def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay(
'Running test of the Neurosurgical Planning tutorial')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome',
'Welcome module', -1)
else:
# otherwise show the sample data module
moduleSelector.selectModule('SampleData')
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume(
)
self.takeScreenshot('NeurosurgicalPlanning-Loaded', 'Data loaded', -1)
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget(
"Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget is not None:
popupWidget.pinPopup(1)
self.takeScreenshot('NeurosurgicalPlanning-Link',
'Link slice viewers', -1)
popupWidget.pinPopup(0)
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# baseline in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(baselineVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-Baseline',
'Baseline in background', -1)
#
# adjust window level on baseline
#
moduleSelector.selectModule('Volumes')
baselineDisplay = baselineVolume.GetDisplayNode()
baselineDisplay.SetAutoWindowLevel(0)
baselineDisplay.SetWindow(2600)
baselineDisplay.SetLevel(1206)
self.takeScreenshot('NeurosurgicalPlanning-WindowLevel',
'Set W/L on baseline', -1)
#
# switch to red slice only
#
lm.setLayout(6)
self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly',
'Set layout to Red Slice only', -1)
#
# segmentation of tumour
#
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, baselineVolume,
baselineVolume.GetName() + '-label')
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# editor module
#
moduleSelector.selectModule('Editor')
self.takeScreenshot('NeurosurgicalPlanning-Editor',
'Showing Editor Module', -1)
# set the slice offset so drawing is right
sliceNode = sliceLogic.GetSliceNode()
sliceOffset = 58.7
sliceNode.SetSliceOffset(sliceOffset)
#
# paint
#
parameterNode = EditUtil.getParameterNode()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.takeScreenshot('NeurosurgicalPlanning-Paint',
'Paint tool in Editor Module', -1)
#
# paint in cystic part of tumor, using converstion from RAS coords to
# avoid slice widget size differences
#
EditUtil.setLabel(293)
displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-11, 73, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-12, 85, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-13, 91, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-15, 78, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintCystic',
'Paint cystic part of tumor', -1)
#
# paint in solid part of tumor
#
EditUtil.setLabel(7)
displayCoords = self.rasToDisplay(-0.5, 118.5, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-7.4, 116, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintSolid',
'Paint solid part of tumor', -1)
#
# paint around the tumor
#
EditUtil.setLabel(295)
rMax = 25
rMin = -50
aMax = 145
aMin = 50
rasStep = 5
# draw the top and bottom
for r in range(rMin, rMax, rasStep):
displayCoords = self.rasToDisplay(r, aMin, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(r, aMax, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
# draw the left and right
for a in range(aMin, aMax, rasStep):
displayCoords = self.rasToDisplay(rMin, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(rMax, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintAround',
'Paint around tumor', -1)
#
# clean up after painting
#
paintTool.cleanup()
paintTool = None
#
# Grow cut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
self.takeScreenshot('NeurosurgicalPlanning-Growcut', 'Growcut', -1)
#
# Merge split volume
#
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
self.takeScreenshot('NeurosurgicalPlanning-SplitMerge', 'SplitMerge',
-1)
#
# go to the data module
#
moduleSelector.selectModule('Data')
self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData',
'SplitMerge results in Data', -1)
#
# Ventricles Segmentation
#
moduleSelector.selectModule('Editor')
#
# select the label volume with the area around the tumor
slicer.util.findChildren(
name='PerStructureVolumesFrame')[0].collapsed = False
treeView = slicer.util.findChildren(name='StructuresView')[0]
selection = qt.QItemSelection()
# selecting the last split volume in the third row
row = 2
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row,
treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 3-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel295.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelOutside',
'Select outside region', -1)
#
# Threshold tool
#
slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect')
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter('ThresholdEffect,min', str(1700))
slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
self.takeScreenshot('NeurosurgicalPlanning-Ventricles',
'Ventricles segmentation', -1)
#
# Save Islands
#
slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect')
saveIslandLogic = EditorLib.SaveIslandEffectLogic(
sliceWidget.sliceLogic())
displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset)
xy = (displayCoords[0], displayCoords[1])
saveIslandLogic.saveIsland(xy)
self.takeScreenshot('NeurosurgicalPlanning-SaveIsland',
'Ventricles save island', -1)
#
# Merge and build
#
slicer.util.findChildren(text='Merge And Build')[0].clicked()
#
# switch to conventional layout
#
lm.setLayout(2)
self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild',
'Merged and built models', -1)
#
# select label volume with label 293, in the second row
#
row = 1
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row,
treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 1-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel293.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelCystic',
'Select cystic region', -1)
#
# Dilate
#
slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect')
EditUtil.setLabel(293)
self.takeScreenshot('NeurosurgicalPlanning-Dilate', 'Dilate tool', -1)
# tutorial says to click apply three times
for d in range(1, 3):
print d
# slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked()
# slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
slicer.modules.EditorWidget.toolsBox.currentOption.onApply()
self.takeScreenshot('NeurosurgicalPlanning-Dilated', 'Dilated tumor',
-1)
return True
def test_SEGExporterSelfTest1(self):
""" Test DICOM import, segmentation, export
"""
self.messageDelay = 50
import os
self.delayDisplay("Starting the DICOM SEG Export test")
#
# first, get the data - a zip file of dicom data
#
filePath = self.logic.downloadSampleData()
self.delayDisplay('Finished with download\n')
self.delayDisplay("Unzipping")
dicomFilesDirectory = self.logic.unzipSampleData(filePath)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatabase'
import shutil
try:
shutil.rmtree(tempDatabaseDirectory)
except OSError:
pass
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
self.logic.importIntoDICOMDatabase(dicomFilesDirectory)
dicomWidget.detailsPopup.open()
# load the data by series UID
mrHeadSeriesUID = "2.16.840.1.113662.4.4168496325.1025306170.548651188813145058"
dicomWidget.detailsPopup.offerLoadables(mrHeadSeriesUID, 'Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
#
# create a label map and set it for editing
#
masterNode = slicer.util.getNode('2: SAG*')
volumesLogic = slicer.modules.volumes.logic()
mergeNode = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, masterNode, masterNode.GetName() + '-label' )
mergeNode.GetDisplayNode().SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( masterNode.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID( mergeNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# go to the editor and do some drawing
#
slicer.util.selectModule('Editor')
import EditorLib
from EditorLib.EditUtil import EditUtil
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter("LabelEffect,paintThreshold", "1")
parameterNode.SetParameter("LabelEffect,paintThresholdMin", "70.0")
parameterNode.SetParameter("LabelEffect,paintThresholdMax", "279.75")
parameterNode.SetParameter("PaintEffect,radius", "40")
parameterNode.SetParameter("PaintEffect,sphere", "1")
self.delayDisplay("Paint some things")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
EditUtil.setLabel(1)
paintTool.paintAddPoint(100,100)
paintTool.paintApply()
EditUtil.setLabel(2)
paintTool.paintAddPoint(200,200)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
# save these to compare with the one we read back
originalSegmentationArray = slicer.util.array(mergeNode.GetID())
originalSegmentationNodeCopy = slicer.vtkMRMLLabelMapVolumeNode()
originalSegmentationNodeCopy.CopyOrientation(mergeNode)
# export the volumes into a SEG
tempSEGDirectory = slicer.app.temporaryPath + '/tempDICOMSEG'
qt.QDir().mkpath(tempSEGDirectory)
segFilePath = os.path.join(tempSEGDirectory, "test.SEG.dcm")
self.delayDisplay('spliting...', 200)
EditUtil.splitPerStructureVolumes(masterNode, mergeNode)
self.delayDisplay('exporting...', 200)
EditUtil.exportAsDICOMSEG(masterNode)
# close scene re-load the input data and SEG
slicer.mrmlScene.Clear(0)
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, tempSEGDirectory, None)
indexer.waitForImportFinished()
mrHeadStudyUID = "2.16.840.1.113662.4.4168496325.1025305873.7118351817185979330"
dicomWidget.detailsPopup.offerLoadables(mrHeadStudyUID, 'Study')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# confirm that segmentations are correctly reloaded
headLabelName = '2: SAG/RF-FAST/VOL/FLIP 30-label'
reloadedLabel = slicer.util.getNode(headLabelName)
reloadedSegmentationArray = slicer.util.array(reloadedLabel.GetID())
import numpy
self.assertTrue(numpy.alltrue(originalSegmentationArray == reloadedSegmentationArray))
geometryWarnings = volumesLogic.CompareVolumeGeometry(mergeNode, reloadedLabel)
print(geometryWarnings)
self.assertTrue(geometryWarnings == '')
# re-export
# close scene re-load the input data and SEG
# confirm that segmentations are available again as per-structure volumes
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def run(self,enableScreenshots=0,screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running test of the Neurosurgical Planning tutorial')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome','Welcome module',-1)
else:
# otherwise show the sample data module
moduleSelector.selectModule('SampleData')
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume()
self.delayDisplay("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
self.takeScreenshot('NeurosurgicalPlanning-Loaded','Data loaded',-1)
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget("Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget != None:
popupWidget.pinPopup(1)
self.takeScreenshot('NeurosurgicalPlanning-Link','Link slice viewers',-1)
popupWidget.pinPopup(0)
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# baseline in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(baselineVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-Baseline','Baseline in background',-1)
#
# adjust window level on baseline
#
moduleSelector.selectModule('Volumes')
baselineDisplay = baselineVolume.GetDisplayNode()
baselineDisplay.SetAutoWindowLevel(0)
baselineDisplay.SetWindow(2600)
baselineDisplay.SetLevel(1206)
self.takeScreenshot('NeurosurgicalPlanning-WindowLevel','Set W/L on baseline',-1)
#
# switch to red slice only
#
lm.setLayout(6)
self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly','Set layout to Red Slice only',-1)
#
# segmentation of tumour
#
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, baselineVolume, baselineVolume.GetName() + '-label' )
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# editor module
#
moduleSelector.selectModule('Editor')
self.takeScreenshot('NeurosurgicalPlanning-Editor','Showing Editor Module',-1)
# set the slice offset so drawing is right
sliceNode = sliceLogic.GetSliceNode()
sliceOffset = 58.7
sliceNode.SetSliceOffset(sliceOffset)
#
# paint
#
parameterNode = EditUtil.getParameterNode()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.takeScreenshot('NeurosurgicalPlanning-Paint','Paint tool in Editor Module',-1)
#
# paint in cystic part of tumor, using converstion from RAS coords to
# avoid slice widget size differences
#
EditUtil.setLabel(293)
displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-11, 73, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-12, 85, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-13, 91, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-15, 78, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintCystic','Paint cystic part of tumor',-1)
#
# paint in solid part of tumor
#
EditUtil.setLabel(7)
displayCoords = self.rasToDisplay(-0.5 , 118.5, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-7.4 , 116, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintSolid','Paint solid part of tumor',-1)
#
# paint around the tumor
#
EditUtil.setLabel(295)
rMax = 25
rMin = -50
aMax = 145
aMin = 50
rasStep = 5
# draw the top and bottom
for r in range(rMin, rMax, rasStep):
displayCoords = self.rasToDisplay(r, aMin, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(r, aMax, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
# draw the left and right
for a in range(aMin, aMax, rasStep):
displayCoords = self.rasToDisplay(rMin, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(rMax, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintAround','Paint around tumor',-1)
#
# clean up after painting
#
paintTool.cleanup()
paintTool = None
#
# Grow cut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
self.takeScreenshot('NeurosurgicalPlanning-Growcut','Growcut',-1)
#
# Merge split volume
#
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
self.takeScreenshot('NeurosurgicalPlanning-SplitMerge','SplitMerge',-1)
#
# go to the data module
#
moduleSelector.selectModule('Data')
self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData','SplitMerge results in Data',-1)
#
# Ventricles Segmentation
#
moduleSelector.selectModule('Editor')
#
# select the label volume with the area around the tumor
slicer.util.findChildren(name='PerStructureVolumesFrame')[0].collapsed = False
treeView = slicer.util.findChildren(name='StructuresView')[0]
selection = qt.QItemSelection()
# selecting the last split volume in the third row
row = 2
rowStart = treeView.model().index(row,0)
rowEnd = treeView.model().index(row,treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 3-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel295.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelOutside','Select outside region',-1)
#
# Threshold tool
#
slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect')
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter('ThresholdEffect,min', str(1700))
slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
self.takeScreenshot('NeurosurgicalPlanning-Ventricles','Ventricles segmentation',-1)
#
# Save Islands
#
slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect')
saveIslandLogic = EditorLib.SaveIslandEffectLogic(sliceWidget.sliceLogic())
displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset)
xy = (displayCoords[0], displayCoords[1])
saveIslandLogic.saveIsland(xy)
self.takeScreenshot('NeurosurgicalPlanning-SaveIsland','Ventricles save island',-1)
#
# Merge and build
#
slicer.util.findChildren(text='Merge And Build')[0].clicked()
#
# switch to conventional layout
#
lm.setLayout(2)
self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild','Merged and built models',-1)
#
# Tractography label map seeding
#
#
# select label volume with label 293, in the second row
#
row = 1
rowStart = treeView.model().index(row,0)
rowEnd = treeView.model().index(row,treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 1-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel293.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelCystic','Select cystic region',-1)
#
# Dilate
#
slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect')
EditUtil.setLabel(293)
self.takeScreenshot('NeurosurgicalPlanning-Dilate','Dilate tool',-1)
# tutorial says to click apply three times
for d in range (1,3):
print d
# slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked()
# slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
slicer.modules.EditorWidget.toolsBox.currentOption.onApply()
self.takeScreenshot('NeurosurgicalPlanning-Dilated','Dilated tumor',-1)
#
# Tractography Label Map Seeding module
#
moduleSelector.selectModule('TractographyLabelMapSeeding')
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeedingModule','Showing Tractography Label Seeding Module',-1)
tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding
parameters = {}
parameters['InputVolume'] = dtiVolume.GetID()
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 1-label")
# VTK6 TODO - set 'InputROIPipelineInfo'
parameters['InputROI'] = baselinelabel293.GetID()
fibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fibers)
parameters['OutputFibers'] = fibers.GetID()
parameters['UseIndexSpace'] = 1
parameters['StoppingValue'] = 0.15
parameters['ROIlabel'] = 293
parameters['StoppingMode'] = 'FractionalAnisotropy'
# defaults
# parameters['ClTh'] = 0.3
# parameters['MinimumLength'] = 20
# parameters['MaximumLength'] = 800
# parameters['StoppingCurvature'] = 0.7
# parameters['IntegrationStepLength'] = 0.5
# parameters['SeedSpacing'] = 2
# and run it
slicer.cli.run(tractographyLabelSeeding, None, parameters)
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeeding','Showing Tractography Label Seeding Results',-1)
#
# tractography fiducial seeding
#
moduleSelector.selectModule('TractographyInteractiveSeeding')
self.takeScreenshot('NeurosurgicalPlanning-TIS','Showing Tractography Interactive Seeding Module',-1)
# DTI in background
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# DTI visible in 3D
sliceNode = sliceLogic.GetSliceNode()
sliceLogic.StartSliceNodeInteraction(128)
sliceNode.SetSliceVisible(1)
sliceLogic.EndSliceNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-TIS-DTI','DTI volume with Tractography Interactive Seeding Module',-1)
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName('F')
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
s = sliceOffset
fidNode.AddFiducial(r,a,s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
self.takeScreenshot('NeurosurgicalPlanning-TIS-Fid1','Fiducial in Tractography Interactive Seeding Module',-1)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation()
wr.setDiffusionTensorVolumeNode(dtiVolume)
# create a fiber bundle
fiducialFibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fiducialFibers)
wr.setFiberBundleNode(fiducialFibers)
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Args','Tractography Interactive Seeding arguments',-1)
self.delayDisplay("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
self.delayDisplay(msg,250)
fidNode.SetNthFiducialPosition(0, r, y, s)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Moved','Moved fiducial and did Tractography Interactive Seeding',-1)
return True
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay("Running test of the Neurosurgical Planning tutorial")
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule("Welcome")
self.delayDisplay("Screenshot")
self.takeScreenshot("NeurosurgicalPlanning-Welcome", "Welcome module", -1)
else:
# otherwise show the sample data module
moduleSelector.selectModule("SampleData")
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume()
self.takeScreenshot("NeurosurgicalPlanning-Loaded", "Data loaded", -1)
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget("Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget is not None:
popupWidget.pinPopup(1)
self.takeScreenshot("NeurosurgicalPlanning-Link", "Link slice viewers", -1)
popupWidget.pinPopup(0)
sliceLogic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# baseline in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(baselineVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot("NeurosurgicalPlanning-Baseline", "Baseline in background", -1)
#
# adjust window level on baseline
#
moduleSelector.selectModule("Volumes")
baselineDisplay = baselineVolume.GetDisplayNode()
baselineDisplay.SetAutoWindowLevel(0)
baselineDisplay.SetWindow(2600)
baselineDisplay.SetLevel(1206)
self.takeScreenshot("NeurosurgicalPlanning-WindowLevel", "Set W/L on baseline", -1)
#
# switch to red slice only
#
lm.setLayout(6)
self.takeScreenshot("NeurosurgicalPlanning-RedSliceOnly", "Set layout to Red Slice only", -1)
#
# segmentation of tumour
#
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, baselineVolume, baselineVolume.GetName() + "-label"
)
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# editor module
#
moduleSelector.selectModule("Editor")
self.takeScreenshot("NeurosurgicalPlanning-Editor", "Showing Editor Module", -1)
# set the slice offset so drawing is right
sliceNode = sliceLogic.GetSliceNode()
sliceOffset = 58.7
sliceNode.SetSliceOffset(sliceOffset)
#
# paint
#
parameterNode = EditUtil.getParameterNode()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget("Red")
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.takeScreenshot("NeurosurgicalPlanning-Paint", "Paint tool in Editor Module", -1)
#
# paint in cystic part of tumor, using converstion from RAS coords to
# avoid slice widget size differences
#
EditUtil.setLabel(293)
displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-11, 73, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-12, 85, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-13, 91, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-15, 78, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot("NeurosurgicalPlanning-PaintCystic", "Paint cystic part of tumor", -1)
#
# paint in solid part of tumor
#
EditUtil.setLabel(7)
displayCoords = self.rasToDisplay(-0.5, 118.5, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-7.4, 116, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot("NeurosurgicalPlanning-PaintSolid", "Paint solid part of tumor", -1)
#
# paint around the tumor
#
EditUtil.setLabel(295)
rMax = 25
rMin = -50
aMax = 145
aMin = 50
rasStep = 5
# draw the top and bottom
for r in range(rMin, rMax, rasStep):
displayCoords = self.rasToDisplay(r, aMin, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(r, aMax, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
# draw the left and right
for a in range(aMin, aMax, rasStep):
displayCoords = self.rasToDisplay(rMin, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(rMax, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot("NeurosurgicalPlanning-PaintAround", "Paint around tumor", -1)
#
# clean up after painting
#
paintTool.cleanup()
paintTool = None
#
# Grow cut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
self.takeScreenshot("NeurosurgicalPlanning-Growcut", "Growcut", -1)
#
# Merge split volume
#
slicer.util.selectModule("Editor")
slicer.util.findChildren(text="Split Merge Volume")[0].clicked()
self.takeScreenshot("NeurosurgicalPlanning-SplitMerge", "SplitMerge", -1)
#
# go to the data module
#
moduleSelector.selectModule("Data")
self.takeScreenshot("NeurosurgicalPlanning-SplitMergeData", "SplitMerge results in Data", -1)
#
# Ventricles Segmentation
#
moduleSelector.selectModule("Editor")
#
# select the label volume with the area around the tumor
slicer.util.findChildren(name="PerStructureVolumesFrame")[0].collapsed = False
treeView = slicer.util.findChildren(name="StructuresView")[0]
selection = qt.QItemSelection()
# selecting the last split volume in the third row
row = 2
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row, treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 3-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel295.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot("NeurosurgicalPlanning-SelOutside", "Select outside region", -1)
#
# Threshold tool
#
slicer.modules.EditorWidget.toolsBox.selectEffect("ThresholdEffect")
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter("ThresholdEffect,min", str(1700))
slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
self.takeScreenshot("NeurosurgicalPlanning-Ventricles", "Ventricles segmentation", -1)
#
# Save Islands
#
slicer.modules.EditorWidget.toolsBox.selectEffect("SaveIslandEffect")
saveIslandLogic = EditorLib.SaveIslandEffectLogic(sliceWidget.sliceLogic())
displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset)
xy = (displayCoords[0], displayCoords[1])
saveIslandLogic.saveIsland(xy)
self.takeScreenshot("NeurosurgicalPlanning-SaveIsland", "Ventricles save island", -1)
#
# Merge and build
#
slicer.util.findChildren(text="Merge And Build")[0].clicked()
#
# switch to conventional layout
#
lm.setLayout(2)
self.takeScreenshot("NeurosurgicalPlanning-MergeAndBuild", "Merged and built models", -1)
#
# select label volume with label 293, in the second row
#
row = 1
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row, treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName("BaselineVolume-region 1-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel293.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot("NeurosurgicalPlanning-SelCystic", "Select cystic region", -1)
#
# Dilate
#
slicer.modules.EditorWidget.toolsBox.selectEffect("DilateEffect")
EditUtil.setLabel(293)
self.takeScreenshot("NeurosurgicalPlanning-Dilate", "Dilate tool", -1)
# tutorial says to click apply three times
for d in range(1, 3):
print d
# slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked()
# slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
slicer.modules.EditorWidget.toolsBox.currentOption.onApply()
self.takeScreenshot("NeurosurgicalPlanning-Dilated", "Dilated tumor", -1)
return True
class ParenchymaWidget(ScriptedLoadableModuleWidget):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent = None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.masterNode = None
self.labelNode = None
self.paint = None
self.paintMode = False
self.correct = None
self.correctMode = False
self.logic = ParenchymaLogic()
self.editUtil = EditUtil()
#self.editUtil = EditorLib.EditUtil.EditUtil()
#self.localParEditorWidget = None
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = True
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene( slicer.mrmlScene )
self.inputSelector.setToolTip( "Pick the input to the algorithm." )
parametersLayout.addRow("Input Volume: ", self.inputSelector)
#self.activeVolume = self.inputSelector.currentNode()
#self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
#self.labelSelector = slicer.qSlicerLabelMapVolumeDisplayWidget()
#parametersLayout.addRow("Label Map: ", self.labelSelector)
#
# Select Button
#
self.selectButton = qt.QPushButton("Select")
self.selectButton.toolTip = "Select the volume."
self.selectButton.enabled = True
parametersLayout.addRow(self.selectButton)
#
# Gradient Button
#
self.gradientButton = qt.QPushButton("Gradient - sergio reimplementation")
self.gradientButton.toolTip = "re-implementation of sergio's gradient."
self.gradientButton.enabled = True
parametersLayout.addRow(self.gradientButton)
#
# Paint Button
#
self.paintButton = qt.QPushButton("Paint")
self.paintButton.toolTip = "Turn on paint."
self.paintButton.enabled = True
self.paintButton.checkable = True
parametersLayout.addRow(self.paintButton)
#
# Apply mask Button
#
self.applyButton = qt.QPushButton("Apply mask")
self.applyButton.toolTip = "Find area of mask."
self.applyButton.enabled = True
parametersLayout.addRow(self.applyButton)
#
# Range for threshold
#
self.threshold = ctk.ctkRangeWidget()
lo, hi = self.getLoHiImageValues()
self.threshold.minimum, self.threshold.maximum = lo, hi
self.threshold.singleStep = (hi - lo) / 1000.
parametersLayout.addRow(self.threshold)
#
# Grow Button
#
self.growButton = qt.QPushButton("Grow with Threshold")
self.growButton.toolTip = "Grow into 3D with connected threshold."
self.growButton.enabled = True
parametersLayout.addRow(self.growButton)
#
# Liver 2D Button
#
self.liver2DButton = qt.QPushButton("Liver 2D")
self.liver2DButton.toolTip = "Grow from mask in 2D, but up down into next slices."
self.liver2DButton.enabled = True
parametersLayout.addRow(self.liver2DButton)
#
# Cross remove Button
#
self.crossButton = qt.QPushButton("Cross remove")
self.crossButton.toolTip = "re-implementation of sergio's cross remove."
self.crossButton.enabled = True
parametersLayout.addRow(self.crossButton)
#
# Connectivity reduction Button
#
self.connectivityButton = qt.QPushButton("Connectivity reduction")
self.connectivityButton.toolTip = "re-implementation of sergio's connectivity reduction."
self.connectivityButton.enabled = True
parametersLayout.addRow(self.connectivityButton)
#
# Paint Button (correction)
#
self.correctButton = qt.QPushButton("Correct")
self.correctButton.toolTip = "Turn on paint for annotating corrections."
self.correctButton.enabled = True
self.correctButton.checkable = True
parametersLayout.addRow(self.correctButton)
#
# Track centroid under mask
#
self.trackMaskButton = qt.QPushButton("Track correction")
self.trackMaskButton.toolTip = "Try to use correction mask, and track the centroid in has inside it"
self.trackMaskButton.enabled = True
parametersLayout.addRow(self.trackMaskButton)
#
# Erase mask (including all under)
#
self.eraseMaskButton = qt.QPushButton("Erase correction")
self.eraseMaskButton.toolTip = "Delete the correction mask to hopefully orphan other areas"
self.eraseMaskButton.enabled = True
parametersLayout.addRow(self.eraseMaskButton)
#
# Remove unconnected
#
self.removeIsolatedButton = qt.QPushButton("Remove unconnected")
self.removeIsolatedButton.toolTip = "try to see just the main blob and remove stuff not connected."
self.removeIsolatedButton.enabled = True
parametersLayout.addRow(self.removeIsolatedButton)
# connections
#buttons
self.selectButton.connect('clicked(bool)', self.onSelectButton)
self.gradientButton.connect('clicked(bool)', self.onGradientButton)
self.paintButton.connect('clicked(bool)', self.onPaintButton)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.growButton.connect('clicked(bool)', self.onGrowButton)
self.liver2DButton.connect('clicked(bool)', self.onliver2DButton)
self.crossButton.connect('clicked(bool)', self.onCrossButton)
self.connectivityButton.connect('clicked(bool)', self.onConnectivityButton)
# correction tools buttons
self.correctButton.connect('clicked(bool)', self.onCorrectButton)
self.trackMaskButton.connect('clicked(bool)', self.onTrackMaskButton)
self.eraseMaskButton.connect('clicked(bool)', self.onEraseMaskButton)
self.removeIsolatedButton.connect('clicked(bool)', self.onRemoveIsolatedButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.threshold.connect('valuesChanged(double,double)', self.onThresholdValuesChanged)
# Creates and adds the custom Editor Widget to the module
#self.localParEditorWidget = ParEditorWidget(parent=self.parent, showVolumesFrame=False)
#self.localParEditorWidget.setup()
#self.localParEditorWidget.enter()
# Add vertical spacer
self.layout.addStretch(1)
# sets the layout to Red Slice Only
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
'''-----------------------------------------------------------------------------'''
def cleanup(self):
pass
def onSelect(self):
self.applyButton.enabled = self.inputSelector.currentNode()
self.masterNode = self.inputSelector.currentNode()
def onSelectButton(self):
self.masterNode = self.inputSelector.currentNode()
lo, hi = self.getLoHiImageValues()
self.threshold.minimum, self.threshold.maximum = lo, hi
self.threshold.singleStep = (hi - lo) / 1000.
#print(self.inputSelector.currentNode())
def onLabelButton(self):
self.labelNode = self.logic.createLabelMap(self.inputSelector.currentNode())
def onProcessFilterButton(self):
self.logic.processFilter(self.masterNode)
def onPaintButton(self):
if self.paintMode:
self.paintMode = False
print("deleting paint")
self.painter.cleanup()
self.painter = None
#self.paint.removeObs()
else:
self.paintMode = True
# just in case?
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( self.masterNode.GetID() )
if self.labelNode == None:
self.labelNode = self.logic.createLabelMap(self.inputSelector.currentNode())
selectionNode.SetReferenceActiveLabelVolumeID( self.labelNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.editUtil.setLabel(1) # green
print("create paint (editor paint effect tool)")
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
self.painter = EditorLib.PaintEffectTool(sliceWidget)
def onApplyButton(self):
self.logic.runMask(self.masterNode, self.labelNode)
mean, std = self.logic.getMeanSD()
max = mean + std
min = mean - std
hi = mean + 4*std
lo = mean - 4*std
self.threshold.minimum, self.threshold.maximum = lo, hi
self.setThresholdValues(min, max)
def onGrowButton(self):
self.logic.runThreshold(self.masterNode, self.labelNode)
def onGradientButton(self):
self.logic.runGradient(self.masterNode)
def onliver2DButton(self):
print("Liver button")
#runFindLiver2D(self,masterNode,labelNode):
self.logic.runFindLiver2D(self.masterNode, self.labelNode)
def onCrossButton(self):
self.logic.runCrossRemove(self.masterNode, self.labelNode, 2) # need to pass in size of cross
def onConnectivityButton(self):
self.logic.runConnectivity(self.masterNode, self.labelNode, 10) # need to pass in number of pixels around it that need to be 1
def onCorrectButton(self):
if self.correctMode:
self.correctMode = False
print("deleting correct")
self.painter.cleanup()
self.painter = None
#self.paint.removeObs()
else:
self.correctMode = True
# just in case?
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( self.masterNode.GetID() )
if self.labelNode == None:
self.labelNode = self.logic.createLabelMap(self.inputSelector.currentNode())
selectionNode.SetReferenceActiveLabelVolumeID( self.labelNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.editUtil.setLabel(5) # red
print("create correct (editor paint effect tool)")
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
self.painter = EditorLib.PaintEffectTool(sliceWidget)
def onTrackMaskButton(self):
self.logic.runTrackMask(self.masterNode, self.labelNode)
def onEraseMaskButton(self):
self.logic.runEraseMask(self.masterNode, self.labelNode)
def onRemoveIsolatedButton(self):
self.logic.runRemoveIsolated(self.masterNode, self.labelNode)
def onEdgeButton(self):
self.logic.runFindEdge(self.masterNode, self.labelNode)
def getLoHiImageValues(self):
backgroundImage = self.masterNode
lo = 0
hi = 100
if backgroundImage:
data = backgroundImage.GetImageData()
lo, hi = data.GetScalarRange()
print('Low: ', lo)
print('High: ', hi)
return lo, hi
def onThresholdValuesChanged(self):
print('value changed')
min = self.threshold.minimumValue
max = self.threshold.maximumValue
print(min, max)
def setThresholdValues(self, min, max):
self.threshold.setMinimumValue( min )
self.threshold.setMaximumValue( max )
def test_ThresholdThreading(self):
"""
Replicate the issue reported in bug 1822 where splitting
a grow-cut produced volume causes a multi-threading related
issue on mac release builds
"""
#
# first, get some sample data
#
self.delayDisplay("Get some data")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
head = sampleDataLogic.downloadMRHead()
#
# now, define an ROI in it
#
roi = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roi)
roi.SetXYZ(-2, 104, -80)
roi.SetRadiusXYZ(30, 30, 30)
#
# apply the cropping to the head
#
cropLogic = slicer.modules.cropvolume.logic()
cvpn = slicer.vtkMRMLCropVolumeParametersNode()
cvpn.SetROINodeID( roi.GetID() )
cvpn.SetInputVolumeNodeID( head.GetID() )
cropLogic.Apply( cvpn )
croppedHead = slicer.mrmlScene.GetNodeByID( cvpn.GetOutputVolumeNodeID() )
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
croppedHeadLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, croppedHead, croppedHead.GetName() + '-label' )
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetActiveVolumeID( croppedHead.GetID() )
selectionNode.SetActiveLabelVolumeID( croppedHeadLabel.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# got to the editor and do some drawing
#
self.delayDisplay("Paint some things")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
EditUtil.setLabel(1)
paintTool.paintAddPoint(100,100)
paintTool.paintApply()
EditUtil.setLabel(2)
paintTool.paintAddPoint(200,200)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
self.delayDisplay("Now grow cut")
#
# now do GrowCut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
#
# now split the volume, merge it back, and see if it looks right
#
preArray = slicer.util.array(croppedHeadLabel.GetName())
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
slicer.util.findChildren(text='Merge All')[0].clicked()
postArray = slicer.util.array(croppedHeadLabel.GetName())
if (postArray - preArray).max() != 0:
print("!$!$!#!@#!@!@$%! Test Failed!!")
else:
print("Ahh... test passed.")
self.assertEqual((postArray - preArray).max(), 0)
self.delayDisplay("Test passed!")
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay(
'Running test of the Neurosurgical Planning tutorial')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(2)
moduleSelector = slicer.util.mainWindow().moduleSelector()
#
# first load the data
#
if self.enableScreenshots == 1:
# for the tutorial, do it through the welcome module
moduleSelector.selectModule('Welcome')
self.delayDisplay("Screenshot")
self.takeScreenshot('NeurosurgicalPlanning-Welcome',
'Welcome module', -1)
else:
# otherwise show the sample data module
moduleSelector.selectModule('SampleData')
# use the sample data module logic to load data for the self test
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting Baseline volume")
baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume(
)
self.delayDisplay("Getting DTI volume")
dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume()
self.takeScreenshot('NeurosurgicalPlanning-Loaded', 'Data loaded', -1)
#
# link the viewers
#
if self.enableScreenshots == 1:
# for the tutorial, pop up the linking control
sliceController = slicer.app.layoutManager().sliceWidget(
"Red").sliceController()
popupWidget = sliceController.findChild("ctkPopupWidget")
if popupWidget != None:
popupWidget.pinPopup(1)
self.takeScreenshot('NeurosurgicalPlanning-Link',
'Link slice viewers', -1)
popupWidget.pinPopup(0)
sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
compositeNode.SetLinkedControl(1)
#
# baseline in the background
#
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(baselineVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-Baseline',
'Baseline in background', -1)
#
# adjust window level on baseline
#
moduleSelector.selectModule('Volumes')
baselineDisplay = baselineVolume.GetDisplayNode()
baselineDisplay.SetAutoWindowLevel(0)
baselineDisplay.SetWindow(2600)
baselineDisplay.SetLevel(1206)
self.takeScreenshot('NeurosurgicalPlanning-WindowLevel',
'Set W/L on baseline', -1)
#
# switch to red slice only
#
lm.setLayout(6)
self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly',
'Set layout to Red Slice only', -1)
#
# segmentation of tumour
#
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, baselineVolume,
baselineVolume.GetName() + '-label')
baselineDisplayNode = baselineVolumeLabel.GetDisplayNode()
baselineDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
baselineVolumeLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# editor module
#
moduleSelector.selectModule('Editor')
self.takeScreenshot('NeurosurgicalPlanning-Editor',
'Showing Editor Module', -1)
# set the slice offset so drawing is right
sliceNode = sliceLogic.GetSliceNode()
sliceOffset = 58.7
sliceNode.SetSliceOffset(sliceOffset)
#
# paint
#
parameterNode = EditUtil.getParameterNode()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.takeScreenshot('NeurosurgicalPlanning-Paint',
'Paint tool in Editor Module', -1)
#
# paint in cystic part of tumor, using converstion from RAS coords to
# avoid slice widget size differences
#
EditUtil.setLabel(293)
displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-11, 73, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-12, 85, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-13, 91, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-15, 78, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintCystic',
'Paint cystic part of tumor', -1)
#
# paint in solid part of tumor
#
EditUtil.setLabel(7)
displayCoords = self.rasToDisplay(-0.5, 118.5, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(-7.4, 116, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintSolid',
'Paint solid part of tumor', -1)
#
# paint around the tumor
#
EditUtil.setLabel(295)
rMax = 25
rMin = -50
aMax = 145
aMin = 50
rasStep = 5
# draw the top and bottom
for r in range(rMin, rMax, rasStep):
displayCoords = self.rasToDisplay(r, aMin, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(r, aMax, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
# draw the left and right
for a in range(aMin, aMax, rasStep):
displayCoords = self.rasToDisplay(rMin, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
displayCoords = self.rasToDisplay(rMax, a, sliceOffset)
paintTool.paintAddPoint(displayCoords[0], displayCoords[1])
paintTool.paintApply()
self.takeScreenshot('NeurosurgicalPlanning-PaintAround',
'Paint around tumor', -1)
#
# clean up after painting
#
paintTool.cleanup()
paintTool = None
#
# Grow cut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
self.takeScreenshot('NeurosurgicalPlanning-Growcut', 'Growcut', -1)
#
# Merge split volume
#
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
self.takeScreenshot('NeurosurgicalPlanning-SplitMerge', 'SplitMerge',
-1)
#
# go to the data module
#
moduleSelector.selectModule('Data')
self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData',
'SplitMerge results in Data', -1)
#
# Ventricles Segmentation
#
moduleSelector.selectModule('Editor')
#
# select the label volume with the area around the tumor
slicer.util.findChildren(
name='PerStructureVolumesFrame')[0].collapsed = False
treeView = slicer.util.findChildren(name='StructuresView')[0]
selection = qt.QItemSelection()
# selecting the last split volume in the third row
row = 2
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row,
treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 3-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel295.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelOutside',
'Select outside region', -1)
#
# Threshold tool
#
slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect')
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter('ThresholdEffect,min', str(1700))
slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
self.takeScreenshot('NeurosurgicalPlanning-Ventricles',
'Ventricles segmentation', -1)
#
# Save Islands
#
slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect')
saveIslandLogic = EditorLib.SaveIslandEffectLogic(
sliceWidget.sliceLogic())
displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset)
xy = (displayCoords[0], displayCoords[1])
saveIslandLogic.saveIsland(xy)
self.takeScreenshot('NeurosurgicalPlanning-SaveIsland',
'Ventricles save island', -1)
#
# Merge and build
#
slicer.util.findChildren(text='Merge And Build')[0].clicked()
#
# switch to conventional layout
#
lm.setLayout(2)
self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild',
'Merged and built models', -1)
#
# Tractography label map seeding
#
#
# select label volume with label 293, in the second row
#
row = 1
rowStart = treeView.model().index(row, 0)
rowEnd = treeView.model().index(row,
treeView.model().columnCount() - 1)
# rowSel = qt.QItemSelection(rowStart, rowEnd)
selection.select(rowStart, rowEnd)
# backup: select the label map in the slice logic too
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 1-label")
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetLabelVolumeID(baselinelabel293.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
self.takeScreenshot('NeurosurgicalPlanning-SelCystic',
'Select cystic region', -1)
#
# Dilate
#
slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect')
EditUtil.setLabel(293)
self.takeScreenshot('NeurosurgicalPlanning-Dilate', 'Dilate tool', -1)
# tutorial says to click apply three times
for d in range(1, 3):
print d
# slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked()
# slicer.modules.EditorWidget.toolsBox.currentTools[0].apply()
slicer.modules.EditorWidget.toolsBox.currentOption.onApply()
self.takeScreenshot('NeurosurgicalPlanning-Dilated', 'Dilated tumor',
-1)
#
# Tractography Label Map Seeding module
#
moduleSelector.selectModule('TractographyLabelMapSeeding')
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeedingModule',
'Showing Tractography Label Seeding Module', -1)
tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding
parameters = {}
parameters['InputVolume'] = dtiVolume.GetID()
baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName(
"BaselineVolume-region 1-label")
# VTK6 TODO - set 'InputROIPipelineInfo'
parameters['InputROI'] = baselinelabel293.GetID()
fibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fibers)
parameters['OutputFibers'] = fibers.GetID()
parameters['UseIndexSpace'] = 1
parameters['StoppingValue'] = 0.15
parameters['ROIlabel'] = 293
parameters['StoppingMode'] = 'FractionalAnisotropy'
# defaults
# parameters['ClTh'] = 0.3
# parameters['MinimumLength'] = 20
# parameters['MaximumLength'] = 800
# parameters['StoppingCurvature'] = 0.7
# parameters['IntegrationStepLength'] = 0.5
# parameters['SeedSpacing'] = 2
# and run it
slicer.cli.run(tractographyLabelSeeding, None, parameters)
self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeeding',
'Showing Tractography Label Seeding Results', -1)
#
# tractography fiducial seeding
#
moduleSelector.selectModule('TractographyInteractiveSeeding')
self.takeScreenshot('NeurosurgicalPlanning-TIS',
'Showing Tractography Interactive Seeding Module',
-1)
# DTI in background
sliceLogic.StartSliceCompositeNodeInteraction(1)
compositeNode.SetBackgroundVolumeID(dtiVolume.GetID())
sliceLogic.EndSliceCompositeNodeInteraction()
# DTI visible in 3D
sliceNode = sliceLogic.GetSliceNode()
sliceLogic.StartSliceNodeInteraction(128)
sliceNode.SetSliceVisible(1)
sliceLogic.EndSliceNodeInteraction()
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-DTI',
'DTI volume with Tractography Interactive Seeding Module', -1)
# place a fiducial
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidNode.SetName('F')
slicer.mrmlScene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(displayNode.GetID())
r = 28.338526
a = 34.064367
s = sliceOffset
fidNode.AddFiducial(r, a, s)
# make it active
selectionNode = slicer.mrmlScene.GetNodeByID(
"vtkMRMLSelectionNodeSingleton")
if (selectionNode != None):
selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID())
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-Fid1',
'Fiducial in Tractography Interactive Seeding Module', -1)
# set up the arguments
wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation(
)
wr.setDiffusionTensorVolumeNode(dtiVolume)
# create a fiber bundle
fiducialFibers = slicer.vtkMRMLFiberBundleNode()
slicer.mrmlScene.AddNode(fiducialFibers)
wr.setFiberBundleNode(fiducialFibers)
wr.setSeedingNode(fidNode)
wr.setMinimumPath(10)
wr.setStoppingValue(0.15)
self.takeScreenshot('NeurosurgicalPlanning-TIS-Args',
'Tractography Interactive Seeding arguments', -1)
self.delayDisplay("Moving the fiducial")
for y in range(-20, 100, 5):
msg = "Moving the fiducial to y = " + str(y)
self.delayDisplay(msg, 250)
fidNode.SetNthFiducialPosition(0, r, y, s)
self.takeScreenshot(
'NeurosurgicalPlanning-TIS-Moved',
'Moved fiducial and did Tractography Interactive Seeding', -1)
return True
class ParenchymaWidget(ScriptedLoadableModuleWidget):
"""Uses ScriptedLoadableModuleWidget base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent=None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.masterNode = None
self.labelNode = None
self.paint = None
self.paintMode = False
self.correct = None
self.correctMode = False
self.logic = ParenchymaLogic()
self.editUtil = EditUtil()
#self.editUtil = EditorLib.EditUtil.EditUtil()
#self.localParEditorWidget = None
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
0)
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = True
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersLayout.addRow("Input Volume: ", self.inputSelector)
#self.activeVolume = self.inputSelector.currentNode()
#self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
#self.labelSelector = slicer.qSlicerLabelMapVolumeDisplayWidget()
#parametersLayout.addRow("Label Map: ", self.labelSelector)
#
# Select Button
#
self.selectButton = qt.QPushButton("Select")
self.selectButton.toolTip = "Select the volume."
self.selectButton.enabled = True
parametersLayout.addRow(self.selectButton)
#
# Gradient Button
#
self.gradientButton = qt.QPushButton(
"Gradient - sergio reimplementation")
self.gradientButton.toolTip = "re-implementation of sergio's gradient."
self.gradientButton.enabled = True
parametersLayout.addRow(self.gradientButton)
#
# Paint Button
#
self.paintButton = qt.QPushButton("Paint")
self.paintButton.toolTip = "Turn on paint."
self.paintButton.enabled = True
self.paintButton.checkable = True
parametersLayout.addRow(self.paintButton)
#
# Apply mask Button
#
self.applyButton = qt.QPushButton("Apply mask")
self.applyButton.toolTip = "Find area of mask."
self.applyButton.enabled = True
parametersLayout.addRow(self.applyButton)
#
# Range for threshold
#
self.threshold = ctk.ctkRangeWidget()
lo, hi = self.getLoHiImageValues()
self.threshold.minimum, self.threshold.maximum = lo, hi
self.threshold.singleStep = (hi - lo) / 1000.
parametersLayout.addRow(self.threshold)
#
# Grow Button
#
self.growButton = qt.QPushButton("Grow with Threshold")
self.growButton.toolTip = "Grow into 3D with connected threshold."
self.growButton.enabled = True
parametersLayout.addRow(self.growButton)
#
# Liver 2D Button
#
self.liver2DButton = qt.QPushButton("Liver 2D")
self.liver2DButton.toolTip = "Grow from mask in 2D, but up down into next slices."
self.liver2DButton.enabled = True
parametersLayout.addRow(self.liver2DButton)
#
# Cross remove Button
#
self.crossButton = qt.QPushButton("Cross remove")
self.crossButton.toolTip = "re-implementation of sergio's cross remove."
self.crossButton.enabled = True
parametersLayout.addRow(self.crossButton)
#
# Connectivity reduction Button
#
self.connectivityButton = qt.QPushButton("Connectivity reduction")
self.connectivityButton.toolTip = "re-implementation of sergio's connectivity reduction."
self.connectivityButton.enabled = True
parametersLayout.addRow(self.connectivityButton)
#
# Paint Button (correction)
#
self.correctButton = qt.QPushButton("Correct")
self.correctButton.toolTip = "Turn on paint for annotating corrections."
self.correctButton.enabled = True
self.correctButton.checkable = True
parametersLayout.addRow(self.correctButton)
#
# Track centroid under mask
#
self.trackMaskButton = qt.QPushButton("Track correction")
self.trackMaskButton.toolTip = "Try to use correction mask, and track the centroid in has inside it"
self.trackMaskButton.enabled = True
parametersLayout.addRow(self.trackMaskButton)
#
# Erase mask (including all under)
#
self.eraseMaskButton = qt.QPushButton("Erase correction")
self.eraseMaskButton.toolTip = "Delete the correction mask to hopefully orphan other areas"
self.eraseMaskButton.enabled = True
parametersLayout.addRow(self.eraseMaskButton)
#
# Remove unconnected
#
self.removeIsolatedButton = qt.QPushButton("Remove unconnected")
self.removeIsolatedButton.toolTip = "try to see just the main blob and remove stuff not connected."
self.removeIsolatedButton.enabled = True
parametersLayout.addRow(self.removeIsolatedButton)
# connections
#buttons
self.selectButton.connect('clicked(bool)', self.onSelectButton)
self.gradientButton.connect('clicked(bool)', self.onGradientButton)
self.paintButton.connect('clicked(bool)', self.onPaintButton)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.growButton.connect('clicked(bool)', self.onGrowButton)
self.liver2DButton.connect('clicked(bool)', self.onliver2DButton)
self.crossButton.connect('clicked(bool)', self.onCrossButton)
self.connectivityButton.connect('clicked(bool)',
self.onConnectivityButton)
# correction tools buttons
self.correctButton.connect('clicked(bool)', self.onCorrectButton)
self.trackMaskButton.connect('clicked(bool)', self.onTrackMaskButton)
self.eraseMaskButton.connect('clicked(bool)', self.onEraseMaskButton)
self.removeIsolatedButton.connect('clicked(bool)',
self.onRemoveIsolatedButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.threshold.connect('valuesChanged(double,double)',
self.onThresholdValuesChanged)
# Creates and adds the custom Editor Widget to the module
#self.localParEditorWidget = ParEditorWidget(parent=self.parent, showVolumesFrame=False)
#self.localParEditorWidget.setup()
#self.localParEditorWidget.enter()
# Add vertical spacer
self.layout.addStretch(1)
# sets the layout to Red Slice Only
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
'''-----------------------------------------------------------------------------'''
def cleanup(self):
pass
def onSelect(self):
self.applyButton.enabled = self.inputSelector.currentNode()
self.masterNode = self.inputSelector.currentNode()
def onSelectButton(self):
self.masterNode = self.inputSelector.currentNode()
lo, hi = self.getLoHiImageValues()
self.threshold.minimum, self.threshold.maximum = lo, hi
self.threshold.singleStep = (hi - lo) / 1000.
#print(self.inputSelector.currentNode())
def onLabelButton(self):
self.labelNode = self.logic.createLabelMap(
self.inputSelector.currentNode())
def onProcessFilterButton(self):
self.logic.processFilter(self.masterNode)
def onPaintButton(self):
if self.paintMode:
self.paintMode = False
print("deleting paint")
self.painter.cleanup()
self.painter = None
#self.paint.removeObs()
else:
self.paintMode = True
# just in case?
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.masterNode.GetID())
if self.labelNode == None:
self.labelNode = self.logic.createLabelMap(
self.inputSelector.currentNode())
selectionNode.SetReferenceActiveLabelVolumeID(
self.labelNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.editUtil.setLabel(1) # green
print("create paint (editor paint effect tool)")
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
self.painter = EditorLib.PaintEffectTool(sliceWidget)
def onApplyButton(self):
self.logic.runMask(self.masterNode, self.labelNode)
mean, std = self.logic.getMeanSD()
max = mean + std
min = mean - std
hi = mean + 4 * std
lo = mean - 4 * std
self.threshold.minimum, self.threshold.maximum = lo, hi
self.setThresholdValues(min, max)
def onGrowButton(self):
self.logic.runThreshold(self.masterNode, self.labelNode)
def onGradientButton(self):
self.logic.runGradient(self.masterNode)
def onliver2DButton(self):
print("Liver button")
#runFindLiver2D(self,masterNode,labelNode):
self.logic.runFindLiver2D(self.masterNode, self.labelNode)
def onCrossButton(self):
self.logic.runCrossRemove(self.masterNode, self.labelNode,
2) # need to pass in size of cross
def onConnectivityButton(self):
self.logic.runConnectivity(
self.masterNode, self.labelNode,
10) # need to pass in number of pixels around it that need to be 1
def onCorrectButton(self):
if self.correctMode:
self.correctMode = False
print("deleting correct")
self.painter.cleanup()
self.painter = None
#self.paint.removeObs()
else:
self.correctMode = True
# just in case?
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.masterNode.GetID())
if self.labelNode == None:
self.labelNode = self.logic.createLabelMap(
self.inputSelector.currentNode())
selectionNode.SetReferenceActiveLabelVolumeID(
self.labelNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.editUtil.setLabel(5) # red
print("create correct (editor paint effect tool)")
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
self.painter = EditorLib.PaintEffectTool(sliceWidget)
def onTrackMaskButton(self):
self.logic.runTrackMask(self.masterNode, self.labelNode)
def onEraseMaskButton(self):
self.logic.runEraseMask(self.masterNode, self.labelNode)
def onRemoveIsolatedButton(self):
self.logic.runRemoveIsolated(self.masterNode, self.labelNode)
def onEdgeButton(self):
self.logic.runFindEdge(self.masterNode, self.labelNode)
def getLoHiImageValues(self):
backgroundImage = self.masterNode
lo = 0
hi = 100
if backgroundImage:
data = backgroundImage.GetImageData()
lo, hi = data.GetScalarRange()
print('Low: ', lo)
print('High: ', hi)
return lo, hi
def onThresholdValuesChanged(self):
print('value changed')
min = self.threshold.minimumValue
max = self.threshold.maximumValue
print(min, max)
def setThresholdValues(self, min, max):
self.threshold.setMinimumValue(min)
self.threshold.setMaximumValue(max)
def test_ThresholdThreading(self):
"""
Replicate the issue reported in bug 1822 where spliting
a grow-cut produced volume causes a multi-threading related
issue on mac release builds
"""
#
# first, get some sample data
#
self.delayDisplay("Get some data")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
head = sampleDataLogic.downloadMRHead()
#
# now, define an ROI in it
#
roi = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roi)
roi.SetXYZ(-2, 104, -80)
roi.SetRadiusXYZ(30, 30, 30)
#
# apply the cropping to the head
#
cropLogic = slicer.modules.cropvolume.logic()
cvpn = slicer.vtkMRMLCropVolumeParametersNode()
cvpn.SetROINodeID(roi.GetID())
cvpn.SetInputVolumeNodeID(head.GetID())
cropLogic.Apply(cvpn)
croppedHead = slicer.mrmlScene.GetNodeByID(
cvpn.GetOutputVolumeNodeID())
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
croppedHeadLabel = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, croppedHead,
croppedHead.GetName() + '-label')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetActiveVolumeID(croppedHead.GetID())
selectionNode.SetActiveLabelVolumeID(croppedHeadLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# got to the editor and do some drawing
#
self.delayDisplay("Paint some things")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
EditUtil.setLabel(1)
paintTool.paintAddPoint(100, 100)
paintTool.paintApply()
EditUtil.setLabel(2)
paintTool.paintAddPoint(200, 200)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
self.delayDisplay("Now grow cut")
#
# now do GrowCut
#
growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic())
growCutLogic.growCut()
#
# now split the volume, merge it back, and see if it looks right
#
preArray = slicer.util.array(croppedHeadLabel.GetName())
slicer.util.selectModule('Editor')
slicer.util.findChildren(text='Split Merge Volume')[0].clicked()
slicer.util.findChildren(text='Merge All')[0].clicked()
postArray = slicer.util.array(croppedHeadLabel.GetName())
if (postArray - preArray).max() != 0:
print("!$!$!#!@#!@!@$%! Test Failed!!")
else:
print("Ahh... test passed.")
self.assertEqual((postArray - preArray).max(), 0)
self.delayDisplay("Test passed!")
def test_SEGExporterSelfTest1(self):
""" Test DICOM import, segmentation, export
"""
self.messageDelay = 50
import os
self.delayDisplay("Starting the DICOM SEG Export test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = ((
'http://slicer.kitware.com/midas3/download/item/220834/PieperMRHead.zip',
'PieperMRHead.zip'), )
self.delayDisplay("Downloading")
for url, name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' %
(name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatabase'
import shutil
shutil.rmtree(tempDatabaseDirectory)
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(
slicer.dicomDatabase.databaseFilename)[0]
else:
originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory,
None)
indexer.waitForImportFinished()
dicomWidget.detailsPopup.open()
# load the data by series UID
mrHeadSeriesUID = "2.16.840.1.113662.4.4168496325.1025306170.548651188813145058"
dicomWidget.detailsPopup.offerLoadables(mrHeadSeriesUID, 'Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
#
# create a label map and set it for editing
#
masterNode = slicer.util.getNode('2: SAG*')
volumesLogic = slicer.modules.volumes.logic()
mergeNode = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, masterNode,
masterNode.GetName() + '-label')
mergeNode.GetDisplayNode().SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(masterNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(mergeNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# go to the editor and do some drawing
#
slicer.util.selectModule('Editor')
import EditorLib
from EditorLib.EditUtil import EditUtil
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter("LabelEffect,paintThreshold", "1")
parameterNode.SetParameter("LabelEffect,paintThresholdMin", "70.0")
parameterNode.SetParameter("LabelEffect,paintThresholdMax",
"279.75")
parameterNode.SetParameter("PaintEffect,radius", "40")
parameterNode.SetParameter("PaintEffect,sphere", "1")
self.delayDisplay("Paint some things")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
EditUtil.setLabel(1)
paintTool.paintAddPoint(100, 100)
paintTool.paintApply()
EditUtil.setLabel(2)
paintTool.paintAddPoint(200, 200)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
# save these to compare with the one we read back
originalSegmentationArray = slicer.util.array(mergeNode.GetID())
originalSegmentationNodeCopy = slicer.vtkMRMLLabelMapVolumeNode()
originalSegmentationNodeCopy.CopyOrientation(mergeNode)
# export the volumes into a SEG
tempSEGDirectory = slicer.app.temporaryPath + '/tempDICOMSEG'
qt.QDir().mkpath(tempSEGDirectory)
segFilePath = os.path.join(tempSEGDirectory, "test.SEG.dcm")
self.delayDisplay('spliting...', 200)
EditUtil.splitPerStructureVolumes(masterNode, mergeNode)
self.delayDisplay('exporting...', 200)
EditUtil.exportAsDICOMSEG(masterNode)
# close scene re-load the input data and SEG
slicer.mrmlScene.Clear(0)
indexer.addDirectory(slicer.dicomDatabase, tempSEGDirectory, None)
indexer.waitForImportFinished()
mrHeadStudyUID = "2.16.840.1.113662.4.4168496325.1025305873.7118351817185979330"
dicomWidget.detailsPopup.offerLoadables(mrHeadStudyUID, 'Study')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# confirm that segmentations are correctly reloaded
headLabelName = '2: SAG/RF-FAST/VOL/FLIP 30-label'
reloadedLabel = slicer.util.getNode(headLabelName)
reloadedSegmentationArray = slicer.util.array(
reloadedLabel.GetID())
import numpy
self.assertTrue(
numpy.alltrue(
originalSegmentationArray == reloadedSegmentationArray))
geometryWarnings = volumesLogic.CompareVolumeGeometry(
mergeNode, reloadedLabel)
print(geometryWarnings)
self.assertTrue(geometryWarnings == '')
# re-export
# close scene re-load the input data and SEG
# confirm that segmentations are available again as per-structure volumes
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))