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MultiVolumeImporter.py
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MultiVolumeImporter.py
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from __main__ import vtk, qt, ctk, slicer
import vtk.util.numpy_support
from MultiVolumeImporter.Helper import Helper
#
# MultiVolumeImporter
#
class MultiVolumeImporter:
def __init__(self, parent):
parent.title = "MultiVolumeImporter"
parent.categories = ["Work in Progress.MultiVolume Support"]
parent.contributors = ["Andrey Fedorov (SPL, BWH)",\
"Jean-Christophe Fillion-Robin (Kitware)", \
"Julien Finet (Kitware)", \
"Steve Pieper (SPL, BWH)",\
"Ron Kikinis (SPL, BWH)"]
parent.index = 0
parent.helpText = """
Support of MultiVolume import in Slicer4
"""
# MultiVolumeExplorer registers the MRML node type this module is using
parent.dependencies = ['MultiVolumeExplorer']
parent.acknowledgementText = """
Development of this module was supported in part by the following grants:
P41EB015898, P41RR019703, R01CA111288 and U01CA151261.
"""
self.parent = parent
#
# qMultiVolumeImporterWidget
#
class MultiVolumeImporterWidget:
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def setup(self):
# Instantiate and connect widgets ...
# Collapsible button
dummyCollapsibleButton = ctk.ctkCollapsibleButton()
dummyCollapsibleButton.text = "Basic settings"
self.layout.addWidget(dummyCollapsibleButton)
dummyFormLayout = qt.QFormLayout(dummyCollapsibleButton)
# add input directory selector
label = qt.QLabel('Input directory:')
self.__fDialog = ctk.ctkDirectoryButton()
self.__fDialog.caption = 'Input DICOM directory'
dummyFormLayout.addRow(label, self.__fDialog)
label = qt.QLabel('Output node:')
self.__vcSelector = slicer.qMRMLNodeComboBox()
self.__vcSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__vcSelector.setMRMLScene(slicer.mrmlScene)
self.__vcSelector.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onMRMLSceneChanged)
self.__vcSelector.addEnabled = 1
dummyFormLayout.addRow(label, self.__vcSelector)
label = qt.QLabel('Input data type:')
self.__modeSelector = qt.QComboBox()
# parameter tuples: long title (for the selector), dicom tag, units, short title
self.__processingModes = []
self.__processingModes.append(['DICOM 4D DCE MRI (GE)', '0018|1060', 'ms', 'DCE'])
self.__processingModes.append(['DICOM variable TE MRI (GE)', '0018|0081', 'ms', 'vTE'])
self.__processingModes.append(['DICOM variable FA MRI (GE)', '0018|1314', 'deg', 'vFA'])
self.__processingModes.append(['DICOM variable TR MRI (GE)', '0018|0080', 'ms', 'vTR'])
self.__processingModes.append(['User-defined DICOM', '??', '??', 'MultiVolumeDICOM'])
self.__processingModes.append(['User-defined non-DICOM', 'N/A', '??', 'MultiVolume'])
for p in self.__processingModes:
print 'Processing mode found: ',p
self.__modeSelector.addItem(p[0])
self.__modeSelector.currentIndex = 0
self.__modeSelector.connect('currentIndexChanged(int)', self.onProcessingModeChanged)
dummyFormLayout.addRow(label, self.__modeSelector)
# Collapsible button
dummyCollapsibleButton = ctk.ctkCollapsibleButton()
dummyCollapsibleButton.text = "Advanced settings"
dummyCollapsibleButton.collapsed = 1
self.layout.addWidget(dummyCollapsibleButton)
dummyFormLayout = qt.QFormLayout(dummyCollapsibleButton)
self.__advancedFrame = dummyCollapsibleButton
# label name and values
label = qt.QLabel('DICOM tag:')
label.toolTip = 'DICOM tag used to separate individual volumes in the series'
self.__dicomTag = qt.QLineEdit()
self.__dicomTag.text = ""
dummyFormLayout.addRow(label, self.__dicomTag)
label = qt.QLabel('Frame identifying units:')
self.__veLabel = qt.QLineEdit()
dummyFormLayout.addRow(label, self.__veLabel)
label = qt.QLabel('Initial value:')
self.__veInitial = qt.QDoubleSpinBox()
self.__veInitial.value = 0
dummyFormLayout.addRow(label, self.__veInitial)
label = qt.QLabel('Step:')
self.__veStep = qt.QDoubleSpinBox()
self.__veStep.value = 1
dummyFormLayout.addRow(label, self.__veStep)
importButton = qt.QPushButton("Import")
importButton.toolTip = "Import the contents of the DICOM directory as a MultiVolume"
self.layout.addWidget(importButton)
importButton.connect('clicked(bool)', self.onImportButtonClicked)
self.__status = qt.QLabel('Status: Idle')
self.layout.addWidget(self.__status)
# Add vertical spacer
self.layout.addStretch(1)
def enter(self):
self.onProcessingModeChanged(self.__modeSelector.currentIndex)
def onProcessingModeChanged(self, idx):
nModes = len(self.__processingModes)
mode = self.__processingModes[idx]
self.__advancedFrame.collapsed = 0
if idx < nModes-2:
self.__advancedFrame.enabled = 0
else:
self.__advancedFrame.enabled = 1
if idx == nModes-1:
self.__dicomTag.enabled = 0
else:
self.__dicomTag.enabled = 1
self.__dicomTag.text = mode[1]
self.__veLabel.text = mode[2]
self.__veInitial.value = 0
self.__veStep.value = 1
def onMRMLSceneChanged(self, mrmlScene):
self.__vcSelector.setMRMLScene(slicer.mrmlScene)
return
def onImportButtonClicked(self):
# check if the output container exists
vcNode = self.__vcSelector.currentNode()
if vcNode == None:
self.__status.text = 'Status: Select output node!'
return
modeIdx = self.__modeSelector.currentIndex
processingMode = self.__processingModes[modeIdx]
# There are two options:
# 1. DICOM series in a directory, with either predefined or custom parse tag
# 2. Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
if modeIdx < len(self.__processingModes)-1:
# DICOM series
# get logic
logic = slicer.modules.multivolumeexplorer.logic()
# create a clean temporary directory
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
tmpDir = tmpDir+'/MultiVolumeImporter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
else:
# clean it up
print 'tmpDir = '+tmpDir
fileNames = os.listdir(tmpDir)
for f in fileNames:
print f,' will be unlinked'
os.unlink(tmpDir+'/'+f)
nFrames = logic.ProcessDICOMSeries(self.__fDialog.directory, tmpDir, self.__dicomTag.text, volumeLabels)
self.__status.text = 'Series processed OK, '+str(nFrames)+' volumes identified'
Helper.Info('Location of files:'+tmpDir)
fileNames = os.listdir(tmpDir)
fileNames.sort()
frameFolder = tmpDir
else:
# each frame is saved as a separate volume
fileNames = os.listdir(self.__fDialog.directory)
fileNames.sort()
frameFolder = self.__fDialog.directory
nFrames = len(fileNames)
volumeLabels.SetNumberOfTuples(nFrames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(nFrames)
for i in range(len(fileNames)):
frameId = self.__veInitial.value+self.__veStep.value*i
volumeLabels.SetComponent(i, 0, frameId)
# read the first frame to get the extent for DWI node
fullName = frameFolder+'/'+fileNames[0]
volumesLogic = slicer.modules.volumes.logic()
frame = volumesLogic.AddArchetypeVolume(fullName, processingMode[3]+' Frame 0', 0)
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
nFrames = len(fileNames)
dwiImage = vtk.vtkImageData()
dwiImage.SetExtent(frameExtent)
dwiImage.SetNumberOfScalarComponents(nFrames)
dwiImage.AllocateScalars()
dwiImageArray = vtk.util.numpy_support.vtk_to_numpy(dwiImage.GetPointData().GetScalars())
# create and initialize a blank DWI node
bValues = vtk.vtkDoubleArray()
bValues.Allocate(nFrames)
bValues.SetNumberOfComponents(1)
bValues.SetNumberOfTuples(nFrames)
gradients = vtk.vtkDoubleArray()
gradients.Allocate(nFrames*3)
gradients.SetNumberOfComponents(3)
gradients.SetNumberOfTuples(nFrames)
bValuesArray = vtk.util.numpy_support.vtk_to_numpy(bValues)
gradientsArray = vtk.util.numpy_support.vtk_to_numpy(gradients)
bValuesArray[:] = 0
gradientsArray[:] = 1
dwiNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLDiffusionWeightedVolumeNode')
dwiNode.SetName(processingMode[3]+'DisplayVolume')
dwiNode.SetScene(slicer.mrmlScene)
dwiNode.SetBValues(bValues)
dwiNode.SetDiffusionGradients(gradients)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
dwiNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
dwiNode.SetIJKToRASMatrix(mat)
self.annihilateScalarNode(frame)
for frameId in range(0,nFrames):
fullName = frameFolder+'/'+fileNames[frameId]
Helper.Info('Processing frame '+str(frameId)+': '+fullName)
frame = volumesLogic.AddArchetypeVolume(fullName, 'Frame'+str(frameId), 0)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
dwiImageArray.T[frameId] = frameImageArray
self.annihilateScalarNode(frame)
dwiDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLDiffusionWeightedVolumeDisplayNode')
dwiDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(dwiDisplayNode)
dwiDisplayNode.SetDefaultColorMap()
dwiNode.SetAndObserveDisplayNodeID(dwiDisplayNode.GetID())
dwiNode.SetAndObserveImageData(dwiImage)
slicer.mrmlScene.AddNode(dwiNode)
Helper.Info('DWI node added to the scene')
vcNode.SetDWVNodeID(dwiNode.GetID())
vcNode.SetLabelArray(volumeLabels)
vcNode.SetLabelName(self.__veLabel.text)
Helper.Info('VC node setup complete!')
Helper.SetBgFgVolumes(dwiNode.GetID(),None)
# leave no trace of the temporary nodes
def annihilateScalarNode(self, node):
dn = node.GetDisplayNode()
sn = node.GetStorageNode()
node.SetAndObserveDisplayNodeID(None)
node.SetAndObserveStorageNodeID(None)
slicer.mrmlScene.RemoveNode(dn)
slicer.mrmlScene.RemoveNode(sn)
slicer.mrmlScene.RemoveNode(node)