MA-2 Upgrade to PySide 6

.gitignore

@@ -105,3 +105,4 @@ ENV/
 data/
 log.txt
 .idea/
+dist

readme.md

@@ -2,22 +2,28 @@
 
 <img src="https://github.com/adamkwolf/3d-nii-visualizer/blob/master/images/visualization.png" style="width: 100px;"/>
 
-### Run with Python
+## Install & Run with Python
 
-1.  Create a virtual environment. Mac can use virtualenv or conda. Windows must use conda.
-2.  Install the dependencies (PyQt5, vtk, and sip) `pip install PyQt5 vtk`
-3.  Start the program `python ./visualizer/brain_tumor_3d.py -i "./sample_data/10labels_example/T1CE.nii.gz" -m "./sample_data/10labels_example/mask.nii.gz"`
+1. Install the dependencies (PySide6, VTK, and sip) `pip install -r requirements.txt`
+2. Start the program `python ./visualizer/brain_tumor_3d.py -i "data.nii.gz" -m "data_mask.nii.gz"`
+
+## Generate PyInstaller Binaries
+
+> **Note**: Must modify the paths in .spec file to match your project directory
 
-### Generate PyInstaller Binaries
-**Note**: Must modify the paths in .spec file to match your project directory
 * Mac: `pyinstaller Theia_Mac.spec`
 * Windows: `pyinstaller Theia_Windows.spec`
 
-### Test
-* `python -m pytest`
+## Test
+
+```shell
+python -m pytest
+```
 
-### Acknowledgements
+## Acknowledgements
 
-[1] S.Bakas et al, "Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features", Nature Scientific Data, 4:170117 (2017) DOI: 10.1038/sdata.2017.117
+[1] S.Bakas et al, "Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features", Nature Scientific Data, 4:
+170117 (2017) DOI: 10.1038/sdata.2017.117
 
-[2] B.Menze et al, "The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)", IEEE Transactions on Medical Imaging 34(10), 1993-2024 (2015) DOI: 10.1109/TMI.2014.2377694
+[2] B.Menze et al, "The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)", IEEE Transactions on Medical Imaging 34(10), 1993-2024 (2015) DOI:
+10.1109/TMI.2014.2377694

requirements.txt

@@ -1,3 +1,4 @@
-PyInstaller==3.3.1
-PyQt5==5.10.1
-vtk==8.1.0
+PyInstaller>=6.9.0
+pyside6>=6.7.2
+vtk>=9.3.1
+qt-material

visualizer/ErrorObserver.py

@@ -14,4 +14,4 @@ def ErrorOccurred(self):
         return occ
 
     def ErrorMessage(self):
-        return self.__ErrorMessage
+        return self.__ErrorMessage

visualizer/MainWindow.py

@@ -1,12 +1,14 @@
 import math
-import time
 import os
+import time
+
+import PySide6.QtCore as Qt
+import PySide6.QtWidgets as QtWidgets
+import vtk
+from vtkmodules.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
 
-import PyQt5.QtWidgets as QtWidgets
-import PyQt5.QtCore as Qt
-from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
-from vtkUtils import *
-from config import *
+from visualizer.config import BRAIN_OPACITY, BRAIN_SMOOTHNESS, MASK_OPACITY, MASK_SMOOTHNESS, APPLICATION_TITLE, MASK_COLORS
+from visualizer.vtkUtils import setup_brain, setup_mask, setup_projection, setup_slicer
 
 
 class MainWindow(QtWidgets.QMainWindow, QtWidgets.QApplication):
@@ -21,21 +23,27 @@ def __init__(self, app):
 
         # setup brain projection and slicer
         self.brain_image_prop = setup_projection(self.brain, self.renderer)
-        self.brain_slicer_props = setup_slicer(self.renderer, self.brain)  # causing issues with rotation
+        self.brain_slicer_props = setup_slicer(
+            self.renderer, self.brain)  # causing issues with rotation
         self.slicer_widgets = []
 
         # brain pickers
         self.brain_threshold_sp = self.create_new_picker(self.brain.scalar_range[1], self.brain.scalar_range[0], 5.0,
                                                          sum(self.brain.scalar_range) / 2, self.brain_threshold_vc)
-        self.brain_opacity_sp = self.create_new_picker(1.0, 0.0, 0.1, BRAIN_OPACITY, self.brain_opacity_vc)
-        self.brain_smoothness_sp = self.create_new_picker(1000, 100, 100, BRAIN_SMOOTHNESS, self.brain_smoothness_vc)
-        self.brain_lut_sp = self.create_new_picker(3.0, 0.0, 0.1, 2.0, self.lut_value_changed)
+        self.brain_opacity_sp = self.create_new_picker(
+            1.0, 0.0, 0.1, BRAIN_OPACITY, self.brain_opacity_vc)
+        self.brain_smoothness_sp = self.create_new_picker(
+            1000, 100, 100, BRAIN_SMOOTHNESS, self.brain_smoothness_vc)
+        self.brain_lut_sp = self.create_new_picker(
+            3.0, 0.0, 0.1, 2.0, self.lut_value_changed)
         self.brain_projection_cb = self.add_brain_projection()
         self.brain_slicer_cb = self.add_brain_slicer()
 
         # mask pickers
-        self.mask_opacity_sp = self.create_new_picker(1.0, 0.0, 0.1, MASK_OPACITY, self.mask_opacity_vc)
-        self.mask_smoothness_sp = self.create_new_picker(1000, 100, 100, MASK_SMOOTHNESS, self.mask_smoothness_vc)
+        self.mask_opacity_sp = self.create_new_picker(
+            1.0, 0.0, 0.1, MASK_OPACITY, self.mask_opacity_vc)
+        self.mask_smoothness_sp = self.create_new_picker(
+            1000, 100, 100, MASK_SMOOTHNESS, self.mask_smoothness_vc)
         self.mask_label_cbs = []
 
         # create grid for all widgets
@@ -59,7 +67,7 @@ def __init__(self, app):
     @staticmethod
     def setup():
         """
-        Create and setup the base vtk and Qt objects for the application
+        Create and set up the base vtk and Qt objects for the application
         """
         renderer = vtk.vtkRenderer()
         frame = QtWidgets.QFrame()
@@ -116,7 +124,8 @@ def add_brain_settings_widget(self):
         brain_group_layout = QtWidgets.QGridLayout()
         brain_group_layout.addWidget(QtWidgets.QLabel("Brain Threshold"), 0, 0)
         brain_group_layout.addWidget(QtWidgets.QLabel("Brain Opacity"), 1, 0)
-        brain_group_layout.addWidget(QtWidgets.QLabel("Brain Smoothness"), 2, 0)
+        brain_group_layout.addWidget(
+            QtWidgets.QLabel("Brain Smoothness"), 2, 0)
         brain_group_layout.addWidget(QtWidgets.QLabel("Image Intensity"), 3, 0)
         brain_group_layout.addWidget(self.brain_threshold_sp, 0, 1, 1, 2)
         brain_group_layout.addWidget(self.brain_opacity_sp, 1, 1, 1, 2)
@@ -130,7 +139,8 @@ def add_brain_settings_widget(self):
         brain_group_layout.addWidget(QtWidgets.QLabel("Sagittal Slice"), 8, 0)
 
         # order is important
-        slicer_funcs = [self.axial_slice_changed, self.coronal_slice_changed, self.sagittal_slice_changed]
+        slicer_funcs = [self.axial_slice_changed,
+                        self.coronal_slice_changed, self.sagittal_slice_changed]
         current_label_row = 6
         # data extent is array [xmin, xmax, ymin, ymax, zmin, zmax)
         # we want all the max values for the range
@@ -139,10 +149,12 @@ def add_brain_settings_widget(self):
             slice_widget = QtWidgets.QSlider(Qt.Qt.Horizontal)
             slice_widget.setDisabled(True)
             self.slicer_widgets.append(slice_widget)
-            brain_group_layout.addWidget(slice_widget, current_label_row, 1, 1, 2)
+            brain_group_layout.addWidget(
+                slice_widget, current_label_row, 1, 1, 2)
             slice_widget.valueChanged.connect(func)
-            slice_widget.setRange(self.brain.extent[extent_index - 1], self.brain.extent[extent_index])
-            slice_widget.setValue(self.brain.extent[extent_index] / 2)
+            slice_widget.setRange(
+                self.brain.extent[extent_index - 1], self.brain.extent[extent_index])
+            slice_widget.setValue(int(self.brain.extent[extent_index] / 2))
             current_label_row += 1
             extent_index -= 2
 
@@ -171,23 +183,28 @@ def add_mask_settings_widget(self):
         mask_settings_group_box = QtWidgets.QGroupBox("Mask Settings")
         mask_settings_layout = QtWidgets.QGridLayout()
         mask_settings_layout.addWidget(QtWidgets.QLabel("Mask Opacity"), 0, 0)
-        mask_settings_layout.addWidget(QtWidgets.QLabel("Mask Smoothness"), 1, 0)
+        mask_settings_layout.addWidget(
+            QtWidgets.QLabel("Mask Smoothness"), 1, 0)
         mask_settings_layout.addWidget(self.mask_opacity_sp, 0, 1)
         mask_settings_layout.addWidget(self.mask_smoothness_sp, 1, 1)
         mask_multi_color_radio = QtWidgets.QRadioButton("Multi Color")
         mask_multi_color_radio.setChecked(True)
-        mask_multi_color_radio.clicked.connect(self.mask_multi_color_radio_checked)
+        mask_multi_color_radio.clicked.connect(
+            self.mask_multi_color_radio_checked)
         mask_single_color_radio = QtWidgets.QRadioButton("Single Color")
-        mask_single_color_radio.clicked.connect(self.mask_single_color_radio_checked)
+        mask_single_color_radio.clicked.connect(
+            self.mask_single_color_radio_checked)
         mask_settings_layout.addWidget(mask_multi_color_radio, 2, 0)
         mask_settings_layout.addWidget(mask_single_color_radio, 2, 1)
         mask_settings_layout.addWidget(self.create_new_separator(), 3, 0, 1, 2)
 
         self.mask_label_cbs = []
         c_col, c_row = 0, 4  # c_row must always be (+1) of last row
         for i in range(1, 11):
-            self.mask_label_cbs.append(QtWidgets.QCheckBox("Label {}".format(i)))
-            mask_settings_layout.addWidget(self.mask_label_cbs[i - 1], c_row, c_col)
+            self.mask_label_cbs.append(
+                QtWidgets.QCheckBox("Label {}".format(i)))
+            mask_settings_layout.addWidget(
+                self.mask_label_cbs[i - 1], c_row, c_col)
             c_row = c_row + 1 if c_col == 1 else c_row
             c_col = 0 if c_col == 1 else 1
 
@@ -238,7 +255,8 @@ def add_brain_projection(self):
     def mask_label_checked(self):
         for i, cb in enumerate(self.mask_label_cbs):
             if cb.isChecked():
-                self.mask.labels[i].property.SetOpacity(self.mask_opacity_sp.value())
+                self.mask.labels[i].property.SetOpacity(
+                    self.mask_opacity_sp.value())
             elif cb.isEnabled():  # labels without data are disabled
                 self.mask.labels[i].property.SetOpacity(0)
         self.render_window.Render()
@@ -257,7 +275,8 @@ def mask_multi_color_radio_checked(self):
 
     def brain_projection_vc(self):
         projection_checked = self.brain_projection_cb.isChecked()
-        self.brain_slicer_cb.setDisabled(projection_checked)  # disable slicer checkbox, cant use both at same time
+        # disable slicer checkbox, cant use both at same time
+        self.brain_slicer_cb.setDisabled(projection_checked)
         self.brain_image_prop.SetOpacity(projection_checked)
         self.render_window.Render()
 
@@ -267,7 +286,8 @@ def brain_slicer_vc(self):
         for widget in self.slicer_widgets:
             widget.setEnabled(slicer_checked)
 
-        self.brain_projection_cb.setDisabled(slicer_checked)  # disable projection checkbox, cant use both at same time
+        # disable projection checkbox, cant use both at same time
+        self.brain_projection_cb.setDisabled(slicer_checked)
         for prop in self.brain_slicer_props:
             prop.GetProperty().SetOpacity(slicer_checked)
         self.render_window.Render()
@@ -308,7 +328,8 @@ def set_axial_view(self):
         self.renderer.ResetCamera()
         fp = self.renderer.GetActiveCamera().GetFocalPoint()
         p = self.renderer.GetActiveCamera().GetPosition()
-        dist = math.sqrt((p[0] - fp[0]) ** 2 + (p[1] - fp[1]) ** 2 + (p[2] - fp[2]) ** 2)
+        dist = math.sqrt((p[0] - fp[0]) ** 2 + (p[1] - fp[1])
+                         ** 2 + (p[2] - fp[2]) ** 2)
         self.renderer.GetActiveCamera().SetPosition(fp[0], fp[1], fp[2] + dist)
         self.renderer.GetActiveCamera().SetViewUp(0.0, 1.0, 0.0)
         self.renderer.GetActiveCamera().Zoom(1.8)
@@ -318,7 +339,8 @@ def set_coronal_view(self):
         self.renderer.ResetCamera()
         fp = self.renderer.GetActiveCamera().GetFocalPoint()
         p = self.renderer.GetActiveCamera().GetPosition()
-        dist = math.sqrt((p[0] - fp[0]) ** 2 + (p[1] - fp[1]) ** 2 + (p[2] - fp[2]) ** 2)
+        dist = math.sqrt((p[0] - fp[0]) ** 2 + (p[1] - fp[1])
+                         ** 2 + (p[2] - fp[2]) ** 2)
         self.renderer.GetActiveCamera().SetPosition(fp[0], fp[2] - dist, fp[1])
         self.renderer.GetActiveCamera().SetViewUp(0.0, 0.5, 0.5)
         self.renderer.GetActiveCamera().Zoom(1.8)
@@ -328,7 +350,8 @@ def set_sagittal_view(self):
         self.renderer.ResetCamera()
         fp = self.renderer.GetActiveCamera().GetFocalPoint()
         p = self.renderer.GetActiveCamera().GetPosition()
-        dist = math.sqrt((p[0] - fp[0]) ** 2 + (p[1] - fp[1]) ** 2 + (p[2] - fp[2]) ** 2)
+        dist = math.sqrt((p[0] - fp[0]) ** 2 + (p[1] - fp[1])
+                         ** 2 + (p[2] - fp[2]) ** 2)
         self.renderer.GetActiveCamera().SetPosition(fp[2] + dist, fp[0], fp[1])
         self.renderer.GetActiveCamera().SetViewUp(0.0, 0.0, 1.0)
         self.renderer.GetActiveCamera().Zoom(1.6)
@@ -338,7 +361,8 @@ def set_sagittal_view(self):
     def create_new_separator():
         horizontal_line = QtWidgets.QWidget()
         horizontal_line.setFixedHeight(1)
-        horizontal_line.setSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed)
+        horizontal_line.setSizePolicy(
+            QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed)
         horizontal_line.setStyleSheet("background-color: #c8c8c8;")
         return horizontal_line
 

visualizer/NiiLabel.py

@@ -5,4 +5,4 @@ def __init__(self, color, opacity, smoothness):
         self.smoother = None
         self.color = color
         self.opacity = opacity
-        self.smoothness = smoothness
+        self.smoothness = smoothness

visualizer/brain_tumor_3d.py

@@ -1,8 +1,12 @@
 import argparse
-import sys
 import os
+import sys
 
-from MainWindow import *
+import vtk
+from PySide6 import QtWidgets
+from qt_material import apply_stylesheet
+
+from visualizer.MainWindow import MainWindow
 
 
 def redirect_vtk_messages():
@@ -19,14 +23,18 @@ def redirect_vtk_messages():
 def verify_type(file):
     ext = os.path.basename(file).split(os.extsep, 1)
     if ext[1] != 'nii.gz':
-        parser.error("File doesn't end with 'nii.gz'. Found: {}".format(ext[1]))
+        parser.error(
+            "File doesn't end with 'nii.gz'. Found: {}".format(ext[1]))
     return file
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description='Reads Nii.gz Files and renders them in 3D.')
-    parser.add_argument('-i', type=lambda fn: verify_type(fn), help='an mri scan (nii.gz)')
-    parser.add_argument('-m', type=lambda fn: verify_type(fn), help='the segmentation mask (nii.gz)')
+    parser = argparse.ArgumentParser(
+        description='Reads Nii.gz Files and renders them in 3D.')
+    parser.add_argument('-i', type=lambda fn: verify_type(fn),
+                        help='an mri scan (nii.gz)')
+    parser.add_argument('-m', type=lambda fn: verify_type(fn),
+                        help='the segmentation mask (nii.gz)')
     args = parser.parse_args()
 
     redirect_vtk_messages()
@@ -36,7 +44,9 @@ def verify_type(file):
     #     read_css = css.read()
     #     app.setStyleSheet(read_css)
 
+    apply_stylesheet(app, theme='light_cyan_500.xml')
+
     app.BRAIN_FILE = args.i
     app.MASK_FILE = args.m
     window = MainWindow(app)
-    sys.exit(app.exec_())
+    sys.exit(app.exec())

visualizer/config.py

@@ -7,12 +7,12 @@
 # default mask settings
 MASK_SMOOTHNESS = 500
 MASK_COLORS = [(1, 0, 0),
-                (0, 1, 0),
-                (1, 1, 0),
-                (0, 0, 1),
-                (1, 0, 1),
-                (0, 1, 1),
-                (1, 0.5, 0.5),
-                (0.5, 1, 0.5),
-                (0.5, 0.5, 1)]  # RGB percentages
+               (0, 1, 0),
+               (1, 1, 0),
+               (0, 0, 1),
+               (1, 0, 1),
+               (0, 1, 1),
+               (1, 0.5, 0.5),
+               (0.5, 1, 0.5),
+               (0.5, 0.5, 1)]  # RGB percentages
 MASK_OPACITY = 1.0