def setNewFiducial(self, newSceneNode):
# Allow click to set the new fiducial to the list
if self.fixed.fiducialList:
self.fixed.fiducialList.RemoveObserver(
vtk.vtkCommand.ModifiedEvent)
self.fixed.fiducialList.AddObserver(vtk.vtkCommand.ModifiedEvent,
self.onMRMLNodeAdded)
self.fixed.fiducialList.UpdateScene(newSceneNode)
collection = vtk.vtkCollection()
self.fixed.fiducialList.GetDirectChildren(collection)
print collection.GetNumberOfItems()
######
# create fiducial in volume labeled with fiducial list index
# add fiducial to appropriate list
# else:
# self.createNewFiducial() (i.e. ignore)
# if volume is not marked done:
# mark volume as done
# else:
# give warning
# if both are marked done:
# reset done flag
# quit
# else:
# self.createNewFiducial()
# elif right-click:
# ignore
# elif ESC:
# remove latest fiducial if lengths not equal (assumes ordered list!!!)
# reset done flags
# elif RET:
# ignore (both fiducials need to be set (i.e. both flags need to == 'done'))
# self.selector.AddNewAnnotationIDToList(self.fixed.newFiducial.GetID())
print "Created a new fiducial node"
def examineForImport(self,fileLists):
""" Returns a list of qSlicerDICOMLoadable
instances corresponding to ways of interpreting the
fileLists parameter.
"""
import vtkSlicerDicomRtImportExportModuleLogic
# Create loadables for each file list
loadables = []
for fileList in fileLists: # Each file list corresponds to one series, so do loadables
# Convert file list to VTK object to be able to pass it for examining
# (VTK class cannot have Qt object as argument, otherwise it is not python wrapped)
vtkFileList = vtk.vtkStringArray()
for file in fileList:
vtkFileList.InsertNextValue(file)
# Examine files
loadablesCollection = vtk.vtkCollection()
slicer.modules.dicomrtimportexport.logic().ExamineForLoad(vtkFileList, loadablesCollection)
for loadableIndex in xrange(0,loadablesCollection.GetNumberOfItems()):
vtkLoadable = loadablesCollection.GetItemAsObject(loadableIndex)
# Create Qt loadable if confidence is greater than 0
if vtkLoadable.GetConfidence() > 0:
# Convert to Qt loadable to pass it back
qtLoadable = slicer.qSlicerDICOMLoadable()
qtLoadable.copyFromVtkLoadable(vtkLoadable)
qtLoadable.tooltip = 'Valid RT object in selection'
qtLoadable.selected = True
loadables.append(qtLoadable)
return loadables
def setNewFiducial(self, newSceneNode):
# Allow click to set the new fiducial to the list
if self.fixed.fiducialList:
self.fixed.fiducialList.RemoveObserver(vtk.vtkCommand.ModifiedEvent)
self.fixed.fiducialList.AddObserver(vtk.vtkCommand.ModifiedEvent, self.onMRMLNodeAdded)
self.fixed.fiducialList.UpdateScene(newSceneNode)
collection = vtk.vtkCollection()
self.fixed.fiducialList.GetDirectChildren(collection)
print collection.GetNumberOfItems()
######
# create fiducial in volume labeled with fiducial list index
# add fiducial to appropriate list
# else:
# self.createNewFiducial() (i.e. ignore)
# if volume is not marked done:
# mark volume as done
# else:
# give warning
# if both are marked done:
# reset done flag
# quit
# else:
# self.createNewFiducial()
# elif right-click:
# ignore
# elif ESC:
# remove latest fiducial if lengths not equal (assumes ordered list!!!)
# reset done flags
# elif RET:
# ignore (both fiducials need to be set (i.e. both flags need to == 'done'))
# self.selector.AddNewAnnotationIDToList(self.fixed.newFiducial.GetID())
print "Created a new fiducial node"
def convertFiducialHierarchyToVtkIdList(hierarchyNode,volumeNode):
'''
'''
outputIds = vtk.vtkIdList()
if not hierarchyNode or not volumeNode:
return outputIds
if isinstance(hierarchyNode,slicer.vtkMRMLAnnotationHierarchyNode) and isinstance(volumeNode,slicer.vtkMRMLScalarVolumeNode):
childrenNodes = vtk.vtkCollection()
image = volumeNode.GetImageData()
hierarchyNode.GetChildrenDisplayableNodes(childrenNodes)
# now we have the children which are fiducialNodes - let's loop!
for n in range(childrenNodes.GetNumberOfItems()):
currentFiducial = childrenNodes.GetItemAsObject(n)
currentCoordinatesRAS = [0,0,0]
# grab the current coordinates
currentFiducial.GetFiducialCoordinates(currentCoordinatesRAS)
# convert the RAS to IJK
currentCoordinatesIJK = Helper.ConvertRAStoIJK(volumeNode,currentCoordinatesRAS)
# strip the last element since we need a 3based tupel
currentCoordinatesIJKlist = (int(currentCoordinatesIJK[0]),int(currentCoordinatesIJK[1]),int(currentCoordinatesIJK[2]))
outputIds.InsertNextId(int(image.ComputePointId(currentCoordinatesIJKlist)))
# IdList was created, return it even if it might be empty
return outputIds
def getRulerNodeForVolumeAndStructure(self,
volumeId,
structureId,
createIfNotExist=True,
callbackWhenRulerModified=None):
""" Search for the right ruler node to be created based on the volume and the selected
structure (Aorta or PA).
It also creates the necessary node hierarchy if it doesn't exist.
:param volumeId:
:param structureId: Aorta (1), PA (2)
:param createIfNotExist: create the ruler node if it doesn't exist yet
:param callbackWhenRulerModified: function to call when the ruler node is modified
:return: node and a boolean indicating if the node has been created now
"""
isNewNode = False
if structureId == 0: # none
return None, isNewNode
if structureId == self.AORTA: # Aorta
#nodeName = volumeId + '_paaRulers_aorta'
nodeName = "A"
elif structureId == self.PA: # 'Pulmonary Arterial':
# nodeName = volumeId + '_paaRulers_pa'
nodeName = "PA"
# Get the node that contains all the rulers for this volume
rulersListNode = self.getRulersListNode(
volumeId, createIfNotExist=createIfNotExist)
node = None
if rulersListNode:
# Search for the node
for i in range(rulersListNode.GetNumberOfChildrenNodes()):
nodeWrapper = rulersListNode.GetNthChildNode(i)
# nodeWrapper is also a HierarchyNode. We need to look for its only child that will be the rulerNode
col = vtk.vtkCollection()
nodeWrapper.GetChildrenDisplayableNodes(col)
rulerNode = col.GetItemAsObject(0)
if rulerNode.GetName() == nodeName:
node = rulerNode
break
if node is None and createIfNotExist:
# Create the node
# Set the active node, so that the new ruler is a child node
annotationsLogic = slicer.modules.annotations.logic()
annotationsLogic.SetActiveHierarchyNodeID(
rulersListNode.GetID())
node = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLAnnotationRulerNode')
node.SetName(nodeName)
self.__changeColor__(node, self.defaultColor)
slicer.mrmlScene.AddNode(node)
isNewNode = True
node.AddObserver(vtk.vtkCommand.ModifiedEvent,
callbackWhenRulerModified)
logging.debug("Created node " + nodeName + " for volume " +
volumeId)
return node, isNewNode
def RemoveModels(modelHierarchyNode):
collection = vtk.vtkCollection()
modelHierarchyNode.GetAssociatedChildrenNodes(collection)
if collection:
nModels = collection.GetNumberOfItems()
for i in range(nModels):
model = collection.GetItemAsObject(i)
slicer.mrmlScene.RemoveNode(model)
return True
def __init__(self, fiducialListNode, dl=0.5):
import numpy
self.dl = dl # desired world space step size (in mm)
self.dt = dl # current guess of parametric stepsize
self.fids = fiducialListNode
# hermite interpolation functions
self.h00 = lambda t: 2 * t ** 3 - 3 * t ** 2 + 1
self.h10 = lambda t: t ** 3 - 2 * t ** 2 + t
self.h01 = lambda t: -2 * t ** 3 + 3 * t ** 2
self.h11 = lambda t: t ** 3 - t ** 2
# n is the number of control points in the piecewise curve
if self.fids.GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
self.fids.GetChildrenDisplayableNodes(collection)
self.n = collection.GetNumberOfItems()
if self.n == 0:
return
self.p = numpy.zeros((self.n, 3))
for i in xrange(self.n):
f = collection.GetItemAsObject(i)
coords = [0, 0, 0]
f.GetFiducialCoordinates(coords)
self.p[i] = coords
else:
# slicer3 style fiducial lists
self.n = self.fids.GetNumberOfFiducials()
n = self.n
if n == 0:
return
# get control point data
# sets self.p
self.p = numpy.zeros((n, 3))
for i in xrange(n):
self.p[i] = self.fids.GetNthFiducialXYZ(i)
# calculate the tangent vectors
# - fm is forward difference
# - m is average of in and out vectors
# - first tangent is out vector, last is in vector
# - sets self.m
n = self.n
fm = numpy.zeros((n, 3))
for i in xrange(0, n - 1):
fm[i] = self.p[i + 1] - self.p[i]
self.m = numpy.zeros((n, 3))
for i in xrange(1, n - 1):
self.m[i] = (fm[i - 1] + fm[i]) / 2.0
self.m[0] = fm[0]
self.m[n - 1] = fm[n - 2]
self.path = [self.p[0]]
self.calculatePath()
def __init__(self, fiducialListNode, dl=0.5):
import numpy
self.dl = dl # desired world space step size (in mm)
self.dt = dl # current guess of parametric stepsize
self.fids = fiducialListNode
# hermite interpolation functions
self.h00 = lambda t: 2 * t**3 - 3 * t**2 + 1
self.h10 = lambda t: t**3 - 2 * t**2 + t
self.h01 = lambda t: -2 * t**3 + 3 * t**2
self.h11 = lambda t: t**3 - t**2
# n is the number of control points in the piecewise curve
if self.fids.GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
self.fids.GetChildrenDisplayableNodes(collection)
self.n = collection.GetNumberOfItems()
if self.n == 0:
return
self.p = numpy.zeros((self.n, 3))
for i in xrange(self.n):
f = collection.GetItemAsObject(i)
coords = [0, 0, 0]
f.GetFiducialCoordinates(coords)
self.p[i] = coords
else:
# slicer3 style fiducial lists
self.n = self.fids.GetNumberOfFiducials()
n = self.n
if n == 0:
return
# get control point data
# sets self.p
self.p = numpy.zeros((n, 3))
for i in xrange(n):
self.p[i] = self.fids.GetNthFiducialXYZ(i)
# calculate the tangent vectors
# - fm is forward difference
# - m is average of in and out vectors
# - first tangent is out vector, last is in vector
# - sets self.m
n = self.n
fm = numpy.zeros((n, 3))
for i in xrange(0, n - 1):
fm[i] = self.p[i + 1] - self.p[i]
self.m = numpy.zeros((n, 3))
for i in xrange(1, n - 1):
self.m[i] = (fm[i - 1] + fm[i]) / 2.
self.m[0] = fm[0]
self.m[n - 1] = fm[n - 2]
self.path = [self.p[0]]
self.calculatePath()
def __init__(self,pytripCube): self.name = pytripCube.patient_name self.pixel_size = pytripCube.pixel_size self.slice_distance = pytripCube.slice_distance self.dimx = pytripCube.dimx self.dimy = pytripCube.dimy self.dimz = pytripCube.dimz self.vois=[] self.vtkCollection = vtk.vtkCollection() self.filePath=''
def getFiducialSliceDisplayableManagerHelper(self,sliceName='Red'):
sliceWidget = slicer.app.layoutManager().sliceWidget(sliceName)
sliceView = sliceWidget.sliceView()
collection = vtk.vtkCollection()
sliceView.getDisplayableManagers(collection)
for i in range(collection.GetNumberOfItems()):
m = collection.GetItemAsObject(i)
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager2D":
return m.GetHelper()
return None
def loadFile(self, title, fileType, nodeComboBox):
manager = slicer.app.ioManager()
loadedNodes = vtk.vtkCollection()
properties = {}
res = manager.openDialog(fileType, slicer.qSlicerFileDialog.Read, properties, loadedNodes)
loadedNode = loadedNodes.GetItemAsObject(0)
if res == True:
nodeComboBox.setCurrentNode(loadedNode)
self.reset3DViews()
return loadedNode
def getFiducialSliceDisplayableManagerHelper(self,sliceName='Red'):
sliceWidget = slicer.app.layoutManager().sliceWidget(sliceName)
sliceView = sliceWidget.sliceView()
collection = vtk.vtkCollection()
sliceView.getDisplayableManagers(collection)
for i in range(collection.GetNumberOfItems()):
m = collection.GetItemAsObject(i)
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager2D":
return m.GetHelper()
return None
def loadFile(self, title, fileType, nodeComboBox):
manager = slicer.app.ioManager()
loadedNodes = vtk.vtkCollection()
properties = {}
res = manager.openDialog(fileType, slicer.qSlicerFileDialog.Read,
properties, loadedNodes)
loadedNode = loadedNodes.GetItemAsObject(0)
if res == True:
nodeComboBox.setCurrentNode(loadedNode)
self.reset3DViews()
return loadedNode
def makeModels(study, finding, colorTable):
if (study == None) | (finding == None) | (colorTable == None):
return
seg = finding.GetSegmentationMappedByStudyNodeID(study.GetID())
if seg:
labelVolume = seg.GetLabelVolumeNode()
#create a temporary model hierarchy for generating models
tempMH = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(tempMH)
if (labelVolume != None) & (tempMH != None):
parameters = {}
parameters['InputVolume'] = labelVolume.GetID()
parameters['ColorTable'] = colorTable.GetID()
parameters['ModelSceneFile'] = tempMH.GetID()
parameters['GenerateAll'] = False
parameters['StartLabel'] = finding.GetColorID()
parameters['EndLabel'] = finding.GetColorID()
parameters['Name'] = labelVolume.GetName() + "_" + finding.GetName()+"_M"
cliModelMaker = None
cliModelMaker = slicer.cli.run(slicer.modules.modelmaker, cliModelMaker, parameters, wait_for_completion = True)
genModelNodes = vtk.vtkCollection()
tempMH.GetChildrenModelNodes(genModelNodes)
if genModelNodes.GetNumberOfItems() > 0:
modelNode = genModelNodes.GetItemAsObject(0)
if modelNode:
if modelNode.IsA('vtkMRMLModelNode'):
hnode = slicer.vtkMRMLHierarchyNode.GetAssociatedHierarchyNode(modelNode.GetScene(), modelNode.GetID())
if hnode:
if seg.GetModelHierarchyNode():
SlicerLongitudinalPETCTModuleViewHelper.removeModelHierarchyAndChildModelNodesFromScene(seg.GetModelHierarchyNode())
hnode.SetName(seg.GetName()+"_Model")
seg.SetAndObserveModelHierarchyNodeID(hnode.GetID())
modelNode.SetName(labelVolume.GetName() + "_" + finding.GetName()+"_M")
if modelNode.GetDisplayNode():
modelNode.GetDisplayNode().SetName(labelVolume.GetName() + "_" + finding.GetName()+"_D")
modelNode.GetDisplayNode().AddViewNodeID(SlicerLongitudinalPETCTModuleViewHelper.getStandardViewNode().GetID())
hnode.SetName(labelVolume.GetName() + "_" + finding.GetName()+"_H")
modelNode.SetHideFromEditors(False)
else:
seg.SetAndObserveModelHierarchyNodeID("")
slicer.mrmlScene.RemoveNode(modelNode)
slicer.mrmlScene.RemoveNode(hnode)
slicer.mrmlScene.RemoveNode(tempMH.GetDisplayNode())
slicer.mrmlScene.RemoveNode(tempMH)
def volumeFiducialsAsList(self,volumeNode):
"""return a list of annotation nodes that are
children of the list associated with the given
volume node"""
children = []
listName = volumeNode.GetName() + "-landmarks"
fidListHierarchyNode = slicer.util.getNode(listName)
if fidListHierarchyNode:
childCollection = vtk.vtkCollection()
fidListHierarchyNode.GetAllChildren(childCollection)
for childIndex in range(childCollection.GetNumberOfItems()):
children.append(childCollection.GetItemAsObject(childIndex))
return children
def widgetVisible(self, fidNode, viewNodeID):
lm = slicer.app.layoutManager()
for v in range(lm.threeDViewCount):
td = lm.threeDWidget(v)
ms = vtk.vtkCollection()
td.getDisplayableManagers(ms)
for i in range(ms.GetNumberOfItems()):
m = ms.GetItemAsObject(i)
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager3D" and m.GetMRMLViewNode().GetID() == viewNodeID:
h = m.GetHelper()
seedWidget = h.GetWidget(fidNode)
return seedWidget.GetEnabled()
return 0
def removeModelHierarchyAndChildModelNodesFromScene(modelHierarchyNode):
if modelHierarchyNode:
cmn = vtk.vtkCollection()
modelHierarchyNode.GetChildrenModelNodes(cmn)
for i in range(cmn.GetNumberOfItems()):
model = cmn.GetItemAsObject(i)
if model.IsA('vtkMRMLModelNode'):
slicer.mrmlScene.RemoveNode(model)
slicer.mrmlScene.RemoveNode(modelHierarchyNode)
def getRulerNodeForVolumeAndStructure(
self, volumeId, structureId, createIfNotExist=True, callbackWhenRulerModified=None
):
""" Search for the right ruler node to be created based on the volume and the selected
structure (Aorta or PA).
It also creates the necessary node hierarchy if it doesn't exist.
:param volumeId:
:param structureId: Aorta (1), PA (2)
:param createIfNotExist: create the ruler node if it doesn't exist yet
:param callbackWhenRulerModified: function to call when the ruler node is modified
:return: node and a boolean indicating if the node has been created now
"""
isNewNode = False
if structureId == 0: # none
return None, isNewNode
if structureId == self.AORTA: # Aorta
# nodeName = volumeId + '_paaRulers_aorta'
nodeName = "A"
elif structureId == self.PA: # 'Pulmonary Arterial':
# nodeName = volumeId + '_paaRulers_pa'
nodeName = "PA"
# Get the node that contains all the rulers for this volume
rulersListNode = self.getRulersListNode(volumeId, createIfNotExist=createIfNotExist)
node = None
if rulersListNode:
# Search for the node
for i in range(rulersListNode.GetNumberOfChildrenNodes()):
nodeWrapper = rulersListNode.GetNthChildNode(i)
# nodeWrapper is also a HierarchyNode. We need to look for its only child that will be the rulerNode
col = vtk.vtkCollection()
nodeWrapper.GetChildrenDisplayableNodes(col)
rulerNode = col.GetItemAsObject(0)
if rulerNode.GetName() == nodeName:
node = rulerNode
break
if node is None and createIfNotExist:
# Create the node
# Set the active node, so that the new ruler is a child node
annotationsLogic = slicer.modules.annotations.logic()
annotationsLogic.SetActiveHierarchyNodeID(rulersListNode.GetID())
node = slicer.mrmlScene.CreateNodeByClass("vtkMRMLAnnotationRulerNode")
node.SetName(nodeName)
self.__changeColor__(node, self.defaultColor)
slicer.mrmlScene.AddNode(node)
isNewNode = True
node.AddObserver(vtk.vtkCommand.ModifiedEvent, callbackWhenRulerModified)
logging.debug("Created node " + nodeName + " for volume " + volumeId)
return node, isNewNode
def onAnnotationsFontSizeChanged(self, size):
lm = slicer.app.layoutManager()
for sliceName in lm.sliceViewNames():
sWidget = lm.sliceWidget(sliceName)
sView = sWidget.sliceView()
DisplayableManagersCollection = vtk.vtkCollection()
sView.getDisplayableManagers(DisplayableManagersCollection)
for DisplayableManagersIndex in range(
DisplayableManagersCollection.GetNumberOfItems()):
AstroDisplayableManager = DisplayableManagersCollection.GetItemAsObject(
DisplayableManagersIndex)
if AstroDisplayableManager.GetClassName(
) == "vtkMRMLAstroTwoDAxesDisplayableManager":
AstroDisplayableManager.SetAnnotationsFontSize(size)
def export(self,exportables):
import vtkSlicerDicomRtImportExportModuleLogic
from vtkSlicerDICOMLibModuleLogicPython import vtkSlicerDICOMExportable
# Convert Qt loadables to VTK ones for the RT export logic
exportablesCollection = vtk.vtkCollection()
for exportable in exportables:
vtkExportable = slicer.vtkSlicerDICOMExportable()
exportable.copyToVtkExportable(vtkExportable)
exportablesCollection.AddItem(vtkExportable)
# Export RT study
message = slicer.modules.dicomrtimportexport.logic().ExportDicomRTStudy(exportablesCollection)
return message
def widgetVisibleOnSlice(self, fidNode, sliceNodeID):
lm = slicer.app.layoutManager()
sliceNames = lm.sliceViewNames()
for sliceName in sliceNames:
sliceWidget = lm.sliceWidget(sliceName)
sliceView = sliceWidget.sliceView()
ms = vtk.vtkCollection()
sliceView.getDisplayableManagers(ms)
for i in range(ms.GetNumberOfItems()):
m = ms.GetItemAsObject(i)
if m.GetClassName() == 'vtkMRMLMarkupsFiducialDisplayableManager2D' and m.GetSliceNode().GetID() == sliceNodeID:
h = m.GetHelper()
seedWidget = h.GetWidget(fidNode)
return seedWidget.GetEnabled()
return 0
def TransformModelHierarchy(modelHierarchyNode, transformNode):
if not transformNode:
return False
# modelLabelNode.SetAndObserveTransformNodeID(transformNode.GetID())
# slicer.vtkSlicerTransformLogic.hardenTransform(modelLabelNode)
collection = vtk.vtkCollection()
modelHierarchyNode.GetAssociatedChildrenNodes(collection)
if collection:
nModels = collection.GetNumberOfItems()
for i in range(nModels):
model = collection.GetItemAsObject(i)
model.SetAndObserveTransformNodeID(transformNode.GetID())
slicer.vtkSlicerTransformLogic.hardenTransform(model)
return True
def volumeFiducialsByName(self,volumeNode):
"""return a dictionary of annotation nodes that are
children of the list associated with the given
volume node, where the keys are fiducial names
and the values are fiducial nodes"""
fiducialsByName = {}
listName = volumeNode.GetName() + "-landmarks"
fidListHierarchyNode = slicer.util.getNode(listName)
if fidListHierarchyNode:
childCollection = vtk.vtkCollection()
fidListHierarchyNode.GetAllChildren(childCollection)
for childIndex in range(childCollection.GetNumberOfItems()):
fiducialNode = childCollection.GetItemAsObject(childIndex)
fiducialsByName[fiducialNode.GetName()] = fiducialNode
return fiducialsByName
def UpdateSelfAndChildMetrics( allMetrics, transformName, absTime, metricsTable ):
if ( PythonMetricsCalculatorLogic.GetMRMLScene() == None or PythonMetricsCalculatorLogic.GetPerkEvaluatorLogic() == None ):
return
# Get the recorded transform node
updatedTransformNode = PythonMetricsCalculatorLogic.GetMRMLScene().GetFirstNode( transformName, "vtkMRMLLinearTransformNode", [ False ] ) # TODO: Is there an error in this function?
# Get all transforms in the scene
transformCollection = vtk.vtkCollection()
PythonMetricsCalculatorLogic.GetPerkEvaluatorLogic().GetSceneVisibleTransformNodes( transformCollection )
# Update all metrics associated with children of the recorded transform
for i in range( transformCollection.GetNumberOfItems() ):
currentTransformNode = transformCollection.GetItemAsObject( i )
if ( PythonMetricsCalculatorLogic.GetPerkEvaluatorLogic().IsSelfOrDescendentTransformNode( updatedTransformNode, currentTransformNode ) ):
PythonMetricsCalculatorLogic.UpdateMetrics( allMetrics, currentTransformNode, absTime, metricsTable )
def onAnnotationsColorChanged(self, color):
lm = slicer.app.layoutManager()
for sliceName in lm.sliceViewNames():
sWidget = lm.sliceWidget(sliceName)
sView = sWidget.sliceView()
DisplayableManagersCollection = vtk.vtkCollection()
sView.getDisplayableManagers(DisplayableManagersCollection)
for DisplayableManagersIndex in range(
DisplayableManagersCollection.GetNumberOfItems()):
AstroDisplayableManager = DisplayableManagersCollection.GetItemAsObject(
DisplayableManagersIndex)
if AstroDisplayableManager.GetClassName() == "vtkMRMLAstroTwoDAxesDisplayableManager" or \
AstroDisplayableManager.GetClassName() == "vtkMRMLAstroBeamDisplayableManager" :
AstroDisplayableManager.SetAnnotationsColor(
color.red() / 255.,
color.green() / 255.,
color.blue() / 255.)
def populateRulers(self, annotationHierarchy, verterbraeNames):
completeVerterbraeNames = []
for verterbraeName in verterbraeNames:
completeVerterbraeNames.append(verterbraeName + "-s")
completeVerterbraeNames.append(verterbraeName + "-i")
if annotationHierarchy != None:
rulerNodes = vtk.vtkCollection()
annotationHierarchy.GetDirectChildren(rulerNodes)
rulerNodeNames = []
for nodeIndex in range(rulerNodes.GetNumberOfItems()):
if rulerNodes.GetItemAsObject(nodeIndex).GetClassName(
) == "vtkMRMLAnnotationRulerNode":
rulerNodeNames.append(
rulerNodes.GetItemAsObject(nodeIndex).GetName())
addedRulerNodesList = []
addedVerterbrae = 200
for completeVerterbraeName in completeVerterbraeNames:
if completeVerterbraeName not in rulerNodeNames:
newRulerNode = slicer.vtkMRMLAnnotationRulerNode()
newRulerNode.SetName(completeVerterbraeName)
newRulerNode.SetPosition1(0, addedVerterbrae, 0)
newRulerNode.SetPosition2(-300, addedVerterbrae, 0)
newRulerNode.SetPointColour([0, 0, 1])
newRulerNode.Initialize(slicer.mrmlScene)
annotationHierarchy.SetAndObserveDisplayNodeID(
newRulerNode.GetDisplayNodeID())
addedVerterbrae -= 50
addedRulerNodesList.append(newRulerNode)
else:
addedVerterbrae = 200
for completeVerterbraeName in completeVerterbraeNames:
newRulerNode = slicer.vtkMRMLAnnotationRulerNode()
newRulerNode.SetName(completeVerterbraeName)
newRulerNode.SetPosition1(0, addedVerterbrae, 0)
newRulerNode.SetPosition2(-300, addedVerterbrae, 0)
newRulerNode.Initialize(slicer.mrmlScene)
annotationHierarchy.SetAndObserveDisplayNodeID(
newRulerNode.GetDisplayNodeID())
addedVerterbrae -= 50
return addedRulerNodesList
def load(self,loadable):
""" Call Reporting logic to load the DICOM SEG object
"""
print('DICOM SEG load()')
labelNodes = vtk.vtkCollection()
uid = None
try:
reportingLogic = slicer.modules.reporting.logic()
uid = loadable.uid
print 'in load(): uid = ', uid
except AttributeError:
return False
res = False
# default color node will be used
res = reportingLogic.DicomSegRead(labelNodes, uid)
print 'Read this many labels:',labelNodes.GetNumberOfItems()
defaultColorNode = reportingLogic.GetDefaultColorNode()
for i in range(labelNodes.GetNumberOfItems()):
# create and initialize the display node to use default color node
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLabelMapVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount()-1)
displayNode.SetAndObserveColorNodeID(defaultColorNode.GetID())
slicer.mrmlScene.AddNode(displayNode)
# assign it to the label node
# this is done here as opposed to Reporting logic to minimize the
# dependencies of the DICOM SEG functionality in the Slicer internals
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNode)
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, labelNode)
return True
def convertFiducialHierarchyToVtkIdList(hierarchyNode, volumeNode):
'''
'''
outputIds = vtk.vtkIdList()
if not hierarchyNode or not volumeNode:
return outputIds
if isinstance(hierarchyNode,
slicer.vtkMRMLAnnotationHierarchyNode) and isinstance(
volumeNode, slicer.vtkMRMLScalarVolumeNode):
childrenNodes = vtk.vtkCollection()
image = volumeNode.GetImageData()
hierarchyNode.GetChildrenDisplayableNodes(childrenNodes)
# now we have the children which are fiducialNodes - let's loop!
for n in range(childrenNodes.GetNumberOfItems()):
currentFiducial = childrenNodes.GetItemAsObject(n)
currentCoordinatesRAS = [0, 0, 0]
# grab the current coordinates
currentFiducial.GetFiducialCoordinates(currentCoordinatesRAS)
# convert the RAS to IJK
currentCoordinatesIJK = Helper.ConvertRAStoIJK(
volumeNode, currentCoordinatesRAS)
# strip the last element since we need a 3based tupel
currentCoordinatesIJKlist = (int(currentCoordinatesIJK[0]),
int(currentCoordinatesIJK[1]),
int(currentCoordinatesIJK[2]))
outputIds.InsertNextId(
int(image.ComputePointId(currentCoordinatesIJKlist)))
# IdList was created, return it even if it might be empty
return outputIds
def onLabelExport(self):
'''
TODO: add a check that the selected label is associated with a volume that
has DICOM.instanceUIDs attribute set
'''
label = self.segmentationSelector.currentNode()
scalar = self.volumeSelector.currentNode()
# assuming here the user does the
if label == None or scalar == None:
self.exportButton.enabled = 0
return
labelImage = label.GetImageData()
scalarImage = label.GetImageData()
lDim = labelImage.GetDimensions()
sDim = scalarImage.GetDimensions()
if lDim[0]!=sDim[0] or lDim[1]!=sDim[1] or lDim[2]!=sDim[2]:
self.__helpLabel.text = 'Geometries do not match'
return
label = self.segmentationSelector.currentNode()
scalar = self.volumeSelector.currentNode()
# need to set up the associated node ID
label.SetAttribute('AssociatedNodeID', scalar.GetID())
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(label)
reportingLogic = slicer.modules.reporting.logic()
dirName = self.outputDir
fileName = reportingLogic.DicomSegWrite(labelCollection, dirName)
if fileName == '':
self.__helpLabel.text = 'Error!'
else:
self.__helpLabel.text = 'Exported to '+fileName.split('/')[-1]
def onLabelExport(self):
'''
TODO: add a check that the selected label is associated with a volume that
has DICOM.instanceUIDs attribute set
'''
label = self.segmentationSelector.currentNode()
scalar = self.volumeSelector.currentNode()
# assuming here the user does the
if label == None or scalar == None:
self.exportButton.enabled = 0
return
labelImage = label.GetImageData()
scalarImage = label.GetImageData()
lDim = labelImage.GetDimensions()
sDim = scalarImage.GetDimensions()
if lDim[0] != sDim[0] or lDim[1] != sDim[1] or lDim[2] != sDim[2]:
self.__helpLabel.text = 'Geometries do not match'
return
label = self.segmentationSelector.currentNode()
scalar = self.volumeSelector.currentNode()
# need to set up the associated node ID
label.SetAttribute('AssociatedNodeID', scalar.GetID())
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(label)
reportingLogic = slicer.modules.reporting.logic()
dirName = self.outputDir
fileName = reportingLogic.DicomSegWrite(labelCollection, dirName)
if fileName == '':
self.__helpLabel.text = 'Error!'
else:
self.__helpLabel.text = 'Exported to ' + fileName.split('/')[-1]
def createFiducialMatrix(self):
self.fiducialMatrixStatus = True
# extracting the effects of transform parameters
transformNode1 = self.templateSelector.currentNode().GetParentTransformNode()
#print transformNode1
shiftTransform1 = [0 , 0, 0]
rotationTransform1 = [[1, 0,0],[0,1,0],[0,0,1]]
#shiftTransform2 = [0, 0, 0]
#rotationTransform2 = [1, 0,0],[0,1,0],[0,0,1]]
if transformNode1 != None:
m = vtk.vtkMatrix4x4()
transformNode1.GetMatrixTransformToWorld(m)
shiftTransform1 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
rotationTransform1 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]]
self.fids = self.inputFiducialsNodeSelector.currentNode();
if self.fids.GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
self.fids.GetChildrenDisplayableNodes(collection)
self.n = collection.GetNumberOfItems()
if self.n == 0:
return
self.p = numpy.zeros((self.n,3))
for i in xrange(self.n):
f = collection.GetItemAsObject(i)
coords = [0,0,0]
# Need to change to consider the transform that is applied to the points
# offset for template width, moving the needle holes in z direction
f.GetFiducialCoordinates(coords)
print coords
coords = numpy.add(coords,[ 0, 0, self.templateWidth])
print coords
self.p[i] = numpy.add(numpy.dot(rotationTransform1,coords),shiftTransform1)
def load(self,loadable):
""" Call Reporting logic to load the DICOM SEG object
"""
print('DICOM SEG load()')
labelNodes = vtk.vtkCollection()
uid = None
try:
reportingLogic = slicer.modules.reporting.logic()
uid = loadable.uid
print 'in load(): uid = ', uid
except AttributeError:
return False
res = False
# default color node will be used
res = reportingLogic.DicomSegRead(labelNodes, uid)
print 'Read this many labels:',labelNodes.GetNumberOfItems()
defaultColorNode = reportingLogic.GetDefaultColorNode()
for i in range(labelNodes.GetNumberOfItems()):
# create and initialize the display node to use default color node
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLabelMapVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount()-1)
displayNode.SetAndObserveColorNodeID(defaultColorNode.GetID())
slicer.mrmlScene.AddNode(displayNode)
# assign it to the label node
# this is done here as opposed to Reporting logic to minimize the
# dependencies of the DICOM SEG functionality in the Slicer internals
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNode)
return True
def start(self, preview=False):
'''
'''
SlicerVmtkCommonLib.Helper.Debug("Starting Level Set Segmentation..")
# first we need the nodes
currentVolumeNode = self.__inputVolumeNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentVesselnessNode = self.__vesselnessVolumeNodeSelector.currentNode(
)
currentStoppersNode = self.__stopperFiducialsNodeSelector.currentNode()
currentLabelMapNode = self.__outputVolumeNodeSelector.currentNode()
currentModelNode = self.__outputModelNodeSelector.currentNode()
if not currentVolumeNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentStoppersNode or currentStoppersNode.GetID(
) == currentSeedsNode.GetID():
# we need a current stopper node
# self.__stopperFiducialsNodeSelector.addNode()
pass
if not currentLabelMapNode or currentLabelMapNode.GetID(
) == currentVolumeNode.GetID():
# we need a current labelMap node
newLabelMapDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLLabelMapVolumeDisplayNode")
newLabelMapDisplayNode.SetScene(slicer.mrmlScene)
newLabelMapDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(newLabelMapDisplayNode)
newLabelMapNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLScalarVolumeNode")
newLabelMapNode.CopyOrientation(currentVolumeNode)
newLabelMapNode.SetScene(slicer.mrmlScene)
newLabelMapNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__outputVolumeNodeSelector.baseName))
newLabelMapNode.LabelMapOn()
newLabelMapNode.SetAndObserveDisplayNodeID(
newLabelMapDisplayNode.GetID())
slicer.mrmlScene.AddNode(newLabelMapNode)
currentLabelMapNode = newLabelMapNode
self.__outputVolumeNodeSelector.setCurrentNode(currentLabelMapNode)
if not currentModelNode:
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelNode")
newModelNode.SetScene(slicer.mrmlScene)
newModelNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__outputModelNodeSelector.baseName))
slicer.mrmlScene.AddNode(newModelNode)
currentModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode(currentModelNode)
# now we need to convert the fiducials to vtkIdLists
seeds = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList(
currentSeedsNode, currentVolumeNode)
# stoppers = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList(currentStoppersNode, currentVolumeNode)
stoppers = vtk.vtkIdList() # TODO
# the input image for the initialization
inputImage = vtk.vtkImageData()
# check if we have a vesselnessNode - this will be our input for the initialization then
if currentVesselnessNode:
# yes, there is one
inputImage.DeepCopy(currentVesselnessNode.GetImageData())
else:
# no, there is none - we use the original image
inputImage.DeepCopy(currentVolumeNode.GetImageData())
inputImage.Update()
# initialization
initImageData = vtk.vtkImageData()
# evolution
evolImageData = vtk.vtkImageData()
# perform the initialization
initImageData.DeepCopy(self.GetLogic().performInitialization(
inputImage, self.__thresholdSlider.minimumValue,
self.__thresholdSlider.maximumValue, seeds, stoppers,
0)) # TODO sidebranch ignore feature
initImageData.Update()
if not initImageData.GetPointData().GetScalars():
# something went wrong, the image is empty
SlicerVmtkCommonLib.Helper.Info(
"Segmentation failed - the output was empty..")
return -1
# check if it is a preview call
if preview:
# if this is a preview call, we want to skip the evolution
evolImageData.DeepCopy(initImageData)
else:
# no preview, run the whole thing! we never use the vesselness node here, just the original one
evolImageData.DeepCopy(self.GetLogic().performEvolution(
currentVolumeNode.GetImageData(), initImageData,
self.__iterationSpinBox.value, self.__inflationSlider.value,
self.__curvatureSlider.value, self.__attractionSlider.value,
'geodesic'))
evolImageData.Update()
# create segmentation labelMap
labelMap = vtk.vtkImageData()
labelMap.DeepCopy(self.GetLogic().buildSimpleLabelMap(
evolImageData, 0, 5))
labelMap.Update()
currentLabelMapNode.CopyOrientation(currentVolumeNode)
# propagate the label map to the node
currentLabelMapNode.SetAndObserveImageData(labelMap)
currentLabelMapNode.Modified()
# deactivate the threshold in the GUI
self.resetThresholdOnDisplayNode()
# self.onInputVolumeChanged()
# show the segmentation results in the GUI
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
if preview and currentVesselnessNode:
# if preview and a vesselnessNode was configured, show it
selectionNode.SetReferenceActiveVolumeID(
currentVesselnessNode.GetID())
else:
# if not preview, show the original volume
if currentVesselnessNode:
selectionNode.SetReferenceSecondaryVolumeID(
currentVesselnessNode.GetID())
selectionNode.SetReferenceActiveVolumeID(currentVolumeNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
currentLabelMapNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection()
# generate 3D model
model = vtk.vtkPolyData()
# we need the ijkToRas transform for the marching cubes call
ijkToRasMatrix = vtk.vtkMatrix4x4()
currentLabelMapNode.GetIJKToRASMatrix(ijkToRasMatrix)
# call marching cubes
model.DeepCopy(self.GetLogic().marchingCubes(evolImageData,
ijkToRasMatrix, 0.0))
model.Update()
# propagate model to nodes
currentModelNode.SetAndObservePolyData(model)
currentModelNode.Modified()
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentModelDisplayNode)
# always configure the displayNode to show the model
currentModelDisplayNode.SetInputPolyData(
currentModelNode.GetPolyData())
currentModelDisplayNode.SetColor(1.0, 0.55, 0.4) # red
currentModelDisplayNode.SetBackfaceCulling(0)
currentModelDisplayNode.SetSliceIntersectionVisibility(0)
currentModelDisplayNode.SetVisibility(1)
currentModelDisplayNode.SetOpacity(1.0)
currentModelDisplayNode.Modified()
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID(
currentModelDisplayNode.GetID())
currentModelNode.Modified()
# fit slice to all sliceviewers
slicer.app.applicationLogic().FitSliceToAll()
# jump all sliceViewers to the first fiducial point, if one was used
if currentSeedsNode:
currentCoordinatesRAS = [0, 0, 0]
if isinstance(currentSeedsNode,
slicer.vtkMRMLAnnotationHierarchyNode):
childrenNodes = vtk.vtkCollection()
currentSeedsNode.GetChildrenDisplayableNodes(childrenNodes)
# now we have the children, let's get the first one
currentFiducial = childrenNodes.GetItemAsObject(0)
# grab the current coordinates
currentFiducial.GetFiducialCoordinates(currentCoordinatesRAS)
elif isinstance(currentSeedsNode,
slicer.vtkMRMLAnnotationFiducialNode):
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates(currentCoordinatesRAS)
numberOfSliceNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLSliceNode')
for n in xrange(numberOfSliceNodes):
sliceNode = slicer.mrmlScene.GetNthNodeByClass(
n, "vtkMRMLSliceNode")
if sliceNode:
sliceNode.JumpSliceByOffsetting(currentCoordinatesRAS[0],
currentCoordinatesRAS[1],
currentCoordinatesRAS[2])
# center 3D view(s) on the new model
if currentCoordinatesRAS:
for d in range(slicer.app.layoutManager().threeDViewCount):
threeDView = slicer.app.layoutManager().threeDWidget(
d).threeDView()
# reset the focal point
threeDView.resetFocalPoint()
# and fly to our seed point
interactor = threeDView.interactor()
renderer = threeDView.renderWindow().GetRenderers(
).GetItemAsObject(0)
interactor.FlyTo(renderer, currentCoordinatesRAS[0],
currentCoordinatesRAS[1],
currentCoordinatesRAS[2])
SlicerVmtkCommonLib.Helper.Debug("End of Level Set Segmentation..")
def start( self, preview=False ):
'''
'''
SlicerVmtkCommonLib.Helper.Debug( "Starting Level Set Segmentation.." )
# first we need the nodes
currentVolumeNode = self.__inputVolumeNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentVesselnessNode = self.__vesselnessVolumeNodeSelector.currentNode()
currentStoppersNode = self.__stopperFiducialsNodeSelector.currentNode()
currentLabelMapNode = self.__outputVolumeNodeSelector.currentNode()
currentModelNode = self.__outputModelNodeSelector.currentNode()
if not currentVolumeNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentStoppersNode or currentStoppersNode.GetID() == currentSeedsNode.GetID():
# we need a current stopper node
# self.__stopperFiducialsNodeSelector.addNode()
pass
if not currentLabelMapNode or currentLabelMapNode.GetID() == currentVolumeNode.GetID():
# we need a current labelMap node
newLabelMapDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLLabelMapVolumeDisplayNode" )
newLabelMapDisplayNode.SetScene( slicer.mrmlScene )
newLabelMapDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode( newLabelMapDisplayNode )
newLabelMapNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLScalarVolumeNode" )
newLabelMapNode.CopyOrientation( currentVolumeNode )
newLabelMapNode.SetScene( slicer.mrmlScene )
newLabelMapNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__outputVolumeNodeSelector.baseName ) )
newLabelMapNode.LabelMapOn()
newLabelMapNode.SetAndObserveDisplayNodeID( newLabelMapDisplayNode.GetID() )
slicer.mrmlScene.AddNode( newLabelMapNode )
currentLabelMapNode = newLabelMapNode
self.__outputVolumeNodeSelector.setCurrentNode( currentLabelMapNode )
if not currentModelNode:
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
newModelNode.SetScene( slicer.mrmlScene )
newModelNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__outputModelNodeSelector.baseName ) )
slicer.mrmlScene.AddNode( newModelNode )
currentModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode( currentModelNode )
# now we need to convert the fiducials to vtkIdLists
seeds = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList( currentSeedsNode, currentVolumeNode )
# stoppers = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList(currentStoppersNode, currentVolumeNode)
stoppers = vtk.vtkIdList() # TODO
# the input image for the initialization
inputImage = vtk.vtkImageData()
# check if we have a vesselnessNode - this will be our input for the initialization then
if currentVesselnessNode:
# yes, there is one
inputImage.DeepCopy( currentVesselnessNode.GetImageData() )
else:
# no, there is none - we use the original image
inputImage.DeepCopy( currentVolumeNode.GetImageData() )
inputImage.Update()
# initialization
initImageData = vtk.vtkImageData()
# evolution
evolImageData = vtk.vtkImageData()
# perform the initialization
initImageData.DeepCopy( self.GetLogic().performInitialization( inputImage,
self.__thresholdSlider.minimumValue,
self.__thresholdSlider.maximumValue,
seeds,
stoppers,
0 ) ) # TODO sidebranch ignore feature
initImageData.Update()
if not initImageData.GetPointData().GetScalars():
# something went wrong, the image is empty
SlicerVmtkCommonLib.Helper.Info( "Segmentation failed - the output was empty.." )
return -1
# check if it is a preview call
if preview:
# if this is a preview call, we want to skip the evolution
evolImageData.DeepCopy( initImageData )
else:
# no preview, run the whole thing! we never use the vesselness node here, just the original one
evolImageData.DeepCopy( self.GetLogic().performEvolution( currentVolumeNode.GetImageData(),
initImageData,
self.__iterationSpinBox.value,
self.__inflationSlider.value,
self.__curvatureSlider.value,
self.__attractionSlider.value,
'geodesic' ) )
evolImageData.Update()
# create segmentation labelMap
labelMap = vtk.vtkImageData()
labelMap.DeepCopy( self.GetLogic().buildSimpleLabelMap( evolImageData, 0, 5 ) )
labelMap.Update()
currentLabelMapNode.CopyOrientation( currentVolumeNode )
# propagate the label map to the node
currentLabelMapNode.SetAndObserveImageData( labelMap )
currentLabelMapNode.Modified()
# deactivate the threshold in the GUI
self.resetThresholdOnDisplayNode()
# self.onInputVolumeChanged()
# show the segmentation results in the GUI
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
if preview and currentVesselnessNode:
# if preview and a vesselnessNode was configured, show it
selectionNode.SetReferenceActiveVolumeID( currentVesselnessNode.GetID() )
else:
# if not preview, show the original volume
if currentVesselnessNode:
selectionNode.SetReferenceSecondaryVolumeID( currentVesselnessNode.GetID() )
selectionNode.SetReferenceActiveVolumeID( currentVolumeNode.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID( currentLabelMapNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection()
# generate 3D model
model = vtk.vtkPolyData()
# we need the ijkToRas transform for the marching cubes call
ijkToRasMatrix = vtk.vtkMatrix4x4()
currentLabelMapNode.GetIJKToRASMatrix( ijkToRasMatrix )
# call marching cubes
model.DeepCopy( self.GetLogic().marchingCubes( evolImageData, ijkToRasMatrix, 0.0 ) )
model.Update()
# propagate model to nodes
currentModelNode.SetAndObservePolyData( model )
currentModelNode.Modified()
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentModelDisplayNode )
# always configure the displayNode to show the model
currentModelDisplayNode.SetInputPolyData( currentModelNode.GetPolyData() )
currentModelDisplayNode.SetColor( 1.0, 0.55, 0.4 ) # red
currentModelDisplayNode.SetBackfaceCulling( 0 )
currentModelDisplayNode.SetSliceIntersectionVisibility( 0 )
currentModelDisplayNode.SetVisibility( 1 )
currentModelDisplayNode.SetOpacity( 1.0 )
currentModelDisplayNode.Modified()
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID( currentModelDisplayNode.GetID() )
currentModelNode.Modified()
# fit slice to all sliceviewers
slicer.app.applicationLogic().FitSliceToAll()
# jump all sliceViewers to the first fiducial point, if one was used
if currentSeedsNode:
currentCoordinatesRAS = [0, 0, 0]
if isinstance( currentSeedsNode, slicer.vtkMRMLAnnotationHierarchyNode ):
childrenNodes = vtk.vtkCollection()
currentSeedsNode.GetChildrenDisplayableNodes( childrenNodes )
# now we have the children, let's get the first one
currentFiducial = childrenNodes.GetItemAsObject( 0 )
# grab the current coordinates
currentFiducial.GetFiducialCoordinates( currentCoordinatesRAS )
elif isinstance( currentSeedsNode, slicer.vtkMRMLAnnotationFiducialNode ):
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates( currentCoordinatesRAS )
numberOfSliceNodes = slicer.mrmlScene.GetNumberOfNodesByClass( 'vtkMRMLSliceNode' )
for n in xrange( numberOfSliceNodes ):
sliceNode = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLSliceNode" )
if sliceNode:
sliceNode.JumpSliceByOffsetting( currentCoordinatesRAS[0], currentCoordinatesRAS[1], currentCoordinatesRAS[2] )
# center 3D view(s) on the new model
if currentCoordinatesRAS:
for d in range( slicer.app.layoutManager().threeDViewCount ):
threeDView = slicer.app.layoutManager().threeDWidget( d ).threeDView()
# reset the focal point
threeDView.resetFocalPoint()
# and fly to our seed point
interactor = threeDView.interactor()
renderer = threeDView.renderWindow().GetRenderers().GetItemAsObject( 0 )
interactor.FlyTo( renderer, currentCoordinatesRAS[0], currentCoordinatesRAS[1], currentCoordinatesRAS[2] )
SlicerVmtkCommonLib.Helper.Debug( "End of Level Set Segmentation.." )
def onRegistrationButtonClicked(self):
print "Hello Registration :) "
self.referenceAttachmentCollapsibleButton.enabled = True
linearTransformExistence = False
linearTransformNodes = slicer.util.getNodes('vtkMRMLlinearTransformNode*')
for linearTransformNode in linearTransformNodes.keys():
if linearTransformNode=='ModelToTemplateTransform':
linearTransformExistence = True
if linearTransformExistence == False:
followupTransform = slicer.vtkMRMLLinearTransformNode()
followupTransform.SetName('ModelToTemplateTransform')
followupTransform.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(followupTransform)
self.followupTransform = followupTransform
self.fiducialListNode = slicer.util.getNode('Template Fiducials')
movingLandmarksListID = self.fiducialListNode.GetID()
modelFiducials = self.modelFiducialSelector.currentNode()
# extracting the effects of transform parameters
transformNode1 = self.templateSelector.currentNode().GetParentTransformNode()
#print transformNode1
shiftTransform1 = [0 , 0, 0]
rotationTransform1 = [[1, 0,0],[0,1,0],[0,0,1]]
#shiftTransform2 = [0, 0, 0]
#rotationTransform2 = [1, 0,0],[0,1,0],[0,0,1]]
if transformNode1 != None:
m = vtk.vtkMatrix4x4()
transformNode1.GetMatrixTransformToWorld(m)
shiftTransform1 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
rotationTransform1 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]]
#transformNode2 = transformNode1.GetParentTransformNode()
#if transformNode2 != None:
#transformNode2.GetMatrixTransformToWorld(m)
#shiftTransform2 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
#rotationTransform2 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]
#shiftTransform = numpy.add(shiftTransform1,shiftTransform2)
# Changing the fiducial coordinates according to the transform
if modelFiducials.GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
modelFiducials.GetChildrenDisplayableNodes(collection)
n = collection.GetNumberOfItems()
if n != 6:
return
# output an error and ask user to select a fiducial with 6 points
listExitence = False
hierarchyNodes = slicer.util.getNodes('vtkMRMLAnnotationHierarchyNode*')
for hierarchyNode in hierarchyNodes.keys():
if hierarchyNode=='New Model Fiducials':
listExitence = True
self.newModelFiducialAnnotationList.RemoveAllChildrenNodes()
if listExitence == False:
newModelFiducialAnnotationList = slicer.vtkMRMLAnnotationHierarchyNode()
newModelFiducialAnnotationList.SetName('New Model Fiducials')
# hide the fiducial list from the scene
newModelFiducialAnnotationList.SetHideFromEditors(1)
newModelFiducialAnnotationList.SetScene(self.scene)
self.scene.AddNode(newModelFiducialAnnotationList)
self.newModelFiducialAnnotationList = newModelFiducialAnnotationList
self.logic.SetActiveHierarchyNodeID(self.newModelFiducialAnnotationList.GetID())
#self.logic.AddHierarchy
#a=self.logic.GetActiveHierarchyNode()
#a.SetName('New Model Fiducials')
p = numpy.zeros((n,3))
for i in xrange(n):
f = collection.GetItemAsObject(i)
coords = [0,0,0]
# Need to change to consider the transform that is applied to the points
f.GetFiducialCoordinates(coords)
newCoords = numpy.add(numpy.dot(rotationTransform1,coords),shiftTransform1)
newfid = slicer.vtkMRMLAnnotationFiducialNode()
newfid.SetFiducialCoordinates(newCoords)
newfid.SetHideFromEditors(0)
newfid.SetName(str(i))
self.scene.AddNode(newfid)
fixedLandmarksListID = self.newModelFiducialAnnotationList.GetID()
self.OutputMessage = ""
parameters = {}
parameters["fixedLandmarks"] = fixedLandmarksListID
parameters["movingLandmarks"] = movingLandmarksListID
parameters["saveTransform"] = self.followupTransform
parameters["transformType"] = "Rigid"
parameters["rms"] = self.RMS
parameters["outputMessage"] = self.OutputMessage
fidreg = slicer.modules.fiducialregistration
self.__cliNode = None
self.__cliNode = slicer.cli.run(fidreg, self.__cliNode, parameters)
print "RMS is", self.RMS
#self.__cliObserverTag = self.__cliNode.AddObserver('ModifiedEvent', self.processRegistrationCompletion)
#self.__registrationStatus.setText('Wait ...')
#self.firstRegButton.setEnabled(0)
stylusNode = self.stylusTrackerSelector.currentNode()
stylusNode.SetAndObserveTransformNodeID(self.followupTransform.GetID())
def onCalculateButton(self):
logic = SpinalCurvatureMeasurementLogic()
(self.superiorAnglesList,
self.inferiorAnglesList) = logic.calculateAngles(
self.inputSelector.currentNode(),
self.projectionPlaneBox.currentText)
superiorAnglesListCount = 0
for superiorAngle in self.superiorAnglesList:
self.angleTable.item(superiorAnglesListCount,
1).setText(str(superiorAngle))
superiorAnglesListCount += 1
inferiorAnglesListCount = 0
for inferiorAngle in self.inferiorAnglesList:
self.angleTable.item(inferiorAnglesListCount,
2).setText(str(inferiorAngle))
inferiorAnglesListCount += 1
# Refresh observers
for rulerNode, tag in self.observerTags:
rulerNode.RemoveObserver(tag)
rulerNodes = vtk.vtkCollection()
self.inputSelector.currentNode().GetDirectChildren(rulerNodes)
rulerNodesList = []
for nodeIndex in range(rulerNodes.GetNumberOfItems()):
if rulerNodes.GetItemAsObject(
nodeIndex).GetClassName() == "vtkMRMLAnnotationRulerNode":
rulerNodesList.append(rulerNodes.GetItemAsObject(nodeIndex))
for rulerNode in rulerNodesList:
def update(caller, ev):
import re
angle = logic.updateAngle(caller,
self.projectionPlaneBox.currentText)
rulerName = caller.GetName()
#nameSearch.group(1) - Region (C, T, or L)
#nameSearch.group(2) - Number (1, 2, 3, etc.)
#nameSearch.group(3) - Superior or Inferior (s or i)
nameSearch = re.search(r"^([CTL])(\d+)-([si])$", rulerName)
if nameSearch != None:
if nameSearch.group(1) == "C":
index = int(nameSearch.group(2)) - 1
elif nameSearch.group(1) == "T":
index = int(nameSearch.group(
2)) + self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE - 1
elif nameSearch.group(1) == "L":
index = int(
nameSearch.group(2)
) + self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE + self.CONST_NUMBER_OF_THORACIC_VERTERBRAE - 1
if nameSearch.group(3) == "s":
self.angleTable.item(index, 1).setText(str(angle))
elif nameSearch.group(3) == "i":
self.angleTable.item(index, 2).setText(str(angle))
tag = rulerNode.AddObserver(rulerNode.ControlPointModifiedEvent,
update)
self.observerTags.append([rulerNode, tag])
def calculateAngles(self, annotationHierarchy, planeOrientation):
import re, math
superiorCervicalAngles = [None
] * self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE
superiorThoracicAngles = [None
] * self.CONST_NUMBER_OF_THORACIC_VERTERBRAE
superiorLumbarAngles = [None] * self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE
inferiorCervicalAngles = [None
] * self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE
inferiorThoracicAngles = [None
] * self.CONST_NUMBER_OF_THORACIC_VERTERBRAE
inferiorLumbarAngles = [None] * self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE
if planeOrientation == "Coronal":
planeNormal = [0, 1, 0]
baseAngleVector = [1, 0, 0]
elif planeOrientation == "Axial":
planeNormal = [0, 0, 1]
baseAngleVector = [1, 0, 0]
else:
planeNormal = [1, 0, 0]
baseAngleVector = [0, 1, 0]
rulerNodes = vtk.vtkCollection()
annotationHierarchy.GetDirectChildren(rulerNodes)
rulerNodesList = []
for nodeIndex in range(rulerNodes.GetNumberOfItems()):
if rulerNodes.GetItemAsObject(
nodeIndex).GetClassName() == "vtkMRMLAnnotationRulerNode":
rulerNodesList.append(rulerNodes.GetItemAsObject(nodeIndex))
for ruler in rulerNodesList:
angle = self.updateAngle(ruler, planeOrientation)
rulerName = ruler.GetName()
#nameSearch.group(1) - Region (C, T, or L)
#nameSearch.group(2) - Number (1, 2, 3, etc.)
#nameSearch.group(3) - Superior or Inferior (s or i)
nameSearch = re.search(r"^([CTL])(\d+)-([si])$", rulerName)
if nameSearch != None:
if nameSearch.group(1) == "C":
if nameSearch.group(3) == "s":
superiorCervicalAngles[int(nameSearch.group(2)) -
1] = angle
elif nameSearch.group(3) == "i":
inferiorCervicalAngles[int(nameSearch.group(2)) -
1] = angle
elif nameSearch.group(1) == "T":
if nameSearch.group(3) == "s":
superiorThoracicAngles[int(nameSearch.group(2)) -
1] = angle
elif nameSearch.group(3) == "i":
inferiorThoracicAngles[int(nameSearch.group(2)) -
1] = angle
elif nameSearch.group(1) == "L":
if nameSearch.group(3) == "s":
superiorLumbarAngles[int(nameSearch.group(2)) -
1] = angle
elif nameSearch.group(3) == "i":
inferiorLumbarAngles[int(nameSearch.group(2)) -
1] = angle
return (superiorCervicalAngles + superiorThoracicAngles +
superiorLumbarAngles, inferiorCervicalAngles +
inferiorThoracicAngles + inferiorLumbarAngles)
def __init__(self, markersFiducialsNode, targetFiducialNode, entryFiducialNode):
self.fids = [markersFiducialsNode, targetFiducialNode, entryFiducialNode]
# Get the point's coordinates in the markers, target and entry fiducials
self.position = [] #save the points' position
for i in range(len(self.fids)):
if self.fids[i].GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
self.fids[i].GetChildrenDisplayableNodes(collection)
self.n = collection.GetNumberOfItems()
if self.n == 0:
return
self.p = numpy.zeros((self.n,3))
for j in xrange(self.n):
f = collection.GetItemAsObject(j)
coords = [0,0,0]
f.GetFiducialCoordinates(coords)
self.p[j] = coords
elif self.fids[i].GetClassName() == 'vtkMRMLMarkupsFiducialNode':
# slicer4 Markups node
self.n = self.fids[i].GetNumberOfFiducials()
n = self.n
if n == 0:
return
# get fiducial positions
# sets self.p
self.p = numpy.zeros((n,3))
for j in xrange(n):
coord = [0.0, 0.0, 0.0]
self.fids[i].GetNthFiducialPosition(j, coord)
self.p[j] = coord
else:
# slicer3 style fiducial lists
self.n = self.fids[i].GetNumberOfFiducials()
n = self.n
if n == 0:
return
#sets self.p
self.p = numpy.zeros((n,3))
for j in xrange(n):
self.p[j] = self.fids[i].GetNthFiducialXYZ(j)
self.position.append(self.p)
#Vectors of the points and the normals of the reference plane
vector1 = self.position[0][0] - self.position[0][1] #a vector in the plane red
vector2 = self.position[0][0] - self.position[0][2] #a vector in the plane red
normalRed = numpy.cross(vector1,vector2) #normal of the plane red using the 'numpy.cross()' to calculate the cross product of two vector
vector3 = self.position[0][3] - self.position[0][4] #a vector in the plane green
normalGreen = numpy.cross(vector3, normalRed) #normal of the plane green
normalBlue = numpy.cross(normalRed, normalGreen)#normal of the plane blue
#Vector of the target and entry point
vectorTargetEntry = self.position[1][0] - self.position[2][0]# the vector the target and entry point
#Distance between target and entry point
distance = round(numpy.linalg.norm(vectorTargetEntry), 1)
#Angles between the puncture path and the reference plane
sinAngleRed = numpy.abs(numpy.dot(vectorTargetEntry, normalRed)) / (numpy.linalg.norm(normalRed)*numpy.linalg.norm(vectorTargetEntry))
sinAngleGreen = numpy.abs(numpy.dot(vectorTargetEntry, normalGreen)) / (numpy.linalg.norm(normalGreen)*numpy.linalg.norm(vectorTargetEntry))
sinAngleBlue = numpy.abs(numpy.dot(vectorTargetEntry, normalBlue)) / (numpy.linalg.norm(normalBlue)*numpy.linalg.norm(vectorTargetEntry))
angleRed = round(numpy.arcsin(sinAngleRed) / numpy.pi * 180.0, 1) # angle of the puncture path relative to the plane red
angleGreen = round(numpy.arcsin(sinAngleGreen) / numpy.pi * 180.0, 1) # angle of the puncture path relative to the plane green
angleBlue = round(numpy.arcsin(sinAngleBlue) / numpy.pi * 180.0, 1) # angle of the puncture path relative to the plane blue
self.normalRed = normalRed
self.normalGreen = normalGreen
self.normalBlue = normalBlue
self.angleRed = angleRed
self.angleGreen = angleGreen
self.angleBlue = angleBlue
self.distance = distance
def DoIt(inputDir, rgbDir, outputDir):
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm) - dcm.rfind('.dcm') == 4:
dcmList.append(inputDir + '/' + dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
print 'Will examine: ', dcmList
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir)
indexer.waitForImportFinished()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
'''
sNode.ResetFileNameList()
for f in loadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(loadables[0].files[0])
sNode.SetSingleFile(0)
inputVolume = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(inputVolume)
'''
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir, 'input_volume.nrrd'))
sNode.WriteData(inputVolume)
#
# Order the input RGBs and rename in a temp directory
#
rgbList = []
for rgb in os.listdir(rgbDir):
if len(rgb) - rgb.rfind('.bmp') == 4:
rgbList.append(rgb)
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
tmpDir = tmpDir + '/PNGStackLabelConverter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
oldFiles = os.listdir(tmpDir)
# just in case there is anything in that directory
for f in oldFiles:
os.unlink(tmpDir + '/' + f)
rgbOrdered = [None] * len(loadables[0].files)
rgbCnt = 0
rgbExt = rgbList[0][rgbList[0].rfind('.') + 1:len(rgbList[0])]
print 'Extension for RGBs: ', rgbExt
dcmFileList = loadables[0].files
rgbRenamedList = []
print 'Number of dcm files: ', len(dcmFileList), ' and rgb files: ', len(
rgbOrdered)
dcmIdx = 0
for dcm in dcmFileList:
rgbIdx = 0
for rgb in rgbList:
dcmPrefix = dcm[dcm.rfind('/') + 1:dcm.rfind('.')]
if rgb.find(dcmPrefix) != -1:
name = string.zfill(str(dcmIdx), 5)
rgbCnt = rgbCnt + 1
src = rgbDir + '/' + rgb
dest = tmpDir + '/' + name + '.' + rgbExt
rgbRenamedList.append(dest)
shutil.copy(src, dest)
break
rgbIdx = rgbIdx + 1
# remove the matched DICOM file from the list
if rgbIdx == len(rgbList):
print('ERROR: failed to find matching label file for DICOM file ' +
dcm)
return
del rgbList[rgbIdx]
dcmIdx = dcmIdx + 1
if len(rgbRenamedList) == 0:
print 'Could not parse the DICOM Study!'
return
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
for f in rgbRenamedList:
sNode.AddFileName(f)
sNode.SetFileName(rgbRenamedList[0])
sNode.SetSingleFile(0)
inputRGBVolume = slicer.vtkMRMLVectorVolumeNode()
sNode.ReadData(inputRGBVolume)
# run the filter
# - extract the RGB portions
extract = vtk.vtkImageExtractComponents()
extract.SetComponents(0, 1, 2)
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
extract.SetInput(inputRGBVolume.GetImageData())
else:
extract.SetInputData(inputRGBVolume.GetImageData())
luminance = vtk.vtkImageLuminance()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
luminance.SetInput(extract.GetOutput())
else:
luminance.SetInputData(extract.GetOutput())
cast = vtk.vtkImageCast()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(luminance.GetOutput())
else:
cast.SetInputData(luminance.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputLabel = slicer.vtkMRMLLabelMapVolumeNode()
outputLabel.SetIJKToRASMatrix(ijkToRAS)
outputLabel.SetAndObserveImageData(cast.GetOutput())
reportingLogic = slicer.modules.reporting.logic()
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(
reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
outputLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir, 'label_output.nrrd'))
sNode.WriteData(outputLabel)
# save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(outputLabel)
slicer.mrmlScene.AddNode(inputVolume)
outputLabel.SetAttribute('AssociatedNodeID', inputVolume.GetID())
slicer.mrmlScene.AddNode(outputLabel)
# initialize the DICOM DB for Reporting logic
settings = qt.QSettings()
dbFileName = settings.value('DatabaseDirectory', '')
if dbFileName == '':
print('ERROR: database must be initialized')
else:
dbFileName = dbFileName + '/ctkDICOM.sql'
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
def LoadAIMFile(newReportID, fileName):
dom = xml.dom.minidom.parse(fileName)
SlicerReportingModuleWidgetHelper.Debug('Parsed AIM report:')
SlicerReportingModuleWidgetHelper.Debug(dom.toxml())
volumeList = []
ddb = slicer.dicomDatabase
volId = 1
volume = None
# get the annotation element and retrieve its name
annotations = dom.getElementsByTagName('ImageAnnotation')
if len(annotations) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM file does not contain any annotations!')
return
ann = annotations[0]
desc = ann.getAttribute('name')
# get the anatomic entity element and initialize the report node based on
# it
anatomics = dom.getElementsByTagName('AnatomicEntity')
if len(anatomics) != 1:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM file does not contain any anatomic entities or contains more than one! This is not supported.')
return
anatomy = anatomics[0]
labelValue = anatomy.getAttribute('codeValue')
labelName = anatomy.getAttribute('codeMeaning')
codingSchemeDesignator = anatomy.getAttribute('codingSchemeDesignator')
if codingSchemeDesignator != '3DSlicer':
SlicerReportingModuleWidgetHelper.WarningPopup('Code scheme designator '+codingSchemeDesignator+' is not supported. Default will be used instead.')
labelValue = "1"
newReport = slicer.mrmlScene.GetNodeByID(newReportID)
newReport.SetFindingLabel(int(labelValue))
# pull all the volumes that are referenced into the scene
for node in dom.getElementsByTagName('ImageSeries'):
instanceUID = node.getAttribute('instanceUID')
filelist = ddb.filesForSeries(instanceUID)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
if len(scalarVolumeLoadables) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('Error loading AIM: Failed to load the volume node reference in the file')
volumeName = scalarVolumeLoadables[0].name
newReport.SetName('Report for Volume '+volumeName)
volume = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volume.SetName(volumeName)
if volume == None:
SlicerReportingModuleWidgetHelper.Error('Failed to read series!')
return
if len(volumeList) != 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('Error importing AIM report: Report references more than one volume, which is not allowed!')
return
volumeList.append(volume)
SlicerReportingModuleWidgetHelper.Debug('Volume read from AIM report:')
slicer.modules.reporting.logic().AddVolumeToReport(volume)
newReport.SetVolumeNodeID(volume.GetID())
if len(volumeList) > 1:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM does not allow to have more than one volume per file!')
return
if len(volumeList) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM file you requested to load does not reference any volumes, cannot process it!')
return
#if volume != None:
# self.__volumeSelector.setCurrentNode(volume)
instanceUIDs = volume.GetAttribute('DICOM.instanceUIDs')
instanceUIDList = instanceUIDs.split()
# AF: GeometricShape is inside geometricShapeCollection, but
# there's no need to parse at that level, I think
#
# geometricShapeCollection
# |
# +-spatialCoordinateCollection
# |
# +-SpatialCoordinate
#
for node in dom.getElementsByTagName('GeometricShape'):
ijCoordList = []
rasPointList = []
uidList = []
elementType = node.getAttribute('xsi:type')
for child in node.childNodes:
if child.nodeName == 'spatialCoordinateCollection':
for coord in child.childNodes:
if coord.nodeName == 'SpatialCoordinate':
ijCoordList.append(float(coord.getAttribute('x')))
ijCoordList.append(float(coord.getAttribute('y')))
uid = coord.getAttribute('imageReferenceUID')
uidList.append(uid)
SlicerReportingModuleWidgetHelper.Debug('Coordinate list: '+str(ijCoordList))
ijk2ras = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(ijk2ras)
# convert each point from IJ to RAS
for ij in range(len(uidList)):
pointUID = uidList[ij]
# locate the UID in the list assigned to the volume
totalSlices = len(instanceUIDList)
for k in range(len(instanceUIDList)):
if pointUID == instanceUIDList[k]:
break
# print "k = ",k,", totalSlices = ",totalSlices
pointIJK = [ijCoordList[ij*2], ijCoordList[ij*2+1], k, 1.]
pointRAS = ijk2ras.MultiplyPoint(pointIJK)
SlicerReportingModuleWidgetHelper.Debug('Input point: '+str(pointIJK))
SlicerReportingModuleWidgetHelper.Debug('Converted point: '+str(pointRAS))
rasPointList.append(pointRAS[0:3])
# instantiate the markup elements
if elementType == 'Point':
SlicerReportingModuleWidgetHelper.Debug("Importing a fiducial!")
if len(ijCoordList) != 2:
SlicerReportingModuleWidgetHelper.Error('Number of coordinates not good for a fiducial')
return
fiducial = slicer.mrmlScene.CreateNodeByClass('vtkMRMLAnnotationFiducialNode')
fiducial.SetReferenceCount(fiducial.GetReferenceCount()-1)
# associate it with the report
fiducial.SetAttribute('ReportingReportNodeID', newReport.GetID())
# associate it with the volume
fiducial.SetAttribute('AssociatedNodeID', volume.GetID())
# ??? Why the API is so inconsistent -- there's no SetPosition1() ???
fiducial.SetFiducialCoordinates(rasPointList[0])
fiducial.Initialize(slicer.mrmlScene)
# adding to hierarchy is handled by the Reporting logic
if elementType == 'MultiPoint':
SlicerReportingModuleWidgetHelper.Debug("Importing a ruler!")
if len(ijCoordList) != 4:
SlicerReportingModuleWidgetHelper.Error('Number of coordinates not good for a ruler')
return
ruler = slicer.mrmlScene.CreateNodeByClass('vtkMRMLAnnotationRulerNode')
ruler.SetReferenceCount(ruler.GetReferenceCount()-1)
# associate it with the report
ruler.SetAttribute('ReportingReportNodeID', newReport.GetID())
# associate it with the volume
ruler.SetAttribute('AssociatedNodeID', volume.GetID())
SlicerReportingModuleWidgetHelper.Debug('Initializing with points '+str(rasPointList[0])+' and '+str(rasPointList[1]))
ruler.SetPosition1(rasPointList[0])
ruler.SetPosition2(rasPointList[1])
ruler.Initialize(slicer.mrmlScene)
# AF: Initialize() adds to the scene ...
for node in dom.getElementsByTagName('Segmentation'):
# read all labels that are available in the SEG object
# check if the referenced volume is already in the scene
# if not, load it
# initialize AssociatedNodeID for the label node to point to the
# reference
SlicerReportingModuleWidgetHelper.Debug('Importing a segmentation')
labelNodes = vtk.vtkCollection()
referenceNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeNode')
referenceNode.SetReferenceCount(referenceNode.GetReferenceCount()-1)
uid = node.getAttribute('sopInstanceUID')
res = False
colorNode = slicer.mrmlScene.GetNodeByID(newReport.GetColorNodeID())
res = slicer.modules.reporting.logic().DicomSegRead(labelNodes, uid, colorNode)
SlicerReportingModuleWidgetHelper.Debug('Read this many labels from the seg object:'+str(labelNodes.GetNumberOfItems()))
if labelNodes.GetNumberOfItems() == 0:
print("Error loading segmentation object, have 0 labels")
else:
# read the reference node
label0 = labelNodes.GetItemAsObject(0)
referenceUIDs = label0.GetAttribute('DICOM.referenceInstanceUIDs')
SlicerReportingModuleWidgetHelper.Debug('Seg object reference uids: '+referenceUIDs)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLabelMapVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount()-1)
displayNode.SetAndObserveColorNodeID(newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('ReportingReportNodeID', newReport.GetID())
labelNode.SetAttribute('AssociatedNodeID', volumeList[0].GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNode)
# AF: this shuould not be necessary with the "proper" AIM input, since
# only one volume should be present in the report, and only one item in
# that volume should be annotated
if 0:
# if referenceUIDs != None:
reader = slicer.vtkMRMLVolumeArchetypeStorageNode()
reader.ResetFileNameList()
for uid in string.split(referenceUIDs, ' '):
fname = slicer.modules.reporting.logic().GetFileNameFromUID(uid)
reader.AddFileName(fname)
reader.SetFileName(string.split(referenceUIDs, ' ')[0])
reader.SetSingleFile(0)
referenceVolume = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeNode')
referenceVolumeUIDs = referenceVolume.GetAttribute('DICOM.instanceUIDs')
reader.ReadData(referenceVolume)
nodeToAdd = referenceVolume
allVolumeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeNode')
allVolumeNodes.SetReferenceCount(allVolumeNodes.GetReferenceCount()-1)
for i in range(allVolumeNodes.GetNumberOfItems()):
v = allVolumeNodes.GetItemAsObject(i)
uids = v.GetAttribute('DICOM.instanceUIDs')
if uids == referenceNodeUIDs:
print('Referenced node is already in the scene!')
nodeToAdd = None
referenceNode = v
break
if nodeToAdd != None:
slicer.mrmlScene.AddNode(nodeToAdd)
slicer.modules.reporting.logic().AddVolumeToReport(referenceNode)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount()-1)
displayNode.SetAndObserveColorNodeID(newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('ReportingReportNodeID', newReport.GetID())
labelNode.SetAttribute('AssociatedNodeID', referenceNode.GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNodes.GetItemAsObject(i))
def LoadAIMFile(newReportID, fileName):
dom = xml.dom.minidom.parse(fileName)
SlicerReportingModuleWidgetHelper.Debug('Parsed AIM report:')
SlicerReportingModuleWidgetHelper.Debug(dom.toxml())
volumeList = []
ddb = slicer.dicomDatabase
volId = 1
volume = None
# get the annotation element and retrieve its name
annotations = dom.getElementsByTagName('ImageAnnotation')
if len(annotations) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM file does not contain any annotations!')
return
ann = annotations[0]
desc = ann.getAttribute('name')
# get the anatomic entity element and initialize the report node based on
# it
anatomics = dom.getElementsByTagName('AnatomicEntity')
if len(anatomics) != 1:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM file does not contain any anatomic entities or contains more than one! This is not supported.'
)
return
anatomy = anatomics[0]
labelValue = anatomy.getAttribute('codeValue')
labelName = anatomy.getAttribute('codeMeaning')
codeSchemeDesignator = anatomy.getAttribute('codeSchemeDesignator')
if codeSchemeDesignator != '3DSlicer':
SlicerReportingModuleWidgetHelper.WarningPopup(
'Code scheme designator ' + codeSchemeDesignator +
' is not supported. Default will be used instead.')
labelValue = "1"
newReport = slicer.mrmlScene.GetNodeByID(newReportID)
newReport.SetFindingLabel(int(labelValue))
# pull all the volumes that are referenced into the scene
for node in dom.getElementsByTagName('ImageSeries'):
instanceUID = node.getAttribute('instanceUID')
filelist = ddb.filesForSeries(instanceUID)
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
if len(scalarVolumeLoadables) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'Error loading AIM: Failed to load the volume node reference in the file'
)
volumeName = scalarVolumeLoadables[0].name
newReport.SetName('Report for Volume ' + volumeName)
volume = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volume.SetName(volumeName)
if volume == None:
SlicerReportingModuleWidgetHelper.Error(
'Failed to read series!')
return
if len(volumeList) != 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'Error importing AIM report: Report references more than one volume, which is not allowed!'
)
return
volumeList.append(volume)
SlicerReportingModuleWidgetHelper.Debug(
'Volume read from AIM report:')
slicer.modules.reporting.logic().InitializeHierarchyForVolume(
volume)
newReport.SetVolumeNodeID(volume.GetID())
if len(volumeList) > 1:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM does not allow to have more than one volume per file!')
return
if len(volumeList) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM file you requested to load does not reference any volumes, cannot process it!'
)
return
#if volume != None:
# self.__volumeSelector.setCurrentNode(volume)
instanceUIDs = volume.GetAttribute('DICOM.instanceUIDs')
instanceUIDList = instanceUIDs.split()
# AF: GeometricShape is inside geometricShapeCollection, but
# there's no need to parse at that level, I think
#
# geometricShapeCollection
# |
# +-spatialCoordinateCollection
# |
# +-SpatialCoordinate
#
for node in dom.getElementsByTagName('GeometricShape'):
ijCoordList = []
rasPointList = []
uidList = []
elementType = node.getAttribute('xsi:type')
for child in node.childNodes:
if child.nodeName == 'spatialCoordinateCollection':
for coord in child.childNodes:
if coord.nodeName == 'SpatialCoordinate':
ijCoordList.append(float(coord.getAttribute('x')))
ijCoordList.append(float(coord.getAttribute('y')))
uid = coord.getAttribute('imageReferenceUID')
uidList.append(uid)
SlicerReportingModuleWidgetHelper.Debug('Coordinate list: ' +
str(ijCoordList))
ijk2ras = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(ijk2ras)
# convert each point from IJ to RAS
for ij in range(len(uidList)):
pointUID = uidList[ij]
# locate the UID in the list assigned to the volume
totalSlices = len(instanceUIDList)
for k in range(len(instanceUIDList)):
if pointUID == instanceUIDList[k]:
break
# print "k = ",k,", totalSlices = ",totalSlices
pointIJK = [
ijCoordList[ij * 2], ijCoordList[ij * 2 + 1], k, 1.
]
pointRAS = ijk2ras.MultiplyPoint(pointIJK)
SlicerReportingModuleWidgetHelper.Debug('Input point: ' +
str(pointIJK))
SlicerReportingModuleWidgetHelper.Debug('Converted point: ' +
str(pointRAS))
rasPointList.append(pointRAS[0:3])
# instantiate the markup elements
if elementType == 'Point':
SlicerReportingModuleWidgetHelper.Debug(
"Importing a fiducial!")
if len(ijCoordList) != 2:
SlicerReportingModuleWidgetHelper.Error(
'Number of coordinates not good for a fiducial')
return
fiducial = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLAnnotationFiducialNode')
fiducial.SetReferenceCount(fiducial.GetReferenceCount() - 1)
# associate it with the volume
fiducial.SetAttribute("AssociatedNodeID", volume.GetID())
# ??? Why the API is so inconsistent -- there's no SetPosition1() ???
fiducial.SetFiducialCoordinates(rasPointList[0])
fiducial.Initialize(slicer.mrmlScene)
# adding to hierarchy is handled by the Reporting logic
if elementType == 'MultiPoint':
SlicerReportingModuleWidgetHelper.Debug("Importing a ruler!")
if len(ijCoordList) != 4:
SlicerReportingModuleWidgetHelper.Error(
'Number of coordinates not good for a ruler')
return
ruler = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLAnnotationRulerNode')
ruler.SetReferenceCount(ruler.GetReferenceCount() - 1)
# associate it with the volume
ruler.SetAttribute("AssociatedNodeID", volume.GetID())
SlicerReportingModuleWidgetHelper.Debug(
'Initializing with points ' + str(rasPointList[0]) +
' and ' + str(rasPointList[1]))
ruler.SetPosition1(rasPointList[0])
ruler.SetPosition2(rasPointList[1])
ruler.Initialize(slicer.mrmlScene)
# AF: Initialize() adds to the scene ...
for node in dom.getElementsByTagName('Segmentation'):
# read all labels that are available in the SEG object
# check if the referenced volume is already in the scene
# if not, load it
# initialize AssociatedNodeID for the label node to point to the
# reference
SlicerReportingModuleWidgetHelper.Debug('Importing a segmentation')
labelNodes = vtk.vtkCollection()
referenceNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLScalarVolumeNode')
referenceNode.SetReferenceCount(referenceNode.GetReferenceCount() -
1)
uid = node.getAttribute('sopInstanceUID')
res = False
colorNode = slicer.mrmlScene.GetNodeByID(
newReport.GetColorNodeID())
res = slicer.modules.reporting.logic().DicomSegRead(
labelNodes, uid, colorNode)
SlicerReportingModuleWidgetHelper.Debug(
'Read this many labels from the seg object:' +
str(labelNodes.GetNumberOfItems()))
# read the reference node
label0 = labelNodes.GetItemAsObject(0)
referenceUIDs = label0.GetAttribute('DICOM.referenceInstanceUIDs')
SlicerReportingModuleWidgetHelper.Debug(
'Seg object reference uids: ' + referenceUIDs)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLLabelMapVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount() -
1)
displayNode.SetAndObserveColorNodeID(
newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('AssociatedNodeID',
volumeList[0].GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNode)
# AF: this shuould not be necessary with the "proper" AIM input, since
# only one volume should be present in the report, and only one item in
# that volume should be annotated
if 0:
# if referenceUIDs != None:
reader = slicer.vtkMRMLVolumeArchetypeStorageNode()
reader.ResetFileNameList()
for uid in string.split(referenceUIDs, ' '):
fname = slicer.modules.reporting.logic(
).GetFileNameFromUID(uid)
reader.AddFileName(fname)
reader.SetFileName(string.split(referenceUIDs, ' ')[0])
reader.SetSingleFile(0)
referenceVolume = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLScalarVolumeNode')
referenceVolumeUIDs = referenceVolume.GetAttribute(
'DICOM.instanceUIDs')
reader.ReadData(referenceVolume)
nodeToAdd = referenceVolume
allVolumeNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLScalarVolumeNode')
allVolumeNodes.SetReferenceCount(
allVolumeNodes.GetReferenceCount() - 1)
for i in range(allVolumeNodes.GetNumberOfItems()):
v = allVolumeNodes.GetItemAsObject(i)
uids = v.GetAttribute('DICOM.instanceUIDs')
if uids == referenceNodeUIDs:
print('Referenced node is already in the scene!')
nodeToAdd = None
referenceNode = v
break
if nodeToAdd != None:
slicer.mrmlScene.AddNode(nodeToAdd)
slicer.modules.reporting.logic().InitializeHierarchyForVolume(
referenceNode)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLScalarVolumeDisplayNode')
displayNode.SetReferenceCount(
displayNode.GetReferenceCount() - 1)
displayNode.SetAndObserveColorNodeID(
newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('AssociatedNodeID',
referenceNode.GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNodes.GetItemAsObject(i))
def DoIt(inputDir, rgbDir, outputDir):
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
print 'Will examine: ',dcmList
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir)
indexer.waitForImportFinished()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
'''
sNode.ResetFileNameList()
for f in loadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(loadables[0].files[0])
sNode.SetSingleFile(0)
inputVolume = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(inputVolume)
'''
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir,'input_volume.nrrd'))
sNode.WriteData(inputVolume)
#
# Order the input RGBs and rename in a temp directory
#
rgbList = []
for rgb in os.listdir(rgbDir):
if len(rgb)-rgb.rfind('.bmp') == 4:
rgbList.append(rgb)
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
tmpDir = tmpDir+'/PNGStackLabelConverter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
oldFiles = os.listdir(tmpDir)
# just in case there is anything in that directory
for f in oldFiles:
os.unlink(tmpDir+'/'+f)
rgbOrdered = [None] * len(loadables[0].files)
rgbCnt = 0
rgbExt = rgbList[0][rgbList[0].rfind('.')+1:len(rgbList[0])]
print 'Extension for RGBs: ',rgbExt
dcmFileList = loadables[0].files
rgbRenamedList = []
print 'Number of dcm files: ',len(dcmFileList), ' and rgb files: ',len(rgbOrdered)
dcmIdx = 0
for dcm in dcmFileList:
rgbIdx = 0
for rgb in rgbList:
dcmPrefix = dcm[dcm.rfind('/')+1:dcm.rfind('.')]
if rgb.find(dcmPrefix) != -1:
name = string.zfill(str(dcmIdx),5)
rgbCnt = rgbCnt+1
src = rgbDir+'/'+rgb
dest = tmpDir+'/'+name+'.'+rgbExt
rgbRenamedList.append(dest)
shutil.copy(src,dest)
break
rgbIdx = rgbIdx+1
# remove the matched DICOM file from the list
if rgbIdx == len(rgbList):
print('ERROR: failed to find matching label file for DICOM file '+dcm)
return
del rgbList[rgbIdx]
dcmIdx = dcmIdx+1
if len(rgbRenamedList) == 0:
print 'Could not parse the DICOM Study!'
return
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
for f in rgbRenamedList:
sNode.AddFileName(f)
sNode.SetFileName(rgbRenamedList[0])
sNode.SetSingleFile(0)
inputRGBVolume = slicer.vtkMRMLVectorVolumeNode()
sNode.ReadData(inputRGBVolume)
# run the filter
# - extract the RGB portions
extract = vtk.vtkImageExtractComponents()
extract.SetComponents(0,1,2)
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
extract.SetInput(inputRGBVolume.GetImageData())
else:
extract.SetInputData(inputRGBVolume.GetImageData())
luminance = vtk.vtkImageLuminance()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
luminance.SetInput(extract.GetOutput())
else:
luminance.SetInputData(extract.GetOutput())
cast = vtk.vtkImageCast()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(luminance.GetOutput())
else:
cast.SetInputData(luminance.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputLabel = slicer.vtkMRMLLabelMapVolumeNode()
outputLabel.SetIJKToRASMatrix(ijkToRAS)
outputLabel.SetAndObserveImageData(cast.GetOutput())
reportingLogic = slicer.modules.reporting.logic()
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
outputLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir,'label_output.nrrd'))
sNode.WriteData(outputLabel)
# save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(outputLabel)
slicer.mrmlScene.AddNode(inputVolume)
outputLabel.SetAttribute('AssociatedNodeID',inputVolume.GetID())
slicer.mrmlScene.AddNode(outputLabel)
# initialize the DICOM DB for Reporting logic
settings = qt.QSettings()
dbFileName = settings.value('DatabaseDirectory','')
if dbFileName =='':
print('ERROR: database must be initialized')
else:
dbFileName = dbFileName +'/ctkDICOM.sql'
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
def DoIt(inputDir, labelFile, outputDir, forceLabel, forceResample):
dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
if not hasattr(slicer.modules, 'reporting'):
print 'The Reporting module has not been loaded into Slicer, script cannot run!\n\tTry setting the --additional-module-path parameter.'
sys.exit(1)
reportingLogic = slicer.modules.reporting.logic()
print('Temporary directory location: '+dbDir1)
qt.QDir().mkpath(dbDir1)
dbDir0 = None
if slicer.dicomDatabase:
dbDir0 = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(dbDir1)
# import DICOM study
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir, None)
indexer.waitForImportFinished()
print('DICOM import finished!')
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
sys.exit(1)
inputVolume = scalarVolumePlugin.load(loadables[0])
print 'Input volume loaded! ID = ', inputVolume.GetID()
# read the label volume
labelVolume = slicer.vtkMRMLLabelMapVolumeNode()
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFile)
sNode.ReadData(labelVolume)
if forceLabel>0:
# print('Forcing label to '+str(forceLabel))
labelImage = labelVolume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(labelImage)
else:
thresh.SetInputData(labelImage)
thresh.ThresholdBetween(1, labelImage.GetScalarRange()[1])
thresh.SetInValue(int(forceLabel))
thresh.SetOutValue(0)
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.Update()
labelImage = thresh.GetOutput()
labelVolume.SetAndObserveImageData(labelImage)
slicer.mrmlScene.AddNode(labelVolume)
print 'Label volume added, id = ', labelVolume.GetID()
# ensure that the label volume scalar type is unsigned short
if labelVolume.GetImageData() != None:
scalarType = labelVolume.GetImageData().GetScalarType()
if scalarType != vtk.VTK_UNSIGNED_SHORT:
print 'Label volume has pixel type of ',vtk.vtkImageScalarTypeNameMacro(scalarType),', casting to unsigned short'
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToUnsignedShort()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(labelVolume.GetImageData())
cast.Update()
labelVolume.SetAndObserveImageData(cast.GetOutput())
else:
cast.SetInputConnection(labelVolume.GetImageDataConnection())
cast.Update()
labelVolume.SetImageDataConnection(cast.GetOutputPort())
if labelVolume.GetImageData().GetScalarType() != vtk.VTK_UNSIGNED_SHORT:
print 'Failed to cast label volume to unsigned short, type is ', vtk.vtkImageScalarTypeNameMacro(labelVolume.GetImageData().GetScalarType())
sys.exit(1)
volumesLogic = slicer.modules.volumes.logic()
geometryCheckString = volumesLogic.CheckForLabelVolumeValidity(inputVolume, labelVolume)
if geometryCheckString != "":
# has the user specified that forced resampling is okay?
if forceResample == False:
print 'Label volume mismatch with input volume:\n',geometryCheckString,'\nForced resample not specified, aborting. Re-run with --force option to ignore geometric inconsistencies'
sys.exit(1)
# resample label to the input volume raster
resampledLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(resampledLabel)
print 'Resampled label added, id = ', resampledLabel.GetID()
resampledLabel = volumesLogic.ResampleVolumeToReferenceVolume(labelVolume, inputVolume)
labelVolume = resampledLabel
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
labelVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
# initialize the DICOM DB for Reporting logic, save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(labelVolume)
print('About to write DICOM SEG!')
dbFileName = slicer.dicomDatabase.databaseFilename
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
dicomWidget.onDatabaseDirectoryChanged(dbDir0)
exit()
def DoIt(inputDir, labelFile, outputDir, forceLabel):
dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
reportingLogic = slicer.modules.reporting.logic()
print('Temporary directory location: '+dbDir1)
qt.QDir().mkpath(dbDir1)
dbDir0 = None
if slicer.dicomDatabase:
dbDir0 = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
try:
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(dbDir1)
# import DICOM study
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir, None)
indexer.waitForImportFinished()
print('DICOM import finished!')
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
slicer.mrmlScene.AddNode(inputVolume)
print('Input volume loaded!')
# read the label volume
labelVolume = slicer.vtkMRMLScalarVolumeNode()
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFile)
sNode.ReadData(labelVolume)
labelVolume.LabelMapOn()
if forceLabel>0:
print('Forcing label to '+str(forceLabel))
labelImage = labelVolume.GetImageData()
thresh = vtk.vtkImageThreshold()
thresh.SetInput(labelImage)
thresh.ThresholdBetween(1, labelImage.GetScalarRange()[1])
thresh.SetInValue(int(forceLabel))
thresh.SetOutValue(0)
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.Update()
labelImage = thresh.GetOutput()
labelVolume.SetAndObserveImageData(labelImage)
slicer.mrmlScene.AddNode(labelVolume)
# resample label to the input volume raster
resampledLabel = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(resampledLabel)
eye = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(eye)
parameters = {}
parameters['inputVolume'] = labelVolume.GetID()
parameters['referenceVolume'] = inputVolume.GetID()
parameters['outputVolume'] = resampledLabel.GetID()
parameters['warpTransform'] = eye.GetID()
parameters['interpolationMode'] = 'NearestNeighbor'
parameters['pixelType'] = 'ushort'
cliNode = None
cliNode = slicer.cli.run(slicer.modules.brainsresample, None, parameters, 1)
labelVolume = resampledLabel
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
labelVolume.LabelMapOn()
labelVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
# initialize the DICOM DB for Reporting logic, save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(labelVolume)
print('About to write DICOM SEG!')
dbFileName = slicer.dicomDatabase.databaseFilename
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
except:
print('Error occurred!')
dicomWidget.onDatabaseDirectoryChanged(dbDir0)
exit()
