ENH: Major update to handle image/mask orientation and more

.gitignore

@@ -7,3 +7,8 @@ __pycache__
 *.swp
 *~
 *.zip
+itk-wheels
+*.tre
+*.mha
+*.nii
+*.code-workspace

README_Dev.md

@@ -1,12 +1,19 @@
+Install the developer build of ITK, ITKMinimalPathExtraction ITKTubetk:
+
+    python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ itk itk-minimalpathextraction itk-tubetk
+
 Setup for editable installation. Changes to code in src are
 immediatelly reflected in the installed version.  Also installs
 all dependencies needed for development and testing:
+
     pip install -e .[dev]
 
 Prior to making a commit, please verify your code is compliant:
+
     pre-commit run --all-files
 
 HINT:
 QT Designer was used to define the layout.  On Windows, to launch
 designer, use this command:
+
     qt6-tools.exe designer pytubeview.ui

data/.gitignore

@@ -6,3 +6,7 @@
 *.nii.gz
 *.mhd
 *.raw
+test*
+CH*
+PCD* 
+UNC*

pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
   'vtk',
   'thedicomsort',
   #'itk',  # Do not install until ITK pypi is updated
+  #'itk-tubetk',  # Do not install until ITK pypi is updated
 ]
 
 [project.scripts]

src/minder3d/lib/sovImageTablePanelWidget.py

@@ -88,10 +88,22 @@ def remove_all(self):
         self.settings.clear_data()
         self.fill_table()
 
+    def close_expanded_table(self):
+        self.enlarged_table.close()
+        self.enlarged_table = None
+
     def expand_table(self):
         if self.enlarged_table is None:
             self.enlarged_table = ImageTablePanelWidget(self.gui, self.state)
             self.enlarged_table.setWindowTitle('Image Table')
+            self.enlarged_table.imageTableExpandButton.setText("CLOSE")
+            self.enlarged_table.imageTableExpandButton.setMinimumWidth(75)
+            self.enlarged_table.imageTableExpandButton.clicked.disconnect()
+            self.enlarged_table.imageTableExpandButton.clicked.connect(
+                self.close_expanded_table
+            )
+            self.enlarged_table.show()
+        else:
             self.enlarged_table.show()
 
     @time_and_log

src/minder3d/lib/sovInfoTablePanelWidget.py

@@ -1,3 +1,5 @@
+import numpy as np
+
 from PySide6.QtWidgets import QTableWidget, QTableWidgetItem, QWidget
 
 from .sovUtils import time_and_log
@@ -20,12 +22,10 @@ def __init__(self, gui, state, parent=None):
         self.gui = gui
         self.state = state
 
-        self.infoTableWidget.setRowCount(3)
+        self.pixel_info_row_start = 0
+
+        self.infoTableWidget.setSizeAdjustPolicy(QTableWidget.AdjustToContents)
         self.infoTableWidget.setColumnCount(2)
-        self.infoTableWidget.setItem(0, 0, QTableWidgetItem('Pixel Coordinate'))
-        self.infoTableWidget.setItem(1, 0, QTableWidgetItem('  Image Value'))
-        self.infoTableWidget.setItem(2, 0, QTableWidgetItem('  Overlay Value'))
-        self.infoTableWidget.setColumnWidth(1, 200)
         self.infoTableWidget.setEditTriggers(QTableWidget.NoEditTriggers)
         self.infoTableWidget.setSelectionMode(QTableWidget.NoSelection)
         self.infoTableWidget.setShowGrid(True)
@@ -37,7 +37,46 @@ def __init__(self, gui, state, parent=None):
 
     @time_and_log
     def update_image(self):
-        pass
+        self.infoTableWidget.clear()
+        self.infoTableWidget.setRowCount(8)
+        self.infoTableWidget.setItem(0, 0, QTableWidgetItem('Image Information'))
+        img = self.state.image[self.state.current_image_num]
+
+        self.infoTableWidget.setItem(1, 0, QTableWidgetItem('  Image Size'))
+        info_str = ', '.join(
+            [f'{x:0.1f}' for x in img.GetLargestPossibleRegion().GetSize()]
+        )
+        self.infoTableWidget.setItem(1, 1, QTableWidgetItem(info_str))
+
+        self.infoTableWidget.setItem(2, 0, QTableWidgetItem('  Image Origin'))
+        info_str = ', '.join(
+            [f'{x:0.1f}' for x in img.GetOrigin()]
+        )
+        self.infoTableWidget.setItem(2, 1, QTableWidgetItem(info_str))
+
+        self.infoTableWidget.setItem(3, 0, QTableWidgetItem('  Image Spacing'))
+        if img.GetSpacing()[0] > 1:
+            info_str = ', '.join(
+                [f'{x:0.1f}' for x in img.GetSpacing()]
+            )
+        else:
+            info_str = ', '.join(
+                [f'{x:0.4f}' for x in img.GetSpacing()]
+            )
+        self.infoTableWidget.setItem(3, 1, QTableWidgetItem(info_str))
+
+        self.infoTableWidget.setItem(4, 0, QTableWidgetItem('  Image Direction'))
+        info_str = ', '.join(
+            [f'{x:0.1f}' for x in np.array(img.GetDirection()).flatten()]
+        )
+        self.infoTableWidget.setItem(4, 1, QTableWidgetItem(info_str))
+
+        self.pixel_info_row_start = 5
+        self.infoTableWidget.setItem(5, 0, QTableWidgetItem('Pixel Coordinate'))
+        self.infoTableWidget.setItem(6, 0, QTableWidgetItem('  Image Value'))
+        self.infoTableWidget.setItem(7, 0, QTableWidgetItem('  Overlay Value'))
+
+        self.infoTableWidget.resizeColumnsToContents()
 
     @time_and_log
     def update_pixel(self):
@@ -54,7 +93,7 @@ def update_pixel(self):
         pos_str = ', '.join(
             [f'{x:0.1f}' for x in self.state.current_pixel_position]
         )
-        self.infoTableWidget.setItem(0, 1, QTableWidgetItem(pos_str))
+        self.infoTableWidget.setItem(self.pixel_info_row_start, 1, QTableWidgetItem(pos_str))
         if (
             self.state.image[self.state.current_image_num]
             .GetLargestPossibleRegion()
@@ -68,13 +107,15 @@ def update_pixel(self):
                 - self.state.image_min[self.state.current_image_num]
             ) < 1:
                 self.infoTableWidget.setItem(
-                    1, 1, QTableWidgetItem(f'{img_val:0.4f}')
+                    self.pixel_info_row_start+1, 1, QTableWidgetItem(f'{img_val:0.4f}')
                 )
             else:
                 self.infoTableWidget.setItem(
-                    1, 1, QTableWidgetItem(f'{img_val:0.1f}')
+                    self.pixel_info_row_start+1, 1, QTableWidgetItem(f'{img_val:0.1f}')
                 )
-            self.infoTableWidget.setItem(2, 1, QTableWidgetItem('0'))
+            self.infoTableWidget.setItem(self.pixel_info_row_start+2, 1, QTableWidgetItem('0'))
         else:
-            self.infoTableWidget.setItem(1, 1, QTableWidgetItem('Outside'))
-            self.infoTableWidget.setItem(2, 1, QTableWidgetItem('Outside'))
+            self.infoTableWidget.setItem(self.pixel_info_row_start+1, 1, QTableWidgetItem('Outside'))
+            self.infoTableWidget.setItem(self.pixel_info_row_start+2, 1, QTableWidgetItem('Outside'))
+
+        self.infoTableWidget.resizeColumnsToContents()

src/minder3d/lib/sovObjectPanelWidget.py

@@ -86,6 +86,8 @@ def update_highlight_selected(self, value):
         """
         self.state.highlight_selected = value
         for selected_id in self.state.selected_ids:
+            if selected_id == -1:
+                continue
             self.gui.log(f'update_highlight_selected: Id={selected_id}')
             so = self.state.scene_list[
                 self.state.scene_list_ids.index(selected_id)
@@ -245,9 +247,12 @@ def rename_selected_object(self):
     def delete_selected_objects(self):
         """Delete the selected objects from the scene.
 
-        This function deletes the selected objects from the scene by removing them from the scene list and updating the GUI accordingly.
+        This function deletes the selected objects from the scene by removing
+        them from the scene list and updating the GUI accordingly.
         """
         for so_id in self.state.selected_ids:
+            if so_id == -1:
+                continue
             scene_idx = self.state.scene_list_ids.index(so_id)
             so = self.state.scene_list[scene_idx]
             so_parent = so.GetParent()
@@ -266,7 +271,7 @@ def delete_selected_objects(self):
 
         self.update_gui = True
 
-        self.update_scene()
+        self.gui.update_scene()
 
     @time_and_log
     def propogate_properties_to_all(self):
@@ -285,7 +290,7 @@ def propogate_properties_to_all(self):
         for idx in range(len(self.state.scene_list)):
             self.state.scene_list_properties[idx]['ColorBy'] = color_by
             self.state.scene_list[idx].GetProperty().SetColor(color)
-            self.redraw_object(self.state.scene_list[idx])
+            self.gui.redraw_object(self.state.scene_list[idx])
 
     @time_and_log
     def propogate_properties_to_similar(self):

src/minder3d/lib/sovOtsuLogic.py

@@ -12,4 +12,5 @@ def run(self, inputImage, numberOfThresholds):
             filter = itk.OtsuMultipleThresholdsImageFilter.New(Input=inputImage)
             filter.SetNumberOfThresholds(numberOfThresholds)
             filter.Update()
-            return filter.GetOutput().astype(np.uint8)
+            img = filter.GetOutput().astype(np.uint8)
+            return img

src/minder3d/lib/sovUtils.py

@@ -222,6 +222,52 @@ def add_objects_in_mask_image_to_scene(mask_image, scene):
         scene.AddChild(mask_so)
 
 
+@time_and_log
+def compress_scene_for_saving(scene):
+    """Compresses a scene for saving.
+
+    It compresses the input scene by removing unnecessary objects and compressing the scene.
+
+    Args:
+        scene: The scene to be compressed.
+    Returns:
+        new_scene: A compressed copy of the scene.
+    """
+    # HERE HERE HERE
+    mask_objects = get_children_as_list(scene, "ImageMask")
+    print("Num mask objects = ", len(mask_objects))
+    mask_image_pointers = list(np.unique([id(mask.GetImage()) for mask in mask_objects]))
+    print("Num mask object pointers = ", len(mask_image_pointers))
+    print("Mask image pointers = ", mask_image_pointers)
+    for mask_object in mask_objects:
+        imgPntr = id(mask_object.GetImage())
+        print("Mask object image pointer = ", imgPntr)
+        if imgPntr not in mask_image_pointers:
+            print("Removing mask object with image pointer = ", imgPntr)
+            #mask_object.GetParent().RemoveChild(mask_object)
+        else:
+            print("Keeping mask object with image pointer = ", imgPntr)
+            #mask_image_pointers.remove(id)
+    return scene
+
+def uncompress_scene_after_loading(scene):
+    """Uncompresses a scene after loading.
+
+    It uncompresses the input scene by adding necessary objects and uncompressing the scene.
+
+    Args:
+        scene: The scene to be uncompressed.
+    Returns:
+        scene: The uncompressed scene.
+    """
+    mask_objects = get_children_as_list(scene, 'ImageMask')
+    print("Num mask objects = ", len(mask_objects))
+    for mask_object in mask_objects:
+        parent = mask_object.GetParent()
+        parent.RemoveChild(mask_object)
+        add_objects_in_mask_image_to_scene(mask_object.GetImage(), parent)
+    return scene
+
 @time_and_log
 def get_children_as_list(
     grp: itk.GroupSpatialObject, child_type: str = ''
@@ -290,6 +336,7 @@ def read_group(filename: str, dims: int = 3) -> itk.GroupSpatialObject:
     try:
         groupFileReader = itk.SpatialObjectReader[dims].New()
         groupFileReader.SetFileName(filename)
+        groupFileReader.SetMetaIOVersion(1)
         groupFileReader.Update()
     except RuntimeError:
         return None
@@ -314,4 +361,5 @@ def write_group(group: itk.GroupSpatialObject, filename: str):
     groupFileWriter = GroupFileWriterType.New()
     groupFileWriter.SetFileName(filename)
     groupFileWriter.SetInput(group)
+    groupFileWriter.SetMetaIOVersion(1)
     groupFileWriter.Update()

src/minder3d/lib/sovView2DPanelWidget.py

@@ -299,13 +299,18 @@ def create_new_image(self):
             self.update_view_plane_coronal(redraw=False)
         elif view_plane == 1:
             self.update_view_plane_sagittal(redraw=False)
-        elif view_plane == 2:
+        else:  # if view_plane == 2:
             self.update_view_plane_axial(redraw=False)
 
         # Sagittal axis is viewed in the negative direction
-        flip[self.state.view2D_csa_axis_order[-1][1]] = not flip[
-            self.state.view2D_csa_axis_order[-1][1]
-        ]
+        #flip[self.state.view2D_csa_axis_order[-1][1]] = not flip[
+            #self.state.view2D_csa_axis_order[-1][1]
+        #]
+        # If coronal axis is data axis 2, then it is viewed in the negative direction
+        if self.state.view2D_csa_axis_order[-1][0] == 2:
+            flip[self.state.view2D_csa_axis_order[-1][0]] = not flip[
+                self.state.view2D_csa_axis_order[-1][0]
+            ]
         self.state.view2D_flip.append(flip)
 
     @time_and_log
@@ -457,6 +462,9 @@ def update_reset(self):
 
     @time_and_log
     def redraw_object(self, so):
+        if self.state.current_image_num < 0:
+            return
+
         if (
             self.state.highlight_selected
             and so.GetId() in self.state.selected_ids

src/minder3d/lib/sovView2DPanelWidget.ui

@@ -455,10 +455,16 @@
          </property>
          <property name="minimumSize">
           <size>
-           <width>35</width>
+           <width>30</width>
            <height>0</height>
           </size>
          </property>
+         <property name="maximumSize">
+          <size>
+           <width>30</width>
+           <height>16777215</height>
+          </size>
+         </property>
          <property name="font">
           <font>
            <pointsize>7</pointsize>

src/minder3d/lib/sovView2DRenderWindowInteractor.py

@@ -35,9 +35,6 @@ def __init__(self, gui, state, parent=None):
             7: 'Crop',
         }
 
-        self.state.view2D_image_axis_order = [0, 1, 2]
-        self.state.view2D_csa_axis_order = [2, 0, 1]
-
         self.current_mouse_mode = 0
 
         self.mouse_pressed = False