Merge pull request #22 from HarryHeres/version/0.2.0

Removing version branch

README.md

@@ -1,11 +1,11 @@
 # SlicerBoneMorphing
 Extension for 3D Slicer for bone mesh morphing.
 
-At the moment, this module specializes for the *humerus* bone, but the use case is not limited to it. 
+At the moment, this module specializes on the *humerus* bone, but the use case is not limited to it. 
 
-## Special thanks 
+## Special thanks 🙏 
 Special thanks goes to my wonderful colleagues [Eva C. Herbst](https://github.com/evaherbst) and [Arthur Porto](https://github.com/agporto) for creating the initial idea and their huge help during the development of this module! 
-Also, I would like to thank [O. Hirose](https://github.com/ohirose) for the research on BCPD/GBCPD and it's implementation (can be found [here](https://github.com/ohirose/bcpd))
+I would also like to thank [O. Hirose](https://github.com/ohirose) for the research on BCPD/GBCPD and it's implementation (can be found [here](https://github.com/ohirose/bcpd))
 
 ## Installation
 **Supported platforms:**
@@ -26,7 +26,7 @@ After a successful installation, the module will be available in the **Morphing*
 ## How to use 
 For guidance on how to use the module, please refer to this [Guide](./docs/how-to-use.md).
 
-## Contributors
+## Contributors ❤️
 A huge thank you to all of the contributors! 
 
 <a href="https://github.com/HarryHeres/SlicerBoneMorphing/graphs/contributors">

SlicerBoneMorphing/Resources/UI/SlicerBoneMorphing.ui

@@ -14,14 +14,14 @@
    <item>
     <widget class="ctkCollapsibleButton" name="visualizationCollapsibleButton">
      <property name="text">
-      <string>Visualization</string>
+      <string>Options</string>
      </property>
      <property name="checked">
       <bool>true</bool>
      </property>
      <layout class="QGridLayout" name="gridLayout">
       <item row="0" column="0">
-       <widget class="QCheckBox" name="visualizationVisualizeCheckBox">
+       <widget class="QCheckBox" name="optionsVisualizeCheckBox">
         <property name="toolTip">
          <string>If checked, the pipeline steps will be visualized using Open3D</string>
         </property>
@@ -30,38 +30,45 @@
         </property>
        </widget>
       </item>
-      <item row="1" column="0" colspan="2">
+      <item row="2" column="0" colspan="2">
        <widget class="QGroupBox" name="visualizationModelColorGroupBox">
         <property name="title">
          <string>Coloring</string>
         </property>
         <layout class="QGridLayout" name="gridLayout_2">
          <item row="0" column="1">
-          <widget class="ctkColorPickerButton" name="visualizationSourceModelColorPickerButton"/>
+          <widget class="ctkColorPickerButton" name="optionsSourceModelColorPickerButton"/>
          </item>
          <item row="0" column="0">
-          <widget class="QLabel" name="visualizationSourceModelColorLabel">
+          <widget class="QLabel" name="optionsSourceModelColorLabel">
            <property name="text">
             <string>Source model color</string>
            </property>
           </widget>
          </item>
          <item row="1" column="0">
-          <widget class="QLabel" name="label_2">
+          <widget class="QLabel" name="optionsTargetModelColorLabel">
            <property name="text">
             <string>Target model color</string>
            </property>
           </widget>
          </item>
          <item row="1" column="1">
-          <widget class="ctkColorPickerButton" name="visualizationTargetModelColorPickerButton"/>
+          <widget class="ctkColorPickerButton" name="optionsTargetModelColorPickerButton"/>
          </item>
         </layout>
        </widget>
       </item>
      </layout>
     </widget>
    </item>
+   <item>
+    <widget class="QCheckBox" name="optionsImportRegistrationModelCheckBox">
+     <property name="text">
+      <string>Import rigid registration model into the scene</string>
+     </property>
+    </widget>
+   </item>
    <item>
     <widget class="ctkCollapsibleButton" name="inputSectionCollapsibleButton">
      <property name="text">
@@ -1397,7 +1404,7 @@
    </hints>
   </connection>
   <connection>
-   <sender>visualizationVisualizeCheckBox</sender>
+   <sender>optionsVisualizeCheckBox</sender>
    <signal>toggled(bool)</signal>
    <receiver>visualizationModelColorGroupBox</receiver>
    <slot>setVisible(bool)</slot>

SlicerBoneMorphing/SlicerBoneMorphing.py

@@ -17,7 +17,7 @@ def __init__(self, parent):
         self.parent.helpText = """
         This module gives a user ability to recreate bone mesh models based on their partial scan.
         Please, start with importing your model and checking out the options on the left side afterwards.
-        Version: 0.2.0-rc.1
+        Version: 0.2.0-rc.2
         """
 
         self.parent.acknowledgementText = """

SlicerBoneMorphing/src/logic/Constants.py

@@ -7,13 +7,15 @@
 
 BCPD_MULTIPLE_VALUES_SEPARATOR = ","
 
-VISUALIZATION_KEY = "visualization"
-VISUALIZATION_KEY_SHOULD_VISUALIZE = "sv"
-VISUALIZATION_KEY_SOURCE_MODEL_COLOR = "smc"
-VISUALIZATION_KEY_TARGET_MODEL_COLOR = "tmc"
-
-VISUALIZATION_DEFAULT_VALUE_SOURCE_MODEL_COLOR = qt.QColor(255, 0, 0, 0)
-VISUALIZATION_DEFAULT_VALUE_TARGET_MODEL_COLOR = qt.QColor(0, 255, 0, 0)
+### OPTIONS ###
+OPTIONS_KEY = "options"
+OPTIONS_KEY_VISUALIZE_RESULTS = "vr"
+OPTIONS_KEY_SOURCE_MODEL_COLOR = "smc"
+OPTIONS_KEY_TARGET_MODEL_COLOR = "tmc"
+OPTIONS_KEY_IMPORT_REGISTRATION_MODEL = "irm"
+
+OPTIONS_DEFAULT_VALUE_SOURCE_MODEL_COLOR = qt.QColor(255, 0, 0, 0)
+OPTIONS_DEFAULT_VALUE_TARGET_MODEL_COLOR = qt.QColor(0, 255, 0, 0)
 
 ### PREPROCESSING PARAMETERS ###
 PREPROCESSING_KEY = "preprocessing"

SlicerBoneMorphing/src/logic/SlicerBoneMorphingLogic.py

@@ -1,13 +1,15 @@
 import src.logic.Constants as const
 import tempfile
 import subprocess
+from subprocess import CalledProcessError
 from vtk.util.numpy_support import vtk_to_numpy
 import vtk
 import glob
 import os
 import numpy as np
 from sys import platform
 from typing import Tuple
+import slicer
 from slicer.ScriptedLoadableModule import ScriptedLoadableModuleLogic
 from slicer import vtkMRMLModelNode
 import slicer.util as su
@@ -17,7 +19,13 @@
 except ModuleNotFoundError:
     print("Module Open3D not found")
     if su.confirmOkCancelDisplay(text="This module requires the 'open3d' Python package. Click OK to install it now.") is True:
-        su.pip_install('open3d===0.16.0')  # Version fix because of silicon based Macs
+        if (platform == 'darwin'):
+            # Must be pin-pointed directly due to defaulting to the 'universal' wheel, which does not work under Rosetta
+            # Submitted at https://github.com/isl-org/Open3D/issues/6994
+            su.pip_install('https://github.com/isl-org/Open3D/releases/download/v0.18.0/open3d-0.18.0-cp39-cp39-macosx_11_0_x86_64.whl')
+        else:
+            su.pip_install('open3d')
+
         import open3d as o3d
     else:
         print("Open3D is not installed, but is required")
@@ -38,7 +46,7 @@ class SlicerBoneMorphingLogic(ScriptedLoadableModuleLogic):
     def __init__(self, parent=None):
         ScriptedLoadableModuleLogic.__init__(self, parent)
 
-    def __visualize(self, source, target, window_name: str = "", source_color=const.VISUALIZATION_DEFAULT_VALUE_TARGET_MODEL_COLOR, target_color=const.VISUALIZATION_KEY_TARGET_MODEL_COLOR):
+    def __visualize(self, source, target, window_name: str = "", source_color=const.OPTIONS_DEFAULT_VALUE_TARGET_MODEL_COLOR, target_color=const.OPTIONS_KEY_TARGET_MODEL_COLOR):
         models = []
 
         if (source is not None):
@@ -81,24 +89,29 @@ def generate_model(
             return const.EXIT_FAILURE, None
 
         source_mesh.transform(result_icp.transformation)
+        options_params = parameters[const.OPTIONS_KEY]
 
-        visualization_params = parameters[const.VISUALIZATION_KEY]
+        if (options_params[const.OPTIONS_KEY_IMPORT_REGISTRATION_MODEL] is True):
+            registration_result = self.__convert_mesh_to_vtk_polydata(source_mesh)
+            registration_node = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode', "_".join([target_model.GetName(), "rigid_registration_result"]))
+            registration_node.SetAndObservePolyData(registration_result)
+            registration_node.CreateDefaultDisplayNodes()
 
-        if (visualization_params[const.VISUALIZATION_KEY_SHOULD_VISUALIZE] is True):
-            self.__visualize(source_mesh, target_mesh, "Preprocessed models", visualization_params[const.VISUALIZATION_KEY_SOURCE_MODEL_COLOR], visualization_params[const.VISUALIZATION_KEY_TARGET_MODEL_COLOR])
+        if (options_params[const.OPTIONS_KEY_VISUALIZE_RESULTS] is True):
+            self.__visualize(source_mesh, target_mesh, "Preprocessed models", options_params[const.OPTIONS_KEY_SOURCE_MODEL_COLOR], options_params[const.OPTIONS_KEY_TARGET_MODEL_COLOR])
 
         # BCPD stage
         deformed = self.__deformable_registration(source_mesh, target_mesh, parameters[const.BCPD_KEY])
         if (deformed is None):
             return const.EXIT_FAILURE, None
 
-        if (visualization_params[const.VISUALIZATION_KEY_SHOULD_VISUALIZE] is True):
-            self.__visualize(deformed, None, "Reconstructed model", visualization_params[const.VISUALIZATION_KEY_SOURCE_MODEL_COLOR], visualization_params[const.VISUALIZATION_KEY_TARGET_MODEL_COLOR])
+        if (options_params[const.OPTIONS_KEY_VISUALIZE_RESULTS] is True):
+            self.__visualize(deformed, None, "Reconstructed model", options_params[const.OPTIONS_KEY_SOURCE_MODEL_COLOR], options_params[const.OPTIONS_KEY_TARGET_MODEL_COLOR])
 
         generated_polydata = self.__postprocess_meshes(deformed, parameters[const.POSTPROCESSING_KEY])
 
-        if (visualization_params[const.VISUALIZATION_KEY_SHOULD_VISUALIZE] is True):
-            self.__visualize(deformed, None, "Postprocessed model", visualization_params[const.VISUALIZATION_KEY_SOURCE_MODEL_COLOR], visualization_params[const.VISUALIZATION_KEY_TARGET_MODEL_COLOR])
+        if (options_params[const.OPTIONS_KEY_VISUALIZE_RESULTS] is True):
+            self.__visualize(deformed, None, "Postprocessed model", options_params[const.OPTIONS_KEY_SOURCE_MODEL_COLOR], options_params[const.OPTIONS_KEY_TARGET_MODEL_COLOR])
 
         return const.EXIT_OK, generated_polydata
 
@@ -375,11 +388,17 @@ def __deformable_registration(
         cmd += f' -o {output_path}'
         print("BCPD: " + cmd)
 
-        subprocess.run(cmd,
-                       shell=True,
-                       check=True,
-                       text=True,
-                       capture_output=True)
+        try:
+            subprocess.run(cmd,
+                           shell=True,
+                           check=True,
+                           text=True,
+                           capture_output=True)
+        except CalledProcessError as e:
+            print("BCPD subprocess returned with error (code {}): {}".format(e.returncode, e.output))
+            print("Process output: {}".format(e.output))
+            print("Errors: {}".format(e.stderr))
+            return None
 
         try:
             bcpdResult = np.loadtxt(output_path + "y.interpolated.txt")

SlicerBoneMorphing/src/widget/SlicerBoneMorphingWidget.py

@@ -53,9 +53,11 @@ def __setup_ui(self) -> None:
         self.__reset_parameters_to_default()
 
     def __reset_parameters_to_default(self) -> None:
-        self.__ui.visualizationVisualizeCheckBox.setChecked(False)
-        self.__ui.visualizationSourceModelColorPickerButton.setColor(const.VISUALIZATION_DEFAULT_VALUE_SOURCE_MODEL_COLOR)
-        self.__ui.visualizationTargetModelColorPickerButton.setColor(const.VISUALIZATION_DEFAULT_VALUE_TARGET_MODEL_COLOR)
+        ## Options ##
+        self.__ui.optionsVisualizeCheckBox.setChecked(False)
+        self.__ui.optionsSourceModelColorPickerButton.setColor(const.OPTIONS_DEFAULT_VALUE_SOURCE_MODEL_COLOR)
+        self.__ui.optionsTargetModelColorPickerButton.setColor(const.OPTIONS_DEFAULT_VALUE_TARGET_MODEL_COLOR)
+        self.__ui.optionsImportRegistrationModelCheckBox.setChecked(False)
 
         ## Preprocessing parameters ##
         self.__ui.preprocessingDownsamplingVoxelSizeDoubleSpinBox.value = const.PREPROCESSING_DEFAULT_VALUE_DOWNSAMPLING_VOXEL_SIZE
@@ -157,18 +159,19 @@ def __parse_parameters(self) -> dict:
             Parsing parameters from the UI user option elements
         """
         params = {}
-        params[const.VISUALIZATION_KEY] = self.__parse_parameters_visualization()
+        params[const.OPTIONS_KEY] = self.__parse_parameters_options()
         params[const.PREPROCESSING_KEY] = self.__parse_parameters_preprocessing()
         params[const.BCPD_KEY] = self.__parse_parameters_bcpd()
         params[const.POSTPROCESSING_KEY] = self.__parse_parameters_postprocessing()
 
         return params
 
-    def __parse_parameters_visualization(self) -> dict:
+    def __parse_parameters_options(self) -> dict:
         params = {}
-        params[const.VISUALIZATION_KEY_SHOULD_VISUALIZE] = self.__ui.visualizationVisualizeCheckBox.checked
-        params[const.VISUALIZATION_KEY_SOURCE_MODEL_COLOR] = self.__ui.visualizationSourceModelColorPickerButton.color
-        params[const.VISUALIZATION_KEY_TARGET_MODEL_COLOR] = self.__ui.visualizationTargetModelColorPickerButton.color
+        params[const.OPTIONS_KEY_VISUALIZE_RESULTS] = self.__ui.optionsVisualizeCheckBox.checked
+        params[const.OPTIONS_KEY_SOURCE_MODEL_COLOR] = self.__ui.optionsSourceModelColorPickerButton.color
+        params[const.OPTIONS_KEY_TARGET_MODEL_COLOR] = self.__ui.optionsTargetModelColorPickerButton.color
+        params[const.OPTIONS_KEY_IMPORT_REGISTRATION_MODEL] = self.__ui.optionsImportRegistrationModelCheckBox.checked
 
         return params
 

docs/how-to-use.md

@@ -1,6 +1,6 @@
 # Guide on how to use the module
-### Visualization
-Here, you can check whether you want to visualize results of each pipeline steps using Open3D.
+### Options 
+Here, you have some pretty self-explanatory options, e.g. visualization of each step of the pipeline.
 
 ### Input section
 - Source = The mean model, i.e. a full humerus
@@ -60,3 +60,4 @@ For these, we let you modify the following parameters:
     - If set to 0, no smoothing is applied 
 
 After the whole process is done, the generated mesh is imported back into the current Slicer scene.
+