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@HarryHeres
HarryHeres committed Aug 31, 2023
1 parent bf51d56 commit 8ba0988
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27 changes: 27 additions & 0 deletions CMakeLists.txt
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cmake_minimum_required(VERSION 3.16.3...3.19.7 FATAL_ERROR)

project(SlicerBoneMorphing)

#-----------------------------------------------------------------------------
# Extension meta-information
set(EXTENSION_HOMEPAGE "https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SlicerBoneMorphing")
set(EXTENSION_CATEGORY "Examples")
set(EXTENSION_CONTRIBUTORS "Jan Heres (West Bohemian University)")
set(EXTENSION_DESCRIPTION "This extensions allows the user to generate and morph bone meshes based on its CT scans")
set(EXTENSION_ICONURL "https://www.example.com/Slicer/Extensions/SlicerBoneMorphing.png")
set(EXTENSION_SCREENSHOTURLS "https://www.example.com/Slicer/Extensions/SlicerBoneMorphing/Screenshots/1.png")
set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies

#-----------------------------------------------------------------------------
# Extension dependencies
find_package(Slicer REQUIRED)
include(${Slicer_USE_FILE})

#-----------------------------------------------------------------------------
# Extension modules
add_subdirectory(SlicerBoneMorphing)
## NEXT_MODULE

#-----------------------------------------------------------------------------
include(${Slicer_EXTENSION_GENERATE_CONFIG})
include(${Slicer_EXTENSION_CPACK})
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31 changes: 31 additions & 0 deletions SlicerBoneMorphing/CMakeLists.txt
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#-----------------------------------------------------------------------------
set(MODULE_NAME SlicerBoneMorphing)

#-----------------------------------------------------------------------------
set(MODULE_PYTHON_SCRIPTS
${MODULE_NAME}.py
)

set(MODULE_PYTHON_RESOURCES
Resources/Icons/${MODULE_NAME}.png
Resources/UI/${MODULE_NAME}.ui
)

#-----------------------------------------------------------------------------
slicerMacroBuildScriptedModule(
NAME ${MODULE_NAME}
SCRIPTS ${MODULE_PYTHON_SCRIPTS}
RESOURCES ${MODULE_PYTHON_RESOURCES}
WITH_GENERIC_TESTS
)

#-----------------------------------------------------------------------------
if(BUILD_TESTING)

# Register the unittest subclass in the main script as a ctest.
# Note that the test will also be available at runtime.
slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)

# Additional build-time testing
add_subdirectory(Testing)
endif()
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280 changes: 280 additions & 0 deletions SlicerBoneMorphing/Resources/UI/SlicerBoneMorphing.ui
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<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>UI</class>
<widget class="qMRMLWidget" name="UI">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>279</width>
<height>286</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<widget class="ctkCollapsibleButton" name="inputsCollapsibleButton">
<property name="text">
<string>Inputs</string>
</property>
<layout class="QFormLayout" name="formLayout_2">
<item row="0" column="0">
<widget class="QLabel" name="label">
<property name="text">
<string>Input volume:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="qMRMLNodeComboBox" name="inputSelector">
<property name="toolTip">
<string>Pick the input to the algorithm.</string>
</property>
<property name="nodeTypes">
<stringlist notr="true">
<string>vtkMRMLScalarVolumeNode</string>
</stringlist>
</property>
<property name="showChildNodeTypes">
<bool>false</bool>
</property>
<property name="addEnabled">
<bool>false</bool>
</property>
<property name="removeEnabled">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_3">
<property name="text">
<string>Image threshold:</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="ctkSliderWidget" name="imageThresholdSliderWidget">
<property name="toolTip">
<string>Set threshold value for computing the output image. Voxels that have intensities lower than this value will set to zero.</string>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="minimum">
<double>-100.000000000000000</double>
</property>
<property name="maximum">
<double>500.000000000000000</double>
</property>
<property name="value">
<double>0.500000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="ctkCollapsibleButton" name="outputsCollapsibleButton">
<property name="text">
<string>Outputs</string>
</property>
<layout class="QFormLayout" name="formLayout_4">
<item row="0" column="0">
<widget class="QLabel" name="label_2">
<property name="text">
<string>Thresholded volume:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="qMRMLNodeComboBox" name="outputSelector">
<property name="toolTip">
<string>Pick the output to the algorithm.</string>
</property>
<property name="nodeTypes">
<stringlist notr="true">
<string>vtkMRMLScalarVolumeNode</string>
</stringlist>
</property>
<property name="showChildNodeTypes">
<bool>false</bool>
</property>
<property name="noneEnabled">
<bool>true</bool>
</property>
<property name="addEnabled">
<bool>true</bool>
</property>
<property name="removeEnabled">
<bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_5">
<property name="text">
<string>Inverted volume:</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="qMRMLNodeComboBox" name="invertedOutputSelector">
<property name="toolTip">
<string>Result with inverted threshold will be written into this volume</string>
</property>
<property name="nodeTypes">
<stringlist notr="true">
<string>vtkMRMLScalarVolumeNode</string>
</stringlist>
</property>
<property name="showChildNodeTypes">
<bool>false</bool>
</property>
<property name="noneEnabled">
<bool>true</bool>
</property>
<property name="addEnabled">
<bool>true</bool>
</property>
<property name="removeEnabled">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="ctkCollapsibleButton" name="advancedCollapsibleButton">
<property name="text">
<string>Advanced</string>
</property>
<property name="collapsed">
<bool>true</bool>
</property>
<layout class="QFormLayout" name="formLayout_3">
<item row="0" column="0">
<widget class="QLabel" name="label_4">
<property name="text">
<string>Invert threshold: </string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QCheckBox" name="invertOutputCheckBox">
<property name="toolTip">
<string>If checked, values above threshold are set to 0. If unchecked, values below are set to 0.</string>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QPushButton" name="applyButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Run the algorithm.</string>
</property>
<property name="text">
<string>Apply</string>
</property>
</widget>
</item>
<item>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
<customwidgets>
<customwidget>
<class>ctkCollapsibleButton</class>
<extends>QWidget</extends>
<header>ctkCollapsibleButton.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>ctkSliderWidget</class>
<extends>QWidget</extends>
<header>ctkSliderWidget.h</header>
</customwidget>
<customwidget>
<class>qMRMLNodeComboBox</class>
<extends>QWidget</extends>
<header>qMRMLNodeComboBox.h</header>
</customwidget>
<customwidget>
<class>qMRMLWidget</class>
<extends>QWidget</extends>
<header>qMRMLWidget.h</header>
<container>1</container>
</customwidget>
</customwidgets>
<resources/>
<connections>
<connection>
<sender>UI</sender>
<signal>mrmlSceneChanged(vtkMRMLScene*)</signal>
<receiver>inputSelector</receiver>
<slot>setMRMLScene(vtkMRMLScene*)</slot>
<hints>
<hint type="sourcelabel">
<x>122</x>
<y>132</y>
</hint>
<hint type="destinationlabel">
<x>248</x>
<y>61</y>
</hint>
</hints>
</connection>
<connection>
<sender>UI</sender>
<signal>mrmlSceneChanged(vtkMRMLScene*)</signal>
<receiver>outputSelector</receiver>
<slot>setMRMLScene(vtkMRMLScene*)</slot>
<hints>
<hint type="sourcelabel">
<x>82</x>
<y>135</y>
</hint>
<hint type="destinationlabel">
<x>220</x>
<y>161</y>
</hint>
</hints>
</connection>
<connection>
<sender>UI</sender>
<signal>mrmlSceneChanged(vtkMRMLScene*)</signal>
<receiver>invertedOutputSelector</receiver>
<slot>setMRMLScene(vtkMRMLScene*)</slot>
<hints>
<hint type="sourcelabel">
<x>161</x>
<y>8</y>
</hint>
<hint type="destinationlabel">
<x>173</x>
<y>176</y>
</hint>
</hints>
</connection>
</connections>
</ui>
21 changes: 21 additions & 0 deletions SlicerBoneMorphing/SlicerBoneMorphing.py
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from slicer.ScriptedLoadableModule import ScriptedLoadableModule

from src.main import *

class SlicerBoneMorphing(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""

def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "Slicer Bone Mesh Module"
self.parent.categories = ["Examples"]
self.parent.dependencies = []
self.parent.contributors = ["Jan Heres"]
self.parent.helpText = """
This is a testing module help text.
"""
self.parent.acknowledgementText = """
Credits: Jan Heres
"""
1 change: 1 addition & 0 deletions SlicerBoneMorphing/Testing/CMakeLists.txt
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add_subdirectory(Python)
2 changes: 2 additions & 0 deletions SlicerBoneMorphing/Testing/Python/CMakeLists.txt
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#slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py)
2 changes: 2 additions & 0 deletions SlicerBoneMorphing/src/CMakeLists.txt
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add_subdirectory(logic)
add_subdirectory(widget)
12 changes: 12 additions & 0 deletions SlicerBoneMorphing/src/logic/SlicerBoneMorphingLogic.py
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from slicer.ScriptedLoadableModule import ScriptedLoadableModuleLogic


class SlicerBoneMorphingLogic(ScriptedLoadableModuleLogic):
"""This class should implement all the actual
computation done by your module. The interface
should be such that other python code can import
this class and make use of the functionality without
requiring an instance of the Widget.
Uses ScriptedLoadableModuleLogic base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
2 changes: 2 additions & 0 deletions SlicerBoneMorphing/src/main.py
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from .widget.SlicerBoneMorphingWidget import SlicerBoneMorphingWidget
from .logic.SlicerBoneMorphingLogic import SlicerBoneMorphingLogic
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