From a802817979c5eabe27cbbe809d32b1d54c9f1552 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Wed, 10 Jul 2024 14:04:51 +0300
Subject: [PATCH 01/44] Aligned stylus.stl with VTK axes Stylus visualization
 is working with Aalto Polaris TODO: add a stylus calibration tab to GUI

---
 icons/stylus.png                              | Bin 0 -> 5395 bytes
 invesalius/data/bases.py                      |  11 +-
 invesalius/data/coregistration.py             |  80 +++++++--
 invesalius/data/viewer_volume.py              |   3 +
 .../data/visualization/probe_visualizer.py    | 166 ++++++++++++++++++
 invesalius/gui/task_navigator.py              |  31 +++-
 invesalius/navigation/navigation.py           |   8 +-
 navigation/ndi_files/Markers/newNBSref.rom    | Bin 0 -> 752 bytes
 navigation/ndi_files/Markers/newNT-115.rom    | Bin 0 -> 752 bytes
 navigation/objects/stylus.stl                 | Bin 55884 -> 55884 bytes
 10 files changed, 278 insertions(+), 21 deletions(-)
 create mode 100644 icons/stylus.png
 create mode 100644 invesalius/data/visualization/probe_visualizer.py
 create mode 100644 navigation/ndi_files/Markers/newNBSref.rom
 create mode 100644 navigation/ndi_files/Markers/newNT-115.rom

diff --git a/icons/stylus.png b/icons/stylus.png
new file mode 100644
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diff --git a/invesalius/data/bases.py b/invesalius/data/bases.py
index aaac61915..cb9e10f04 100644
--- a/invesalius/data/bases.py
+++ b/invesalius/data/bases.py
@@ -212,19 +212,16 @@ def object_registration(
         fids_raw[ic, :] = dco.dynamic_reference_m2(coords[ic, :], coords[3, :])[:3]
 
     # compute initial alignment of probe fixed in the object in source frame
-
-    # XXX: Some duplicate processing is done here: the Euler angles are calculated once by
-    #      the lines below, and then again in dco.coordinates_to_transformation_matrix.
-    #
-    a, b, g = np.radians(coords[3, 3:])
-    r_s0_raw = tr.euler_matrix(a, b, g, axes="rzyx")
-
     s0_raw = dco.coordinates_to_transformation_matrix(
         position=coords[3, :3],
         orientation=coords[3, 3:],
         axes="rzyx",
     )
 
+    # copy rotation submatrix from s0_raw
+    r_s0_raw = np.eye(4)
+    r_s0_raw[:3, :3] = s0_raw[:3, :3]
+
     # compute change of basis for object fiducials in source frame
     base_obj_raw, q_obj_raw = base_creation(fids_raw[:3, :3])
     r_obj_raw = np.identity(4)
diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index f5594f46d..7302920fa 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -170,6 +170,49 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
 
     return m_target_in_tracker
 
+def corregistrate_probe(m_change, coord_raw, ref_mode_id):
+    m_probe = compute_marker_transformation(coord_raw, 0) 
+    #print(f"raw angles: {np.degrees(tr.euler_from_matrix(m_probe,axes='rzyx'))}")
+
+    # transform probe to reference system if dynamic ref_mode
+    if ref_mode_id:
+        m_probe_ref = object_to_reference(coord_raw, m_probe)
+    else:
+        m_probe_ref = m_probe
+
+    # invert y coordinate
+    m_probe_ref[2, -1] = -m_probe_ref[2, -1]
+
+    # Manual method:
+    # Hold stylus in line with head (pointing up)
+    # Save the euler-angle from the print statement below into up_trk:
+    print(f"up_trk angles: {np.degrees(tr.euler_from_matrix(m_probe_ref,axes='rzyx'))}")
+    # this gets the angle of stylus relative to head
+
+    # orientation 'stylus pointing up along head' in tracker system 
+    up_trk = tr.euler_matrix(*np.radians([90.0, 6, 18.0]), axes='rzyx')[:3,:3] 
+    
+    # orientation 'stylus pointing up along head' in vtk-coordinate system
+    up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
+    
+    # Rotation or change of basis matrix from tracker to VTK coordinate system
+    R = up_vtk @ np.linalg.inv(up_trk)
+
+    # rotate new orientation to vtk space
+    r_img = R @ m_probe_ref[:3,:3]
+
+    # translate and rotate m_probe_ref from tracker to image space
+    m_img = m_change @ m_probe_ref 
+    m_img[:3, :3] = r_img[:3, :3]
+
+    # compute rotation angles
+    angles = np.degrees(tr.euler_from_matrix(m_img, axes='sxyz'))
+
+    # create output coordinate list
+    coord = np.array([ m_img[0, -1], m_img[1, -1], m_img[2, -1],
+        angles[0], angles[1], angles[2] ])
+
+    return coord, m_img
 
 def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id, icp):
     m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
@@ -191,16 +234,16 @@ def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id, icp):
     m_img = apply_icp(m_img, icp)
 
     # compute rotation angles
-    angles = tr.euler_from_matrix(m_img, axes="sxyz")
+    angles = np.degrees(tr.euler_from_matrix(m_img, axes="sxyz"))
 
     # create output coordinate list
     coord = (
         m_img[0, -1],
         m_img[1, -1],
         m_img[2, -1],
-        np.degrees(angles[0]),
-        np.degrees(angles[1]),
-        np.degrees(angles[2]),
+        angles[0],
+        angles[1],
+        angles[2],
     )
 
     return coord, m_img
@@ -236,16 +279,16 @@ def corregistrate_dynamic(inp, coord_raw, ref_mode_id, icp):
     m_img = apply_icp(m_img, icp)
 
     # compute rotation angles
-    angles = tr.euler_from_matrix(m_img, axes="sxyz")
+    angles = np.degrees(tr.euler_from_matrix(m_img, axes="sxyz"))
 
     # create output coordinate list
     coord = (
         m_img[0, -1],
         m_img[1, -1],
         m_img[2, -1],
-        np.degrees(angles[0]),
-        np.degrees(angles[1]),
-        np.degrees(angles[2]),
+        angles[0],
+        angles[1],
+        angles[2],
     )
 
     return coord, m_img
@@ -349,9 +392,17 @@ def run(self):
 
                 # print(f"Set the coordinate")
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
+                
+                m_change = coreg_data[0] 
+                coords, m_imgs = corregistrate_probe(
+                    m_change, coord_raw, self.ref_mode_id
+                )
                 coord, m_img = corregistrate_object_dynamic(
                     coreg_data, coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
                 )
+                
+                coords = np.stack((coords, coord))
+                m_imgs = np.stack((m_imgs, m_img))
 
                 # XXX: This is not the best place to do the logic related to approaching the target when the
                 #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
@@ -376,7 +427,7 @@ def run(self):
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
                 # self.pipeline.set_message(m_img_flip)
 
-                self.coord_queue.put_nowait([coord, marker_visibilities, m_img, view_obj])
+                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs, view_obj])
                 # print('CoordCoreg: put {}'.format(count))
                 # count += 1
 
@@ -425,14 +476,23 @@ def run(self):
                 # print(f"Set the coordinate")
                 # print(self.icp, self.m_icp)
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
+
+                m_change = coreg_data[0]
+                coords, m_imgs = corregistrate_probe(
+                    m_change, coord_raw, self.ref_mode_id
+                )
                 coord, m_img = corregistrate_dynamic(
                     coreg_data, coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
                 )
+
+                coords = np.stack((coords, coord))
+                m_imgs = np.stack((m_imgs, m_img))
+
                 # print("Coord: ", coord)
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
 
-                self.coord_queue.put_nowait([coord, marker_visibilities, m_img, view_obj])
+                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs, view_obj])
 
                 if self.view_tracts:
                     self.coord_tracts_queue.put_nowait(m_img_flip)
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index 60a204388..8aaaa058d 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -98,6 +98,7 @@
 from invesalius.data.markers.surface_geometry import SurfaceGeometry
 from invesalius.data.ruler_volume import GenericLeftRulerVolume
 from invesalius.data.visualization.coil_visualizer import CoilVisualizer
+from invesalius.data.visualization.probe_visualizer import ProbeVisualizer
 from invesalius.data.visualization.marker_visualizer import MarkerVisualizer
 from invesalius.data.visualization.vector_field_visualizer import VectorFieldVisualizer
 from invesalius.gui.widgets.canvas_renderer import CanvasRendererCTX
@@ -312,6 +313,8 @@ def __init__(self, parent):
             actor_factory=self.actor_factory,
             vector_field_visualizer=self.vector_field_visualizer,
         )
+        
+        self.probe_visualizer = ProbeVisualizer(self.ren, self.interactor)
 
         self.seed_offset = const.SEED_OFFSET
         self.radius_list = vtkIdList()
diff --git a/invesalius/data/visualization/probe_visualizer.py b/invesalius/data/visualization/probe_visualizer.py
new file mode 100644
index 000000000..1579c1199
--- /dev/null
+++ b/invesalius/data/visualization/probe_visualizer.py
@@ -0,0 +1,166 @@
+import os
+import vtk
+
+import invesalius.data.vtk_utils as vtku
+from invesalius.pubsub import pub as Publisher
+from invesalius import inv_paths
+
+class ProbeVisualizer:
+    """
+    A class for visualizing probe in the volume viewer.
+    """
+
+    def __init__(self, renderer, interactor):
+        self.renderer = renderer
+        self.interactor = interactor
+
+        self.probe_actor = None
+        self.probe_path = os.path.join(inv_paths.OBJ_DIR, "stylus.stl")
+        self.show_probe = False
+        self.is_navigating = False
+
+        self.AddProbeActor(self.probe_path)
+        self.__bind_events()
+
+    def __bind_events(self):
+        Publisher.subscribe(self.ShowProbe, 'Show probe in viewer volume')
+        Publisher.subscribe(self.UpdateProbePose, 'Update probe pose')
+        Publisher.subscribe(self.OnNavigationStatus, 'Navigation status')
+
+    def OnNavigationStatus(self, nav_status, vis_status):
+        self.is_navigating = nav_status  # show probe when start navigation
+        if self.probe_actor is not None: # and hide it when stop navigation
+            Publisher.sendMessage('Press show-probe button',pressed=nav_status)
+            self.ShowProbe(self.is_navigating)
+            self.interactor.Render()
+
+    def ShowProbe(self, state):
+        self.show_probe = state
+
+        if self.probe_actor:
+            self.probe_actor.SetVisibility(self.show_probe)
+            self.interactor.Render()
+    
+    def AddProbeActor(self, probe_path):
+        vtk_colors = vtk.vtkNamedColors()
+        obj_polydata = vtku.CreateObjectPolyData(probe_path)
+             
+        # This rotation is done so that the probe visibility icon in viewer_volume doesn't need to be rotated
+        transform = vtk.vtkTransform()
+        transform.RotateZ(-150)
+        
+        transform_filt = vtk.vtkTransformPolyDataFilter()
+        transform_filt.SetTransform(transform)
+        transform_filt.SetInputData(obj_polydata)
+        transform_filt.Update()
+
+        obj_mapper = vtk.vtkPolyDataMapper()
+        obj_mapper.SetInputData(transform_filt.GetOutput())
+        obj_mapper.ScalarVisibilityOff()
+
+        probe_actor = vtk.vtkActor()
+        probe_actor.SetMapper(obj_mapper)
+        probe_actor.GetProperty().SetAmbientColor(vtk_colors.GetColor3d('GhostWhite'))
+        probe_actor.GetProperty().SetSpecular(30)
+        probe_actor.GetProperty().SetSpecularPower(80)
+        probe_actor.GetProperty().SetOpacity(.4)
+        probe_actor.SetVisibility(0)
+
+        self.probe_actor = probe_actor
+        self.renderer.AddActor(self.probe_actor)
+
+    def RemoveProbeActor(self):
+        if self.probe_actor is not None:
+            self.renderer.RemoveActor(self.probe_actor)
+            self.probe_actor = None
+
+    def UpdateProbePose(self, m_img, coord):
+        m_img_flip = m_img.copy() 
+        m_img_flip[1, -1] = -m_img_flip[1, -1]
+
+        m_img_vtk = vtku.numpy_to_vtkMatrix4x4(m_img_flip)
+
+        self.probe_actor.SetUserMatrix(m_img_vtk)
+
+"""
+Code used to shrink and align old stylus.stl file. 
+May be useful for aligning other stl files into VTK in the future.
+This computes the main axes of the object and position of the tip
+then rotates and translates to align with vtk axes 
+
+    import numpy as np
+
+    import invesalius.data.coordinates as dco
+    import invesalius.constants as const
+    import invesalius.data.polydata_utils as pu
+
+    obj_polydata = vtku.CreateObjectPolyData(probe_path) # STL file to be aligned
+    #Shrink object
+    scale_factor = 0.1
+    shrink_transform = vtk.vtkTransform()
+    shrink_transform.Scale(scale_factor, scale_factor, scale_factor)
+
+    shrink_transform_filt = vtk.vtkTransformPolyDataFilter()
+    shrink_transform_filt.SetTransform(shrink_transform)
+    shrink_transform_filt.SetInputData(obj_polydata)
+    shrink_transform_filt.Update()
+
+    obj_polydata = shrink_transform_filt.GetOutput() #replace original with shrunk
+
+    # Rotate to align obj_axes and translate tip to origin
+    obj_axes, tip = self.__calculate_pca(obj_polydata)
+
+    obj_to_vtk = np.linalg.inv(obj_axes) 
+    rotation = vtk.vtkMatrix4x4() 
+    rotation.SetElement(3, 3, 1) #affine transformation: last row is [0 0 0 1]
+    for i in range(3): # copy obj_to_vtk to vtk_matrix
+        for j in range(3):
+            rotation.SetElement(i, j, obj_to_vtk[i, j])
+            rotation.SetElement(3, j, 0) #last column
+        rotation.SetElement(i, 3, 0) # last row
+
+    transform = vtk.vtkTransform()
+    transform.Translate(-obj_to_vtk@tip) #change to vtk basis before translating
+    transform.Concatenate(rotation)
+
+    transform_filt = vtk.vtkTransformPolyDataFilter()
+    transform_filt.SetTransform(transform)
+    transform_filt.SetInputData(obj_polydata)
+    transform_filt.Update()
+
+    # Write the aligned object into a new STL file
+    output_path = os.path.join(inv_paths.OBJ_DIR, "stylus2.stl")
+    stl_writer = vtk.vtkSTLWriter()
+    stl_writer.SetFileTypeToBinary()
+    stl_writer.SetFileName(output_path)
+    stl_writer.SetInputData(transform_filt.GetOutput())
+    stl_writer.Write()
+
+    # Helper function
+    def __calculate_pca(self, polydata): 
+        #Calculate 3 principal axes of object from vtk polydata with principal component analysis.
+        #Returns the object axes in the desired xyz-order in a 3x3 matrix:
+        #    x-column: Secondary axis (lateral axis of object)
+        #    y-column: Principal axis (longitudinal axis of object)
+        #    z-column: Tertiary axis (normal to object)
+        #Google aircraft axes for analogue
+
+        points = np.array(polydata.GetPoints().GetData())
+
+        # Center the points
+        centroid = np.mean(points, axis=0)
+        centered_points = points - centroid
+
+        # Perform PCA
+        covariance_matrix = np.cov(centered_points, rowvar=False)
+        eigenvalues, eigenvectors = np.linalg.eigh(covariance_matrix)
+        #eigh returns vectors in ascending order (ie. principal axis is the last one)
+        
+        # Permute, so that y-column is the principal axis and x-column secondary axis
+        eigenvectors[:, [0, 1, 2]] = eigenvectors[:, [1, 2, 0]]
+        
+        # the tip is the point furthest along principal axis 
+        # for another STL object tip could be in opposite direction so would use argmin instead
+        tip = points[np.argmax(np.dot(centered_points, eigenvectors[:,1]))]
+        return eigenvectors, tip
+"""
\ No newline at end of file
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 58c0f0762..1cdadb3b3 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1241,6 +1241,18 @@ def __init__(self, parent, nav_hub):
         show_coil_button.Bind(wx.EVT_TOGGLEBUTTON, self.OnShowCoil)
         self.show_coil_button = show_coil_button
 
+        # Toggle button for showing probe during navigation
+        tooltip = _("Show probe") #LUKATODO: get proper png
+        BMP_SHOW_PROBE = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("stylus.png")), wx.BITMAP_TYPE_PNG)
+        show_probe_button = wx.ToggleButton(self, -1, "", style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
+        show_probe_button.SetBackgroundColour(GREY_COLOR)
+        show_probe_button.SetBitmap(BMP_SHOW_PROBE)
+        show_probe_button.SetToolTip(tooltip)
+        show_probe_button.Enable(True)
+        self.UpdateToggleButton(show_probe_button, False) #the probe is hidden at start
+        show_probe_button.Bind(wx.EVT_TOGGLEBUTTON, self.OnShowProbe)
+        self.show_probe_button = show_probe_button
+
         # Toggle Button to use serial port to trigger pulse signal and create markers
         tooltip = _("Enable serial port communication to trigger pulse and create markers")
         BMP_PORT = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("wave.png")), wx.BITMAP_TYPE_PNG)
@@ -1379,6 +1391,7 @@ def __init__(self, parent, nav_hub):
                 (efield_checkbox),
                 (lock_to_target_button),
                 (show_coil_button),
+                (show_probe_button),
                 (show_motor_map_button),
             ]
         )
@@ -1422,8 +1435,10 @@ def __bind_events(self):
         Publisher.subscribe(self.UpdateTractsVisualization, "Update tracts visualization")
 
         # Externally press/unpress and enable/disable buttons.
-        Publisher.subscribe(self.PressShowCoilButton, "Press show-coil button")
-        Publisher.subscribe(self.EnableShowCoilButton, "Enable show-coil button")
+        Publisher.subscribe(self.PressShowProbeButton, 'Press show-probe button')
+
+        Publisher.subscribe(self.PressShowCoilButton, 'Press show-coil button')
+        Publisher.subscribe(self.EnableShowCoilButton, 'Enable show-coil button')
 
         Publisher.subscribe(self.PressTrackObjectButton, "Press track object button")
         Publisher.subscribe(self.EnableTrackObjectButton, "Enable track object button")
@@ -1721,7 +1736,17 @@ def EnableShowCoilButton(self, enabled=False):
     def OnShowCoil(self, evt=None):
         self.UpdateToggleButton(self.show_coil_button)
         pressed = self.show_coil_button.GetValue()
-        Publisher.sendMessage("Show coil in viewer volume", state=pressed)
+        Publisher.sendMessage('Show coil in viewer volume', state=pressed)
+    
+    # 'Show probe' button
+    def PressShowProbeButton(self, pressed=False):
+        self.UpdateToggleButton(self.show_probe_button, pressed)
+        self.OnShowProbe()
+
+    def OnShowProbe(self, evt=None):
+        self.UpdateToggleButton(self.show_probe_button)
+        pressed = self.show_probe_button.GetValue()
+        Publisher.sendMessage('Show probe in viewer volume', state=pressed)
 
     # 'Serial Port Com'
     def OnEnableSerialPort(self, evt, ctrl):
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 7f74a2889..17a36c033 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -141,7 +141,10 @@ def run(self):
             got_coords = False
             object_visible_flag = False
             try:
-                coord, marker_visibilities, m_img, view_obj = self.coord_queue.get_nowait()
+                coords, marker_visibilities, m_imgs, view_obj = self.coord_queue.get_nowait()
+                coord = coords[1] # main coil
+                m_img = m_imgs[1]
+
                 got_coords = True
                 object_visible_flag = marker_visibilities[2]
 
@@ -217,6 +220,9 @@ def run(self):
                         "Update volume viewer pointer",
                         position=[coord[0], -coord[1], coord[2]],
                     )
+                
+                wx.CallAfter(Publisher.sendMessage, 'Update probe pose', m_img=m_imgs[0], coord=coords[0])
+                
                 # Render the volume viewer and the slice viewers.
                 wx.CallAfter(Publisher.sendMessage, "Render volume viewer")
                 wx.CallAfter(Publisher.sendMessage, "Update slice viewer")
diff --git a/navigation/ndi_files/Markers/newNBSref.rom b/navigation/ndi_files/Markers/newNBSref.rom
new file mode 100644
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From 7286afef4f9c7bf47d37799bb9643e5caa33b7ed Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 11 Jul 2024 12:45:51 +0300
Subject: [PATCH 02/44] added r_change to navigation code, now add GUI to
 record r_change

---
 invesalius/data/coregistration.py   | 26 ++++++++++++++++----------
 invesalius/navigation/navigation.py | 28 ++++++++++++++++++++++++++--
 2 files changed, 42 insertions(+), 12 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 7302920fa..dca96614f 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -170,7 +170,7 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
 
     return m_target_in_tracker
 
-def corregistrate_probe(m_change, coord_raw, ref_mode_id):
+def corregistrate_probe(m_change, r_change, coord_raw, ref_mode_id):
     m_probe = compute_marker_transformation(coord_raw, 0) 
     #print(f"raw angles: {np.degrees(tr.euler_from_matrix(m_probe,axes='rzyx'))}")
 
@@ -200,9 +200,13 @@ def corregistrate_probe(m_change, coord_raw, ref_mode_id):
 
     # rotate new orientation to vtk space
     r_img = R @ m_probe_ref[:3,:3]
+    
 
-    # translate and rotate m_probe_ref from tracker to image space
+    # translate m_probe_ref from tracker to image space
     m_img = m_change @ m_probe_ref 
+   
+    # rotate m_probe_ref from tracker to image space 
+    #r_img = r_change @ m_probe_ref[:3,:3]
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles
@@ -392,13 +396,14 @@ def run(self):
 
                 # print(f"Set the coordinate")
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
-                
-                m_change = coreg_data[0] 
+
+                #m_change = coreg_data[1]
+                #r_change = coreg_data[0] # currently used for probe only 
                 coords, m_imgs = corregistrate_probe(
-                    m_change, coord_raw, self.ref_mode_id
+                    coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
-                coord, m_img = corregistrate_object_dynamic(
-                    coreg_data, coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
+                coord, m_img = corregistrate_dynamic(
+                    coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
                 )
                 
                 coords = np.stack((coords, coord))
@@ -477,12 +482,13 @@ def run(self):
                 # print(self.icp, self.m_icp)
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
-                m_change = coreg_data[0]
+                #m_change = coreg_data[1]
+                #r_change = coreg_data[0] # currently used for probe only 
                 coords, m_imgs = corregistrate_probe(
-                    m_change, coord_raw, self.ref_mode_id
+                    coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
                 coord, m_img = corregistrate_dynamic(
-                    coreg_data, coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
+                    coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
                 )
 
                 coords = np.stack((coords, coord))
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 17a36c033..e33403213 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -246,6 +246,7 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.object_registration = None
         self.track_obj = False
         self.m_change = None
+        self.r_change = None
         self.obj_data = None
         self.all_fiducials = np.zeros((6, 6))
         self.event = threading.Event()
@@ -411,6 +412,29 @@ def EstimateTrackerToInVTransformationMatrix(self, tracker, image):
             self.all_fiducials[3:, :].T, self.all_fiducials[:3, :].T, shear=False, scale=False
         )
 
+    def SetStylusOrientation(self, coord_raw):
+        if self.m_change is not None:
+            m_probe = dcr.compute_marker_transformation(coord_raw, 0) 
+
+            # transform probe to reference system if dynamic ref_mode
+            if self.ref_mode_id:
+                up_trk = dcr.object_to_reference(coord_raw, m_probe)[:3, :3]
+            else:
+                up_trk = m_probe[:3, :3]
+            # up_trk is orientation 'stylus pointing up along head' in tracker system 
+            
+            # orientation 'stylus pointing up along head' in vtk-coordinate system
+            up_vtk = np.eye(3)
+            up_vtk[:, [1,2]] = up_vtk[:, [2,1]] #swap last 2 columns
+            up_vtk[:, 2] *= -1  # flip last column
+
+            # above is identical to:
+            #up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
+
+            # Rotation from tracker to VTK coordinate system
+            self.r_change = up_vtk @ np.linalg.inv(up_trk)
+        
+
     def StartNavigation(self, tracker, icp):
         # initialize jobs list
         jobs_list = []
@@ -448,7 +472,7 @@ def StartNavigation(self, tracker, icp):
                 # object_registration[0] is object 3x3 fiducial matrix and object_registration[1] is 3x3 orientation matrix
                 obj_fiducials, obj_orients, obj_ref_mode, obj_name = self.object_registration
 
-                coreg_data = [self.m_change, obj_ref_mode]
+                coreg_data = [self.r_change, self.m_change, obj_ref_mode]
 
                 if self.ref_mode_id:
                     coord_raw, marker_visibilities = tracker.TrackerCoordinates.GetCoordinates()
@@ -483,7 +507,7 @@ def StartNavigation(self, tracker, icp):
                     )
                 )
         else:
-            coreg_data = (self.m_change, 0)
+            coreg_data = (self.r_change, self.m_change, 0)
             queues = [self.coord_queue, self.coord_tracts_queue, self.icp_queue, self.efield_queue]
             jobs_list.append(
                 dcr.CoordinateCorregistrateNoObject(

From 147c5d62ef2a516f67fc5aa8773e98d2f0f124eb Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 11 Jul 2024 13:47:24 +0300
Subject: [PATCH 03/44] StylusPage records coord_raw for Navigation

---
 invesalius/gui/task_navigator.py | 68 ++++++++++++++++++++++++++++++--
 1 file changed, 65 insertions(+), 3 deletions(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 1cdadb3b3..c7cb8b6ac 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -320,6 +320,7 @@ def __init__(self, parent, nav_hub):
         book.AddPage(ImagePage(book, nav_hub), _("Image"))
         book.AddPage(TrackerPage(book, nav_hub), _("Patient"))
         book.AddPage(RefinePage(book, nav_hub), _("Refine"))
+        book.AddPage(StylusPage(book, nav_hub), _("Stylus"))
         book.AddPage(StimulatorPage(book, nav_hub), _("TMS Coil"))
 
         book.SetSelection(0)
@@ -335,6 +336,7 @@ def __init__(self, parent, nav_hub):
     def __bind_events(self):
         Publisher.subscribe(self._FoldTracker, "Move to tracker page")
         Publisher.subscribe(self._FoldRefine, "Move to refine page")
+        Publisher.subscribe(self._FoldStylus, "Move to stylus page")
         Publisher.subscribe(self._FoldStimulator, "Move to stimulator page")
         Publisher.subscribe(self._FoldImage, "Move to image page")
 
@@ -357,7 +359,7 @@ def OnPageChanged(self, evt):
             Publisher.sendMessage("Update UI for refine tab")
 
         # new page validations
-        if (old_page == 1) and (new_page == 2 or new_page == 3):
+        if (old_page == 1) and (new_page > 1):
             # Do not allow user to move to other (forward) tabs if tracker fiducials not done.
             if self.image.AreImageFiducialsSet() and not self.tracker.AreTrackerFiducialsSet():
                 self.book.SetSelection(1)
@@ -374,9 +376,12 @@ def _FoldTracker(self):
     def _FoldRefine(self):
         self.book.SetSelection(2)
 
-    def _FoldStimulator(self):
+    def _FoldStylus(self):
         self.book.SetSelection(3)
 
+    def _FoldStimulator(self):
+        self.book.SetSelection(4)
+
 
 class ImagePage(wx.Panel):
     def __init__(self, parent, nav_hub):
@@ -989,13 +994,70 @@ def OnBack(self, evt):
         Publisher.sendMessage("Move to tracker page")
 
     def OnNext(self, evt):
-        Publisher.sendMessage("Move to stimulator page")
+        Publisher.sendMessage('Move to stylus page')
 
     def OnRefine(self, evt):
         self.icp.RegisterICP(self.navigation, self.tracker)
         if self.icp.use_icp:
             self.OnUpdateUI()
 
+class StylusPage(wx.Panel):
+    def __init__(self, parent, nav_hub):
+
+        wx.Panel.__init__(self, parent)
+        self.navigation = nav_hub.navigation
+        self.tracker = nav_hub.tracker
+
+        border = wx.FlexGridSizer(1,3, 5)
+        
+        lbl = wx.StaticText(self, -1, _("Calibrate stylus with head"))
+        lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
+        self.lbl = lbl
+
+        lbl_rec = wx.StaticText(self, -1, _("Calibrate stylus with physical head"))
+        btn_rec = wx.Button(self, -1, _("Record"))
+        btn_rec.SetToolTip("Record stylus orientation relative to head")
+        btn_rec.Bind(wx.EVT_BUTTON, self.onRecord)
+
+        border.AddMany([
+            (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 10),
+            (lbl_rec, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5),
+            (btn_rec, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 5)
+        ])
+
+        next_button = wx.Button(self, label="Next")
+        next_button.Bind(wx.EVT_BUTTON, partial(self.OnNext))
+
+        bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        bottom_sizer.Add(next_button)
+        
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.AddMany([
+            (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 10),
+            (bottom_sizer, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.TOP, 20)
+        ])
+        
+        self.SetSizerAndFit(main_sizer)
+        self.Layout()
+        self.__bind_events()
+
+    def __bind_events(self):
+        pass #Publisher.subscribe(self.OnCloseProject, 'Remove object data')
+
+    def onRecord(self, evt):
+        marker_visibilities, _, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1) #ref_mode is irrelevant here
+        if marker_visibilities[0] and marker_visibilities[1]: #if probe and head are visible
+            self.navigation.SetStylusOrientation(coord_raw)
+            return True
+        else:
+            wx.MessageBox(_("Probe or head not visible to tracker!"), _("InVesalius 3"))            
+            return False
+
+    def OnBack(self, evt):
+        Publisher.sendMessage('Move to refine page')
+ 
+    def OnNext(self, evt):
+        Publisher.sendMessage('Move to stimulator page')
 
 class StimulatorPage(wx.Panel):
     def __init__(self, parent, nav_hub):

From 7dd3e61f122511769bf0c0f9daab3d24a27caeac Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 11 Jul 2024 14:43:20 +0300
Subject: [PATCH 04/44] Clean up corregistrate_probe

---
 invesalius/data/coregistration.py | 21 +--------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index dca96614f..2532420e4 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -183,30 +183,11 @@ def corregistrate_probe(m_change, r_change, coord_raw, ref_mode_id):
     # invert y coordinate
     m_probe_ref[2, -1] = -m_probe_ref[2, -1]
 
-    # Manual method:
-    # Hold stylus in line with head (pointing up)
-    # Save the euler-angle from the print statement below into up_trk:
-    print(f"up_trk angles: {np.degrees(tr.euler_from_matrix(m_probe_ref,axes='rzyx'))}")
-    # this gets the angle of stylus relative to head
-
-    # orientation 'stylus pointing up along head' in tracker system 
-    up_trk = tr.euler_matrix(*np.radians([90.0, 6, 18.0]), axes='rzyx')[:3,:3] 
-    
-    # orientation 'stylus pointing up along head' in vtk-coordinate system
-    up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
-    
-    # Rotation or change of basis matrix from tracker to VTK coordinate system
-    R = up_vtk @ np.linalg.inv(up_trk)
-
-    # rotate new orientation to vtk space
-    r_img = R @ m_probe_ref[:3,:3]
-    
-
     # translate m_probe_ref from tracker to image space
     m_img = m_change @ m_probe_ref 
    
     # rotate m_probe_ref from tracker to image space 
-    #r_img = r_change @ m_probe_ref[:3,:3]
+    r_img = r_change @ m_probe_ref[:3,:3]
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles

From 754b07fbeae032c59110772e9b00b74ffec16c0f Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 11 Jul 2024 15:02:15 +0300
Subject: [PATCH 05/44] using _ to discard the returned variable resulted in a
 wxPython error! Use __ instead

---
 invesalius/gui/task_navigator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index c7cb8b6ac..d017d1b05 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1045,7 +1045,7 @@ def __bind_events(self):
         pass #Publisher.subscribe(self.OnCloseProject, 'Remove object data')
 
     def onRecord(self, evt):
-        marker_visibilities, _, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1) #ref_mode is irrelevant here
+        marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1)
         if marker_visibilities[0] and marker_visibilities[1]: #if probe and head are visible
             self.navigation.SetStylusOrientation(coord_raw)
             return True

From 8e0ddb11f4dfc16634f3cb201d2ae36fbb6cfab2 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 11 Jul 2024 18:12:15 +0300
Subject: [PATCH 06/44] add illustration of how to align the stylus with head

---
 icons/align.png                     | Bin 0 -> 26370 bytes
 invesalius/gui/task_navigator.py    |  35 +++++++++++++++++++++-------
 invesalius/navigation/navigation.py |  11 +++------
 3 files changed, 30 insertions(+), 16 deletions(-)
 create mode 100644 icons/align.png

diff --git a/icons/align.png b/icons/align.png
new file mode 100644
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z=Yg>Rqm6lyN&^n)!!Tc8pSInyBfW<nsyAT3|5@jV3oqt5)AZX%M55B;5<-{+qGt?Y
zN3-i!>=p3<&~RSlOpOm1*>{M~o~NrbiEmk?UCbM;=tye}x1!xu9b15)!Up~Fo1EcD
zh@i>#icb@REfRH!oAE9LKq-r{yzp%uYW>+Ui6*w@W3`j_nzPJ-b!t5G{f}%b)M~z5
zjHGe_pyb`g;sU9;@3Cg?kMo3z`p|k#3Cg*K;Z8pdiaG-Xu-`yi#Yj`Nr%p%VF>=w)
zV><@Qn{#`b>e_l%)N^ojK4Uxf@4C-$sewEZtMYnzs4!r2TtQ%IX}BIUQYNLfGip(%
z7IQz}R*j~2^+#Q;GMBrU{<%cjI`Yk;ovR#Y5?RS08M;zu>x7x49;yOE=RS^@icL}Y
t&EWQ3@3d6)q5~9G|Nr=C#h~tS<->)180n|8fK3=!%JLfT%VjM>{s*|M5z7Do

literal 0
HcmV?d00001

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index d017d1b05..a04f25bc6 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1003,38 +1003,50 @@ def OnRefine(self, evt):
 
 class StylusPage(wx.Panel):
     def __init__(self, parent, nav_hub):
-
         wx.Panel.__init__(self, parent)
         self.navigation = nav_hub.navigation
         self.tracker = nav_hub.tracker
 
         border = wx.FlexGridSizer(1,3, 5)
-        
+        self.border = border
+
+        self.success = False
+
         lbl = wx.StaticText(self, -1, _("Calibrate stylus with head"))
         lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
         self.lbl = lbl
+        self.help_img = wx.Image(os.path.join(inv_paths.ICON_DIR,"align.png"), wx.BITMAP_TYPE_ANY)
+        
+        #first show help in grayscale. when record successful: make it green
+        self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToGreyscale(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
 
-        lbl_rec = wx.StaticText(self, -1, _("Calibrate stylus with physical head"))
+        lbl_rec = wx.StaticText(self, -1, _("Point stylus up relative to head, like so:"))
         btn_rec = wx.Button(self, -1, _("Record"))
         btn_rec.SetToolTip("Record stylus orientation relative to head")
         btn_rec.Bind(wx.EVT_BUTTON, self.onRecord)
+        
+        self.btn_rec = btn_rec
 
-        border.AddMany([
+        self.border.AddMany([
             (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 10),
             (lbl_rec, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5),
+            (self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5),      
             (btn_rec, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 5)
         ])
-
+        
+        back_button = wx.Button(self, label="Back")
+        back_button.Bind(wx.EVT_BUTTON, partial(self.OnBack))
         next_button = wx.Button(self, label="Next")
         next_button.Bind(wx.EVT_BUTTON, partial(self.OnNext))
 
         bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        bottom_sizer.Add(back_button)
         bottom_sizer.Add(next_button)
-        
+
         main_sizer = wx.BoxSizer(wx.VERTICAL)
         main_sizer.AddMany([
             (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 10),
-            (bottom_sizer, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.TOP, 20)
+            (bottom_sizer, 0, wx.ALIGN_CENTER | wx.CENTER | wx.TOP, 20)
         ])
         
         self.SetSizerAndFit(main_sizer)
@@ -1048,6 +1060,13 @@ def onRecord(self, evt):
         marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1)
         if marker_visibilities[0] and marker_visibilities[1]: #if probe and head are visible
             self.navigation.SetStylusOrientation(coord_raw)
+            if not self.success: #only show green first time
+                self.success = True
+                #show green for success
+                self.help.Destroy()
+                self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToBitmap(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
+                self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
+                self.Layout()
             return True
         else:
             wx.MessageBox(_("Probe or head not visible to tracker!"), _("InVesalius 3"))            
@@ -1304,7 +1323,7 @@ def __init__(self, parent, nav_hub):
         self.show_coil_button = show_coil_button
 
         # Toggle button for showing probe during navigation
-        tooltip = _("Show probe") #LUKATODO: get proper png
+        tooltip = _("Show probe")
         BMP_SHOW_PROBE = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("stylus.png")), wx.BITMAP_TYPE_PNG)
         show_probe_button = wx.ToggleButton(self, -1, "", style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
         show_probe_button.SetBackgroundColour(GREY_COLOR)
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index e33403213..6536693cf 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -421,15 +421,10 @@ def SetStylusOrientation(self, coord_raw):
                 up_trk = dcr.object_to_reference(coord_raw, m_probe)[:3, :3]
             else:
                 up_trk = m_probe[:3, :3]
-            # up_trk is orientation 'stylus pointing up along head' in tracker system 
             
-            # orientation 'stylus pointing up along head' in vtk-coordinate system
-            up_vtk = np.eye(3)
-            up_vtk[:, [1,2]] = up_vtk[:, [2,1]] #swap last 2 columns
-            up_vtk[:, 2] *= -1  # flip last column
-
-            # above is identical to:
-            #up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
+            # up_trk: orientation 'stylus pointing up along head' in tracker space 
+            # up_vtk: orientation 'stylus pointing up along head' in vtk space
+            up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
 
             # Rotation from tracker to VTK coordinate system
             self.r_change = up_vtk @ np.linalg.inv(up_trk)

From a241a2867faff276fd5aa80c3145aea3af3e8ae5 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Fri, 12 Jul 2024 12:07:40 +0300
Subject: [PATCH 07/44] Reduce vertical gaps between GUI components. This has
 been tested on both Windows and Ubuntu 22

---
 invesalius/gui/task_navigator.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index a04f25bc6..6fc319dd6 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1028,10 +1028,10 @@ def __init__(self, parent, nav_hub):
         self.btn_rec = btn_rec
 
         self.border.AddMany([
-            (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 10),
-            (lbl_rec, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5),
-            (self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5),      
-            (btn_rec, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 5)
+            (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2),
+            (lbl_rec, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2),
+            (self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1),      
+            (btn_rec, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 1)
         ])
         
         back_button = wx.Button(self, label="Back")
@@ -1045,8 +1045,8 @@ def __init__(self, parent, nav_hub):
 
         main_sizer = wx.BoxSizer(wx.VERTICAL)
         main_sizer.AddMany([
-            (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 10),
-            (bottom_sizer, 0, wx.ALIGN_CENTER | wx.CENTER | wx.TOP, 20)
+            (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 1),
+            (bottom_sizer, 0, wx.ALIGN_CENTER | wx.CENTER | wx.TOP, 1)
         ])
         
         self.SetSizerAndFit(main_sizer)
@@ -1065,7 +1065,7 @@ def onRecord(self, evt):
                 #show green for success
                 self.help.Destroy()
                 self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToBitmap(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
-                self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
+                self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1)
                 self.Layout()
             return True
         else:

From 218ab9e9ecbbcc1f98f954a82feb59f7f0c8a4a2 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Fri, 12 Jul 2024 13:35:20 +0300
Subject: [PATCH 08/44] save stylus orientation (r_change) to config.json

---
 invesalius/gui/task_navigator.py    | 20 ++++++++++----------
 invesalius/navigation/navigation.py |  8 ++++++++
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 6fc319dd6..f8b8623bc 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1059,18 +1059,18 @@ def __bind_events(self):
     def onRecord(self, evt):
         marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1)
         if marker_visibilities[0] and marker_visibilities[1]: #if probe and head are visible
-            self.navigation.SetStylusOrientation(coord_raw)
-            if not self.success: #only show green first time
-                self.success = True
-                #show green for success
-                self.help.Destroy()
-                self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToBitmap(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
-                self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1)
-                self.Layout()
-            return True
+            if self.navigation.SetStylusOrientation(coord_raw): # if successfully created r_change
+                # Save to config.json file
+                ses.Session().SetConfig('navigation-stylus', {'r_change': self.navigation.r_change.tolist()})
+
+                if not self.success: #only show green on first successful record
+                    self.success = True
+                    self.help.Destroy() #show a colored (green) bitmap as opposed to grayscale
+                    self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToBitmap(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
+                    self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1)
+                    self.Layout()
         else:
             wx.MessageBox(_("Probe or head not visible to tracker!"), _("InVesalius 3"))            
-            return False
 
     def OnBack(self, evt):
         Publisher.sendMessage('Move to refine page')
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 6536693cf..989380093 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -345,6 +345,11 @@ def LoadConfig(self):
             object_name,
         )
 
+        # Try to load stylus orientation data
+        stylus_data = session.GetConfig('navigation-stylus')
+        if stylus_data is not None:
+            self.r_change = np.array(stylus_data['r_change'])
+
     def CoilAtTarget(self, state):
         self.coil_at_target = state
 
@@ -428,6 +433,9 @@ def SetStylusOrientation(self, coord_raw):
 
             # Rotation from tracker to VTK coordinate system
             self.r_change = up_vtk @ np.linalg.inv(up_trk)
+            return True
+        else:
+            return False
         
 
     def StartNavigation(self, tracker, icp):

From 929f3aa746f787788d72d4077c061a927f0c03c5 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Fri, 12 Jul 2024 13:40:45 +0300
Subject: [PATCH 09/44] Handle the case where manual stylus calibration is
 skipped. Print out a warning in this case, but allow navigation to work as
 normal

---
 invesalius/data/coregistration.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 2532420e4..8e862b122 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -171,8 +171,11 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
     return m_target_in_tracker
 
 def corregistrate_probe(m_change, r_change, coord_raw, ref_mode_id):
+    if r_change is None:
+        #utils.debug("STYLUS ORIENTATION NOT DEFINED!")
+        r_change = np.eye(3)
+
     m_probe = compute_marker_transformation(coord_raw, 0) 
-    #print(f"raw angles: {np.degrees(tr.euler_from_matrix(m_probe,axes='rzyx'))}")
 
     # transform probe to reference system if dynamic ref_mode
     if ref_mode_id:
@@ -383,7 +386,7 @@ def run(self):
                 coords, m_imgs = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
-                coord, m_img = corregistrate_dynamic(
+                coord, m_img = corregistrate_object_dynamic(
                     coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
                 )
                 

From e888ddff0a437015856b9e2d8ae83f0627074cec Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 18 Jul 2024 10:26:06 +0300
Subject: [PATCH 10/44] Rename r_change to r_stylus (this is the rotation
 matrix to orient the stylus in vtk)

---
 invesalius/data/coregistration.py   | 13 ++++++++-----
 invesalius/gui/task_navigator.py    | 10 +++++-----
 invesalius/navigation/navigation.py | 10 +++++-----
 3 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 8e862b122..484786b42 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -170,10 +170,10 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
 
     return m_target_in_tracker
 
-def corregistrate_probe(m_change, r_change, coord_raw, ref_mode_id):
-    if r_change is None:
+def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id):
+    if r_stylus is None:
         #utils.debug("STYLUS ORIENTATION NOT DEFINED!")
-        r_change = np.eye(3)
+        r_stylus = np.eye(3)
 
     m_probe = compute_marker_transformation(coord_raw, 0) 
 
@@ -190,7 +190,7 @@ def corregistrate_probe(m_change, r_change, coord_raw, ref_mode_id):
     m_img = m_change @ m_probe_ref 
    
     # rotate m_probe_ref from tracker to image space 
-    r_img = r_change @ m_probe_ref[:3,:3]
+    r_img = r_stylus @ m_probe_ref[:3,:3]
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles
@@ -382,7 +382,7 @@ def run(self):
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
                 #m_change = coreg_data[1]
-                #r_change = coreg_data[0] # currently used for probe only 
+                #r_stylus = coreg_data[0] # currently used for probe only 
                 coords, m_imgs = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
@@ -467,6 +467,9 @@ def run(self):
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
                 #m_change = coreg_data[1]
+                #r_stylus = coreg_data[0] # currently used for probe only 
+                coords, m_imgs = corregistrate_probe(coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id)
+                coord, m_img = corregistrate_dynamic(coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp])
                 #r_change = coreg_data[0] # currently used for probe only 
                 coords, m_imgs = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index f8b8623bc..573c618c1 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1010,7 +1010,7 @@ def __init__(self, parent, nav_hub):
         border = wx.FlexGridSizer(1,3, 5)
         self.border = border
 
-        self.success = False
+        self.done = False
 
         lbl = wx.StaticText(self, -1, _("Calibrate stylus with head"))
         lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
@@ -1059,12 +1059,12 @@ def __bind_events(self):
     def onRecord(self, evt):
         marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1)
         if marker_visibilities[0] and marker_visibilities[1]: #if probe and head are visible
-            if self.navigation.SetStylusOrientation(coord_raw): # if successfully created r_change
+            if self.navigation.SetStylusOrientation(coord_raw): # if successfully created r_stylus
                 # Save to config.json file
-                ses.Session().SetConfig('navigation-stylus', {'r_change': self.navigation.r_change.tolist()})
+                ses.Session().SetConfig('navigation-stylus', {'r_stylus': self.navigation.r_stylus.tolist()})
 
-                if not self.success: #only show green on first successful record
-                    self.success = True
+                if not self.done: #only show green on first record
+                    self.done = True
                     self.help.Destroy() #show a colored (green) bitmap as opposed to grayscale
                     self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToBitmap(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
                     self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1)
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 989380093..779e756c2 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -246,7 +246,7 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.object_registration = None
         self.track_obj = False
         self.m_change = None
-        self.r_change = None
+        self.r_stylus = None
         self.obj_data = None
         self.all_fiducials = np.zeros((6, 6))
         self.event = threading.Event()
@@ -348,7 +348,7 @@ def LoadConfig(self):
         # Try to load stylus orientation data
         stylus_data = session.GetConfig('navigation-stylus')
         if stylus_data is not None:
-            self.r_change = np.array(stylus_data['r_change'])
+            self.r_stylus = np.array(stylus_data['r_stylus'])
 
     def CoilAtTarget(self, state):
         self.coil_at_target = state
@@ -432,7 +432,7 @@ def SetStylusOrientation(self, coord_raw):
             up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
 
             # Rotation from tracker to VTK coordinate system
-            self.r_change = up_vtk @ np.linalg.inv(up_trk)
+            self.r_stylus = up_vtk @ np.linalg.inv(up_trk)
             return True
         else:
             return False
@@ -475,7 +475,7 @@ def StartNavigation(self, tracker, icp):
                 # object_registration[0] is object 3x3 fiducial matrix and object_registration[1] is 3x3 orientation matrix
                 obj_fiducials, obj_orients, obj_ref_mode, obj_name = self.object_registration
 
-                coreg_data = [self.r_change, self.m_change, obj_ref_mode]
+                coreg_data = [self.r_stylus, self.m_change, obj_ref_mode]
 
                 if self.ref_mode_id:
                     coord_raw, marker_visibilities = tracker.TrackerCoordinates.GetCoordinates()
@@ -510,7 +510,7 @@ def StartNavigation(self, tracker, icp):
                     )
                 )
         else:
-            coreg_data = (self.r_change, self.m_change, 0)
+            coreg_data = (self.r_stylus, self.m_change, 0)
             queues = [self.coord_queue, self.coord_tracts_queue, self.icp_queue, self.efield_queue]
             jobs_list.append(
                 dcr.CoordinateCorregistrateNoObject(

From 8731817bc113ea98beb6a021d221bc3e4398e271 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 18 Jul 2024 12:26:51 +0300
Subject: [PATCH 11/44] Cleaning up, RUFF formatting

---
 invesalius/data/coregistration.py             |  63 +++++-----
 invesalius/data/viewer_volume.py              |   2 +-
 .../data/visualization/probe_visualizer.py    |  31 ++---
 invesalius/gui/task_navigator.py              | 110 +++++++++++-------
 invesalius/navigation/navigation.py           |  23 ++--
 navigation/ndi_files/Markers/NBSref.rom       | Bin 752 -> 752 bytes
 navigation/ndi_files/Markers/NT-115.rom       | Bin 752 -> 752 bytes
 navigation/ndi_files/Markers/newNBSref.rom    | Bin 752 -> 0 bytes
 navigation/ndi_files/Markers/newNT-115.rom    | Bin 752 -> 0 bytes
 9 files changed, 134 insertions(+), 95 deletions(-)
 delete mode 100644 navigation/ndi_files/Markers/newNBSref.rom
 delete mode 100644 navigation/ndi_files/Markers/newNT-115.rom

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 484786b42..31886097d 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -170,12 +170,13 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
 
     return m_target_in_tracker
 
+
 def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id):
     if r_stylus is None:
-        #utils.debug("STYLUS ORIENTATION NOT DEFINED!")
+        # utils.debug("STYLUS ORIENTATION NOT DEFINED!")
         r_stylus = np.eye(3)
 
-    m_probe = compute_marker_transformation(coord_raw, 0) 
+    m_probe = compute_marker_transformation(coord_raw, 0)
 
     # transform probe to reference system if dynamic ref_mode
     if ref_mode_id:
@@ -187,21 +188,28 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id):
     m_probe_ref[2, -1] = -m_probe_ref[2, -1]
 
     # translate m_probe_ref from tracker to image space
-    m_img = m_change @ m_probe_ref 
-   
-    # rotate m_probe_ref from tracker to image space 
-    r_img = r_stylus @ m_probe_ref[:3,:3]
+    m_img = m_change @ m_probe_ref
+
+    # rotate m_probe_ref from tracker to image space
+    r_img = r_stylus @ m_probe_ref[:3, :3]
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles
-    angles = np.degrees(tr.euler_from_matrix(m_img, axes='sxyz'))
+    angles = np.degrees(tr.euler_from_matrix(m_img, axes="sxyz"))
 
     # create output coordinate list
-    coord = np.array([ m_img[0, -1], m_img[1, -1], m_img[2, -1],
-        angles[0], angles[1], angles[2] ])
+    coord = (
+        m_img[0, -1],
+        m_img[1, -1],
+        m_img[2, -1],
+        angles[0],
+        angles[1],
+        angles[2],
+    )
 
     return coord, m_img
 
+
 def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id, icp):
     m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
 
@@ -381,17 +389,16 @@ def run(self):
                 # print(f"Set the coordinate")
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
-                #m_change = coreg_data[1]
-                #r_stylus = coreg_data[0] # currently used for probe only 
-                coords, m_imgs = corregistrate_probe(
+                # m_change = coreg_data[1], r_stylus = coreg_data[0] (r_stylus used for probe only)
+                coord_probe, m_img_probe = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
-                coord, m_img = corregistrate_object_dynamic(
+                coord_coil, m_img_coil = corregistrate_object_dynamic(
                     coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
                 )
-                
-                coords = np.stack((coords, coord))
-                m_imgs = np.stack((m_imgs, m_img))
+
+                coords = [coord_probe, coord_coil]
+                m_imgs = [m_img_probe, m_img_coil]
 
                 # XXX: This is not the best place to do the logic related to approaching the target when the
                 #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
@@ -403,22 +410,23 @@ def run(self):
                 #
                 if self.tracker_id == const.DEBUGTRACKAPPROACH and self.target is not None:
                     if self.last_coord is None:
-                        self.last_coord = np.array(coord)
+                        self.last_coord = np.array(coord_coil)
                     else:
                         coord = self.last_coord + (self.target - self.last_coord) * 0.05
+                        coords[1] = coord
                         self.last_coord = coord
 
                     angles = [np.radians(coord[3]), np.radians(coord[4]), np.radians(coord[5])]
                     translate = coord[0:3]
-                    m_img = tr.compose_matrix(angles=angles, translate=translate)
+                    m_imgs[1] = tr.compose_matrix(angles=angles, translate=translate)
+
+                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs, view_obj])
+
+                coord = coords[1]  # main coil
+                m_img = m_imgs[1]
 
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
-                # self.pipeline.set_message(m_img_flip)
-
-                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs, view_obj])
-                # print('CoordCoreg: put {}'.format(count))
-                # count += 1
 
                 if self.view_tracts:
                     self.coord_tracts_queue.put_nowait(m_img_flip)
@@ -466,11 +474,10 @@ def run(self):
                 # print(self.icp, self.m_icp)
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
-                #m_change = coreg_data[1]
-                #r_stylus = coreg_data[0] # currently used for probe only 
-                coords, m_imgs = corregistrate_probe(coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id)
-                coord, m_img = corregistrate_dynamic(coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp])
-                #r_change = coreg_data[0] # currently used for probe only 
+                # NOTE: THIS THREAD WILL BE REFACTORED/DELETED SOON (with multicoil PR)
+
+                # m_change = coreg_data[1]
+                # r_stylus = coreg_data[0] # currently used for probe only
                 coords, m_imgs = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index 8aaaa058d..5634af961 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -313,7 +313,7 @@ def __init__(self, parent):
             actor_factory=self.actor_factory,
             vector_field_visualizer=self.vector_field_visualizer,
         )
-        
+
         self.probe_visualizer = ProbeVisualizer(self.ren, self.interactor)
 
         self.seed_offset = const.SEED_OFFSET
diff --git a/invesalius/data/visualization/probe_visualizer.py b/invesalius/data/visualization/probe_visualizer.py
index 1579c1199..4101a96cc 100644
--- a/invesalius/data/visualization/probe_visualizer.py
+++ b/invesalius/data/visualization/probe_visualizer.py
@@ -1,9 +1,11 @@
 import os
+
 import vtk
 
 import invesalius.data.vtk_utils as vtku
-from invesalius.pubsub import pub as Publisher
 from invesalius import inv_paths
+from invesalius.pubsub import pub as Publisher
+
 
 class ProbeVisualizer:
     """
@@ -23,14 +25,14 @@ def __init__(self, renderer, interactor):
         self.__bind_events()
 
     def __bind_events(self):
-        Publisher.subscribe(self.ShowProbe, 'Show probe in viewer volume')
-        Publisher.subscribe(self.UpdateProbePose, 'Update probe pose')
-        Publisher.subscribe(self.OnNavigationStatus, 'Navigation status')
+        Publisher.subscribe(self.ShowProbe, "Show probe in viewer volume")
+        Publisher.subscribe(self.UpdateProbePose, "Update probe pose")
+        Publisher.subscribe(self.OnNavigationStatus, "Navigation status")
 
     def OnNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status  # show probe when start navigation
-        if self.probe_actor is not None: # and hide it when stop navigation
-            Publisher.sendMessage('Press show-probe button',pressed=nav_status)
+        if self.probe_actor is not None:  # and hide it when stop navigation
+            Publisher.sendMessage("Press show-probe button", pressed=nav_status)
             self.ShowProbe(self.is_navigating)
             self.interactor.Render()
 
@@ -40,15 +42,15 @@ def ShowProbe(self, state):
         if self.probe_actor:
             self.probe_actor.SetVisibility(self.show_probe)
             self.interactor.Render()
-    
+
     def AddProbeActor(self, probe_path):
         vtk_colors = vtk.vtkNamedColors()
         obj_polydata = vtku.CreateObjectPolyData(probe_path)
-             
-        # This rotation is done so that the probe visibility icon in viewer_volume doesn't need to be rotated
+
+        # This rotation is done so that the probe visibility icon in viewer_volume doesn"t need to be rotated
         transform = vtk.vtkTransform()
         transform.RotateZ(-150)
-        
+
         transform_filt = vtk.vtkTransformPolyDataFilter()
         transform_filt.SetTransform(transform)
         transform_filt.SetInputData(obj_polydata)
@@ -60,10 +62,10 @@ def AddProbeActor(self, probe_path):
 
         probe_actor = vtk.vtkActor()
         probe_actor.SetMapper(obj_mapper)
-        probe_actor.GetProperty().SetAmbientColor(vtk_colors.GetColor3d('GhostWhite'))
+        probe_actor.GetProperty().SetAmbientColor(vtk_colors.GetColor3d("GhostWhite"))
         probe_actor.GetProperty().SetSpecular(30)
         probe_actor.GetProperty().SetSpecularPower(80)
-        probe_actor.GetProperty().SetOpacity(.4)
+        probe_actor.GetProperty().SetOpacity(0.4)
         probe_actor.SetVisibility(0)
 
         self.probe_actor = probe_actor
@@ -75,13 +77,14 @@ def RemoveProbeActor(self):
             self.probe_actor = None
 
     def UpdateProbePose(self, m_img, coord):
-        m_img_flip = m_img.copy() 
+        m_img_flip = m_img.copy()
         m_img_flip[1, -1] = -m_img_flip[1, -1]
 
         m_img_vtk = vtku.numpy_to_vtkMatrix4x4(m_img_flip)
 
         self.probe_actor.SetUserMatrix(m_img_vtk)
 
+
 """
 Code used to shrink and align old stylus.stl file. 
 May be useful for aligning other stl files into VTK in the future.
@@ -163,4 +166,4 @@ def __calculate_pca(self, polydata):
         # for another STL object tip could be in opposite direction so would use argmin instead
         tip = points[np.argmax(np.dot(centered_points, eigenvectors[:,1]))]
         return eigenvectors, tip
-"""
\ No newline at end of file
+"""
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 573c618c1..ba1b79f22 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -994,20 +994,21 @@ def OnBack(self, evt):
         Publisher.sendMessage("Move to tracker page")
 
     def OnNext(self, evt):
-        Publisher.sendMessage('Move to stylus page')
+        Publisher.sendMessage("Move to stylus page")
 
     def OnRefine(self, evt):
         self.icp.RegisterICP(self.navigation, self.tracker)
         if self.icp.use_icp:
             self.OnUpdateUI()
 
+
 class StylusPage(wx.Panel):
     def __init__(self, parent, nav_hub):
         wx.Panel.__init__(self, parent)
         self.navigation = nav_hub.navigation
         self.tracker = nav_hub.tracker
 
-        border = wx.FlexGridSizer(1,3, 5)
+        border = wx.FlexGridSizer(1, 3, 5)
         self.border = border
 
         self.done = False
@@ -1015,25 +1016,33 @@ def __init__(self, parent, nav_hub):
         lbl = wx.StaticText(self, -1, _("Calibrate stylus with head"))
         lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
         self.lbl = lbl
-        self.help_img = wx.Image(os.path.join(inv_paths.ICON_DIR,"align.png"), wx.BITMAP_TYPE_ANY)
-        
-        #first show help in grayscale. when record successful: make it green
-        self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToGreyscale(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
+        self.help_img = wx.Image(os.path.join(inv_paths.ICON_DIR, "align.png"), wx.BITMAP_TYPE_ANY)
+
+        # first show help in grayscale. when record successful: make it green to show success
+        self.help = wx.GenericStaticBitmap(
+            self,
+            -1,
+            self.help_img.ConvertToGreyscale(),
+            (10, 5),
+            (self.help_img.GetWidth(), self.help_img.GetHeight()),
+        )
 
         lbl_rec = wx.StaticText(self, -1, _("Point stylus up relative to head, like so:"))
         btn_rec = wx.Button(self, -1, _("Record"))
         btn_rec.SetToolTip("Record stylus orientation relative to head")
         btn_rec.Bind(wx.EVT_BUTTON, self.onRecord)
-        
+
         self.btn_rec = btn_rec
 
-        self.border.AddMany([
-            (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2),
-            (lbl_rec, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2),
-            (self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1),      
-            (btn_rec, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 1)
-        ])
-        
+        self.border.AddMany(
+            [
+                (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2),
+                (lbl_rec, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2),
+                (self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1),
+                (btn_rec, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 1),
+            ]
+        )
+
         back_button = wx.Button(self, label="Back")
         back_button.Bind(wx.EVT_BUTTON, partial(self.OnBack))
         next_button = wx.Button(self, label="Next")
@@ -1044,39 +1053,54 @@ def __init__(self, parent, nav_hub):
         bottom_sizer.Add(next_button)
 
         main_sizer = wx.BoxSizer(wx.VERTICAL)
-        main_sizer.AddMany([
-            (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 1),
-            (bottom_sizer, 0, wx.ALIGN_CENTER | wx.CENTER | wx.TOP, 1)
-        ])
-        
+        main_sizer.AddMany(
+            [
+                (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 1),
+                (bottom_sizer, 0, wx.ALIGN_CENTER | wx.CENTER | wx.TOP, 1),
+            ]
+        )
+
         self.SetSizerAndFit(main_sizer)
         self.Layout()
         self.__bind_events()
 
     def __bind_events(self):
-        pass #Publisher.subscribe(self.OnCloseProject, 'Remove object data')
+        pass  # Publisher.subscribe(self.OnCloseProject, 'Remove object data')
 
     def onRecord(self, evt):
-        marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(ref_mode_id=0, n_samples=1)
-        if marker_visibilities[0] and marker_visibilities[1]: #if probe and head are visible
-            if self.navigation.SetStylusOrientation(coord_raw): # if successfully created r_stylus
+        marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(
+            ref_mode_id=0, n_samples=1
+        )
+        if marker_visibilities[0] and marker_visibilities[1]:  # if probe and head are visible
+            if self.navigation.SetStylusOrientation(coord_raw):  # if successfully created r_stylus
                 # Save to config.json file
-                ses.Session().SetConfig('navigation-stylus', {'r_stylus': self.navigation.r_stylus.tolist()})
+                ses.Session().SetConfig(
+                    "navigation-stylus", {"r_stylus": self.navigation.r_stylus.tolist()}
+                )
 
-                if not self.done: #only show green on first record
+                if not self.done:  # only show green on first record
                     self.done = True
-                    self.help.Destroy() #show a colored (green) bitmap as opposed to grayscale
-                    self.help = wx.GenericStaticBitmap(self, -1, self.help_img.ConvertToBitmap(), (10, 5), (self.help_img.GetWidth(), self.help_img.GetHeight()))
-                    self.border.Insert(2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1)
+                    self.help.Destroy()  # show a colored (green) bitmap as opposed to grayscale
+                    self.help = wx.GenericStaticBitmap(
+                        self,
+                        -1,
+                        self.help_img.ConvertToBitmap(),
+                        (10, 5),
+                        (self.help_img.GetWidth(), self.help_img.GetHeight()),
+                    )
+                    self.border.Insert(
+                        2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1
+                    )
                     self.Layout()
         else:
-            wx.MessageBox(_("Probe or head not visible to tracker!"), _("InVesalius 3"))            
+            wx.MessageBox(_("Probe or head not visible to tracker!"), _("InVesalius 3"))
 
     def OnBack(self, evt):
-        Publisher.sendMessage('Move to refine page')
- 
+        Publisher.sendMessage("Move to refine page")
+
     def OnNext(self, evt):
-        Publisher.sendMessage('Move to stimulator page')
+        Publisher.sendMessage("Move to stimulator page")
+
 
 class StimulatorPage(wx.Panel):
     def __init__(self, parent, nav_hub):
@@ -1324,13 +1348,17 @@ def __init__(self, parent, nav_hub):
 
         # Toggle button for showing probe during navigation
         tooltip = _("Show probe")
-        BMP_SHOW_PROBE = wx.Bitmap(str(inv_paths.ICON_DIR.joinpath("stylus.png")), wx.BITMAP_TYPE_PNG)
-        show_probe_button = wx.ToggleButton(self, -1, "", style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE)
+        BMP_SHOW_PROBE = wx.Bitmap(
+            str(inv_paths.ICON_DIR.joinpath("stylus.png")), wx.BITMAP_TYPE_PNG
+        )
+        show_probe_button = wx.ToggleButton(
+            self, -1, "", style=pbtn.PB_STYLE_SQUARE, size=ICON_SIZE
+        )
         show_probe_button.SetBackgroundColour(GREY_COLOR)
         show_probe_button.SetBitmap(BMP_SHOW_PROBE)
         show_probe_button.SetToolTip(tooltip)
         show_probe_button.Enable(True)
-        self.UpdateToggleButton(show_probe_button, False) #the probe is hidden at start
+        self.UpdateToggleButton(show_probe_button, False)  # the probe is hidden at start
         show_probe_button.Bind(wx.EVT_TOGGLEBUTTON, self.OnShowProbe)
         self.show_probe_button = show_probe_button
 
@@ -1516,10 +1544,10 @@ def __bind_events(self):
         Publisher.subscribe(self.UpdateTractsVisualization, "Update tracts visualization")
 
         # Externally press/unpress and enable/disable buttons.
-        Publisher.subscribe(self.PressShowProbeButton, 'Press show-probe button')
+        Publisher.subscribe(self.PressShowProbeButton, "Press show-probe button")
 
-        Publisher.subscribe(self.PressShowCoilButton, 'Press show-coil button')
-        Publisher.subscribe(self.EnableShowCoilButton, 'Enable show-coil button')
+        Publisher.subscribe(self.PressShowCoilButton, "Press show-coil button")
+        Publisher.subscribe(self.EnableShowCoilButton, "Enable show-coil button")
 
         Publisher.subscribe(self.PressTrackObjectButton, "Press track object button")
         Publisher.subscribe(self.EnableTrackObjectButton, "Enable track object button")
@@ -1817,8 +1845,8 @@ def EnableShowCoilButton(self, enabled=False):
     def OnShowCoil(self, evt=None):
         self.UpdateToggleButton(self.show_coil_button)
         pressed = self.show_coil_button.GetValue()
-        Publisher.sendMessage('Show coil in viewer volume', state=pressed)
-    
+        Publisher.sendMessage("Show coil in viewer volume", state=pressed)
+
     # 'Show probe' button
     def PressShowProbeButton(self, pressed=False):
         self.UpdateToggleButton(self.show_probe_button, pressed)
@@ -1827,7 +1855,7 @@ def PressShowProbeButton(self, pressed=False):
     def OnShowProbe(self, evt=None):
         self.UpdateToggleButton(self.show_probe_button)
         pressed = self.show_probe_button.GetValue()
-        Publisher.sendMessage('Show probe in viewer volume', state=pressed)
+        Publisher.sendMessage("Show probe in viewer volume", state=pressed)
 
     # 'Serial Port Com'
     def OnEnableSerialPort(self, evt, ctrl):
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 779e756c2..dd9911556 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -142,7 +142,7 @@ def run(self):
             object_visible_flag = False
             try:
                 coords, marker_visibilities, m_imgs, view_obj = self.coord_queue.get_nowait()
-                coord = coords[1] # main coil
+                coord = coords[1]  # main coil
                 m_img = m_imgs[1]
 
                 got_coords = True
@@ -220,9 +220,11 @@ def run(self):
                         "Update volume viewer pointer",
                         position=[coord[0], -coord[1], coord[2]],
                     )
-                
-                wx.CallAfter(Publisher.sendMessage, 'Update probe pose', m_img=m_imgs[0], coord=coords[0])
-                
+
+                wx.CallAfter(
+                    Publisher.sendMessage, "Update probe pose", m_img=m_imgs[0], coord=coords[0]
+                )
+
                 # Render the volume viewer and the slice viewers.
                 wx.CallAfter(Publisher.sendMessage, "Render volume viewer")
                 wx.CallAfter(Publisher.sendMessage, "Update slice viewer")
@@ -346,9 +348,9 @@ def LoadConfig(self):
         )
 
         # Try to load stylus orientation data
-        stylus_data = session.GetConfig('navigation-stylus')
+        stylus_data = session.GetConfig("navigation-stylus")
         if stylus_data is not None:
-            self.r_stylus = np.array(stylus_data['r_stylus'])
+            self.r_stylus = np.array(stylus_data["r_stylus"])
 
     def CoilAtTarget(self, state):
         self.coil_at_target = state
@@ -419,24 +421,23 @@ def EstimateTrackerToInVTransformationMatrix(self, tracker, image):
 
     def SetStylusOrientation(self, coord_raw):
         if self.m_change is not None:
-            m_probe = dcr.compute_marker_transformation(coord_raw, 0) 
+            m_probe = dcr.compute_marker_transformation(coord_raw, 0)
 
             # transform probe to reference system if dynamic ref_mode
             if self.ref_mode_id:
                 up_trk = dcr.object_to_reference(coord_raw, m_probe)[:3, :3]
             else:
                 up_trk = m_probe[:3, :3]
-            
-            # up_trk: orientation 'stylus pointing up along head' in tracker space 
+
+            # up_trk: orientation 'stylus pointing up along head' in tracker space
             # up_vtk: orientation 'stylus pointing up along head' in vtk space
-            up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes='rxyz')[:3,:3]
+            up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes="rxyz")[:3, :3]
 
             # Rotation from tracker to VTK coordinate system
             self.r_stylus = up_vtk @ np.linalg.inv(up_trk)
             return True
         else:
             return False
-        
 
     def StartNavigation(self, tracker, icp):
         # initialize jobs list
diff --git a/navigation/ndi_files/Markers/NBSref.rom b/navigation/ndi_files/Markers/NBSref.rom
index 426497352428f907d17cdc11fbe454259bcb17ae..820d7b8fb8ba90b312873f65f47e58b9ef42fc3a 100644
GIT binary patch
literal 752
zcmeZs@nqmLVPIfnU|?W^Pz+2e6Ro3wd=?;P24Wy^0F$@~4hDvqb1xq}Z}r|WwR(c>
z{q=Va&RKQi;9o1xJ?31e9p_a|cG{V8$<D|5spC4inTG_eKkUP0)KC#;lkMEavu&xh
z!vA`EV%S5)UpU>#$OKIa2o>@`zzO8$B^AR3{hWe}Qq$mEFoTm32vCK9DGiHQ1A`{I
HGHUYy)`&GM

literal 752
zcmeZs@nra6%D}+Lz`(!^p%|D{CR#@U`797IAj#kWBCrDmN09h~@7#wPJc}F|Hdq}L
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zW4CWqbU;FYk%^gwl?}yec_82fisU5~!^Qoaf{Rkq;9M|+lMw<?M6roAFleHvp#cW~
Drein(

diff --git a/navigation/ndi_files/Markers/NT-115.rom b/navigation/ndi_files/Markers/NT-115.rom
index dd67e7678f81e19cc69ba5f696e62ab4b1736e4b..a5868cbad4f5c0951eee19a8349d2c1d43bff1e3 100644
GIT binary patch
delta 124
zcmeys`hk_r&&88LLwO>bjTr+20|x`cveKm*3=Cq2-vs73PFQ{%$TkJD3vCZM2K@*G
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delta 117
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diff --git a/navigation/ndi_files/Markers/newNBSref.rom b/navigation/ndi_files/Markers/newNBSref.rom
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From 2a4ce4c4550c40b4ea76d1c3e403be231b1688d9 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 18 Jul 2024 21:28:59 +0300
Subject: [PATCH 12/44] Completely replace corregistrate_dynamic by
 corregistrate_probe. These functions were identical, except for r_img in
 corregistrate_probe... This rotation does not change ICP behavior since ICP
 only affects the translation

---
 invesalius/data/bases.py            |  4 +--
 invesalius/data/coregistration.py   | 53 ++++-------------------------
 invesalius/data/viewer_volume.py    |  2 +-
 invesalius/gui/dialogs.py           |  4 +--
 invesalius/navigation/navigation.py |  2 +-
 5 files changed, 11 insertions(+), 54 deletions(-)

diff --git a/invesalius/data/bases.py b/invesalius/data/bases.py
index cb9e10f04..485bdecf6 100644
--- a/invesalius/data/bases.py
+++ b/invesalius/data/bases.py
@@ -137,9 +137,7 @@ def calculate_fre(
 
     dist = np.zeros([3, 1])
     for i in range(0, 6, 2):
-        p_m, _ = dcr.corregistrate_dynamic(
-            (m_change, 0), fiducials_raw[i : i + 2], ref_mode_id, icp
-        )
+        p_m, _ = dcr.corregistrate_probe(m_change, None, fiducials_raw[i : i + 2], ref_mode_id, icp)
         dist[int(i / 2)] = np.sqrt(np.sum(np.power((p_m[:3] - fiducials[int(i / 2), :]), 2)))
 
     return float(np.sqrt(np.sum(dist**2) / 3))
diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 31886097d..927209231 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -171,7 +171,7 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
     return m_target_in_tracker
 
 
-def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id):
+def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, None]):
     if r_stylus is None:
         # utils.debug("STYLUS ORIENTATION NOT DEFINED!")
         r_stylus = np.eye(3)
@@ -189,6 +189,7 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id):
 
     # translate m_probe_ref from tracker to image space
     m_img = m_change @ m_probe_ref
+    m_img = apply_icp(m_img, icp)
 
     # rotate m_probe_ref from tracker to image space
     r_img = r_stylus @ m_probe_ref[:3, :3]
@@ -254,42 +255,6 @@ def compute_marker_transformation(coord_raw, obj_ref_mode):
     return m_probe
 
 
-def corregistrate_dynamic(inp, coord_raw, ref_mode_id, icp):
-    m_change, obj_ref_mode = inp
-
-    # transform raw marker coordinate to object center
-    m_probe = compute_marker_transformation(coord_raw, obj_ref_mode)
-
-    # transform object center to reference marker if specified as dynamic reference
-    if ref_mode_id:
-        m_ref = compute_marker_transformation(coord_raw, 1)
-        m_probe_ref = np.linalg.inv(m_ref) @ m_probe
-    else:
-        m_probe_ref = m_probe
-
-    # invert y coordinate
-    m_probe_ref[2, -1] = -m_probe_ref[2, -1]
-
-    # corregistrate from tracker to image space
-    m_img = m_change @ m_probe_ref
-    m_img = apply_icp(m_img, icp)
-
-    # compute rotation angles
-    angles = np.degrees(tr.euler_from_matrix(m_img, axes="sxyz"))
-
-    # create output coordinate list
-    coord = (
-        m_img[0, -1],
-        m_img[1, -1],
-        m_img[2, -1],
-        angles[0],
-        angles[1],
-        angles[2],
-    )
-
-    return coord, m_img
-
-
 def apply_icp(m_img, icp):
     use_icp, m_icp = icp
     if use_icp:
@@ -476,18 +441,14 @@ def run(self):
 
                 # NOTE: THIS THREAD WILL BE REFACTORED/DELETED SOON (with multicoil PR)
 
-                # m_change = coreg_data[1]
-                # r_stylus = coreg_data[0] # currently used for probe only
-                coords, m_imgs = corregistrate_probe(
+                # m_change = coreg_data[1], r_stylus = coreg_data[0]
+                coord, m_img = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
-                coord, m_img = corregistrate_dynamic(
-                    coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
-                )
-
-                coords = np.stack((coords, coord))
-                m_imgs = np.stack((m_imgs, m_img))
 
+                # temporary hack to follow old code structure, will be refactored soon
+                coords = [coord, coord]
+                m_imgs = [m_img, m_img]
                 # print("Coord: ", coord)
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index 5634af961..4d22607d6 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -98,8 +98,8 @@
 from invesalius.data.markers.surface_geometry import SurfaceGeometry
 from invesalius.data.ruler_volume import GenericLeftRulerVolume
 from invesalius.data.visualization.coil_visualizer import CoilVisualizer
-from invesalius.data.visualization.probe_visualizer import ProbeVisualizer
 from invesalius.data.visualization.marker_visualizer import MarkerVisualizer
+from invesalius.data.visualization.probe_visualizer import ProbeVisualizer
 from invesalius.data.visualization.vector_field_visualizer import VectorFieldVisualizer
 from invesalius.gui.widgets.canvas_renderer import CanvasRendererCTX
 from invesalius.i18n import tr as _
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 4aed757c6..2fafc9cd0 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -4474,9 +4474,7 @@ def RemoveSinglePointActor(self) -> None:
 
     def GetCurrentCoord(self) -> Tuple[Tuple, List[bool]]:
         coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
-        coord, _ = dcr.corregistrate_dynamic(
-            (self.m_change, 0), coord_raw, const.DEFAULT_REF_MODE, [None, None]
-        )
+        coord, _ = dcr.corregistrate_probe(self.m_change, None, coord_raw, const.DEFAULT_REF_MODE)
         return coord[:3], marker_visibilities
 
     def AddMarker(self, size: int, colour: Tuple[int, int, int], coord: np.ndarray) -> None:
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index dd9911556..a5c4a54ca 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -142,7 +142,7 @@ def run(self):
             object_visible_flag = False
             try:
                 coords, marker_visibilities, m_imgs, view_obj = self.coord_queue.get_nowait()
-                coord = coords[1]  # main coil
+                coord = coords[1]  # main coil (or stylus if view_obj=False)
                 m_img = m_imgs[1]
 
                 got_coords = True

From 5e5271bfce3fd2c9bb75d613c67ac159a6c53206 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sat, 20 Jul 2024 19:41:35 +0300
Subject: [PATCH 13/44] Refactor 'Track coil' button behavior: this determines
 (on the fly) whether to follow the coil or probe with marker. Join the two
 Corregistrate threads into one. Edit CoilVisualizer and GUI to work with this
 change.

Please excuse some stray comments and var-definitions (eg. n_coils)... I will clean these up in future multicoil PR.
---
 invesalius/data/coregistration.py             | 145 ++++++++--------
 .../data/visualization/coil_visualizer.py     |  26 ++-
 invesalius/gui/preferences.py                 |   5 +-
 invesalius/gui/task_navigator.py              |  14 +-
 invesalius/navigation/navigation.py           | 158 +++++++++---------
 5 files changed, 168 insertions(+), 180 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 927209231..3d7fe6e50 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -48,7 +48,6 @@ def object_marker_to_center(coord_raw, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw
     :return: 4 x 4 numpy double array
     :rtype: numpy.ndarray
     """
-
     as1, bs1, gs1 = np.radians(coord_raw[obj_ref_mode, 3:])
     r_probe = tr.euler_matrix(as1, bs1, gs1, "rzyx")
     t_probe_raw = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
@@ -211,17 +210,17 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     return coord, m_img
 
 
-def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id, icp):
+def corregistrate_object_dynamic(inp, coord_raw, i_obj, icp):
+    """
+    Corregistrate the object at coord_raw[i_obj] in dynamic ref_mode
+    """
     m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
 
     # transform raw marker coordinate to object center
-    m_probe = object_marker_to_center(coord_raw, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw)
+    m_probe = object_marker_to_center(coord_raw, i_obj, t_obj_raw, s0_raw, r_s0_raw)
 
-    # transform object center to reference marker if specified as dynamic reference
-    if ref_mode_id:
-        m_probe_ref = object_to_reference(coord_raw, m_probe)
-    else:
-        m_probe_ref = m_probe
+    # transform object center to reference marker
+    m_probe_ref = object_to_reference(coord_raw, m_probe)
 
     # invert y coordinate
     m_probe_ref[2, -1] = -m_probe_ref[2, -1]
@@ -246,6 +245,38 @@ def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id, icp):
     return coord, m_img
 
 
+def corregistrate_object_static(inp, coord_raw, i_obj, icp):
+    """
+    Corregistrate the object at coord_raw[i_obj] in static ref_mode
+    """
+    m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
+
+    # transform raw marker coordinate to object center
+    m_probe = object_marker_to_center(coord_raw, i_obj, t_obj_raw, s0_raw, r_s0_raw)
+
+    # invert y coordinate
+    m_probe[2, -1] = -m_probe[2, -1]
+
+    # corregistrate from tracker to image space
+    m_img = tracker_to_image(m_change, m_probe, r_obj_img, m_obj_raw, s0_dyn)
+    m_img = apply_icp(m_img, icp)
+
+    # compute rotation angles
+    angles = np.degrees(tr.euler_from_matrix(m_img, axes="sxyz"))
+
+    # create output coordinate list
+    coord = (
+        m_img[0, -1],
+        m_img[1, -1],
+        m_img[2, -1],
+        angles[0],
+        angles[1],
+        angles[2],
+    )
+
+    return coord, m_img
+
+
 def compute_marker_transformation(coord_raw, obj_ref_mode):
     m_probe = dco.coordinates_to_transformation_matrix(
         position=coord_raw[obj_ref_mode, :3],
@@ -299,6 +330,7 @@ def __init__(
         self,
         ref_mode_id,
         tracker,
+        n_coils,
         coreg_data,
         view_tracts,
         queues,
@@ -312,6 +344,7 @@ def __init__(
         threading.Thread.__init__(self, name="CoordCoregObject")
         self.ref_mode_id = ref_mode_id
         self.tracker = tracker
+        self.n_coils = n_coils
         self.coreg_data = coreg_data
         self.coord_queue = queues[0]
         self.view_tracts = view_tracts
@@ -340,9 +373,20 @@ def __init__(
 
     def run(self):
         coreg_data = self.coreg_data
-        view_obj = 1
+        corregistrate_object = (
+            corregistrate_object_dynamic if self.ref_mode_id else corregistrate_object_static
+        )
+
+        # compute n_coils_effective, the no. of coils to actually process:
+        # check how many coords we get from tracker (-2 for probe & head)
+        n_coils_trk = self.tracker.TrackerCoordinates.GetCoordinates()[0].shape[0] - 2
+
+        obj_ref_mode = coreg_data[2]
+        # if obj_ref_mode=0: only coregister one coil
+        # else: process the other (n_coils - 1) coils too
+        # min(obj_ref_mode, 1) = 0 if obj_ref_mode==0 else 1
+        n_coils_effective = min(n_coils_trk, 1 + min(obj_ref_mode, 1) * (self.n_coils - 1))
 
-        # print('CoordCoreg: event {}'.format(self.event.is_set()))
         while not self.event.is_set():
             try:
                 if not self.icp_queue.empty():
@@ -351,20 +395,27 @@ def run(self):
                 if not self.object_at_target_queue.empty():
                     self.target_flag = self.object_at_target_queue.get_nowait()
 
-                # print(f"Set the coordinate")
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
-                # m_change = coreg_data[1], r_stylus = coreg_data[0] (r_stylus used for probe only)
+                # m_change = coreg_data[1], r_stylus = coreg_data[0]
                 coord_probe, m_img_probe = corregistrate_probe(
                     coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
                 )
-                coord_coil, m_img_coil = corregistrate_object_dynamic(
-                    coreg_data[1:], coord_raw, self.ref_mode_id, [self.use_icp, self.m_icp]
+                coord_coil, m_img_coil = corregistrate_object(
+                    coreg_data[1:], coord_raw, obj_ref_mode, [self.use_icp, self.m_icp]
                 )
 
                 coords = [coord_probe, coord_coil]
                 m_imgs = [m_img_probe, m_img_coil]
 
+                # the possible other coils are i_obj=3 onwards at coord_raw[i_obj]
+                for i_obj in range(3, n_coils_effective + 2):
+                    coord_coil, m_img_coil = corregistrate_object(
+                        coreg_data[1:], coord_raw, i_obj, [self.use_icp, self.m_icp]
+                    )
+                    coords.append(coord_coil)
+                    m_imgs.append(m_img_coil)
+
                 # XXX: This is not the best place to do the logic related to approaching the target when the
                 #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
                 #      the tracker space where it is hard to make the tracker approach the target in the image space.
@@ -385,10 +436,12 @@ def run(self):
                     translate = coord[0:3]
                     m_imgs[1] = tr.compose_matrix(angles=angles, translate=translate)
 
-                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs, view_obj])
+                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs])
 
                 coord = coords[1]  # main coil
                 m_img = m_imgs[1]
+                # LUKATODO: should coord = coords[track_coil]
+                # should the stuff below ever be done for stylus, but not coil?
 
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
@@ -403,65 +456,3 @@ def run(self):
                 pass
             # The sleep has to be in both threads
             sleep(self.sle)
-
-
-class CoordinateCorregistrateNoObject(threading.Thread):
-    def __init__(
-        self, ref_mode_id, tracker, coreg_data, view_tracts, queues, event, sle, icp, e_field_loaded
-    ):
-        threading.Thread.__init__(self, name="CoordCoregNoObject")
-        self.ref_mode_id = ref_mode_id
-        self.tracker = tracker
-        self.coreg_data = coreg_data
-        self.coord_queue = queues[0]
-        self.view_tracts = view_tracts
-        self.coord_tracts_queue = queues[1]
-        self.event = event
-        self.sle = sle
-        self.icp_queue = queues[2]
-        self.use_icp = icp.use_icp
-        self.m_icp = icp.m_icp
-        self.efield_queue = queues[3]
-        self.e_field_loaded = e_field_loaded
-
-    def run(self):
-        coreg_data = self.coreg_data
-        view_obj = 0
-
-        # print('CoordCoreg: event {}'.format(self.event.is_set()))
-        while not self.event.is_set():
-            try:
-                if self.icp_queue.empty():
-                    None
-                else:
-                    self.use_icp, self.m_icp = self.icp_queue.get_nowait()
-                # print(f"Set the coordinate")
-                # print(self.icp, self.m_icp)
-                coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
-
-                # NOTE: THIS THREAD WILL BE REFACTORED/DELETED SOON (with multicoil PR)
-
-                # m_change = coreg_data[1], r_stylus = coreg_data[0]
-                coord, m_img = corregistrate_probe(
-                    coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
-                )
-
-                # temporary hack to follow old code structure, will be refactored soon
-                coords = [coord, coord]
-                m_imgs = [m_img, m_img]
-                # print("Coord: ", coord)
-                m_img_flip = m_img.copy()
-                m_img_flip[1, -1] = -m_img_flip[1, -1]
-
-                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs, view_obj])
-
-                if self.view_tracts:
-                    self.coord_tracts_queue.put_nowait(m_img_flip)
-                if self.e_field_loaded:
-                    self.efield_queue.put_nowait([m_img, coord])
-                if not self.icp_queue.empty():
-                    self.icp_queue.task_done()
-            except queue.Full:
-                pass
-            # The sleep has to be in both threads
-            sleep(self.sle)
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index f1dd39aad..cf4bd10f5 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -35,14 +35,20 @@ def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer)
         # The vector field visualizer is used to show a vector field relative to the coil.
         self.vector_field_visualizer = vector_field_visualizer
 
+        # Number of coils is by default 1
+        self.n_coils = 1
+
         # The actor for showing the actual coil in the volume viewer.
         self.coil_actor = None
+        self.coil_actors = []
 
         # The actor for showing the center of the actual coil in the volume viewer.
         self.coil_center_actor = None
+        self.coil_center_actors = []
 
         # The actor for showing the target coil in the volume viewer.
         self.target_coil_actor = None
+        self.target_coil_actors = []
 
         # The assembly for showing the vector field relative to the coil in the volume viewer.
         self.vector_field_assembly = self.vector_field_visualizer.CreateVectorFieldAssembly()
@@ -72,6 +78,9 @@ def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer)
 
         self.LoadConfig()
 
+        self.AddCoilActor(self.coil_path)
+        self.ShowCoil(False)
+
         self.__bind_events()
 
     def __bind_events(self):
@@ -79,6 +88,7 @@ def __bind_events(self):
         Publisher.subscribe(self.OnNavigationStatus, "Navigation status")
         Publisher.subscribe(self.TrackObject, "Track object")
         Publisher.subscribe(self.ShowCoil, "Show coil in viewer volume")
+        Publisher.subscribe(self.SetCoilCount, "Set coil count")
         Publisher.subscribe(self.ConfigureCoil, "Configure coil")
         Publisher.subscribe(self.UpdateCoilPose, "Update coil pose")
         Publisher.subscribe(self.UpdateVectorField, "Update vector field")
@@ -162,6 +172,9 @@ def SetCoilAtTarget(self, state):
         self.target_coil_actor.GetProperty().SetDiffuseColor(target_coil_color)
         self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color)
 
+    def SetCoilCount(self, n_coils):
+        self.n_coils = n_coils
+
     def RemoveCoilActor(self):
         self.renderer.RemoveActor(self.coil_actor)
         self.renderer.RemoveActor(self.coil_center_actor)
@@ -186,16 +199,11 @@ def OnNavigationStatus(self, nav_status, vis_status):
     def TrackObject(self, enabled):
         self.track_object_pressed = enabled
 
-        if self.coil_path is None:
-            return
-
-        # Remove the previous coil actor if it exists.
-        if self.coil_actor is not None:
-            self.RemoveCoilActor()
-
-        # If enabled, add a new coil actor.
+        # Hide coil vector_field if it exists. LUKATODO: what is this vector field?
         if enabled:
-            self.AddCoilActor(self.coil_path)
+            self.vector_field_assembly.SetVisibility(1)
+        else:
+            self.vector_field_assembly.SetVisibility(0)
 
     # Called when 'show coil' button is pressed in the user interface or in code.
     def ShowCoil(self, state):
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index d08e9422b..de232ee19 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1356,10 +1356,7 @@ def OnChooseTracker(self, evt, ctrl):
             self.ShowParent()
 
     def OnChooseReferenceMode(self, evt, ctrl):
-        # Probably need to refactor object registration as a whole to use the
-        # OnChooseReferenceMode function which was used earlier. It can be found in
-        # the deprecated code in ObjectRegistrationPanel in task_navigator.py.
-        pass
+        Navigation().SetReferenceMode(evt.GetSelection())
 
     def HideParent(self):  # hide preferences dialog box
         self.GetGrandParent().Hide()
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index ba1b79f22..4dd844a32 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1342,7 +1342,7 @@ def __init__(self, parent, nav_hub):
         show_coil_button.SetBitmap(BMP_SHOW_COIL)
         show_coil_button.SetToolTip(tooltip)
         show_coil_button.SetValue(False)
-        show_coil_button.Enable(False)
+        show_coil_button.Enable(True)
         show_coil_button.Bind(wx.EVT_TOGGLEBUTTON, self.OnShowCoil)
         self.show_coil_button = show_coil_button
 
@@ -1713,12 +1713,11 @@ def OnCheckStatus(self, nav_status, vis_status):
             self.EnableToggleButton(self.checkbox_serial_port, 1)
             self.UpdateToggleButton(self.checkbox_serial_port)
 
-        # Enable/Disable track-object checkbox if navigation is off/on and object registration is valid.
+        # Enable/Disable track-object checkbox if object registration is valid.
         obj_registration = self.navigation.GetObjectRegistration()
-        enable_track_object = (
-            obj_registration is not None and obj_registration[0] is not None and not nav_status
-        )
+        enable_track_object = obj_registration is not None and obj_registration[0] is not None
         self.EnableTrackObjectButton(enable_track_object)
+        self.EnableShowCoilButton(enable_track_object)
 
     # Robot
     def OnRobotStatus(self, data):
@@ -1819,10 +1818,7 @@ def OnTrackObjectButton(self, evt=None, ctrl=None):
         if not pressed:
             Publisher.sendMessage("Press target mode button", pressed=pressed)
 
-        # Disable or enable 'Show coil' button, based on if 'Track object' button is pressed.
-        Publisher.sendMessage("Enable show-coil button", enabled=pressed)
-
-        # Also, automatically press or unpress 'Show coil' button.
+        # Automatically press or unpress 'Show coil' button.
         Publisher.sendMessage("Press show-coil button", pressed=pressed)
 
         self.SaveConfig()
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index a5c4a54ca..f63f1811d 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -135,18 +135,28 @@ def __init__(self, vis_queues, vis_components, event, sle, neuronavigation_api):
         self.sle = sle
         self.event = event
         self.neuronavigation_api = neuronavigation_api
+        self.navigation = Navigation()
 
     def run(self):
         while not self.event.is_set():
             got_coords = False
-            object_visible_flag = False
             try:
-                coords, marker_visibilities, m_imgs, view_obj = self.coord_queue.get_nowait()
-                coord = coords[1]  # main coil (or stylus if view_obj=False)
-                m_img = m_imgs[1]
-
+                coords, marker_visibilities, m_imgs = self.coord_queue.get_nowait()
                 got_coords = True
-                object_visible_flag = marker_visibilities[2]
+
+                probe_visible = marker_visibilities[0]
+                coil_visible = marker_visibilities[2]
+
+                # automatically track either coil or stylus if only one of them is visible, otherise use navigation.track_obj
+                track_coil = (
+                    (coil_visible or not probe_visible)
+                    if (coil_visible ^ probe_visible)
+                    else self.navigation.track_obj
+                )
+
+                # choose which object to track in slices and viewer_volume pointer
+                coord = coords[track_coil]  # main-coil if track_coil else stylus
+                m_img = m_imgs[track_coil]
 
                 # use of CallAfter is mandatory otherwise crashes the wx interface
                 if self.view_tracts:
@@ -183,15 +193,32 @@ def run(self):
                 # new marker is created, it is created in the current position of the object.
                 wx.CallAfter(Publisher.sendMessage, "Set cross focal point", position=coord)
 
-                if self.e_field_loaded and object_visible_flag:
+                wx.CallAfter(
+                    Publisher.sendMessage,
+                    "Update volume viewer pointer",
+                    position=[coord[0], -coord[1], coord[2]],
+                )
+
+                if coil_visible:
+                    wx.CallAfter(
+                        Publisher.sendMessage, "Update coil pose", m_img=m_imgs[1], coord=coords[1]
+                    )
                     wx.CallAfter(
                         Publisher.sendMessage,
-                        "Update point location for e-field calculation",
-                        m_img=m_img,
-                        coord=coord,
-                        queue_IDs=self.e_field_IDs_queue,
+                        "Update object arrow matrix",
+                        m_img=m_imgs[1],
+                        coord=coords[1],
+                        flag=self.peel_loaded,
                     )
-                    if not self.e_field_norms_queue.empty():
+
+                    if self.e_field_loaded:
+                        wx.CallAfter(
+                            Publisher.sendMessage,
+                            "Update point location for e-field calculation",
+                            m_img=m_imgs[1],
+                            coord=coords[1],
+                            queue_IDs=self.e_field_IDs_queue,
+                        )
                         try:
                             enorm_data = self.e_field_norms_queue.get_nowait()
                             wx.CallAfter(
@@ -200,31 +227,16 @@ def run(self):
                                 enorm_data=enorm_data,
                                 plot_vector=self.plot_efield_vectors,
                             )
-                        finally:
+                        except queue.Empty:
+                            pass
+                        else:
                             self.e_field_norms_queue.task_done()
 
-                if view_obj:
-                    wx.CallAfter(
-                        Publisher.sendMessage, "Update coil pose", m_img=m_img, coord=coord
-                    )
-                    wx.CallAfter(
-                        Publisher.sendMessage,
-                        "Update object arrow matrix",
-                        m_img=m_img,
-                        coord=coord,
-                        flag=self.peel_loaded,
-                    )
-                else:
+                if probe_visible:
                     wx.CallAfter(
-                        Publisher.sendMessage,
-                        "Update volume viewer pointer",
-                        position=[coord[0], -coord[1], coord[2]],
+                        Publisher.sendMessage, "Update probe pose", m_img=m_imgs[0], coord=coords[0]
                     )
 
-                wx.CallAfter(
-                    Publisher.sendMessage, "Update probe pose", m_img=m_imgs[0], coord=coords[0]
-                )
-
                 # Render the volume viewer and the slice viewers.
                 wx.CallAfter(Publisher.sendMessage, "Render volume viewer")
                 wx.CallAfter(Publisher.sendMessage, "Update slice viewer")
@@ -245,6 +257,8 @@ def __init__(self, pedal_connector, neuronavigation_api):
 
         self.correg = None
         self.target = None
+        self.n_coils = 1
+        self.obj_registrations = []
         self.object_registration = None
         self.track_obj = False
         self.m_change = None
@@ -463,71 +477,53 @@ def StartNavigation(self, tracker, icp):
         ]
 
         Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components)
-        errors = False
-
-        if self.track_obj:
-            # if object tracking is selected
-            if self.object_registration is None:
-                # check if object registration was performed
-                wx.MessageBox(_("Perform coil registration before navigation."), _("InVesalius 3"))
-                errors = True
-            else:
-                # if object registration was correctly performed continue with navigation
-                # object_registration[0] is object 3x3 fiducial matrix and object_registration[1] is 3x3 orientation matrix
-                obj_fiducials, obj_orients, obj_ref_mode, obj_name = self.object_registration
 
-                coreg_data = [self.r_stylus, self.m_change, obj_ref_mode]
+        # LUKATODO: object_registration --> coil_registrations
+        if self.object_registration is None:
+            # check if object registration was performed
+            wx.MessageBox(_("Perform coil registration before navigation."), _("InVesalius 3"))
+        else:
+            # if object registration was correctly performed continue with navigation
+            # object_registration[0] is object 3x3 fiducial matrix and object_registration[1] is 3x3 orientation matrix
+            obj_fiducials, obj_orients, obj_ref_mode, obj_name = self.object_registration
 
-                if self.ref_mode_id:
-                    coord_raw, marker_visibilities = tracker.TrackerCoordinates.GetCoordinates()
-                else:
-                    coord_raw = np.array([None])
+            coreg_data = [self.r_stylus, self.m_change, obj_ref_mode]
 
-                self.obj_data = db.object_registration(
-                    obj_fiducials, obj_orients, coord_raw, self.m_change
-                )
-                coreg_data.extend(self.obj_data)
-
-                queues = [
-                    self.coord_queue,
-                    self.coord_tracts_queue,
-                    self.icp_queue,
-                    self.object_at_target_queue,
-                    self.efield_queue,
-                ]
-                jobs_list.append(
-                    dcr.CoordinateCorregistrate(
-                        self.ref_mode_id,
-                        tracker,
-                        coreg_data,
-                        self.view_tracts,
-                        queues,
-                        self.event,
-                        self.sleep_nav,
-                        tracker.tracker_id,
-                        self.target,
-                        icp,
-                        self.e_field_loaded,
-                    )
-                )
-        else:
-            coreg_data = (self.r_stylus, self.m_change, 0)
-            queues = [self.coord_queue, self.coord_tracts_queue, self.icp_queue, self.efield_queue]
+            if self.ref_mode_id:
+                coord_raw, marker_visibilities = tracker.TrackerCoordinates.GetCoordinates()
+            else:
+                coord_raw = np.array([None])
+
+            # LUKATODO: NOTE: coil does not need to be visible here, we only need the head coord for obj_data:
+            self.obj_data = db.object_registration(
+                obj_fiducials, obj_orients, coord_raw, self.m_change
+            )
+            coreg_data.extend(self.obj_data)
+
+            queues = [
+                self.coord_queue,
+                self.coord_tracts_queue,
+                self.icp_queue,
+                self.object_at_target_queue,
+                self.efield_queue,
+            ]
             jobs_list.append(
-                dcr.CoordinateCorregistrateNoObject(
+                dcr.CoordinateCorregistrate(
                     self.ref_mode_id,
                     tracker,
+                    self.n_coils,
                     coreg_data,
                     self.view_tracts,
                     queues,
                     self.event,
                     self.sleep_nav,
+                    tracker.tracker_id,
+                    self.target,
                     icp,
                     self.e_field_loaded,
                 )
             )
 
-        if not errors:
             # TODO: Test the serial port thread
             if self.serial_port_in_use:
                 self.serial_port_connection = spc.SerialPortConnection(

From 97b9bcd7bb16739908cac5c2d2909759690f49ab Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Mon, 22 Jul 2024 19:09:37 +0300
Subject: [PATCH 14/44] Simplify how r_stylus is saved to file: move r_stylus
 to 'navigation' object and remove bogus 'navigation-stylus' object

---
 invesalius/gui/task_navigator.py    | 34 ++++++++++++--------------
 invesalius/navigation/navigation.py | 37 ++++++++++++++++-------------
 2 files changed, 35 insertions(+), 36 deletions(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 4dd844a32..556136129 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1071,27 +1071,23 @@ def onRecord(self, evt):
         marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(
             ref_mode_id=0, n_samples=1
         )
+
         if marker_visibilities[0] and marker_visibilities[1]:  # if probe and head are visible
-            if self.navigation.SetStylusOrientation(coord_raw):  # if successfully created r_stylus
-                # Save to config.json file
-                ses.Session().SetConfig(
-                    "navigation-stylus", {"r_stylus": self.navigation.r_stylus.tolist()}
+            if self.navigation.SetStylusOrientation(coord_raw) and not self.done:
+                # if successfully created r_stylus in navigation for the first time: make the illustration green to show success
+                self.done = True
+                self.help.Destroy()  # show a colored (green) bitmap as opposed to grayscale
+                self.help = wx.GenericStaticBitmap(
+                    self,
+                    -1,
+                    self.help_img.ConvertToBitmap(),
+                    (10, 5),
+                    (self.help_img.GetWidth(), self.help_img.GetHeight()),
                 )
-
-                if not self.done:  # only show green on first record
-                    self.done = True
-                    self.help.Destroy()  # show a colored (green) bitmap as opposed to grayscale
-                    self.help = wx.GenericStaticBitmap(
-                        self,
-                        -1,
-                        self.help_img.ConvertToBitmap(),
-                        (10, 5),
-                        (self.help_img.GetWidth(), self.help_img.GetHeight()),
-                    )
-                    self.border.Insert(
-                        2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1
-                    )
-                    self.Layout()
+                self.border.Insert(
+                    2, self.help, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 1
+                )
+                self.Layout()
         else:
             wx.MessageBox(_("Probe or head not visible to tracker!"), _("InVesalius 3"))
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index f63f1811d..a4512cc83 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -347,24 +347,21 @@ def LoadConfig(self):
         session = ses.Session()
         state = session.GetConfig("navigation")
 
-        if state is None:
-            return
-
-        object_fiducials = np.array(state["object_fiducials"])
-        object_orientations = np.array(state["object_orientations"])
-        object_reference_mode = state["object_reference_mode"]
-        object_name = state["object_name"].encode(const.FS_ENCODE)
-        self.object_registration = (
-            object_fiducials,
-            object_orientations,
-            object_reference_mode,
-            object_name,
-        )
+        if state is not None:
+            object_fiducials = np.array(state["object_fiducials"])
+            object_orientations = np.array(state["object_orientations"])
+            object_reference_mode = state["object_reference_mode"]
+            object_name = state["object_name"].encode(const.FS_ENCODE)
+            self.object_registration = (
+                object_fiducials,
+                object_orientations,
+                object_reference_mode,
+                object_name,
+            )
 
-        # Try to load stylus orientation data
-        stylus_data = session.GetConfig("navigation-stylus")
-        if stylus_data is not None:
-            self.r_stylus = np.array(stylus_data["r_stylus"])
+            # Try to load stylus orientation data
+            if "r_stylus" in state:
+                self.r_stylus = np.array(state["r_stylus"])
 
     def CoilAtTarget(self, state):
         self.coil_at_target = state
@@ -449,6 +446,12 @@ def SetStylusOrientation(self, coord_raw):
 
             # Rotation from tracker to VTK coordinate system
             self.r_stylus = up_vtk @ np.linalg.inv(up_trk)
+
+            # Save r_stylus to config file
+            session = ses.Session()
+            if (nav_config := session.GetConfig("navigation")) is not None:
+                nav_config["r_stylus"] = self.r_stylus.tolist()
+                session.SetConfig("navigation", nav_config)
             return True
         else:
             return False

From 515c1bd90b809ba573ca9a529b700235ad330d7a Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Tue, 23 Jul 2024 16:39:50 +0300
Subject: [PATCH 15/44] Remove behavior where probe is automatically
 shown/hidden when navigation is started/stopped. Automatically show
 coil/probe when Track coil is pressed/unpressed

---
 invesalius/data/visualization/probe_visualizer.py | 8 --------
 invesalius/gui/task_navigator.py                  | 3 ++-
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/invesalius/data/visualization/probe_visualizer.py b/invesalius/data/visualization/probe_visualizer.py
index 4101a96cc..3627bf7b3 100644
--- a/invesalius/data/visualization/probe_visualizer.py
+++ b/invesalius/data/visualization/probe_visualizer.py
@@ -27,14 +27,6 @@ def __init__(self, renderer, interactor):
     def __bind_events(self):
         Publisher.subscribe(self.ShowProbe, "Show probe in viewer volume")
         Publisher.subscribe(self.UpdateProbePose, "Update probe pose")
-        Publisher.subscribe(self.OnNavigationStatus, "Navigation status")
-
-    def OnNavigationStatus(self, nav_status, vis_status):
-        self.is_navigating = nav_status  # show probe when start navigation
-        if self.probe_actor is not None:  # and hide it when stop navigation
-            Publisher.sendMessage("Press show-probe button", pressed=nav_status)
-            self.ShowProbe(self.is_navigating)
-            self.interactor.Render()
 
     def ShowProbe(self, state):
         self.show_probe = state
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 556136129..07a683ae3 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1814,8 +1814,9 @@ def OnTrackObjectButton(self, evt=None, ctrl=None):
         if not pressed:
             Publisher.sendMessage("Press target mode button", pressed=pressed)
 
-        # Automatically press or unpress 'Show coil' button.
+        # Automatically press or unpress 'Show coil' and 'Show probe' button.
         Publisher.sendMessage("Press show-coil button", pressed=pressed)
+        Publisher.sendMessage("Press show-probe button", pressed=(not pressed))
 
         self.SaveConfig()
 

From 9274b2913e93984fae17a79c187c92af6c34d4fe Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 25 Jul 2024 12:47:15 +0300
Subject: [PATCH 16/44] Now works with tracker coordinate system where stylus
 points in x-axis as opposed to y-axis. Also, removed unnecessary disabling of
 'Track coil' button before navigation.

---
 invesalius/data/coregistration.py   | 5 ++++-
 invesalius/gui/task_navigator.py    | 2 --
 invesalius/navigation/navigation.py | 7 +++++--
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 3d7fe6e50..73e08b91f 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -190,8 +190,11 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     m_img = m_change @ m_probe_ref
     m_img = apply_icp(m_img, icp)
 
+    # Rotate from trk system where stylus points in x-axis to vtk-system where stylus points in y-axis
+    R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
+
     # rotate m_probe_ref from tracker to image space
-    r_img = r_stylus @ m_probe_ref[:3, :3]
+    r_img = r_stylus @ R @ m_probe_ref[:3, :3] @ np.linalg.inv(R)
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 07a683ae3..6827644d0 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1302,8 +1302,6 @@ def __init__(self, parent, nav_hub):
         track_object_button.SetBackgroundColour(GREY_COLOR)
         track_object_button.SetBitmap(BMP_TRACK)
         track_object_button.SetValue(False)
-        if not self.track_obj:
-            track_object_button.Enable(False)
         track_object_button.SetToolTip(tooltip)
         track_object_button.Bind(
             wx.EVT_TOGGLEBUTTON, partial(self.OnTrackObjectButton, ctrl=track_object_button)
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index a4512cc83..ab89e2e0d 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -444,9 +444,12 @@ def SetStylusOrientation(self, coord_raw):
             # up_vtk: orientation 'stylus pointing up along head' in vtk space
             up_vtk = tr.euler_matrix(*np.radians([90.0, 0.0, 0.0]), axes="rxyz")[:3, :3]
 
-            # Rotation from tracker to VTK coordinate system
-            self.r_stylus = up_vtk @ np.linalg.inv(up_trk)
+            # Rotate 90 degrees around z-axis from trk system where stylus points in x-axis
+            # to vtk-system where stylus points in y-axis
+            R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
 
+            # Rotation from tracker to VTK coordinate system
+            self.r_stylus = up_vtk @ np.linalg.inv(R @ up_trk @ np.linalg.inv(R))
             # Save r_stylus to config file
             session = ses.Session()
             if (nav_config := session.GetConfig("navigation")) is not None:

From 81f6da53816efebf4707579e7b584530a1102789 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Tue, 23 Jul 2024 21:30:35 +0300
Subject: [PATCH 17/44] Start work on multicoil. Add n_coils variable to
 tracker connection init dialogs. Polaris init dialog now asks for n_coils
 Coil ROM files.

---
 invesalius/data/tracker_connection.py | 27 +++++++------
 invesalius/gui/dialogs.py             | 58 +++++++++++++++------------
 invesalius/navigation/tracker.py      |  4 +-
 3 files changed, 49 insertions(+), 40 deletions(-)

diff --git a/invesalius/data/tracker_connection.py b/invesalius/data/tracker_connection.py
index f1270ca67..ddb1132ab 100644
--- a/invesalius/data/tracker_connection.py
+++ b/invesalius/data/tracker_connection.py
@@ -30,7 +30,7 @@
 
 
 class TrackerConnection:
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         self.connection = None
         self.configuration = None
         self.model = model
@@ -80,7 +80,7 @@ class OptitrackTrackerConnection(TrackerConnection):
     loads User Profile (Rigid bodies information).
     """
 
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         super().__init__(model)
 
     def Configure(self):
@@ -127,7 +127,7 @@ def Disconnect(self):
 
 
 class ClaronTrackerConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         super().__init__(model)
 
     def Configure(self):
@@ -167,7 +167,7 @@ def Disconnect(self):
 
 
 class PolhemusTrackerConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         assert model in [
             "fastrak",
             "isotrak",
@@ -355,7 +355,7 @@ def Disconnect(self):
 
 
 class CameraTrackerConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         super().__init__(model)
 
     def Configure(self):
@@ -383,11 +383,12 @@ def Disconnect(self):
 
 
 class PolarisTrackerConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
+        self.n_coils = n_coils
         super().__init__(model)
 
     def Configure(self):
-        dialog = dlg.ConfigurePolarisDialog()
+        dialog = dlg.ConfigurePolarisDialog(self.n_coils)
         status = dialog.ShowModal()
 
         success = status == ID_OK
@@ -447,11 +448,11 @@ def Disconnect(self):
 
 
 class PolarisP4TrackerConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         super().__init__(model)
 
     def Configure(self):
-        dialog = dlg.ConfigurePolarisDialog()
+        dialog = dlg.ConfigurePolarisDialog(1)
         status = dialog.ShowModal()
 
         success = status == ID_OK
@@ -507,7 +508,7 @@ def Disconnect(self):
 
 
 class DebugTrackerRandomConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         super().__init__(model)
 
     def Configure(self):
@@ -525,7 +526,7 @@ def Disconnect(self):
 
 
 class DebugTrackerApproachConnection(TrackerConnection):
-    def __init__(self, model=None):
+    def __init__(self, model=None, n_coils=1):
         super().__init__(model)
 
     def Configure(self):
@@ -556,7 +557,7 @@ def Disconnect(self):
 }
 
 
-def CreateTrackerConnection(tracker_id):
+def CreateTrackerConnection(tracker_id, n_coils):
     """
     Initialize spatial tracker connection for coordinate detection during navigation.
 
@@ -578,5 +579,5 @@ def CreateTrackerConnection(tracker_id):
     else:
         model = None
 
-    tracker_connection = tracker_connection_class(model=model)
+    tracker_connection = tracker_connection_class(model=model, n_coils=n_coils)
     return tracker_connection
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 2fafc9cd0..5360205ce 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -6800,13 +6800,14 @@ def GetValue(self) -> Optional[Union[np.ndarray, List]]:
 
 
 class ConfigurePolarisDialog(wx.Dialog):
-    def __init__(self, title: str = _("Configure NDI Polaris")):
+    def __init__(self, n_coils, title: str = _("Configure NDI Polaris")):
+        self.n_coils = n_coils
         wx.Dialog.__init__(
             self,
             wx.GetApp().GetTopWindow(),
             -1,
             title,
-            size=wx.Size(1000, 200),
+            size=wx.Size(1000, 200 + (n_coils - 1) * 50),
             style=wx.DEFAULT_DIALOG_STYLE
             | wx.FRAME_FLOAT_ON_PARENT
             | wx.STAY_ON_TOP
@@ -6858,14 +6859,14 @@ def _init_gui(self) -> None:
         session = ses.Session()
         last_ndi_probe_marker = session.GetConfig("last_ndi_probe_marker", "")
         last_ndi_ref_marker = session.GetConfig("last_ndi_ref_marker", "")
-        last_ndi_obj_marker = session.GetConfig("last_ndi_obj_marker", "")
+        last_ndi_obj_markers = session.GetConfig("last_ndi_obj_markers", "")
 
         if not last_ndi_probe_marker:
             last_ndi_probe_marker = inv_paths.NDI_MAR_DIR_PROBE
         if not last_ndi_ref_marker:
             last_ndi_ref_marker = inv_paths.NDI_MAR_DIR_REF
-        if not last_ndi_obj_marker:
-            last_ndi_obj_marker = inv_paths.NDI_MAR_DIR_OBJ
+        if not last_ndi_obj_markers:
+            last_ndi_obj_markers = self.n_coils * [inv_paths.NDI_MAR_DIR_OBJ]
 
         self.dir_probe = wx.FilePickerCtrl(
             self,
@@ -6891,18 +6892,24 @@ def _init_gui(self) -> None:
         row_ref.Add(wx.StaticText(self, wx.ID_ANY, "Reference ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
         row_ref.Add(self.dir_ref, 0, wx.ALL | wx.CENTER | wx.EXPAND)
 
-        self.dir_obj = wx.FilePickerCtrl(
-            self,
-            path=last_ndi_obj_marker,
-            style=wx.FLP_USE_TEXTCTRL | wx.FLP_SMALL,
-            wildcard="Rom files (*.rom)|*.rom",
-            message="Select the ROM file of the object",
-            size=(700, -1),
-        )
-        # self.dir_probe.Bind(wx.EVT_FILEPICKER_CHANGED, self.Selected)
-        row_obj = wx.BoxSizer(wx.VERTICAL)
-        row_obj.Add(wx.StaticText(self, wx.ID_ANY, "Coil ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
-        row_obj.Add(self.dir_obj, 0, wx.ALL | wx.CENTER | wx.EXPAND)
+
+        self.dir_objs = []
+        row_objs = []
+        for i in range(self.n_coils):
+            dir_obj = wx.FilePickerCtrl(
+                self,
+                path=last_ndi_obj_markers[i],
+                style=wx.FLP_USE_TEXTCTRL | wx.FLP_SMALL,
+                wildcard="Rom files (*.rom)|*.rom",
+                message="Select the ROM file of the object",
+                size=(700, -1),
+            )
+            self.dir_objs.append(dir_obj)
+
+            row_obj = wx.BoxSizer(wx.VERTICAL)
+            row_obj.Add(wx.StaticText(self, wx.ID_ANY, "Coil ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
+            row_obj.Add(dir_obj, 0, wx.ALL | wx.CENTER | wx.EXPAND)
+            row_objs.append(row_obj)
 
         btn_ok = wx.Button(self, wx.ID_OK)
         btn_ok.SetHelpText("")
@@ -6925,8 +6932,9 @@ def _init_gui(self) -> None:
         main_sizer.Add(row_probe, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
         main_sizer.Add((5, 5))
         main_sizer.Add(row_ref, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
-        main_sizer.Add((5, 5))
-        main_sizer.Add(row_obj, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+        for row_obj in row_objs:
+            main_sizer.Add((5, 5))
+            main_sizer.Add(row_obj, 1, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
         main_sizer.Add((15, 15))
         main_sizer.Add(btnsizer, 0, wx.EXPAND)
         main_sizer.Add((5, 5))
@@ -6942,17 +6950,17 @@ def OnChoicePort(self, evt: wx.CommandEvent, ctrl: wx.ComboBox) -> None:
     def GetValue(self) -> Tuple[str, str, str, str]:
         fn_probe = self.dir_probe.GetPath()
         fn_ref = self.dir_ref.GetPath()
-        fn_obj = self.dir_obj.GetPath()
+        fn_objs = [dir_obj.GetPath() for dir_obj in self.dir_objs]
 
-        if fn_probe and fn_ref and fn_obj:
+        if fn_probe and fn_ref and fn_objs:
             session = ses.Session()
-            session.SetConfig("last_ndi_probe_marker", self.dir_probe.GetPath())
-            session.SetConfig("last_ndi_ref_marker", self.dir_ref.GetPath())
-            session.SetConfig("last_ndi_obj_marker", self.dir_obj.GetPath())
+            session.SetConfig("last_ndi_probe_marker", fn_probe)
+            session.SetConfig("last_ndi_ref_marker", fn_ref)
+            session.SetConfig("last_ndi_obj_markers", fn_objs)
 
         com_port = self.com_ports.GetValue()
 
-        return com_port, fn_probe, fn_ref, fn_obj
+        return com_port, fn_probe, fn_ref, fn_objs
 
 
 class SetCOMPort(wx.Dialog):
diff --git a/invesalius/navigation/tracker.py b/invesalius/navigation/tracker.py
index 051654569..f5fd83637 100644
--- a/invesalius/navigation/tracker.py
+++ b/invesalius/navigation/tracker.py
@@ -92,9 +92,9 @@ def LoadState(self):
 
         self.SetTracker(tracker_id=self.tracker_id, configuration=configuration)
 
-    def SetTracker(self, tracker_id, configuration=None):
+    def SetTracker(self, tracker_id, n_coils=1, configuration=None):
         if tracker_id:
-            self.tracker_connection = tc.CreateTrackerConnection(tracker_id)
+            self.tracker_connection = tc.CreateTrackerConnection(tracker_id, n_coils)
 
             # Configure tracker.
             if configuration is not None:

From d99784235f2e8630cec47e744b67a96e2a3bfb5d Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Tue, 23 Jul 2024 09:27:02 +0300
Subject: [PATCH 18/44] Larger refactor.

Rename/repurpose obj_ref_mode to obj_id (this is the index of an object in coord_raw).

Use dicts throughout code so that coils can be controlled by name. Simplify CoilVisualizer and coregistration.

Add coil selection buttons to Preferences ObjectTab.
---
 invesalius/data/coregistration.py             | 131 +++---
 invesalius/data/viewer_volume.py              |   4 +-
 .../data/visualization/coil_visualizer.py     | 206 +++------
 invesalius/gui/dialogs.py                     |  58 ++-
 invesalius/gui/preferences.py                 | 436 +++++++++++-------
 invesalius/gui/task_navigator.py              | 150 +++---
 invesalius/navigation/navigation.py           | 199 +++++---
 invesalius/session.py                         |  10 +-
 8 files changed, 655 insertions(+), 539 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 73e08b91f..576b5de99 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -31,14 +31,14 @@
 # TODO: Replace the use of degrees by radians in every part of the navigation pipeline
 
 
-def object_marker_to_center(coord_raw, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw):
+def object_marker_to_center(coord_raw, obj_id, t_obj_raw, s0_raw, r_s0_raw):
     """Translate and rotate the raw coordinate given by the tracking device to the reference system created during
     the object registration.
 
     :param coord_raw: Coordinates returned by the tracking device
     :type coord_raw: numpy.ndarray
-    :param obj_ref_mode:
-    :type obj_ref_mode: int
+    :param obj_id:
+    :type obj_id: int
     :param t_obj_raw:
     :type t_obj_raw: numpy.ndarray
     :param s0_raw:
@@ -48,9 +48,9 @@ def object_marker_to_center(coord_raw, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw
     :return: 4 x 4 numpy double array
     :rtype: numpy.ndarray
     """
-    as1, bs1, gs1 = np.radians(coord_raw[obj_ref_mode, 3:])
+    as1, bs1, gs1 = np.radians(coord_raw[obj_id, 3:])
     r_probe = tr.euler_matrix(as1, bs1, gs1, "rzyx")
-    t_probe_raw = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
+    t_probe_raw = tr.translation_matrix(coord_raw[obj_id, :3])
     t_offset_aux = np.linalg.inv(r_s0_raw) @ r_probe @ t_obj_raw
     t_offset = np.identity(4)
     t_offset[:, -1] = t_offset_aux[:, -1]
@@ -213,14 +213,14 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     return coord, m_img
 
 
-def corregistrate_object_dynamic(inp, coord_raw, i_obj, icp):
+def corregistrate_object_dynamic(m_change, obj_data, coord_raw, icp):
     """
-    Corregistrate the object at coord_raw[i_obj] in dynamic ref_mode
+    Corregistrate the object define by obj_data in dynamic ref_mode
     """
-    m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
+    obj_id, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = obj_data
 
     # transform raw marker coordinate to object center
-    m_probe = object_marker_to_center(coord_raw, i_obj, t_obj_raw, s0_raw, r_s0_raw)
+    m_probe = object_marker_to_center(coord_raw, obj_id, t_obj_raw, s0_raw, r_s0_raw)
 
     # transform object center to reference marker
     m_probe_ref = object_to_reference(coord_raw, m_probe)
@@ -248,14 +248,14 @@ def corregistrate_object_dynamic(inp, coord_raw, i_obj, icp):
     return coord, m_img
 
 
-def corregistrate_object_static(inp, coord_raw, i_obj, icp):
+def corregistrate_object_static(m_change, obj_data, coord_raw, icp):
     """
-    Corregistrate the object at coord_raw[i_obj] in static ref_mode
+    Corregistrate the object define by obj_data in static ref_mode
     """
-    m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
+    obj_id, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = obj_data
 
     # transform raw marker coordinate to object center
-    m_probe = object_marker_to_center(coord_raw, i_obj, t_obj_raw, s0_raw, r_s0_raw)
+    m_probe = object_marker_to_center(coord_raw, obj_id, t_obj_raw, s0_raw, r_s0_raw)
 
     # invert y coordinate
     m_probe[2, -1] = -m_probe[2, -1]
@@ -280,10 +280,10 @@ def corregistrate_object_static(inp, coord_raw, i_obj, icp):
     return coord, m_img
 
 
-def compute_marker_transformation(coord_raw, obj_ref_mode):
+def compute_marker_transformation(coord_raw, obj_id):
     m_probe = dco.coordinates_to_transformation_matrix(
-        position=coord_raw[obj_ref_mode, :3],
-        orientation=coord_raw[obj_ref_mode, 3:],
+        position=coord_raw[obj_id, :3],
+        orientation=coord_raw[obj_id, 3:],
         axes="rzyx",
     )
     return m_probe
@@ -335,6 +335,7 @@ def __init__(
         tracker,
         n_coils,
         coreg_data,
+        obj_datas,
         view_tracts,
         queues,
         event,
@@ -347,8 +348,11 @@ def __init__(
         threading.Thread.__init__(self, name="CoordCoregObject")
         self.ref_mode_id = ref_mode_id
         self.tracker = tracker
-        self.n_coils = n_coils
+        self.n_coils = (
+            n_coils  # LUKATODO: remove n_coils since this is just equal to len(obj_datas)
+        )
         self.coreg_data = coreg_data
+        self.obj_datas = obj_datas
         self.coord_queue = queues[0]
         self.view_tracts = view_tracts
         self.coord_tracts_queue = queues[1]
@@ -375,21 +379,13 @@ def __init__(
             self.target[1] = -self.target[1]
 
     def run(self):
-        coreg_data = self.coreg_data
+        m_change, r_stylus = self.coreg_data
+        obj_datas = self.obj_datas
+
         corregistrate_object = (
             corregistrate_object_dynamic if self.ref_mode_id else corregistrate_object_static
         )
 
-        # compute n_coils_effective, the no. of coils to actually process:
-        # check how many coords we get from tracker (-2 for probe & head)
-        n_coils_trk = self.tracker.TrackerCoordinates.GetCoordinates()[0].shape[0] - 2
-
-        obj_ref_mode = coreg_data[2]
-        # if obj_ref_mode=0: only coregister one coil
-        # else: process the other (n_coils - 1) coils too
-        # min(obj_ref_mode, 1) = 0 if obj_ref_mode==0 else 1
-        n_coils_effective = min(n_coils_trk, 1 + min(obj_ref_mode, 1) * (self.n_coils - 1))
-
         while not self.event.is_set():
             try:
                 if not self.icp_queue.empty():
@@ -400,51 +396,29 @@ def run(self):
 
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
-                # m_change = coreg_data[1], r_stylus = coreg_data[0]
                 coord_probe, m_img_probe = corregistrate_probe(
-                    coreg_data[1], coreg_data[0], coord_raw, self.ref_mode_id
-                )
-                coord_coil, m_img_coil = corregistrate_object(
-                    coreg_data[1:], coord_raw, obj_ref_mode, [self.use_icp, self.m_icp]
+                    m_change, r_stylus, coord_raw, self.ref_mode_id
                 )
 
-                coords = [coord_probe, coord_coil]
-                m_imgs = [m_img_probe, m_img_coil]
+                coords = {"probe": coord_probe}
+                m_imgs = {"probe": m_img_probe}
 
-                # the possible other coils are i_obj=3 onwards at coord_raw[i_obj]
-                for i_obj in range(3, n_coils_effective + 2):
+                for coil_name in obj_datas:
                     coord_coil, m_img_coil = corregistrate_object(
-                        coreg_data[1:], coord_raw, i_obj, [self.use_icp, self.m_icp]
+                        m_change, obj_datas[coil_name], coord_raw, [self.use_icp, self.m_icp]
                     )
-                    coords.append(coord_coil)
-                    m_imgs.append(m_img_coil)
-
-                # XXX: This is not the best place to do the logic related to approaching the target when the
-                #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
-                #      the tracker space where it is hard to make the tracker approach the target in the image space.
-                #      Ideally, the transformation from the tracker space to the image space (the function
-                #      corregistrate_object_dynamic above) would be encapsulated in a class together with the
-                #      tracker, and then the whole class would be mocked when using the debug tracker. However,
-                #      those abstractions do not currently exist and doing them would need a larger refactoring.
-                #
-                if self.tracker_id == const.DEBUGTRACKAPPROACH and self.target is not None:
-                    if self.last_coord is None:
-                        self.last_coord = np.array(coord_coil)
-                    else:
-                        coord = self.last_coord + (self.target - self.last_coord) * 0.05
-                        coords[1] = coord
-                        self.last_coord = coord
-
-                    angles = [np.radians(coord[3]), np.radians(coord[4]), np.radians(coord[5])]
-                    translate = coord[0:3]
-                    m_imgs[1] = tr.compose_matrix(angles=angles, translate=translate)
-
+                    coords[coil_name] = coord_coil
+                    m_imgs[coil_name] = m_img_coil
+                
                 self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs])
-
-                coord = coords[1]  # main coil
-                m_img = m_imgs[1]
-                # LUKATODO: should coord = coords[track_coil]
-                # should the stuff below ever be done for stylus, but not coil?
+                
+                # LUKATODO: Refactor so that all coils are processed
+                # we need tracts, efield, etc. for all coils. what about stylus?
+               
+                # LUKATODO: coords is unordered so this randomly gives probe/somecoil...
+                #coord = coords.values()[1]
+                coord = coords["coil1"]
+                m_img = m_imgs["coil1"]
 
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
@@ -457,5 +431,30 @@ def run(self):
                     self.icp_queue.task_done()
             except queue.Full:
                 pass
+
             # The sleep has to be in both threads
             sleep(self.sle)
+                
+                
+            # LUKATODO: move below Debug approach to UpdateNavigationScene
+            # Better way to do debug approach...? Just change the main_coil coord in UpdateNavigationScene...
+            """
+            # XXX: This is not the best place to do the logic related to approaching the target when the
+            #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
+            #      the tracker space where it is hard to make the tracker approach the target in the image space.
+            #      Ideally, the transformation from the tracker space to the image space (the function
+            #      corregistrate_object_dynamic above) would be encapsulated in a class together with the
+            #      tracker, and then the whole class would be mocked when using the debug tracker. However,
+            #      those abstractions do not currently exist and doing them would need a larger refactoring.
+                if self.tracker_id == const.DEBUGTRACKAPPROACH and self.target is not None:
+                if self.last_coord is None:
+                    self.last_coord = np.array(coord_coil)
+                else:
+                    coord = self.last_coord + (self.target - self.last_coord) * 0.05
+                    coords[1] = coord
+                    self.last_coord = coord
+
+                angles = [np.radians(coord[3]), np.radians(coord[4]), np.radians(coord[5])]
+                translate = coord[0:3]
+                m_imgs[1] = tr.compose_matrix(angles=angles, translate=translate)
+            """
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index 4d22607d6..b2e8baab7 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -343,9 +343,7 @@ def __init__(self, parent):
         self.positions_above_threshold = None
         self.cell_id_indexes_above_threshold = None
 
-        # Automatically enable and press 'Track object' button.
-        Publisher.sendMessage("Enable track object button", enabled=True)
-        Publisher.sendMessage("Press track object button", pressed=True)
+        # LUKATODO: delete this?
         Publisher.sendMessage("Press target mode button", pressed=False)
 
     def UpdateCanvas(self):
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index cf4bd10f5..35d0ea0ed 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -35,20 +35,11 @@ def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer)
         # The vector field visualizer is used to show a vector field relative to the coil.
         self.vector_field_visualizer = vector_field_visualizer
 
-        # Number of coils is by default 1
-        self.n_coils = 1
-
-        # The actor for showing the actual coil in the volume viewer.
-        self.coil_actor = None
-        self.coil_actors = []
-
-        # The actor for showing the center of the actual coil in the volume viewer.
-        self.coil_center_actor = None
-        self.coil_center_actors = []
+        # Keyed by coil name, each coil has a dict holding its coil actor, coil center actor, coil path.
+        self.coils = {}
 
         # The actor for showing the target coil in the volume viewer.
         self.target_coil_actor = None
-        self.target_coil_actors = []
 
         # The assembly for showing the vector field relative to the coil in the volume viewer.
         self.vector_field_assembly = self.vector_field_visualizer.CreateVectorFieldAssembly()
@@ -59,26 +50,10 @@ def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer)
 
         self.coil_at_target = False
 
-        self.coil_path = None
-        self.coil_polydata = None
-
-        # Show coil button status
-        self.show_coil_pressed = False
-
-        # Track object button status
-        self.track_object_pressed = False
-
-        # Is this the first time show coil button has been pressed
-        self.initial_button_press = True
-
-        # Is this the initial project that was loaded
-        self.initial_project = True
-
         self.is_navigating = False
 
         self.LoadConfig()
 
-        self.AddCoilActor(self.coil_path)
         self.ShowCoil(False)
 
         self.__bind_events()
@@ -86,58 +61,22 @@ def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer)
     def __bind_events(self):
         Publisher.subscribe(self.SetCoilAtTarget, "Coil at target")
         Publisher.subscribe(self.OnNavigationStatus, "Navigation status")
-        Publisher.subscribe(self.TrackObject, "Track object")
         Publisher.subscribe(self.ShowCoil, "Show coil in viewer volume")
-        Publisher.subscribe(self.SetCoilCount, "Set coil count")
-        Publisher.subscribe(self.ConfigureCoil, "Configure coil")
-        Publisher.subscribe(self.UpdateCoilPose, "Update coil pose")
+        Publisher.subscribe(lambda n_coils: self.RemoveCoil(), "Reset coil selection")
+        Publisher.subscribe(self.SelectCoil, "Select coil")
+        Publisher.subscribe(self.UpdateCoilPoses, "Update coil poses")
         Publisher.subscribe(self.UpdateVectorField, "Update vector field")
-        Publisher.subscribe(self.OnSetTrackerFiducials, "Tracker fiducials set")
-        Publisher.subscribe(self.OnResetTrackerFiducials, "Reset tracker fiducials")
-        Publisher.subscribe(self.OnLoadProject, "Project loaded successfully")
-
-    def SaveConfig(self):
-        coil_path = self.coil_path.decode(const.FS_ENCODE) if self.coil_path is not None else None
-
-        session = ses.Session()
-        session.SetConfig("coil_path", coil_path)
 
     def LoadConfig(self):
         session = ses.Session()
-        coil_path_unencoded = session.GetConfig("coil_path")
-
-        if coil_path_unencoded is None:
-            return
-
-        self.coil_path = coil_path_unencoded.encode(const.FS_ENCODE)
-        self.coil_polydata = pu.LoadPolydata(path=coil_path_unencoded)
-
-    def OnSetTrackerFiducials(self):
-        self.tracker_fiducials_set = True
-
-        # If the track coil button is not pressed, press it after tracker fiducials have been set
-        if not self.track_object_pressed:
-            Publisher.sendMessage("Press track object button", pressed=True)
-
-        elif not self.show_coil_pressed:
-            Publisher.sendMessage("Press show-coil button", pressed=True)
-        else:
-            self.ShowCoil(self.show_coil_pressed)
-
-    def OnResetTrackerFiducials(self):
-        self.tracker_fiducials_set = False
-
-        # If the show coil button is pressed, press it again to hide the coil
-        if self.show_coil_pressed:
-            Publisher.sendMessage("Press show-coil button", pressed=False)
 
-    def OnLoadProject(self):
-        # When loading some other than the initially loaded project, reset some instance variables
-        if self.initial_project:
-            self.initial_project = False
-        else:
-            self.tracker_fiducials_set = False
-            # self.initial_button_press = True
+        # Get the list of coil names of coils selected for navigation
+        selected_coils = (session.GetConfig("navigation") or {}).get("selected_coils", [])
+        
+        saved_registrations = session.GetConfig("coil_registrations") or {}
+        for coil_name in selected_coils:
+            if (coil := saved_registrations.get(coil_name, None)) is not None:
+                self.AddCoil(coil_name, coil["path"])
 
     def UpdateVectorField(self):
         """
@@ -170,59 +109,24 @@ def SetCoilAtTarget(self, state):
 
         # Set the color of both target coil (representing the target) and the coil center (representing the actual coil).
         self.target_coil_actor.GetProperty().SetDiffuseColor(target_coil_color)
-        self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color)
-
-    def SetCoilCount(self, n_coils):
-        self.n_coils = n_coils
-
-    def RemoveCoilActor(self):
-        self.renderer.RemoveActor(self.coil_actor)
-        self.renderer.RemoveActor(self.coil_center_actor)
-        # TODO: Vector field assembly follows a different pattern for removal, should unify.
-        self.vector_field_assembly.SetVisibility(0)
-
-        self.coil_actor = None
-        self.coil_center_actor = None
-
-    def ConfigureCoil(self, coil_path=None, polydata=None):
-        self.coil_path = coil_path
-        self.coil_polydata = polydata
-
-        self.SaveConfig()
+        #self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color)
 
     def OnNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status
-        if self.is_navigating and self.coil_actor is not None:
-            self.coil_actor.SetVisibility(self.show_coil_pressed)
-
-    # Called when 'track object' button is pressed in the user interface or in code.
-    def TrackObject(self, enabled):
-        self.track_object_pressed = enabled
-
-        # Hide coil vector_field if it exists. LUKATODO: what is this vector field?
-        if enabled:
-            self.vector_field_assembly.SetVisibility(1)
-        else:
-            self.vector_field_assembly.SetVisibility(0)
 
     # Called when 'show coil' button is pressed in the user interface or in code.
-    def ShowCoil(self, state):
-        self.show_coil_pressed = state
-
-        # Initially, if the tracker fiducials are not set but the show coil button is pressed,
-        # press it again to hide the coil
-        if not self.tracker_fiducials_set and self.show_coil_pressed and self.initial_button_press:
-            self.initial_button_press = False
-
-            # Press the show coil button to turn it off
-            Publisher.sendMessage("Press show-coil button", pressed=False)
-            return
-
+    # LUKATODO: Right-click 'show coil' button to open combobox to choose specific coil to show/hide
+    def ShowCoil(self, state, coil_name=None):
+        if coil_name is None:  # Show/hide all coils
+            for coil in self.coils.values():
+                coil["actor"].SetVisibility(state)
+        elif (coil := self.coils.get(coil_name, None)) is not None:
+            coil["actor"].SetVisibility(state)
+
+        # LUKATODO: target?
         if self.target_coil_actor is not None:
-            self.target_coil_actor.SetVisibility(self.show_coil_pressed)
-
-        if self.coil_actor:
-            self.coil_actor.SetVisibility(self.show_coil_pressed)
+            self.target_coil_actor.SetVisibility(state)
+        self.vector_field_assembly.SetVisibility(state)
 
         if not self.is_navigating:
             self.interactor.Render()
@@ -286,7 +190,14 @@ def RemoveTargetCoil(self):
         self.renderer.RemoveActor(self.target_coil_actor)
         self.target_coil_actor = None
 
-    def AddCoilActor(self, coil_path):
+    # Called when a coil is (un)selected for navigation
+    def SelectCoil(self, coil_name, coil_registration):
+        if coil_registration is not None:  # coil is selected
+            self.AddCoil(coil_name, coil_registration["path"])
+        else:  # coil is unselected
+            self.RemoveCoil(coil_name)
+
+    def AddCoil(self, coil_name, coil_path):
         """
         Add actors for actual coil, coil center, and x, y, and z-axes to the renderer.
         """
@@ -320,8 +231,6 @@ def AddCoilActor(self, coil_path):
         coil_actor.GetProperty().SetOpacity(0.4)
         coil_actor.SetVisibility(0)
 
-        self.coil_actor = coil_actor
-
         # Create an actor for the coil center.
         coil_center_actor = self.actor_factory.CreateTorus(
             position=[0.0, 0.0, 0.0],
@@ -329,25 +238,48 @@ def AddCoilActor(self, coil_path):
             colour=vtk_colors.GetColor3d("Red"),
             scale=0.5,
         )
-        self.coil_center_actor = coil_center_actor
-
-        self.renderer.AddActor(self.coil_actor)
-        self.renderer.AddActor(self.coil_center_actor)
-        # TODO: Vector field assembly follows a different pattern for addition, should unify.
-        self.vector_field_assembly.SetVisibility(1)
 
-    def UpdateCoilPose(self, m_img, coord):
+        self.renderer.AddActor(coil_actor)
+        self.renderer.AddActor(coil_center_actor)
+        
+        self.coils[coil_name] = {}
+        self.coils[coil_name]["actor"] = coil_actor
+        self.coils[coil_name]["center_actor"] = coil_center_actor
+        self.coils[coil_name]["path"] = coil_path
+
+        # LUKATODO: Vector field assembly follows a different pattern for addition, should unify.
+        # self.vector_field_assembly.SetVisibility(1)
+
+    def RemoveCoil(self, coil_name=None):
+        if coil_name is not None:
+            coil = self.coils.pop(coil_name)
+            self.renderer.RemoveActor(coil["actor"])
+            self.renderer.RemoveActor(coil["center_actor"])
+        else:  # Remove all coils
+            for coil in self.coils.values():
+                self.renderer.RemoveActor(coil["actor"])
+                self.renderer.RemoveActor(coil["center_actor"])
+            # LUKATODO: what about target_actors and other things?
+            self.coils = {}
+
+        # self.vector_field_assembly.SetVisibility(0)
+
+    def UpdateCoilPoses(self, m_imgs, coords):
         """
         During navigation, use updated coil pose to perform the following tasks:
 
         - Update actor positions for coil, coil center, and coil orientation axes.
         """
-        m_img_flip = m_img.copy()
-        m_img_flip[1, -1] = -m_img_flip[1, -1]
 
-        m_img_vtk = vtku.numpy_to_vtkMatrix4x4(m_img_flip)
+        for name, m_img in m_imgs.items():
+            m_img_flip = m_img.copy()
+            m_img_flip[1, -1] = -m_img_flip[1, -1]
+
+            m_img_vtk = vtku.numpy_to_vtkMatrix4x4(m_img_flip)
+
+            # Update actor positions for coil, coil center, and coil orientation axes.
+            self.coils[name]["actor"].SetUserMatrix(m_img_vtk)
+            self.coils[name]["center_actor"].SetUserMatrix(m_img_vtk)
 
-        # Update actor positions for coil, coil center, and coil orientation axes.
-        self.coil_actor.SetUserMatrix(m_img_vtk)
-        self.coil_center_actor.SetUserMatrix(m_img_vtk)
-        self.vector_field_assembly.SetUserMatrix(m_img_vtk)
+            # LUKATODO: what to do with this??? Is mtms field needed? If not, just delete vector_field_assembly...?
+            # self.vector_field_assembly[name].SetUserMatrix(m_img_vtk)
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 5360205ce..7e3462a76 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -3890,7 +3890,7 @@ def __init__(
 
         self.tracker_id = tracker.GetTrackerId()
         self.show_sensor_options: bool = self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
-        self.obj_ref_id = 2
+        self.obj_id = 2  # the index of the object in coord_raw
         self.coil_path = None
         self.polydata = None
 
@@ -3922,22 +3922,26 @@ def _init_gui(self) -> None:
         self.ball_actors: List[Optional[vtkActor]] = [None] * 4
         self.txt_coord = [list(), list(), list(), list()]
 
-        # ComboBox for tracker reference mode
-        tooltip = _("Choose the object reference mode")
+        # ComboBox for object index in coord_raw (0 for static, 2 for dynamic, 3, 4, ... for multiple coils)
+        # Check how many coords the tracker gives, ie. coord_raw.shape[0]
+        max_obj_id = self.tracker.GetTrackerCoordinates(ref_mode_id=0)[2].shape[0]
+        tooltip = _(
+            "Choose the coil index in coord_raw. Choose 0 for static mode, 2 for dynamic mode and 3 onwards for multiple coils."
+        )
         choice_ref = wx.ComboBox(
             self,
             -1,
             "",
             size=wx.Size(90, 23),
-            choices=const.REF_MODE,
+            choices=["0"] + [str(i) for i in range(2, max_obj_id)],
             style=wx.CB_DROPDOWN | wx.CB_READONLY,
         )
         choice_ref.SetToolTip(tooltip)
-        choice_ref.Bind(wx.EVT_COMBOBOX, self.OnChooseReferenceMode)
+        choice_ref.Bind(wx.EVT_COMBOBOX, self.OnChooseObjID)
         choice_ref.SetSelection(1)
         choice_ref.Enable(True)
         if self.tracker_id == const.PATRIOT or self.tracker_id == const.ISOTRAKII:
-            self.obj_ref_id = 0
+            self.obj_id = 0
             choice_ref.SetSelection(0)
             choice_ref.Enable(False)
 
@@ -4012,12 +4016,20 @@ def _init_gui(self) -> None:
         group_sizer = wx.FlexGridSizer(rows=1, cols=2, hgap=50, vgap=5)
         group_sizer.AddMany([(coord_sizer, 0, wx.LEFT, 20), (extra_sizer, 0, wx.LEFT, 10)])
 
+        name_sizer = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
+        lbl_name = wx.StaticText(self, -1, _("Name the coil:"))
+        self.name_box = name_box = wx.TextCtrl(self, -1, _("coil1"))
+        name_sizer.AddMany(
+            [(lbl_name, 1, wx.ALIGN_CENTER_VERTICAL), (name_box, 1, wx.ALIGN_CENTER_VERTICAL)]
+        )
+        # LUKATODO: Add warning about overwriting old coil
+
         main_sizer = wx.BoxSizer(wx.VERTICAL)
         main_sizer.Add(self.interactor, 0, wx.EXPAND)
         main_sizer.Add(
             group_sizer, 0, wx.EXPAND | wx.GROW | wx.LEFT | wx.TOP | wx.RIGHT | wx.BOTTOM, 10
         )
-
+        main_sizer.Add(name_sizer, 0, wx.EXPAND)
         self.SetSizer(main_sizer)
         main_sizer.Fit(self)
 
@@ -4204,8 +4216,8 @@ def SetObjectFiducial(self, fiducial_index: int) -> None:
         #      mode" principle above, but it's hard to come up with a simple change to increase the consistency
         #      and not change the function to the point of potentially breaking it.)
         #
-        if self.obj_ref_id and fiducial_index == const.OBJECT_FIDUCIAL_FIXED:
-            coord = coord_raw[self.obj_ref_id, :]
+        if self.obj_id and fiducial_index == const.OBJECT_FIDUCIAL_FIXED:
+            coord = coord_raw[self.obj_id, :]
         else:
             coord = coord_raw[0, :]
 
@@ -4241,7 +4253,7 @@ def ResetObjectFiducial(self, index: int) -> None:
     def OnReset(self, evt: wx.CommandEvent) -> None:
         self.ResetObjectFiducials()
 
-    def OnChooseReferenceMode(self, evt: wx.CommandEvent) -> None:
+    def OnChooseObjID(self, evt: wx.CommandEvent) -> None:
         # When ref mode is changed the tracker coordinates are set to nan
         # This is for Polhemus FASTRAK wrapper, where the sensor attached to the object can be the stylus (Static
         # reference - Selection 0 - index 0 for coordinates) or can be a 3rd sensor (Dynamic reference - Selection 1 -
@@ -4249,13 +4261,12 @@ def OnChooseReferenceMode(self, evt: wx.CommandEvent) -> None:
         # I use the index 2 directly here to send to the coregistration module where it is possible to access without
         # any conditional statement the correct index of coordinates.
 
-        if evt.GetSelection() == 1:
-            self.obj_ref_id = 2
-            if self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS:
-                self.choice_sensor.Show(True)
-        else:
-            self.obj_ref_id = 0
+        if evt.GetSelection() == 0:
+            self.obj_id = 0
             self.choice_sensor.Show(False)
+        else:
+            self.obj_id = evt.GetSelection() + 1
+            self.choice_sensor.Show(self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS)
 
         self.ResetObjectFiducials()
 
@@ -4264,14 +4275,22 @@ def OnChooseReferenceMode(self, evt: wx.CommandEvent) -> None:
 
     def OnChoiceFTSensor(self, evt: wx.CommandEvent) -> None:
         if evt.GetSelection():
-            self.obj_ref_id = 3
+            self.obj_id = 3
         else:
-            self.obj_ref_id = 0
+            self.obj_id = 0
 
     def GetValue(
         self,
     ) -> Tuple[np.ndarray, np.ndarray, int, Optional[bytes], Optional[vtkPolyData]]:
-        return self.obj_fiducials, self.obj_orients, self.obj_ref_id, self.coil_path, self.polydata
+        coil_name = self.name_box.GetValue().strip()
+        return (
+            coil_name,
+            self.coil_path,
+            self.obj_fiducials,
+            self.obj_orients,
+            self.obj_id,
+            self.tracker_id,
+        )
 
     def OnOk(self, evt: wx.CommandEvent) -> None:
         if evt.GetId() == wx.ID_OK:
@@ -6892,7 +6911,6 @@ def _init_gui(self) -> None:
         row_ref.Add(wx.StaticText(self, wx.ID_ANY, "Reference ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
         row_ref.Add(self.dir_ref, 0, wx.ALL | wx.CENTER | wx.EXPAND)
 
-
         self.dir_objs = []
         row_objs = []
         for i in range(self.n_coils):
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index de232ee19..4e28f5db3 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -877,61 +877,86 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         self.pedal_connector = pedal_connector
         self.neuronavigation_api = neuronavigation_api
         self.navigation = navigation
-        self.obj_fiducials = None
-        self.obj_orients = None
-        self.obj_ref_mode = None
-        self.coil_path = None
+        self.coil_registrations = self.session.GetConfig("coil_registrations") or {}
         self.__bind_events()
         self.timestamp = const.TIMESTAMP
+
         self.LoadConfig()
 
-        # Buttons for TMS coil configuration
+        # Sizer for displaying instructions
+        top_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, ("Instructions"))
+        inner_top_sizer = wx.FlexGridSizer(1, 3, 1, 1)
+        self.instruction_lbl = wx.StaticText(
+            self,
+            -1,
+            _(
+                f"Choose {navigation.n_coils} coils to use below. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. Unused coils can be deleted by right-clicking the button."
+            ),
+        )
+        # instruction_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL))
+        inner_top_sizer.Add(self.instruction_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
+        top_sizer.Add(inner_top_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        # Sizer for choosing which coils to use in navigation
+        self.sel_sizer = sel_sizer = wx.StaticBoxSizer(
+            wx.VERTICAL,
+            self,
+            _(
+                f"TMS coil selection ({len(navigation.coil_registrations)} out of {navigation.n_coils})"
+            ),
+        )
+        self.inner_sel_sizer = inner_sel_sizer = wx.FlexGridSizer(10, 1, 1)
+
+        self.no_coils_lbl = None
+        if len(self.coil_registrations) == 0:
+            self.no_coils_lbl = wx.StaticText(
+                self, -1, _("No coils found in config.json. Create or load new coils below.")
+            )
+            inner_sel_sizer.Add(self.no_coils_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
+        sel_sizer.Add(inner_sel_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        # Add a button for each coil in coil_registrations
+        self.coil_btns = {}
+        for coil_name in self.coil_registrations:
+            self.AddCoilButton(coil_name)
+
+        # Sizer for TMS coil configuration
         tooltip = _("New TMS coil configuration")
         btn_new = wx.Button(self, -1, _("New"), size=wx.Size(65, 23))
         btn_new.SetToolTip(tooltip)
         btn_new.Enable(1)
         btn_new.Bind(wx.EVT_BUTTON, self.OnCreateNewCoil)
-        self.btn_new = btn_new
-
-        tooltip = _("Load TMS coil configuration from a file")
-        btn_load = wx.Button(self, -1, _("Load"), size=wx.Size(65, 23))
-        btn_load.SetToolTip(tooltip)
-        btn_load.Enable(1)
-        btn_load.Bind(wx.EVT_BUTTON, self.OnLoadCoil)
-        self.btn_load = btn_load
-
-        tooltip = _("Save current TMS coil configuration to a file")
-        btn_save = wx.Button(self, -1, _("Save"), size=wx.Size(65, 23))
-        btn_save.SetToolTip(tooltip)
-        btn_save.Enable(1)
-        btn_save.Bind(wx.EVT_BUTTON, self.OnSaveCoil)
-        self.btn_save = btn_save
-
-        self.config_txt = config_txt = wx.StaticText(self, -1, "None")
-        data = self.navigation.GetObjectRegistration()
-        self.OnObjectUpdate(data)
-
-        lbl = wx.StaticText(self, -1, _("Current Configuration:"))
-        lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
-
-        # Empty cell for the grid sizer
-        empty_cell = (0, 0)
-
-        load_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, _("TMS coil registration"))
-        inner_load_sizer = wx.FlexGridSizer(2, 4, 5)
-        inner_load_sizer.AddMany(
+
+        lbl_new = wx.StaticText(self, -1, _("Create or edit a coil configuration: "))
+
+        coil_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, _("TMS coil registration"))
+        inner_coil_sizer = wx.FlexGridSizer(2, 4, 5)
+        inner_coil_sizer.AddMany(
             [
-                (lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                (config_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (lbl_new, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
                 (btn_new, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                empty_cell,
-                (btn_load, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                empty_cell,
-                (btn_save, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                empty_cell,
             ]
         )
-        load_sizer.Add(inner_load_sizer, 0, wx.ALL | wx.EXPAND, 10)
+        coil_sizer.Add(inner_coil_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.AddMany(
+            [
+                (top_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (coil_sizer, 0, wx.ALL | wx.EXPAND, 10),
+            ]
+        )
+        self.SetSizerAndFit(main_sizer)
+
+        # Press the buttons for coils that were selected in config file
+        state = self.session.GetConfig("navigation", {})
+        for coil_name in state.get("selected_coils", []):
+            self.coil_btns[coil_name][0].SetValue(True)
+        self.Layout()
+
+        # LUKATODO: move the following into ObjectCalibrationDialog (along with the relevant funcs)
+        """
         # Change angles threshold
         text_angles = wx.StaticText(self, -1, _("Angle threshold (degrees):"))
         spin_size_angles = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23))
@@ -1003,18 +1028,42 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
                 (line_timestamp, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 20),
             ]
         )
+        """
 
-        main_sizer = wx.BoxSizer(wx.VERTICAL)
-        main_sizer.AddMany(
-            [(load_sizer, 0, wx.ALL | wx.EXPAND, 10), (conf_sizer, 0, wx.ALL | wx.EXPAND, 10)]
-        )
-        self.SetSizerAndFit(main_sizer)
-        self.Layout()
+    def AddCoilButton(self, coil_name):
+        if self.no_coils_lbl is not None:
+            self.no_coils_lbl.Destroy()  # Remove obsolete message
+            self.no_coils_lbl = None
+
+        # Create a new button with coil_name if it doesn't already exist
+        if coil_name not in self.coil_btns:
+            coil_btn = wx.ToggleButton(self, -1, coil_name[:8], size=wx.Size(88, 17))
+            coil_btn.SetToolTip(coil_name)
+            coil_btn.Bind(
+                wx.EVT_TOGGLEBUTTON, lambda event, name=coil_name: self.OnSelectCoil(event, name)
+            )
+            coil_btn.Bind(
+                wx.EVT_RIGHT_DOWN, lambda event, name=coil_name: self.OnRightClickCoil(event, name)
+            )
+            self.coil_btns[coil_name] = (coil_btn, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
+
+            self.inner_sel_sizer.Add(coil_btn, 1, wx.EXPAND, 5)
 
     def __bind_events(self):
-        Publisher.subscribe(self.OnObjectUpdate, "Update object registration")
+        Publisher.subscribe(self.OnSetCoilCount, "Reset coil selection")
+
+    def OnSetCoilCount(self, n_coils):
+        self.instruction_lbl.SetLabel(
+            f"Choose {n_coils} coils to use below. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. A coil can be deleted or its index can be changed by right-clicking its button."
+        )
+        self.sel_sizer.GetStaticBox().SetLabel(f"TMS coil selection (0 out of {n_coils})")
+        # Reset (enable and unpress) all coil-buttons
+        for btn, *junk in self.coil_btns.values():
+            btn.Enable()
+            btn.SetValue(False)
 
     def LoadConfig(self):
+        # LUKATODO: ???
         self.angle_threshold = (
             self.session.GetConfig("angle_threshold") or const.DEFAULT_ANGLE_THRESHOLD
         )
@@ -1022,20 +1071,123 @@ def LoadConfig(self):
             self.session.GetConfig("distance_threshold") or const.DEFAULT_DISTANCE_THRESHOLD
         )
 
-        state = self.session.GetConfig("navigation")
+    def OnSelectCoil(self, event, name):
+        coil_registration = None
+        navigation = self.navigation
+
+        if event.GetSelection():  # If coil is selected
+            coil_registration = self.coil_registrations[name]
+
+            # Check that the index of the chosen coil does not conflict with other selected coils
+            obj_id = coil_registration["obj_id"]
+            selected_registrations = navigation.coil_registrations
+            conflicting_coil_name = next(
+                (
+                    coil_name
+                    for coil_name, registration in selected_registrations.items()
+                    if registration["obj_id"] == obj_id
+                ),
+                None,
+            )
+            if conflicting_coil_name is not None:
+                wx.MessageBox(
+                    _(
+                        f"Cannot select this coil, its index (obj_id = {obj_id}) conflicts with selected coil: {conflicting_coil_name}"
+                    ),
+                    _("InVesalius 3"),
+                )
+                event.GetEventObject().SetValue(False)  # Unpress the button
+                return
+
+            # Check that the tracker used to configure the coil matches the currently used tracker
+            elif (obj_tracker_id := coil_registration["tracker_id"]) != self.tracker.tracker_id:
+                wx.MessageBox(
+                    _(
+                        f"Cannot select this coil, its tracker [{const.TRACKERS[obj_tracker_id - 1]}] does not match the selected tracker [{const.TRACKERS[self.tracker.tracker_id - 1]}]"
+                    ),
+                    _("InVesalius 3"),
+                )
+                event.GetEventObject().SetValue(False)  # Unpress the button
+                return
 
-        if state is not None:
-            object_fiducials = np.array(state["object_fiducials"])
-            object_orientations = np.array(state["object_orientations"])
-            object_reference_mode = state["object_reference_mode"]
-            object_name = state["object_name"].encode(const.FS_ENCODE)
+        # Select/Unselect coil
+        Publisher.sendMessage("Select coil", coil_name=name, coil_registration=coil_registration)
+        # LUKATODO: Is there a delay here? Is "Select coil" performed first everywhere and then only this?
+        n_coils_selected = len(navigation.coil_registrations)
+        n_coils = navigation.n_coils
+        # Update label telling how many coils to select
+        self.sel_sizer.GetStaticBox().SetLabel(
+            f"TMS coil selection ({n_coils_selected} out of {n_coils})"
+        )
 
-            self.obj_fiducials, self.obj_orients, self.obj_ref_mode, self.coil_path = (
-                object_fiducials,
-                object_orientations,
-                object_reference_mode,
-                object_name,
+        if n_coils_selected == n_coils:
+            Publisher.sendMessage(
+                "Coil selection done", done=True
+            )  # Inform task_navigator that selection is done
+            Publisher.sendMessage("Update status text in GUI", label=_("Ready"))
+
+            # Allow only n_coils buttons to be pressed, so disable unpressed buttons
+            for btn, *junk in self.coil_btns.values():
+                btn.Enable(btn.GetValue())
+        else:  # Enable all buttons
+            Publisher.sendMessage(
+                "Coil selection done", done=False
+            )
+            for btn, *junk in self.coil_btns.values():
+                btn.Enable(True)
+
+    def OnChoiceObjID(self, event, name):
+        obj_id = 0 if event.GetSelection() == 0 else event.GetSelection() + 1
+        self.coil_registrations[name]["obj_id"] = obj_id
+        self.session.SetConfig("coil_registrations", self.coil_registrations)
+
+        # Unselect the coil, because the new id may cause conflicts
+        Publisher.sendMessage("Select coil", coil_name=name, coil_registration=None)
+
+        self.coil_btns[name][0].SetValue(False)
+        for btn, *junk in self.coil_btns.values():  # Enable all coil-buttons
+            btn.Enable(True)
+        event.GetEventObject().Destroy()  # Delete the obj_id combobox
+
+    def OnRightClickCoil(self, event, name):
+        def SetObjID(event, name):
+            # Largest valid obj_id with the currently used Tracker (ie. coord_raw.shape[0])
+            max_obj_id = self.tracker.GetTrackerCoordinates(ref_mode_id=0)[2].shape[0]
+
+            choice_obj_id = wx.ComboBox(
+                self,
+                -1,
+                f"{str(self.coil_registrations[name]['obj_id'])}",
+                size=wx.Size(90, 23),
+                choices=["0"] + [str(id) for id in range(2, max_obj_id)],
+                style=wx.CB_DROPDOWN | wx.CB_READONLY,
             )
+            tooltip = "Choose the coil index in coord_raw with the current tracker. Choose 0 for static mode, 2 for dynamic mode and 3 onwards for multiple coils."
+            choice_obj_id.SetToolTip(tooltip)
+            choice_obj_id.Bind(
+                wx.EVT_COMBOBOX, (lambda event, name=name: self.OnChoiceObjID(event, name))
+            )
+
+        def DeleteCoil(event, name):
+            del self.coil_registrations[name]
+
+            # Remove the coil-button
+            self.coil_btns[name][0].Destroy()
+            del self.coil_btns[name]
+
+            # Remove the coil from the config file
+            self.session.SetConfig("coil_registrations", self.coil_registrations)
+
+            # Remove coil from navigation and CoilVisualizer
+            Publisher.sendMessage("Select coil", coil_name=name, coil_registration=None)
+
+        menu = wx.Menu()
+        delete_coil = menu.Append(wx.ID_ANY, "Delete coil")
+        set_obj_id = menu.Append(wx.ID_ANY, "Set coil index")
+        self.Bind(wx.EVT_MENU, (lambda event, name=name: DeleteCoil(event, name)), delete_coil)
+        self.Bind(wx.EVT_MENU, (lambda event, name=name: SetObjID(event, name)), set_obj_id)
+        self.PopupMenu(menu, event.GetPosition())
+        menu.Destroy()
 
     def OnCreateNewCoil(self, event=None):
         if self.tracker.IsTrackerInitialized():
@@ -1044,28 +1196,32 @@ def OnCreateNewCoil(self, event=None):
             )
             try:
                 if dialog.ShowModal() == wx.ID_OK:
-                    obj_fiducials, obj_orients, obj_ref_mode, coil_path, polydata = (
+                    (coil_name, coil_path, obj_fiducials, obj_orients, obj_id, tracker_id) = (
                         dialog.GetValue()
                     )
 
-                    self.neuronavigation_api.update_coil_mesh(polydata)
+                    # LUKATODO: update coil mesh elsewhere
+                    # self.neuronavigation_api.update_coil_mesh(polydata)
 
                     if np.isfinite(obj_fiducials).all() and np.isfinite(obj_orients).all():
-                        Publisher.sendMessage(
-                            "Update object registration",
-                            data=(obj_fiducials, obj_orients, obj_ref_mode, coil_path),
-                        )
-                        Publisher.sendMessage("Update status text in GUI", label=_("Ready"))
-                        Publisher.sendMessage(
-                            "Configure coil",
-                            coil_path=coil_path,
-                            polydata=polydata,
-                        )
+                        coil_registration = {  # LUKATODO: angle_threshold, dist_threshold, time_interval
+                            "fiducials": obj_fiducials.tolist(),
+                            "orientations": obj_orients.tolist(),
+                            "obj_id": obj_id,
+                            "tracker_id": tracker_id,
+                            "path": coil_path.decode(const.FS_ENCODE),
+                        }
+                        self.coil_registrations[coil_name] = coil_registration
+                        self.session.SetConfig("coil_registrations", self.coil_registrations)
+                        self.AddCoilButton(coil_name)  # Add a button for this coil to GUI
+                        self.Layout()
+
+                        # Update the coil registration in Navigation if coil_name was selected
+                        if self.coil_btns[coil_name][0].GetValue():
+                            self.navigation.coil_registrations[coil_name] = coil_registration
 
                         # Automatically enable and check 'Track object' checkbox and uncheck 'Disable Volume Camera' checkbox.
-                        Publisher.sendMessage("Enable track object button", enabled=True)
-                        Publisher.sendMessage("Press track object button", pressed=True)
-
+                        # LUKATODO: delete the below with dependencies
                         Publisher.sendMessage("Press target mode button", pressed=False)
 
             except wx.PyAssertionError:  # TODO FIX: win64
@@ -1074,87 +1230,6 @@ def OnCreateNewCoil(self, event=None):
         else:
             dlg.ShowNavigationTrackerWarning(0, "choose")
 
-    def OnLoadCoil(self, event=None):
-        filename = dlg.ShowLoadSaveDialog(
-            message=_("Load object registration"), wildcard=_("Registration files (*.obr)|*.obr")
-        )
-        # data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\anat_reg_improve_20200609'
-        # coil_path = 'magstim_coil_dell_laptop.obr'
-        # filename = os.path.join(data_dir, coil_path)
-
-        try:
-            if filename:
-                with open(filename) as text_file:
-                    data = [s.split("\t") for s in text_file.readlines()]
-
-                registration_coordinates = np.array(data[1:]).astype(np.float32)
-                obj_fiducials = registration_coordinates[:, :3]
-                obj_orients = registration_coordinates[:, 3:]
-
-                coil_path = data[0][1].encode(const.FS_ENCODE)
-                obj_ref_mode = int(data[0][-1])
-
-                if not os.path.exists(coil_path):
-                    coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
-
-                polydata = vtk_utils.CreateObjectPolyData(coil_path)
-                if polydata:
-                    self.neuronavigation_api.update_coil_mesh(polydata)
-                else:
-                    coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
-
-                Publisher.sendMessage(
-                    "Update object registration",
-                    data=(obj_fiducials, obj_orients, obj_ref_mode, coil_path),
-                )
-                Publisher.sendMessage(
-                    "Update status text in GUI", label=_("Object file successfully loaded")
-                )
-                Publisher.sendMessage(
-                    "Configure coil",
-                    coil_path=coil_path,
-                    polydata=polydata,
-                )
-
-                # Automatically enable and check 'Track object' checkbox and uncheck 'Disable Volume Camera' checkbox.
-                Publisher.sendMessage("Enable track object button", enabled=True)
-                Publisher.sendMessage("Press track object button", pressed=True)
-                Publisher.sendMessage("Press target mode button", pressed=False)
-
-                msg = _("Object file successfully loaded")
-                wx.MessageBox(msg, _("InVesalius 3"))
-        except Exception:
-            wx.MessageBox(_("Object registration file incompatible."), _("InVesalius 3"))
-            Publisher.sendMessage("Update status text in GUI", label="")
-
-    def OnSaveCoil(self, evt):
-        obj_fiducials, obj_orients, obj_ref_mode, coil_path = (
-            self.navigation.GetObjectRegistration()
-        )
-        if np.isnan(obj_fiducials).any() or np.isnan(obj_orients).any():
-            wx.MessageBox(_("Digitize all object fiducials before saving"), _("Save error"))
-        else:
-            filename = dlg.ShowLoadSaveDialog(
-                message=_("Save object registration as..."),
-                wildcard=_("Registration files (*.obr)|*.obr"),
-                style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
-                default_filename="object_registration.obr",
-                save_ext="obr",
-            )
-            if filename:
-                hdr = (
-                    "Object"
-                    + "\t"
-                    + utils.decode(coil_path, const.FS_ENCODE)
-                    + "\t"
-                    + "Reference"
-                    + "\t"
-                    + str("%d" % obj_ref_mode)
-                )
-                data = np.hstack([obj_fiducials, obj_orients])
-                np.savetxt(filename, data, fmt="%.4f", delimiter="\t", newline="\n", header=hdr)
-                wx.MessageBox(_("Object file successfully saved"), _("Save"))
-
     def OnSelectAngleThreshold(self, evt, ctrl):
         self.angle_threshold = ctrl.GetValue()
         Publisher.sendMessage("Update angle threshold", angle=self.angle_threshold)
@@ -1170,13 +1245,6 @@ def OnSelectDistanceThreshold(self, evt, ctrl):
     def OnSelectTimestamp(self, evt, ctrl):
         self.timestamp = ctrl.GetValue()
 
-    def OnObjectUpdate(self, data=None):
-        if data:
-            label = os.path.basename(data[-1])
-        else:
-            label = "None"
-        self.config_txt.SetLabel(label)
-
 
 class TrackerTab(wx.Panel):
     def __init__(self, parent, tracker, robot):
@@ -1188,8 +1256,28 @@ def __init__(self, parent, tracker, robot):
         self.robot = robot
         self.robot_ip = None
         self.matrix_tracker_to_robot = None
+        self.n_coils = 1
         self.state = self.LoadConfig()
 
+        # ComboBox for choosing the no. of coils to track
+        n_coils_options = [str(n) for n in range(1, 10)]
+        select_n_coils_elem = wx.ComboBox(
+            self,
+            -1,
+            "",
+            size=(145, -1),
+            choices=n_coils_options,
+            style=wx.CB_DROPDOWN | wx.CB_READONLY,
+        )
+        tooltip = _("Choose the number of coils to track")
+        select_n_coils_elem.SetToolTip(tooltip)
+        select_n_coils_elem.SetSelection(self.n_coils - 1)
+        select_n_coils_elem.Bind(
+            wx.EVT_COMBOBOX, partial(self.OnChooseNoOfCoils, ctrl=select_n_coils_elem)
+        )
+
+        select_n_coils_label = wx.StaticText(self, -1, _("Choose the number of coils to track:"))
+
         # ComboBox for spatial tracker device selection
         tracker_options = [_("Select")] + self.tracker.get_trackers()
         select_tracker_elem = wx.ComboBox(
@@ -1206,7 +1294,6 @@ def __init__(self, parent, tracker, robot):
         select_tracker_elem.Bind(
             wx.EVT_COMBOBOX, partial(self.OnChooseTracker, ctrl=select_tracker_elem)
         )
-        self.select_tracker_elem = select_tracker_elem
 
         select_tracker_label = wx.StaticText(self, -1, _("Choose the tracking device: "))
 
@@ -1229,9 +1316,11 @@ def __init__(self, parent, tracker, robot):
 
         choice_ref_label = wx.StaticText(self, -1, _("Choose the navigation reference mode: "))
 
-        ref_sizer = wx.FlexGridSizer(rows=2, cols=2, hgap=5, vgap=5)
+        ref_sizer = wx.FlexGridSizer(rows=3, cols=2, hgap=5, vgap=5)
         ref_sizer.AddMany(
             [
+                (select_n_coils_label, wx.LEFT),
+                (select_n_coils_elem, wx.RIGHT),
                 (select_tracker_label, wx.LEFT),
                 (select_tracker_elem, wx.RIGHT),
                 (choice_ref_label, wx.LEFT),
@@ -1323,6 +1412,8 @@ def LoadConfig(self):
         session = ses.Session()
         state = session.GetConfig("robot")
 
+        self.n_coils = max(1, len((session.GetConfig("navigation") or {}).get("selected_coils", [])))
+
         if state is None:
             return False
 
@@ -1331,6 +1422,17 @@ def LoadConfig(self):
 
         return True
 
+    def OnChooseNoOfCoils(self, evt, ctrl):
+        if hasattr(evt, "GetSelection"):
+            choice = evt.GetSelection()
+            print(f"choice: {choice}")
+            self.n_coils = choice + 1
+        else:
+            self.n_coils = 1
+        ctrl.SetSelection(self.n_coils - 1)
+        Publisher.sendMessage("Reset coil selection", n_coils=self.n_coils)
+        Publisher.sendMessage("Coil selection done", done=False)
+
     def OnChooseTracker(self, evt, ctrl):
         if sys.platform == "darwin":
             wx.CallAfter(self.GetParent().Hide)
@@ -1345,9 +1447,11 @@ def OnChooseTracker(self, evt, ctrl):
 
         self.tracker.DisconnectTracker()
         self.tracker.ResetTrackerFiducials()
-        self.tracker.SetTracker(choice)
+        self.tracker.SetTracker(choice, n_coils=self.n_coils)
         Publisher.sendMessage("Update status text in GUI", label=_("Ready"))
         Publisher.sendMessage("Tracker changed")
+        Publisher.sendMessage("Reset coil selection", n_coils=self.n_coils)
+        Publisher.sendMessage("Coil selection done", done=False)
         ctrl.SetSelection(self.tracker.tracker_id)
         Publisher.sendMessage("End busy cursor")
         if sys.platform == "darwin":
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 6827644d0..645128234 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -166,12 +166,12 @@ def __init__(self, parent):
         fold_panel.AddFoldPanelWindow(item, ntw, spacing=0, leftSpacing=0, rightSpacing=0)
         fold_panel.Expand(fold_panel.GetFoldPanel(0))
 
-        item = fold_panel.AddFoldPanel(_("Navigation"), collapsed=True)
-        self.__id_nav = item.GetId()
-        ntw = NavigationPanel(parent=item, nav_hub=nav_hub)
+        self.nav_panel = nav_panel = fold_panel.AddFoldPanel(_("Navigation"), collapsed=True)
+        self.__id_nav = nav_panel.GetId()
+        ntw = NavigationPanel(parent=nav_panel, nav_hub=nav_hub)
 
-        fold_panel.ApplyCaptionStyle(item, style)
-        fold_panel.AddFoldPanelWindow(item, ntw, spacing=0, leftSpacing=0, rightSpacing=0)
+        fold_panel.ApplyCaptionStyle(nav_panel, style)
+        fold_panel.AddFoldPanelWindow(nav_panel, ntw, spacing=0, leftSpacing=0, rightSpacing=0)
         self.fold_panel.Bind(fpb.EVT_CAPTIONBAR, self.OnFoldPressCaption)
 
         sizer = wx.BoxSizer(wx.VERTICAL)
@@ -194,6 +194,7 @@ def __bind_events(self):
         # Publisher.subscribe(self.OnHideDbs, "Hide dbs folder")
         Publisher.subscribe(self.OpenNavigation, "Open navigation menu")
         Publisher.subscribe(self.OnEnableState, "Enable state project")
+        Publisher.subscribe(self.CollapseNavigation, "Coil selection done")
 
     def __calc_best_size(self, panel):
         parent = panel.GetParent()
@@ -272,17 +273,19 @@ def OnShowCoil(self, evt=None):
         pressed = self.show_coil_button.GetValue()
         Publisher.sendMessage("Show coil in viewer volume", state=pressed)
 
+    def CollapseNavigation(self, done):
+        if not done: # Coil selection is no longer complete, so hide navigation panel
+            self.fold_panel.Collapse(self.nav_panel)
+
     def OnFoldPressCaption(self, evt):
         id = evt.GetTag().GetId()
         expanded = evt.GetFoldStatus()
 
-        if id == self.__id_nav:
-            status = self.CheckRegistration()  # noqa: F841
-
-        if not expanded:
-            self.fold_panel.Expand(evt.GetTag())
-        else:
+        if expanded:
             self.fold_panel.Collapse(evt.GetTag())
+        elif id != self.__id_nav or self.CheckRegistration():
+            # Only expand navigation panel if coil selection/registration is done
+            self.fold_panel.Expand(evt.GetTag())
 
     def ResizeFPB(self):
         sizeNeeded = self.fold_panel.GetPanelsLength(0, 0)[2]
@@ -293,7 +296,7 @@ def CheckRegistration(self):
         return (
             self.tracker.AreTrackerFiducialsSet()
             and self.image.AreImageFiducialsSet()
-            and self.navigation.GetObjectRegistration() is not None
+            and self.navigation.CoilSelectionDone()
         )
 
     def OpenNavigation(self):
@@ -1065,7 +1068,7 @@ def __init__(self, parent, nav_hub):
         self.__bind_events()
 
     def __bind_events(self):
-        pass  # Publisher.subscribe(self.OnCloseProject, 'Remove object data')
+        pass
 
     def onRecord(self, evt):
         marker_visibilities, __, coord_raw = self.tracker.GetTrackerCoordinates(
@@ -1103,51 +1106,39 @@ def __init__(self, parent, nav_hub):
         wx.Panel.__init__(self, parent)
         self.navigation = nav_hub.navigation
 
-        border = wx.FlexGridSizer(2, 3, 5)
-        object_reg = self.navigation.GetObjectRegistration()
-        self.object_reg = object_reg
+        border = wx.FlexGridSizer(1, 2, 1)
+        self.coil_registrations = []
 
-        lbl = wx.StaticText(self, -1, _("No TMS coil configured!"))
-        lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
+        lbl = wx.StaticText(self, -1, _("Coil selection done, ready for navigation!"))
+        # lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
         self.lbl = lbl
 
-        config_txt = wx.StaticText(self, -1, "")
-        self.config_txt = config_txt
-        self.config_txt.Hide()
-
-        lbl_edit = wx.StaticText(self, -1, _("Edit Configuration:"))
-        btn_edit = wx.Button(self, -1, _("Preferences"))
+        btn_edit = wx.Button(self, -1, _("Edit selection in Preferences"))
         btn_edit.SetToolTip("Open preferences menu")
         btn_edit.Bind(wx.EVT_BUTTON, self.OnEditPreferences)
 
         border.AddMany(
             [
-                (lbl, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 10),
-                (0, 0),
-                (config_txt, 1, wx.EXPAND | wx.LEFT | wx.ALIGN_CENTER_VERTICAL, 10),
-                (0, 0),
-                (lbl_edit, 1, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL, 10),
-                (btn_edit, 0, wx.EXPAND | wx.ALL | wx.ALIGN_LEFT, 10),
+                (lbl, 1, wx.EXPAND),
+                (btn_edit, 1, wx.EXPAND),
             ]
         )
 
         next_button = wx.Button(self, label="Proceed to navigation")
         next_button.Bind(wx.EVT_BUTTON, partial(self.OnNext))
-        if self.object_reg is None:
-            next_button.Disable()
+        if not self.navigation.CoilSelectionDone():
+            self.lbl.SetLabel("Please select which coil(s) to track")
+            next_button.Enable(False)
         self.next_button = next_button
 
         bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        bottom_sizer.Add(next_button)
-
-        if self.object_reg is not None:
-            self.OnObjectUpdate()
+        bottom_sizer.Add(next_button, 1, wx.EXPAND)
 
         main_sizer = wx.BoxSizer(wx.VERTICAL)
         main_sizer.AddMany(
             [
-                (border, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 10),
-                (bottom_sizer, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.TOP, 20),
+                (border, 0, wx.EXPAND, 5),
+                (bottom_sizer, 0, wx.EXPAND, 5),
             ]
         )
 
@@ -1156,27 +1147,24 @@ def __init__(self, parent, nav_hub):
         self.__bind_events()
 
     def __bind_events(self):
-        Publisher.subscribe(self.OnObjectUpdate, "Update object registration")
+        Publisher.subscribe(self.CoilSelectionDone, "Coil selection done")
         Publisher.subscribe(self.OnCloseProject, "Close project data")
         Publisher.subscribe(self.OnCloseProject, "Remove object data")
 
     def OnCloseProject(self):
+        Publisher.sendMessage("Enable start navigation button", enabled=False)
+        # LUKATODO: delete the below?
         Publisher.sendMessage("Press track object button", pressed=False)
         Publisher.sendMessage("Enable track object button", enabled=False)
 
-    def UpdateObjectRegistration(self):
-        self.object_reg = self.navigation.GetObjectRegistration()
-
-    def OnObjectUpdate(self, data=None):
-        self.lbl.SetLabel("Current Configuration:")
-        self.UpdateObjectRegistration()
-        if self.object_reg is not None:
-            self.config_txt.SetLabelText(os.path.basename(self.object_reg[-1]))
+    def CoilSelectionDone(self, done):
+        if done:
+            self.lbl.SetLabel("Coil selection done, ready for navigation!")
         else:
-            self.config_txt.SetLabelText("None")
+            self.lbl.SetLabel("Please select which coil(s) to track")
+
+        self.next_button.Enable(done)
         self.lbl.Show()
-        self.config_txt.Show()
-        self.next_button.Enable()
 
     def OnEditPreferences(self, evt):
         Publisher.sendMessage("Open preferences menu", page=3)
@@ -1301,6 +1289,7 @@ def __init__(self, parent, nav_hub):
         )
         track_object_button.SetBackgroundColour(GREY_COLOR)
         track_object_button.SetBitmap(BMP_TRACK)
+        track_object_button.Enable(True)
         track_object_button.SetValue(False)
         track_object_button.SetToolTip(tooltip)
         track_object_button.Bind(
@@ -1582,7 +1571,6 @@ def SaveConfig(self):
         state = {
             "track_object": {
                 "checked": track_object.GetValue(),
-                "enabled": track_object.IsEnabled(),
             }
         }
 
@@ -1593,13 +1581,9 @@ def LoadConfig(self):
         session = ses.Session()
         state = session.GetConfig("object_registration_panel")
 
-        if state is None:
-            return
-
-        track_object = state["track_object"]
-
-        self.EnableTrackObjectButton(track_object["enabled"])
-        self.PressTrackObjectButton(track_object["checked"])
+        if state is not None:
+            track_object = state["track_object"]
+            self.PressTrackObjectButton(track_object["checked"])
 
     # Toggle Button Helpers
     def UpdateToggleButton(self, ctrl, state=None):
@@ -1707,12 +1691,6 @@ def OnCheckStatus(self, nav_status, vis_status):
             self.EnableToggleButton(self.checkbox_serial_port, 1)
             self.UpdateToggleButton(self.checkbox_serial_port)
 
-        # Enable/Disable track-object checkbox if object registration is valid.
-        obj_registration = self.navigation.GetObjectRegistration()
-        enable_track_object = obj_registration is not None and obj_registration[0] is not None
-        self.EnableTrackObjectButton(enable_track_object)
-        self.EnableShowCoilButton(enable_track_object)
-
     # Robot
     def OnRobotStatus(self, data):
         if data:
@@ -2076,6 +2054,29 @@ def __init__(self, parent, nav_hub):
         sizer_delete = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
         sizer_delete.AddMany([(btn_delete_single, 1, wx.RIGHT), (btn_delete_all, 0, wx.LEFT)])
 
+        # Combobox to choose the main coil (ie. the coil which to track with pointer and to use for marker creation)
+        #LUKATODO: how to ensure the choices are updated when coil selection changes
+        self.select_main_coil = select_main_coil = wx.ComboBox(
+            self,
+            -1,
+            "",
+            size=(145, -1),
+            choices=list(self.navigation.coil_registrations),
+            style=wx.CB_DROPDOWN | wx.CB_READONLY,
+        )
+        maincoil_tooltip = "Select which coil to record markers with"
+        select_main_coil.SetToolTip(maincoil_tooltip)
+        select_main_coil.Bind(
+            wx.EVT_COMBOBOX, partial(self.OnChooseMainCoil, ctrl=select_main_coil)
+        )
+
+        # If main coil is defined, set this in the combobox        
+        if (main_coil := self.navigation.main_coil) is not None:
+            main_coil_index = select_main_coil.FindString(main_coil)
+            select_main_coil.SetSelection(main_coil_index)
+        sizer_main_coil = wx.FlexGridSizer(rows=1, cols=1, hgap=5, vgap=5)
+        sizer_main_coil.Add(select_main_coil)
+
         screen_width, screen_height = wx.DisplaySize()
 
         # The marker list height is set to 120 pixels (accommodating 4 markers) if the screen height is
@@ -2138,6 +2139,7 @@ def __init__(self, parent, nav_hub):
         group_sizer.Add(sizer_create, 0, wx.TOP | wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
         group_sizer.Add(sizer_btns, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
         group_sizer.Add(sizer_delete, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
+        group_sizer.Add(sizer_main_coil, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
         group_sizer.Add(marker_list_ctrl, 0, wx.EXPAND | wx.ALL, 5)
         group_sizer.Fit(self)
 
@@ -2175,6 +2177,9 @@ def __bind_events(self):
         Publisher.subscribe(self.CreateMarkerEfield, "Create Marker from tangential")
         Publisher.subscribe(self.UpdateCortexMarker, "Update Cortex Marker")
 
+        # Update main_coil combobox
+        Publisher.subscribe(self.UpdateMainCoilCombobox, "Coil selection done")
+
         # Update marker_list_ctrl
         Publisher.subscribe(self._AddMarker, "Add marker")
         Publisher.subscribe(self._DeleteMarker, "Delete marker")
@@ -2585,6 +2590,23 @@ def OnCreateCoilTargetFromCoilPose(self, evt):
 
         self.markers.CreateCoilTargetFromCoilPose(marker)
 
+    def UpdateMainCoilCombobox(self, done):
+        select_main_coil = self.select_main_coil
+        if done:
+            select_main_coil.Clear()
+            select_main_coil.AppendItems(list(self.navigation.coil_registrations))
+            main_coil_index = select_main_coil.FindString(self.navigation.main_coil)
+            select_main_coil.SetSelection(main_coil_index)
+        else:
+            select_main_coil.Clear()
+
+    def OnChooseMainCoil(self, evt, ctrl):
+        choice = evt.GetSelection()
+        main_coil = ctrl.GetString(choice)
+        self.navigation.SetMainCoil(main_coil)
+        ctrl.SetSelection(choice)
+
+
     def ChangeLabel(self, evt):
         list_index = self.marker_list_ctrl.GetFocusedItem()
         if list_index == -1:
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index ab89e2e0d..2f9be266c 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -145,7 +145,9 @@ def run(self):
                 got_coords = True
 
                 probe_visible = marker_visibilities[0]
-                coil_visible = marker_visibilities[2]
+
+                #LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
+                coil_visible = marker_visibilities[2] # LUKATODO: will static mode work with this?
 
                 # automatically track either coil or stylus if only one of them is visible, otherise use navigation.track_obj
                 track_coil = (
@@ -153,10 +155,16 @@ def run(self):
                     if (coil_visible ^ probe_visible)
                     else self.navigation.track_obj
                 )
-
+                main_coil = self.navigation.main_coil
+                track_this = main_coil if track_coil else "probe"
                 # choose which object to track in slices and viewer_volume pointer
-                coord = coords[track_coil]  # main-coil if track_coil else stylus
-                m_img = m_imgs[track_coil]
+                coord = coords[track_this]  # main-coil if track_coil else stylus
+                m_img = m_imgs[track_this]
+                #LUKATODO: do Debug approach here
+
+                # Remove probe, so that coords/m_imgs only contain coils
+                probe_coord = coords.pop("probe")
+                probe_m_img = m_imgs.pop("probe")
 
                 # use of CallAfter is mandatory otherwise crashes the wx interface
                 if self.view_tracts:
@@ -200,14 +208,18 @@ def run(self):
                 )
 
                 if coil_visible:
+                    # Check pubsub "Update coil pose" dependencies
                     wx.CallAfter(
-                        Publisher.sendMessage, "Update coil pose", m_img=m_imgs[1], coord=coords[1]
+                        Publisher.sendMessage, "Update coil poses", m_imgs=m_imgs, coords=coords
+                    )
+                    wx.CallAfter( # LUKATODO: this is just for viewer_volume...
+                        Publisher.sendMessage, "Update coil pose", m_img=m_imgs[main_coil], coord=coords[main_coil]
                     )
                     wx.CallAfter(
-                        Publisher.sendMessage,
+                        Publisher.sendMessage, #LUKATODO: what is this?
                         "Update object arrow matrix",
-                        m_img=m_imgs[1],
-                        coord=coords[1],
+                        m_img=m_imgs[main_coil],
+                        coord=coords[main_coil],
                         flag=self.peel_loaded,
                     )
 
@@ -215,8 +227,8 @@ def run(self):
                         wx.CallAfter(
                             Publisher.sendMessage,
                             "Update point location for e-field calculation",
-                            m_img=m_imgs[1],
-                            coord=coords[1],
+                            m_img=m_imgs[main_coil],
+                            coord=coords[main_coil],
                             queue_IDs=self.e_field_IDs_queue,
                         )
                         try:
@@ -234,7 +246,7 @@ def run(self):
 
                 if probe_visible:
                     wx.CallAfter(
-                        Publisher.sendMessage, "Update probe pose", m_img=m_imgs[0], coord=coords[0]
+                        Publisher.sendMessage, "Update probe pose", m_img=probe_m_img, coord=probe_coord
                     )
 
                 # Render the volume viewer and the slice viewers.
@@ -255,15 +267,14 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.pedal_connector = pedal_connector
         self.neuronavigation_api = neuronavigation_api
 
-        self.correg = None
         self.target = None
         self.n_coils = 1
-        self.obj_registrations = []
-        self.object_registration = None
+        self.coil_registrations = {}
+        self.main_coil = None  # Which coil to track with pointer
         self.track_obj = False
         self.m_change = None
         self.r_stylus = None
-        self.obj_data = None
+
         self.all_fiducials = np.zeros((6, 6))
         self.event = threading.Event()
         self.coord_queue = QueueCustom(maxsize=1)
@@ -319,50 +330,66 @@ def __init__(self, pedal_connector, neuronavigation_api):
 
     def __bind_events(self):
         Publisher.subscribe(self.CoilAtTarget, "Coil at target")
+        Publisher.subscribe(self.SetNoOfCoils, "Reset coil selection")
+        Publisher.subscribe(self.SelectCoil, "Select coil")
         Publisher.subscribe(self.UpdateSerialPort, "Update serial port")
-        Publisher.subscribe(self.UpdateObjectRegistration, "Update object registration")
         Publisher.subscribe(self.TrackObject, "Track object")
 
-    def SaveConfig(self):
-        # XXX: This shouldn't be needed, but task_navigator.py currently calls UpdateObjectRegistration with
-        #   None parameter when the project is closed, crashing without this checks.
-        if self.object_registration is None:
-            return
-
-        object_fiducials, object_orientations, object_reference_mode, object_name = (
-            self.object_registration
-        )
-
-        state = {
-            "object_fiducials": object_fiducials.tolist(),
-            "object_orientations": object_orientations.tolist(),
-            "object_reference_mode": object_reference_mode,
-            "object_name": object_name.decode(const.FS_ENCODE),
-        }
-
+    def SaveConfig(self, key=None, value=None):
+        """
+        Save either the whole state, or a specific key-value pair into navigation configuration
+        """
         session = ses.Session()
-        session.SetConfig("navigation", state)
+        if key is None:  # Save the whole state
+            state = {"selected_coils": list(self.coil_registrations)}
+            if self.r_stylus is not None:
+                state["r_stylus"] = self.r_stylus.tolist()
+            session.SetConfig("navigation", state)
+
+        elif value is not None:
+            state = session.GetConfig("navigation") or {}
+            state[key] = value
+            session.SetConfig("navigation", state)
 
     def LoadConfig(self):
         session = ses.Session()
         state = session.GetConfig("navigation")
 
+        # Get the dict of all coil_registrations saved to config file
+        saved_coil_registrations = session.GetConfig("coil_registrations")
+
         if state is not None:
-            object_fiducials = np.array(state["object_fiducials"])
-            object_orientations = np.array(state["object_orientations"])
-            object_reference_mode = state["object_reference_mode"]
-            object_name = state["object_name"].encode(const.FS_ENCODE)
-            self.object_registration = (
-                object_fiducials,
-                object_orientations,
-                object_reference_mode,
-                object_name,
-            )
+            # Try to load selected_coils, the list of names of coils to use for navigation
+            if ("selected_coils" in state) and (saved_coil_registrations is not None):
+                selected_coils = state["selected_coils"]
+                self.coil_registrations = {
+                    coil_name: saved_coil_registrations[coil_name]
+                    for coil_name in selected_coils
+                    if coil_name in saved_coil_registrations
+                }
+                if self.coil_registrations:
+                    self.main_coil = state.get("main_coil", None) or next(iter(self.coil_registrations))
+                    self.n_coils = len(self.coil_registrations)
 
             # Try to load stylus orientation data
             if "r_stylus" in state:
                 self.r_stylus = np.array(state["r_stylus"])
 
+    def CoilSelectionDone(self):
+        return len(self.coil_registrations) == self.n_coils
+
+    def SelectCoil(self, coil_name, coil_registration):
+        if coil_registration is not None:  # Add the coil to selection
+            self.coil_registrations[coil_name] = coil_registration
+            if self.main_coil is None:
+                self.main_coil = coil_name
+        else:  # Remove the coil from selection
+            self.coil_registrations.pop(coil_name, None)
+            if self.main_coil == coil_name:
+                self.main_coil = None
+
+        self.SaveConfig("selected_coils", list(self.coil_registrations.keys()))
+
     def CoilAtTarget(self, state):
         self.coil_at_target = state
 
@@ -375,20 +402,24 @@ def UpdateSerialPort(self, serial_port_in_use, com_port=None, baud_rate=None):
         self.com_port = com_port
         self.baud_rate = baud_rate
 
-    def UpdateObjectRegistration(self, data=None):
-        self.object_registration = data
-
-        self.SaveConfig()
-
-    def GetObjectRegistration(self):
-        return self.object_registration
-
     def TrackObject(self, enabled=False):
         self.track_obj = enabled
 
     def SetLockToTarget(self, value):
         self.lock_to_target = value
 
+    def SetNoOfCoils(self, n_coils):
+        self.n_coils = n_coils
+
+        # Reset coil selection
+        self.coil_registrations = {}
+        self.main_coil = None
+        self.SaveConfig("selected_coils", [])
+
+    def SetMainCoil(self, main_coil):
+        self.main_coil = main_coil
+        self.SaveConfig("main_coil", main_coil)
+
     def SetReferenceMode(self, value):
         self.ref_mode_id = value
 
@@ -451,10 +482,7 @@ def SetStylusOrientation(self, coord_raw):
             # Rotation from tracker to VTK coordinate system
             self.r_stylus = up_vtk @ np.linalg.inv(R @ up_trk @ np.linalg.inv(R))
             # Save r_stylus to config file
-            session = ses.Session()
-            if (nav_config := session.GetConfig("navigation")) is not None:
-                nav_config["r_stylus"] = self.r_stylus.tolist()
-                session.SetConfig("navigation", nav_config)
+            self.SaveConfig("r_stylus", self.r_stylus.tolist())
             return True
         else:
             return False
@@ -484,28 +512,48 @@ def StartNavigation(self, tracker, icp):
 
         Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components)
 
-        # LUKATODO: object_registration --> coil_registrations
-        if self.object_registration is None:
-            # check if object registration was performed
-            wx.MessageBox(_("Perform coil registration before navigation."), _("InVesalius 3"))
+        if not self.CoilSelectionDone():
+            wx.MessageBox(
+                _(
+                    f"No. of coils to track is {self.n_coils}, but no. of coils registered is {len(self.coil_registrations)}"
+                ),
+                _("InVesalius 3"),
+            )
         else:
-            # if object registration was correctly performed continue with navigation
-            # object_registration[0] is object 3x3 fiducial matrix and object_registration[1] is 3x3 orientation matrix
-            obj_fiducials, obj_orients, obj_ref_mode, obj_name = self.object_registration
-
-            coreg_data = [self.r_stylus, self.m_change, obj_ref_mode]
-
-            if self.ref_mode_id:
-                coord_raw, marker_visibilities = tracker.TrackerCoordinates.GetCoordinates()
-            else:
-                coord_raw = np.array([None])
+            # Pre-compute obj_datas: data/matrices for each coil to be used in coregistration
+            # data is accessed from dict by coil name
+            obj_datas = {}
+            for coil_name in self.coil_registrations:
+                if self.ref_mode_id:
+                    coord_raw, marker_visibilities = tracker.TrackerCoordinates.GetCoordinates()
+                else:
+                    coord_raw = np.array([None])
+
+                coil_registration = self.coil_registrations[coil_name]
+                obj_id = coil_registration["obj_id"]
+
+                # Check that the object index is in range of Tracker coordinates
+                if obj_id >= coord_raw.shape[0]:
+                    wx.MessageBox(
+                        _(
+                            f"Coil index {obj_id} for coil {coil_name} is out of range of current Tracker! Change the coil index in Preferences - TMS Coil tab"
+                        ),
+                        _("InVesalius 3"),
+                    )
+                    return
+
+                # Pre-compute obj_datas: data/matrices for each coil to be used in coregistration
+                obj_data = (obj_id,) + db.object_registration(
+                    np.array(coil_registration["fiducials"]),
+                    np.array(coil_registration["orientations"]),
+                    coord_raw,
+                    self.m_change,
+                )
+                obj_datas[coil_name] = obj_data
 
-            # LUKATODO: NOTE: coil does not need to be visible here, we only need the head coord for obj_data:
-            self.obj_data = db.object_registration(
-                obj_fiducials, obj_orients, coord_raw, self.m_change
-            )
-            coreg_data.extend(self.obj_data)
+            coreg_data = [self.m_change, self.r_stylus]
 
+            # LUKATODO: coord_queue is accounted for but what about others for multicoil?
             queues = [
                 self.coord_queue,
                 self.coord_tracts_queue,
@@ -519,6 +567,7 @@ def StartNavigation(self, tracker, icp):
                     tracker,
                     self.n_coils,
                     coreg_data,
+                    obj_datas,
                     self.view_tracts,
                     queues,
                     self.event,
diff --git a/invesalius/session.py b/invesalius/session.py
index 7d03b479f..2d7e003bd 100644
--- a/invesalius/session.py
+++ b/invesalius/session.py
@@ -110,20 +110,14 @@ def SetConfig(self, key: str, value: Any) -> None:
         self.WriteConfigFile()
 
     def GetConfig(self, key: str, default_value: Any = None) -> Any:
-        if key in self._config:
-            return self._config[key]
-        else:
-            return default_value
+        return self._config.get(key, default_value)
 
     def SetState(self, key: str, value: Any) -> None:
         self._state[key] = value
         self.WriteStateFile()
 
     def GetState(self, key: str, default_value: Any = None) -> Any:
-        if key in self._state:
-            return self._state[key]
-        else:
-            return default_value
+        return self._state.get(key, default_value)
 
     def IsOpen(self) -> bool:
         import invesalius.constants as const

From d215fff1672a92241b8263ebe624c22ad03b3df9 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Mon, 12 Aug 2024 19:56:16 +0300
Subject: [PATCH 19/44] Cleaning up.

Improve ObjectTab init by using LoadConfig. Remove self.track_obj state var from GUI, it is a property of Navigation class.

Addition: load/save coil from/to OBR file.
---
 invesalius/data/coordinates.py                |   5 +-
 invesalius/data/coregistration.py             |  17 +-
 .../data/visualization/coil_visualizer.py     |  14 +-
 invesalius/gui/preferences.py                 | 217 +++++++++++++-----
 invesalius/gui/task_navigator.py              |  47 ++--
 invesalius/navigation/navigation.py           |  41 ++--
 6 files changed, 212 insertions(+), 129 deletions(-)

diff --git a/invesalius/data/coordinates.py b/invesalius/data/coordinates.py
index 68222da11..dc05158b2 100644
--- a/invesalius/data/coordinates.py
+++ b/invesalius/data/coordinates.py
@@ -538,6 +538,9 @@ def DebugCoordRandom(tracker_connection: "TrackerConnection", tracker_id: int, r
     coord4 = np.array(
         [uniform(*dx), uniform(*dx), uniform(*dx), uniform(*dt), uniform(*dt), uniform(*dt)]
     )
+    coord5 = np.array(
+        [uniform(*dx), uniform(*dx), uniform(*dx), uniform(*dt), uniform(*dt), uniform(*dt)]
+    )
 
     sleep(0.15)
 
@@ -557,7 +560,7 @@ def DebugCoordRandom(tracker_connection: "TrackerConnection", tracker_id: int, r
     # is not possible to registering without markers.
     marker_visibilities = [True, True, True]
 
-    return np.vstack([coord1, coord2, coord3, coord4]), marker_visibilities
+    return np.vstack([coord1, coord2, coord3, coord4, coord5]), marker_visibilities
 
 
 def coordinates_to_transformation_matrix(
diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 576b5de99..ca5389bef 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -333,7 +333,6 @@ def __init__(
         self,
         ref_mode_id,
         tracker,
-        n_coils,
         coreg_data,
         obj_datas,
         view_tracts,
@@ -348,9 +347,6 @@ def __init__(
         threading.Thread.__init__(self, name="CoordCoregObject")
         self.ref_mode_id = ref_mode_id
         self.tracker = tracker
-        self.n_coils = (
-            n_coils  # LUKATODO: remove n_coils since this is just equal to len(obj_datas)
-        )
         self.coreg_data = coreg_data
         self.obj_datas = obj_datas
         self.coord_queue = queues[0]
@@ -413,12 +409,13 @@ def run(self):
                 self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs])
                 
                 # LUKATODO: Refactor so that all coils are processed
-                # we need tracts, efield, etc. for all coils. what about stylus?
-               
-                # LUKATODO: coords is unordered so this randomly gives probe/somecoil...
-                #coord = coords.values()[1]
-                coord = coords["coil1"]
-                m_img = m_imgs["coil1"]
+                # we need tracts, efield, etc. for all coils. 
+                # what about icp for stylus?
+
+                # LUKATODO: this is an arbitrary coil... 
+                main_coil = next(iter(obj_datas)) 
+                coord = coords[main_coil]
+                m_img = m_imgs[main_coil]
 
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 35d0ea0ed..a1abe6a32 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -62,7 +62,7 @@ def __bind_events(self):
         Publisher.subscribe(self.SetCoilAtTarget, "Coil at target")
         Publisher.subscribe(self.OnNavigationStatus, "Navigation status")
         Publisher.subscribe(self.ShowCoil, "Show coil in viewer volume")
-        Publisher.subscribe(lambda n_coils: self.RemoveCoil(), "Reset coil selection")
+        Publisher.subscribe(self.ResetCoilVisualizer, "Reset coil selection")
         Publisher.subscribe(self.SelectCoil, "Select coil")
         Publisher.subscribe(self.UpdateCoilPoses, "Update coil poses")
         Publisher.subscribe(self.UpdateVectorField, "Update vector field")
@@ -71,9 +71,9 @@ def LoadConfig(self):
         session = ses.Session()
 
         # Get the list of coil names of coils selected for navigation
-        selected_coils = (session.GetConfig("navigation") or {}).get("selected_coils", [])
+        selected_coils = (session.GetConfig("navigation", {})).get("selected_coils", [])
         
-        saved_registrations = session.GetConfig("coil_registrations") or {}
+        saved_registrations = session.GetConfig("coil_registrations", {})
         for coil_name in selected_coils:
             if (coil := saved_registrations.get(coil_name, None)) is not None:
                 self.AddCoil(coil_name, coil["path"])
@@ -115,7 +115,7 @@ def OnNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status
 
     # Called when 'show coil' button is pressed in the user interface or in code.
-    # LUKATODO: Right-click 'show coil' button to open combobox to choose specific coil to show/hide
+    # LUKATODO: Right-click 'show coil' button to open combobox to choose specific coil to show/hide?
     def ShowCoil(self, state, coil_name=None):
         if coil_name is None:  # Show/hide all coils
             for coil in self.coils.values():
@@ -229,7 +229,7 @@ def AddCoil(self, coil_name, coil_path):
         coil_actor.GetProperty().SetSpecular(30)
         coil_actor.GetProperty().SetSpecularPower(80)
         coil_actor.GetProperty().SetOpacity(0.4)
-        coil_actor.SetVisibility(0)
+        coil_actor.SetVisibility(1)
 
         # Create an actor for the coil center.
         coil_center_actor = self.actor_factory.CreateTorus(
@@ -262,8 +262,12 @@ def RemoveCoil(self, coil_name=None):
             # LUKATODO: what about target_actors and other things?
             self.coils = {}
 
+        self.interactor.Render()
         # self.vector_field_assembly.SetVisibility(0)
 
+    def ResetCoilVisualizer(self, n_coils):
+        self.RemoveCoil() # Remove all coils
+
     def UpdateCoilPoses(self, m_imgs, coords):
         """
         During navigation, use updated coil pose to perform the following tasks:
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 4e28f5db3..a80f99a22 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -877,11 +877,8 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         self.pedal_connector = pedal_connector
         self.neuronavigation_api = neuronavigation_api
         self.navigation = navigation
-        self.coil_registrations = self.session.GetConfig("coil_registrations") or {}
+        self.coil_registrations = {} 
         self.__bind_events()
-        self.timestamp = const.TIMESTAMP
-
-        self.LoadConfig()
 
         # Sizer for displaying instructions
         top_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, ("Instructions"))
@@ -890,7 +887,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             self,
             -1,
             _(
-                f"Choose {navigation.n_coils} coils to use below. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. Unused coils can be deleted by right-clicking the button."
+                f"Choose {navigation.n_coils} coils to use. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. Unused coils can be deleted by right-clicking its button."
             ),
         )
         # instruction_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL))
@@ -906,7 +903,9 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             ),
         )
         self.inner_sel_sizer = inner_sel_sizer = wx.FlexGridSizer(10, 1, 1)
-
+        
+        # Coils are selected by toggling coil-buttons
+        self.coil_btns = {}
         self.no_coils_lbl = None
         if len(self.coil_registrations) == 0:
             self.no_coils_lbl = wx.StaticText(
@@ -915,48 +914,42 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             inner_sel_sizer.Add(self.no_coils_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
         sel_sizer.Add(inner_sel_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
-        # Add a button for each coil in coil_registrations
-        self.coil_btns = {}
-        for coil_name in self.coil_registrations:
-            self.AddCoilButton(coil_name)
-
         # Sizer for TMS coil configuration
         tooltip = _("New TMS coil configuration")
         btn_new = wx.Button(self, -1, _("New"), size=wx.Size(65, 23))
         btn_new.SetToolTip(tooltip)
         btn_new.Enable(1)
         btn_new.Bind(wx.EVT_BUTTON, self.OnCreateNewCoil)
-
         lbl_new = wx.StaticText(self, -1, _("Create or edit a coil configuration: "))
 
+        tooltip = _("Load TMS coil configuration from an OBR file")
+        btn_load = wx.Button(self, -1, _("Load"), size=wx.Size(65, 23))
+        btn_load.SetToolTip(tooltip)
+        btn_load.Enable(1)
+        btn_load.Bind(wx.EVT_BUTTON, self.OnLoadCoilFromOBR)
+        lbl_load = wx.StaticText(self, -1, _("Load configuration from file: "))
+
         coil_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, _("TMS coil registration"))
         inner_coil_sizer = wx.FlexGridSizer(2, 4, 5)
         inner_coil_sizer.AddMany(
             [
                 (lbl_new, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
                 (btn_new, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (lbl_load, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (btn_load, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
             ]
         )
         coil_sizer.Add(inner_coil_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
-        main_sizer = wx.BoxSizer(wx.VERTICAL)
-        main_sizer.AddMany(
-            [
-                (top_sizer, 0, wx.ALL | wx.EXPAND, 10),
-                (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
-                (coil_sizer, 0, wx.ALL | wx.EXPAND, 10),
-            ]
+        # Angle/Dist thresholds, timestamp interval
+        self.angle_threshold = (
+            self.session.GetConfig("angle_threshold", const.DEFAULT_ANGLE_THRESHOLD)
+        )
+        self.distance_threshold = (
+            self.session.GetConfig("distance_threshold", const.DEFAULT_DISTANCE_THRESHOLD)
         )
-        self.SetSizerAndFit(main_sizer)
 
-        # Press the buttons for coils that were selected in config file
-        state = self.session.GetConfig("navigation", {})
-        for coil_name in state.get("selected_coils", []):
-            self.coil_btns[coil_name][0].SetValue(True)
-        self.Layout()
 
-        # LUKATODO: move the following into ObjectCalibrationDialog (along with the relevant funcs)
-        """
         # Change angles threshold
         text_angles = wx.StaticText(self, -1, _("Angle threshold (degrees):"))
         spin_size_angles = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23))
@@ -981,19 +974,6 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             wx.EVT_SPINCTRL, partial(self.OnSelectDistanceThreshold, ctrl=spin_size_dist)
         )
 
-        # Change timestamp interval
-        text_timestamp = wx.StaticText(self, -1, _("Timestamp interval (s):"))
-        spin_timestamp_dist = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23), inc=0.1)
-        spin_timestamp_dist.SetRange(0.5, 60.0)
-        spin_timestamp_dist.SetValue(self.timestamp)
-        spin_timestamp_dist.Bind(
-            wx.EVT_TEXT, partial(self.OnSelectTimestamp, ctrl=spin_timestamp_dist)
-        )
-        spin_timestamp_dist.Bind(
-            wx.EVT_SPINCTRL, partial(self.OnSelectTimestamp, ctrl=spin_timestamp_dist)
-        )
-        self.spin_timestamp_dist = spin_timestamp_dist
-
         # Create a horizontal sizer to threshold configs
         line_angle_threshold = wx.BoxSizer(wx.HORIZONTAL)
         line_angle_threshold.AddMany(
@@ -1011,24 +991,30 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             ]
         )
 
-        line_timestamp = wx.BoxSizer(wx.HORIZONTAL)
-        line_timestamp.AddMany(
-            [
-                (text_timestamp, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, 5),
-                (spin_timestamp_dist, 0, wx.ALL | wx.EXPAND | wx.GROW, 5),
-            ]
-        )
-
         # Add line sizers into main sizer
         conf_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, _("Settings"))
         conf_sizer.AddMany(
             [
                 (line_angle_threshold, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 20),
                 (line_dist_threshold, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 20),
-                (line_timestamp, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 20),
             ]
         )
-        """
+
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.AddMany(
+            [
+                (top_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (coil_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (conf_sizer, 0, wx.ALL | wx.EXPAND, 10),
+            ]
+        )
+        self.SetSizerAndFit(main_sizer)
+        
+        self.LoadConfig()
+        self.Layout()       
+
+
 
     def AddCoilButton(self, coil_name):
         if self.no_coils_lbl is not None:
@@ -1063,13 +1049,30 @@ def OnSetCoilCount(self, n_coils):
             btn.SetValue(False)
 
     def LoadConfig(self):
-        # LUKATODO: ???
-        self.angle_threshold = (
-            self.session.GetConfig("angle_threshold") or const.DEFAULT_ANGLE_THRESHOLD
-        )
-        self.distance_threshold = (
-            self.session.GetConfig("distance_threshold") or const.DEFAULT_DISTANCE_THRESHOLD
+        state = self.session.GetConfig("navigation", {})
+        self.coil_registrations = self.session.GetConfig("coil_registrations", {})  
+        # Add a button for each coil 
+        for coil_name in self.coil_registrations:
+            self.AddCoilButton(coil_name)
+        
+        # Press the buttons for coils that were selected in config file
+        selected_coils = state.get("selected_coils", []) 
+        for coil_name in selected_coils:
+            self.coil_btns[coil_name][0].SetValue(True)
+
+        n_coils_selected = len(selected_coils)
+        n_coils = state.get("n_coils", 1)
+
+        # Update label
+        self.sel_sizer.GetStaticBox().SetLabel(
+            f"TMS coil selection ({n_coils_selected} out of {n_coils})"
         )
+        
+        if n_coils_selected == n_coils:
+            # Allow only n_coils buttons to be pressed, so disable unpressed buttons
+            for btn, *junk in self.coil_btns.values():
+                btn.Enable(btn.GetValue())
+
 
     def OnSelectCoil(self, event, name):
         coil_registration = None
@@ -1112,7 +1115,7 @@ def OnSelectCoil(self, event, name):
 
         # Select/Unselect coil
         Publisher.sendMessage("Select coil", coil_name=name, coil_registration=coil_registration)
-        # LUKATODO: Is there a delay here? Is "Select coil" performed first everywhere and then only this?
+        
         n_coils_selected = len(navigation.coil_registrations)
         n_coils = navigation.n_coils
         # Update label telling how many coils to select
@@ -1184,12 +1187,17 @@ def DeleteCoil(event, name):
         menu = wx.Menu()
         delete_coil = menu.Append(wx.ID_ANY, "Delete coil")
         set_obj_id = menu.Append(wx.ID_ANY, "Set coil index")
+        save_coil = menu.Append(wx.ID_ANY, "Save coil to OBR file")
+        
         self.Bind(wx.EVT_MENU, (lambda event, name=name: DeleteCoil(event, name)), delete_coil)
         self.Bind(wx.EVT_MENU, (lambda event, name=name: SetObjID(event, name)), set_obj_id)
+        self.Bind(wx.EVT_MENU, (lambda event, name=name: self.OnSaveCoilToOBR(event, name)), save_coil)
         self.PopupMenu(menu, event.GetPosition())
         menu.Destroy()
 
     def OnCreateNewCoil(self, event=None):
+        # Create a coil registration and save it by the given name 
+        # Also used to edit coil registrations by overwriting to the same name
         if self.tracker.IsTrackerInitialized():
             dialog = dlg.ObjectCalibrationDialog(
                 self.tracker, self.pedal_connector, self.neuronavigation_api
@@ -1204,7 +1212,7 @@ def OnCreateNewCoil(self, event=None):
                     # self.neuronavigation_api.update_coil_mesh(polydata)
 
                     if np.isfinite(obj_fiducials).all() and np.isfinite(obj_orients).all():
-                        coil_registration = {  # LUKATODO: angle_threshold, dist_threshold, time_interval
+                        coil_registration = {
                             "fiducials": obj_fiducials.tolist(),
                             "orientations": obj_orients.tolist(),
                             "obj_id": obj_id,
@@ -1216,11 +1224,10 @@ def OnCreateNewCoil(self, event=None):
                         self.AddCoilButton(coil_name)  # Add a button for this coil to GUI
                         self.Layout()
 
-                        # Update the coil registration in Navigation if coil_name was selected
+                        # Update the coil registration in Navigation if we just edited an existing coil_name
                         if self.coil_btns[coil_name][0].GetValue():
                             self.navigation.coil_registrations[coil_name] = coil_registration
 
-                        # Automatically enable and check 'Track object' checkbox and uncheck 'Disable Volume Camera' checkbox.
                         # LUKATODO: delete the below with dependencies
                         Publisher.sendMessage("Press target mode button", pressed=False)
 
@@ -1230,6 +1237,91 @@ def OnCreateNewCoil(self, event=None):
         else:
             dlg.ShowNavigationTrackerWarning(0, "choose")
 
+    def OnLoadCoilFromOBR(self, event=None):
+        filename = dlg.ShowLoadSaveDialog(
+            message=_("Load object registration"), wildcard=_("Registration files (*.obr)|*.obr")
+        )
+        # data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\anat_reg_improve_20200609'
+        # coil_path = 'magstim_coil_dell_laptop.obr'
+        # filename = os.path.join(data_dir, coil_path)
+
+        try:
+            if filename:
+                with open(filename, "r") as text_file:
+                    data = [s.split("\t") for s in text_file.readlines()]
+
+                registration_coordinates = np.array(data[1:]).astype(np.float32)
+                obj_fiducials = registration_coordinates[:, :3]
+                obj_orients = registration_coordinates[:, 3:]
+
+                coil_name = data[0][0][2:]
+                coil_path = data[0][1].encode(const.FS_ENCODE)
+                tracker_id = int(data[0][3])
+                obj_id = int(data[0][-1])
+
+                if not os.path.exists(coil_path):
+                    coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
+
+                polydata = vtk_utils.CreateObjectPolyData(coil_path)
+                if not polydata:
+                    coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
+
+                # LUKATODO: what is neuronavigation_api.update_coil_mesh ?
+                #if polydata:
+                #    self.neuronavigation_api.update_coil_mesh(polydata)
+
+                if np.isfinite(obj_fiducials).all() and np.isfinite(obj_orients).all():
+                    coil_registration = {
+                        "fiducials": obj_fiducials.tolist(),
+                        "orientations": obj_orients.tolist(),
+                        "obj_id": obj_id,
+                        "tracker_id": tracker_id,
+                        "path": coil_path.decode(const.FS_ENCODE),
+                    }
+                    self.coil_registrations[coil_name] = coil_registration
+                    self.session.SetConfig("coil_registrations", self.coil_registrations)
+                    self.AddCoilButton(coil_name)  # Add a button for this coil to GUI
+                    self.Layout()
+
+                Publisher.sendMessage(
+                    "Update status text in GUI", label=_("Object file successfully loaded")
+                )
+
+                msg = _("Object file successfully loaded")
+                wx.MessageBox(msg, _("InVesalius 3"))
+        except:
+            wx.MessageBox(_("Object registration file incompatible."), _("InVesalius 3"))
+            Publisher.sendMessage("Update status text in GUI", label="")
+
+    def OnSaveCoilToOBR(self, evt, coil_name):
+        coil_registration = self.coil_registrations[coil_name]
+        
+        filename = dlg.ShowLoadSaveDialog(
+            message=_("Save object registration as..."),
+            wildcard=_("Registration files (*.obr)|*.obr"),
+            style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
+            default_filename="object_registration.obr",
+            save_ext="obr",
+        )
+        if filename:
+            hdr = (
+                coil_name 
+                + "\t"
+                + utils.decode(coil_registration["path"], const.FS_ENCODE)
+                + "\t"
+                + "Tracker"
+                + "\t"
+                + str("%d" % coil_registration["tracker_id"])
+                + "\t"
+                + "Index"
+                + "\t"
+                + str("%d" % coil_registration["obj_id"])
+            )
+            data = np.hstack([coil_registration["fiducials"], coil_registration["orientations"]])
+            np.savetxt(filename, data, fmt="%.4f", delimiter="\t", newline="\n", header=hdr)
+            wx.MessageBox(_("Object file successfully saved"), _("Save"))
+
+
     def OnSelectAngleThreshold(self, evt, ctrl):
         self.angle_threshold = ctrl.GetValue()
         Publisher.sendMessage("Update angle threshold", angle=self.angle_threshold)
@@ -1410,9 +1502,9 @@ def __bind_events(self):
 
     def LoadConfig(self):
         session = ses.Session()
-        state = session.GetConfig("robot")
+        self.n_coils = session.GetConfig("navigation", {}).get("n_coils", 1)
 
-        self.n_coils = max(1, len((session.GetConfig("navigation") or {}).get("selected_coils", [])))
+        state = session.GetConfig("robot")
 
         if state is None:
             return False
@@ -1425,7 +1517,6 @@ def LoadConfig(self):
     def OnChooseNoOfCoils(self, evt, ctrl):
         if hasattr(evt, "GetSelection"):
             choice = evt.GetSelection()
-            print(f"choice: {choice}")
             self.n_coils = choice + 1
         else:
             self.n_coils = 1
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 645128234..a3064d502 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -179,7 +179,6 @@ def __init__(self, parent):
         self.SetSizer(sizer)
         sizer.Fit(self)
 
-        self.track_obj = False
         gbs.Add(fold_panel, (0, 0), flag=wx.EXPAND)
         gbs.Layout()
         sizer.Fit(self)
@@ -1109,7 +1108,7 @@ def __init__(self, parent, nav_hub):
         border = wx.FlexGridSizer(1, 2, 1)
         self.coil_registrations = []
 
-        lbl = wx.StaticText(self, -1, _("Coil selection done, ready for navigation!"))
+        lbl = wx.StaticText(self, -1, _(f"Ready for navigation with {self.navigation.n_coils} coil{'' if self.navigation.n_coils == 1 else 's'}!"))
         # lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
         self.lbl = lbl
 
@@ -1159,7 +1158,7 @@ def OnCloseProject(self):
 
     def CoilSelectionDone(self, done):
         if done:
-            self.lbl.SetLabel("Coil selection done, ready for navigation!")
+            self.lbl.SetLabel(f"Ready for navigation with {self.navigation.n_coils} coil{'' if self.navigation.n_coils == 1 else 's'}!")
         else:
             self.lbl.SetLabel("Please select which coil(s) to track")
 
@@ -1240,7 +1239,6 @@ def __init__(self, parent, nav_hub):
 
         self.nav_status = False
         self.target_mode = False
-        self.track_obj = False
 
         self.navigation_status = False
 
@@ -1565,25 +1563,11 @@ def __bind_events(self):
         Publisher.subscribe(self.EnableACT, "Enable ACT")
         Publisher.subscribe(self.UpdateACTData, "Update ACT data")
 
-    # Config
-    def SaveConfig(self):
-        track_object = self.track_object_button
-        state = {
-            "track_object": {
-                "checked": track_object.GetValue(),
-            }
-        }
-
-        session = ses.Session()
-        session.SetConfig("object_registration_panel", state)
-
     def LoadConfig(self):
         session = ses.Session()
-        state = session.GetConfig("object_registration_panel")
-
-        if state is not None:
-            track_object = state["track_object"]
-            self.PressTrackObjectButton(track_object["checked"])
+        state = session.GetConfig("navigation", {})
+        track_coil = state.get("track_coil", False)
+        self.PressTrackObjectButton(track_coil)
 
     # Toggle Button Helpers
     def UpdateToggleButton(self, ctrl, state=None):
@@ -1775,12 +1759,10 @@ def EnableACT(self, data):
     def EnableTrackObjectButton(self, enabled):
         self.EnableToggleButton(self.track_object_button, enabled)
         self.UpdateToggleButton(self.track_object_button)
-        self.SaveConfig()
 
     def PressTrackObjectButton(self, pressed):
         self.UpdateToggleButton(self.track_object_button, pressed)
         self.OnTrackObjectButton()
-        self.SaveConfig()
 
     def OnTrackObjectButton(self, evt=None, ctrl=None):
         if ctrl is not None:
@@ -1788,13 +1770,12 @@ def OnTrackObjectButton(self, evt=None, ctrl=None):
         pressed = self.track_object_button.GetValue()
         Publisher.sendMessage("Track object", enabled=pressed)
         if not pressed:
-            Publisher.sendMessage("Press target mode button", pressed=pressed)
+            Publisher.sendMessage("Press target mode button", pressed=False)
 
         # Automatically press or unpress 'Show coil' and 'Show probe' button.
         Publisher.sendMessage("Press show-coil button", pressed=pressed)
         Publisher.sendMessage("Press show-probe button", pressed=(not pressed))
 
-        self.SaveConfig()
 
     # 'Lock to Target' button
     def OnLockToTargetButton(self, evt, ctrl):
@@ -1856,7 +1837,6 @@ def OnEfieldCheckbox(self, evt, ctrl):
 
     # 'Target mode' button
     def TrackObject(self, enabled):
-        self.track_obj = enabled
         self.UpdateTargetButton()
 
     def ShowTargetButton(self):
@@ -1867,7 +1847,7 @@ def HideTargetButton(self):
 
     def UpdateTargetButton(self):
         # Enable or disable 'Target mode' button based on if target is selected and if 'Track object' button is pressed.
-        enabled = self.target_selected and self.track_obj
+        enabled = self.target_selected and self.navigation.track_coil
         self.EnableToggleButton(self.target_mode_button, enabled)
 
     def PressTargetModeButton(self, pressed):
@@ -2054,8 +2034,7 @@ def __init__(self, parent, nav_hub):
         sizer_delete = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
         sizer_delete.AddMany([(btn_delete_single, 1, wx.RIGHT), (btn_delete_all, 0, wx.LEFT)])
 
-        # Combobox to choose the main coil (ie. the coil which to track with pointer and to use for marker creation)
-        #LUKATODO: how to ensure the choices are updated when coil selection changes
+        # Combobox for choosing the main coil (ie. the coil which to track with pointer and to use for marker creation)
         self.select_main_coil = select_main_coil = wx.ComboBox(
             self,
             -1,
@@ -2070,10 +2049,12 @@ def __init__(self, parent, nav_hub):
             wx.EVT_COMBOBOX, partial(self.OnChooseMainCoil, ctrl=select_main_coil)
         )
 
-        # If main coil is defined, set this in the combobox        
-        if (main_coil := self.navigation.main_coil) is not None:
+        # If main coil is defined, select this in the combobox        
+        nav_state = self.session.GetConfig("navigation", {})
+        if (main_coil := nav_state.get("main_coil", None)) is not None:
             main_coil_index = select_main_coil.FindString(main_coil)
             select_main_coil.SetSelection(main_coil_index)
+
         sizer_main_coil = wx.FlexGridSizer(rows=1, cols=1, hgap=5, vgap=5)
         sizer_main_coil.Add(select_main_coil)
 
@@ -2331,7 +2312,7 @@ def __list_fiducial_labels():
     def UpdateCurrentCoord(self, position):
         self.current_position = list(position[:3])
         self.current_orientation = list(position[3:])
-        if not self.navigation.track_obj:
+        if not self.navigation.track_coil:
             self.current_orientation = None, None, None
 
     def UpdateNavigationStatus(self, nav_status, vis_status):
@@ -3057,7 +3038,7 @@ def OnCreateMarker(
         if marker_type is None:
             marker_type = (
                 MarkerType.COIL_TARGET
-                if self.nav_status and self.navigation.track_obj
+                if self.nav_status and self.navigation.track_coil
                 else MarkerType.LANDMARK
             )
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 2f9be266c..42db8cad9 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -145,21 +145,21 @@ def run(self):
                 got_coords = True
 
                 probe_visible = marker_visibilities[0]
-
-                #LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
                 coil_visible = marker_visibilities[2] # LUKATODO: will static mode work with this?
+                #LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
 
-                # automatically track either coil or stylus if only one of them is visible, otherise use navigation.track_obj
+                # automatically track either coil or stylus if only one of them is visible, otherise use navigation.track_coil
                 track_coil = (
                     (coil_visible or not probe_visible)
                     if (coil_visible ^ probe_visible)
-                    else self.navigation.track_obj
+                    else self.navigation.track_coil
                 )
                 main_coil = self.navigation.main_coil
                 track_this = main_coil if track_coil else "probe"
                 # choose which object to track in slices and viewer_volume pointer
-                coord = coords[track_this]  # main-coil if track_coil else stylus
+                coord = coords[track_this]
                 m_img = m_imgs[track_this]
+                
                 #LUKATODO: do Debug approach here
 
                 # Remove probe, so that coords/m_imgs only contain coils
@@ -270,8 +270,8 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.target = None
         self.n_coils = 1
         self.coil_registrations = {}
+        self.track_coil = False
         self.main_coil = None  # Which coil to track with pointer
-        self.track_obj = False
         self.m_change = None
         self.r_stylus = None
 
@@ -341,13 +341,15 @@ def SaveConfig(self, key=None, value=None):
         """
         session = ses.Session()
         if key is None:  # Save the whole state
-            state = {"selected_coils": list(self.coil_registrations)}
+            state = {"selected_coils": list(self.coil_registrations), "n_coils": self.n_coils, "track_coil": self.track_coil}
+            if self.main_coil is not None:
+                state["main_coil"] = self.main_coil
             if self.r_stylus is not None:
                 state["r_stylus"] = self.r_stylus.tolist()
             session.SetConfig("navigation", state)
 
-        elif value is not None:
-            state = session.GetConfig("navigation") or {}
+        elif value is not None: # Save a specific state attribute
+            state = session.GetConfig("navigation", {})
             state[key] = value
             session.SetConfig("navigation", state)
 
@@ -359,7 +361,11 @@ def LoadConfig(self):
         saved_coil_registrations = session.GetConfig("coil_registrations")
 
         if state is not None:
-            # Try to load selected_coils, the list of names of coils to use for navigation
+            self.main_coil = state.get("main_coil", None)
+            self.n_coils = state.get("n_coils", 1)
+            self.track_coil = state.get("track_coil", False)
+
+            # Try to load selected_coils (the list of names of coils to use for navigation)
             if ("selected_coils" in state) and (saved_coil_registrations is not None):
                 selected_coils = state["selected_coils"]
                 self.coil_registrations = {
@@ -369,8 +375,7 @@ def LoadConfig(self):
                 }
                 if self.coil_registrations:
                     self.main_coil = state.get("main_coil", None) or next(iter(self.coil_registrations))
-                    self.n_coils = len(self.coil_registrations)
-
+            
             # Try to load stylus orientation data
             if "r_stylus" in state:
                 self.r_stylus = np.array(state["r_stylus"])
@@ -387,8 +392,9 @@ def SelectCoil(self, coil_name, coil_registration):
             self.coil_registrations.pop(coil_name, None)
             if self.main_coil == coil_name:
                 self.main_coil = None
-
-        self.SaveConfig("selected_coils", list(self.coil_registrations.keys()))
+                self.SaveConfig()
+        
+        self.SaveConfig()
 
     def CoilAtTarget(self, state):
         self.coil_at_target = state
@@ -403,18 +409,20 @@ def UpdateSerialPort(self, serial_port_in_use, com_port=None, baud_rate=None):
         self.baud_rate = baud_rate
 
     def TrackObject(self, enabled=False):
-        self.track_obj = enabled
+        self.track_coil = enabled
+        self.SaveConfig()
 
     def SetLockToTarget(self, value):
         self.lock_to_target = value
 
     def SetNoOfCoils(self, n_coils):
         self.n_coils = n_coils
+        self.SaveConfig("n_coils", n_coils)
 
         # Reset coil selection
         self.coil_registrations = {}
         self.main_coil = None
-        self.SaveConfig("selected_coils", [])
+        self.SaveConfig()
 
     def SetMainCoil(self, main_coil):
         self.main_coil = main_coil
@@ -565,7 +573,6 @@ def StartNavigation(self, tracker, icp):
                 dcr.CoordinateCorregistrate(
                     self.ref_mode_id,
                     tracker,
-                    self.n_coils,
                     coreg_data,
                     obj_datas,
                     self.view_tracts,

From d47431e6dc27f953ad04bac0f153f66b1dc812e9 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Wed, 14 Aug 2024 19:41:27 +0300
Subject: [PATCH 20/44] Added a warning before overwriting old coil
 registrations, other minor fixes

---
 invesalius/data/bases.py                      |  4 +-
 invesalius/data/coregistration.py             | 58 ++++++++----------
 invesalius/data/viewer_volume.py              |  2 +-
 .../data/visualization/coil_visualizer.py     | 12 ++--
 invesalius/gui/dialogs.py                     |  1 -
 invesalius/gui/preferences.py                 | 61 +++++++++++++++----
 invesalius/gui/task_navigator.py              |  3 -
 invesalius/navigation/navigation.py           | 12 ++--
 8 files changed, 88 insertions(+), 65 deletions(-)

diff --git a/invesalius/data/bases.py b/invesalius/data/bases.py
index 485bdecf6..b4444a764 100644
--- a/invesalius/data/bases.py
+++ b/invesalius/data/bases.py
@@ -174,7 +174,7 @@ def calculate_fre(
 def transform_icp(m_img: np.ndarray, m_icp: np.ndarray) -> np.ndarray:
     coord_img = [m_img[0, -1], -m_img[1, -1], m_img[2, -1], 1]
     m_img[0, -1], m_img[1, -1], m_img[2, -1], _ = m_icp @ coord_img
-    m_img[0, -1], m_img[1, -1], m_img[2, -1] = m_img[0, -1], -m_img[1, -1], m_img[2, -1]
+    m_img[1, -1] = -m_img[1, -1]
 
     return m_img
 
@@ -182,7 +182,7 @@ def transform_icp(m_img: np.ndarray, m_icp: np.ndarray) -> np.ndarray:
 def inverse_transform_icp(m_img: np.ndarray, m_icp: np.ndarray) -> np.ndarray:
     coord_img = [m_img[0, -1], -m_img[1, -1], m_img[2, -1], 1]
     m_img[0, -1], m_img[1, -1], m_img[2, -1], _ = np.linalg.inv(m_icp) @ coord_img
-    m_img[0, -1], m_img[1, -1], m_img[2, -1] = m_img[0, -1], -m_img[1, -1], m_img[2, -1]
+    m_img[1, -1] = -m_img[1, -1]
 
     return m_img
 
diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index ca5389bef..a0e431e6c 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -393,7 +393,7 @@ def run(self):
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
                 coord_probe, m_img_probe = corregistrate_probe(
-                    m_change, r_stylus, coord_raw, self.ref_mode_id
+                    m_change, r_stylus, coord_raw, self.ref_mode_id, icp=[self.use_icp, self.m_icp]
                 )
 
                 coords = {"probe": coord_probe}
@@ -405,18 +405,34 @@ def run(self):
                     )
                     coords[coil_name] = coord_coil
                     m_imgs[coil_name] = m_img_coil
-                
-                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs])
-                
-                # LUKATODO: Refactor so that all coils are processed
-                # we need tracts, efield, etc. for all coils. 
-                # what about icp for stylus?
 
-                # LUKATODO: this is an arbitrary coil... 
-                main_coil = next(iter(obj_datas)) 
+
+                # LUKATODO: this is an arbitrary coil, so efields/tracts work correctly with 1 coil but may bug out when using multiple
+                main_coil = next(iter(obj_datas))
                 coord = coords[main_coil]
                 m_img = m_imgs[main_coil]
 
+                # XXX: This is not the best place to do the logic related to approaching the target when the
+                #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
+                #      the tracker space where it is hard to make the tracker approach the target in the image space.
+                #      Ideally, the transformation from the tracker space to the image space (the function
+                #      corregistrate_object_dynamic above) would be encapsulated in a class together with the
+                #      tracker, and then the whole class would be mocked when using the debug tracker.
+                if self.tracker_id == const.DEBUGTRACKAPPROACH and self.target is not None:
+                    if self.last_coord is None:
+                        self.last_coord = np.array(coord)
+                    else:
+                        coord = self.last_coord + (self.target - self.last_coord) * 0.05
+                        coords[main_coil] = coord
+                        self.last_coord = coord
+                    
+                    angles = [np.radians(coord[3]), np.radians(coord[4]), np.radians(coord[5])]
+                    translate = coord[0:3]
+                    m_imgs[main_coil] = tr.compose_matrix(angles=angles, translate=translate)
+                
+                self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs])
+
+                # Compute data for efield/tracts 
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
 
@@ -431,27 +447,3 @@ def run(self):
 
             # The sleep has to be in both threads
             sleep(self.sle)
-                
-                
-            # LUKATODO: move below Debug approach to UpdateNavigationScene
-            # Better way to do debug approach...? Just change the main_coil coord in UpdateNavigationScene...
-            """
-            # XXX: This is not the best place to do the logic related to approaching the target when the
-            #      debug tracker is in use. However, the trackers (including the debug trackers) operate in
-            #      the tracker space where it is hard to make the tracker approach the target in the image space.
-            #      Ideally, the transformation from the tracker space to the image space (the function
-            #      corregistrate_object_dynamic above) would be encapsulated in a class together with the
-            #      tracker, and then the whole class would be mocked when using the debug tracker. However,
-            #      those abstractions do not currently exist and doing them would need a larger refactoring.
-                if self.tracker_id == const.DEBUGTRACKAPPROACH and self.target is not None:
-                if self.last_coord is None:
-                    self.last_coord = np.array(coord_coil)
-                else:
-                    coord = self.last_coord + (self.target - self.last_coord) * 0.05
-                    coords[1] = coord
-                    self.last_coord = coord
-
-                angles = [np.radians(coord[3]), np.radians(coord[4]), np.radians(coord[5])]
-                translate = coord[0:3]
-                m_imgs[1] = tr.compose_matrix(angles=angles, translate=translate)
-            """
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index b2e8baab7..3a125fd0e 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -2173,7 +2173,7 @@ def GetEnorm(self, enorm_data, plot_vector):
             if session.GetConfig("debug_efield"):
                 self.e_field_norms = enorm_data[3][self.Id_list, 0]
                 self.e_field_col1 = enorm_data[3][self.Id_list, 1]
-                self.e_field_col2 = enorm_data[3][self.Id_list, 1]
+                self.e_field_col2 = enorm_data[3][self.Id_list, 1] #LUKATODO: is this a typo?
                 self.e_field_col3 = enorm_data[3][self.Id_list, 3]
                 self.Idmax = np.array(self.Id_list[np.array(self.e_field_norms).argmax()])
                 max = np.array(self.e_field_norms).argmax()
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index a1abe6a32..5c159fd52 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -252,14 +252,14 @@ def AddCoil(self, coil_name, coil_path):
 
     def RemoveCoil(self, coil_name=None):
         if coil_name is not None:
-            coil = self.coils.pop(coil_name)
-            self.renderer.RemoveActor(coil["actor"])
-            self.renderer.RemoveActor(coil["center_actor"])
+            coil = self.coils.pop(coil_name, None)
+            if coil is not None:
+                self.renderer.RemoveActor(coil["actor"])
+                self.renderer.RemoveActor(coil["center_actor"])
         else:  # Remove all coils
             for coil in self.coils.values():
                 self.renderer.RemoveActor(coil["actor"])
                 self.renderer.RemoveActor(coil["center_actor"])
-            # LUKATODO: what about target_actors and other things?
             self.coils = {}
 
         self.interactor.Render()
@@ -285,5 +285,5 @@ def UpdateCoilPoses(self, m_imgs, coords):
             self.coils[name]["actor"].SetUserMatrix(m_img_vtk)
             self.coils[name]["center_actor"].SetUserMatrix(m_img_vtk)
 
-            # LUKATODO: what to do with this??? Is mtms field needed? If not, just delete vector_field_assembly...?
-            # self.vector_field_assembly[name].SetUserMatrix(m_img_vtk)
+            # LUKATODO
+            self.vector_field_assembly[name].SetUserMatrix(m_img_vtk)
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 7e3462a76..e7e431aeb 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -4022,7 +4022,6 @@ def _init_gui(self) -> None:
         name_sizer.AddMany(
             [(lbl_name, 1, wx.ALIGN_CENTER_VERTICAL), (name_box, 1, wx.ALIGN_CENTER_VERTICAL)]
         )
-        # LUKATODO: Add warning about overwriting old coil
 
         main_sizer = wx.BoxSizer(wx.VERTICAL)
         main_sizer.Add(self.interactor, 0, wx.EXPAND)
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index a80f99a22..a79c8c7bb 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -887,7 +887,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             self,
             -1,
             _(
-                f"Choose {navigation.n_coils} coils to use. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. Unused coils can be deleted by right-clicking its button."
+                f"Choose {navigation.n_coils} coils to use. If there are not enough options, create coil configurations below. You can edit configurations by overwriting them. Unused coils can be deleted by right-clicking its button."
             ),
         )
         # instruction_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL))
@@ -1074,11 +1074,11 @@ def LoadConfig(self):
                 btn.Enable(btn.GetValue())
 
 
-    def OnSelectCoil(self, event, name):
+    def OnSelectCoil(self, event=None, name=None, select=False):
         coil_registration = None
         navigation = self.navigation
 
-        if event.GetSelection():  # If coil is selected
+        if select or (event is not None and event.GetSelection()):  # If coil is selected
             coil_registration = self.coil_registrations[name]
 
             # Check that the index of the chosen coil does not conflict with other selected coils
@@ -1145,11 +1145,9 @@ def OnChoiceObjID(self, event, name):
         self.session.SetConfig("coil_registrations", self.coil_registrations)
 
         # Unselect the coil, because the new id may cause conflicts
-        Publisher.sendMessage("Select coil", coil_name=name, coil_registration=None)
-
         self.coil_btns[name][0].SetValue(False)
-        for btn, *junk in self.coil_btns.values():  # Enable all coil-buttons
-            btn.Enable(True)
+        self.OnSelectCoil(name=name, select=False)
+
         event.GetEventObject().Destroy()  # Delete the obj_id combobox
 
     def OnRightClickCoil(self, event, name):
@@ -1208,6 +1206,21 @@ def OnCreateNewCoil(self, event=None):
                         dialog.GetValue()
                     )
 
+                    if coil_name in self.coil_registrations:
+                        # Warn that we are overwriting an old registration
+                        dialog = wx.TextEntryDialog(
+                            None,
+                            _("A registration with this name already exists. Enter a new name or overwrite an old coil registration"),
+                            _("Warning: Coil Name Conflict"),
+                            value=coil_name,
+                        )
+                        if dialog.ShowModal() == wx.ID_OK:
+                            coil_name = dialog.GetValue().strip()  # Update coil_name with user input
+                        else:
+                            return  # Cancel the operation if the user closes the dialog or cancels
+                        dialog.Destroy()
+
+
                     # LUKATODO: update coil mesh elsewhere
                     # self.neuronavigation_api.update_coil_mesh(polydata)
 
@@ -1222,11 +1235,14 @@ def OnCreateNewCoil(self, event=None):
                         self.coil_registrations[coil_name] = coil_registration
                         self.session.SetConfig("coil_registrations", self.coil_registrations)
                         self.AddCoilButton(coil_name)  # Add a button for this coil to GUI
-                        self.Layout()
 
-                        # Update the coil registration in Navigation if we just edited an existing coil_name
-                        if self.coil_btns[coil_name][0].GetValue():
-                            self.navigation.coil_registrations[coil_name] = coil_registration
+                        # if we just edited a currently selected coil_name, unselect it (to avoid possible conflicts caused by new registration)
+                        coil_btn = self.coil_btns[coil_name][0]
+                        if coil_btn.GetValue():
+                            coil_btn.SetValue(False)
+                            self.OnSelectCoil(name=coil_name, select=False)
+                        
+                        self.Layout()
 
                         # LUKATODO: delete the below with dependencies
                         Publisher.sendMessage("Press target mode button", pressed=False)
@@ -1259,6 +1275,20 @@ def OnLoadCoilFromOBR(self, event=None):
                 tracker_id = int(data[0][3])
                 obj_id = int(data[0][-1])
 
+                if coil_name in self.coil_registrations:
+                    # Warn that we are overwriting an old registration
+                    dialog = wx.TextEntryDialog(
+                        None,
+                        _("A registration with this name already exists. Enter a new name or overwrite an old coil registration"),
+                        _("Warning: Coil Name Conflict"),
+                        value=coil_name,
+                    )
+                    if dialog.ShowModal() == wx.ID_OK:
+                        coil_name = dialog.GetValue().strip()  # Update coil_name with user input
+                    else:
+                        return  # Cancel the operation if the user closes the dialog or cancels
+                    dialog.Destroy()
+
                 if not os.path.exists(coil_path):
                     coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
 
@@ -1281,6 +1311,15 @@ def OnLoadCoilFromOBR(self, event=None):
                     self.coil_registrations[coil_name] = coil_registration
                     self.session.SetConfig("coil_registrations", self.coil_registrations)
                     self.AddCoilButton(coil_name)  # Add a button for this coil to GUI
+
+                    # if we just overwrote a currently selected coil_name, unselect it (to avoid possible conflicts caused by this loaded registration)
+                    coil_btn = self.coil_btns[coil_name][0]
+                    if coil_btn.GetValue():
+                        coil_btn.SetValue(False)
+                        self.OnSelectCoil(name=coil_name, select=False)
+                    elif self.navigation.CoilSelectionDone():
+                        coil_btn.Enable(False)
+
                     self.Layout()
 
                 Publisher.sendMessage(
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index a3064d502..ae2ab9425 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1152,9 +1152,6 @@ def __bind_events(self):
 
     def OnCloseProject(self):
         Publisher.sendMessage("Enable start navigation button", enabled=False)
-        # LUKATODO: delete the below?
-        Publisher.sendMessage("Press track object button", pressed=False)
-        Publisher.sendMessage("Enable track object button", enabled=False)
 
     def CoilSelectionDone(self, done):
         if done:
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 42db8cad9..2c20fcb9a 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -145,10 +145,10 @@ def run(self):
                 got_coords = True
 
                 probe_visible = marker_visibilities[0]
-                coil_visible = marker_visibilities[2] # LUKATODO: will static mode work with this?
+                coil_visible = marker_visibilities[2]
                 #LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
 
-                # automatically track either coil or stylus if only one of them is visible, otherise use navigation.track_coil
+                # automatically track either coil or stylus if only one of them is visible, otherwise use navigation.track_coil
                 track_coil = (
                     (coil_visible or not probe_visible)
                     if (coil_visible ^ probe_visible)
@@ -158,10 +158,7 @@ def run(self):
                 track_this = main_coil if track_coil else "probe"
                 # choose which object to track in slices and viewer_volume pointer
                 coord = coords[track_this]
-                m_img = m_imgs[track_this]
                 
-                #LUKATODO: do Debug approach here
-
                 # Remove probe, so that coords/m_imgs only contain coils
                 probe_coord = coords.pop("probe")
                 probe_m_img = m_imgs.pop("probe")
@@ -212,11 +209,11 @@ def run(self):
                     wx.CallAfter(
                         Publisher.sendMessage, "Update coil poses", m_imgs=m_imgs, coords=coords
                     )
-                    wx.CallAfter( # LUKATODO: this is just for viewer_volume...
+                    wx.CallAfter( # LUKATODO: this is just for viewer_volume... which will be updated later to support multicoil (target, tracts & efield)
                         Publisher.sendMessage, "Update coil pose", m_img=m_imgs[main_coil], coord=coords[main_coil]
                     )
                     wx.CallAfter(
-                        Publisher.sendMessage, #LUKATODO: what is this?
+                        Publisher.sendMessage,
                         "Update object arrow matrix",
                         m_img=m_imgs[main_coil],
                         coord=coords[main_coil],
@@ -561,7 +558,6 @@ def StartNavigation(self, tracker, icp):
 
             coreg_data = [self.m_change, self.r_stylus]
 
-            # LUKATODO: coord_queue is accounted for but what about others for multicoil?
             queues = [
                 self.coord_queue,
                 self.coord_tracts_queue,

From 1ad1eb9d007962cb6397857b0cc3b2999e20ac19 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Fri, 16 Aug 2024 21:31:13 +0300
Subject: [PATCH 21/44] Remove icp_queue (which was only used in
 CoordinateCorregistrate thread) since the ICP data is constant once created.
 The ICP data is passed to coregistration when the navigation is started, so
 it is up to date with the ICP data defined in Refine tab.

---
 invesalius/data/coregistration.py             | 24 +++++--------
 .../data/visualization/coil_visualizer.py     | 10 +++---
 .../navigation/iterativeclosestpoint.py       |  1 -
 invesalius/navigation/navigation.py           | 36 +++++++++++--------
 4 files changed, 36 insertions(+), 35 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index a0e431e6c..6e4e5d1c3 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -350,14 +350,13 @@ def __init__(
         self.coreg_data = coreg_data
         self.obj_datas = obj_datas
         self.coord_queue = queues[0]
-        self.view_tracts = view_tracts
         self.coord_tracts_queue = queues[1]
-        self.efield_queue = queues[4]
+        self.view_tracts = view_tracts
+        self.object_at_target_queue = queues[2]
+        self.efield_queue = queues[3]
         self.e_field_loaded = e_field_loaded
         self.event = event
         self.sle = sle
-        self.icp_queue = queues[2]
-        self.object_at_target_queue = queues[3]
         self.use_icp = icp.use_icp
         self.m_icp = icp.m_icp
         self.last_coord = None
@@ -382,18 +381,16 @@ def run(self):
             corregistrate_object_dynamic if self.ref_mode_id else corregistrate_object_static
         )
 
+        icp = (self.use_icp, self.m_icp)
         while not self.event.is_set():
             try:
-                if not self.icp_queue.empty():
-                    self.use_icp, self.m_icp = self.icp_queue.get_nowait()
-
                 if not self.object_at_target_queue.empty():
                     self.target_flag = self.object_at_target_queue.get_nowait()
 
                 coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
                 coord_probe, m_img_probe = corregistrate_probe(
-                    m_change, r_stylus, coord_raw, self.ref_mode_id, icp=[self.use_icp, self.m_icp]
+                    m_change, r_stylus, coord_raw, self.ref_mode_id, icp=icp
                 )
 
                 coords = {"probe": coord_probe}
@@ -401,12 +398,11 @@ def run(self):
 
                 for coil_name in obj_datas:
                     coord_coil, m_img_coil = corregistrate_object(
-                        m_change, obj_datas[coil_name], coord_raw, [self.use_icp, self.m_icp]
+                        m_change, obj_datas[coil_name], coord_raw, icp
                     )
                     coords[coil_name] = coord_coil
                     m_imgs[coil_name] = m_img_coil
 
-
                 # LUKATODO: this is an arbitrary coil, so efields/tracts work correctly with 1 coil but may bug out when using multiple
                 main_coil = next(iter(obj_datas))
                 coord = coords[main_coil]
@@ -425,14 +421,14 @@ def run(self):
                         coord = self.last_coord + (self.target - self.last_coord) * 0.05
                         coords[main_coil] = coord
                         self.last_coord = coord
-                    
+
                     angles = [np.radians(coord[3]), np.radians(coord[4]), np.radians(coord[5])]
                     translate = coord[0:3]
                     m_imgs[main_coil] = tr.compose_matrix(angles=angles, translate=translate)
-                
+
                 self.coord_queue.put_nowait([coords, marker_visibilities, m_imgs])
 
-                # Compute data for efield/tracts 
+                # Compute data for efield/tracts
                 m_img_flip = m_img.copy()
                 m_img_flip[1, -1] = -m_img_flip[1, -1]
 
@@ -440,8 +436,6 @@ def run(self):
                     self.coord_tracts_queue.put_nowait(m_img_flip)
                 if self.e_field_loaded:
                     self.efield_queue.put_nowait([m_img, coord])
-                if not self.icp_queue.empty():
-                    self.icp_queue.task_done()
             except queue.Full:
                 pass
 
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 5c159fd52..2e7d1411d 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -72,7 +72,7 @@ def LoadConfig(self):
 
         # Get the list of coil names of coils selected for navigation
         selected_coils = (session.GetConfig("navigation", {})).get("selected_coils", [])
-        
+
         saved_registrations = session.GetConfig("coil_registrations", {})
         for coil_name in selected_coils:
             if (coil := saved_registrations.get(coil_name, None)) is not None:
@@ -109,7 +109,7 @@ def SetCoilAtTarget(self, state):
 
         # Set the color of both target coil (representing the target) and the coil center (representing the actual coil).
         self.target_coil_actor.GetProperty().SetDiffuseColor(target_coil_color)
-        #self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color)
+        # self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color) # LUKATODO
 
     def OnNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status
@@ -241,7 +241,7 @@ def AddCoil(self, coil_name, coil_path):
 
         self.renderer.AddActor(coil_actor)
         self.renderer.AddActor(coil_center_actor)
-        
+
         self.coils[coil_name] = {}
         self.coils[coil_name]["actor"] = coil_actor
         self.coils[coil_name]["center_actor"] = coil_center_actor
@@ -266,7 +266,7 @@ def RemoveCoil(self, coil_name=None):
         # self.vector_field_assembly.SetVisibility(0)
 
     def ResetCoilVisualizer(self, n_coils):
-        self.RemoveCoil() # Remove all coils
+        self.RemoveCoil()  # Remove all coils
 
     def UpdateCoilPoses(self, m_imgs, coords):
         """
@@ -286,4 +286,4 @@ def UpdateCoilPoses(self, m_imgs, coords):
             self.coils[name]["center_actor"].SetUserMatrix(m_img_vtk)
 
             # LUKATODO
-            self.vector_field_assembly[name].SetUserMatrix(m_img_vtk)
+            self.vector_field_assembly.SetUserMatrix(m_img_vtk)
diff --git a/invesalius/navigation/iterativeclosestpoint.py b/invesalius/navigation/iterativeclosestpoint.py
index eb513eb5a..bce7eb163 100644
--- a/invesalius/navigation/iterativeclosestpoint.py
+++ b/invesalius/navigation/iterativeclosestpoint.py
@@ -96,7 +96,6 @@ def RegisterICP(self, navigation, tracker):
 
     def SetICP(self, navigation, use_icp):
         self.use_icp = use_icp
-        navigation.icp_queue.put_nowait([self.use_icp, self.m_icp])
 
         self.SaveState()
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 2c20fcb9a..2beb92c6e 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -128,7 +128,6 @@ def __init__(self, vis_queues, vis_components, event, sle, neuronavigation_api):
             self.coord_queue,
             self.serial_port_queue,
             self.tracts_queue,
-            self.icp_queue,
             self.e_field_norms_queue,
             self.e_field_IDs_queue,
         ) = vis_queues
@@ -146,7 +145,7 @@ def run(self):
 
                 probe_visible = marker_visibilities[0]
                 coil_visible = marker_visibilities[2]
-                #LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
+                # LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
 
                 # automatically track either coil or stylus if only one of them is visible, otherwise use navigation.track_coil
                 track_coil = (
@@ -158,7 +157,7 @@ def run(self):
                 track_this = main_coil if track_coil else "probe"
                 # choose which object to track in slices and viewer_volume pointer
                 coord = coords[track_this]
-                
+
                 # Remove probe, so that coords/m_imgs only contain coils
                 probe_coord = coords.pop("probe")
                 probe_m_img = m_imgs.pop("probe")
@@ -209,8 +208,11 @@ def run(self):
                     wx.CallAfter(
                         Publisher.sendMessage, "Update coil poses", m_imgs=m_imgs, coords=coords
                     )
-                    wx.CallAfter( # LUKATODO: this is just for viewer_volume... which will be updated later to support multicoil (target, tracts & efield)
-                        Publisher.sendMessage, "Update coil pose", m_img=m_imgs[main_coil], coord=coords[main_coil]
+                    wx.CallAfter(  # LUKATODO: this is just for viewer_volume... which will be updated later to support multicoil (target, tracts & efield)
+                        Publisher.sendMessage,
+                        "Update coil pose",
+                        m_img=m_imgs[main_coil],
+                        coord=coords[main_coil],
                     )
                     wx.CallAfter(
                         Publisher.sendMessage,
@@ -243,7 +245,10 @@ def run(self):
 
                 if probe_visible:
                     wx.CallAfter(
-                        Publisher.sendMessage, "Update probe pose", m_img=probe_m_img, coord=probe_coord
+                        Publisher.sendMessage,
+                        "Update probe pose",
+                        m_img=probe_m_img,
+                        coord=probe_coord,
                     )
 
                 # Render the volume viewer and the slice viewers.
@@ -275,7 +280,6 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.all_fiducials = np.zeros((6, 6))
         self.event = threading.Event()
         self.coord_queue = QueueCustom(maxsize=1)
-        self.icp_queue = QueueCustom(maxsize=1)
         self.object_at_target_queue = QueueCustom(maxsize=1)
         self.efield_queue = QueueCustom(maxsize=1)
         self.e_field_norms_queue = QueueCustom(maxsize=1)
@@ -338,14 +342,18 @@ def SaveConfig(self, key=None, value=None):
         """
         session = ses.Session()
         if key is None:  # Save the whole state
-            state = {"selected_coils": list(self.coil_registrations), "n_coils": self.n_coils, "track_coil": self.track_coil}
+            state = {
+                "selected_coils": list(self.coil_registrations),
+                "n_coils": self.n_coils,
+                "track_coil": self.track_coil,
+            }
             if self.main_coil is not None:
                 state["main_coil"] = self.main_coil
             if self.r_stylus is not None:
                 state["r_stylus"] = self.r_stylus.tolist()
             session.SetConfig("navigation", state)
 
-        elif value is not None: # Save a specific state attribute
+        elif value is not None:  # Save a specific state attribute
             state = session.GetConfig("navigation", {})
             state[key] = value
             session.SetConfig("navigation", state)
@@ -371,8 +379,10 @@ def LoadConfig(self):
                     if coil_name in saved_coil_registrations
                 }
                 if self.coil_registrations:
-                    self.main_coil = state.get("main_coil", None) or next(iter(self.coil_registrations))
-            
+                    self.main_coil = state.get("main_coil", None) or next(
+                        iter(self.coil_registrations)
+                    )
+
             # Try to load stylus orientation data
             if "r_stylus" in state:
                 self.r_stylus = np.array(state["r_stylus"])
@@ -390,7 +400,7 @@ def SelectCoil(self, coil_name, coil_registration):
             if self.main_coil == coil_name:
                 self.main_coil = None
                 self.SaveConfig()
-        
+
         self.SaveConfig()
 
     def CoilAtTarget(self, state):
@@ -510,7 +520,6 @@ def StartNavigation(self, tracker, icp):
             self.coord_queue,
             self.serial_port_queue,
             self.tracts_queue,
-            self.icp_queue,
             self.e_field_norms_queue,
             self.e_field_IDs_queue,
         ]
@@ -561,7 +570,6 @@ def StartNavigation(self, tracker, icp):
             queues = [
                 self.coord_queue,
                 self.coord_tracts_queue,
-                self.icp_queue,
                 self.object_at_target_queue,
                 self.efield_queue,
             ]

From 6f6a95083290960e81c42673f55e3ffb8319c361 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sun, 18 Aug 2024 14:32:48 +0300
Subject: [PATCH 22/44] Maximize viewer volume when target mode is set. Remove
 obsolete functions

---
 invesalius/gui/default_viewers.py | 85 ++++---------------------------
 1 file changed, 10 insertions(+), 75 deletions(-)

diff --git a/invesalius/gui/default_viewers.py b/invesalius/gui/default_viewers.py
index e5d9d4368..0f55f9ebb 100644
--- a/invesalius/gui/default_viewers.py
+++ b/invesalius/gui/default_viewers.py
@@ -158,8 +158,18 @@ def __bind_events_wx(self):
         self.aui_manager.Bind(wx.aui.EVT_AUI_PANE_RESTORE, self.OnRestore)
 
     def __bind_events(self):
+        Publisher.subscribe(self.MaximizeViewerVolume, "Set target mode")
         Publisher.subscribe(self._Exit, "Exit")
 
+    def MaximizeViewerVolume(self, enabled=True):
+        if enabled:
+            self.aui_manager.MaximizePane(self.aui_manager.GetAllPanes()[-1]) # Viewer volume is the last pane
+            Publisher.sendMessage("Show raycasting widget")
+        else:
+            self.aui_manager.RestoreMaximizedPane()
+            Publisher.sendMessage("Hide raycasting widget")
+        self.aui_manager.Update()
+
     def OnMaximize(self, evt):
         if evt.GetPane().name == self.s4.name:
             Publisher.sendMessage("Show raycasting widget")
@@ -168,84 +178,9 @@ def OnRestore(self, evt):
         if evt.GetPane().name == self.s4.name:
             Publisher.sendMessage("Hide raycasting widget")
 
-    def __init_four_way_splitter(self):
-        splitter = fws.FourWaySplitter(self, style=wx.SP_LIVE_UPDATE)
-
-        sizer = wx.BoxSizer(wx.HORIZONTAL)
-        sizer.Add(splitter, 1, wx.EXPAND)
-        self.SetSizer(sizer)
-
-        p1 = slice_viewer.Viewer(self, "AXIAL")
-        splitter.AppendWindow(p1)
-
-        p2 = slice_viewer.Viewer(self, "CORONAL")
-        splitter.AppendWindow(p2)
-
-        p3 = slice_viewer.Viewer(self, "SAGITAL")
-        splitter.AppendWindow(p3)
-
-        p4 = volume_viewer.Viewer(self)
-        splitter.AppendWindow(p4)
-
     def _Exit(self):
         self.aui_manager.UnInit()
 
-    def __init_mix(self):
-        aui_manager = wx.aui.AuiManager()
-        aui_manager.SetManagedWindow(self)
-
-        splitter = fws.FourWaySplitter(self, style=wx.SP_LIVE_UPDATE)
-
-        sizer = wx.BoxSizer(wx.HORIZONTAL)
-        sizer.Add(splitter, 1, wx.EXPAND)
-        self.SetSizer(sizer)
-
-        p1 = slice_viewer.Viewer(self, "AXIAL")
-        aui_manager.AddPane(
-            p1,
-            wx.aui.AuiPaneInfo()
-            .Name("Axial Slice")
-            .Caption(_("Axial slice"))
-            .MaximizeButton(True)
-            .CloseButton(False),
-        )
-
-        p2 = slice_viewer.Viewer(self, "CORONAL")
-        aui_manager.AddPane(
-            p2,
-            wx.aui.AuiPaneInfo()
-            .Name("Coronal Slice")
-            .Caption(_("Coronal slice"))
-            .MaximizeButton(True)
-            .CloseButton(False),
-        )
-
-        p3 = slice_viewer.Viewer(self, "SAGITAL")
-        aui_manager.AddPane(
-            p3,
-            wx.aui.AuiPaneInfo()
-            .Name("Sagittal Slice")
-            .Caption(_("Sagittal slice"))
-            .MaximizeButton(True)
-            .CloseButton(False),
-        )
-
-        # p4 = volume_viewer.Viewer(self)
-        aui_manager.AddPane(
-            VolumeViewerCover,
-            wx.aui.AuiPaneInfo()
-            .Name("Volume")
-            .Caption(_("Volume"))
-            .MaximizeButton(True)
-            .CloseButton(False),
-        )
-
-        splitter.AppendWindow(p1)
-        splitter.AppendWindow(p2)
-        splitter.AppendWindow(p3)
-
-        aui_manager.Update()
-
 
 class VolumeInteraction(wx.Panel):
     def __init__(self, parent, id):

From 23606da39589c9823c96e744be1d90ee4e3be397 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sun, 18 Aug 2024 20:16:21 +0300
Subject: [PATCH 23/44] Minor fixes to ensure target mode works as normal with
 a single coil

---
 invesalius/data/coregistration.py                |  2 +-
 invesalius/data/visualization/coil_visualizer.py |  5 +++--
 invesalius/navigation/navigation.py              |  5 ++++-
 invesalius/navigation/robot.py                   | 12 ++++++------
 4 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 6e4e5d1c3..7565adf29 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -125,7 +125,7 @@ def image_to_tracker(m_change, coord_raw, target, icp, obj_data):
     :return: The transformation matrices from invesalius coordinate system to tracker coordinate system
     :rtype: numpy.ndarray
     """
-    t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = obj_data
+    obj_id, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = obj_data
     m_target_in_image = dco.coordinates_to_transformation_matrix(
         position=target[:3],
         orientation=target[3:],
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 2e7d1411d..0caebbea5 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -136,7 +136,8 @@ def AddTargetCoil(self, m_target):
 
         vtk_colors = vtk.vtkNamedColors()
 
-        decoded_path = self.coil_path.decode("utf-8")
+        # LUKATODO: this is an arbitrary coil... but works for single coil mode
+        decoded_path = next(iter(self.coils.values()))["path"]
 
         coil_filename = os.path.basename(decoded_path)
         coil_dir = os.path.dirname(decoded_path)
@@ -175,7 +176,7 @@ def AddTargetCoil(self, m_target):
         self.target_coil_actor.GetProperty().SetSpecular(0.5)
         self.target_coil_actor.GetProperty().SetSpecularPower(10)
         self.target_coil_actor.GetProperty().SetOpacity(0.3)
-        self.target_coil_actor.SetVisibility(self.show_coil_pressed)
+        self.target_coil_actor.SetVisibility(True) #LUKATODO
         self.target_coil_actor.SetUserMatrix(m_target)
 
         self.renderer.AddActor(self.target_coil_actor)
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 2beb92c6e..5f8bc82af 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -276,6 +276,7 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.main_coil = None  # Which coil to track with pointer
         self.m_change = None
         self.r_stylus = None
+        self.obj_datas = None # This is accessed by the robot, gets value at StartNavigation
 
         self.all_fiducials = np.zeros((6, 6))
         self.event = threading.Event()
@@ -564,7 +565,9 @@ def StartNavigation(self, tracker, icp):
                     self.m_change,
                 )
                 obj_datas[coil_name] = obj_data
-
+            
+            self.obj_datas = obj_datas
+            
             coreg_data = [self.m_change, self.r_stylus]
 
             queues = [
diff --git a/invesalius/navigation/robot.py b/invesalius/navigation/robot.py
index 96c60686d..d8108d309 100644
--- a/invesalius/navigation/robot.py
+++ b/invesalius/navigation/robot.py
@@ -162,6 +162,11 @@ def SendTargetToRobot(self):
         if self.target is None:
             return False
 
+        navigation = self.navigation
+        # XXX: These are needed for computing the target in tracker coordinate system. Ensure that they are set.
+        if navigation.m_change is None or navigation.obj_datas is not None:
+            return False
+
         # Compute the target in tracker coordinate system.
         coord_raw, marker_visibilities = self.tracker.TrackerCoordinates.GetCoordinates()
 
@@ -170,13 +175,8 @@ def SendTargetToRobot(self):
         #   to avoid modifying it.
         target = self.target[:]
         target[1] = -target[1]
-
-        # XXX: These are needed for computing the target in tracker coordinate system. Ensure that they are set.
-        if self.navigation.m_change is None or self.navigation.obj_data is None:
-            return False
-
         m_target = dcr.image_to_tracker(
-            self.navigation.m_change, coord_raw, target, self.icp, self.navigation.obj_data
+            navigation.m_change, coord_raw, target, self.icp, navigation.obj_datas[navigation.main_coil]
         )
 
         Publisher.sendMessage(

From efcf2afb51c03c9f8543838d82509af96ea254b6 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Tue, 20 Aug 2024 11:44:28 +0300
Subject: [PATCH 24/44] Update PolarisCoord to receive multiple coil
 coordinates. Improve Polaris ROM init dialog. Update handling of
 marker_visibilities to support multiple coils.

---
 invesalius/data/coordinates.py        | 21 ++++++++++++---------
 invesalius/data/tracker_connection.py | 10 ++++++----
 invesalius/data/viewer_volume.py      |  4 ++--
 invesalius/gui/dialogs.py             | 21 +++++++++------------
 invesalius/navigation/navigation.py   | 19 ++++++-------------
 invesalius/navigation/tracker.py      |  2 +-
 6 files changed, 36 insertions(+), 41 deletions(-)

diff --git a/invesalius/data/coordinates.py b/invesalius/data/coordinates.py
index dc05158b2..ab45149fa 100644
--- a/invesalius/data/coordinates.py
+++ b/invesalius/data/coordinates.py
@@ -253,15 +253,18 @@ def PolarisCoord(tracker_connection: "TrackerConnection", tracker_id: int, ref_m
     angles_ref = np.degrees(tr.euler_from_quaternion(ref[2:6], axes="rzyx"))
     trans_ref = np.array(ref[6:9]).astype(float)
     coord2 = np.hstack((trans_ref, angles_ref))
+    
+    obj_coords = []
+    for i in range(trck.objs.size()):
+        obj = trck.objs[i].decode(const.FS_ENCODE).split(",") 
+        angles_obj = np.degrees(tr.euler_from_quaternion(obj[2:6], axes="rzyx"))
+        trans_obj = np.array(obj[6:9]).astype(float)
+        obj_coords.append(np.hstack((trans_obj, angles_obj)))
+    
+    coord = np.vstack([coord1, coord2, *obj_coords])
+    marker_visibilities = [trck.probeID, trck.refID] + list(trck.objIDs)
 
-    obj = trck.obj.decode(const.FS_ENCODE).split(",")
-    angles_obj = np.degrees(tr.euler_from_quaternion(obj[2:6], axes="rzyx"))
-    trans_obj = np.array(obj[6:9]).astype(float)
-    coord3 = np.hstack((trans_obj, angles_obj))
-
-    coord = np.vstack([coord1, coord2, coord3])
-
-    return coord, [trck.probeID, trck.refID, trck.objID]
+    return coord, marker_visibilities  
 
 
 def CameraCoord(tracker_connection: "TrackerConnection", tracker_id: int, ref_mode):
@@ -558,7 +561,7 @@ def DebugCoordRandom(tracker_connection: "TrackerConnection", tracker_id: int, r
 
     # Always make the markers visible when using debug tracker; this enables registration, as it
     # is not possible to registering without markers.
-    marker_visibilities = [True, True, True]
+    marker_visibilities = [True, True, True, True, True]
 
     return np.vstack([coord1, coord2, coord3, coord4, coord5]), marker_visibilities
 
diff --git a/invesalius/data/tracker_connection.py b/invesalius/data/tracker_connection.py
index ddb1132ab..253e1060b 100644
--- a/invesalius/data/tracker_connection.py
+++ b/invesalius/data/tracker_connection.py
@@ -393,13 +393,13 @@ def Configure(self):
 
         success = status == ID_OK
         if success:
-            com_port, probe_dir, ref_dir, obj_dir = dialog.GetValue()
+            com_port, probe_dir, ref_dir, obj_dirs = dialog.GetValue()
 
             self.configuration = {
                 "com_port": com_port,
                 "probe_dir": probe_dir,
                 "ref_dir": ref_dir,
-                "obj_dir": obj_dir,
+                "obj_dirs": obj_dirs,
             }
         else:
             self.lib_mode = None
@@ -427,9 +427,11 @@ def Connect(self):
             com_port = self.configuration["com_port"].encode(const.FS_ENCODE)
             probe_dir = self.configuration["probe_dir"].encode(const.FS_ENCODE)
             ref_dir = self.configuration["ref_dir"].encode(const.FS_ENCODE)
-            obj_dir = self.configuration["obj_dir"].encode(const.FS_ENCODE)
+            obj_dirs = pypolaris.StringVector() # SWIG fails to convert python list to vector<string>, so we directly create StringVector
+            for obj_dir in self.configuration["obj_dirs"]:
+                obj_dirs.append(obj_dir.encode(const.FS_ENCODE))
 
-            if connection.Initialize(com_port, probe_dir, ref_dir, obj_dir) != 0:
+            if connection.Initialize(com_port, probe_dir, ref_dir, obj_dirs) != 0:
                 lib_mode = None
                 print("Could not connect to polaris tracker.")
             else:
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index 3a125fd0e..b9efe56c9 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -599,7 +599,7 @@ def DeletePointer(self):
         self.UpdateRender()
 
     def OnSensors(self, marker_visibilities):
-        probe_id, ref_id, obj_id = marker_visibilities
+        probe_id, ref_id, *coil_ids = marker_visibilities
 
         if not self.probe:
             self.probe = True
@@ -616,7 +616,7 @@ def OnSensors(self, marker_visibilities):
             colour2 = green_color
         else:
             colour2 = red_color
-        if obj_id:
+        if any(coil_ids): #LUKATODO: add subscript to show how many coils are visible (green when all visible, orange when some not)
             colour3 = green_color
         else:
             colour3 = red_color
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index e7e431aeb..dac174de4 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -3960,12 +3960,10 @@ def _init_gui(self) -> None:
         choice_sensor.Bind(wx.EVT_COMBOBOX, self.OnChoiceFTSensor)
         self.choice_sensor = choice_sensor
 
-        # Show tracker reference mode and sensor selection for certain trackers only
+        # Show sensor selection for certain trackers only
         if self.show_sensor_options:
-            choice_ref.Show(True)
             choice_sensor.Show(True)
         else:
-            choice_ref.Show(False)
             choice_sensor.Show(False)
 
         tooltip = _("Reset all fiducials")
@@ -4197,13 +4195,13 @@ def SetObjectFiducial(self, fiducial_index: int) -> None:
         )
 
         # If coil or probe markers are not visible, show a warning and return early.
-        probe_visible, _, coil_visible = marker_visibilities
+        probe_visible, head_visible, *coils_visible = marker_visibilities
 
         if not probe_visible:
             ShowNavigationTrackerWarning(0, "probe marker not visible")
             return
 
-        if not coil_visible:
+        if not coils_visible[self.obj_id - 2]:
             ShowNavigationTrackerWarning(0, "coil marker not visible")
             return
 
@@ -4664,7 +4662,7 @@ def HandleContinuousAcquisition(self, evt: wx.TimerEvent) -> None:
     def CreatePoint(self, evt: Optional[wx.CommandEvent] = None) -> None:
         current_coord, marker_visibilities = self.GetCurrentCoord()
 
-        probe_visible, head_visible, _ = marker_visibilities
+        probe_visible, head_visible, *coils_visible = marker_visibilities
 
         if probe_visible and head_visible:
             self.AddMarker(3, (1, 0, 0), current_coord)
@@ -6877,14 +6875,13 @@ def _init_gui(self) -> None:
         session = ses.Session()
         last_ndi_probe_marker = session.GetConfig("last_ndi_probe_marker", "")
         last_ndi_ref_marker = session.GetConfig("last_ndi_ref_marker", "")
-        last_ndi_obj_markers = session.GetConfig("last_ndi_obj_markers", "")
-
+        last_ndi_obj_markers = session.GetConfig("last_ndi_obj_markers", [])
         if not last_ndi_probe_marker:
             last_ndi_probe_marker = inv_paths.NDI_MAR_DIR_PROBE
         if not last_ndi_ref_marker:
             last_ndi_ref_marker = inv_paths.NDI_MAR_DIR_REF
-        if not last_ndi_obj_markers:
-            last_ndi_obj_markers = self.n_coils * [inv_paths.NDI_MAR_DIR_OBJ]
+        while len(last_ndi_obj_markers) < self.n_coils:
+            last_ndi_obj_markers.append(inv_paths.NDI_MAR_DIR_OBJ)
 
         self.dir_probe = wx.FilePickerCtrl(
             self,
@@ -6918,13 +6915,13 @@ def _init_gui(self) -> None:
                 path=last_ndi_obj_markers[i],
                 style=wx.FLP_USE_TEXTCTRL | wx.FLP_SMALL,
                 wildcard="Rom files (*.rom)|*.rom",
-                message="Select the ROM file of the object",
+                message=f"Select the ROM file of coil {i+1}",
                 size=(700, -1),
             )
             self.dir_objs.append(dir_obj)
 
             row_obj = wx.BoxSizer(wx.VERTICAL)
-            row_obj.Add(wx.StaticText(self, wx.ID_ANY, "Coil ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
+            row_obj.Add(wx.StaticText(self, wx.ID_ANY, f"Coil {i+1} ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
             row_obj.Add(dir_obj, 0, wx.ALL | wx.CENTER | wx.EXPAND)
             row_objs.append(row_obj)
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 5f8bc82af..837c6a730 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -144,17 +144,10 @@ def run(self):
                 got_coords = True
 
                 probe_visible = marker_visibilities[0]
-                coil_visible = marker_visibilities[2]
-                # LUKATODO: this goes all the way to the wrappers, but should have coils_visible dict...
-
-                # automatically track either coil or stylus if only one of them is visible, otherwise use navigation.track_coil
-                track_coil = (
-                    (coil_visible or not probe_visible)
-                    if (coil_visible ^ probe_visible)
-                    else self.navigation.track_coil
-                )
+                coil_visible = any(marker_visibilities[2:])  # is any coil visible?
+
                 main_coil = self.navigation.main_coil
-                track_this = main_coil if track_coil else "probe"
+                track_this = main_coil if self.navigation.track_coil else "probe"
                 # choose which object to track in slices and viewer_volume pointer
                 coord = coords[track_this]
 
@@ -276,7 +269,7 @@ def __init__(self, pedal_connector, neuronavigation_api):
         self.main_coil = None  # Which coil to track with pointer
         self.m_change = None
         self.r_stylus = None
-        self.obj_datas = None # This is accessed by the robot, gets value at StartNavigation
+        self.obj_datas = None  # This is accessed by the robot, gets value at StartNavigation
 
         self.all_fiducials = np.zeros((6, 6))
         self.event = threading.Event()
@@ -565,9 +558,9 @@ def StartNavigation(self, tracker, icp):
                     self.m_change,
                 )
                 obj_datas[coil_name] = obj_data
-            
+
             self.obj_datas = obj_datas
-            
+
             coreg_data = [self.m_change, self.r_stylus]
 
             queues = [
diff --git a/invesalius/navigation/tracker.py b/invesalius/navigation/tracker.py
index f5fd83637..75ba6f047 100644
--- a/invesalius/navigation/tracker.py
+++ b/invesalius/navigation/tracker.py
@@ -199,7 +199,7 @@ def SetTrackerFiducial(self, ref_mode_id, fiducial_index):
         )
 
         # If probe or head markers are not visible, show a warning and return early.
-        probe_visible, head_visible, _ = marker_visibilities
+        probe_visible, head_visible, *coils_visible = marker_visibilities
 
         if not probe_visible:
             dlg.ShowNavigationTrackerWarning(0, "probe marker not visible")

From 6e09feb6df8659ff491a7a2f5cef70efd2f82992 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 22 Aug 2024 10:29:07 +0300
Subject: [PATCH 25/44] Rotate stylus NT-115.rom to point in x-axis. Restore
 NBSref.rom to old form.

---
 navigation/ndi_files/Markers/NBSref.rom | Bin 752 -> 752 bytes
 navigation/ndi_files/Markers/NT-115.rom | Bin 752 -> 752 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/navigation/ndi_files/Markers/NBSref.rom b/navigation/ndi_files/Markers/NBSref.rom
index 820d7b8fb8ba90b312873f65f47e58b9ef42fc3a..426497352428f907d17cdc11fbe454259bcb17ae 100644
GIT binary patch
literal 752
zcmeZs@nra6%D}+Lz`(!^p%|D{CR#@U`797IAj#kWBCrDmN09h~@7#wPJc}F|Hdq}L
zcvO7QhMD^iL)Qz31OH18#9f`@)ZnxAU`9ZM(-X_+Lkvwf9KXG2bAC8$%Heg>dyn8^
zW4CWqbU;FYk%^gwl?}yec_82fisU5~!^Qoaf{Rkq;9M|+lMw<?M6roAFleHvp#cW~
Drein(

literal 752
zcmeZs@nqmLVPIfnU|?W^Pz+2e6Ro3wd=?;P24Wy^0F$@~4hDvqb1xq}Z}r|WwR(c>
z{q=Va&RKQi;9o1xJ?31e9p_a|cG{V8$<D|5spC4inTG_eKkUP0)KC#;lkMEavu&xh
z!vA`EV%S5)UpU>#$OKIa2o>@`zzO8$B^AR3{hWe}Qq$mEFoTm32vCK9DGiHQ1A`{I
HGHUYy)`&GM

diff --git a/navigation/ndi_files/Markers/NT-115.rom b/navigation/ndi_files/Markers/NT-115.rom
index a5868cbad4f5c0951eee19a8349d2c1d43bff1e3..6081243760b646a3b15a5817f4d92b8e4caae760 100644
GIT binary patch
delta 84
zcmeys`hk_r&&87=M{y#XlK}&R*kJ~ShLvvua~v5MOyTUHAAyGpZ4Vs;iO-6xIDGcZ
eI!6$DV&lPy6F4VFF-lDKW0aWKy?wGK({TVV<srua

delta 84
zcmeys`hk_r&&88LLwO>blfkmmr5X$jVu#-Z<~UARejLa)1+xon4><<?2n4gwo>_Nr
fR%8X3J+blN#0i{}qZlP7`!PyP?A|_Elj%4Bh9@II


From 120869f8d22e1719e5bf4362cec409dcfbd2b329 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 22 Aug 2024 16:39:11 +0300
Subject: [PATCH 26/44] Reset tracker connection when n_coils is changed. This
 is necessary for Polaris to load ROM new files.

---
 invesalius/gui/preferences.py    | 7 +++++++
 invesalius/gui/task_navigator.py | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index a79c8c7bb..0d210dc72 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1554,11 +1554,18 @@ def LoadConfig(self):
         return True
 
     def OnChooseNoOfCoils(self, evt, ctrl):
+        old_n_coils = self.n_coils
         if hasattr(evt, "GetSelection"):
             choice = evt.GetSelection()
             self.n_coils = choice + 1
         else:
             self.n_coils = 1
+
+        if self.n_coils != old_n_coils: # if n_coils was changed reset connection
+            tracker_id = self.tracker.tracker_id
+            self.tracker.DisconnectTracker()
+            self.tracker.SetTracker(tracker_id, n_coils=self.n_coils)
+
         ctrl.SetSelection(self.n_coils - 1)
         Publisher.sendMessage("Reset coil selection", n_coils=self.n_coils)
         Publisher.sendMessage("Coil selection done", done=False)
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index ae2ab9425..f57f37cd3 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1766,7 +1766,7 @@ def OnTrackObjectButton(self, evt=None, ctrl=None):
             self.UpdateToggleButton(ctrl)
         pressed = self.track_object_button.GetValue()
         Publisher.sendMessage("Track object", enabled=pressed)
-        if not pressed:
+        if not pressed and self.target_mode_button.GetValue():
             Publisher.sendMessage("Press target mode button", pressed=False)
 
         # Automatically press or unpress 'Show coil' and 'Show probe' button.

From 7df6426049b608c54ef32f6dd23c75c5eafce214 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 22 Aug 2024 17:09:31 +0300
Subject: [PATCH 27/44] Clean comments and RUFF format

---
 invesalius/data/coordinates.py                |  8 +--
 invesalius/data/tracker_connection.py         |  2 +-
 invesalius/data/viewer_volume.py              |  7 +-
 .../data/visualization/coil_visualizer.py     | 10 +--
 invesalius/gui/default_viewers.py             |  4 +-
 invesalius/gui/dialogs.py                     |  4 +-
 invesalius/gui/preferences.py                 | 71 +++++++++----------
 invesalius/gui/task_navigator.py              | 18 +++--
 invesalius/navigation/robot.py                |  6 +-
 9 files changed, 71 insertions(+), 59 deletions(-)

diff --git a/invesalius/data/coordinates.py b/invesalius/data/coordinates.py
index ab45149fa..09365e3c4 100644
--- a/invesalius/data/coordinates.py
+++ b/invesalius/data/coordinates.py
@@ -253,18 +253,18 @@ def PolarisCoord(tracker_connection: "TrackerConnection", tracker_id: int, ref_m
     angles_ref = np.degrees(tr.euler_from_quaternion(ref[2:6], axes="rzyx"))
     trans_ref = np.array(ref[6:9]).astype(float)
     coord2 = np.hstack((trans_ref, angles_ref))
-    
+
     obj_coords = []
     for i in range(trck.objs.size()):
-        obj = trck.objs[i].decode(const.FS_ENCODE).split(",") 
+        obj = trck.objs[i].decode(const.FS_ENCODE).split(",")
         angles_obj = np.degrees(tr.euler_from_quaternion(obj[2:6], axes="rzyx"))
         trans_obj = np.array(obj[6:9]).astype(float)
         obj_coords.append(np.hstack((trans_obj, angles_obj)))
-    
+
     coord = np.vstack([coord1, coord2, *obj_coords])
     marker_visibilities = [trck.probeID, trck.refID] + list(trck.objIDs)
 
-    return coord, marker_visibilities  
+    return coord, marker_visibilities
 
 
 def CameraCoord(tracker_connection: "TrackerConnection", tracker_id: int, ref_mode):
diff --git a/invesalius/data/tracker_connection.py b/invesalius/data/tracker_connection.py
index 253e1060b..f93dabed9 100644
--- a/invesalius/data/tracker_connection.py
+++ b/invesalius/data/tracker_connection.py
@@ -427,7 +427,7 @@ def Connect(self):
             com_port = self.configuration["com_port"].encode(const.FS_ENCODE)
             probe_dir = self.configuration["probe_dir"].encode(const.FS_ENCODE)
             ref_dir = self.configuration["ref_dir"].encode(const.FS_ENCODE)
-            obj_dirs = pypolaris.StringVector() # SWIG fails to convert python list to vector<string>, so we directly create StringVector
+            obj_dirs = pypolaris.StringVector()  # SWIG fails to convert python list to vector<string>, so we directly create StringVector
             for obj_dir in self.configuration["obj_dirs"]:
                 obj_dirs.append(obj_dir.encode(const.FS_ENCODE))
 
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index b9efe56c9..b085aaf4e 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -343,7 +343,6 @@ def __init__(self, parent):
         self.positions_above_threshold = None
         self.cell_id_indexes_above_threshold = None
 
-        # LUKATODO: delete this?
         Publisher.sendMessage("Press target mode button", pressed=False)
 
     def UpdateCanvas(self):
@@ -616,7 +615,9 @@ def OnSensors(self, marker_visibilities):
             colour2 = green_color
         else:
             colour2 = red_color
-        if any(coil_ids): #LUKATODO: add subscript to show how many coils are visible (green when all visible, orange when some not)
+        if any(
+            coil_ids
+        ):  # LUKATODO: add subscript to show how many coils are visible (green when all visible, orange when some not)
             colour3 = green_color
         else:
             colour3 = red_color
@@ -2173,7 +2174,7 @@ def GetEnorm(self, enorm_data, plot_vector):
             if session.GetConfig("debug_efield"):
                 self.e_field_norms = enorm_data[3][self.Id_list, 0]
                 self.e_field_col1 = enorm_data[3][self.Id_list, 1]
-                self.e_field_col2 = enorm_data[3][self.Id_list, 1] #LUKATODO: is this a typo?
+                self.e_field_col2 = enorm_data[3][self.Id_list, 1]  # LUKATODO: is this a typo?
                 self.e_field_col3 = enorm_data[3][self.Id_list, 3]
                 self.Idmax = np.array(self.Id_list[np.array(self.e_field_norms).argmax()])
                 max = np.array(self.e_field_norms).argmax()
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 0caebbea5..4cf3dae27 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -109,13 +109,13 @@ def SetCoilAtTarget(self, state):
 
         # Set the color of both target coil (representing the target) and the coil center (representing the actual coil).
         self.target_coil_actor.GetProperty().SetDiffuseColor(target_coil_color)
-        # self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color) # LUKATODO
+        # self.coil_center_actor.GetProperty().SetDiffuseColor(target_coil_color) # LUKATODO: use main_coil from navigation?
 
     def OnNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status
 
     # Called when 'show coil' button is pressed in the user interface or in code.
-    # LUKATODO: Right-click 'show coil' button to open combobox to choose specific coil to show/hide?
+    # LUKATODO: Right-click 'show coil' button to open combobox for choosing specific coil to show/hide
     def ShowCoil(self, state, coil_name=None):
         if coil_name is None:  # Show/hide all coils
             for coil in self.coils.values():
@@ -126,7 +126,7 @@ def ShowCoil(self, state, coil_name=None):
         # LUKATODO: target?
         if self.target_coil_actor is not None:
             self.target_coil_actor.SetVisibility(state)
-        self.vector_field_assembly.SetVisibility(state)
+        # self.vector_field_assembly.SetVisibility(state) # LUKATODO: Keep this hidden for now
 
         if not self.is_navigating:
             self.interactor.Render()
@@ -176,7 +176,7 @@ def AddTargetCoil(self, m_target):
         self.target_coil_actor.GetProperty().SetSpecular(0.5)
         self.target_coil_actor.GetProperty().SetSpecularPower(10)
         self.target_coil_actor.GetProperty().SetOpacity(0.3)
-        self.target_coil_actor.SetVisibility(True) #LUKATODO
+        self.target_coil_actor.SetVisibility(True)
         self.target_coil_actor.SetUserMatrix(m_target)
 
         self.renderer.AddActor(self.target_coil_actor)
@@ -287,4 +287,4 @@ def UpdateCoilPoses(self, m_imgs, coords):
             self.coils[name]["center_actor"].SetUserMatrix(m_img_vtk)
 
             # LUKATODO
-            self.vector_field_assembly.SetUserMatrix(m_img_vtk)
+            # self.vector_field_assembly.SetUserMatrix(m_img_vtk)
diff --git a/invesalius/gui/default_viewers.py b/invesalius/gui/default_viewers.py
index 0f55f9ebb..1812c987f 100644
--- a/invesalius/gui/default_viewers.py
+++ b/invesalius/gui/default_viewers.py
@@ -163,7 +163,9 @@ def __bind_events(self):
 
     def MaximizeViewerVolume(self, enabled=True):
         if enabled:
-            self.aui_manager.MaximizePane(self.aui_manager.GetAllPanes()[-1]) # Viewer volume is the last pane
+            self.aui_manager.MaximizePane(
+                self.aui_manager.GetAllPanes()[-1]
+            )  # Viewer volume is the last pane
             Publisher.sendMessage("Show raycasting widget")
         else:
             self.aui_manager.RestoreMaximizedPane()
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index dac174de4..7bd4640f8 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -6921,7 +6921,9 @@ def _init_gui(self) -> None:
             self.dir_objs.append(dir_obj)
 
             row_obj = wx.BoxSizer(wx.VERTICAL)
-            row_obj.Add(wx.StaticText(self, wx.ID_ANY, f"Coil {i+1} ROM file:"), 0, wx.TOP | wx.RIGHT, 5)
+            row_obj.Add(
+                wx.StaticText(self, wx.ID_ANY, f"Coil {i+1} ROM file:"), 0, wx.TOP | wx.RIGHT, 5
+            )
             row_obj.Add(dir_obj, 0, wx.ALL | wx.CENTER | wx.EXPAND)
             row_objs.append(row_obj)
 
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 0d210dc72..154d37072 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -877,7 +877,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         self.pedal_connector = pedal_connector
         self.neuronavigation_api = neuronavigation_api
         self.navigation = navigation
-        self.coil_registrations = {} 
+        self.coil_registrations = {}
         self.__bind_events()
 
         # Sizer for displaying instructions
@@ -903,7 +903,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             ),
         )
         self.inner_sel_sizer = inner_sel_sizer = wx.FlexGridSizer(10, 1, 1)
-        
+
         # Coils are selected by toggling coil-buttons
         self.coil_btns = {}
         self.no_coils_lbl = None
@@ -942,14 +942,13 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         coil_sizer.Add(inner_coil_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
         # Angle/Dist thresholds, timestamp interval
-        self.angle_threshold = (
-            self.session.GetConfig("angle_threshold", const.DEFAULT_ANGLE_THRESHOLD)
+        self.angle_threshold = self.session.GetConfig(
+            "angle_threshold", const.DEFAULT_ANGLE_THRESHOLD
         )
-        self.distance_threshold = (
-            self.session.GetConfig("distance_threshold", const.DEFAULT_DISTANCE_THRESHOLD)
+        self.distance_threshold = self.session.GetConfig(
+            "distance_threshold", const.DEFAULT_DISTANCE_THRESHOLD
         )
 
-
         # Change angles threshold
         text_angles = wx.StaticText(self, -1, _("Angle threshold (degrees):"))
         spin_size_angles = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23))
@@ -1010,11 +1009,9 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             ]
         )
         self.SetSizerAndFit(main_sizer)
-        
-        self.LoadConfig()
-        self.Layout()       
-
 
+        self.LoadConfig()
+        self.Layout()
 
     def AddCoilButton(self, coil_name):
         if self.no_coils_lbl is not None:
@@ -1050,13 +1047,13 @@ def OnSetCoilCount(self, n_coils):
 
     def LoadConfig(self):
         state = self.session.GetConfig("navigation", {})
-        self.coil_registrations = self.session.GetConfig("coil_registrations", {})  
-        # Add a button for each coil 
+        self.coil_registrations = self.session.GetConfig("coil_registrations", {})
+        # Add a button for each coil
         for coil_name in self.coil_registrations:
             self.AddCoilButton(coil_name)
-        
+
         # Press the buttons for coils that were selected in config file
-        selected_coils = state.get("selected_coils", []) 
+        selected_coils = state.get("selected_coils", [])
         for coil_name in selected_coils:
             self.coil_btns[coil_name][0].SetValue(True)
 
@@ -1067,13 +1064,12 @@ def LoadConfig(self):
         self.sel_sizer.GetStaticBox().SetLabel(
             f"TMS coil selection ({n_coils_selected} out of {n_coils})"
         )
-        
+
         if n_coils_selected == n_coils:
             # Allow only n_coils buttons to be pressed, so disable unpressed buttons
             for btn, *junk in self.coil_btns.values():
                 btn.Enable(btn.GetValue())
 
-
     def OnSelectCoil(self, event=None, name=None, select=False):
         coil_registration = None
         navigation = self.navigation
@@ -1115,7 +1111,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
 
         # Select/Unselect coil
         Publisher.sendMessage("Select coil", coil_name=name, coil_registration=coil_registration)
-        
+
         n_coils_selected = len(navigation.coil_registrations)
         n_coils = navigation.n_coils
         # Update label telling how many coils to select
@@ -1133,9 +1129,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
             for btn, *junk in self.coil_btns.values():
                 btn.Enable(btn.GetValue())
         else:  # Enable all buttons
-            Publisher.sendMessage(
-                "Coil selection done", done=False
-            )
+            Publisher.sendMessage("Coil selection done", done=False)
             for btn, *junk in self.coil_btns.values():
                 btn.Enable(True)
 
@@ -1186,15 +1180,17 @@ def DeleteCoil(event, name):
         delete_coil = menu.Append(wx.ID_ANY, "Delete coil")
         set_obj_id = menu.Append(wx.ID_ANY, "Set coil index")
         save_coil = menu.Append(wx.ID_ANY, "Save coil to OBR file")
-        
+
         self.Bind(wx.EVT_MENU, (lambda event, name=name: DeleteCoil(event, name)), delete_coil)
         self.Bind(wx.EVT_MENU, (lambda event, name=name: SetObjID(event, name)), set_obj_id)
-        self.Bind(wx.EVT_MENU, (lambda event, name=name: self.OnSaveCoilToOBR(event, name)), save_coil)
+        self.Bind(
+            wx.EVT_MENU, (lambda event, name=name: self.OnSaveCoilToOBR(event, name)), save_coil
+        )
         self.PopupMenu(menu, event.GetPosition())
         menu.Destroy()
 
     def OnCreateNewCoil(self, event=None):
-        # Create a coil registration and save it by the given name 
+        # Create a coil registration and save it by the given name
         # Also used to edit coil registrations by overwriting to the same name
         if self.tracker.IsTrackerInitialized():
             dialog = dlg.ObjectCalibrationDialog(
@@ -1210,17 +1206,20 @@ def OnCreateNewCoil(self, event=None):
                         # Warn that we are overwriting an old registration
                         dialog = wx.TextEntryDialog(
                             None,
-                            _("A registration with this name already exists. Enter a new name or overwrite an old coil registration"),
+                            _(
+                                "A registration with this name already exists. Enter a new name or overwrite an old coil registration"
+                            ),
                             _("Warning: Coil Name Conflict"),
                             value=coil_name,
                         )
                         if dialog.ShowModal() == wx.ID_OK:
-                            coil_name = dialog.GetValue().strip()  # Update coil_name with user input
+                            coil_name = (
+                                dialog.GetValue().strip()
+                            )  # Update coil_name with user input
                         else:
                             return  # Cancel the operation if the user closes the dialog or cancels
                         dialog.Destroy()
 
-
                     # LUKATODO: update coil mesh elsewhere
                     # self.neuronavigation_api.update_coil_mesh(polydata)
 
@@ -1241,11 +1240,8 @@ def OnCreateNewCoil(self, event=None):
                         if coil_btn.GetValue():
                             coil_btn.SetValue(False)
                             self.OnSelectCoil(name=coil_name, select=False)
-                        
-                        self.Layout()
 
-                        # LUKATODO: delete the below with dependencies
-                        Publisher.sendMessage("Press target mode button", pressed=False)
+                        self.Layout()
 
             except wx.PyAssertionError:  # TODO FIX: win64
                 pass
@@ -1279,7 +1275,9 @@ def OnLoadCoilFromOBR(self, event=None):
                     # Warn that we are overwriting an old registration
                     dialog = wx.TextEntryDialog(
                         None,
-                        _("A registration with this name already exists. Enter a new name or overwrite an old coil registration"),
+                        _(
+                            "A registration with this name already exists. Enter a new name or overwrite an old coil registration"
+                        ),
                         _("Warning: Coil Name Conflict"),
                         value=coil_name,
                     )
@@ -1297,7 +1295,7 @@ def OnLoadCoilFromOBR(self, event=None):
                     coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
 
                 # LUKATODO: what is neuronavigation_api.update_coil_mesh ?
-                #if polydata:
+                # if polydata:
                 #    self.neuronavigation_api.update_coil_mesh(polydata)
 
                 if np.isfinite(obj_fiducials).all() and np.isfinite(obj_orients).all():
@@ -1334,7 +1332,7 @@ def OnLoadCoilFromOBR(self, event=None):
 
     def OnSaveCoilToOBR(self, evt, coil_name):
         coil_registration = self.coil_registrations[coil_name]
-        
+
         filename = dlg.ShowLoadSaveDialog(
             message=_("Save object registration as..."),
             wildcard=_("Registration files (*.obr)|*.obr"),
@@ -1344,7 +1342,7 @@ def OnSaveCoilToOBR(self, evt, coil_name):
         )
         if filename:
             hdr = (
-                coil_name 
+                coil_name
                 + "\t"
                 + utils.decode(coil_registration["path"], const.FS_ENCODE)
                 + "\t"
@@ -1360,7 +1358,6 @@ def OnSaveCoilToOBR(self, evt, coil_name):
             np.savetxt(filename, data, fmt="%.4f", delimiter="\t", newline="\n", header=hdr)
             wx.MessageBox(_("Object file successfully saved"), _("Save"))
 
-
     def OnSelectAngleThreshold(self, evt, ctrl):
         self.angle_threshold = ctrl.GetValue()
         Publisher.sendMessage("Update angle threshold", angle=self.angle_threshold)
@@ -1561,7 +1558,7 @@ def OnChooseNoOfCoils(self, evt, ctrl):
         else:
             self.n_coils = 1
 
-        if self.n_coils != old_n_coils: # if n_coils was changed reset connection
+        if self.n_coils != old_n_coils:  # if n_coils was changed reset connection
             tracker_id = self.tracker.tracker_id
             self.tracker.DisconnectTracker()
             self.tracker.SetTracker(tracker_id, n_coils=self.n_coils)
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index f57f37cd3..3498e06cd 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -273,7 +273,7 @@ def OnShowCoil(self, evt=None):
         Publisher.sendMessage("Show coil in viewer volume", state=pressed)
 
     def CollapseNavigation(self, done):
-        if not done: # Coil selection is no longer complete, so hide navigation panel
+        if not done:  # Coil selection is no longer complete, so hide navigation panel
             self.fold_panel.Collapse(self.nav_panel)
 
     def OnFoldPressCaption(self, evt):
@@ -1108,7 +1108,13 @@ def __init__(self, parent, nav_hub):
         border = wx.FlexGridSizer(1, 2, 1)
         self.coil_registrations = []
 
-        lbl = wx.StaticText(self, -1, _(f"Ready for navigation with {self.navigation.n_coils} coil{'' if self.navigation.n_coils == 1 else 's'}!"))
+        lbl = wx.StaticText(
+            self,
+            -1,
+            _(
+                f"Ready for navigation with {self.navigation.n_coils} coil{'' if self.navigation.n_coils == 1 else 's'}!"
+            ),
+        )
         # lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
         self.lbl = lbl
 
@@ -1155,7 +1161,9 @@ def OnCloseProject(self):
 
     def CoilSelectionDone(self, done):
         if done:
-            self.lbl.SetLabel(f"Ready for navigation with {self.navigation.n_coils} coil{'' if self.navigation.n_coils == 1 else 's'}!")
+            self.lbl.SetLabel(
+                f"Ready for navigation with {self.navigation.n_coils} coil{'' if self.navigation.n_coils == 1 else 's'}!"
+            )
         else:
             self.lbl.SetLabel("Please select which coil(s) to track")
 
@@ -1773,7 +1781,6 @@ def OnTrackObjectButton(self, evt=None, ctrl=None):
         Publisher.sendMessage("Press show-coil button", pressed=pressed)
         Publisher.sendMessage("Press show-probe button", pressed=(not pressed))
 
-
     # 'Lock to Target' button
     def OnLockToTargetButton(self, evt, ctrl):
         self.UpdateToggleButton(ctrl)
@@ -2046,7 +2053,7 @@ def __init__(self, parent, nav_hub):
             wx.EVT_COMBOBOX, partial(self.OnChooseMainCoil, ctrl=select_main_coil)
         )
 
-        # If main coil is defined, select this in the combobox        
+        # If main coil is defined, select this in the combobox
         nav_state = self.session.GetConfig("navigation", {})
         if (main_coil := nav_state.get("main_coil", None)) is not None:
             main_coil_index = select_main_coil.FindString(main_coil)
@@ -2584,7 +2591,6 @@ def OnChooseMainCoil(self, evt, ctrl):
         self.navigation.SetMainCoil(main_coil)
         ctrl.SetSelection(choice)
 
-
     def ChangeLabel(self, evt):
         list_index = self.marker_list_ctrl.GetFocusedItem()
         if list_index == -1:
diff --git a/invesalius/navigation/robot.py b/invesalius/navigation/robot.py
index d8108d309..a3eb1c1d6 100644
--- a/invesalius/navigation/robot.py
+++ b/invesalius/navigation/robot.py
@@ -176,7 +176,11 @@ def SendTargetToRobot(self):
         target = self.target[:]
         target[1] = -target[1]
         m_target = dcr.image_to_tracker(
-            navigation.m_change, coord_raw, target, self.icp, navigation.obj_datas[navigation.main_coil]
+            navigation.m_change,
+            coord_raw,
+            target,
+            self.icp,
+            navigation.obj_datas[navigation.main_coil],
         )
 
         Publisher.sendMessage(

From 6f4c7dd973dc1110cee7e15cdf7e943c8e302ae5 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sun, 25 Aug 2024 19:40:44 +0300
Subject: [PATCH 28/44] Add popup-menu to show/hide specific coil. Menu is
 shown when the Show-coil button is right-clicked

---
 .../data/visualization/coil_visualizer.py     | 20 ++++++++++++-----
 invesalius/gui/task_navigator.py              | 22 +++++++++++++++----
 2 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 4cf3dae27..658a6da3b 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -114,18 +114,26 @@ def SetCoilAtTarget(self, state):
     def OnNavigationStatus(self, nav_status, vis_status):
         self.is_navigating = nav_status
 
-    # Called when 'show coil' button is pressed in the user interface or in code.
-    # LUKATODO: Right-click 'show coil' button to open combobox for choosing specific coil to show/hide
     def ShowCoil(self, state, coil_name=None):
         if coil_name is None:  # Show/hide all coils
             for coil in self.coils.values():
                 coil["actor"].SetVisibility(state)
+                coil["center_actor"].SetVisibility(state)
+            if self.target_coil_actor is not None:  # LUKATODO: target mode...
+                self.target_coil_actor.SetVisibility(state)
         elif (coil := self.coils.get(coil_name, None)) is not None:
-            coil["actor"].SetVisibility(state)
+            # Just toggle the visibility when dealing with specific coils
+            new_state = not coil["actor"].GetVisibility()
+            coil["actor"].SetVisibility(new_state)
+            coil["center_actor"].SetVisibility(new_state)
+
+            # If all coils are hidden/shown, update the color of Show-coil button
+            coils_visible = [coil["actor"].GetVisibility() for coil in self.coils.values()]
+            if not any(coils_visible):  # all coils are hidden
+                Publisher.sendMessage("Press show-coil button", pressed=False)
+            elif all(coils_visible):  # all coils are shown
+                Publisher.sendMessage("Press show-coil button", pressed=True)
 
-        # LUKATODO: target?
-        if self.target_coil_actor is not None:
-            self.target_coil_actor.SetVisibility(state)
         # self.vector_field_assembly.SetVisibility(state) # LUKATODO: Keep this hidden for now
 
         if not self.is_navigating:
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 3498e06cd..6f4d885ef 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -259,7 +259,6 @@ def OnEnableSerialPort(self, evt, ctrl):
             Publisher.sendMessage("Update serial port", serial_port_in_use=False)
 
     # 'Show coil' button
-
     # Called when the 'Show coil' button is pressed elsewhere in code.
     def PressShowCoilButton(self, pressed=False):
         self.show_coil_button.SetValue(pressed)
@@ -270,7 +269,7 @@ def EnableShowCoilButton(self, enabled=False):
 
     def OnShowCoil(self, evt=None):
         pressed = self.show_coil_button.GetValue()
-        Publisher.sendMessage("Show coil in viewer volume", state=pressed)
+        Publisher.sendMessage("Show coil in viewer volume", state=pressed, coil_name=None)
 
     def CollapseNavigation(self, done):
         if not done:  # Coil selection is no longer complete, so hide navigation panel
@@ -1330,6 +1329,7 @@ def __init__(self, parent, nav_hub):
         show_coil_button.SetValue(False)
         show_coil_button.Enable(True)
         show_coil_button.Bind(wx.EVT_TOGGLEBUTTON, self.OnShowCoil)
+        show_coil_button.Bind(wx.EVT_RIGHT_DOWN, self.ShowCoilChoice)
         self.show_coil_button = show_coil_button
 
         # Toggle button for showing probe during navigation
@@ -1796,10 +1796,24 @@ def EnableShowCoilButton(self, enabled=False):
         self.EnableToggleButton(self.show_coil_button, enabled)
         self.UpdateToggleButton(self.show_coil_button)
 
-    def OnShowCoil(self, evt=None):
+    def ShowCoilChoice(self, evt):
+        coil_names = list(self.navigation.coil_registrations)
+
+        show_coil_menu = wx.Menu()
+        for coil_name in coil_names:
+            item = wx.MenuItem(show_coil_menu, wx.ID_ANY, coil_name)
+            self.Bind(
+                wx.EVT_MENU, lambda evt, name=coil_name: self.OnShowCoil(coil_name=name), item
+            )
+            show_coil_menu.Append(item)
+
+        self.PopupMenu(show_coil_menu, evt.GetPosition())
+        show_coil_menu.Destroy()
+
+    def OnShowCoil(self, evt=None, coil_name=None):
         self.UpdateToggleButton(self.show_coil_button)
         pressed = self.show_coil_button.GetValue()
-        Publisher.sendMessage("Show coil in viewer volume", state=pressed)
+        Publisher.sendMessage("Show coil in viewer volume", state=pressed, coil_name=coil_name)
 
     # 'Show probe' button
     def PressShowProbeButton(self, pressed=False):

From 5a7ec8e1c50d3ec502ff287c9244c9e11bc7c1fa Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Mon, 26 Aug 2024 21:38:51 +0300
Subject: [PATCH 29/44] Specify which coil is connected to the robot. Add a
 check that robot.coil_name is specified and in navigation.coil_registrations
 before robot can be used

---
 invesalius/gui/preferences.py       | 61 +++++++++++++++++++++++++++--
 invesalius/gui/task_navigator.py    |  2 +
 invesalius/navigation/navigation.py | 11 ++++++
 invesalius/navigation/robot.py      | 11 +++++-
 4 files changed, 80 insertions(+), 5 deletions(-)

diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 154d37072..f603dae55 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -877,10 +877,11 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         self.pedal_connector = pedal_connector
         self.neuronavigation_api = neuronavigation_api
         self.navigation = navigation
+        self.robot = Robot()
         self.coil_registrations = {}
         self.__bind_events()
 
-        # Sizer for displaying instructions
+        ### Sizer for displaying instructions
         top_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, ("Instructions"))
         inner_top_sizer = wx.FlexGridSizer(1, 3, 1, 1)
         self.instruction_lbl = wx.StaticText(
@@ -894,7 +895,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         inner_top_sizer.Add(self.instruction_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
         top_sizer.Add(inner_top_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
-        # Sizer for choosing which coils to use in navigation
+        ### Sizer for choosing which coils to use in navigation
         self.sel_sizer = sel_sizer = wx.StaticBoxSizer(
             wx.VERTICAL,
             self,
@@ -914,7 +915,50 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             inner_sel_sizer.Add(self.no_coils_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
         sel_sizer.Add(inner_sel_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
-        # Sizer for TMS coil configuration
+        ### Sizer for choosing which coil is attached to the robot
+        self.robot_sizer = robot_sizer = wx.StaticBoxSizer(
+            wx.VERTICAL,
+            self,
+            _("Robot coil selection"),
+        )
+        self.inner_robot_sizer = inner_robot_sizer = wx.FlexGridSizer(2, 1, 1)
+
+        self.not_connected_txt = None
+        self.choice_robot_coil = None
+        if not self.robot.IsConnected():
+            self.not_connected_txt = wx.StaticText(self, -1, "Robot is not connected")
+            inner_robot_sizer.Add(
+                self.not_connected_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
+            )
+        else:
+            choice_robot_coil_lbl = wx.StaticText(self, -1, _("Coil attached to robot: "))
+            self.choice_robot_coil = choice_robot_coil = wx.ComboBox(
+                self,
+                -1,
+                f"{self.robot.coil_name or ''}",
+                size=wx.Size(90, 23),
+                choices=list(
+                    self.navigation.coil_registrations
+                ),  # List of coils selected for navigation
+                style=wx.CB_DROPDOWN | wx.CB_READONLY,
+            )
+
+            choice_robot_coil.SetToolTip(
+                "Specify which coil is attached to the robot",
+            )
+
+            choice_robot_coil.Bind(wx.EVT_COMBOBOX, (lambda event: self.OnChoiceRobotCoil(event)))
+
+            inner_robot_sizer.AddMany(
+                [
+                    (choice_robot_coil_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                    (choice_robot_coil, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                ]
+            )
+
+        robot_sizer.Add(inner_robot_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        ### Sizer for TMS coil configuration
         tooltip = _("New TMS coil configuration")
         btn_new = wx.Button(self, -1, _("New"), size=wx.Size(65, 23))
         btn_new.SetToolTip(tooltip)
@@ -941,6 +985,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         )
         coil_sizer.Add(inner_coil_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
+        ### Sizer for settings (conf_sizer)
         # Angle/Dist thresholds, timestamp interval
         self.angle_threshold = self.session.GetConfig(
             "angle_threshold", const.DEFAULT_ANGLE_THRESHOLD
@@ -1004,6 +1049,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             [
                 (top_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (robot_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (coil_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (conf_sizer, 0, wx.ALL | wx.EXPAND, 10),
             ]
@@ -1013,6 +1059,10 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         self.LoadConfig()
         self.Layout()
 
+    def OnChoiceRobotCoil(self, event):
+        robot_coil_name = event.GetEventObject().GetStringSelection()
+        self.robot.SetCoilName(robot_coil_name)
+
     def AddCoilButton(self, coil_name):
         if self.no_coils_lbl is not None:
             self.no_coils_lbl.Destroy()  # Remove obsolete message
@@ -1114,11 +1164,16 @@ def OnSelectCoil(self, event=None, name=None, select=False):
 
         n_coils_selected = len(navigation.coil_registrations)
         n_coils = navigation.n_coils
+
         # Update label telling how many coils to select
         self.sel_sizer.GetStaticBox().SetLabel(
             f"TMS coil selection ({n_coils_selected} out of {n_coils})"
         )
 
+        # Update robot coil combobox
+        if self.choice_robot_coil is not None:
+            self.choice_robot_coil.Set(list(navigation.coil_registrations))
+            self.choice_robot_coil.SetStringSelection(self.robot.coil_name or "")
         if n_coils_selected == n_coils:
             Publisher.sendMessage(
                 "Coil selection done", done=True
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 6f4d885ef..7b3b2fb56 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1692,11 +1692,13 @@ def UpdateRobotButtons(self):
         #   - Target is set
         #   - Target mode is on
         #   - Robot is connected
+        #   - The name of the coil attached to robot is specified
         track_target_button_enabled = (
             self.nav_status
             and self.target_selected
             and self.target_mode
             and self.robot.IsConnected()
+            and self.robot.coil_name in self.navigation.coil_registrations
         )
         self.EnableRobotTrackTargetButton(enabled=track_target_button_enabled)
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 837c6a730..85e59b8c3 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -562,6 +562,17 @@ def StartNavigation(self, tracker, icp):
             self.obj_datas = obj_datas
 
             coreg_data = [self.m_change, self.r_stylus]
+            
+            
+            # LUKATODO: where does robot get actual data?
+
+            robot = Robot()
+            if robot.coil_name in self.coil_registrations:
+                # Tell robot at which index (obj_id) to find its coil in
+                Publisher.sendMessage(
+                    "Neuronavigation to Robot: Set coil index",
+                    data=self.coil_registrations[robot.coil_name]["obj_id"],
+                )
 
             queues = [
                 self.coord_queue,
diff --git a/invesalius/navigation/robot.py b/invesalius/navigation/robot.py
index a3eb1c1d6..6a4619a16 100644
--- a/invesalius/navigation/robot.py
+++ b/invesalius/navigation/robot.py
@@ -43,9 +43,10 @@ def __init__(self, tracker, navigation, icp):
         self.tracker = tracker
         self.navigation = navigation
         self.icp = icp
-
         self.enabled_in_gui = False
 
+        self.coil_name = None
+
         self.is_robot_connected = False
         self.robot_ip = None
         self.matrix_tracker_to_robot = None
@@ -142,6 +143,9 @@ def AbortRobotConfiguration(self):
     def IsConnected(self):
         return self.is_robot_connected
 
+    def IsReady(self): # LUKATODO: use this check before enabling robot for navigation...
+        self.IsConnected() and (self.coil_name in self.navigation.coil_registrations)
+
     def SetRobotIP(self, data):
         if data is not None:
             self.robot_ip = data
@@ -157,6 +161,9 @@ def InitializeRobot(self):
         )
         print("Robot initialized")
 
+    def SetCoilName(self, name):
+        self.coil_name = name
+
     def SendTargetToRobot(self):
         # If the target is not set, return early.
         if self.target is None:
@@ -180,7 +187,7 @@ def SendTargetToRobot(self):
             coord_raw,
             target,
             self.icp,
-            navigation.obj_datas[navigation.main_coil],
+            navigation.obj_datas[self.coil_name],
         )
 
         Publisher.sendMessage(

From af8646ed55d07936c65f671ca16cb0fae6256ad0 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Wed, 28 Aug 2024 19:17:40 +0300
Subject: [PATCH 30/44] Change GUI to its old form for single coil mode

---
 invesalius/gui/dialogs.py           |  35 ++-
 invesalius/gui/preferences.py       | 329 ++++++++++++++++++----------
 invesalius/gui/task_navigator.py    |  40 ++--
 invesalius/navigation/navigation.py |   8 +-
 4 files changed, 270 insertions(+), 142 deletions(-)

diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 7bd4640f8..2cc8edcf7 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -3881,10 +3881,12 @@ class ObjectCalibrationDialog(wx.Dialog):
     def __init__(
         self,
         tracker: "Tracker",
+        n_coils: "int",
         pedal_connector: "PedalConnector",
         neuronavigation_api: "NeuronavigationApi",
     ):
         self.tracker = tracker
+        self.n_coils = n_coils
         self.pedal_connector = pedal_connector
         self.neuronavigation_api = neuronavigation_api
 
@@ -3928,7 +3930,7 @@ def _init_gui(self) -> None:
         tooltip = _(
             "Choose the coil index in coord_raw. Choose 0 for static mode, 2 for dynamic mode and 3 onwards for multiple coils."
         )
-        choice_ref = wx.ComboBox(
+        choice_obj_id = wx.ComboBox(
             self,
             -1,
             "",
@@ -3936,14 +3938,15 @@ def _init_gui(self) -> None:
             choices=["0"] + [str(i) for i in range(2, max_obj_id)],
             style=wx.CB_DROPDOWN | wx.CB_READONLY,
         )
-        choice_ref.SetToolTip(tooltip)
-        choice_ref.Bind(wx.EVT_COMBOBOX, self.OnChooseObjID)
-        choice_ref.SetSelection(1)
-        choice_ref.Enable(True)
+        choice_obj_id.SetToolTip(tooltip)
+        choice_obj_id.Bind(wx.EVT_COMBOBOX, self.OnChooseObjID)
+        choice_obj_id.SetSelection(1)
+        choice_obj_id.Enable(True)
+
         if self.tracker_id == const.PATRIOT or self.tracker_id == const.ISOTRAKII:
             self.obj_id = 0
-            choice_ref.SetSelection(0)
-            choice_ref.Enable(False)
+            choice_obj_id.SetSelection(0)
+            choice_obj_id.Enable(False)
 
         # ComboBox for sensor selection for FASTRAK
         tooltip = _("Choose the FASTRAK sensor port")
@@ -3977,7 +3980,7 @@ def _init_gui(self) -> None:
         btn_ok.SetToolTip(tooltip)
 
         extra_sizer = wx.FlexGridSizer(cols=1, hgap=5, vgap=10)
-        extra_sizer.AddMany([choice_ref, btn_reset, btn_ok, choice_sensor])
+        extra_sizer.AddMany([choice_obj_id, btn_reset, btn_ok, choice_sensor])
 
         # Buttons for object fiducials
         self.buttons = OrderedFiducialButtons(
@@ -4026,7 +4029,13 @@ def _init_gui(self) -> None:
         main_sizer.Add(
             group_sizer, 0, wx.EXPAND | wx.GROW | wx.LEFT | wx.TOP | wx.RIGHT | wx.BOTTOM, 10
         )
-        main_sizer.Add(name_sizer, 0, wx.EXPAND)
+        if self.n_coils > 1:  # Multicoil
+            main_sizer.Add(name_sizer, 0, wx.EXPAND)
+        else:  # Single coil mode
+            # Hide obj_id combobox
+            choice_obj_id.Enable(False)
+            choice_obj_id.Show(False)
+
         self.SetSizer(main_sizer)
         main_sizer.Fit(self)
 
@@ -4255,8 +4264,6 @@ def OnChooseObjID(self, evt: wx.CommandEvent) -> None:
         # This is for Polhemus FASTRAK wrapper, where the sensor attached to the object can be the stylus (Static
         # reference - Selection 0 - index 0 for coordinates) or can be a 3rd sensor (Dynamic reference - Selection 1 -
         # index 2 for coordinates)
-        # I use the index 2 directly here to send to the coregistration module where it is possible to access without
-        # any conditional statement the correct index of coordinates.
 
         if evt.GetSelection() == 0:
             self.obj_id = 0
@@ -4279,7 +4286,11 @@ def OnChoiceFTSensor(self, evt: wx.CommandEvent) -> None:
     def GetValue(
         self,
     ) -> Tuple[np.ndarray, np.ndarray, int, Optional[bytes], Optional[vtkPolyData]]:
-        coil_name = self.name_box.GetValue().strip()
+        if self.n_coils > 1:
+            coil_name = self.name_box.GetValue().strip()
+        else:
+            coil_name = "default_coil"
+
         return (
             coil_name,
             self.coil_path,
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index f603dae55..f784f683b 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -881,112 +881,51 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         self.coil_registrations = {}
         self.__bind_events()
 
-        ### Sizer for displaying instructions
-        top_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, ("Instructions"))
-        inner_top_sizer = wx.FlexGridSizer(1, 3, 1, 1)
-        self.instruction_lbl = wx.StaticText(
-            self,
-            -1,
-            _(
-                f"Choose {navigation.n_coils} coils to use. If there are not enough options, create coil configurations below. You can edit configurations by overwriting them. Unused coils can be deleted by right-clicking its button."
-            ),
-        )
-        # instruction_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL))
-        inner_top_sizer.Add(self.instruction_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
-        top_sizer.Add(inner_top_sizer, 0, wx.ALL | wx.EXPAND, 10)
-
-        ### Sizer for choosing which coils to use in navigation
-        self.sel_sizer = sel_sizer = wx.StaticBoxSizer(
-            wx.VERTICAL,
-            self,
-            _(
-                f"TMS coil selection ({len(navigation.coil_registrations)} out of {navigation.n_coils})"
-            ),
-        )
-        self.inner_sel_sizer = inner_sel_sizer = wx.FlexGridSizer(10, 1, 1)
-
-        # Coils are selected by toggling coil-buttons
-        self.coil_btns = {}
-        self.no_coils_lbl = None
-        if len(self.coil_registrations) == 0:
-            self.no_coils_lbl = wx.StaticText(
-                self, -1, _("No coils found in config.json. Create or load new coils below.")
-            )
-            inner_sel_sizer.Add(self.no_coils_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
-        sel_sizer.Add(inner_sel_sizer, 0, wx.ALL | wx.EXPAND, 10)
+        ### Sizer for TMS coil configuration ###
+        self.config_lbl = wx.StaticText(self, -1, _("Current Configuration:"))
+        self.config_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
 
-        ### Sizer for choosing which coil is attached to the robot
-        self.robot_sizer = robot_sizer = wx.StaticBoxSizer(
-            wx.VERTICAL,
+        self.config_txt = wx.StaticText(
             self,
-            _("Robot coil selection"),
+            -1,
+            f"{os.path.basename(self.coil_registrations.get('default_coil', {}).get('path', 'None'))}",
         )
-        self.inner_robot_sizer = inner_robot_sizer = wx.FlexGridSizer(2, 1, 1)
 
-        self.not_connected_txt = None
-        self.choice_robot_coil = None
-        if not self.robot.IsConnected():
-            self.not_connected_txt = wx.StaticText(self, -1, "Robot is not connected")
-            inner_robot_sizer.Add(
-                self.not_connected_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
-            )
-        else:
-            choice_robot_coil_lbl = wx.StaticText(self, -1, _("Coil attached to robot: "))
-            self.choice_robot_coil = choice_robot_coil = wx.ComboBox(
-                self,
-                -1,
-                f"{self.robot.coil_name or ''}",
-                size=wx.Size(90, 23),
-                choices=list(
-                    self.navigation.coil_registrations
-                ),  # List of coils selected for navigation
-                style=wx.CB_DROPDOWN | wx.CB_READONLY,
-            )
-
-            choice_robot_coil.SetToolTip(
-                "Specify which coil is attached to the robot",
-            )
-
-            choice_robot_coil.Bind(wx.EVT_COMBOBOX, (lambda event: self.OnChoiceRobotCoil(event)))
-
-            inner_robot_sizer.AddMany(
-                [
-                    (choice_robot_coil_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                    (choice_robot_coil, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                ]
-            )
-
-        robot_sizer.Add(inner_robot_sizer, 0, wx.ALL | wx.EXPAND, 10)
-
-        ### Sizer for TMS coil configuration
         tooltip = _("New TMS coil configuration")
         btn_new = wx.Button(self, -1, _("New"), size=wx.Size(65, 23))
         btn_new.SetToolTip(tooltip)
         btn_new.Enable(1)
         btn_new.Bind(wx.EVT_BUTTON, self.OnCreateNewCoil)
-        lbl_new = wx.StaticText(self, -1, _("Create or edit a coil configuration: "))
 
         tooltip = _("Load TMS coil configuration from an OBR file")
         btn_load = wx.Button(self, -1, _("Load"), size=wx.Size(65, 23))
         btn_load.SetToolTip(tooltip)
         btn_load.Enable(1)
         btn_load.Bind(wx.EVT_BUTTON, self.OnLoadCoilFromOBR)
-        lbl_load = wx.StaticText(self, -1, _("Load configuration from file: "))
+
+        tooltip = _("Save current TMS coil configuration to a file")
+        btn_save = wx.Button(self, -1, _("Save"), size=wx.Size(65, 23))
+        btn_save.SetToolTip(tooltip)
+        btn_save.Enable(1)
+        btn_save.Bind(wx.EVT_BUTTON, self.OnSaveCoilToOBR)
 
         coil_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, _("TMS coil registration"))
-        inner_coil_sizer = wx.FlexGridSizer(2, 4, 5)
+        inner_coil_sizer = wx.FlexGridSizer(3, 4, 5)
         inner_coil_sizer.AddMany(
             [
-                (lbl_new, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (self.config_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (self.config_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                ((0, 0), 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
                 (btn_new, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                (lbl_load, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
                 (btn_load, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (btn_save, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
             ]
         )
         coil_sizer.Add(inner_coil_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
-        ### Sizer for settings (conf_sizer)
-        # Angle/Dist thresholds, timestamp interval
+        ### Sizer for settings (conf_sizer) ###
+
+        # Angle/Dist thresholds
         self.angle_threshold = self.session.GetConfig(
             "angle_threshold", const.DEFAULT_ANGLE_THRESHOLD
         )
@@ -1035,23 +974,104 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             ]
         )
 
-        # Add line sizers into main sizer
         conf_sizer = wx.StaticBoxSizer(wx.VERTICAL, self, _("Settings"))
         conf_sizer.AddMany(
             [
-                (line_angle_threshold, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 20),
-                (line_dist_threshold, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 20),
+                (line_angle_threshold, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 10),
+                (line_dist_threshold, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, 10),
             ]
         )
 
+        ### Sizer for displaying instructions (multicoil) ###
+        self.instruction_sizer = instruction_sizer = wx.StaticBoxSizer(
+            wx.VERTICAL, self, ("Instructions for using multiple coils")
+        )
+        inner_instruction_sizer = wx.FlexGridSizer(1, 3, 1, 1)
+        self.instruction_lbl = wx.StaticText(
+            self,
+            -1,
+            _(
+                f"Choose {navigation.n_coils} coils to use. If there are not enough options, create coil configurations below. You can edit configurations by overwriting them. Unused coils can be deleted by right-clicking its button."
+            ),
+        )
+        # instruction_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL))
+        inner_instruction_sizer.Add(
+            self.instruction_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
+        )
+        instruction_sizer.Add(inner_instruction_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        ### Sizer for choosing which coils to use in navigation (multicoil)
+        self.sel_sizer = sel_sizer = wx.StaticBoxSizer(
+            wx.VERTICAL,
+            self,
+            _(
+                f"TMS coil selection ({len(navigation.coil_registrations)} out of {navigation.n_coils})"
+            ),
+        )
+        self.inner_sel_sizer = inner_sel_sizer = wx.FlexGridSizer(10, 1, 1)
+
+        # Coils are selected by toggling coil-buttons
+        self.coil_btns = {}
+        self.no_coils_lbl = None
+        if len(self.coil_registrations) == 0:
+            self.no_coils_lbl = wx.StaticText(
+                self, -1, _("No coils found in config.json. Create or load new coils below.")
+            )
+            inner_sel_sizer.Add(self.no_coils_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
+        sel_sizer.Add(inner_sel_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        ### Sizer for choosing which coil is attached to the robot (multicoil) ###
+        self.robot_sizer = robot_sizer = wx.StaticBoxSizer(
+            wx.VERTICAL,
+            self,
+            _("Robot coil selection"),
+        )
+        self.inner_robot_sizer = inner_robot_sizer = wx.FlexGridSizer(2, 1, 1)
+
+        self.not_connected_txt = None
+        self.choice_robot_coil = None
+        if not self.robot.IsConnected():
+            self.not_connected_txt = wx.StaticText(self, -1, "Robot is not connected")
+            inner_robot_sizer.Add(
+                self.not_connected_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
+            )
+        else:
+            choice_robot_coil_lbl = wx.StaticText(self, -1, _("Coil attached to robot: "))
+            self.choice_robot_coil = choice_robot_coil = wx.ComboBox(
+                self,
+                -1,
+                f"{self.robot.coil_name or ''}",
+                size=wx.Size(90, 23),
+                choices=list(
+                    self.navigation.coil_registrations
+                ),  # List of coils selected for navigation
+                style=wx.CB_DROPDOWN | wx.CB_READONLY,
+            )
+
+            choice_robot_coil.SetToolTip(
+                "Specify which coil is attached to the robot",
+            )
+
+            choice_robot_coil.Bind(wx.EVT_COMBOBOX, (lambda event: self.OnChoiceRobotCoil(event)))
+
+            inner_robot_sizer.AddMany(
+                [
+                    (choice_robot_coil_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                    (choice_robot_coil, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                ]
+            )
+
+        robot_sizer.Add(inner_robot_sizer, 0, wx.ALL | wx.EXPAND, 10)
+
+        ### Main sizer that contains all of the above GUI sizers ###
         main_sizer = wx.BoxSizer(wx.VERTICAL)
         main_sizer.AddMany(
             [
-                (top_sizer, 0, wx.ALL | wx.EXPAND, 10),
-                (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
-                (robot_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (coil_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (conf_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (instruction_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (robot_sizer, 0, wx.ALL | wx.EXPAND, 10),
             ]
         )
         self.SetSizerAndFit(main_sizer)
@@ -1086,14 +1106,43 @@ def __bind_events(self):
         Publisher.subscribe(self.OnSetCoilCount, "Reset coil selection")
 
     def OnSetCoilCount(self, n_coils):
-        self.instruction_lbl.SetLabel(
-            f"Choose {n_coils} coils to use below. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. A coil can be deleted or its index can be changed by right-clicking its button."
-        )
-        self.sel_sizer.GetStaticBox().SetLabel(f"TMS coil selection (0 out of {n_coils})")
-        # Reset (enable and unpress) all coil-buttons
-        for btn, *junk in self.coil_btns.values():
-            btn.Enable()
-            btn.SetValue(False)
+        if n_coils == 1:
+            self.config_txt.Show(True)
+            self.config_lbl.Show(True)
+
+            # Hide multicoil GUI elements
+            self.instruction_sizer.GetStaticBox().Show(False)
+            self.instruction_sizer.ShowItems(False)
+
+            self.sel_sizer.GetStaticBox().Show(False)
+            self.sel_sizer.ShowItems(False)
+
+            self.robot_sizer.GetStaticBox().Show(False)
+            self.robot_sizer.ShowItems(False)
+
+        else:
+            self.config_txt.Show(False)
+            self.config_lbl.Show(False)
+            # Multicoil mode
+            self.instruction_lbl.SetLabel(
+                f"Choose {n_coils} coils to use below. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. A coil can be deleted or its index can be changed by right-clicking its button."
+            )
+            self.sel_sizer.GetStaticBox().SetLabel(f"TMS coil selection (0 out of {n_coils})")
+            # Reset (enable and unpress) all coil-buttons
+            for btn, *junk in self.coil_btns.values():
+                btn.Enable()
+                btn.SetValue(False)
+
+            # Show multicoil GUI elements
+            self.instruction_sizer.GetStaticBox().Show(True)
+            self.instruction_sizer.ShowItems(True)
+
+            self.sel_sizer.GetStaticBox().Show(True)
+            self.sel_sizer.ShowItems(True)
+
+            self.robot_sizer.GetStaticBox().Show(True)
+            self.robot_sizer.ShowItems(True)
+        self.Layout()
 
     def LoadConfig(self):
         state = self.session.GetConfig("navigation", {})
@@ -1109,8 +1158,12 @@ def LoadConfig(self):
 
         n_coils_selected = len(selected_coils)
         n_coils = state.get("n_coils", 1)
+        self.OnSetCoilCount(n_coils)
 
-        # Update label
+        # Update labels
+        self.config_txt.SetLabel(
+            f"{os.path.basename(self.coil_registrations.get('default_coil', {}).get('path', 'None'))}"
+        )
         self.sel_sizer.GetStaticBox().SetLabel(
             f"TMS coil selection ({n_coils_selected} out of {n_coils})"
         )
@@ -1121,10 +1174,19 @@ def LoadConfig(self):
                 btn.Enable(btn.GetValue())
 
     def OnSelectCoil(self, event=None, name=None, select=False):
+        if name is None:
+            if not select:  # Unselect all coils
+                Publisher.sendMessage("Reset coil selection", n_coils=self.navigation.n_coils)
+            return
+
         coil_registration = None
         navigation = self.navigation
 
         if select or (event is not None and event.GetSelection()):  # If coil is selected
+            # Press the coil button here in case selection was done via code without pressing button
+            coil_btn = self.coil_btns[name][0]
+            coil_btn.SetValue(True)
+
             coil_registration = self.coil_registrations[name]
 
             # Check that the index of the chosen coil does not conflict with other selected coils
@@ -1145,7 +1207,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
                     ),
                     _("InVesalius 3"),
                 )
-                event.GetEventObject().SetValue(False)  # Unpress the button
+                event.GetEventObject().SetValue(False)  # Unpress the coil-button
                 return
 
             # Check that the tracker used to configure the coil matches the currently used tracker
@@ -1165,7 +1227,10 @@ def OnSelectCoil(self, event=None, name=None, select=False):
         n_coils_selected = len(navigation.coil_registrations)
         n_coils = navigation.n_coils
 
-        # Update label telling how many coils to select
+        # Update labels telling which coil is selected (for single coil mode) and how many coils to select (for multicoil mode)
+        self.config_txt.SetLabel(
+            f"{os.path.basename(self.coil_registrations.get('default_coil', {}).get('path', 'None'))}"
+        )
         self.sel_sizer.GetStaticBox().SetLabel(
             f"TMS coil selection ({n_coils_selected} out of {n_coils})"
         )
@@ -1239,7 +1304,9 @@ def DeleteCoil(event, name):
         self.Bind(wx.EVT_MENU, (lambda event, name=name: DeleteCoil(event, name)), delete_coil)
         self.Bind(wx.EVT_MENU, (lambda event, name=name: SetObjID(event, name)), set_obj_id)
         self.Bind(
-            wx.EVT_MENU, (lambda event, name=name: self.OnSaveCoilToOBR(event, name)), save_coil
+            wx.EVT_MENU,
+            (lambda event, name=name: self.OnSaveCoilToOBR(event, coil_name=name)),
+            save_coil,
         )
         self.PopupMenu(menu, event.GetPosition())
         menu.Destroy()
@@ -1249,7 +1316,10 @@ def OnCreateNewCoil(self, event=None):
         # Also used to edit coil registrations by overwriting to the same name
         if self.tracker.IsTrackerInitialized():
             dialog = dlg.ObjectCalibrationDialog(
-                self.tracker, self.pedal_connector, self.neuronavigation_api
+                self.tracker,
+                self.navigation.n_coils,
+                self.pedal_connector,
+                self.neuronavigation_api,
             )
             try:
                 if dialog.ShowModal() == wx.ID_OK:
@@ -1257,7 +1327,7 @@ def OnCreateNewCoil(self, event=None):
                         dialog.GetValue()
                     )
 
-                    if coil_name in self.coil_registrations:
+                    if coil_name in self.coil_registrations and coil_name != "default_coil":
                         # Warn that we are overwriting an old registration
                         dialog = wx.TextEntryDialog(
                             None,
@@ -1296,7 +1366,13 @@ def OnCreateNewCoil(self, event=None):
                             coil_btn.SetValue(False)
                             self.OnSelectCoil(name=coil_name, select=False)
 
-                        self.Layout()
+                    if self.navigation.n_coils == 1:
+                        # Select the coil that was created for navigation
+                        self.OnSelectCoil(name="default_coil", select=True)
+                        # Hide the coil-button
+                        coil_btn.Show(False)
+
+                    self.Layout()
 
             except wx.PyAssertionError:  # TODO FIX: win64
                 pass
@@ -1308,9 +1384,6 @@ def OnLoadCoilFromOBR(self, event=None):
         filename = dlg.ShowLoadSaveDialog(
             message=_("Load object registration"), wildcard=_("Registration files (*.obr)|*.obr")
         )
-        # data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\anat_reg_improve_20200609'
-        # coil_path = 'magstim_coil_dell_laptop.obr'
-        # filename = os.path.join(data_dir, coil_path)
 
         try:
             if filename:
@@ -1325,8 +1398,14 @@ def OnLoadCoilFromOBR(self, event=None):
                 coil_path = data[0][1].encode(const.FS_ENCODE)
                 tracker_id = int(data[0][3])
                 obj_id = int(data[0][-1])
+                coil_name = "default_coil" if self.navigation.n_coils == 1 else coil_name
+
+                # Handle old OBR file which lacks coil_name and tracker information
+                if len(data[0]) < 6:
+                    coil_name = "default_coil"
+                    tracker_id = self.tracker.tracker_id
 
-                if coil_name in self.coil_registrations:
+                if coil_name in self.coil_registrations and coil_name != "default_coil":
                     # Warn that we are overwriting an old registration
                     dialog = wx.TextEntryDialog(
                         None,
@@ -1373,6 +1452,15 @@ def OnLoadCoilFromOBR(self, event=None):
                     elif self.navigation.CoilSelectionDone():
                         coil_btn.Enable(False)
 
+                    if self.navigation.n_coils == 1:
+                        # Select the coil that was just loaded for navigation
+                        self.OnSelectCoil(
+                            name="default_coil", select=False
+                        )  # We have to unselect 1st since single coil mode causes edge-case bug
+                        self.OnSelectCoil(name="default_coil", select=True)
+                        # Hide the coil-button
+                        coil_btn.Show(False)
+
                     self.Layout()
 
                 Publisher.sendMessage(
@@ -1385,8 +1473,30 @@ def OnLoadCoilFromOBR(self, event=None):
             wx.MessageBox(_("Object registration file incompatible."), _("InVesalius 3"))
             Publisher.sendMessage("Update status text in GUI", label="")
 
-    def OnSaveCoilToOBR(self, evt, coil_name):
-        coil_registration = self.coil_registrations[coil_name]
+    def OnSaveCoilToOBR(self, evt, coil_name=None):
+        if coil_name is None:
+            if self.navigation.n_coils > 1 and self.coil_registrations:
+                # Specify the coil name if multicoil mode and if any exist
+                dialog = wx.SingleChoiceDialog(
+                    None,
+                    _("Select which coil registration to save"),
+                    _("Saving coil registration"),
+                    choices=list(self.coil_registrations),
+                )
+                if dialog.ShowModal() == wx.ID_OK:
+                    coil_name = dialog.GetStringSelection()
+                else:
+                    return  # Cancel the operation if the user closes the dialog or cancels
+                dialog.Destroy()
+            else:
+                # In single coil mode there is only one coil to save
+                coil_name = next(iter(self.coil_registrations), None)
+
+        coil_registration = self.coil_registrations.get(coil_name, None)
+
+        if coil_registration is None:  # No registration found by this name
+            wx.MessageBox(_("Failed to save registration: No registration to save!"), _("Save"))
+            return
 
         filename = dlg.ShowLoadSaveDialog(
             message=_("Save object registration as..."),
@@ -1425,9 +1535,6 @@ def OnSelectDistanceThreshold(self, evt, ctrl):
 
         self.session.SetConfig("distance_threshold", self.distance_threshold)
 
-    def OnSelectTimestamp(self, evt, ctrl):
-        self.timestamp = ctrl.GetValue()
-
 
 class TrackerTab(wx.Panel):
     def __init__(self, parent, tracker, robot):
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 7b3b2fb56..d47d29eb8 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1117,35 +1117,28 @@ def __init__(self, parent, nav_hub):
         # lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
         self.lbl = lbl
 
-        btn_edit = wx.Button(self, -1, _("Edit selection in Preferences"))
+        btn_edit = wx.Button(self, -1, _("Edit coil registration in Preferences"))
         btn_edit.SetToolTip("Open preferences menu")
         btn_edit.Bind(wx.EVT_BUTTON, self.OnEditPreferences)
 
-        border.AddMany(
-            [
-                (lbl, 1, wx.EXPAND),
-                (btn_edit, 1, wx.EXPAND),
-            ]
-        )
-
         next_button = wx.Button(self, label="Proceed to navigation")
         next_button.Bind(wx.EVT_BUTTON, partial(self.OnNext))
         if not self.navigation.CoilSelectionDone():
-            self.lbl.SetLabel("Please select which coil(s) to track")
+            self.lbl.SetLabel("Please select a coil registration")
             next_button.Enable(False)
         self.next_button = next_button
 
-        bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        bottom_sizer.Add(next_button, 1, wx.EXPAND)
-
-        main_sizer = wx.BoxSizer(wx.VERTICAL)
-        main_sizer.AddMany(
+        border.AddMany(
             [
-                (border, 0, wx.EXPAND, 5),
-                (bottom_sizer, 0, wx.EXPAND, 5),
+                (lbl, 1, wx.EXPAND),
+                (btn_edit, 1, wx.EXPAND),
+                (next_button, 1, wx.EXPAND),
             ]
         )
 
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.Add(border, 0, wx.EXPAND, 5)
+
         self.SetSizerAndFit(main_sizer)
         self.Layout()
         self.__bind_events()
@@ -1532,6 +1525,8 @@ def __bind_events(self):
         # Externally press/unpress and enable/disable buttons.
         Publisher.subscribe(self.PressShowProbeButton, "Press show-probe button")
 
+        Publisher.subscribe(self.OnCoilSelectionDone, "Coil selection done")
+
         Publisher.subscribe(self.PressShowCoilButton, "Press show-coil button")
         Publisher.subscribe(self.EnableShowCoilButton, "Enable show-coil button")
 
@@ -1680,6 +1675,10 @@ def OnCheckStatus(self, nav_status, vis_status):
             self.EnableToggleButton(self.checkbox_serial_port, 1)
             self.UpdateToggleButton(self.checkbox_serial_port)
 
+    def OnCoilSelectionDone(self, done):
+        self.PressTrackObjectButton(done)
+        self.PressShowCoilButton(pressed=done)
+
     # Robot
     def OnRobotStatus(self, data):
         if data:
@@ -2075,6 +2074,9 @@ def __init__(self, parent, nav_hub):
             main_coil_index = select_main_coil.FindString(main_coil)
             select_main_coil.SetSelection(main_coil_index)
 
+        # Hide main_coil combobox if single coil mode
+        select_main_coil.Show(nav_state.get("n_coils", 1) != 1)
+
         sizer_main_coil = wx.FlexGridSizer(rows=1, cols=1, hgap=5, vgap=5)
         sizer_main_coil.Add(select_main_coil)
 
@@ -2601,6 +2603,12 @@ def UpdateMainCoilCombobox(self, done):
         else:
             select_main_coil.Clear()
 
+        if self.navigation.n_coils == 1:  # Single coil: hide main coil combobox
+            select_main_coil.Hide()
+        else:
+            select_main_coil.Show()
+        self.Layout()
+
     def OnChooseMainCoil(self, evt, ctrl):
         choice = evt.GetSelection()
         main_coil = ctrl.GetString(choice)
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 85e59b8c3..d2de3e01a 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -362,6 +362,9 @@ def LoadConfig(self):
         if state is not None:
             self.main_coil = state.get("main_coil", None)
             self.n_coils = state.get("n_coils", 1)
+            if self.n_coils == 1:
+                self.main_coil = "default_coil"
+
             self.track_coil = state.get("track_coil", False)
 
             # Try to load selected_coils (the list of names of coils to use for navigation)
@@ -373,7 +376,7 @@ def LoadConfig(self):
                     if coil_name in saved_coil_registrations
                 }
                 if self.coil_registrations:
-                    self.main_coil = state.get("main_coil", None) or next(
+                    self.main_coil = self.main_coil or next(
                         iter(self.coil_registrations)
                     )
 
@@ -562,8 +565,7 @@ def StartNavigation(self, tracker, icp):
             self.obj_datas = obj_datas
 
             coreg_data = [self.m_change, self.r_stylus]
-            
-            
+
             # LUKATODO: where does robot get actual data?
 
             robot = Robot()

From 694f95448a71079aee774d3156dc5e9a3a6f9df8 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 29 Aug 2024 21:01:20 +0300
Subject: [PATCH 31/44] Save/load robot coil name (the coil attached to robot)
 to config file. Add CoilSelectionDone function to simplify preferences code

---
 invesalius/gui/preferences.py  | 40 ++++++++++++++++++----------------
 invesalius/navigation/robot.py | 32 +++++++++++++++++----------
 2 files changed, 42 insertions(+), 30 deletions(-)

diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index f784f683b..b16398b9b 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1169,9 +1169,20 @@ def LoadConfig(self):
         )
 
         if n_coils_selected == n_coils:
-            # Allow only n_coils buttons to be pressed, so disable unpressed buttons
-            for btn, *junk in self.coil_btns.values():
-                btn.Enable(btn.GetValue())
+            self.CoilSelectionDone()
+
+    def CoilSelectionDone(self):
+        if self.navigation.n_coils == 1: # Tell the robot the coil name
+            self.robot.SetCoilName(next(iter(self.navigation.coil_registrations)))
+
+        Publisher.sendMessage(
+            "Coil selection done", done=True
+        )
+        Publisher.sendMessage("Update status text in GUI", label=_("Ready"))
+
+        # Allow only n_coils buttons to be pressed, so disable unpressed coil-buttons
+        for btn, *junk in self.coil_btns.values():
+            btn.Enable(btn.GetValue())
 
     def OnSelectCoil(self, event=None, name=None, select=False):
         if name is None:
@@ -1239,15 +1250,9 @@ def OnSelectCoil(self, event=None, name=None, select=False):
         if self.choice_robot_coil is not None:
             self.choice_robot_coil.Set(list(navigation.coil_registrations))
             self.choice_robot_coil.SetStringSelection(self.robot.coil_name or "")
-        if n_coils_selected == n_coils:
-            Publisher.sendMessage(
-                "Coil selection done", done=True
-            )  # Inform task_navigator that selection is done
-            Publisher.sendMessage("Update status text in GUI", label=_("Ready"))
 
-            # Allow only n_coils buttons to be pressed, so disable unpressed buttons
-            for btn, *junk in self.coil_btns.values():
-                btn.Enable(btn.GetValue())
+        if n_coils_selected == n_coils:
+            self.CoilSelectionDone()
         else:  # Enable all buttons
             Publisher.sendMessage("Coil selection done", done=False)
             for btn, *junk in self.coil_btns.values():
@@ -1547,7 +1552,7 @@ def __init__(self, parent, tracker, robot):
         self.robot_ip = None
         self.matrix_tracker_to_robot = None
         self.n_coils = 1
-        self.state = self.LoadConfig()
+        self.LoadConfig()
 
         # ComboBox for choosing the no. of coils to track
         n_coils_options = [str(n) for n in range(1, 10)]
@@ -1704,13 +1709,10 @@ def LoadConfig(self):
 
         state = session.GetConfig("robot")
 
-        if state is None:
-            return False
-
-        self.robot_ip = state["robot_ip"]
-        self.matrix_tracker_to_robot = np.array(state["tracker_to_robot"])
-
-        return True
+        self.robot_ip = state.get("robot_ip", None)
+        self.matrix_tracker_to_robot = state.get("tracker_to_robot", None)
+        if self.matrix_tracker_to_robot is not None:
+            self.matrix_tracker_to_robot = np.array(self.matrix_tracker_to_robot)
 
     def OnChooseNoOfCoils(self, evt, ctrl):
         old_n_coils = self.n_coils
diff --git a/invesalius/navigation/robot.py b/invesalius/navigation/robot.py
index 6a4619a16..cc3b87302 100644
--- a/invesalius/navigation/robot.py
+++ b/invesalius/navigation/robot.py
@@ -82,24 +82,33 @@ def __bind_events(self):
 
         Publisher.subscribe(self.TrackerFiducialsSet, "Tracker fiducials set")
 
-    def SaveConfig(self):
-        matrix_tracker_to_robot = self.matrix_tracker_to_robot.tolist()
-
-        state = {"robot_ip": self.robot_ip, "tracker_to_robot": matrix_tracker_to_robot}
+    def SaveConfig(self, key=None, value=None):
         session = ses.Session()
+        if key is None or value is None:
+            # Save the whole state
+            state = {"robot_ip": self.robot_ip, "tracker_to_robot": self.matrix_tracker_to_robot.tolist()}
+            if self.coil_name is not None:
+                state["robot_coil"] = self.coil_name
+        else:
+            state = session.GetConfig("robot", {})
+            state[key] = value
+
         session.SetConfig("robot", state)
 
     def LoadConfig(self):
         session = ses.Session()
-        state = session.GetConfig("robot")
-
-        if state is None:
-            return False
+        state = session.GetConfig("robot", {})
+        
+        self.coil_name = state.get("robot_coil", None)
+        
+        self.robot_ip = state.get("robot_ip", None)
 
-        self.robot_ip = state["robot_ip"]
-        self.matrix_tracker_to_robot = np.array(state["tracker_to_robot"])
+        self.matrix_tracker_to_robot = state.get("tracker_to_robot", None)
+        if self.matrix_tracker_to_robot is not None:
+            self.matrix_tracker_to_robot = np.array(self.matrix_tracker_to_robot)
 
-        return True
+        success = (self.robot_ip is not None and self.matrix_tracker_to_robot is not None)
+        return success
 
     def OnRobotConnectionStatus(self, data):
         # TODO: Is this check necessary?
@@ -163,6 +172,7 @@ def InitializeRobot(self):
 
     def SetCoilName(self, name):
         self.coil_name = name
+        self.SaveConfig("robot_coil", name)
 
     def SendTargetToRobot(self):
         # If the target is not set, return early.

From 9621084334d7617808afd1186a22468ffcb76091 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sat, 31 Aug 2024 11:25:36 +0300
Subject: [PATCH 32/44] Improve preferences wording and layout. Simplified
 LoadConfig. Removed the following:   Messy multicoil instructions (there will
 be separate documentation for that)   Unnecessary feature of changing the
 index (obj_id) of a registration

---
 invesalius/gui/preferences.py | 129 +++++++++-------------------------
 1 file changed, 33 insertions(+), 96 deletions(-)

diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index b16398b9b..dd48363d7 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -133,11 +133,6 @@ def LoadPreferences(self):
         console_logging = log.invLogger.GetConfig("console_logging")
         console_logging_level = log.invLogger.GetConfig("console_logging_level")
 
-        mode = session.GetConfig("mode")
-
-        if mode == const.MODE_NAVIGATOR:
-            self.object_tab.LoadConfig()
-
         values = {
             const.RENDERING: rendering,
             const.SURFACE_INTERPOLATION: surface_interpolation,
@@ -903,7 +898,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         btn_load.Enable(1)
         btn_load.Bind(wx.EVT_BUTTON, self.OnLoadCoilFromOBR)
 
-        tooltip = _("Save current TMS coil configuration to a file")
+        tooltip = _("Save TMS coil configuration to a file")
         btn_save = wx.Button(self, -1, _("Save"), size=wx.Size(65, 23))
         btn_save.SetToolTip(tooltip)
         btn_save.Enable(1)
@@ -982,24 +977,6 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             ]
         )
 
-        ### Sizer for displaying instructions (multicoil) ###
-        self.instruction_sizer = instruction_sizer = wx.StaticBoxSizer(
-            wx.VERTICAL, self, ("Instructions for using multiple coils")
-        )
-        inner_instruction_sizer = wx.FlexGridSizer(1, 3, 1, 1)
-        self.instruction_lbl = wx.StaticText(
-            self,
-            -1,
-            _(
-                f"Choose {navigation.n_coils} coils to use. If there are not enough options, create coil configurations below. You can edit configurations by overwriting them. Unused coils can be deleted by right-clicking its button."
-            ),
-        )
-        # instruction_lbl.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL))
-        inner_instruction_sizer.Add(
-            self.instruction_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
-        )
-        instruction_sizer.Add(inner_instruction_sizer, 0, wx.ALL | wx.EXPAND, 10)
-
         ### Sizer for choosing which coils to use in navigation (multicoil)
         self.sel_sizer = sel_sizer = wx.StaticBoxSizer(
             wx.VERTICAL,
@@ -1030,7 +1007,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
 
         self.not_connected_txt = None
         self.choice_robot_coil = None
-        if not self.robot.IsConnected():
+        if self.robot.IsConnected():
             self.not_connected_txt = wx.StaticText(self, -1, "Robot is not connected")
             inner_robot_sizer.Add(
                 self.not_connected_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
@@ -1068,10 +1045,9 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
         main_sizer.AddMany(
             [
                 (coil_sizer, 0, wx.ALL | wx.EXPAND, 10),
-                (conf_sizer, 0, wx.ALL | wx.EXPAND, 10),
-                (instruction_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (sel_sizer, 0, wx.ALL | wx.EXPAND, 10),
                 (robot_sizer, 0, wx.ALL | wx.EXPAND, 10),
+                (conf_sizer, 0, wx.ALL | wx.EXPAND, 10),
             ]
         )
         self.SetSizerAndFit(main_sizer)
@@ -1083,7 +1059,7 @@ def OnChoiceRobotCoil(self, event):
         robot_coil_name = event.GetEventObject().GetStringSelection()
         self.robot.SetCoilName(robot_coil_name)
 
-    def AddCoilButton(self, coil_name):
+    def AddCoilButton(self, coil_name, show_button=True):
         if self.no_coils_lbl is not None:
             self.no_coils_lbl.Destroy()  # Remove obsolete message
             self.no_coils_lbl = None
@@ -1098,6 +1074,7 @@ def AddCoilButton(self, coil_name):
             coil_btn.Bind(
                 wx.EVT_RIGHT_DOWN, lambda event, name=coil_name: self.OnRightClickCoil(event, name)
             )
+            coil_btn.Show(show_button) 
             self.coil_btns[coil_name] = (coil_btn, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
 
             self.inner_sel_sizer.Add(coil_btn, 1, wx.EXPAND, 5)
@@ -1105,65 +1082,57 @@ def AddCoilButton(self, coil_name):
     def __bind_events(self):
         Publisher.subscribe(self.OnSetCoilCount, "Reset coil selection")
 
-    def OnSetCoilCount(self, n_coils):
-        if n_coils == 1:
-            self.config_txt.Show(True)
-            self.config_lbl.Show(True)
+    def ShowMulticoilGUI(self, show_multicoil):
+        # Show/hide singlecoil configuration text
+        self.config_txt.Show(not show_multicoil)
+        self.config_lbl.Show(not show_multicoil)
 
-            # Hide multicoil GUI elements
-            self.instruction_sizer.GetStaticBox().Show(False)
-            self.instruction_sizer.ShowItems(False)
+        # Show/hide multicoil GUI elements
+        self.sel_sizer.GetStaticBox().Show(show_multicoil)
+        self.sel_sizer.ShowItems(show_multicoil)
 
-            self.sel_sizer.GetStaticBox().Show(False)
-            self.sel_sizer.ShowItems(False)
+        self.robot_sizer.GetStaticBox().Show(show_multicoil)
+        self.robot_sizer.ShowItems(show_multicoil)
+        
+        self.Layout()
 
-            self.robot_sizer.GetStaticBox().Show(False)
-            self.robot_sizer.ShowItems(False)
 
-        else:
-            self.config_txt.Show(False)
-            self.config_lbl.Show(False)
-            # Multicoil mode
-            self.instruction_lbl.SetLabel(
-                f"Choose {n_coils} coils to use below. If there are not enough options, create coil configurations below. Here you can also edit configurations by using the same name. A coil can be deleted or its index can be changed by right-clicking its button."
-            )
+    def OnSetCoilCount(self, n_coils):
+        multicoil_mode = n_coils > 1 
+
+        if multicoil_mode:
+            # Update multicoil GUI elements
             self.sel_sizer.GetStaticBox().SetLabel(f"TMS coil selection (0 out of {n_coils})")
+            
             # Reset (enable and unpress) all coil-buttons
             for btn, *junk in self.coil_btns.values():
                 btn.Enable()
                 btn.SetValue(False)
 
-            # Show multicoil GUI elements
-            self.instruction_sizer.GetStaticBox().Show(True)
-            self.instruction_sizer.ShowItems(True)
-
-            self.sel_sizer.GetStaticBox().Show(True)
-            self.sel_sizer.ShowItems(True)
-
-            self.robot_sizer.GetStaticBox().Show(True)
-            self.robot_sizer.ShowItems(True)
-        self.Layout()
+        self.ShowMulticoilGUI(multicoil_mode)
 
     def LoadConfig(self):
         state = self.session.GetConfig("navigation", {})
+        n_coils = state.get("n_coils", 1)
+        multicoil_mode = n_coils > 1
+        self.ShowMulticoilGUI(multicoil_mode)
+
         self.coil_registrations = self.session.GetConfig("coil_registrations", {})
         # Add a button for each coil
         for coil_name in self.coil_registrations:
-            self.AddCoilButton(coil_name)
+            self.AddCoilButton(coil_name, show_button=multicoil_mode)
 
         # Press the buttons for coils that were selected in config file
         selected_coils = state.get("selected_coils", [])
         for coil_name in selected_coils:
             self.coil_btns[coil_name][0].SetValue(True)
 
-        n_coils_selected = len(selected_coils)
-        n_coils = state.get("n_coils", 1)
-        self.OnSetCoilCount(n_coils)
-
         # Update labels
         self.config_txt.SetLabel(
             f"{os.path.basename(self.coil_registrations.get('default_coil', {}).get('path', 'None'))}"
         )
+        
+        n_coils_selected = len(selected_coils)
         self.sel_sizer.GetStaticBox().SetLabel(
             f"TMS coil selection ({n_coils_selected} out of {n_coils})"
         )
@@ -1194,10 +1163,6 @@ def OnSelectCoil(self, event=None, name=None, select=False):
         navigation = self.navigation
 
         if select or (event is not None and event.GetSelection()):  # If coil is selected
-            # Press the coil button here in case selection was done via code without pressing button
-            coil_btn = self.coil_btns[name][0]
-            coil_btn.SetValue(True)
-
             coil_registration = self.coil_registrations[name]
 
             # Check that the index of the chosen coil does not conflict with other selected coils
@@ -1231,6 +1196,9 @@ def OnSelectCoil(self, event=None, name=None, select=False):
                 )
                 event.GetEventObject().SetValue(False)  # Unpress the button
                 return
+            
+            # Press the coil button here in case selection was done via code without pressing button
+            self.coil_btns[name][0].SetValue(True)
 
         # Select/Unselect coil
         Publisher.sendMessage("Select coil", coil_name=name, coil_registration=coil_registration)
@@ -1258,36 +1226,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
             for btn, *junk in self.coil_btns.values():
                 btn.Enable(True)
 
-    def OnChoiceObjID(self, event, name):
-        obj_id = 0 if event.GetSelection() == 0 else event.GetSelection() + 1
-        self.coil_registrations[name]["obj_id"] = obj_id
-        self.session.SetConfig("coil_registrations", self.coil_registrations)
-
-        # Unselect the coil, because the new id may cause conflicts
-        self.coil_btns[name][0].SetValue(False)
-        self.OnSelectCoil(name=name, select=False)
-
-        event.GetEventObject().Destroy()  # Delete the obj_id combobox
-
     def OnRightClickCoil(self, event, name):
-        def SetObjID(event, name):
-            # Largest valid obj_id with the currently used Tracker (ie. coord_raw.shape[0])
-            max_obj_id = self.tracker.GetTrackerCoordinates(ref_mode_id=0)[2].shape[0]
-
-            choice_obj_id = wx.ComboBox(
-                self,
-                -1,
-                f"{str(self.coil_registrations[name]['obj_id'])}",
-                size=wx.Size(90, 23),
-                choices=["0"] + [str(id) for id in range(2, max_obj_id)],
-                style=wx.CB_DROPDOWN | wx.CB_READONLY,
-            )
-            tooltip = "Choose the coil index in coord_raw with the current tracker. Choose 0 for static mode, 2 for dynamic mode and 3 onwards for multiple coils."
-            choice_obj_id.SetToolTip(tooltip)
-            choice_obj_id.Bind(
-                wx.EVT_COMBOBOX, (lambda event, name=name: self.OnChoiceObjID(event, name))
-            )
-
         def DeleteCoil(event, name):
             del self.coil_registrations[name]
 
@@ -1303,11 +1242,9 @@ def DeleteCoil(event, name):
 
         menu = wx.Menu()
         delete_coil = menu.Append(wx.ID_ANY, "Delete coil")
-        set_obj_id = menu.Append(wx.ID_ANY, "Set coil index")
         save_coil = menu.Append(wx.ID_ANY, "Save coil to OBR file")
 
         self.Bind(wx.EVT_MENU, (lambda event, name=name: DeleteCoil(event, name)), delete_coil)
-        self.Bind(wx.EVT_MENU, (lambda event, name=name: SetObjID(event, name)), set_obj_id)
         self.Bind(
             wx.EVT_MENU,
             (lambda event, name=name: self.OnSaveCoilToOBR(event, coil_name=name)),

From 9ac50ee71bf85a30fa363481b84ff223072eae37 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sat, 31 Aug 2024 13:39:37 +0300
Subject: [PATCH 33/44] Add getter for robot coil name. Remove unused
 neuronavigation_api variables.

---
 invesalius/gui/dialogs.py           |  3 --
 invesalius/gui/preferences.py       | 53 +++++++++++------------------
 invesalius/gui/task_navigator.py    |  4 +--
 invesalius/navigation/navigation.py | 15 ++++----
 invesalius/navigation/robot.py      | 16 ++++++---
 5 files changed, 41 insertions(+), 50 deletions(-)

diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 2cc8edcf7..1f1e98aed 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -124,7 +124,6 @@
     from invesalius.navigation.navigation import Navigation
     from invesalius.navigation.robot import Robot
     from invesalius.navigation.tracker import Tracker
-    from invesalius.net.neuronavigation_api import NeuronavigationApi
     from invesalius.net.pedal_connection import PedalConnector
     from typings.wx.type_defs import ColourType  # type: ignore
 
@@ -3883,12 +3882,10 @@ def __init__(
         tracker: "Tracker",
         n_coils: "int",
         pedal_connector: "PedalConnector",
-        neuronavigation_api: "NeuronavigationApi",
     ):
         self.tracker = tracker
         self.n_coils = n_coils
         self.pedal_connector = pedal_connector
-        self.neuronavigation_api = neuronavigation_api
 
         self.tracker_id = tracker.GetTrackerId()
         self.show_sensor_options: bool = self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index dd48363d7..2fee720ef 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -60,9 +60,7 @@ def __init__(
 
             self.navigation_tab = NavigationTab(self.book, navigation)
             self.tracker_tab = TrackerTab(self.book, tracker, robot)
-            self.object_tab = ObjectTab(
-                self.book, navigation, tracker, pedal_connector, neuronavigation_api
-            )
+            self.object_tab = ObjectTab(self.book, navigation, tracker, pedal_connector)
 
             self.book.AddPage(self.navigation_tab, _("Navigation"))
             self.book.AddPage(self.tracker_tab, _("Tracker"))
@@ -861,7 +859,7 @@ def LoadConfig(self):
 
 
 class ObjectTab(wx.Panel):
-    def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation_api):
+    def __init__(self, parent, navigation, tracker, pedal_connector):
         wx.Panel.__init__(self, parent)
 
         self.session = ses.Session()
@@ -870,7 +868,6 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
 
         self.tracker = tracker
         self.pedal_connector = pedal_connector
-        self.neuronavigation_api = neuronavigation_api
         self.navigation = navigation
         self.robot = Robot()
         self.coil_registrations = {}
@@ -1007,7 +1004,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
 
         self.not_connected_txt = None
         self.choice_robot_coil = None
-        if self.robot.IsConnected():
+        if not self.robot.IsConnected():
             self.not_connected_txt = wx.StaticText(self, -1, "Robot is not connected")
             inner_robot_sizer.Add(
                 self.not_connected_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
@@ -1017,7 +1014,7 @@ def __init__(self, parent, navigation, tracker, pedal_connector, neuronavigation
             self.choice_robot_coil = choice_robot_coil = wx.ComboBox(
                 self,
                 -1,
-                f"{self.robot.coil_name or ''}",
+                f"{self.robot.GetCoilName() or ''}",
                 size=wx.Size(90, 23),
                 choices=list(
                     self.navigation.coil_registrations
@@ -1074,7 +1071,7 @@ def AddCoilButton(self, coil_name, show_button=True):
             coil_btn.Bind(
                 wx.EVT_RIGHT_DOWN, lambda event, name=coil_name: self.OnRightClickCoil(event, name)
             )
-            coil_btn.Show(show_button) 
+            coil_btn.Show(show_button)
             self.coil_btns[coil_name] = (coil_btn, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5)
 
             self.inner_sel_sizer.Add(coil_btn, 1, wx.EXPAND, 5)
@@ -1093,17 +1090,16 @@ def ShowMulticoilGUI(self, show_multicoil):
 
         self.robot_sizer.GetStaticBox().Show(show_multicoil)
         self.robot_sizer.ShowItems(show_multicoil)
-        
-        self.Layout()
 
+        self.Layout()
 
     def OnSetCoilCount(self, n_coils):
-        multicoil_mode = n_coils > 1 
+        multicoil_mode = n_coils > 1
 
         if multicoil_mode:
             # Update multicoil GUI elements
             self.sel_sizer.GetStaticBox().SetLabel(f"TMS coil selection (0 out of {n_coils})")
-            
+
             # Reset (enable and unpress) all coil-buttons
             for btn, *junk in self.coil_btns.values():
                 btn.Enable()
@@ -1131,7 +1127,7 @@ def LoadConfig(self):
         self.config_txt.SetLabel(
             f"{os.path.basename(self.coil_registrations.get('default_coil', {}).get('path', 'None'))}"
         )
-        
+
         n_coils_selected = len(selected_coils)
         self.sel_sizer.GetStaticBox().SetLabel(
             f"TMS coil selection ({n_coils_selected} out of {n_coils})"
@@ -1141,12 +1137,10 @@ def LoadConfig(self):
             self.CoilSelectionDone()
 
     def CoilSelectionDone(self):
-        if self.navigation.n_coils == 1: # Tell the robot the coil name
+        if self.navigation.n_coils == 1:  # Tell the robot the coil name
             self.robot.SetCoilName(next(iter(self.navigation.coil_registrations)))
 
-        Publisher.sendMessage(
-            "Coil selection done", done=True
-        )
+        Publisher.sendMessage("Coil selection done", done=True)
         Publisher.sendMessage("Update status text in GUI", label=_("Ready"))
 
         # Allow only n_coils buttons to be pressed, so disable unpressed coil-buttons
@@ -1196,7 +1190,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
                 )
                 event.GetEventObject().SetValue(False)  # Unpress the button
                 return
-            
+
             # Press the coil button here in case selection was done via code without pressing button
             self.coil_btns[name][0].SetValue(True)
 
@@ -1217,7 +1211,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
         # Update robot coil combobox
         if self.choice_robot_coil is not None:
             self.choice_robot_coil.Set(list(navigation.coil_registrations))
-            self.choice_robot_coil.SetStringSelection(self.robot.coil_name or "")
+            self.choice_robot_coil.SetStringSelection(self.robot.GetCoilName() or "")
 
         if n_coils_selected == n_coils:
             self.CoilSelectionDone()
@@ -1261,7 +1255,6 @@ def OnCreateNewCoil(self, event=None):
                 self.tracker,
                 self.navigation.n_coils,
                 self.pedal_connector,
-                self.neuronavigation_api,
             )
             try:
                 if dialog.ShowModal() == wx.ID_OK:
@@ -1283,12 +1276,10 @@ def OnCreateNewCoil(self, event=None):
                             coil_name = (
                                 dialog.GetValue().strip()
                             )  # Update coil_name with user input
+                            dialog.Destroy()
                         else:
+                            dialog.Destroy()
                             return  # Cancel the operation if the user closes the dialog or cancels
-                        dialog.Destroy()
-
-                    # LUKATODO: update coil mesh elsewhere
-                    # self.neuronavigation_api.update_coil_mesh(polydata)
 
                     if np.isfinite(obj_fiducials).all() and np.isfinite(obj_orients).all():
                         coil_registration = {
@@ -1308,11 +1299,11 @@ def OnCreateNewCoil(self, event=None):
                             coil_btn.SetValue(False)
                             self.OnSelectCoil(name=coil_name, select=False)
 
-                    if self.navigation.n_coils == 1:
-                        # Select the coil that was created for navigation
-                        self.OnSelectCoil(name="default_coil", select=True)
-                        # Hide the coil-button
-                        coil_btn.Show(False)
+                        if self.navigation.n_coils == 1:
+                            # Select the coil that was created for navigation
+                            self.OnSelectCoil(name=coil_name, select=True)
+                            # Hide the coil-button
+                            coil_btn.Show(False)
 
                     self.Layout()
 
@@ -1370,10 +1361,6 @@ def OnLoadCoilFromOBR(self, event=None):
                 if not polydata:
                     coil_path = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
 
-                # LUKATODO: what is neuronavigation_api.update_coil_mesh ?
-                # if polydata:
-                #    self.neuronavigation_api.update_coil_mesh(polydata)
-
                 if np.isfinite(obj_fiducials).all() and np.isfinite(obj_orients).all():
                     coil_registration = {
                         "fiducials": obj_fiducials.tolist(),
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index d47d29eb8..8a4af02b9 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1691,13 +1691,13 @@ def UpdateRobotButtons(self):
         #   - Target is set
         #   - Target mode is on
         #   - Robot is connected
-        #   - The name of the coil attached to robot is specified
+        #   - The name of the coil attached to robot is being tracked
         track_target_button_enabled = (
             self.nav_status
             and self.target_selected
             and self.target_mode
             and self.robot.IsConnected()
-            and self.robot.coil_name in self.navigation.coil_registrations
+            and self.robot.GetCoilName() in self.navigation.coil_registrations
         )
         self.EnableRobotTrackTargetButton(enabled=track_target_button_enabled)
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index d2de3e01a..de82f0f95 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -47,6 +47,7 @@
 from invesalius.net.pedal_connection import PedalConnector
 from invesalius.pubsub import pub as Publisher
 from invesalius.utils import Singleton
+import invesalius.data.polydata_utils as pu
 
 
 class NavigationHub(metaclass=Singleton):
@@ -376,9 +377,7 @@ def LoadConfig(self):
                     if coil_name in saved_coil_registrations
                 }
                 if self.coil_registrations:
-                    self.main_coil = self.main_coil or next(
-                        iter(self.coil_registrations)
-                    )
+                    self.main_coil = self.main_coil or next(iter(self.coil_registrations))
 
             # Try to load stylus orientation data
             if "r_stylus" in state:
@@ -432,6 +431,10 @@ def SetMainCoil(self, main_coil):
         self.main_coil = main_coil
         self.SaveConfig("main_coil", main_coil)
 
+        # Send the polydata of the main coil to the connection
+        polydata = pu.LoadPolydata(self.coil_registrations[main_coil]["path"])
+        self.neuronavigation_api.update_coil_mesh(polydata)
+
     def SetReferenceMode(self, value):
         self.ref_mode_id = value
 
@@ -566,14 +569,12 @@ def StartNavigation(self, tracker, icp):
 
             coreg_data = [self.m_change, self.r_stylus]
 
-            # LUKATODO: where does robot get actual data?
-
             robot = Robot()
-            if robot.coil_name in self.coil_registrations:
+            if robot.GetCoilName() in self.coil_registrations:
                 # Tell robot at which index (obj_id) to find its coil in
                 Publisher.sendMessage(
                     "Neuronavigation to Robot: Set coil index",
-                    data=self.coil_registrations[robot.coil_name]["obj_id"],
+                    data=self.coil_registrations[robot.GetCoilName()]["obj_id"],
                 )
 
             queues = [
diff --git a/invesalius/navigation/robot.py b/invesalius/navigation/robot.py
index cc3b87302..c1c17a59d 100644
--- a/invesalius/navigation/robot.py
+++ b/invesalius/navigation/robot.py
@@ -86,7 +86,10 @@ def SaveConfig(self, key=None, value=None):
         session = ses.Session()
         if key is None or value is None:
             # Save the whole state
-            state = {"robot_ip": self.robot_ip, "tracker_to_robot": self.matrix_tracker_to_robot.tolist()}
+            state = {
+                "robot_ip": self.robot_ip,
+                "tracker_to_robot": self.matrix_tracker_to_robot.tolist(),
+            }
             if self.coil_name is not None:
                 state["robot_coil"] = self.coil_name
         else:
@@ -98,16 +101,16 @@ def SaveConfig(self, key=None, value=None):
     def LoadConfig(self):
         session = ses.Session()
         state = session.GetConfig("robot", {})
-        
+
         self.coil_name = state.get("robot_coil", None)
-        
+
         self.robot_ip = state.get("robot_ip", None)
 
         self.matrix_tracker_to_robot = state.get("tracker_to_robot", None)
         if self.matrix_tracker_to_robot is not None:
             self.matrix_tracker_to_robot = np.array(self.matrix_tracker_to_robot)
 
-        success = (self.robot_ip is not None and self.matrix_tracker_to_robot is not None)
+        success = self.robot_ip is not None and self.matrix_tracker_to_robot is not None
         return success
 
     def OnRobotConnectionStatus(self, data):
@@ -152,7 +155,7 @@ def AbortRobotConfiguration(self):
     def IsConnected(self):
         return self.is_robot_connected
 
-    def IsReady(self): # LUKATODO: use this check before enabling robot for navigation...
+    def IsReady(self):  # LUKATODO: use this check before enabling robot for navigation...
         self.IsConnected() and (self.coil_name in self.navigation.coil_registrations)
 
     def SetRobotIP(self, data):
@@ -170,6 +173,9 @@ def InitializeRobot(self):
         )
         print("Robot initialized")
 
+    def GetCoilName(self):
+        return self.coil_name
+
     def SetCoilName(self, name):
         self.coil_name = name
         self.SaveConfig("robot_coil", name)

From 0b49e178131c24ac682b3e2ccfd108f5913e1003 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Sun, 1 Sep 2024 22:00:53 +0300
Subject: [PATCH 34/44] Show/hide robot coil combobox when robot is
 connected/disconnected. RUFF format

---
 invesalius/gui/preferences.py       | 76 +++++++++++++++++------------
 invesalius/navigation/navigation.py |  4 +-
 2 files changed, 46 insertions(+), 34 deletions(-)

diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 2fee720ef..804434cf6 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1002,38 +1002,34 @@ def __init__(self, parent, navigation, tracker, pedal_connector):
         )
         self.inner_robot_sizer = inner_robot_sizer = wx.FlexGridSizer(2, 1, 1)
 
-        self.not_connected_txt = None
-        self.choice_robot_coil = None
-        if not self.robot.IsConnected():
-            self.not_connected_txt = wx.StaticText(self, -1, "Robot is not connected")
-            inner_robot_sizer.Add(
-                self.not_connected_txt, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5
-            )
-        else:
-            choice_robot_coil_lbl = wx.StaticText(self, -1, _("Coil attached to robot: "))
-            self.choice_robot_coil = choice_robot_coil = wx.ComboBox(
-                self,
-                -1,
-                f"{self.robot.GetCoilName() or ''}",
-                size=wx.Size(90, 23),
-                choices=list(
-                    self.navigation.coil_registrations
-                ),  # List of coils selected for navigation
-                style=wx.CB_DROPDOWN | wx.CB_READONLY,
-            )
+        self.robot_lbl = wx.StaticText(self, -1, _("Robot is connected. Coil attached to robot: "))
+        self.choice_robot_coil = choice_robot_coil = wx.ComboBox(
+            self,
+            -1,
+            f"{self.robot.GetCoilName() or ''}",
+            size=wx.Size(90, 23),
+            choices=list(
+                self.navigation.coil_registrations
+            ),  # List of coils selected for navigation
+            style=wx.CB_DROPDOWN | wx.CB_READONLY,
+        )
 
-            choice_robot_coil.SetToolTip(
-                "Specify which coil is attached to the robot",
-            )
+        choice_robot_coil.SetToolTip(
+            "Specify which coil is attached to the robot",
+        )
 
-            choice_robot_coil.Bind(wx.EVT_COMBOBOX, (lambda event: self.OnChoiceRobotCoil(event)))
+        choice_robot_coil.Bind(wx.EVT_COMBOBOX, self.OnChoiceRobotCoil)
 
-            inner_robot_sizer.AddMany(
-                [
-                    (choice_robot_coil_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                    (choice_robot_coil, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
-                ]
-            )
+        if not self.robot.IsConnected():
+            self.robot_lbl.SetLabel("Robot is not connected")
+            choice_robot_coil.Show(False)  # Hide the combobox
+
+        inner_robot_sizer.AddMany(
+            [
+                (self.robot_lbl, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+                (choice_robot_coil, 1, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, 5),
+            ]
+        )
 
         robot_sizer.Add(inner_robot_sizer, 0, wx.ALL | wx.EXPAND, 10)
 
@@ -1052,6 +1048,22 @@ def __init__(self, parent, navigation, tracker, pedal_connector):
         self.LoadConfig()
         self.Layout()
 
+    def __bind_events(self):
+        Publisher.subscribe(self.OnSetCoilCount, "Reset coil selection")
+        Publisher.subscribe(
+            self.OnRobotConnectionStatus, "Robot to Neuronavigation: Robot connection status"
+        )
+
+    def OnRobotConnectionStatus(self, data):
+        if data is None:
+            return
+
+        self.choice_robot_coil.Show(data)
+        if data:
+            self.robot_lbl.SetLabel("Robot is connected. Coil attached to robot: ")
+        else:
+            self.robot_lbl.SetLabel("Robot is not connected.")
+
     def OnChoiceRobotCoil(self, event):
         robot_coil_name = event.GetEventObject().GetStringSelection()
         self.robot.SetCoilName(robot_coil_name)
@@ -1076,9 +1088,6 @@ def AddCoilButton(self, coil_name, show_button=True):
 
             self.inner_sel_sizer.Add(coil_btn, 1, wx.EXPAND, 5)
 
-    def __bind_events(self):
-        Publisher.subscribe(self.OnSetCoilCount, "Reset coil selection")
-
     def ShowMulticoilGUI(self, show_multicoil):
         # Show/hide singlecoil configuration text
         self.config_txt.Show(not show_multicoil)
@@ -1091,6 +1100,9 @@ def ShowMulticoilGUI(self, show_multicoil):
         self.robot_sizer.GetStaticBox().Show(show_multicoil)
         self.robot_sizer.ShowItems(show_multicoil)
 
+        # Show the robot coil combobox only if the robot is connected
+        self.choice_robot_coil.Show(show_multicoil and self.robot.IsConnected())
+
         self.Layout()
 
     def OnSetCoilCount(self, n_coils):
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index de82f0f95..0c18d59ef 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -28,6 +28,7 @@
 import invesalius.data.bases as db
 import invesalius.data.coregistration as dcr
 import invesalius.data.e_field as e_field
+import invesalius.data.polydata_utils as pu
 import invesalius.data.serial_port_connection as spc
 import invesalius.data.slice_ as sl
 import invesalius.data.tractography as dti
@@ -47,7 +48,6 @@
 from invesalius.net.pedal_connection import PedalConnector
 from invesalius.pubsub import pub as Publisher
 from invesalius.utils import Singleton
-import invesalius.data.polydata_utils as pu
 
 
 class NavigationHub(metaclass=Singleton):
@@ -571,7 +571,7 @@ def StartNavigation(self, tracker, icp):
 
             robot = Robot()
             if robot.GetCoilName() in self.coil_registrations:
-                # Tell robot at which index (obj_id) to find its coil in
+                # Tell robot at which index (obj_id) to find its coil in (relevant when there are multiple coils)
                 Publisher.sendMessage(
                     "Neuronavigation to Robot: Set coil index",
                     data=self.coil_registrations[robot.GetCoilName()]["obj_id"],

From 238073e34347594f37288a9bdfed80853674ba06 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 5 Sep 2024 14:01:44 +0300
Subject: [PATCH 35/44] Minor fix

---
 invesalius/gui/preferences.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 804434cf6..3941d4776 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1643,7 +1643,7 @@ def LoadConfig(self):
         session = ses.Session()
         self.n_coils = session.GetConfig("navigation", {}).get("n_coils", 1)
 
-        state = session.GetConfig("robot")
+        state = session.GetConfig("robot", {})
 
         self.robot_ip = state.get("robot_ip", None)
         self.matrix_tracker_to_robot = state.get("tracker_to_robot", None)

From 733dbe5dc80742e9fe053025170edfd26093a68c Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 5 Sep 2024 14:19:44 +0300
Subject: [PATCH 36/44] Minor change to improve code readability

---
 invesalius/gui/task_navigator.py    | 2 +-
 invesalius/navigation/navigation.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index 8a4af02b9..f7cb633cc 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1697,7 +1697,7 @@ def UpdateRobotButtons(self):
             and self.target_selected
             and self.target_mode
             and self.robot.IsConnected()
-            and self.robot.GetCoilName() in self.navigation.coil_registrations
+            and self.robot.IsReady()
         )
         self.EnableRobotTrackTargetButton(enabled=track_target_button_enabled)
 
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 0c18d59ef..f0e77a826 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -570,7 +570,7 @@ def StartNavigation(self, tracker, icp):
             coreg_data = [self.m_change, self.r_stylus]
 
             robot = Robot()
-            if robot.GetCoilName() in self.coil_registrations:
+            if robot.IsReady():
                 # Tell robot at which index (obj_id) to find its coil in (relevant when there are multiple coils)
                 Publisher.sendMessage(
                     "Neuronavigation to Robot: Set coil index",

From 64dcc188ab53dd6cd444248a666d86009ed3a047 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Thu, 5 Sep 2024 14:50:55 +0300
Subject: [PATCH 37/44] Hide name box during coil registration if in single
 coil mode

---
 invesalius/gui/dialogs.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 1f1e98aed..e8507a416 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -4032,6 +4032,8 @@ def _init_gui(self) -> None:
             # Hide obj_id combobox
             choice_obj_id.Enable(False)
             choice_obj_id.Show(False)
+            name_sizer.Show(False)
+            name_sizer.ShowItems(False)
 
         self.SetSizer(main_sizer)
         main_sizer.Fit(self)

From 2cf113388334a1b21722f88d09e9b45b85c1444e Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Fri, 6 Sep 2024 18:33:11 +0300
Subject: [PATCH 38/44] Fix stylus orientation. The issue was that the vtk
 y-axis is flipped.

---
 invesalius/data/coregistration.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 7565adf29..099ec4097 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -193,8 +193,12 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     # Rotate from trk system where stylus points in x-axis to vtk-system where stylus points in y-axis
     R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
 
+    # Reflect/flip the orientation in the vtk y-axis (ie. over vtk xz-plane) at the end
+    y_flip = np.eye(3)
+    y_flip[1] = -y_flip[1]
+
     # rotate m_probe_ref from tracker to image space
-    r_img = r_stylus @ R @ m_probe_ref[:3, :3] @ np.linalg.inv(R)
+    r_img = y_flip @ r_stylus @ R @ m_probe_ref[:3, :3] @ np.linalg.inv(R)
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles

From e2220566ef2b1ebddf590ee6c4f8283c74f1e350 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Mon, 9 Sep 2024 15:27:31 +0300
Subject: [PATCH 39/44] Before this commit, the stylus was correctly oriented
 with MRI heads. Now it is correctly oriented with NIFTI heads. TODO: unify
 the orientation of MRI and NIFTI heads in vtk?

---
 invesalius/data/coregistration.py   | 7 ++-----
 invesalius/navigation/navigation.py | 8 ++++++--
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/invesalius/data/coregistration.py b/invesalius/data/coregistration.py
index 099ec4097..f5720b2b5 100644
--- a/invesalius/data/coregistration.py
+++ b/invesalius/data/coregistration.py
@@ -174,6 +174,7 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     if r_stylus is None:
         # utils.debug("STYLUS ORIENTATION NOT DEFINED!")
         r_stylus = np.eye(3)
+        r_stylus[0] = -r_stylus[0]  # Flip over vtk x-axis
 
     m_probe = compute_marker_transformation(coord_raw, 0)
 
@@ -193,12 +194,8 @@ def corregistrate_probe(m_change, r_stylus, coord_raw, ref_mode_id, icp=[None, N
     # Rotate from trk system where stylus points in x-axis to vtk-system where stylus points in y-axis
     R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
 
-    # Reflect/flip the orientation in the vtk y-axis (ie. over vtk xz-plane) at the end
-    y_flip = np.eye(3)
-    y_flip[1] = -y_flip[1]
-
     # rotate m_probe_ref from tracker to image space
-    r_img = y_flip @ r_stylus @ R @ m_probe_ref[:3, :3] @ np.linalg.inv(R)
+    r_img = r_stylus @ R @ m_probe_ref[:3, :3] @ np.linalg.inv(R)
     m_img[:3, :3] = r_img[:3, :3]
 
     # compute rotation angles
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index f0e77a826..1aefce10e 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -494,8 +494,12 @@ def SetStylusOrientation(self, coord_raw):
             # to vtk-system where stylus points in y-axis
             R = tr.euler_matrix(*np.radians([0, 0, -90]), axes="rxyz")[:3, :3]
 
-            # Rotation from tracker to VTK coordinate system
-            self.r_stylus = up_vtk @ np.linalg.inv(R @ up_trk @ np.linalg.inv(R))
+            # Reflect/flip the orientation in the vtk x-axis
+            x_flip = np.eye(3)
+            x_flip[0] = -x_flip[0]
+
+            # Rotation from tracker to VTK coordinate system (apply x_flip to orient stylus with NIFTI file)
+            self.r_stylus = x_flip @ up_vtk @ np.linalg.inv(R @ up_trk @ np.linalg.inv(R))
             # Save r_stylus to config file
             self.SaveConfig("r_stylus", self.r_stylus.tolist())
             return True

From b15cb299abcebb74bfcd034a515dd254a5d48d39 Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Tue, 10 Sep 2024 12:07:03 +0300
Subject: [PATCH 40/44] Add check to prevent delayed rendering of coil/probe
 when navigating. Remove obj_id=0 choice in multicoil mode. Automatically
 select a coil for navigation when it's created. Other fixes related to edge
 cases in coil creation/selection in multicoil mode

---
 .../data/visualization/coil_visualizer.py     |  3 +-
 .../data/visualization/probe_visualizer.py    |  7 +++-
 invesalius/gui/dialogs.py                     | 32 ++++++++++---------
 invesalius/gui/preferences.py                 | 21 ++++++++----
 4 files changed, 40 insertions(+), 23 deletions(-)

diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 658a6da3b..0aa7b1d1c 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -271,8 +271,9 @@ def RemoveCoil(self, coil_name=None):
                 self.renderer.RemoveActor(coil["center_actor"])
             self.coils = {}
 
-        self.interactor.Render()
         # self.vector_field_assembly.SetVisibility(0)
+        if not self.is_navigating:
+            self.interactor.Render()
 
     def ResetCoilVisualizer(self, n_coils):
         self.RemoveCoil()  # Remove all coils
diff --git a/invesalius/data/visualization/probe_visualizer.py b/invesalius/data/visualization/probe_visualizer.py
index 3627bf7b3..0c6764e8d 100644
--- a/invesalius/data/visualization/probe_visualizer.py
+++ b/invesalius/data/visualization/probe_visualizer.py
@@ -27,13 +27,18 @@ def __init__(self, renderer, interactor):
     def __bind_events(self):
         Publisher.subscribe(self.ShowProbe, "Show probe in viewer volume")
         Publisher.subscribe(self.UpdateProbePose, "Update probe pose")
+        Publisher.subscribe(self.OnNavigationStatus, "Navigation status")
+
+    def OnNavigationStatus(self, nav_status, vis_status):
+        self.is_navigating = nav_status
 
     def ShowProbe(self, state):
         self.show_probe = state
 
         if self.probe_actor:
             self.probe_actor.SetVisibility(self.show_probe)
-            self.interactor.Render()
+            if not self.is_navigating:
+                self.interactor.Render()
 
     def AddProbeActor(self, probe_path):
         vtk_colors = vtk.vtkNamedColors()
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index e8507a416..900657b98 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -3888,8 +3888,10 @@ def __init__(
         self.pedal_connector = pedal_connector
 
         self.tracker_id = tracker.GetTrackerId()
-        self.show_sensor_options: bool = self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
         self.obj_id = 2  # the index of the object in coord_raw
+        self.show_sensor_options: bool = (
+            self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS and self.obj_id == 0
+        )
         self.coil_path = None
         self.polydata = None
 
@@ -3927,17 +3929,22 @@ def _init_gui(self) -> None:
         tooltip = _(
             "Choose the coil index in coord_raw. Choose 0 for static mode, 2 for dynamic mode and 3 onwards for multiple coils."
         )
+
+        # Static mode obj_id=0 (case where stylus is attached to coil) is only feasible for single coil-mode, so hide it in multicoil mode
+        choices = ["0"] if self.n_coils == 1 else []
+        choices += [str(i) for i in range(2, max_obj_id)]
+
         choice_obj_id = wx.ComboBox(
             self,
             -1,
             "",
             size=wx.Size(90, 23),
-            choices=["0"] + [str(i) for i in range(2, max_obj_id)],
+            choices=choices,
             style=wx.CB_DROPDOWN | wx.CB_READONLY,
         )
         choice_obj_id.SetToolTip(tooltip)
         choice_obj_id.Bind(wx.EVT_COMBOBOX, self.OnChooseObjID)
-        choice_obj_id.SetSelection(1)
+        choice_obj_id.SetStringSelection(str(self.obj_id))
         choice_obj_id.Enable(True)
 
         if self.tracker_id == const.PATRIOT or self.tracker_id == const.ISOTRAKII:
@@ -4259,21 +4266,16 @@ def OnReset(self, evt: wx.CommandEvent) -> None:
         self.ResetObjectFiducials()
 
     def OnChooseObjID(self, evt: wx.CommandEvent) -> None:
-        # When ref mode is changed the tracker coordinates are set to nan
-        # This is for Polhemus FASTRAK wrapper, where the sensor attached to the object can be the stylus (Static
-        # reference - Selection 0 - index 0 for coordinates) or can be a 3rd sensor (Dynamic reference - Selection 1 -
-        # index 2 for coordinates)
+        self.obj_id = int(evt.GetEventObject().GetStringSelection())
 
-        if evt.GetSelection() == 0:
-            self.obj_id = 0
-            self.choice_sensor.Show(False)
-        else:
-            self.obj_id = evt.GetSelection() + 1
-            self.choice_sensor.Show(self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS)
+        # choice_sensor is only shown for relevant trackers like Polhemus FASTRAK
+        # If obj_id=0, (ie. the stylus is attached to the coil), the sensor is not used, so hide this
+        self.choice_sensor.Show(
+            self.obj_id == 0 and self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
+        )
 
+        # When obj_id is changed the object fiducials are reset
         self.ResetObjectFiducials()
-
-        # Used to update choice sensor controls
         self.Layout()
 
     def OnChoiceFTSensor(self, evt: wx.CommandEvent) -> None:
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 3941d4776..70aa4f3c5 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1189,7 +1189,9 @@ def OnSelectCoil(self, event=None, name=None, select=False):
                     ),
                     _("InVesalius 3"),
                 )
-                event.GetEventObject().SetValue(False)  # Unpress the coil-button
+                self.coil_btns[name][0].SetValue(
+                    False
+                )  # Unpress the coil-button since its selection just failed
                 return
 
             # Check that the tracker used to configure the coil matches the currently used tracker
@@ -1200,7 +1202,7 @@ def OnSelectCoil(self, event=None, name=None, select=False):
                     ),
                     _("InVesalius 3"),
                 )
-                event.GetEventObject().SetValue(False)  # Unpress the button
+                self.coil_btns[name][0].SetValue(False)  # Unpress the button
                 return
 
             # Press the coil button here in case selection was done via code without pressing button
@@ -1234,6 +1236,8 @@ def OnSelectCoil(self, event=None, name=None, select=False):
 
     def OnRightClickCoil(self, event, name):
         def DeleteCoil(event, name):
+            # Unselect the coil first
+            self.OnSelectCoil(name, select=False)
             del self.coil_registrations[name]
 
             # Remove the coil-button
@@ -1311,11 +1315,16 @@ def OnCreateNewCoil(self, event=None):
                             coil_btn.SetValue(False)
                             self.OnSelectCoil(name=coil_name, select=False)
 
-                        if self.navigation.n_coils == 1:
-                            # Select the coil that was created for navigation
+                        # Select the coil that was just created (if all coils have not been selected)
+                        if len(self.navigation.coil_registrations) < self.navigation.n_coils:
                             self.OnSelectCoil(name=coil_name, select=True)
-                            # Hide the coil-button
-                            coil_btn.Show(False)
+                        else:
+                            coil_btn.Enable(
+                                False
+                            )  # All coils have been selected so disable the new button
+
+                        # Show button only in multicoil mode
+                        coil_btn.Show(self.navigation.n_coils > 1)
 
                     self.Layout()
 

From 43160da5e6e31cef9c651239bc21f81a3e308caa Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Wed, 11 Sep 2024 10:00:37 +0300
Subject: [PATCH 41/44] Show coil center/target even when coil is hidden.
 Handle exceptions when loading state file. Update environment.yml. Minor
 refactors ie. naming changes.

---
 environment.yml                                 |  2 +-
 invesalius/data/viewer_volume.py                |  3 +--
 .../data/visualization/coil_visualizer.py       | 17 ++++++++---------
 .../data/visualization/probe_visualizer.py      |  5 ++---
 invesalius/gui/preferences.py                   |  2 +-
 invesalius/gui/task_navigator.py                |  7 +++++--
 invesalius/navigation/image.py                  |  7 ++++++-
 invesalius/navigation/iterativeclosestpoint.py  |  5 ++++-
 invesalius/navigation/navigation.py             |  2 +-
 invesalius/navigation/tracker.py                |  5 ++++-
 10 files changed, 33 insertions(+), 22 deletions(-)

diff --git a/environment.yml b/environment.yml
index af1f2b6c6..0b7a6b404 100644
--- a/environment.yml
+++ b/environment.yml
@@ -29,7 +29,7 @@ dependencies:
     - pyclaron
     - polhemusFT
     - polhemus
-    - pypolaris==0.0.7
+    - pypolaris==0.0.8
     - scikit-image==0.24.0
     - scikit-learn==1.5.0
     - torch==2.3.1
diff --git a/invesalius/data/viewer_volume.py b/invesalius/data/viewer_volume.py
index b085aaf4e..b3ef7cfb3 100644
--- a/invesalius/data/viewer_volume.py
+++ b/invesalius/data/viewer_volume.py
@@ -309,12 +309,11 @@ def __init__(self, parent):
         # An object to manage visualizing coils in the 3D viewer.
         self.coil_visualizer = CoilVisualizer(
             renderer=self.ren,
-            interactor=self.interactor,
             actor_factory=self.actor_factory,
             vector_field_visualizer=self.vector_field_visualizer,
         )
 
-        self.probe_visualizer = ProbeVisualizer(self.ren, self.interactor)
+        self.probe_visualizer = ProbeVisualizer(self.ren)
 
         self.seed_offset = const.SEED_OFFSET
         self.radius_list = vtkIdList()
diff --git a/invesalius/data/visualization/coil_visualizer.py b/invesalius/data/visualization/coil_visualizer.py
index 0aa7b1d1c..e1370120e 100644
--- a/invesalius/data/visualization/coil_visualizer.py
+++ b/invesalius/data/visualization/coil_visualizer.py
@@ -21,9 +21,8 @@ class CoilVisualizer:
     # Color for the marker for target when the coil at the target.
     COIL_AT_TARGET_COLOR = vtk.vtkNamedColors().GetColor3d("Green")
 
-    def __init__(self, renderer, interactor, actor_factory, vector_field_visualizer):
+    def __init__(self, renderer, actor_factory, vector_field_visualizer):
         self.renderer = renderer
-        self.interactor = interactor
         self.tracker = Tracker()
 
         # Keeps track of whether tracker fiducials have been set.
@@ -95,7 +94,7 @@ def UpdateVectorField(self):
 
         # If not navigating, render the scene.
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def SetCoilAtTarget(self, state):
         self.coil_at_target = state
@@ -118,14 +117,14 @@ def ShowCoil(self, state, coil_name=None):
         if coil_name is None:  # Show/hide all coils
             for coil in self.coils.values():
                 coil["actor"].SetVisibility(state)
-                coil["center_actor"].SetVisibility(state)
+                coil["center_actor"].SetVisibility(True)  # Always show the center donut actor
             if self.target_coil_actor is not None:  # LUKATODO: target mode...
-                self.target_coil_actor.SetVisibility(state)
+                self.target_coil_actor.SetVisibility(True)  # Keep target visible for now
         elif (coil := self.coils.get(coil_name, None)) is not None:
             # Just toggle the visibility when dealing with specific coils
             new_state = not coil["actor"].GetVisibility()
             coil["actor"].SetVisibility(new_state)
-            coil["center_actor"].SetVisibility(new_state)
+            coil["center_actor"].SetVisibility(True)  # Always show the center donut actor
 
             # If all coils are hidden/shown, update the color of Show-coil button
             coils_visible = [coil["actor"].GetVisibility() for coil in self.coils.values()]
@@ -137,7 +136,7 @@ def ShowCoil(self, state, coil_name=None):
         # self.vector_field_assembly.SetVisibility(state) # LUKATODO: Keep this hidden for now
 
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def AddTargetCoil(self, m_target):
         self.RemoveTargetCoil()
@@ -190,7 +189,7 @@ def AddTargetCoil(self, m_target):
         self.renderer.AddActor(self.target_coil_actor)
 
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def RemoveTargetCoil(self):
         if self.target_coil_actor is None:
@@ -273,7 +272,7 @@ def RemoveCoil(self, coil_name=None):
 
         # self.vector_field_assembly.SetVisibility(0)
         if not self.is_navigating:
-            self.interactor.Render()
+            Publisher.sendMessage("Render volume viewer")
 
     def ResetCoilVisualizer(self, n_coils):
         self.RemoveCoil()  # Remove all coils
diff --git a/invesalius/data/visualization/probe_visualizer.py b/invesalius/data/visualization/probe_visualizer.py
index 0c6764e8d..e721d1177 100644
--- a/invesalius/data/visualization/probe_visualizer.py
+++ b/invesalius/data/visualization/probe_visualizer.py
@@ -12,9 +12,8 @@ class ProbeVisualizer:
     A class for visualizing probe in the volume viewer.
     """
 
-    def __init__(self, renderer, interactor):
+    def __init__(self, renderer):
         self.renderer = renderer
-        self.interactor = interactor
 
         self.probe_actor = None
         self.probe_path = os.path.join(inv_paths.OBJ_DIR, "stylus.stl")
@@ -38,7 +37,7 @@ def ShowProbe(self, state):
         if self.probe_actor:
             self.probe_actor.SetVisibility(self.show_probe)
             if not self.is_navigating:
-                self.interactor.Render()
+                Publisher.sendMessage("Render volume viewer")
 
     def AddProbeActor(self, probe_path):
         vtk_colors = vtk.vtkNamedColors()
diff --git a/invesalius/gui/preferences.py b/invesalius/gui/preferences.py
index 70aa4f3c5..58e4c461a 100644
--- a/invesalius/gui/preferences.py
+++ b/invesalius/gui/preferences.py
@@ -1260,7 +1260,7 @@ def DeleteCoil(event, name):
             (lambda event, name=name: self.OnSaveCoilToOBR(event, coil_name=name)),
             save_coil,
         )
-        self.PopupMenu(menu, event.GetPosition())
+        self.PopupMenu(menu)
         menu.Destroy()
 
     def OnCreateNewCoil(self, event=None):
diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index f7cb633cc..d073c5f97 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1074,7 +1074,7 @@ def onRecord(self, evt):
         )
 
         if marker_visibilities[0] and marker_visibilities[1]:  # if probe and head are visible
-            if self.navigation.SetStylusOrientation(coord_raw) and not self.done:
+            if self.navigation.OnRecordStylusOrientation(coord_raw) and not self.done:
                 # if successfully created r_stylus in navigation for the first time: make the illustration green to show success
                 self.done = True
                 self.help.Destroy()  # show a colored (green) bitmap as opposed to grayscale
@@ -2135,7 +2135,10 @@ def __init__(self, parent, nav_hub):
         )
 
         # In the future, it would be better if the panel could initialize itself based on markers in MarkersControl
-        self.markers.LoadState()
+        try:
+            self.markers.LoadState()
+        except:
+            self.session.DeleteStateFile()  # Delete state file if it is erroneous
 
         # Add all lines into main sizer
         group_sizer = wx.BoxSizer(wx.VERTICAL)
diff --git a/invesalius/navigation/image.py b/invesalius/navigation/image.py
index b60693e69..bef95a675 100644
--- a/invesalius/navigation/image.py
+++ b/invesalius/navigation/image.py
@@ -128,9 +128,14 @@ def UpdateFiducialMarkers(self):
     def OnStateProject(self, state):
         if state:
             if self.load_from_state:
-                self.LoadState()
                 self.load_from_state = False
+                try:
+                    self.LoadState()
+                except:
+                    ses.Session.DeleteStateFile()
+                    self.LoadProject()  # Load project if failed to load from state
             else:
                 self.LoadProject()
+
         self.SaveState()
         self.UpdateFiducialMarkers()
diff --git a/invesalius/navigation/iterativeclosestpoint.py b/invesalius/navigation/iterativeclosestpoint.py
index bce7eb163..d695d83fb 100644
--- a/invesalius/navigation/iterativeclosestpoint.py
+++ b/invesalius/navigation/iterativeclosestpoint.py
@@ -32,7 +32,10 @@ def __init__(self):
         self.m_icp = None
         self.icp_fre = None
 
-        self.LoadState()
+        try:
+            self.LoadState()
+        except:
+            ses.Session().DeleteStateFile()
 
     def SaveState(self):
         m_icp = self.m_icp.tolist() if self.m_icp is not None else None
diff --git a/invesalius/navigation/navigation.py b/invesalius/navigation/navigation.py
index 1aefce10e..1895e99af 100644
--- a/invesalius/navigation/navigation.py
+++ b/invesalius/navigation/navigation.py
@@ -476,7 +476,7 @@ def EstimateTrackerToInVTransformationMatrix(self, tracker, image):
             self.all_fiducials[3:, :].T, self.all_fiducials[:3, :].T, shear=False, scale=False
         )
 
-    def SetStylusOrientation(self, coord_raw):
+    def OnRecordStylusOrientation(self, coord_raw):
         if self.m_change is not None:
             m_probe = dcr.compute_marker_transformation(coord_raw, 0)
 
diff --git a/invesalius/navigation/tracker.py b/invesalius/navigation/tracker.py
index 75ba6f047..a3a789403 100644
--- a/invesalius/navigation/tracker.py
+++ b/invesalius/navigation/tracker.py
@@ -51,7 +51,10 @@ def __init__(self):
 
         self.TrackerCoordinates = dco.TrackerCoordinates()
 
-        self.LoadState()
+        try:
+            self.LoadState()
+        except:
+            ses.Session().DeleteStateFile()
 
     def SaveState(self):
         tracker_id = self.tracker_id

From a9a5a9b8c89e3f613b4b3a48e8addc7cba20f11d Mon Sep 17 00:00:00 2001
From: Tolonen Luka <luka.tolonen@gmail.com>
Date: Wed, 11 Sep 2024 17:23:56 +0300
Subject: [PATCH 42/44] Remove incomplete robot check that causes bug with
 single robot

---
 invesalius/gui/task_navigator.py | 1 -
 invesalius/navigation/robot.py   | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/invesalius/gui/task_navigator.py b/invesalius/gui/task_navigator.py
index d073c5f97..a222616c6 100644
--- a/invesalius/gui/task_navigator.py
+++ b/invesalius/gui/task_navigator.py
@@ -1697,7 +1697,6 @@ def UpdateRobotButtons(self):
             and self.target_selected
             and self.target_mode
             and self.robot.IsConnected()
-            and self.robot.IsReady()
         )
         self.EnableRobotTrackTargetButton(enabled=track_target_button_enabled)
 
diff --git a/invesalius/navigation/robot.py b/invesalius/navigation/robot.py
index c1c17a59d..996e06a6a 100644
--- a/invesalius/navigation/robot.py
+++ b/invesalius/navigation/robot.py
@@ -156,7 +156,7 @@ def IsConnected(self):
         return self.is_robot_connected
 
     def IsReady(self):  # LUKATODO: use this check before enabling robot for navigation...
-        self.IsConnected() and (self.coil_name in self.navigation.coil_registrations)
+        return self.IsConnected() and (self.coil_name in self.navigation.coil_registrations)
 
     def SetRobotIP(self, data):
         if data is not None:
@@ -187,7 +187,7 @@ def SendTargetToRobot(self):
 
         navigation = self.navigation
         # XXX: These are needed for computing the target in tracker coordinate system. Ensure that they are set.
-        if navigation.m_change is None or navigation.obj_datas is not None:
+        if navigation.m_change is None or navigation.obj_datas is None:
             return False
 
         # Compute the target in tracker coordinate system.

From a5699ee29c777e791bfc9f0e1bb30becd9c4d3a9 Mon Sep 17 00:00:00 2001
From: Renan <renan_hiroshi@hotmail.com>
Date: Mon, 30 Sep 2024 20:32:33 +0300
Subject: [PATCH 43/44] FIX: tracker device polhemus

---
 invesalius/gui/dialogs.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 900657b98..f97a9c3d1 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -3890,7 +3890,7 @@ def __init__(
         self.tracker_id = tracker.GetTrackerId()
         self.obj_id = 2  # the index of the object in coord_raw
         self.show_sensor_options: bool = (
-            self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS and self.obj_id == 0
+            self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
         )
         self.coil_path = None
         self.polydata = None
@@ -4212,13 +4212,14 @@ def SetObjectFiducial(self, fiducial_index: int) -> None:
         # If coil or probe markers are not visible, show a warning and return early.
         probe_visible, head_visible, *coils_visible = marker_visibilities
 
-        if not probe_visible:
-            ShowNavigationTrackerWarning(0, "probe marker not visible")
-            return
+        if not self.show_sensor_options:
+            if not probe_visible:
+                ShowNavigationTrackerWarning(0, "probe marker not visible")
+                return
 
-        if not coils_visible[self.obj_id - 2]:
-            ShowNavigationTrackerWarning(0, "coil marker not visible")
-            return
+            if not coils_visible[self.obj_id - 2]:
+                ShowNavigationTrackerWarning(0, "coil marker not visible")
+                return
 
         # XXX: The condition below happens when setting the "fixed" coordinate in the object calibration.
         #      The case is not handled by GetTrackerCoordinates function, therefore redo some computation

From f30bd29e8dfa02cdbe7c53fc2dce89936d3acf0f Mon Sep 17 00:00:00 2001
From: Renan <renan_hiroshi@hotmail.com>
Date: Mon, 30 Sep 2024 20:32:46 +0300
Subject: [PATCH 44/44] Ruff

---
 invesalius/gui/dialogs.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index f97a9c3d1..59f218cf2 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -3889,9 +3889,7 @@ def __init__(
 
         self.tracker_id = tracker.GetTrackerId()
         self.obj_id = 2  # the index of the object in coord_raw
-        self.show_sensor_options: bool = (
-            self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
-        )
+        self.show_sensor_options: bool = self.tracker_id in const.TRACKERS_WITH_SENSOR_OPTIONS
         self.coil_path = None
         self.polydata = None