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SingleSliceSegmentation.py
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SingleSliceSegmentation.py
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from __future__ import print_function
import os
import vtk, qt, ctk, slicer
import logging
import numpy as np
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
DEFAULT_INPUT_IMAGE_NAME = "Image_Image"
#
# SingleSliceSegmentation
#
class SingleSliceSegmentation(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 = "Single Slice Segmentation"
self.parent.categories = ["Ultrasound"]
self.parent.dependencies = []
self.parent.contributors = ["Tamas Ungi (Queen's University)"] # replace with "Firstname Lastname (Organization)"
self.parent.helpText = """
This is an example of scripted loadable module bundled in an extension.
It performs a simple thresholding on the input volume and optionally captures a screenshot.
"""
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = """
This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.
and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
""" # replace with organization, grant and thanks.
def setup(self):
# Register subject hierarchy plugin
import SubjectHierarchyPlugins
scriptedPlugin = slicer.qSlicerSubjectHierarchyScriptedPlugin(None)
scriptedPlugin.setPythonSource(SubjectHierarchyPlugins.SegmentEditorSubjectHierarchyPlugin.filePath)
#
# SingleSliceSegmentationWidget
#
class SingleSliceSegmentationWidget(ScriptedLoadableModuleWidget, VTKObservationMixin):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
ATTRIBUTE_PREFIX = 'SingleSliceSegmentation_'
EXPORT_FOLDER = ATTRIBUTE_PREFIX + 'FilenamePrefix'
INPUT_BROWSER = ATTRIBUTE_PREFIX + 'InputBrowser'
INPUT_SKIP_NUMBER = ATTRIBUTE_PREFIX + 'InputSkipNumber'
DEFAULT_INPUT_SKIP_NUMBER = 4
INPUT_LAST_INDEX = ATTRIBUTE_PREFIX + 'InputLastIndex'
INPUT_IMAGE_ID = ATTRIBUTE_PREFIX + 'InputImageId'
SEGMENTATION = ATTRIBUTE_PREFIX + 'Segmentation'
OUTPUT_BROWSER = ATTRIBUTE_PREFIX + 'OutputBrowser'
ORIGINAL_IMAGE_INDEX = ATTRIBUTE_PREFIX + 'OriginalImageIndex'
def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
VTKObservationMixin.__init__(self)
self.logic = SingleSliceSegmentationLogic()
# Members
self.parameterSetNode = None
self.editor = None
self.ui = None
self.lastForegroundOpacity = 0.3 # Default value for CT/MRI overlay
# Shortcuts
self.shortcutS = qt.QShortcut(slicer.util.mainWindow())
self.shortcutS.setKey(qt.QKeySequence('s'))
self.shortcutD = qt.QShortcut(slicer.util.mainWindow())
self.shortcutD.setKey(qt.QKeySequence('d'))
self.shortcutC = qt.QShortcut(slicer.util.mainWindow())
self.shortcutC.setKey(qt.QKeySequence('c'))
self.shortcutA = qt.QShortcut(slicer.util.mainWindow())
self.shortcutA.setKey(qt.QKeySequence('a'))
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer)
uiWidget = slicer.util.loadUI(self.resourcePath('UI/SingleSliceSegmentation.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
# Set up widgets
self.ui.inputSequenceBrowserSelector.setMRMLScene(slicer.mrmlScene)
self.ui.inputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.ui.inputSegmentationSelector.setMRMLScene(slicer.mrmlScene)
self.ui.segmentationBrowserSelector.setMRMLScene(slicer.mrmlScene)
# connections
# Observe scene end import event and call onSceneEndImport when it happens
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndImportEvent, self.onSceneEndImport)
self.ui.inputSequenceBrowserSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputBrowserChanged)
self.ui.inputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputVolumeChanged)
self.ui.inputSegmentationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSegmentationChanged)
self.ui.segmentationBrowserSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSegmentationBrowserChanged)
self.ui.skipImagesSpinBox.connect("valueChanged(int)", self.onSkipImagesNumChanged)
self.ui.captureButton.connect('clicked(bool)', self.onCaptureButton)
self.ui.clearSegmentationButton.connect('clicked(bool)', self.onClearButton)
self.ui.skipImageButton.connect('clicked(bool)', self.onSkipButton)
self.ui.outputDirectoryButton.connect('directoryChanged(QString)', self.onExportFolderChanged)
self.ui.convertSegButton.connect('clicked(bool)', self.onConvertButton)
self.ui.exportButton.connect('clicked(bool)', self.onExportButton)
self.ui.layoutSelectButton.connect('clicked(bool)', self.onLayoutSelectButton)
self.ui.overlayButton.connect('clicked(bool)', self.onOverlayClicked)
self.ui.editor.setMRMLScene(slicer.mrmlScene)
import qSlicerSegmentationsEditorEffectsPythonQt
# TODO: For some reason the instance() function cannot be called as a class function although it's static
factory = qSlicerSegmentationsEditorEffectsPythonQt.qSlicerSegmentEditorEffectFactory()
self.effectFactorySingleton = factory.instance()
self.effectFactorySingleton.connect('effectRegistered(QString)', self.editorEffectRegistered)
# Add custom layout to layout selection menu
customLayout = """
<layout type="horizontal" split="true">
<item>
<view class="vtkMRMLSliceNode" singletontag="Red">
<property name="orientation" action="default">Axial</property>
<property name="viewlabel" action="default">R</property>
<property name="viewcolor" action="default">#F34A33</property>
</view>
</item>
<item>
<view class="vtkMRMLViewNode" singletontag="1">
<property name="viewlabel" action="default">1</property>
</view>
</item>
</layout>
"""
customLayoutId = 501
layoutManager = slicer.app.layoutManager()
layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
viewToolBar = slicer.util.mainWindow().findChild('QToolBar', 'ViewToolBar')
layoutMenu = viewToolBar.widgetForAction(viewToolBar.actions()[0]).menu()
layoutSwitchActionParent = layoutMenu
layoutSwitchAction = layoutSwitchActionParent.addAction("red + 3D side by side") # add inside layout list
layoutSwitchAction.setData(customLayoutId)
# layoutSwitchAction.setIcon(qt.QIcon(':Icons/Go.png'))
layoutSwitchAction.setToolTip('3D and slice view')
layoutSwitchAction.connect('triggered()', lambda layoutId=customLayoutId: slicer.app.layoutManager().setLayout(layoutId))
customLayout = """
<layout type="horizontal" split="true">
<item>
<view class="vtkMRMLSliceNode" singletontag="Red">
<property name="orientation" action="default">Axial</property>
<property name="viewlabel" action="default">R</property>
<property name="viewcolor" action="default">#F34A33</property>
</view>
</item>
<item>
<layout type=\"horizontal\">
<item>
<view class="vtkMRMLViewNode" singletontag="1">
<property name="viewlabel" action="default">1</property>
</view>
</item>
<item>
<view class="vtkMRMLViewNode" singletontag="2" type="secondary">
<property name="viewlabel" action="default">2</property>
</view>
</item>
</layout>
</item>
</layout>
"""
customLayoutId = 502
layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
layoutSwitchActionParent = layoutMenu
layoutSwitchAction = layoutSwitchActionParent.addAction("red + stacked dual 3D") # add inside layout list
layoutSwitchAction.setData(customLayoutId)
# layoutSwitchAction.setIcon(qt.QIcon(':Icons/Go.png'))
layoutSwitchAction.setToolTip('Dual 3D and slice view')
layoutSwitchAction.connect('triggered()',
lambda layoutId=customLayoutId: slicer.app.layoutManager().setLayout(layoutId))
def cleanup(self):
self.effectFactorySingleton.disconnect('effectRegistered(QString)', self.editorEffectRegistered)
def onExportFolderChanged(self, text):
"""Save the filename prefix in application settings"""
settings = qt.QSettings()
settings.setValue(self.EXPORT_FOLDER, text)
def onInputBrowserChanged(self, currentNode):
browserNodes = slicer.util.getNodesByClass('vtkMRMLSequenceBrowserNode')
for browser in browserNodes:
browser.SetAttribute(self.INPUT_BROWSER, "False")
if currentNode is None:
return
currentNode.SetAttribute(self.INPUT_BROWSER, "True")
savedSkip = currentNode.GetAttribute(self.INPUT_SKIP_NUMBER)
if savedSkip is not None:
slicer.modules.singleslicesegmentation.widgetRepresentation().self().ui.skipImagesSpinBox.value = int(savedSkip)
else:
numSkip = slicer.modules.singleslicesegmentation.widgetRepresentation().self().ui.skipImagesSpinBox.value
currentNode.SetAttribute(self.INPUT_SKIP_NUMBER, str(numSkip))
logging.debug("onSequenceBrowserSelected: {}".format(currentNode.GetName()))
def onInputVolumeChanged(self, currentNode):
# todo: delete after testing parameter node
# volumeNodes = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')
# for volume in volumeNodes:
# volume.SetAttribute(self.INPUT_IMAGE, "False")
if currentNode is None:
self.parameterSetNode.RemoveAttribute(self.INPUT_IMAGE_ID)
else:
self.parameterSetNode.SetAttribute(self.INPUT_IMAGE_ID, currentNode.GetID())
def onSegmentationChanged(self, currentNode):
segmentationNodes = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')
for segmentation in segmentationNodes:
segmentation.SetAttribute(self.SEGMENTATION, "False")
if currentNode is None:
return
else:
currentNode.SetAttribute(self.SEGMENTATION, "True")
def onSegmentationBrowserChanged(self, currentNode):
browserNodes = slicer.util.getNodesByClass('vtkMRMLSequenceBrowserNode')
for browser in browserNodes:
browser.SetAttribute(self.OUTPUT_BROWSER, "False")
if currentNode is None:
return
else:
currentNode.SetAttribute(self.OUTPUT_BROWSER, "True")
def onImageChange(self, browserNode):
inputImageIndex = browserNode.GetSelectedItemNumber()
if inputImageIndex is not None:
inputBrowserNode.SetAttribute(self.ORIGINAL_IMAGE_INDEX, str(inputImageIndex))
def onSkipImagesNumChanged(self, value):
inputBrowserNode = self.ui.inputSequenceBrowserSelector.currentNode()
if inputBrowserNode is not None:
inputBrowserNode.SetAttribute(self.INPUT_SKIP_NUMBER, str(value))
def onCaptureButton(self):
"""
Callback function for capture button or hotkey to trigger either saving of a new segmentation (if the input image sequence
browser is selected) or overwriting an existing segmentation (if the segmentation sequence is selected).
:returns: None
"""
inputBrowserNode = self.ui.inputSequenceBrowserSelector.currentNode()
inputImage = self.ui.inputVolumeSelector.currentNode()
outputBrowserNode = self.ui.segmentationBrowserSelector.currentNode()
selectedSegmentation = self.ui.inputSegmentationSelector.currentNode()
numSkip = slicer.modules.singleslicesegmentation.widgetRepresentation().self().ui.skipImagesSpinBox.value
if inputBrowserNode is None:
logging.error("No browser node selected!")
return
if selectedSegmentation is None:
logging.error("No segmentation selected!")
return
if outputBrowserNode is None:
logging.error("No segmentation sequence browser selected!")
return
original_index_str = selectedSegmentation.GetAttribute(self.ORIGINAL_IMAGE_INDEX)
# If input sequence browser is selected in the toolbar, always consider this a new segmentation. This is needed in case
# a scene was loaded with segmentation attribute ORIGINAL_IMAGE_INDEX not None.
activeBrowserNode = slicer.modules.sequences.toolBar().activeBrowserNode()
if activeBrowserNode == inputBrowserNode:
original_index_str = None
if original_index_str is None or original_index_str == "None" or original_index_str == "": # new segmentation
inputImageIndex = inputBrowserNode.GetSelectedItemNumber()
selectedSegmentation.SetAttribute(self.ORIGINAL_IMAGE_INDEX, str(inputImageIndex))
self.logic.captureSlice(outputBrowserNode, selectedSegmentation, inputImage)
self.logic.eraseCurrentSegmentation(selectedSegmentation)
selectedSegmentation.SetAttribute(self.ORIGINAL_IMAGE_INDEX, "None")
currentItemNum = inputBrowserNode.GetSelectedItemNumber()
newItemNum = inputBrowserNode.SelectNextItem(numSkip)
else: # overwrite segmentation
self.logic.captureSlice(outputBrowserNode, selectedSegmentation, inputImage)
currentItemNum = outputBrowserNode.GetSelectedItemNumber()
newItemNum = outputBrowserNode.SelectNextItem()
# Check if sequence browser wrapped around. If yes, pop up message box to ask if user wants to continue.
if newItemNum < currentItemNum:
logging.debug("Sequence wrapped around!")
msgBox = qt.QMessageBox()
msgBox.setText("Sequence wrapped around!")
msgBox.setInformativeText("Please save the scene before closing the application!")
msgBox.setStandardButtons(qt.QMessageBox.Ok)
msgBox.setDefaultButton(qt.QMessageBox.Ok)
msgBox.exec_()
def onClearButton(self):
"""
Callback function for "delete" button. Clears segmentation canvas.
:returns: none
"""
selectedSegmentation = self.ui.inputSegmentationSelector.currentNode()
if selectedSegmentation is None:
logging.error("No segmentation selected!")
return
self.logic.eraseCurrentSegmentation(selectedSegmentation)
def onSkipButton(self):
"""
Callback function for skip button or hotkey. If input sequence browser is active, skips specified number of frames without
recording any segmentation. If output sequence browser is active, moves to the next output frame without skipping any frames
because the user is probably editing/overwriting existing segmentations.
:returns: None
"""
inputBrowserNode = self.ui.inputSequenceBrowserSelector.currentNode()
selectedSegmentation = self.ui.inputSegmentationSelector.currentNode()
outputBrowserNode = self.ui.segmentationBrowserSelector.currentNode()
numSkip = slicer.modules.singleslicesegmentation.widgetRepresentation().self().ui.skipImagesSpinBox.value
if inputBrowserNode is None:
logging.error("No browser node selected!")
return
if selectedSegmentation is None:
logging.error("No segmentation selected!")
return
activeBrowserNode = slicer.modules.sequences.toolBar().activeBrowserNode()
if activeBrowserNode == outputBrowserNode:
currentItemNum = outputBrowserNode.GetSelectedItemNumber()
newItemNum = outputBrowserNode.SelectNextItem()
else:
self.logic.eraseCurrentSegmentation(selectedSegmentation)
currentItemNum = inputBrowserNode.GetSelectedItemNumber()
newItemNum = inputBrowserNode.SelectNextItem(numSkip)
# Check if sequence browser wrapped around. If yes, pop up message box to ask if user wants to continue.
if newItemNum < currentItemNum:
logging.debug("Sequence wrapped around!")
msgBox = qt.QMessageBox()
msgBox.setText("Sequence wrapped around!")
msgBox.setInformativeText("Please save the scene before closing the application!")
msgBox.setStandardButtons(qt.QMessageBox.Ok)
msgBox.setDefaultButton(qt.QMessageBox.Ok)
msgBox.exec_()
def onConvertButton(self):
"""
Callback function for convert button.
Converts all segmentations in the segmentation sequence browser to a sequence of scalar volumes.
"""
inputBrowserNode = self.ui.segmentationBrowserSelector.currentNode()
if inputBrowserNode is None:
logging.error("No browser node selected!")
return
segmentationNode = self.ui.inputSegmentationSelector.currentNode()
if segmentationNode is None:
logging.error("No segmentation selected!")
return
ultrasoundNode = self.ui.inputVolumeSelector.currentNode()
if ultrasoundNode is None:
logging.error("No ultrasound volume selected!")
return
value = self.ui.convertValueSpinBox.value
self.logic.convertSegmentationSequenceToVolumeSequence(inputBrowserNode, segmentationNode, ultrasoundNode, value)
def onExportButton(self):
selectedSegmentationSequence = self.ui.segmentationBrowserSelector.currentNode()
selectedSegmentation = self.ui.inputSegmentationSelector.currentNode()
selectedImage = self.ui.inputVolumeSelector.currentNode()
selectedImageSequence = self.ui.inputSequenceBrowserSelector.currentNode()
outputFolder = self.ui.outputDirectoryButton.directory
baseName = self.ui.filenamePrefixEdit.text
if selectedSegmentation is None:
logging.error("No segmentation selected!")
return
if selectedSegmentationSequence is None:
logging.error("No segmentation sequence browser selected!")
return
if selectedImage is None:
logging.error("No image selected!")
return
if selectedImage is None:
logging.error("No image sequence browser selected!")
return
if self.ui.exportTransformCheckBox.checked:
self.logic.exportNumpySlice(selectedImage,
selectedImageSequence,
selectedSegmentation,
selectedSegmentationSequence,
outputFolder,
baseName)
self.logic.exportTransformToWorldSequence(selectedImage,
selectedImageSequence,
selectedSegmentation,
selectedSegmentationSequence,
outputFolder,
baseName)
else:
self.logic.exportPngSequence(selectedImage,
selectedImageSequence,
selectedSegmentation,
selectedSegmentationSequence,
outputFolder,
baseName)
def onLayoutSelectButton(self):
layoutManager = slicer.app.layoutManager()
currentLayout = layoutManager.layout
# place skeleton model in first 3d view
skeleton_volume = slicer.util.getFirstNodeByName("SkeletonModel")
viewNode = layoutManager.threeDWidget(0).mrmlViewNode()
if skeleton_volume is not None:
displayNode = skeleton_volume.GetDisplayNode()
displayNode.SetViewNodeIDs([viewNode.GetID()])
# place reconstructed volume in second 3d view
# hacky but necessary way to ensure that we grab the correct browser node
i = 1
found = False
browser = slicer.util.getFirstNodeByClassByName('vtkMRMLSequenceBrowserNode', 'LandmarkingScan')
while not found and i < 6:
if browser == None:
browser = slicer.util.getFirstNodeByClassByName('vtkMRMLSequenceBrowserNode', 'LandmarkingScan_{}'.format(str(i)))
if browser != None:
found = True
else:
found = True
i += 1
if browser is not None:
spine_volume = slicer.util.getFirstNodeByName(browser.GetName() + 'ReconstructionResults')
if layoutManager.threeDWidget(1) is not None:
viewNode = layoutManager.threeDWidget(1).mrmlViewNode()
else:
newView = slicer.vtkMRMLViewNode()
newView = slicer.mrmlScene.AddNode(newView)
newWidget = slicer.qMRMLThreeDWidget()
newWidget.setMRMLScene(slicer.mrmlScene)
newWidget.setMRMLViewNode(newView)
if spine_volume is not None:
displayNode = slicer.modules.volumerendering.logic().GetFirstVolumeRenderingDisplayNode(spine_volume)
displayNode.SetViewNodeIDs([viewNode.GetID()])
spine_volume.SetDisplayVisibility(1)
if currentLayout == 501:
layoutManager.setLayout(502) # switch to dual 3d + red slice layout
elif currentLayout == 502:
layoutManager.setLayout(6) # switch to red slice only layout
else:
layoutManager.setLayout(501) # switch to custom layout with 3d viewer
def onOverlayClicked(self):
# show/hide foreground image
layoutManager = slicer.app.layoutManager()
compositeNode = layoutManager.sliceWidget('Red').sliceLogic().GetSliceCompositeNode()
currentOpacity = compositeNode.GetForegroundOpacity()
if currentOpacity == 0:
compositeNode.SetForegroundOpacity(self.lastForegroundOpacity)
else:
self.lastForegroundOpacity = currentOpacity
compositeNode.SetForegroundOpacity(0.0)
# Segment Editor Functionalities
def editorEffectRegistered(self):
self.editor.updateEffectList()
def selectParameterNode(self):
# Select parameter set node if one is found in the scene, and create one otherwise
segmentEditorSingletonTag = "SegmentEditor"
segmentEditorNode = slicer.mrmlScene.GetSingletonNode(segmentEditorSingletonTag, "vtkMRMLSegmentEditorNode")
if segmentEditorNode is None:
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
segmentEditorNode.SetSingletonTag(segmentEditorSingletonTag)
segmentEditorNode = slicer.mrmlScene.AddNode(segmentEditorNode)
if self.parameterSetNode == segmentEditorNode:
# nothing changed
return
self.parameterSetNode = segmentEditorNode
self.ui.editor.setMRMLSegmentEditorNode(self.parameterSetNode)
def getCompositeNode(self, layoutName):
""" use the Red slice composite node to define the active volumes """
count = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLSliceCompositeNode')
for n in range(count):
compNode = slicer.mrmlScene.GetNthNodeByClass(n, 'vtkMRMLSliceCompositeNode')
if layoutName and compNode.GetLayoutName() != layoutName:
continue
return compNode
def getDefaultMasterVolumeNodeID(self):
layoutManager = slicer.app.layoutManager()
# Use first background volume node in any of the displayed layouts
for layoutName in layoutManager.sliceViewNames():
compositeNode = self.getCompositeNode(layoutName)
if compositeNode.GetBackgroundVolumeID():
return compositeNode.GetBackgroundVolumeID()
# Use first background volume node in any of the displayed layouts
for layoutName in layoutManager.sliceViewNames():
compositeNode = self.getCompositeNode(layoutName)
if compositeNode.GetForegroundVolumeID():
return compositeNode.GetForegroundVolumeID()
# Not found anything
return None
def enter(self):
"""Runs whenever the module is reopened"""
logging.debug('Entered SingleSliceSegmentation module widget')
# Prevent segmentation master volume to be created in the wrong position.
# Todo: Instead of this, the input image should be kept transformed, and the segmentation also transformed
# inputImageNode = slicer.util.getFirstNodeByName(DEFAULT_INPUT_IMAGE_NAME)
# if inputImageNode is not None and inputImageNode.GetClassName() == 'vtkMRMLScalarVolumeNode':
# inputImageNode.SetAndObserveTransformNodeID(None)
if self.ui.editor.turnOffLightboxes():
slicer.util.warningDisplay('Segment Editor is not compatible with slice viewers in light box mode.'
'Views are being reset.', windowTitle='Segment Editor')
# Allow switching between effects and selected segment using keyboard shortcuts
self.ui.editor.installKeyboardShortcuts()
# Set parameter set node if absent
self.selectParameterNode()
self.ui.editor.updateWidgetFromMRML()
# Update UI
slicer.modules.sequences.setToolBarVisible(True)
self.updateSelections()
self.connectKeyboardShortcuts()
# Collapse input group if all is selected
if self.ui.inputSequenceBrowserSelector.currentNode() is not None and\
self.ui.inputVolumeSelector.currentNode() is not None and\
self.ui.inputSegmentationSelector.currentNode() is not None and\
self.ui.segmentationBrowserSelector.currentNode() is not None:
self.ui.inputCollapsibleButton.collapsed = True
else:
self.ui.inputCollapsibleButton.collapsed = False
# If no segmentation node exists then create one so that the user does not have to create one manually
if not self.ui.editor.segmentationNodeID():
segmentationNode = slicer.mrmlScene.GetFirstNode(None, "vtkMRMLSegmentationNode")
if not segmentationNode:
segmentationNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
self.ui.editor.setSegmentationNode(segmentationNode)
if not self.ui.editor.sourceVolumeNodeID():
masterVolumeNodeID = self.getDefaultMasterVolumeNodeID()
self.ui.editor.setSourceVolumeNodeID(masterVolumeNodeID)
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(6)
redController = slicer.app.layoutManager().sliceWidget('Red').sliceController()
redController.fitSliceToBackground()
def connectKeyboardShortcuts(self):
self.shortcutS.connect('activated()', self.onSkipButton)
self.shortcutD.connect('activated()', self.onClearButton)
self.shortcutC.connect('activated()', self.onCaptureButton)
self.shortcutA.connect('activated()', self.onOverlayClicked)
def disconnectKeyboardShortcuts(self):
self.shortcutS.activated.disconnect()
self.shortcutD.activated.disconnect()
self.shortcutC.activated.disconnect()
self.shortcutA.activated.disconnect()
def exit(self):
self.ui.editor.setActiveEffect(None)
self.ui.editor.uninstallKeyboardShortcuts()
self.ui.editor.removeViewObservations()
self.disconnectKeyboardShortcuts()
def onSceneStartClose(self, caller, event):
self.parameterSetNode = None
self.ui.editor.setSegmentationNode(None)
self.ui.editor.removeViewObservations()
def onSceneEndClose(self, caller, event):
if self.parent.isEntered:
self.selectParameterNode()
self.ui.editor.updateWidgetFromMRML()
def onSceneEndImport(self, caller, event):
if self.parent.isEntered:
self.selectParameterNode()
self.ui.editor.updateWidgetFromMRML()
self.updateSelections()
def updateSelections(self):
browserNodes = slicer.util.getNodesByClass('vtkMRMLSequenceBrowserNode')
for browser in browserNodes:
if browser.GetAttribute(self.INPUT_BROWSER) == "True":
self.ui.inputSequenceBrowserSelector.setCurrentNode(browser)
slicer.modules.sequences.setToolBarActiveBrowserNode(browser)
self.ui.inputCollapsibleButton.collapsed = True
selectedItem = browser.GetAttribute(self.INPUT_LAST_INDEX)
if selectedItem is not None:
browser.SetSelectedItemNumber(int(selectedItem))
skipNumber = browser.GetAttribute(self.INPUT_SKIP_NUMBER)
if skipNumber is None:
skipNumber = self.DEFAULT_INPUT_SKIP_NUMBER
self.ui.skipImagesSpinBox.value = int(skipNumber)
if browser.GetAttribute(self.OUTPUT_BROWSER) == "True":
self.ui.segmentationBrowserSelector.setCurrentNode(browser)
segmentationNodes = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')
for segmentation in segmentationNodes:
if segmentation.GetAttribute(self.SEGMENTATION) == "True":
self.ui.inputSegmentationSelector.setCurrentNode(segmentation)
self.logic.eraseCurrentSegmentation(segmentation)
self.ui.editor.setSegmentationNode(segmentation)
inputImageAttribute = self.parameterSetNode.GetAttribute(self.INPUT_IMAGE_ID)
if inputImageAttribute is not None:
inputImageNode = slicer.mrmlScene.GetNodeByID(inputImageAttribute)
if inputImageNode is not None:
self.ui.inputVolumeSelector.setCurrentNode(inputImageNode)
layoutManager = slicer.app.layoutManager()
sliceLogic = layoutManager.sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetBackgroundVolumeID(inputImageNode.GetID())
self.ui.editor.setSourceVolumeNode(inputImageNode)
# Update export folder value if path is found in application settings
exportFolder = slicer.app.settings().value(self.EXPORT_FOLDER)
if exportFolder is not None:
self.ui.outputDirectoryButton.directory = exportFolder
#
# SingleSliceSegmentationLogic
#
class SingleSliceSegmentationLogic(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
"""
def __init__(self, parent=None):
ScriptedLoadableModuleLogic.__init__(self, parent)
def exportSlice(self,
selectedImage,
selectedSegmentation,
outputFolder,
filenamePrefix,
itemNumber):
if not os.path.exists(outputFolder):
logging.error("Export folder does not exist {}".format(outputFolder))
return
ic = vtk.vtkImageCast()
ic.SetOutputScalarTypeToUnsignedChar()
ic.Update()
png_writer = vtk.vtkPNGWriter()
labelmapNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(
selectedSegmentation, labelmapNode, selectedImage)
segmentedImageData = labelmapNode.GetImageData()
ultrasoundData = selectedImage.GetImageData()
seg_file_name = filenamePrefix + "_%04d_segmentation" % itemNumber + ".png"
img_file_name = filenamePrefix + "_%04d_ultrasound" % itemNumber + ".png"
seg_fullname = os.path.join(outputFolder, seg_file_name)
img_fullname = os.path.join(outputFolder, img_file_name)
ic.SetInputData(segmentedImageData)
ic.Update()
png_writer.SetInputData(ic.GetOutput())
png_writer.SetFileName(seg_fullname)
png_writer.Update()
png_writer.Write()
ic.SetInputData(ultrasoundData)
ic.Update()
png_writer.SetInputData(ic.GetOutput())
png_writer.SetFileName(img_fullname)
png_writer.Update()
png_writer.Write()
num_segments = selectedSegmentation.GetSegmentation().GetNumberOfSegments()
# Assuming we are working with one (or the first) segment
# Erases the current segmentation
for i in range(num_segments):
segmentId = selectedSegmentation.GetSegmentation().GetNthSegmentID(i)
labelMapRep = selectedSegmentation.GetBinaryLabelmapRepresentation(segmentId)
labelMapRep.Initialize()
labelMapRep.Modified()
selectedSegmentation.Modified()
def convertSegmentationSequenceToVolumeSequence(self, inputBrowserNode, segmentationNode, ultrasoundNode, value):
"""
Converts a segmentation sequence to a volume sequence
"""
print(f"inputBrowserNode: {inputBrowserNode.GetName()}")
print(f"segmentationNode: {segmentationNode.GetName()}")
print(f"ultrasoundNode: {ultrasoundNode.GetName()}")
print(f"value: {value}")
# Add a new sequence node to the scene and add it to the inputBrowserNode
volumeSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode", "SegmentationVolumeSequence")
inputBrowserNode.AddSynchronizedSequenceNode(volumeSequenceNode)
# Iterate through ever item in the inputBrowserNode and convert the segmentation to a volume
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
scalarVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLScalarVolumeNode', "SegmentationVolume")
scalarVolumeNode.CreateDefaultDisplayNodes()
inputBrowserNode.AddProxyNode(scalarVolumeNode, volumeSequenceNode, False)
segmentationSequence = inputBrowserNode.GetSequenceNode(segmentationNode)
if segmentationSequence is None:
logging.error(f"No segmentation sequence found for segmentation {segmentationNode.GetName()}")
return
# Iterate through every item in the inputBrowserNode and convert the segmentation to a volume
for itemIndex in range(inputBrowserNode.GetNumberOfItems()):
inputBrowserNode.SetSelectedItemNumber(itemIndex)
currentSegmentation = segmentationSequence.GetNthDataNode(itemIndex)
slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(
currentSegmentation, labelmapVolumeNode, slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY)
# slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(
# currentSegmentation, labelmapVolumeNode, ultrasoundNode)
arrayLabelmap = slicer.util.array(labelmapVolumeNode.GetID())
if arrayLabelmap is not None:
arrayLabelmap[arrayLabelmap != 0] = 1
arrayLabelmap *= value
else:
arrayLabelmap = slicer.util.array(ultrasoundNode.GetID())
arrayLabelmap[:, :, :] = 0
slicer.util.updateVolumeFromArray(scalarVolumeNode, arrayLabelmap)
indexValue = segmentationSequence.GetNthIndexValue(itemIndex)
volumeSequenceNode.SetDataNodeAtValue(scalarVolumeNode, indexValue)
slicer.app.processEvents()
def exportNumpySlice(self,
selectedImage,
selectedImageSequence,
selectedSegmentation,
selectedSegmentationSequence,
outputFolder,
baseName):
if not os.path.exists(outputFolder):
logging.error("Export folder does not exist {}".format(outputFolder))
return
labelmapNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
seg_file_name = baseName + "_segmentation"
img_file_name = baseName + "_ultrasound"
ind_file_name = baseName + "_indices"
seg_fullname = os.path.join(outputFolder, seg_file_name)
img_fullname = os.path.join(outputFolder, img_file_name)
ind_fullname = os.path.join(outputFolder, ind_file_name)
# Get whole image volume (each frame in the original recording)
num_items = selectedImageSequence.GetNumberOfItems()
selectedImageSequence.SelectFirstItem()
img_numpy_size = slicer.util.arrayFromVolume(selectedImage).shape
img_seq_numpy = np.zeros((num_items, img_numpy_size[1], img_numpy_size[2], 1), dtype=np.uint8)
for i in range(num_items):
img_numpy = slicer.util.arrayFromVolume(selectedImage)
resize_img_numpy = np.expand_dims(img_numpy, axis=3)
img_seq_numpy[i, ...] = resize_img_numpy
selectedImageSequence.SelectNextItem()
slicer.app.processEvents()
np.save(img_fullname, img_seq_numpy)
# Get each segmentation at the right spot in volume the same size as the images, and store all original indices
num_items = selectedSegmentationSequence.GetNumberOfItems()
selectedSegmentationSequence.SelectFirstItem()
seg_seq_numpy = np.zeros(img_seq_numpy.shape, dtype=np.uint8)
originalIndices = np.array([], dtype=np.uint8)
for i in range(num_items):
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(selectedSegmentation,
labelmapNode, selectedImage)
seg_numpy = slicer.util.arrayFromVolume(labelmapNode)
resize_seg_numpy = np.expand_dims(seg_numpy, axis=3)
segmentationIndex = int(selectedSegmentation.GetAttribute(SingleSliceSegmentationWidget.ORIGINAL_IMAGE_INDEX))
originalIndices = np.append(originalIndices, segmentationIndex)
seg_seq_numpy[segmentationIndex, ...] = resize_seg_numpy
selectedSegmentationSequence.SelectNextItem()
slicer.app.processEvents()
np.save(seg_fullname, seg_seq_numpy)
np.save(ind_fullname, originalIndices)
def exportPngSequence(self,
selectedImage,
selectedImageSequence,
selectedSegmentation,
selectedSegmentationSequence,
outputFolder,
baseName):
if not os.path.exists(outputFolder):
logging.error("Export folder does not exist {}".format(outputFolder))
return
imageCast = vtk.vtkImageCast()
imageCast.SetOutputScalarTypeToUnsignedChar()
imageCast.Update()
pngWriter = vtk.vtkPNGWriter()
labelmapNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
num_items = selectedSegmentationSequence.GetNumberOfItems()
selectedSegmentationSequence.SelectFirstItem()
for i in range(num_items):
originalIndex = selectedSegmentation.GetAttribute(SingleSliceSegmentationWidget.ORIGINAL_IMAGE_INDEX)
if originalIndex == None:
logging.warning("Input image index attribute not found in segmentation. Input sequence will not be used.")
else:
try:
selectedImageSequence.SetSelectedItemNumber(int(originalIndex))
except:
logging.error(f"Original image not found for segmentation {i} - skipping")
continue
slicer.modules.sequences.logic().UpdateAllProxyNodes()
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(selectedSegmentation,
labelmapNode,
selectedImage)
segmentedImageData = labelmapNode.GetImageData()
ultrasoundData = selectedImage.GetImageData()
segmentationFileName = baseName + "_%04d_segmentation" % i + ".png"
ultrasoundFileName = baseName + "_%04d_ultrasound" % i + ".png"
segmentationFullname = os.path.join(outputFolder, segmentationFileName)
ultrasoundFullname = os.path.join(outputFolder, ultrasoundFileName)
imageCast.SetInputData(segmentedImageData)
imageCast.Update()
pngWriter.SetInputData(imageCast.GetOutput())
pngWriter.SetFileName(segmentationFullname)
pngWriter.Update()
pngWriter.Write()
imageCast.SetInputData(ultrasoundData)
imageCast.Update()
pngWriter.SetInputData(imageCast.GetOutput())
pngWriter.SetFileName(ultrasoundFullname)
pngWriter.Update()
pngWriter.Write()
selectedSegmentationSequence.SelectNextItem()
slicer.modules.sequences.logic().UpdateAllProxyNodes()
def exportTransformToWorldSequence(self,
selectedImage,
selectedImageSequence,
selectedSegmentation,
selectedSegmentationSequence,
outputFolder,
baseName):
if not os.path.exists(outputFolder):
logging.error("Export folder does not exist {}".format(outputFolder))
return
# Find out if selectedImage is transformed by an transform node in the scene
# If so, we will use that transform to get the transform to world for each frame
imageTransformID = selectedImage.GetTransformNodeID()
if imageTransformID is None:
logging.warning("Image is not transformed; no transform to world will be exported.")
return
else:
imageTransform = slicer.mrmlScene.GetNodeByID(imageTransformID)
num_items = selectedImageSequence.GetNumberOfItems()
selectedImageSequence.SelectFirstItem()
transforms_seq_numpy = np.zeros((num_items, 4, 4))
for i in range(num_items):
# Get landmarking scan transform, get TransformToWorld
transformToWorld = vtk.vtkMatrix4x4()
imageTransform.GetMatrixTransformToWorld(transformToWorld)
transformToWorld_numpy = slicer.util.arrayFromVTKMatrix(transformToWorld)
transforms_seq_numpy[i, ...] = transformToWorld_numpy
selectedImageSequence.SelectNextItem()
slicer.app.processEvents()
# Save stacked transforms as output numpy array.
transformFileName = baseName + "_transform.npy"
transformFullname = os.path.join(outputFolder, transformFileName)
np.save(transformFullname, transforms_seq_numpy)
def captureSlice(self, segmentationSequenceBrowser, selectedSegmentation, inputImage):
"""
Saves current segmentation in the selected segmentation sequence browser.
If the current input image index is already associated with a saved segmentation, that saved segmentation will be replaced
to avoid saving two different segmentations for the same input image.
:param segmentationSequenceBrowser: Output sequence browser for segmentations
:param selectedSegmentation: Output segmentation node, proxy node of one of the sequences in segmentationSequenceBrowser
:param inputImage: Input volume node, proxy node of one of the sequences in segmentationSequenceBrowser
"""
# Find sequences in selected browser associated with then inputImage and selectedSegmentation as proxy nodes
inputImageSequenceNode = segmentationSequenceBrowser.GetSequenceNode(inputImage)
if inputImageSequenceNode is None:
logging.error("Sequence not found for input image: {}".format(inputImage.GetName()))
return
segmentationSequenceNode = segmentationSequenceBrowser.GetSequenceNode(selectedSegmentation)
if segmentationSequenceNode is None:
logging.error("Sequence not found for segmentation: {}".format(selectedSegmentation.GetName()))
return