def updateSelection(self, row):
self.targetTable.clearSelection()
first = self.targetTable.model().index(row, 0)
second = self.targetTable.model().index(row, 1)
selection = qt.QItemSelection(first, second)
self.targetTable.selectionModel().select(selection, qt.QItemSelectionModel.Select)
def selectStructure(self, idx):
"""programmatically select the specified structure"""
selectionModel = self.structuresView.selectionModel()
selectionModel.select(qt.QItemSelection(self.structures.index(idx,0),
self.structures.index(idx,4)),
selectionModel.ClearAndSelect)
selectionModel.setCurrentIndex(self.structures.index(idx,0), selectionModel.NoUpdate)
self.structuresView.activated(self.structures.index(idx,0))
def _selectAllSeries(self, selected):
if selected:
m = self._seriesTableModel
itemSelection = \
qt.QItemSelection(m.index(0, 0), m.index(m.rowCount()-1, m.columnCount()-1))
self._seriesTable.selectionModel().select(
itemSelection,
qt.QItemSelectionModel.Select | qt.QItemSelectionModel.Rows)
else:
self._seriesTable.selectionModel().clearSelection()
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 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 setup(self):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer).
# Additional widgets can be instantiated manually and added to self.layout.
uiWidget = slicer.util.loadUI(
self.resourcePath('UI/antsRegistration.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
# Set custom UI components
self.ui.stagesTableWidget = StagesTable()
stagesTableLayout = qt.QVBoxLayout(self.ui.stagesFrame)
stagesTableLayout.addWidget(self.ui.stagesTableWidget)
self.ui.metricsTableWidget = MetricsTable()
metricsTableLayout = qt.QVBoxLayout(self.ui.metricsFrame)
metricsTableLayout.addWidget(self.ui.metricsTableWidget)
self.ui.levelsTableWidget = LevelsTable()
levelsTableLayout = qt.QVBoxLayout(self.ui.levelsFrame)
levelsTableLayout.addWidget(self.ui.levelsTableWidget)
self.ui.cliWidget = slicer.modules.antsregistrationcli.createNewWidgetRepresentation(
)
self.layout.addWidget(self.ui.cliWidget.children()[3]) # progress bar
self._cliObserver = None
# Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's
# "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's.
# "setMRMLScene(vtkMRMLScene*)" slot.
uiWidget.setMRMLScene(slicer.mrmlScene)
# Create logic class. Logic implements all computations that should be possible to run
# in batch mode, without a graphical user interface.
self.logic = antsRegistrationLogic()
self.ui.stagesPresetsComboBox.addItems(
['Select...'] + PresetManager().getPresetNames())
# Connections
# These connections ensure that we update parameter node when scene is closed
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent,
self.onSceneStartClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent,
self.onSceneEndClose)
# These connections ensure that whenever user changes some settings on the GUI, that is saved in the MRML scene
# (in the selected parameter node).
self.ui.stagesTableWidget.view.selectionModel(
).selectionChanged.connect(self.updateParameterNodeFromGUI)
self.ui.outputInterpolationComboBox.connect(
"currentIndexChanged(int)", self.updateParameterNodeFromGUI)
self.ui.outputTransformComboBox.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.updateParameterNodeFromGUI)
self.ui.outputVolumeComboBox.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.updateParameterNodeFromGUI)
self.ui.initialTransformTypeComboBox.connect(
"currentIndexChanged(int)", self.updateParameterNodeFromGUI)
self.ui.initialTransformNodeComboBox.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.updateParameterNodeFromGUI)
self.ui.dimensionalitySpinBox.connect("valueChanged(int)",
self.updateParameterNodeFromGUI)
self.ui.histogramMatchingCheckBox.connect(
"toggled(bool)", self.updateParameterNodeFromGUI)
self.ui.outputDisplacementFieldCheckBox.connect(
"toggled(bool)", self.updateParameterNodeFromGUI)
self.ui.winsorizeRangeWidget.connect("rangeChanged(double,double)",
self.updateParameterNodeFromGUI)
self.ui.computationPrecisionComboBox.connect(
"currentIndexChanged(int)", self.updateParameterNodeFromGUI)
self.ui.fixedImageNodeComboBox.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.updateStagesFromFixedMovingNodes)
self.ui.movingImageNodeComboBox.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.updateStagesFromFixedMovingNodes)
# Stages Parameter
self.ui.stagesTableWidget.removeButton.clicked.connect(
self.onRemoveStageButtonClicked)
self.ui.metricsTableWidget.removeButton.clicked.connect(
self.updateStagesParameterFromGUI)
self.ui.levelsTableWidget.removeButton.clicked.connect(
self.updateStagesParameterFromGUI)
self.ui.stagesTableWidget.model.itemChanged.connect(
self.updateStagesParameterFromGUI)
self.ui.metricsTableWidget.model.itemChanged.connect(
self.updateStagesParameterFromGUI)
self.ui.levelsTableWidget.model.itemChanged.connect(
self.updateStagesParameterFromGUI)
self.ui.fixedMaskComboBox.connect("currentNodeChanged(vtkMRMLNode*)",
self.updateStagesParameterFromGUI)
self.ui.movingMaskComboBox.connect("currentNodeChanged(vtkMRMLNode*)",
self.updateStagesParameterFromGUI)
self.ui.levelsTableWidget.smoothingSigmasUnitComboBox.currentTextChanged.connect(
self.updateStagesParameterFromGUI)
self.ui.levelsTableWidget.convergenceThresholdSpinBox.valueChanged.connect(
self.updateStagesParameterFromGUI)
self.ui.levelsTableWidget.convergenceWindowSizeSpinBox.valueChanged.connect(
self.updateStagesParameterFromGUI)
self.ui.metricsTableWidget.linkStagesPushButton.toggled.connect(
self.updateStagesParameterFromGUI)
self.ui.levelsTableWidget.linkStagesPushButton.toggled.connect(
self.updateStagesParameterFromGUI)
self.ui.linkMaskingStagesPushButton.toggled.connect(
self.updateStagesParameterFromGUI)
# Preset Stages
self.ui.stagesPresetsComboBox.currentTextChanged.connect(
self.onPresetSelected)
# Buttons
self.ui.stagesTableWidget.savePresetPushButton.connect(
'clicked(bool)', self.onSavePresetPushButton)
self.ui.runRegistrationButton.connect('clicked(bool)',
self.onRunRegistrationButton)
# Make sure parameter node is initialized (needed for module reload)
self.initializeParameterNode()
# Init tables
self.ui.stagesTableWidget.view.selectionModel().emitSelectionChanged(
self.ui.stagesTableWidget.view.selectionModel().selection,
qt.QItemSelection())
self.ui.metricsTableWidget.view.selectionModel().emitSelectionChanged(
self.ui.metricsTableWidget.view.selectionModel().selection,
qt.QItemSelection())