def setCropButtonClicked(self):
vol = self.inputSelector.currentNode()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('CropVolume')
cropVolumeNode = slicer.vtkMRMLCropVolumeParametersNode()
cropVolumeNode.SetScene(slicer.mrmlScene)
cropVolumeNode.SetName('ChangeTracker_CropVolume_node')
cropVolumeNode.SetIsotropicResampling(True)
cropVolumeNode.SetSpacingScalingConst(0.5)
slicer.mrmlScene.AddNode(cropVolumeNode)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic = slicer.modules.cropvolume.logic()
cropVolumeLogic.Apply(cropVolumeNode)
#self.delayDisplay('First test passed, closing the scene and running again')
# test clearing the scene and running a second time
slicer.mrmlScene.Clear(0)
# the module will re-add the removed parameters node
mainWindow.moduleSelector().selectModule('Transforms')
mainWindow.moduleSelector().selectModule('CropVolume')
cropVolumeNode = slicer.mrmlScene.GetNodeByID(
'vtkMRMLCropVolumeParametersNode1')
#vol = SampleData.downloadSample("MRHead")
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic.Apply(cropVolumeNode)
def createUserInterface( self ):
'''
'''
self.__layout = super( EMSegmentQuickStep4, self ).createUserInterface()
# deactivate next button since it is the last step
self.buttonBoxHints = self.NextButtonDisabled
# the ROI parameters
voiGroupBox = qt.QGroupBox()
voiGroupBox.setTitle( 'Define VOI' )
self.__layout.addWidget( voiGroupBox )
voiGroupBoxLayout = qt.QFormLayout( voiGroupBox )
self.__roiWidget = slicer.modulewidget.qMRMLAnnotationROIWidget()
self.__roiWidget.toolTip = 'Select a sub-volume for segmentation. Then, only the selected area will be segmented. By default, the complete volume will be segmented.'
voiGroupBoxLayout.addWidget( self.__roiWidget )
self.__roi = slicer.vtkMRMLAnnotationROINode()
self.__roi.SetXYZ( [0, 0, 0] );
self.__roi.SetRadiusXYZ( 100, 100, 100 );
self.__roi.Initialize( slicer.mrmlScene )
self.__roi.AddObserver( vtk.vtkCommand.ModifiedEvent, self.updateMRMLFromROI )
self.__roiWidget.setMRMLAnnotationROINode( self.__roi )
self.__roiWidget.setDisplayClippingBox( 0 )
def test_CropVolumeSelfTest(self):
"""
Replicate the crashe in issue 3117
"""
print("Running CropVolumeSelfTest Test case:")
vol = self.downloadMRHead()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('CropVolume')
cropVolumeNode = slicer.vtkMRMLCropVolumeParametersNode()
cropVolumeNode.SetScene(slicer.mrmlScene)
cropVolumeNode.SetName('ChangeTracker_CropVolume_node')
cropVolumeNode.SetIsotropicResampling(True)
cropVolumeNode.SetSpacingScalingConst(0.5)
slicer.mrmlScene.AddNode(cropVolumeNode)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic = slicer.modules.cropvolume.logic()
cropVolumeLogic.Apply(cropVolumeNode)
slicer.mrmlScene.RemoveNode(roi)
self.delayDisplay('Test passed')
def test_VolumeClipWithRoi1(self):
# Download MRHead from sample data
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
self.delayDisplay("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
# Create output volume
outputVolume = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolume)
# Create clipping ROI
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetXYZ(36, 17, -10)
roiNode.SetRadiusXYZ(25, 40, 65)
roiNode.Initialize(slicer.mrmlScene)
fillValue = 17
clipOutsideSurface = True
logic = VolumeClipWithRoiLogic()
logic.clipVolumeWithRoi(roiNode, mrHeadVolume, fillValue,
clipOutsideSurface, outputVolume)
self.delayDisplay("Test passed!")
def test_CropVolumeSelfTest(self):
"""
Replicate the crashe in issue 3117
"""
print("Running CropVolumeSelfTest Test case:")
vol = self.downloadMRHead()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('CropVolume')
cropVolumeNode = slicer.vtkMRMLCropVolumeParametersNode()
cropVolumeNode.SetScene(slicer.mrmlScene)
cropVolumeNode.SetName('ChangeTracker_CropVolume_node')
cropVolumeNode.SetIsotropicResampling(True)
cropVolumeNode.SetSpacingScalingConst(0.5)
slicer.mrmlScene.AddNode(cropVolumeNode)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic = slicer.modules.cropvolume.logic()
cropVolumeLogic.Apply(cropVolumeNode)
slicer.mrmlScene.RemoveNode(roi)
self.delayDisplay('Test passed')
def test_ROISegmentation(self, samplevolume, labelmapSelector):
roiSNode = slicer.vtkMRMLAnnotationROINode()
roiBNode = slicer.vtkMRMLAnnotationROINode()
roiSNode.SetXYZ(-5.12, 26.72, 27.54)
roiSNode.SetRadiusXYZ(7.87, 7.87, 9.84)
roiBNode.SetXYZ(-3.93, 26.71, 28.72)
roiBNode.SetRadiusXYZ(20.07, 18.88, 19.67)
roiBNode.Initialize(slicer.mrmlScene)
roiBNode.Initialize(slicer.mrmlScene)
logic = ROISegmentation1Logic()
logic.roiSegment(samplevolume, roiSNode, roiBNode, labelmapSelector)
self.delayDisplay("test passed.")
def test_CropVolumeSelfTest(self):
"""
Replicate the crashe in issue 3117
"""
print("Running CropVolumeSelfTest Test case:")
vol = self.downloadMRHead()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('CropVolume')
cropVolumeNode = slicer.vtkMRMLCropVolumeParametersNode()
cropVolumeNode.SetScene(slicer.mrmlScene)
cropVolumeNode.SetName('ChangeTracker_CropVolume_node')
cropVolumeNode.SetIsotropicResampling(True)
cropVolumeNode.SetSpacingScalingConst(0.5)
slicer.mrmlScene.AddNode(cropVolumeNode)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic = slicer.modules.cropvolume.logic()
cropVolumeLogic.Apply(cropVolumeNode)
self.delayDisplay(
'First test passed, closing the scene and running again')
# test clearing the scene and running a second time
slicer.mrmlScene.Clear(0)
# the module will re-add the removed parameters node
cropVolumeNode = slicer.mrmlScene.GetNodeByID(
'vtkMRMLCropVolumeParametersNode1')
vol = self.downloadMRHead()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic.Apply(cropVolumeNode)
self.delayDisplay('Test passed')
def updateWidgetFromParameterNode(self, parameterNode):
roiNode = parameterNode.GetNodeReference('roiNode')
if not roiNode:
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.Initialize(slicer.mrmlScene)
parameterNode.SetNodeReferenceID('roiNode', roiNode.GetID())
roiNode.SetRadiusXYZ(50, 50, 100)
# initialize slightly off-center, as spine is usually towards posterior side of the image
roiNode.SetXYZ(0, -50, 0)
self.__roiSelector.setCurrentNode(roiNode)
self.onROIChanged()
def test_CropVolumeSelfTest(self):
"""
Replicate the crashe in issue 3117
"""
print("Running CropVolumeSelfTest Test case:")
vol = self.downloadMRHead()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('CropVolume')
cropVolumeNode = slicer.vtkMRMLCropVolumeParametersNode()
cropVolumeNode.SetScene(slicer.mrmlScene)
cropVolumeNode.SetName('ChangeTracker_CropVolume_node')
cropVolumeNode.SetIsotropicResampling(True)
cropVolumeNode.SetSpacingScalingConst(0.5)
slicer.mrmlScene.AddNode(cropVolumeNode)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic = slicer.modules.cropvolume.logic()
cropVolumeLogic.Apply(cropVolumeNode)
self.delayDisplay('First test passed, closing the scene and running again')
# test clearing the scene and running a second time
slicer.mrmlScene.Clear(0)
# the module will re-add the removed parameters node
cropVolumeNode = slicer.mrmlScene.GetNodeByID('vtkMRMLCropVolumeParametersNode1')
vol = self.downloadMRHead()
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
cropVolumeNode.SetInputVolumeNodeID(vol.GetID())
cropVolumeNode.SetROINodeID(roi.GetID())
cropVolumeLogic.Apply(cropVolumeNode)
self.delayDisplay('Test passed')
def updateWidgetFromParameterNode(self, parameterNode):
roiNodeID = parameterNode.GetParameter('roiNodeID')
if roiNodeID != '':
self.__roi = slicer.mrmlScene.GetNodeByID(roiNodeID)
self.__roiSelector.setCurrentNode(Helper.getNodeByID(self.__roi.GetID()))
else:
roi = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roi)
parameterNode.SetParameter('roiNodeID', roi.GetID())
self.__roiSelector.setCurrentNode(roi)
self.onROIChanged()
def updateWidgetFromParameterNode(self, parameterNode):
roiNodeID = parameterNode.GetParameter("roiNodeID")
if roiNodeID != "":
self.__roi = slicer.mrmlScene.GetNodeByID(roiNodeID)
self.__roiSelector.setCurrentNode(Helper.getNodeByID(self.__roi.GetID()))
else:
roi = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roi)
parameterNode.SetParameter("roiNodeID", roi.GetID())
self.__roiSelector.setCurrentNode(roi)
self.onROIChanged()
def updateWidgetFromParameterNode(self, parameterNode):
roiNodeID = parameterNode.GetParameter('roiNodeID')
if roiNodeID != '':
self.__roi = slicer.mrmlScene.GetNodeByID(roiNodeID)
self.__roiSelector.setCurrentNode(Helper.getNodeByID(self.__roi.GetID()))
else:
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
parameterNode.SetParameter('roiNodeID', roi.GetID())
self.__roiSelector.setCurrentNode(roi)
self.onROIChanged()
def updateWidgetFromParameterNode(self, parameterNode):
""" Effectively creates the ROI node upon entry, and then uses onROIChanged
to calculate its intial position.
"""
roiNodeID = parameterNode.GetParameter('roiNodeID')
if roiNodeID != '':
self.__roi = slicer.mrmlScene.GetNodeByID(roiNodeID)
self.__roiSelector.setCurrentNode(Helper.getNodeByID(self.__roi.GetID()))
else:
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
parameterNode.SetParameter('roiNodeID', roi.GetID())
self.__roiSelector.setCurrentNode(roi)
self.onROIChanged()
def updateWidgetFromParameterNode(self, parameterNode):
roiNodeID = parameterNode.GetParameter('roiNodeID')
if roiNodeID != '':
self.__roi = slicer.mrmlScene.GetNodeByID(roiNodeID)
self.__roiSelector.setCurrentNode(Helper.getNodeByID(self.__roi.GetID()))
else:
roi = slicer.vtkMRMLAnnotationROINode()
roi.Initialize(slicer.mrmlScene)
parameterNode.SetParameter('roiNodeID', roi.GetID())
self.__roiSelector.setCurrentNode(roi)
baselineROIVolume = Helper.getNodeByID(parameterNode.GetParameter('baselineVolumeID'))
baselineROIRange = baselineROIVolume.GetImageData().GetScalarRange()
self.__roiVolume = baselineROIVolume
self.__corticalRange.minimum = -1000
self.__corticalRange.maximum = baselineROIRange[1]
vl = slicer.modules.volumes.logic()
self.__corticalNode = vl.CreateAndAddLabelVolume(slicer.mrmlScene, baselineROIVolume, 'corticalROI_segmentation')
#self.__cancellousNode = vl.CreateAndAddLabelVolume(slicer.mrmlScene, baselineROIVolume, 'cancellousROI_segmentation')
Helper.SetLabelVolume(None)
labelsColorNode = slicer.modules.colors.logic().GetColorTableNodeID(10)
self.__corticalNode.GetDisplayNode().SetAndObserveColorNodeID(labelsColorNode)
Helper.SetLabelVolume(self.__corticalNode.GetID())
thresholdRange = str(0.5*(baselineROIRange[0]+baselineROIRange[1]))+','+str(baselineROIRange[1])
if thresholdRange != '':
rangeArray = string.split(thresholdRange, ',')
#self.__corticalRange.minimumValue = float(rangeArray[0])
self.__corticalRange.minimumValue = 150
self.__corticalRange.maximumValue = float(rangeArray[1])
#self.__cancellousRange.minimumValue = float(rangeArray[0])
#self.__cancellousRange.maximumValue = float(rangeArray[1])
else:
Helper.Error('Unexpected parameter values!')
#self.onCancellousChanged()
self.onCorticalChanged()
def refineLandmark(self, state):
"""Refine the specified landmark"""
# Refine landmark, or if none, do nothing
# Crop images around the fiducial
# Affine registration of the cropped images
# Transform the fiducial using the transformation
#
# No need to take into account the current transformation because landmarks are in World RAS
timing = False
if self.VerboseMode == "Verbose":
timing = True
if state.fixed == None or state.moving == None or state.fixedFiducials == None or state.movingFiducials == None or state.currentLandmarkName == None:
print "Cannot refine landmarks. Images or landmarks not selected."
return
print("Refining landmark " +
state.currentLandmarkName) + " using " + self.name
start = time.time()
volumes = (state.fixed, state.moving)
(fixedVolume, movingVolume) = volumes
slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)
landmarks = state.logic.landmarksForVolumes(volumes)
cvpn = slicer.vtkMRMLCropVolumeParametersNode()
cvpn.SetInterpolationMode(1)
cvpn.SetVoxelBased(1)
fixedPoint = [
0,
] * 3
movingPoint = [
0,
] * 3
(fixedFiducial, movingFiducial) = landmarks[state.currentLandmarkName]
(fixedList, fixedIndex) = fixedFiducial
(movingList, movingIndex) = movingFiducial
# define an roi for the fixed
if timing: roiStart = time.time()
roiFixed = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiFixed)
fixedList.GetNthFiducialPosition(fixedIndex, fixedPoint)
roiFixed.SetDisplayVisibility(0)
roiFixed.SelectableOff()
roiFixed.SetXYZ(fixedPoint)
roiFixed.SetRadiusXYZ(30, 30, 30)
# crop the fixed. note we hide the display node temporarily to avoid the automated
# window level calculation on temporary nodes created by cloning
cvpn.SetROINodeID(roiFixed.GetID())
cvpn.SetInputVolumeNodeID(fixedVolume.GetID())
fixedDisplayNode = fixedVolume.GetDisplayNode()
fixedVolume.SetAndObserveDisplayNodeID(
'This is not a valid DisplayNode ID')
if timing: roiEnd = time.time()
if timing: cropStart = time.time()
state.logic.cropLogic.Apply(cvpn)
if timing: cropEnd = time.time()
croppedFixedVolume = slicer.mrmlScene.GetNodeByID(
cvpn.GetOutputVolumeNodeID())
fixedVolume.SetAndObserveDisplayNodeID(fixedDisplayNode.GetID())
# define an roi for the moving
if timing: roi2Start = time.time()
roiMoving = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiMoving)
movingList.GetNthFiducialPosition(movingIndex, movingPoint)
roiMoving.SetDisplayVisibility(0)
roiMoving.SelectableOff()
roiMoving.SetXYZ(movingPoint)
if self.LocalBRAINSFitMode == "Small":
roiMoving.SetRadiusXYZ(45, 45, 45)
else:
roiMoving.SetRadiusXYZ(60, 60, 60)
# crop the moving. note we hide the display node temporarily to avoid the automated
# window level calculation on temporary nodes created by cloning
cvpn.SetROINodeID(roiMoving.GetID())
cvpn.SetInputVolumeNodeID(movingVolume.GetID())
movingDisplayNode = movingVolume.GetDisplayNode()
movingVolume.SetAndObserveDisplayNodeID(
'This is not a valid DisplayNode ID')
if timing: roi2End = time.time()
if timing: crop2Start = time.time()
state.logic.cropLogic.Apply(cvpn)
if timing: crop2End = time.time()
croppedMovingVolume = slicer.mrmlScene.GetNodeByID(
cvpn.GetOutputVolumeNodeID())
movingVolume.SetAndObserveDisplayNodeID(movingDisplayNode.GetID())
if timing:
print 'Time to set up fixed ROI was ' + str(roiEnd -
roiStart) + ' seconds'
if timing:
print 'Time to set up moving ROI was ' + str(
roi2End - roi2Start) + ' seconds'
if timing:
print 'Time to crop fixed volume ' + str(cropEnd -
cropStart) + ' seconds'
if timing:
print 'Time to crop moving volume ' + str(crop2End -
crop2Start) + ' seconds'
#
transform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transform)
matrix = vtk.vtkMatrix4x4()
# define the registration parameters
minPixelSpacing = min(croppedFixedVolume.GetSpacing())
parameters = {}
parameters['fixedVolume'] = croppedFixedVolume.GetID()
parameters['movingVolume'] = croppedMovingVolume.GetID()
parameters['linearTransform'] = transform.GetID()
parameters['useRigid'] = True
parameters['initializeTransformMode'] = 'useGeometryAlign'
parameters['samplingPercentage'] = 0.2
parameters['minimumStepLength'] = 0.1 * minPixelSpacing
parameters['maximumStepLength'] = minPixelSpacing
# run the registration
if timing: regStart = time.time()
slicer.cli.run(slicer.modules.brainsfit,
None,
parameters,
wait_for_completion=True)
if timing: regEnd = time.time()
if timing:
print 'Time for local registration ' + str(regEnd -
regStart) + ' seconds'
# apply the local transform to the landmark
#print transform
if timing: resultStart = time.time()
transform.GetMatrixTransformToWorld(matrix)
matrix.Invert()
tp = [
0,
] * 4
tp = matrix.MultiplyPoint(fixedPoint + [
1,
])
#print fixedPoint, movingPoint, tp[:3]
movingList.SetNthFiducialPosition(movingIndex, tp[0], tp[1], tp[2])
if timing: resultEnd = time.time()
if timing:
print 'Time for transforming landmark was ' + str(
resultEnd - resultStart) + ' seconds'
# clean up cropped volmes, need to reset the foreground/background display before we delete it
if timing: cleanUpStart = time.time()
slicer.mrmlScene.RemoveNode(croppedFixedVolume)
slicer.mrmlScene.RemoveNode(croppedMovingVolume)
slicer.mrmlScene.RemoveNode(roiFixed)
slicer.mrmlScene.RemoveNode(roiMoving)
slicer.mrmlScene.RemoveNode(transform)
roiFixed = None
roiMoving = None
transform = None
matrix = None
if timing: cleanUpEnd = time.time()
if timing:
print 'Cleanup took ' + str(cleanUpEnd - cleanUpStart) + ' seconds'
end = time.time()
print 'Refined landmark ' + state.currentLandmarkName + ' in ' + str(
end - start) + ' seconds'
slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)
def createUserInterface(self):
'''
'''
self.__layout = super(EMSegmentDefineMiscParametersStep,
self).createUserInterface()
# deactivate next button since it is the last step
self.buttonBoxHints = self.NextButtonDisabled
# the ROI parameters
voiGroupBox = qt.QGroupBox()
voiGroupBox.setTitle('Define VOI')
self.__layout.addWidget(voiGroupBox)
voiGroupBoxLayout = qt.QFormLayout(voiGroupBox)
self.__roiWidget = slicer.modulewidget.qMRMLAnnotationROIWidget()
self.__roiWidget.toolTip = 'Select a sub-volume for segmentation. Then, only the selected area will be segmented. By default, the complete volume will be segmented.'
voiGroupBoxLayout.addWidget(self.__roiWidget)
self.__roi = slicer.vtkMRMLAnnotationROINode()
self.__roi.SetXYZ([0, 0, 0])
self.__roi.SetRadiusXYZ(100, 100, 100)
self.__roi.Initialize(slicer.mrmlScene)
# since revision 21159 taken out SetVisibility was Replaced with SetDisplayVisibility
# however when setting it I got a message that int values was not correct
# self.__roi.SetDisplayVisibility( 0 )
self.__roi.AddObserver(vtk.vtkCommand.ModifiedEvent,
self.updateMRMLFromROI)
self.__roiWidget.setMRMLAnnotationROINode(self.__roi)
self.__roiWidget.setDisplayClippingBox(0)
#
# save groupbox
#
saveGroupBox = qt.QGroupBox()
saveGroupBox.setTitle('Save')
self.__layout.addWidget(saveGroupBox)
saveGroupBoxLayout = qt.QFormLayout(saveGroupBox)
self.__saveButton = qt.QPushButton('Create')
self.__saveButton.toolTip = 'Create a template file which can be shared and used to re-apply the configured task.'
saveGroupBoxLayout.addRow("Create Template File:", self.__saveButton)
self.__saveButton.connect('clicked()', self.onSaveButtonClicked)
self.__saveIntermediateResultsCheckBox = qt.QCheckBox()
self.__saveIntermediateResultsCheckBox.toolTip = 'Toggle to save intermediate results as well.'
saveGroupBoxLayout.addRow("Save Intermediate Results:",
self.__saveIntermediateResultsCheckBox)
self.__saveIntermediateResultsCheckBox.connect('stateChanged(int)',
self.propagateToMRML)
self.__selectDirectoryButton = qt.QPushButton('Select')
self.__selectDirectoryButton.toolTip = 'Select a directory to save intermediate results, if selected.'
saveGroupBoxLayout.addRow("Select Intermediate Directory:",
self.__selectDirectoryButton)
self.__selectDirectoryButton.connect(
'clicked()', self.onSelectDirectoryButtonClicked)
#
# post processing groupbox
#
postProcessingGroupBox = qt.QGroupBox()
postProcessingGroupBox.setTitle('Postprocessing')
self.__layout.addWidget(postProcessingGroupBox)
postProcessingGroupBoxLayout = qt.QFormLayout(postProcessingGroupBox)
self.__subparcellationCheckBox = qt.QCheckBox()
self.__subparcellationCheckBox.toolTip = 'Enable subpacellation.'
postProcessingGroupBoxLayout.addRow("Subparcellation enabled:",
self.__subparcellationCheckBox)
self.__subparcellationCheckBox.connect('stateChanged(int)',
self.propagateToMRML)
self.__minimumIslandSizeSpinBox = qt.QSpinBox()
self.__minimumIslandSizeSpinBox.toolTip = 'Configure the minimum island size.'
self.__minimumIslandSizeSpinBox.minimum = 0
self.__minimumIslandSizeSpinBox.maximum = 200
self.__minimumIslandSizeSpinBox.singleStep = 1
postProcessingGroupBoxLayout.addRow("Minimum island size:",
self.__minimumIslandSizeSpinBox)
self.__minimumIslandSizeSpinBox.connect('stateChanged(int)',
self.propagateToMRML)
self.__twoDIslandNeighborhoodCheckBox = qt.QCheckBox()
self.__twoDIslandNeighborhoodCheckBox.toolTip = 'Enable 2D Island Neighborhood'
postProcessingGroupBoxLayout.addRow(
"2D Island Neighborhood:", self.__twoDIslandNeighborhoodCheckBox)
self.__twoDIslandNeighborhoodCheckBox.connect('stateChanged(int)',
self.propagateToMRML)
#
# Misc. groupbox
#
miscGroupBox = qt.QGroupBox()
miscGroupBox.setTitle('Misc.')
self.__layout.addWidget(miscGroupBox)
miscGroupBoxLayout = qt.QFormLayout(miscGroupBox)
self.__multithreadingCheckBox = qt.QCheckBox()
self.__multithreadingCheckBox.toolTip = 'Enhance speed by using multiple threads.'
miscGroupBoxLayout.addRow("Multi-threading enabled:",
self.__multithreadingCheckBox)
self.__multithreadingCheckBox.connect('stateChanged(int)',
self.propagateToMRML)
def step2_3(self):
'''Step 2: 5 - 10'''
key = 'step2_3'
# 5. Convert ex 2d contour to ex 3d contour
slicer.util.loadVolume(os.path.join(self.nii_folder, 'ex_2d_contour.nii'))
slicer.util.loadVolume(os.path.join(self.nii_folder, 'ex_3d.nii'))
output = dict(
warpImg(
inImg=os.path.join(self.nii_folder, 'ex_2d_contour.nii'),
refImg=os.path.join(self.nii_folder, '(ex_3d)_to_(ex_2d).nii'),
outImg=os.path.join(self.nii_folder, 'ex_3d_contour_blocky.nii'),
pixelT='uchar',
tfmFile=os.path.join(self.tfm_folder, 'identity.tfm'),
intplMode='NearestNeighbor', # US spelling
labelMap=True))
# LabelMapSmoothing
output.update(
labelMapSmoothing(inImg=os.path.join(self.nii_folder,
'ex_3d_contour_blocky.nii'),
outImg=os.path.join(self.nii_folder,
'ex_3d_contour.nii'),
sigma=2))
slicer.mrmlScene.Clear(0)
# 6. Crop ex 3d as a reference image
slicer.util.loadVolume(
os.path.join(self.nii_folder, '(ex_3d)_to_(ex_2d).nii'))
selectModule(slicer.modules.cropvolume)
# Create an Annotation ROI Node
roiNode = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiNode)
# Create an output volume node
outputNode = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputNode)
outputNode.SetName('(ex_3d)_to_(ex_2d)_cropped')
# Set the parameters. Note that the positions of the
# widgets might be dependent on the Slicer version
w = slicer.modules.cropvolume.widgetRepresentation()
w.children()[2].children()[5].setCurrentNode(roiNode)
w.children()[2].children()[10].setCurrentNode(outputNode)
# Manually adjust the ROI
try:
_ = input("Please adjust the cropping volume \n\
1. Use the control points to crop ex_3d; \n\
2. Click 'Apply' in the 'Crop Volume' module; \n\
3. Press ENTER to continue. ")
except:
# In case of an EOF error (empty string)
pass
# print("Cropping the volume")
# Simulate the click
# w.findChildren('QPushButton', 'CropButton')[0].animateClick()
print('*' * 20, 'Done', '*' * 20)
# Save node
ex_3d_cropped_path = os.path.join(self.nii_folder, 'ex_3d_cropped.nii')
saved = slicer.util.saveNode(outputNode, ex_3d_cropped_path)
if saved:
output.update({ex_3d_cropped_path: True})
slicer.util.saveNode(
roiNode, os.path.join(self.temp_folder, 'ex_3d_cropped_roi.acsv'))
# To load the annotation node
# slicer.util.loadAnnotationROI(os.path.join(self.temp_folder, 'ex_3d_cropped_roi.acsv'))
selectModule(slicer.modules.pyregpipe)
# 7. Filter in 3d
# in_3d_log_path = os.path.join(self.nii_folder, 'in_3d_log.nii')
# genLogMacro(infile=os.path.join(self.nii_folder, 'in_3d.nii'),
# outfile=in_3d_log_path,
# macroPath=os.path.join(self.script_folder, 'in_3d_log.imj'))
# filterLoG(macro_path=os.path.join(self.script_folder, 'in_3d_log.imj'),
# exe_path=self.imagej_path)
# copyHeader(os.path.join(self.nii_folder, 'in_3d_log.nii'),
# os.path.join(self.nii_folder, 'in_3d.nii'),
# self.nii_folder,
# self.temp_folder)
# if os.path.exists(in_3d_log_path):
# output.update({os.path.join(self.nii_folder, 'in_3d_log.nii'):True})
output.update(
logFilter(inFile=os.path.join(self.nii_folder, 'in_3d.nii'),
outFile=os.path.join(self.nii_folder, 'in_3d_log.nii')))
# 8. Filter ex 3d cropped
# ex_3d_cropped_log_path = os.path.join(self.nii_folder,
# 'ex_3d_cropped_log.nii')
# genLogMacro(infile=os.path.join(self.nii_folder, 'ex_3d_cropped.nii'),
# outfile=ex_3d_cropped_log_path,
# macroPath=os.path.join(self.script_folder, 'ex_3d_log.imj'))
# filterLoG(macro_path=os.path.join(self.script_folder, 'ex_3d_log.imj'),
# exe_path=self.imagej_path)
# copyHeader(os.path.join(self.nii_folder, 'ex_3d_cropped_log.nii'),
# os.path.join(self.nii_folder, 'ex_3d_cropped.nii'),
# self.nii_folder,
# self.temp_folder)
# if os.path.exists(ex_3d_cropped_log_path):
# output.update({ex_3d_cropped_log_path: True})
output.update(
logFilter(inFile=os.path.join(self.nii_folder, 'ex_3d_cropped.nii'),
outFile=os.path.join(self.nii_folder,
'ex_3d_cropped_log.nii')))
# 9. Mask in 3d log with manual contour
output.update(
maskVolume(infile=os.path.join(self.nii_folder, 'in_3d_log.nii'),
contFile=os.path.join(self.nii_folder, 'in_3d_contour.nii'),
outFile=os.path.join(self.nii_folder,
'in_3d_log_masked.nii'),
label=1))
# 10. mask ex 3d cropped log with the manual contour
output.update(
maskVolume(infile=os.path.join(self.nii_folder,
'ex_3d_cropped_log.nii'),
contFile=os.path.join(self.nii_folder, 'ex_3d_contour.nii'),
outFile=os.path.join(self.nii_folder,
'ex_3d_cropped_log_masked.nii'),
label=1))
update(self, key, output)
def createUserInterface( self ):
'''
'''
self.__layout = super( EMSegmentDefineMiscParametersStep, self ).createUserInterface()
# deactivate next button since it is the last step
self.buttonBoxHints = self.NextButtonDisabled
# the ROI parameters
voiGroupBox = qt.QGroupBox()
voiGroupBox.setTitle( 'Define VOI' )
self.__layout.addWidget( voiGroupBox )
voiGroupBoxLayout = qt.QFormLayout( voiGroupBox )
self.__roiWidget = slicer.modulewidget.qMRMLAnnotationROIWidget()
self.__roiWidget.toolTip = 'Select a sub-volume for segmentation. Then, only the selected area will be segmented. By default, the complete volume will be segmented.'
voiGroupBoxLayout.addWidget( self.__roiWidget )
self.__roi = slicer.vtkMRMLAnnotationROINode()
self.__roi.SetXYZ( [0, 0, 0] );
self.__roi.SetRadiusXYZ( 100, 100, 100 )
self.__roi.Initialize( slicer.mrmlScene )
# since revision 21159 taken out SetVisibility was Replaced with SetDisplayVisibility
# however when setting it I got a message that int values was not correct
# self.__roi.SetDisplayVisibility( 0 )
self.__roi.AddObserver( vtk.vtkCommand.ModifiedEvent, self.updateMRMLFromROI )
self.__roiWidget.setMRMLAnnotationROINode( self.__roi )
self.__roiWidget.setDisplayClippingBox( 0 )
#
# save groupbox
#
saveGroupBox = qt.QGroupBox()
saveGroupBox.setTitle( 'Save' )
self.__layout.addWidget( saveGroupBox )
saveGroupBoxLayout = qt.QFormLayout ( saveGroupBox )
self.__saveButton = qt.QPushButton( 'Create' )
self.__saveButton.toolTip = 'Create a template file which can be shared and used to re-apply the configured task.'
saveGroupBoxLayout.addRow( "Create Template File:", self.__saveButton )
self.__saveButton.connect( 'clicked()', self.onSaveButtonClicked )
self.__saveIntermediateResultsCheckBox = qt.QCheckBox()
self.__saveIntermediateResultsCheckBox.toolTip = 'Toggle to save intermediate results as well.'
saveGroupBoxLayout.addRow( "Save Intermediate Results:", self.__saveIntermediateResultsCheckBox )
self.__saveIntermediateResultsCheckBox.connect( 'stateChanged(int)', self.propagateToMRML )
self.__selectDirectoryButton = qt.QPushButton( 'Select' )
self.__selectDirectoryButton.toolTip = 'Select a directory to save intermediate results, if selected.'
saveGroupBoxLayout.addRow( "Select Intermediate Directory:", self.__selectDirectoryButton )
self.__selectDirectoryButton.connect( 'clicked()', self.onSelectDirectoryButtonClicked )
#
# post processing groupbox
#
postProcessingGroupBox = qt.QGroupBox()
postProcessingGroupBox.setTitle( 'Postprocessing' )
self.__layout.addWidget( postProcessingGroupBox )
postProcessingGroupBoxLayout = qt.QFormLayout( postProcessingGroupBox )
self.__subparcellationCheckBox = qt.QCheckBox()
self.__subparcellationCheckBox.toolTip = 'Enable subpacellation.'
postProcessingGroupBoxLayout.addRow( "Subparcellation enabled:", self.__subparcellationCheckBox )
self.__subparcellationCheckBox.connect( 'stateChanged(int)', self.propagateToMRML )
self.__minimumIslandSizeSpinBox = qt.QSpinBox()
self.__minimumIslandSizeSpinBox.toolTip = 'Configure the minimum island size.'
self.__minimumIslandSizeSpinBox.minimum = 0
self.__minimumIslandSizeSpinBox.maximum = 200
self.__minimumIslandSizeSpinBox.singleStep = 1
postProcessingGroupBoxLayout.addRow( "Minimum island size:", self.__minimumIslandSizeSpinBox )
self.__minimumIslandSizeSpinBox.connect( 'stateChanged(int)', self.propagateToMRML )
self.__twoDIslandNeighborhoodCheckBox = qt.QCheckBox()
self.__twoDIslandNeighborhoodCheckBox.toolTip = 'Enable 2D Island Neighborhood'
postProcessingGroupBoxLayout.addRow( "2D Island Neighborhood:", self.__twoDIslandNeighborhoodCheckBox )
self.__twoDIslandNeighborhoodCheckBox.connect( 'stateChanged(int)', self.propagateToMRML )
#
# Misc. groupbox
#
miscGroupBox = qt.QGroupBox()
miscGroupBox.setTitle( 'Misc.' )
self.__layout.addWidget( miscGroupBox )
miscGroupBoxLayout = qt.QFormLayout( miscGroupBox )
self.__multithreadingCheckBox = qt.QCheckBox()
self.__multithreadingCheckBox.toolTip = 'Enhance speed by using multiple threads.'
miscGroupBoxLayout.addRow( "Multi-threading enabled:", self.__multithreadingCheckBox )
self.__multithreadingCheckBox.connect( 'stateChanged(int)', self.propagateToMRML )
def refineLandmark(self, state):
"""Refine the specified landmark"""
# Refine landmark, or if none, do nothing
# Crop images around the fiducial
# Affine registration of the cropped images
# Transform the fiducial using the transformation
#
# No need to take into account the current transformation because landmarks are in World RAS
timing = False
if self.VerboseMode == "Verbose":
timing = True
if state.logic.cropLogic is None:
print("Cannot refine landmarks. CropVolume module is not available.")
if state.fixed == None or state.moving == None or state.fixedFiducials == None or state.movingFiducials == None or state.currentLandmarkName == None:
print "Cannot refine landmarks. Images or landmarks not selected."
return
print ("Refining landmark " + state.currentLandmarkName) + " using " + self.name
start = time.time()
volumes = (state.fixed, state.moving)
(fixedVolume, movingVolume) = volumes
slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)
landmarks = state.logic.landmarksForVolumes(volumes)
cvpn = slicer.vtkMRMLCropVolumeParametersNode()
cvpn.SetInterpolationMode(1)
cvpn.SetVoxelBased(1)
fixedPoint = [0,]*3
movingPoint = [0,]*3
(fixedFiducial, movingFiducial) = landmarks[state.currentLandmarkName]
(fixedList,fixedIndex) = fixedFiducial
(movingList, movingIndex) = movingFiducial
# define an roi for the fixed
if timing: roiStart = time.time()
roiFixed = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiFixed)
fixedList.GetNthFiducialPosition(fixedIndex,fixedPoint)
roiFixed.SetDisplayVisibility(0)
roiFixed.SelectableOff()
roiFixed.SetXYZ(fixedPoint)
roiFixed.SetRadiusXYZ(30, 30, 30)
# crop the fixed. note we hide the display node temporarily to avoid the automated
# window level calculation on temporary nodes created by cloning
cvpn.SetROINodeID( roiFixed.GetID() )
cvpn.SetInputVolumeNodeID( fixedVolume.GetID() )
fixedDisplayNode = fixedVolume.GetDisplayNode()
fixedVolume.SetAndObserveDisplayNodeID('This is not a valid DisplayNode ID')
if timing: roiEnd = time.time()
if timing: cropStart = time.time()
state.logic.cropLogic.Apply( cvpn )
if timing: cropEnd = time.time()
croppedFixedVolume = slicer.mrmlScene.GetNodeByID( cvpn.GetOutputVolumeNodeID() )
fixedVolume.SetAndObserveDisplayNodeID(fixedDisplayNode.GetID())
# define an roi for the moving
if timing: roi2Start = time.time()
roiMoving = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiMoving)
movingList.GetNthFiducialPosition(movingIndex,movingPoint)
roiMoving.SetDisplayVisibility(0)
roiMoving.SelectableOff()
roiMoving.SetXYZ(movingPoint)
if self.LocalBRAINSFitMode == "Small":
roiMoving.SetRadiusXYZ(45, 45, 45)
else:
roiMoving.SetRadiusXYZ(60, 60, 60)
# crop the moving. note we hide the display node temporarily to avoid the automated
# window level calculation on temporary nodes created by cloning
cvpn.SetROINodeID( roiMoving.GetID() )
cvpn.SetInputVolumeNodeID( movingVolume.GetID() )
movingDisplayNode = movingVolume.GetDisplayNode()
movingVolume.SetAndObserveDisplayNodeID('This is not a valid DisplayNode ID')
if timing: roi2End = time.time()
if timing: crop2Start = time.time()
state.logic.cropLogic.Apply( cvpn )
if timing: crop2End = time.time()
croppedMovingVolume = slicer.mrmlScene.GetNodeByID( cvpn.GetOutputVolumeNodeID() )
movingVolume.SetAndObserveDisplayNodeID(movingDisplayNode.GetID())
if timing: print 'Time to set up fixed ROI was ' + str(roiEnd - roiStart) + ' seconds'
if timing: print 'Time to set up moving ROI was ' + str(roi2End - roi2Start) + ' seconds'
if timing: print 'Time to crop fixed volume ' + str(cropEnd - cropStart) + ' seconds'
if timing: print 'Time to crop moving volume ' + str(crop2End - crop2Start) + ' seconds'
#
transform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transform)
matrix = vtk.vtkMatrix4x4()
# define the registration parameters
minPixelSpacing = min(croppedFixedVolume.GetSpacing())
parameters = {}
parameters['fixedVolume'] = croppedFixedVolume.GetID()
parameters['movingVolume'] = croppedMovingVolume.GetID()
parameters['linearTransform'] = transform.GetID()
parameters['useRigid'] = True
parameters['initializeTransformMode'] = 'useGeometryAlign';
parameters['samplingPercentage'] = 0.2
parameters['minimumStepLength'] = 0.1 * minPixelSpacing
parameters['maximumStepLength'] = minPixelSpacing
# run the registration
if timing: regStart = time.time()
slicer.cli.run(slicer.modules.brainsfit, None, parameters, wait_for_completion=True)
if timing: regEnd = time.time()
if timing: print 'Time for local registration ' + str(regEnd - regStart) + ' seconds'
# apply the local transform to the landmark
#print transform
if timing: resultStart = time.time()
transform.GetMatrixTransformToWorld(matrix)
matrix.Invert()
tp = [0,]*4
tp = matrix.MultiplyPoint(fixedPoint + [1,])
#print fixedPoint, movingPoint, tp[:3]
movingList.SetNthFiducialPosition(movingIndex, tp[0], tp[1], tp[2])
if timing: resultEnd = time.time()
if timing: print 'Time for transforming landmark was ' + str(resultEnd - resultStart) + ' seconds'
# clean up cropped volmes, need to reset the foreground/background display before we delete it
if timing: cleanUpStart = time.time()
slicer.mrmlScene.RemoveNode(croppedFixedVolume)
slicer.mrmlScene.RemoveNode(croppedMovingVolume)
slicer.mrmlScene.RemoveNode(roiFixed)
slicer.mrmlScene.RemoveNode(roiMoving)
slicer.mrmlScene.RemoveNode(transform)
roiFixed = None
roiMoving = None
transform = None
matrix = None
if timing: cleanUpEnd = time.time()
if timing: print 'Cleanup took ' + str(cleanUpEnd - cleanUpStart) + ' seconds'
end = time.time()
print 'Refined landmark ' + state.currentLandmarkName + ' in ' + str(end - start) + ' seconds'
slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)