From f428bc2671d928c5547c2b0d03e123e87294e039 Mon Sep 17 00:00:00 2001
From: Alex Liberzon <alexlib@users.noreply.github.com>
Date: Thu, 28 Mar 2024 23:14:36 +0200
Subject: [PATCH] added notebook to test calibration using Ron code

improved scipy_optimize to work also with 3D body and not only multiplane
---
 pyptv/calibration_gui.py     | 12 +++---
 pyptv/ptv.py                 | 11 ++++-
 pyptv/pyptv_gui.py           |  6 ++-
 pyptv/test_calibration.ipynb | 83 ++++++++++++++++++++++++++++++++++++
 4 files changed, 102 insertions(+), 10 deletions(-)
 create mode 100644 pyptv/test_calibration.ipynb

diff --git a/pyptv/calibration_gui.py b/pyptv/calibration_gui.py
index d757bce..4882734 100644
--- a/pyptv/calibration_gui.py
+++ b/pyptv/calibration_gui.py
@@ -569,7 +569,7 @@ def _button_showimg_fired(self):
         self.cal_images = []
         for i in range(len(self.camera)):
             imname = self.calParams.img_cal_name[i]
-            im = imread(imname)
+            im = imread(imname, as_gray=True)
             # im = ImageData.fromfile(imname).data
             if im.ndim > 2:
                 im = rgb2gray(im[:,:,:3])
@@ -980,10 +980,10 @@ def _button_fine_orient_fired(self):
                 print("Before scipy calibration")
                 print(self.cals[i_cam].get_pos())
                 
-                ptv.py_calibration(
+                residuals = ptv.py_calibration(
                     self.cals[i_cam],
-                    all_known,
-                    all_detected[:, 1:],
+                    self.cal_points["pos"],
+                    targs,
                     self.cpar,
                     flags,
                 ) 
@@ -1016,8 +1016,8 @@ def _button_fine_orient_fired(self):
             self.camera[i_cam].drawquiver(
                 x,
                 y,
-                x + scale * residuals[: len(x), 0],
-                y + scale * residuals[: len(x), 1],
+                x + scale * residuals[:len(x), 0],
+                y + scale * residuals[:len(x), 1],
                 "red",
             )
             # self.camera[i]._plot.index_mapper.range.set_bounds(0, self.h_pixel)
diff --git a/pyptv/ptv.py b/pyptv/ptv.py
index c499d15..2465bae 100644
--- a/pyptv/ptv.py
+++ b/pyptv/ptv.py
@@ -470,9 +470,16 @@ def py_calibration(cal, XYZ, xy, cpar, flags):
     """ Performs calibration of the selected cameras using Scipy"""
     
     x0 = calibration_to_array(cal)
-    sol = minimize(error_function, x0, args=(cal, XYZ, xy, cpar), method='Nelder-Mead', tol=1e-5)
+    xy = np.array([_.pos() for _ in xy]) # we get targs not arrays
+    sol = minimize(error_function, x0, args=(cal, XYZ, xy, cpar), method='Nelder-Mead', tol=1e-6)
     array_to_calibration(sol.x, cal) # cal is updated in place
-    # return cal
+        
+    targets = arr_metric_to_pixel(
+        image_coordinates(XYZ, cal, cpar.get_multimedia_params()),
+    cpar,
+    )
+        
+    return targets - xy
 
 
 def py_multiplanecalibration(exp):
diff --git a/pyptv/pyptv_gui.py b/pyptv/pyptv_gui.py
index 2acf058..98efe93 100644
--- a/pyptv/pyptv_gui.py
+++ b/pyptv/pyptv_gui.py
@@ -596,7 +596,8 @@ def init_action(self, info):
                     getattr(
                         mainGui.exp1.active_params.m_params,
                         f"Name_{i+1}_Image",
-                    )
+                    ),
+                    as_gray=True,
                 )
                 if im.ndim > 2:
                     im = rgb2gray(im)
@@ -1517,7 +1518,8 @@ def main():
         # exp_path = software_path.parent / "test_cavity"
         # exp_path = Path('/home/user/Downloads/one-dot-example/working_folder')
         # exp_path = Path('/home/user/Downloads/test_crossing_particle')
-        exp_path = Path('/home/user/Downloads/rbc300')
+        # exp_path = Path('/home/user/Downloads/rbc300')
+        exp_path = Path('/home/user/Downloads/For_Alex_test_34/')
         print(f"Without input, PyPTV fallbacks to a default {exp_path} \n")
 
     if not exp_path.is_dir() or not exp_path.exists():
diff --git a/pyptv/test_calibration.ipynb b/pyptv/test_calibration.ipynb
new file mode 100644
index 0000000..85ffa42
--- /dev/null
+++ b/pyptv/test_calibration.ipynb
@@ -0,0 +1,83 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# main\n",
+    "from test_calibration import *\n",
+    "%matplotlib qt\n",
+    "\n",
+    "from pathlib import Path\n",
+    "working_path = Path('/home/user/Downloads/For_Alex_test_34')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(<Figure size 640x480 with 1 Axes>,\n",
+       " <Axes3D: xlabel='X', ylabel='Z', zlabel='Y'>)"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "calblock = read_calblock(working_path / 'cal' / 'target_on_a_side.txt')\n",
+    "result = read_dt_lsq(working_path / 'res' / 'rt_is.123456789')\n",
+    "pairs = pair_cal_points(calblock, result, max_dist = 3.0)\n",
+    "plot_cal_points(pairs)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(<Figure size 640x480 with 1 Axes>, <Axes: >)"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "plot_cal_err_histogram(pairs)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pyptv25",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}