def ReadImageSlicer(FileName):
mrml = slicer.vtkMRMLScene()
vl = slicer.vtkSlicerVolumesLogic()
vl.SetAndObserveMRMLScene(mrml)
n = vl.AddArchetypeVolume(FileName, 'CTC')
i = n.GetImageData()
return i
def onCentrar(self):
volumenCentrar = self.imagenSelector.currentNode()
lm = slicer.app.layoutManager()
origenVolumen = volumenCentrar.GetOrigin()
volumeLogic = slicer.vtkSlicerVolumesLogic()
origenCentro = [0, 0, 0]
volumeLogic.GetVolumeCenteredOrigin(volumenCentrar, origenCentro)
traslacion = [0, 0, 0]
volumenCentrar.SetOrigin(origenCentro)
lm.resetSliceViews()
for i in range(3):
traslacion[i] = origenCentro[i] - origenVolumen[i]
T = slicer.vtkMRMLTransformNode()
I = slicer.vtkMRMLTransformNode()
transmatrix = vtk.vtkMatrix4x4()
transform = vtk.vtkTransform()
T.SetAndObserveTransformToParent(transform)
T.SetName('centrarTransformacionSeeg')
I.SetName('CentrarTInversaSeeg')
transmatrix.DeepCopy((1, 0, 0, traslacion[0], 0, 1, 0, traslacion[1],
0, 0, 1, traslacion[2], 0, 0, 0, 1))
transform.SetMatrix(transmatrix)
inv = transform.GetInverse()
I.SetAndObserveTransformToParent(inv)
slicer.mrmlScene.AddNode(T)
slicer.mrmlScene.AddNode(I)
def SaveLabelMapContours(labelMapContours, outputSegmentationsDir, fileFormat, logFilePath):
volumesLogic = slicer.vtkSlicerVolumesLogic()
for labelMapContour in labelMapContours:
volumesLogic.CenterVolume(labelMapContour)
savenamelabel = labelMapContour.GetName()
savenamelabel = ''.join(x for x in savenamelabel if x not in "',;\/:*?<>|") + fileFormat
savelabel = slicer.util.saveNode(labelMapContour, os.path.join(outputSegmentationsDir, savenamelabel), properties={"filetype": fileFormat})
if not savelabel:
with open(logFilePath,mode='a') as logfile: logfile.write("\tSAVEERROR: Could not save data" + labelMapContour.GetName() + '\n')
def saveVolumes(self, listVolumes, outputDir, isLabelMap=False):
volumesLogic = slicer.vtkSlicerVolumesLogic()
for volume in listVolumes:
if self.converterSettings["centerlabels"] and isLabelMap:
volumesLogic.CenterVolume(volume)
elif self.converterSettings["centerimages"] and not isLabelMap:
volumesLogic.CenterVolume(volume)
savename = volume.GetName()
savename = ''.join(x for x in savename if x not in "',;\/:*?<>|") + self.converterSettings["fileformat"]
savevol = slicer.util.saveNode(volume, os.path.join(outputDir, savename), properties={"filetype": self.converterSettings["fileformat"]})
if not savevol:
with open(self.logFilePath,mode='a') as logfile: logfile.write("\tSAVEERROR: Could not save data" + volume.GetName() + '\n')
def SaveLabelMapContours(labelMapContours, outputSegmentationsDir, fileFormat,
logFilePath):
volumesLogic = slicer.vtkSlicerVolumesLogic()
for labelMapContour in labelMapContours:
volumesLogic.CenterVolume(labelMapContour)
savenamelabel = labelMapContour.GetName()
savenamelabel = ''.join(
x for x in savenamelabel if x not in "',;\/:*?<>|") + fileFormat
savelabel = slicer.util.saveNode(labelMapContour,
os.path.join(outputSegmentationsDir,
savenamelabel),
properties={"filetype": fileFormat})
if not savelabel:
with open(logFilePath, mode='a') as logfile:
logfile.write("\tSAVEERROR: Could not save data" +
labelMapContour.GetName() + '\n')
def loadVolumeFromHierarchyNode(self, hierarchyNode):
#Look for existing associated nodes:
if hierarchyNode.GetAssociatedNodeID():
volume = slicer.util.getNode(hierarchyNode.GetAssociatedNodeID())
if volume:
return volume
filePath = hierarchyNode.GetAttribute('FilePath')
volume = None
if filePath:
#Special case for ctx files
if filePath.find('ctx') > -1:
import LoadCTX
loadLogic = LoadCTX.LoadCTXLogic()
volume = slicer.util.getNode(loadLogic.loadCube(filePath, 0))
if volume:
#Write it in hierarchy node for later use
hierarchyNode.SetAssociatedNodeID(volume.GetID())
return volume
elif filePath.find('cbt') > -1:
import LoadCTX
loadLogic = LoadCTX.LoadCTXLogic()
volume = slicer.util.getNode(loadLogic.loadCube(filePath, 3))
if volume:
#Write it in hierarchy node for later use
hierarchyNode.SetAssociatedNodeID(volume.GetID())
return volume
else:
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetMRMLScene(slicer.mrmlScene)
slicerVolumeName = os.path.splitext(os.path.basename(filePath))[0]
volume = volumesLogic.AddArchetypeVolume(filePath, slicerVolumeName)
if not volume:
print "Can't load volume " + os.path.basename(filePath)
return None
#Write it in hierarchy node for later use
hierarchyNode.SetAssociatedNodeID(volume.GetID())
else:
print "Can't get file Path from: " + hierarchyNode.GetNameWithoutPostfix()
return None
return volume
def saveVolumes(self, listVolumes, outputDir, isLabelMap=False):
volumesLogic = slicer.vtkSlicerVolumesLogic()
for volume in listVolumes:
if self.converterSettings["centerlabels"] and isLabelMap:
volumesLogic.CenterVolume(volume)
elif self.converterSettings["centerimages"] and not isLabelMap:
volumesLogic.CenterVolume(volume)
savename = volume.GetName()
savename = ''.join(x for x in savename if x not in "',;\/:*?<>|"
) + self.converterSettings["fileformat"]
savevol = slicer.util.saveNode(
volume,
os.path.join(outputDir, savename),
properties={"filetype": self.converterSettings["fileformat"]})
if not savevol:
with open(self.logFilePath, mode='a') as logfile:
logfile.write("\tSAVEERROR: Could not save data" +
volume.GetName() + '\n')
def modelHandler(imageNode, labelNode, Zind):
sliceZImageNode = extractMaxZSlice(imageNode, Zind)
sliceZLabelNode = extractMaxZSlice(labelNode, Zind)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720,660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti=vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
return finalImage
def GeoDistorsionShow3D(self, inputSelectorGeoDistorsionResult,
OutputDirectory):
### Output : image 3D avec code couleur en fonction du fait que les sphères ont des déformations géométrique en dessus ou en dessous des valeurs de tolérance ####
print(u"Début de la fonction Show3D")
time1 = time.time()
if not inputSelectorGeoDistorsionResult:
nom_image_IRMrecal = "Resultat_DisGeo_CT_MRI" + str(
date.day) + str(date.month) + str(date.year)
else:
nom_image_IRMrecal = inputSelectorGeoDistorsionResult
############# Récupération du chemin de sauvegarde de l'image résultat (3D) #############
ThreeDImagesavepath = OutputDirectory.directory + "/3DImageResult" + str(
date.day) + str(date.month) + str(date.year) + ".png"
############# Récupération de l'image résultat des test précédent et création de 3 volumes pour les 3 conditions de tolérance #############
volumeNode1 = slicer.util.getNode(nom_image_IRMrecal)
labelVolumeNode1 = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLLabelMapVolumeNode")
slicer.vtkSlicerVolumesLogic().CreateLabelVolumeFromVolume(
slicer.mrmlScene, labelVolumeNode1, volumeNode1)
volumeNode2 = slicer.util.getNode(nom_image_IRMrecal)
labelVolumeNode2 = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLLabelMapVolumeNode")
slicer.vtkSlicerVolumesLogic().CreateLabelVolumeFromVolume(
slicer.mrmlScene, labelVolumeNode2, volumeNode2)
volumeNode3 = slicer.util.getNode(nom_image_IRMrecal)
labelVolumeNode3 = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLLabelMapVolumeNode")
slicer.vtkSlicerVolumesLogic().CreateLabelVolumeFromVolume(
slicer.mrmlScene, labelVolumeNode3, volumeNode3)
############# Création de 3 segmentations basée sur les valeurs de tolérance 6; 13 et 14 du test précédent #############
thresholdValue1 = 6
voxelArray = slicer.util.arrayFromVolume(volumeNode1)
labelVoxelArray = slicer.util.arrayFromVolume(labelVolumeNode1)
labelVoxelArray[voxelArray == thresholdValue1] = 100
labelVoxelArray[voxelArray != thresholdValue1] = 0
slicer.util.arrayFromVolumeModified(labelVolumeNode1)
thresholdValue2 = 13
voxelArray = slicer.util.arrayFromVolume(volumeNode2)
labelVoxelArray = slicer.util.arrayFromVolume(labelVolumeNode2)
labelVoxelArray[voxelArray == thresholdValue2] = 100
labelVoxelArray[voxelArray != thresholdValue2] = 0
slicer.util.arrayFromVolumeModified(labelVolumeNode2)
thresholdValue3 = 14
voxelArray = slicer.util.arrayFromVolume(volumeNode3)
labelVoxelArray = slicer.util.arrayFromVolume(labelVolumeNode3)
labelVoxelArray[voxelArray == thresholdValue3] = 100
labelVoxelArray[voxelArray != thresholdValue3] = 0
slicer.util.arrayFromVolumeModified(labelVolumeNode3)
############# Création de 3 segments issus des 3 segmentations précédentes, coloriage en fonction de la tolérance ou non au test #############
segmentationNode1 = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentID = slicer.modules.segmentations.logic(
).ImportLabelmapToSegmentationNode(labelVolumeNode1, segmentationNode1)
segmentation = segmentationNode1.GetSegmentation()
segment = segmentation.GetSegment(segmentation.GetNthSegmentID(0))
segment.SetColor(0, 1, 0)
segmentationNode2 = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(
labelVolumeNode2, segmentationNode2)
segmentation = segmentationNode2.GetSegmentation()
segment = segmentation.GetSegment(segmentation.GetNthSegmentID(0))
try: # condition pour éviter plantage dans le cas où il n'y ait pas de sphères avec des distortions < 2mm
segment.SetColor(1, 0.70, 0) # couleur R, V, B
except:
print("Il n'y a pas de sphère avec une distortion inférieur à 2mm")
sphere2exist = False
else:
sphere2exist = True
segmentationNode3 = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(
labelVolumeNode3, segmentationNode3)
segmentation = segmentationNode3.GetSegmentation()
segment = segmentation.GetSegment(segmentation.GetNthSegmentID(0))
try: # condition pour éviter plantage dans le cas où il n'y ait pas de sphères avec des distortions > 2mm
segment.SetColor(1, 0, 0) # couleur R, V, B
except:
print("Il n'y a pas de sphère avec une distortion supérieur à 2mm")
sphere3exist = False
else:
sphere3exist = True
############# Représentation 3d des volumes segmentés et coloriés #############
segmentationNode1.CreateClosedSurfaceRepresentation()
if sphere2exist == True:
segmentationNode2.CreateClosedSurfaceRepresentation()
if sphere3exist == True:
segmentationNode3.CreateClosedSurfaceRepresentation()
############# Copie d'écran du résultat et sauvegarde de l'image dans le dossier de résultat global #############
ThreeDImage = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage()
ThreeDImage.save(ThreeDImagesavepath)
time2 = time.time()
TimeForrunFunction = time2 - time1
print("\n")
print(
u"La fonction de représentation 3D des sphères s'est bien executée (temps = "
+ str(TimeForrunFunction) + " secondes)")
print("\n")
print(
u"Si dans la représentation 3D des sphères sont de couleurs rouges, merci de prévenir Cyril Jaudet au 5690 ou Aurélien Corroyer-Dulmont au 5768"
)
print("\n")
print(
u"Si besoin d’aide ou d’informations sur comment fonctionne le programme : Cyril Jaudet (5690) ou Aurélien Corroyer-Dulmont (5768)"
)
def modelHandler(ImageFilePath, imageNode, labelNode, imgOutputDir,
IDcurrPatient, Zind):
"""
imageBuffer = vtk.vtkImageData()
label = growCut(imageNode.GetImageData(),labelNode.GetImageData(),imageBuffer)
q = labelNode.GetImageData()
q.DeepCopy(label)
if labelNode.GetImageDataConnection():
labelNode.GetImageDataConnection().GetProducer().Update()
if labelNode.GetImageData().GetPointData().GetScalars() != None:
labelNode.GetImageData().GetPointData().GetScalars().Modified()
labelNode.GetImageData().Modified()
labelNode.Modified()
pdb.set_trace()
"""
imageSeriesDescription = os.path.basename(ImageFilePath).replace(
'.nrrd', '')
imagePatientID = os.path.basename(
os.path.dirname(os.path.dirname(os.path.dirname((ImageFilePath)))))
imageStudyDate = os.path.basename(
os.path.dirname(os.path.dirname((ImageFilePath))))
imagePatientID_StudyDate = imagePatientID + '_' + imageStudyDate
inputImage = su.PullFromSlicer(imageNode.GetName())
inputLabel = su.PullFromSlicer(labelNode.GetName())
pixelID = inputImage.GetPixelIDValue()
FlipYAxis = sitk.FlipImageFilter()
FlipYAxis.SetFlipAxes([False, True, False])
sizeZ = list(inputImage.GetSize())
sizeZ[2] = 0
indexZ = [0, 0, Zind]
ExtractorZ = sitk.ExtractImageFilter()
ExtractorZ.SetSize(sizeZ)
ExtractorZ.SetIndex(indexZ)
sliceZImage = ExtractorZ.Execute(inputImage)
sliceZLabel = ExtractorZ.Execute(inputLabel)
imageName = 'Axial_Slice_Image' + IDcurrPatient
labelName = 'Axial_Slice_Label' + IDcurrPatient
su.PushToSlicer(sliceZImage, imageName)
su.PushToSlicer(sliceZLabel, labelName)
sliceZImageNode = slicer.util.getNode(imageName)
sliceZLabelNode = slicer.util.getNode(labelName)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
#sliceZLabelNode = binarizeLabelMapToValue(sliceZLabelNode, labelValue=296)
#labelNode = binarizeLabelMapToValue(labelNode, labelValue=296)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720, 660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
#finalImagePath = str(os.path.join(imgOutputDir, IDcurrPatient + '_axial_sliceZ.png'))
finalImagePath = str(
os.path.join(
imgOutputDir,
imagePatientID_StudyDate + '_' + imageSeriesDescription + '.png'))
writer = vtk.vtkPNGWriter()
writer.SetFileName(finalImagePath)
writer.SetInputData(finalImage)
writer.Write()
def modelHandler(imageNode, labelNode, Zind):
sliceZImageNode = extractMaxZSlice(imageNode, Zind)
sliceZLabelNode = extractMaxZSlice(labelNode, Zind)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720, 660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
return finalImage
def modelHandler(ImageFilePath, imageNode, labelNode, imgOutputDir, IDcurrPatient, Zind):
"""
imageBuffer = vtk.vtkImageData()
label = growCut(imageNode.GetImageData(),labelNode.GetImageData(),imageBuffer)
q = labelNode.GetImageData()
q.DeepCopy(label)
if labelNode.GetImageDataConnection():
labelNode.GetImageDataConnection().GetProducer().Update()
if labelNode.GetImageData().GetPointData().GetScalars() != None:
labelNode.GetImageData().GetPointData().GetScalars().Modified()
labelNode.GetImageData().Modified()
labelNode.Modified()
pdb.set_trace()
"""
imageSeriesDescription = os.path.basename(ImageFilePath).replace('.nrrd','')
imagePatientID = os.path.basename(os.path.dirname(os.path.dirname(os.path.dirname((ImageFilePath)))))
imageStudyDate = os.path.basename(os.path.dirname(os.path.dirname((ImageFilePath))))
imagePatientID_StudyDate = imagePatientID + '_' + imageStudyDate
inputImage = su.PullFromSlicer(imageNode.GetName())
inputLabel = su.PullFromSlicer(labelNode.GetName())
pixelID = inputImage.GetPixelIDValue()
FlipYAxis = sitk.FlipImageFilter()
FlipYAxis.SetFlipAxes([False, True, False])
sizeZ = list(inputImage.GetSize())
sizeZ[2] = 0
indexZ = [0, 0, Zind]
ExtractorZ = sitk.ExtractImageFilter()
ExtractorZ.SetSize(sizeZ)
ExtractorZ.SetIndex(indexZ)
sliceZImage = ExtractorZ.Execute(inputImage)
sliceZLabel = ExtractorZ.Execute(inputLabel)
imageName = 'Axial_Slice_Image' + IDcurrPatient
labelName = 'Axial_Slice_Label' + IDcurrPatient
su.PushToSlicer(sliceZImage, imageName)
su.PushToSlicer(sliceZLabel, labelName)
sliceZImageNode = slicer.util.getNode(imageName)
sliceZLabelNode = slicer.util.getNode(labelName)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
#sliceZLabelNode = binarizeLabelMapToValue(sliceZLabelNode, labelValue=296)
#labelNode = binarizeLabelMapToValue(labelNode, labelValue=296)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720,660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti=vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
#finalImagePath = str(os.path.join(imgOutputDir, IDcurrPatient + '_axial_sliceZ.png'))
finalImagePath = str(os.path.join(imgOutputDir, imagePatientID_StudyDate + '_' + imageSeriesDescription +'.png'))
writer=vtk.vtkPNGWriter()
writer.SetFileName(finalImagePath)
writer.SetInputData(finalImage)
writer.Write()
def createLabelMap(self, dataNode, labelNode, outputDir, IDcurrPatient):
"""
self.sliceXarray = numpy.rollaxis(self.sliceXarray,1)[:,:,None] #512,36,1
#self.sliceXarray = self.sliceXarray[:,:,None]
self.sliceYarray = numpy.rollaxis(self.sliceYarray,1)[:,:,None] #512,36,1
#self.sliceYarray = self.sliceYarray[:,:,None]
#self.slizeZarray = numpy.rot90(self.sliceZarray)
self.sliceZarray = self.sliceZarray[:,:,None] #512,512,1
self.sliceXnode = slicer.vtkMRMLScalarVolumeNode()
self.sliceYnode = slicer.vtkMRMLScalarVolumeNode()
self.sliceZnode = slicer.vtkMRMLScalarVolumeNode()
self.sliceXnode.SetName('SliceX')
self.sliceYnode.SetName('SliceY')
self.sliceZnode.SetName('SliceZ')
self.sliceXNodeDisplayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(self.sliceXNodeDisplayNode)
self.sliceXnode.SetAndObserveDisplayNodeID(self.sliceXNodeDisplayNode.GetID())
self.sliceYNodeDisplayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(self.sliceYNodeDisplayNode)
self.sliceYnode.SetAndObserveDisplayNodeID(self.sliceYNodeDisplayNode.GetID())
self.sliceZNodeDisplayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(self.sliceZNodeDisplayNode)
self.sliceZnode.SetAndObserveDisplayNodeID(self.sliceZNodeDisplayNode.GetID())
"""
imageFilePath = dataNode.GetStorageNode().GetFileName()
imageName = os.path.basename(imageFilePath).replace('.nrrd','')
reconDir = os.path.dirname(imageFilePath)
studyDir = os.path.dirname(reconDir)
segDir = [dirpath for dirpath in glob.glob(os.path.join(studyDir,'*')) if 'Segmentations' in dirpath][0]
resourcesDir = [dirpath for dirpath in glob.glob(os.path.join(studyDir,'*')) if 'Resources' in dirpath][0]
spacing = dataNode.GetSpacing()
origin = dataNode.GetOrigin()
#pdb.set_trace()
arrays = []
for r,d,f in os.walk(studyDir):
[arrays.append(os.path.join(r,file)) for file in fnmatch.filter(f, '*.npy')]
try:
name = os.path.basename(arrays[0]).replace('.npy', '')
except IndexError:
print(IDcurrPatient, ': FAILED TO PROCESS NPY FILE')
return
arr = numpy.load(arrays[0])
#arr = numpy.ascontiguousarray(arr)
#nump_arr = reversedim(arr,0)
nump_arr = numpy.swapaxes(arr, 0, 2)
#nump_arr = nump_arr[...,::-1]
#nump_arr = numpy.rollaxis(numpy.rollaxis(nump_arr,2),2,1)
self.labelMapnode = slicer.vtkMRMLScalarVolumeNode()
self.labelMapnode.SetName('labelMap')
self.labelMapnode.LabelMapOn()
self.labelMapnodeDisplayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(self.labelMapnodeDisplayNode)
self.labelMapnode.SetAndObserveDisplayNodeID(self.labelMapnodeDisplayNode.GetID())
self.labelMapnodeDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
try:
self.labelMapnode = renderArray(self, nump_arr, self.labelMapnode, dataNode, shape=nump_arr.shape, spacing=spacing, origin=origin)
except ValueError:
print(IDcurrPatient, ': FAILED TO CONVERT TO LABEL MAP')
return
#self.sliceXnode = self.renderSlice(self.sliceXarray, self.sliceXnode, self.dataNode, shape=self.sliceXarray.shape, spacing=(x,z,1))
#self.sliceYnode = self.renderSlice(self.sliceYarray, self.sliceYnode, self.dataNode, shape=self.sliceYarray.shape, spacing=(y,z,1))
#self.sliceZnode = self.renderSlice(self.sliceZarray, self.sliceZnode, self.dataNode, shape=self.sliceZarray.shape, spacing=(x,y,1))
self.labelMapnode = binarizeLabelMapToValue(self.labelMapnode)
self.labelMapnodeDisplayNode.SetInputImageDataConnection(self.labelMapnode.GetImageDataConnection())
self.labelMapnodeDisplayNode.UpdateImageDataPipeline()
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.CenterVolume(dataNode)
volumesLogic.CenterVolume(self.labelMapnode)
labelMapNodeFileName = os.path.join(segDir, imageName + '_labelMap.nrrd')
saveLabelMap = slicer.util.saveNode(self.labelMapnode, labelMapNodeFileName, properties={"filetype": ".nrrd"})
#saveNode = slicer.util.saveNode(dataNode, imageFilePath, properties={"filetype": ".nrrd"})
arraysName = os.path.basename(arrays[0])
shutil.move(arrays[0],os.path.join(resourcesDir,arraysName))
labelMapNodeSITK = sitk.ReadImage(str(labelMapNodeFileName))
FlipZAxis = sitk.FlipImageFilter()
FlipZAxis.SetDebug(False)
FlipZAxis.SetFlipAxes([False, False, True])
FlipZAxis.SetFlipAboutOrigin(True)
FlipZAxis.SetNumberOfThreads(4)
labelMapNodeSITK = FlipZAxis.Execute(labelMapNodeSITK)
FlipZAxis.Execute(labelMapNodeSITK)
sitk.WriteImage(labelMapNodeSITK, str(labelMapNodeFileName) )
"""