Clean comments and RUFF format

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):

invesalius/data/tracker_connection.py

@@ -428,7 +428,7 @@ 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))
 

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()

invesalius/data/visualization/coil_visualizer.py

@@ -110,13 +110,13 @@ 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():
@@ -127,7 +127,7 @@ 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()
@@ -177,7 +177,7 @@ 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)
@@ -288,4 +288,4 @@ 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)

invesalius/gui/default_viewers.py

@@ -161,7 +161,9 @@ 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()

invesalius/gui/dialogs.py

@@ -6867,7 +6867,9 @@ 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)
 

invesalius/gui/preferences.py

@@ -468,7 +468,7 @@ 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
@@ -494,7 +494,7 @@ 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
@@ -533,14 +533,13 @@ 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))
@@ -601,11 +600,9 @@ 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:
@@ -641,13 +638,13 @@ 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)
 
@@ -658,13 +655,12 @@ 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
@@ -706,7 +702,7 @@ 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
@@ -724,9 +720,7 @@ 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)
 
@@ -777,15 +771,17 @@ 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(
@@ -801,17 +797,20 @@ 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)
 
@@ -832,11 +831,8 @@ 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
@@ -870,7 +866,9 @@ 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,
                     )
@@ -888,7 +886,7 @@ 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():
@@ -925,7 +923,7 @@ 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"),
@@ -935,7 +933,7 @@ def OnSaveCoilToOBR(self, evt, coil_name):
         )
         if filename:
             hdr = (
-                coil_name 
+                coil_name
                 + "\t"
                 + utils.decode(coil_registration["path"], const.FS_ENCODE)
                 + "\t"
@@ -951,7 +949,6 @@ 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)
@@ -1152,7 +1149,7 @@ 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)

invesalius/gui/task_navigator.py

@@ -276,7 +276,7 @@ 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):
@@ -1112,7 +1112,13 @@ 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
 
@@ -1159,7 +1165,9 @@ 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")
 
@@ -1727,7 +1735,6 @@ 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)
@@ -1972,7 +1979,7 @@ 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)
@@ -2489,7 +2496,6 @@ 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: