def onSaveButtonClicked(self):
bundle = EditUtil.EditUtil().getParameterNode().GetParameter('QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
j = {}
j['layers'] = layers
j['username'] = self.setupUserName.text
j['sourcetile'] = self.tilename
j['generator'] = "3DSlicer-4.5.0 with SlicerPathology v1.0a"
j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory, labelName + '.tif')
print "labelFileName : "+labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "successful writing "+labelFileName
else:
print "failed writing "+labelFileName
jstr = json.dumps(j,sort_keys=True, indent=4, separators=(',', ': '))
f = open(os.path.join(self.dataDirButton.directory, self.tilename + '.json'),'w')
f.write(jstr)
f.close()
def readFrame(self, file):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
sNode.SetFileName(file)
sNode.SetSingleFile(0)
frame = slicer.vtkMRMLScalarVolumeNode()
success = sNode.ReadData(frame)
return (success, frame)
def onSaveButtonClicked(self):
import zipfile
bundle = EditUtil.EditUtil().getParameterNode().GetParameter('QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
self.j['layers'] = layers
self.j['username'] = self.setupUserName.text
self.j['sourcetile'] = self.tilename
self.j['generator'] = slicer.app.applicationVersion
self.j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
zfname = os.path.join(self.dataDirButton.directory, self.tilename + '.zip')
print "zipfile name"
print zfname
zf = zipfile.ZipFile(zfname, mode='w')
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory, labelName + '.tif')
print "labelFileName : "+labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "adding "+labelFileName+" to zipfile"
zf.write(labelFileName)
os.remove(labelFileName)
else:
print "failed writing "+labelFileName
jstr = json.dumps(self.j,sort_keys=True, indent=4, separators=(',', ': '))
mfname = os.path.join(self.dataDirButton.directory, 'manifest.json')
f = open(mfname,'w')
f.write(jstr)
f.close()
zf.write(mfname)
zf.close()
os.remove(mfname)
def onClick(caller, event):
coordinates = self.interactor.GetLastEventPosition()
ctrlKey = self.interactor.GetControlKey()
rasPoint = ConvertCoordinates2RAS(coordinates)
ijkPoint = ConvertCoordinates2IJK(coordinates)
ijk = [int(round(i)) for i in ijkPoint[0:3]]
labeledImage = self.LabeledVolumeSelector.currentNode(
).GetImageData() #GetImageData()
selectedImage = self.SelectedVolumeSelector.currentNode(
).GetImageData()
pointId = labeledImage.ComputePointId(ijk) #*
targetLabel = int(
round(
labeledImage.GetScalarComponentAsFloat(
ijk[0], ijk[1], ijk[2], 0)))
selectedLabel = int(
round(
selectedImage.GetScalarComponentAsFloat(
ijk[0], ijk[1], ijk[2], 0)))
labeledArray = slicer.util.arrayFromVolume(
self.LabeledVolumeSelector.currentNode())
labeledSlice = labeledArray[ijk[2], ...]
selectedArray = slicer.util.arrayFromVolume(
self.SelectedVolumeSelector.currentNode())
selectedSlice = selectedArray[ijk[2], ...]
if not ctrlKey:
selectedSlice[labeledSlice == targetLabel] = targetLabel
else:
selectedSlice[selectedSlice == selectedLabel] = 0
self.SelectedVolumeSelector.currentNode().Modified()
storageNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
storageNode.SetFileName(self.SaveFile) #SAVE
storageNode.WriteData(
self.SelectedVolumeSelector.currentNode())
print("SAVED")
def onSaveButtonClicked(self):
bundle = EditUtil.EditUtil().getParameterNode().GetParameter(
'QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
j = {}
j['layers'] = layers
j['username'] = self.setupUserName.text
j['sourcetile'] = self.tilename
j['generator'] = "3DSlicer-4.5.0 with SlicerPathology v1.0a"
j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory,
labelName + '.tif')
print "labelFileName : " + labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "successful writing " + labelFileName
else:
print "failed writing " + labelFileName
jstr = json.dumps(j, sort_keys=True, indent=4, separators=(',', ': '))
f = open(
os.path.join(self.dataDirButton.directory,
self.tilename + '.json'), 'w')
f.write(jstr)
f.close()
def load(self, loadable):
"""Load the selection as a MultiVolume, if multivolume attribute is
present
"""
mvNode = ''
try:
mvNode = loadable.multivolume
except AttributeError:
return None
nFrames = int(mvNode.GetAttribute('MultiVolume.NumberOfFrames'))
files = string.split(mvNode.GetAttribute('MultiVolume.FrameFileList'),
',')
nFiles = len(files)
filesPerFrame = nFiles / nFrames
frames = []
baseName = loadable.name
loadAsVolumeSequence = hasattr(
loadable, 'loadAsVolumeSequence') and loadable.loadAsVolumeSequence
if loadAsVolumeSequence:
volumeSequenceNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSequenceNode",
slicer.mrmlScene.GenerateUniqueName(baseName))
volumeSequenceNode.SetIndexName("")
volumeSequenceNode.SetIndexUnit("")
else:
mvImage = vtk.vtkImageData()
mvImageArray = None
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
instanceUIDs = ""
for file in files:
uid = slicer.dicomDatabase.fileValue(file,
self.tags['instanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1]
mvNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
progressbar = slicer.util.createProgressDialog(
labelText="Loading " + baseName,
value=0,
maximum=nFrames,
windowModality=qt.Qt.WindowModal)
try:
# read each frame into scalar volume
for frameNumber in range(nFrames):
progressbar.value = frameNumber
slicer.app.processEvents()
if progressbar.wasCanceled:
break
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
frameFileList = files[frameNumber *
filesPerFrame:(frameNumber + 1) *
filesPerFrame]
# sv plugin will sort the filenames by geometric order
svLoadables = scalarVolumePlugin.examine([frameFileList])
if len(svLoadables) == 0:
raise IOError("volume frame %d is invalid" % frameNumber)
frame = scalarVolumePlugin.load(svLoadables[0])
if frame.GetImageData() == None:
raise IOError("volume frame %d is invalid" % frameNumber)
if loadAsVolumeSequence:
# Load into volume sequence
# volumeSequenceNode.SetDataNodeAtValue would deep-copy the volume frame.
# To avoid memory reallocation, add an empty node and shallow-copy the contents
# of the volume frame.
# Create an empty volume node in the sequence node
proxyVolume = slicer.mrmlScene.AddNewNodeByClass(
frame.GetClassName())
indexValue = str(frameNumber)
volumeSequenceNode.SetDataNodeAtValue(
proxyVolume, indexValue)
slicer.mrmlScene.RemoveNode(proxyVolume)
# Update the data node
shallowCopy = True
volumeSequenceNode.UpdateDataNodeAtValue(
frame, indexValue, shallowCopy)
else:
# Load into multi-volume
if frameNumber == 0:
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1] * frameExtent[
3] * frameExtent[5]
mvImage.SetExtent(frameExtent)
if vtk.VTK_MAJOR_VERSION <= 5:
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.SetScalarType(
frame.GetImageData().GetScalarType())
mvImage.AllocateScalars()
else:
mvImage.AllocateScalars(
frame.GetImageData().GetScalarType(), nFrames)
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars())
mvNode.SetScene(slicer.mrmlScene)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameNumber] = frameImageArray
# Remove temporary volume node
if frame.GetDisplayNode():
slicer.mrmlScene.RemoveNode(frame.GetDisplayNode())
if frame.GetStorageNode():
slicer.mrmlScene.RemoveNode(frame.GetStorageNode())
slicer.mrmlScene.RemoveNode(frame)
if loadAsVolumeSequence:
# Finalize volume sequence import
# For user convenience, add a browser node and show the volume in the slice viewer.
# Add browser node
sequenceBrowserNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSequenceBrowserNode',
slicer.mrmlScene.GenerateUniqueName(baseName + " browser"))
sequenceBrowserNode.SetAndObserveMasterSequenceNodeID(
volumeSequenceNode.GetID())
# If save changes are allowed then proxy nodes are updated using shallow copy, which is much
# faster for images. Images are usually not modified, so the risk of accidentally modifying
# data in the sequence is low.
sequenceBrowserNode.SetSaveChanges(volumeSequenceNode, True)
# Show frame number in proxy volume node name
sequenceBrowserNode.SetOverwriteProxyName(
volumeSequenceNode, True)
# Automatically select the volume to display
imageProxyVolumeNode = sequenceBrowserNode.GetProxyNode(
volumeSequenceNode)
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(
imageProxyVolumeNode.GetID())
appLogic.PropagateVolumeSelection()
# Show sequence browser toolbar
sequenceBrowserModule = slicer.modules.sequencebrowser
if sequenceBrowserModule.autoShowToolBar:
sequenceBrowserModule.setToolBarActiveBrowserNode(
sequenceBrowserNode)
sequenceBrowserModule.setToolBarVisible(True)
else:
# Finalize multi-volume import
mvDisplayNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(mvNode)
#
# automatically select the volume to display
#
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(mvNode.GetID())
appLogic.PropagateVolumeSelection()
# file list is no longer needed - remove the attribute
mvNode.RemoveAttribute('MultiVolume.FrameFileList')
except Exception as e:
logging.error("Failed to read a multivolume: {0}".format(
e.message))
import traceback
traceback.print_exc()
mvNode = None
finally:
progressbar.close()
return mvNode
if len(dcm)-dcm.rfind('.dcm') == 4:
rwvmList.append(rwvmDir+'/'+dcm)
rwvmList = rwvmList[:1]
rwvmPlugin = slicer.modules.dicomPlugins['DICOMRWVMPlugin']()
# index input DICOM series
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, petDir)
indexer.waitForImportFinished()
indexer.addDirectory(slicer.dicomDatabase, rwvmDir)
indexer.waitForImportFinished()
loadables = rwvmPlugin.examine([rwvmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
# load input DICOM volume
dcmVolume = rwvmPlugin.load(loadables[0])
# save DICOM volume as single file nrrd format
dcmStorage = slicer.vtkMRMLVolumeArchetypeStorageNode()
dcmStorage.SetWriteFileFormat('nrrd')
dcmStorage.SetFileName(os.path.join(outputDir,'SUVbw.nrrd'))
dcmStorage.WriteData(dcmVolume)
sys.exit()
def SaveEditorButtonClicked(self):
storageNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
storageNode.SetFileName(self.SaveFile)
storageNode.WriteData(self.SelectedVolumeSelector.currentNode())
print("SAVED EDITOR")
def load(self,loadable):
"""Load the selection as a MultiVolume, if multivolume attribute is
present
"""
mvNode = ''
try:
mvNode = loadable.multivolume
except AttributeError:
return None
nFrames = int(mvNode.GetAttribute('MultiVolume.NumberOfFrames'))
files = mvNode.GetAttribute('MultiVolume.FrameFileList').split(',')
nFiles = len(files)
filesPerFrame = int(nFiles/nFrames)
frames = []
baseName = loadable.name
loadAsVolumeSequence = hasattr(loadable, 'loadAsVolumeSequence') and loadable.loadAsVolumeSequence
if loadAsVolumeSequence:
volumeSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode",
slicer.mrmlScene.GenerateUniqueName(baseName))
volumeSequenceNode.SetIndexName("")
volumeSequenceNode.SetIndexUnit("")
else:
mvImage = vtk.vtkImageData()
mvImageArray = None
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
instanceUIDs = ""
for file in files:
uid = slicer.dicomDatabase.fileValue(file,self.tags['instanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid+" "
instanceUIDs = instanceUIDs[:-1]
mvNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
progressbar = slicer.util.createProgressDialog(labelText="Loading "+baseName,
value=0, maximum=nFrames,
windowModality = qt.Qt.WindowModal)
try:
# read each frame into scalar volume
for frameNumber in range(nFrames):
progressbar.value = frameNumber
slicer.app.processEvents()
if progressbar.wasCanceled:
break
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList();
frameFileList = files[frameNumber*filesPerFrame:(frameNumber+1)*filesPerFrame]
# sv plugin will sort the filenames by geometric order
svLoadables = scalarVolumePlugin.examine([frameFileList])
if len(svLoadables) == 0:
raise IOError("volume frame %d is invalid" % frameNumber)
frame = scalarVolumePlugin.load(svLoadables[0])
if frame.GetImageData() == None:
raise IOError("volume frame %d is invalid" % frameNumber)
if loadAsVolumeSequence:
# Load into volume sequence
# volumeSequenceNode.SetDataNodeAtValue would deep-copy the volume frame.
# To avoid memory reallocation, add an empty node and shallow-copy the contents
# of the volume frame.
# Create an empty volume node in the sequence node
proxyVolume = slicer.mrmlScene.AddNewNodeByClass(frame.GetClassName())
indexValue = str(frameNumber)
volumeSequenceNode.SetDataNodeAtValue(proxyVolume, indexValue)
slicer.mrmlScene.RemoveNode(proxyVolume)
# Update the data node
shallowCopy = True
volumeSequenceNode.UpdateDataNodeAtValue(frame, indexValue, shallowCopy)
else:
# Load into multi-volume
if frameNumber == 0:
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
mvImage.SetExtent(frameExtent)
if vtk.VTK_MAJOR_VERSION <= 5:
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.SetScalarType(frame.GetImageData().GetScalarType())
mvImage.AllocateScalars()
else:
mvImage.AllocateScalars(frame.GetImageData().GetScalarType(), nFrames)
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mvNode.SetScene(slicer.mrmlScene)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameNumber] = frameImageArray
# Remove temporary volume node
if frame.GetDisplayNode():
slicer.mrmlScene.RemoveNode(frame.GetDisplayNode())
if frame.GetStorageNode():
slicer.mrmlScene.RemoveNode(frame.GetStorageNode())
slicer.mrmlScene.RemoveNode(frame)
if loadAsVolumeSequence:
# Finalize volume sequence import
# For user convenience, add a browser node and show the volume in the slice viewer.
# Add browser node
sequenceBrowserNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceBrowserNode',
slicer.mrmlScene.GenerateUniqueName(baseName + " browser"))
sequenceBrowserNode.SetAndObserveMasterSequenceNodeID(volumeSequenceNode.GetID())
# If save changes are allowed then proxy nodes are updated using shallow copy, which is much
# faster for images. Images are usually not modified, so the risk of accidentally modifying
# data in the sequence is low.
sequenceBrowserNode.SetSaveChanges(volumeSequenceNode, True)
# Show frame number in proxy volume node name
sequenceBrowserNode.SetOverwriteProxyName(volumeSequenceNode, True);
# Automatically select the volume to display
imageProxyVolumeNode = sequenceBrowserNode.GetProxyNode(volumeSequenceNode)
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(imageProxyVolumeNode.GetID())
appLogic.PropagateVolumeSelection()
# Show sequence browser toolbar
sequenceBrowserModule = slicer.modules.sequencebrowser
if sequenceBrowserModule.autoShowToolBar:
sequenceBrowserModule.setToolBarActiveBrowserNode(sequenceBrowserNode)
sequenceBrowserModule.setToolBarVisible(True)
else:
# Finalize multi-volume import
mvDisplayNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(mvNode)
#
# automatically select the volume to display
#
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(mvNode.GetID())
appLogic.PropagateVolumeSelection()
# file list is no longer needed - remove the attribute
mvNode.RemoveAttribute('MultiVolume.FrameFileList')
except Exception as e:
logging.error("Failed to read a multivolume: {0}".format(e.message))
import traceback
traceback.print_exc()
mvNode = None
finally:
progressbar.close()
return mvNode
def onSaveButtonClicked(self):
import zipfile
import os.path
import uuid
bundle = EditUtil.EditUtil().getParameterNode().GetParameter('QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
self.j['layers'] = layers
self.j['username'] = self.setupUserName.text
self.j['sourcetile'] = self.tilename
self.j['generator'] = slicer.app.applicationVersion
self.j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
self.j['execution_id'] = self.setupExecutionID.text + "-"+ uuid.uuid4().get_urn()
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
zfname = os.path.join(self.dataDirButton.directory, self.tilename + "_" + datetime.datetime.now().strftime("%Y%m%d%H%M%S") + '.zip')
print "zipfile name"
print zfname
zf = zipfile.ZipFile(zfname, mode='w')
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fg = red_cn.GetForegroundVolumeID()
ff = slicer.util.getNode(fg)
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName("original.tif")
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(ff)
zf.write("original.tif")
os.remove("original.tif")
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory, labelName + '.tif')
compFileName = os.path.join(self.dataDirButton.directory, labelName + '-comp.tif')
sNode.SetFileName(labelFileName)
success = sNode.WriteData(label)
if success:
print "adding "+labelFileName+" to zipfile"
zf.write(labelFileName,os.path.basename(labelFileName))
os.remove(labelFileName)
else:
print "failed writing "+labelFileName
comp = self.WriteLonI(label.GetImageData(),ff.GetImageData())
volumeNode = slicer.vtkMRMLVectorVolumeNode()
volumeNode.SetName("COMP")
volumeNode.SetAndObserveImageData(comp)
sNode.SetFileName(compFileName)
success = sNode.WriteData(volumeNode)
if success:
print "adding "+compFileName+" to zipfile"
zf.write(compFileName,os.path.basename(compFileName))
os.remove(compFileName)
else:
print "failed writing "+compFileName
jstr = json.dumps(self.j,sort_keys=True, indent=4, separators=(',', ': '))
mfname = os.path.join(self.dataDirButton.directory, 'manifest.json')
f = open(mfname,'w')
f.write(jstr)
f.close()
zf.write(mfname,os.path.basename(mfname))
zf.close()
os.remove(mfname)
if len(dcm) - dcm.rfind('.dcm') == 4:
rwvmList.append(rwvmDir + '/' + dcm)
rwvmList = rwvmList[:1]
rwvmPlugin = slicer.modules.dicomPlugins['DICOMRWVMPlugin']()
# index input DICOM series
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, petDir)
indexer.waitForImportFinished()
indexer.addDirectory(slicer.dicomDatabase, rwvmDir)
indexer.waitForImportFinished()
loadables = rwvmPlugin.examine([rwvmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
# load input DICOM volume
dcmVolume = rwvmPlugin.load(loadables[0])
# save DICOM volume as single file nrrd format
dcmStorage = slicer.vtkMRMLVolumeArchetypeStorageNode()
dcmStorage.SetWriteFileFormat('nrrd')
dcmStorage.SetFileName(os.path.join(outputDir, 'SUVbw.nrrd'))
dcmStorage.WriteData(dcmVolume)
sys.exit()
def load(self,loadable):
"""Load the selection as a MultiVolume, if multivolume attribute is
present
"""
mvNode = ''
try:
mvNode = loadable.multivolume
except AttributeError:
return None
nFrames = int(mvNode.GetAttribute('MultiVolume.NumberOfFrames'))
files = string.split(mvNode.GetAttribute('MultiVolume.FrameFileList'),',')
nFiles = len(files)
filesPerFrame = nFiles/nFrames
frames = []
mvImage = vtk.vtkImageData()
mvImageArray = None
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
instanceUIDs = ""
for file in files:
uid = slicer.dicomDatabase.fileValue(file,self.tags['instanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid+" "
instanceUIDs = instanceUIDs[:-1]
mvNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
# read each frame into scalar volume
for frameNumber in range(nFrames):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList();
frameFileList = files[frameNumber*filesPerFrame:(frameNumber+1)*filesPerFrame]
# sv plugin will sort the filenames by geometric order
svLoadables = scalarVolumePlugin.examine([frameFileList])
if len(svLoadables) == 0:
return None
for f in svLoadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(frameFileList[0]) # only used when num files/frame = 1
sNode.SetSingleFile(0)
frame = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(frame)
if frame.GetImageData() == None:
logging.error('Failed to read a multivolume frame!')
return None
if frameNumber == 0:
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
mvImage.SetExtent(frameExtent)
if vtk.VTK_MAJOR_VERSION <= 5:
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.SetScalarType(frame.GetImageData().GetScalarType())
mvImage.AllocateScalars()
else:
mvImage.AllocateScalars(frame.GetImageData().GetScalarType(), nFrames)
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mvNode.SetScene(slicer.mrmlScene)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameNumber] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount()-1)
mvDisplayNode.SetScene(slicer.mrmlScene)
mvDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(mvDisplayNode)
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(mvNode)
#
# automatically select the volume to display
#
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(mvNode.GetID())
appLogic.PropagateVolumeSelection()
# file list is no longer needed - remove the attribute
mvNode.RemoveAttribute('MultiVolume.FrameFileList')
return mvNode
