def setUp(self):
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
dti = sampleDataLogic.downloadMRHead()
self.file_name = dti.GetStorageNode().GetFileName()
self.ritk = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
self.ritk.SetUseOrientationFromFile(True)
self.ritk.SetUseNativeOriginOn();
self.ritk.SetOutputScalarTypeToNative()
self.ritk.SetDesiredCoordinateOrientationToNative()
self.ritk.SetArchetype(self.file_name)
self.ritk.Update()
self.rnrrd = slicer.vtkNRRDReader()
self.rnrrd.SetFileName(self.file_name)
self.rnrrd.Update()
def loadFilesWithSeriesReader(self,imageIOName,files,name):
""" Explicitly use the named imageIO to perform the loading
"""
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
reader.SetArchetype(files[0]);
for f in files:
reader.AddFileName(slicer.util.toVTKString(f))
reader.SetSingleFile(0);
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
if imageIOName == "GDCM":
reader.SetDICOMImageIOApproachToGDCM()
elif imageIOName == "DCMTK":
reader.SetDICOMImageIOApproachToDCMTK()
else:
raise Exception("Invalid imageIOName of %s" % imageIOName)
logging.info("Loading with imageIOName: %s" % imageIOName)
reader.Update()
slicer.modules.reader = reader
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorStrings = (imageIOName, vtk.vtkErrorCode.GetStringFromErrorCode(reader.GetErrorCode()))
logging.error("Could not read scalar volume using %s approach. Error is: %s" % errorStrings)
return
imageChangeInformation = vtk.vtkImageChangeInformation()
imageChangeInformation.SetInputConnection(reader.GetOutputPort())
imageChangeInformation.SetOutputSpacing( 1, 1, 1 )
imageChangeInformation.SetOutputOrigin( 0, 0, 0 )
imageChangeInformation.Update()
name = slicer.mrmlScene.GenerateUniqueName(slicer.util.toVTKString(name))
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", name)
volumeNode.SetAndObserveImageData(imageChangeInformation.GetOutputDataObject(0))
slicer.vtkMRMLVolumeArchetypeStorageNode.SetMetaDataDictionaryFromReader(volumeNode, reader)
volumeNode.SetRASToIJKMatrix(reader.GetRasToIjkMatrix())
volumeNode.CreateDefaultDisplayNodes()
slicer.modules.DICOMInstance.reader = reader
slicer.modules.DICOMInstance.imageChangeInformation = imageChangeInformation
return(volumeNode)
def loadFilesWithSeriesReader(self,imageIOName,files,name):
""" Explicitly use the named imageIO to perform the loading
"""
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
reader.SetArchetype(files[0]);
for f in files:
reader.AddFileName(slicer.util.toVTKString(f))
reader.SetSingleFile(0);
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
if imageIOName == "GDCM":
reader.SetDICOMImageIOApproachToGDCM()
elif imageIOName == "DCMTK":
reader.SetDICOMImageIOApproachToDCMTK()
else:
raise Exception("Invalid imageIOName of %s" % imageIOName)
logging.info("Loading with imageIOName: %s" % imageIOName)
reader.Update()
slicer.modules.reader = reader
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorStrings = (imageIOName, vtk.vtkErrorCode.GetStringFromErrorCode(reader.GetErrorCode()))
logging.error("Could not read scalar volume using %s approach. Error is: %s" % errorStrings)
return
imageChangeInformation = vtk.vtkImageChangeInformation()
imageChangeInformation.SetInputConnection(reader.GetOutputPort())
imageChangeInformation.SetOutputSpacing( 1, 1, 1 )
imageChangeInformation.SetOutputOrigin( 0, 0, 0 )
imageChangeInformation.Update()
name = slicer.mrmlScene.GenerateUniqueName(slicer.util.toVTKString(name))
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", name)
volumeNode.SetAndObserveImageData(imageChangeInformation.GetOutputDataObject(0))
slicer.vtkMRMLVolumeArchetypeStorageNode.SetMetaDataDictionaryFromReader(volumeNode, reader)
volumeNode.SetRASToIJKMatrix(reader.GetRasToIjkMatrix())
volumeNode.CreateDefaultDisplayNodes()
slicer.modules.DICOMInstance.reader = reader
slicer.modules.DICOMInstance.imageChangeInformation = imageChangeInformation
return(volumeNode)
def loadBabies(self,directoryPath,pattern,maxIndex=None):
self.images = []
filePaths = []
index = 1
import os.path
while True:
filePath = os.path.join(directoryPath, pattern % index)
if not os.path.exists(filePath):
break
filePaths.append(filePath)
index += 1
if maxIndex and index > maxIndex:
break
if len(filePaths) == 0:
return
middleBabyPath = filePaths[len(filePaths)/2]
babyVolume = self.babyVolume(middleBabyPath)
#transtor = slicer.vtkMRMLTransformStorageNode()
reader = reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
reader.SetSingleFile(1)
reader.SetUseOrientationFromFile(1)
#reader.SetDesiredCoordinateOrientationToAxial()
reader.SetOutputScalarTypeToNative()
reader.SetUseNativeOriginOn()
changeInfo = vtk.vtkImageChangeInformation()
changeInfo.SetInputConnection( reader.GetOutputPort() )
changeInfo.SetOutputSpacing( 1, 1, 1 )
changeInfo.SetOutputOrigin( 0, 0, 0 )
self.images = {}
self.rasToIJKs = {}
#self.toTemplate = {}
for filePath in filePaths:
print("Loading %s" % filePath)
reader.SetArchetype(filePath)
changeInfo.Update()
self.rasToIJKs[filePath] = vtk.vtkMatrix4x4()
self.rasToIJKs[filePath].DeepCopy(reader.GetRasToIjkMatrix())
self.images[filePath] = vtk.vtkImageData()
self.images[filePath].DeepCopy(changeInfo.GetOutput())
def setUp(self):
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
dti = sampleDataLogic.downloadMRHead()
self.file_name = dti.GetStorageNode().GetFileName()
self.ritk = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
self.ritk.SetUseOrientationFromFile(True)
self.ritk.SetUseNativeOriginOn()
self.ritk.SetOutputScalarTypeToNative()
self.ritk.SetDesiredCoordinateOrientationToNative()
self.ritk.SetArchetype(self.file_name)
self.ritk.Update()
self.rnrrd = slicer.vtkNRRDReader()
self.rnrrd.SetFileName(self.file_name)
self.rnrrd.Update()
self.assertTrue(
compare_vtk_matrix(self.ritk.GetRasToIjkMatrix(),
self.rnrrd.GetRasToIjkMatrix()))
def setUp(self):
from SampleData import SampleDataLogic
brainSource = SampleDataLogic().sourceForSampleName('MRHead')
self.file_name = SampleDataLogic().downloadSourceIntoCache(
brainSource)[0]
self.ritk = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
self.ritk.SetUseOrientationFromFile(True)
self.ritk.SetUseNativeOriginOn()
self.ritk.SetOutputScalarTypeToNative()
self.ritk.SetDesiredCoordinateOrientationToNative()
self.ritk.SetArchetype(self.file_name)
self.ritk.Update()
self.rnrrd = teem.vtkTeemNRRDReader()
self.rnrrd.SetFileName(self.file_name)
self.rnrrd.Update()
self.assertTrue(
compare_vtk_matrix(self.ritk.GetRasToIjkMatrix(),
self.rnrrd.GetRasToIjkMatrix()))
def setUp(self):
from SampleData import SampleDataLogic
brainSource = SampleDataLogic().sourceForSampleName('MRHead')
self.file_name = SampleDataLogic().downloadSourceIntoCache(brainSource)[0]
self.ritk = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
self.ritk.SetUseOrientationFromFile(True)
self.ritk.SetUseNativeOriginOn();
self.ritk.SetOutputScalarTypeToNative()
self.ritk.SetDesiredCoordinateOrientationToNative()
self.ritk.SetArchetype(self.file_name)
self.ritk.Update()
self.rnrrd = teem.vtkTeemNRRDReader()
self.rnrrd.SetFileName(self.file_name)
self.rnrrd.Update()
self.assertTrue(
compare_vtk_matrix(
self.ritk.GetRasToIjkMatrix(),
self.rnrrd.GetRasToIjkMatrix()
)
)
def load(self, loadable):
"""Load the selection
"""
filePath = loadable.files[0]
metadata = self.getMetadata(filePath)
import vtkITK
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
reader.SetArchetype(filePath)
reader.AddFileName(filePath)
reader.SetSingleFile(True)
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
# GDCM is not particularly better in this than DCMTK, we just select one explicitly
# so that we know which one is used
reader.SetDICOMImageIOApproachToGDCM()
reader.Update()
imageData = reader.GetOutput()
from __main__ import vtk
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorString = vtk.vtkErrorCode.GetStringFromErrorCode(
reader.GetErrorCode())
raise ValueError(
"Could not read image {0} from file {1}. Error is: {2}".format(
loadable.name, filePath, errorString))
# Image origin and spacing is stored in IJK to RAS matrix
imageData.SetSpacing(1.0, 1.0, 1.0)
imageData.SetOrigin(0.0, 0.0, 0.0)
volumeNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLScalarVolumeNode",
slicer.mrmlScene.GenerateUniqueName(loadable.name))
# I axis: scanline index (lateralSpacing)
# J axis: sound propagation (axialSpacing)
# K axis: slice (sliceSpacing)
lateralSpacing = metadata['PixelSpacing'][1]
axialSpacing = metadata['PixelSpacing'][0]
sliceSpacing = metadata['SpacingBetweenSlices']
ijkToRas = vtk.vtkMatrix4x4()
ijkToRas.SetElement(0, 0, -1)
ijkToRas.SetElement(1, 1, -1) # so that J axis points toward posterior
volumeNode.SetIJKToRASMatrix(ijkToRas)
volumeNode.SetSpacing(lateralSpacing, axialSpacing, sliceSpacing)
extent = imageData.GetExtent()
volumeNode.SetOrigin(
(extent[1] - extent[0] + 1) * 0.5 * lateralSpacing, 0,
-(extent[5] - extent[2] + 1) * 0.5 * sliceSpacing)
volumeNode.SetAndObserveImageData(imageData)
# Apply scan conversion transform
acquisitionTransform = self.createAcquisitionTransform(
volumeNode, metadata)
volumeNode.SetAndObserveTransformNodeID(acquisitionTransform.GetID())
# Create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, volumeNode)
# Place transform in the same subject hierarchy folder as the volume node
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
volumeParentItemId = shNode.GetItemParent(
shNode.GetItemByDataNode(volumeNode))
shNode.SetItemParent(shNode.GetItemByDataNode(acquisitionTransform),
volumeParentItemId)
# Show in slice views
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(volumeNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(1)
return volumeNode
def load(self,loadable):
"""Load the selection
"""
outputSequenceNodes = []
for filePath in loadable.files:
import vtkITK
if loadable.grayscale:
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
else:
reader = vtkITK.vtkITKArchetypeImageSeriesVectorReaderFile()
reader.SetArchetype(filePath)
reader.AddFileName(filePath)
reader.SetSingleFile(True)
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
# GDCM is not particularly better in this than DCMTK, we just select one explicitly
# so that we know which one is used
reader.SetDICOMImageIOApproachToGDCM()
reader.Update()
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorString = vtk.vtkErrorCode.GetStringFromErrorCode(reader.GetErrorCode())
raise ValueError("Could not read image {0} from file {1}. Error is: {2}".format(loadable.name, filePath, errorString))
volume = reader.GetOutput()
[spacingX, spacingY, frameTimeMsec] = volume.GetSpacing()
volume.SetSpacing(1.0, 1.0, 1.0)
outputSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode")
if frameTimeMsec == 1.0:
# frame time is not found, set it to 1.0fps
frameTime = 1
outputSequenceNode.SetIndexName("frame")
outputSequenceNode.SetIndexUnit("")
playbackRateFps = 10
else:
frameTime = frameTimeMsec * 0.001
outputSequenceNode.SetIndexName("time")
outputSequenceNode.SetIndexUnit("s")
playbackRateFps = 1.0/frameTime
if loadable.grayscale:
tempFrameVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
else:
tempFrameVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLVectorVolumeNode")
# Rotate 180deg, otherwise the image would appear upside down
ijkToRAS = vtk.vtkMatrix4x4()
ijkToRAS.SetElement(0,0,-1.0)
ijkToRAS.SetElement(1,1,-1.0)
tempFrameVolume.SetIJKToRASMatrix(ijkToRAS)
tempFrameVolume.SetSpacing(spacingX, spacingY, 1.0)
numberOfFrames = volume.GetDimensions()[2]
extent = volume.GetExtent()
numberOfFrames = extent[5]-extent[4]+1
for frame in range(numberOfFrames):
crop = vtk.vtkImageClip()
crop.SetInputData(volume)
crop.SetOutputWholeExtent(extent[0], extent[1], extent[2], extent[3], extent[4]+frame, extent[4]+frame)
crop.ClipDataOn()
crop.Update()
croppedOutput = crop.GetOutput()
croppedOutput.SetExtent(extent[0], extent[1], extent[2], extent[3], 0, 0)
tempFrameVolume.SetAndObserveImageData(croppedOutput)
if type(frameTime)==int:
timeStampSec = str(frame * frameTime)
else:
timeStampSec = "{:.3f}".format(frame * frameTime)
outputSequenceNode.SetDataNodeAtValue(tempFrameVolume, timeStampSec)
slicer.mrmlScene.RemoveNode(tempFrameVolume)
if len(loadable.files) == 1:
outputSequenceNode.SetName(loadable.name)
else:
ds = dicom.read_file(filePath, stop_before_pixels=True)
if hasattr(ds, 'PositionerPrimaryAngle') and hasattr(ds, 'PositionerSecondaryAngle'):
outputSequenceNode.SetName('{0} ({1}/{2})'.format(loadable.name, ds.PositionerPrimaryAngle,ds.PositionerSecondaryAngle))
else:
outputSequenceNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(outputSequenceNode)
# Create storage node that allows saving node as nrrd
outputSequenceStorageNode = slicer.vtkMRMLVolumeSequenceStorageNode()
slicer.mrmlScene.AddNode(outputSequenceStorageNode)
outputSequenceNode.SetAndObserveStorageNodeID(outputSequenceStorageNode.GetID())
outputSequenceNodes.append(outputSequenceNode)
if not hasattr(loadable, 'createBrowserNode') or loadable.createBrowserNode:
# Add a browser node and show the volume in the slice viewer for user convenience
outputSequenceBrowserNode = slicer.vtkMRMLSequenceBrowserNode()
outputSequenceBrowserNode.SetName(slicer.mrmlScene.GenerateUniqueName(loadable.name+' browser'))
outputSequenceBrowserNode.SetPlaybackRateFps(playbackRateFps)
slicer.mrmlScene.AddNode(outputSequenceBrowserNode)
# Add all sequences to the sequence browser
first = True
for outputSequenceNode in outputSequenceNodes:
#outputSequenceBrowserNode.SetAndObserveMasterSequenceNodeID(outputSequenceNode.GetID())
outputSequenceBrowserNode.AddSynchronizedSequenceNode(outputSequenceNode)
proxyVolumeNode = outputSequenceBrowserNode.GetProxyNode(outputSequenceNode)
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, proxyVolumeNode)
if first:
first = False
# Automatically select the volume to display
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(proxyVolumeNode.GetID())
appLogic.PropagateVolumeSelection()
appLogic.FitSliceToAll()
slicer.modules.sequences.setToolBarActiveBrowserNode(outputSequenceBrowserNode)
# Show sequence browser toolbar
slicer.modules.sequences.showSequenceBrowser(outputSequenceBrowserNode)
return outputSequenceNode