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Add Codes for Tutorial 02. Interact, Debug & Pipeline
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‎.gitignore

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# Large Figures' Folder (all saved on GoogleDrive)
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_Figures/
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# PyCharm Files
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.idea/
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]

‎02__Interact_Debug_&_Pipeline/CMakeLists.txt

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cmake_minimum_required(VERSION 3.16.3...3.19.7 FATAL_ERROR)
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project(SL_Tutorials)
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#-----------------------------------------------------------------------------
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# Extension meta-information
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set(EXTENSION_HOMEPAGE "https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SL_Tutorials")
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set(EXTENSION_CATEGORY "Tutorials")
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set(EXTENSION_CONTRIBUTORS "Sen Li (ETS)")
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set(EXTENSION_DESCRIPTION "This is an example of a simple extension")
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set(EXTENSION_ICONURL "https://www.example.com/Slicer/Extensions/SL_Tutorials.png")
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set(EXTENSION_SCREENSHOTURLS "https://www.example.com/Slicer/Extensions/SL_Tutorials/Screenshots/1.png")
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set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies
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#-----------------------------------------------------------------------------
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# Extension dependencies
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find_package(Slicer REQUIRED)
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include(${Slicer_USE_FILE})
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#-----------------------------------------------------------------------------
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# Extension modules
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add_subdirectory(t_ApplyThreshold)
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## NEXT_MODULE
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#-----------------------------------------------------------------------------
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include(${Slicer_EXTENSION_GENERATE_CONFIG})
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include(${Slicer_EXTENSION_CPACK})

‎02__Interact_Debug_&_Pipeline/README.md

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## <a href="/README.md" style="text-decoration:none">Step 02: Interact, Debug & Pipeline</a>
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<img src="/SL__Summary.png" alt="isolated" width="800"/>

‎02__Interact_Debug_&_Pipeline/SL_Tutorials.png

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‎02__Interact_Debug_&_Pipeline/SL__Summary.png

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‎02__Interact_Debug_&_Pipeline/t_ApplyThreshold/CMakeLists.txt

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#-----------------------------------------------------------------------------
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set(MODULE_NAME t_ApplyThreshold)
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#-----------------------------------------------------------------------------
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set(MODULE_PYTHON_SCRIPTS
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${MODULE_NAME}.py
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)
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set(MODULE_PYTHON_RESOURCES
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Resources/Icons/${MODULE_NAME}.png
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Resources/UI/${MODULE_NAME}.ui
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)
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#-----------------------------------------------------------------------------
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slicerMacroBuildScriptedModule(
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NAME ${MODULE_NAME}
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SCRIPTS ${MODULE_PYTHON_SCRIPTS}
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RESOURCES ${MODULE_PYTHON_RESOURCES}
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WITH_GENERIC_TESTS
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)
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#-----------------------------------------------------------------------------
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if(BUILD_TESTING)
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# Register the unittest subclass in the main script as a ctest.
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# Note that the test will also be available at runtime.
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slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)
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# Additional build-time testing
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add_subdirectory(Testing)
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endif()

‎02__Interact_Debug_&_Pipeline/t_ApplyThreshold/Resources/Icons/t_ApplyThreshold.png

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‎02__Interact_Debug_&_Pipeline/t_ApplyThreshold/Resources/UI/t_ApplyThreshold.ui

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

‎02__Interact_Debug_&_Pipeline/t_ApplyThreshold/Testing/CMakeLists.txt

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add_subdirectory(Python)

‎02__Interact_Debug_&_Pipeline/t_ApplyThreshold/Testing/Python/CMakeLists.txt

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#slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py)

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