def loadPhilipsAffinity3DUS(self, loadable):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
name = slicer.util.toVTKString(loadable.name)
filePath = loadable.files[0]
fileList = vtk.vtkStringArray()
fileList.InsertNextValue(slicer.util.toVTKString(filePath))
volumesLogic = slicer.modules.volumes.logic()
outputVolume = volumesLogic.AddArchetypeScalarVolume(
filePath, name, 0, fileList)
# Override spacing, as GDCM cannot retreive image spacing correctly for this type of image
ds = dicom.read_file(filePath, stop_before_pixels=True)
outputSpacingStr = ds[findPrivateTag(ds, 0x200d, 0x03,
"Philips US Imaging DD 036")]
outputVolume.SetSpacing(float(outputSpacingStr[0]),
float(outputSpacingStr[1]),
float(outputSpacingStr[2]))
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
appLogic.PropagateVolumeSelection(0)
appLogic.FitSliceToAll()
return outputVolume
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 loadEigenArtemis3DUS(self, loadable):
name = slicer.util.toVTKString(loadable.name)
filePath = loadable.files[0]
fileList = vtk.vtkStringArray()
fileList.InsertNextValue(slicer.util.toVTKString(filePath))
volumesLogic = slicer.modules.volumes.logic()
outputVolume = volumesLogic.AddArchetypeScalarVolume(
filePath, name, 0, fileList)
outputVolume.SetSpacing(loadable.spacing, loadable.spacing,
loadable.spacing)
outputVolume.SetOrigin(loadable.origin[0], loadable.origin[1],
loadable.origin[2])
ijk2ras = vtk.vtkMatrix4x4()
outputVolume.GetIJKToRASMatrix(ijk2ras)
rot = vtk.vtkMatrix4x4()
rot.DeepCopy((0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1))
ijk2ras_updated = vtk.vtkMatrix4x4()
ijk2ras.Multiply4x4(rot, ijk2ras, ijk2ras_updated)
outputVolume.SetIJKToRASMatrix(ijk2ras_updated)
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
appLogic.PropagateVolumeSelection(0)
appLogic.FitSliceToAll()
return outputVolume
def loadFilesWithArchetype(self,files,name):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
fileList = vtk.vtkStringArray()
for f in files:
fileList.InsertNextValue(f)
volumesLogic = slicer.modules.volumes.logic()
return (volumesLogic.AddArchetypeVolume( files[0], name, 0, fileList ))
def loadFilesWithArchetype(self, files, name):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
fileList = vtk.vtkStringArray()
for f in files:
fileList.InsertNextValue(f)
volumesLogic = slicer.modules.volumes.logic()
return (volumesLogic.AddArchetypeVolume(files[0], name, 0, fileList))
def loadFilesWithArchetype(self):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
fileList = vtk.vtkStringArray()
for f in self.files:
fileList.InsertNextValue(f)
vl = slicer.modules.volumes.logic()
self.volumeNode = vl.AddArchetypeVolume( self.files[0], self.name, 0, fileList )
def loadFilesWithArchetype(self):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
fileList = vtk.vtkStringArray()
for f in self.files:
fileList.InsertNextValue(f)
vl = slicer.modules.volumes.logic()
self.volumeNode = vl.AddArchetypeVolume( self.files[0], self.name, 0, fileList )
def loadFiles(self, files, name):
fileList = vtk.vtkStringArray()
for f in files:
fileList.InsertNextValue(f)
vl = slicer.modules.volumes.logic()
# TODO: pass in fileList once it is known to be in the right order
volumeNode = vl.AddArchetypeVolume( files[0], name, 0 )
# automatically select the volume to display
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(volumeNode.GetID())
appLogic.PropagateVolumeSelection()
def InitializeMetricsTable( metricsTable ):
if ( metricsTable == None ):
return
metricsTable.GetTable().Initialize()
# TODO: Make the more robust (e.g. qSlicerMetricsTableWidget::METRIC_TABLE_COLUMNS)
metricsTableColumnNames = [ "MetricName", "MetricRoles", "MetricUnit", "MetricValue" ]
for columnName in metricsTableColumnNames:
column = vtk.vtkStringArray()
column.SetName( columnName )
metricsTable.GetTable().AddColumn( column )
def loadFilesWithArchetype(self,files,name):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
#name = slicer.util.unicodeify(name)
name = name.encode('latin1', 'ignore')
fileList = vtk.vtkStringArray()
for f in files:
fileList.InsertNextValue(f)
volumesLogic = slicer.modules.volumes.logic()
return(volumesLogic.AddArchetypeScalarVolume(files[0],name,0,fileList))
def loadFilesWithArchetype(self,files,name):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
#name = slicer.util.unicodeify(name)
name = name.encode('latin1', 'ignore')
fileList = vtk.vtkStringArray()
for f in files:
fileList.InsertNextValue(f)
volumesLogic = slicer.modules.volumes.logic()
return(volumesLogic.AddArchetypeScalarVolume(files[0],name,0,fileList))
def requestDeviceIDsCompleted(self, object=None, event=None, caller=None):
wasBlocked = self.deviceIDComboBox.blockSignals(True)
self.deviceIDComboBox.clear()
deviceIDs = vtk.vtkStringArray()
self.plusRemoteNode.GetDeviceIDs(deviceIDs)
currentDeviceID = self.plusRemoteNode.GetCurrentDeviceID()
for valueIndex in range(deviceIDs.GetNumberOfValues()):
deviceID = deviceIDs.GetValue(valueIndex)
self.deviceIDComboBox.addItem(deviceID)
currentIndex = self.deviceIDComboBox.findText(currentDeviceID)
self.deviceIDComboBox.setCurrentIndex(currentIndex)
self.deviceIDComboBox.blockSignals(wasBlocked)
self.onDeviceIdChanged()
def ConvertStructureSetToLabelmap(self):
import vtkSlicerDicomRtImportExportModuleLogic
import vtkSegmentationCore
import vtkSlicerSegmentationsModuleMRML
import vtkSlicerSegmentationsModuleLogic
labelmapsToSave = []
# Get all segmentation nodes from the scene
segmentationNodes = slicer.util.getNodes('vtkMRMLSegmentationNode*')
for segmentationNode in segmentationNodes.values():
logging.info(' Converting structure set ' + segmentationNode.GetName())
# Set referenced volume as rasterization reference
referenceVolume = vtkSlicerDicomRtImportExportModuleLogic.vtkSlicerDicomRtImportExportModuleLogic.GetReferencedVolumeByDicomForSegmentation(segmentationNode)
if referenceVolume == None:
logging.error('No reference volume found for segmentation ' + segmentationNode.GetName())
continue
# Perform conversion
binaryLabelmapRepresentationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()
segmentation = segmentationNode.GetSegmentation()
segmentation.CreateRepresentation(binaryLabelmapRepresentationName)
# Create labelmap volume nodes from binary labelmaps
segmentIDs = vtk.vtkStringArray()
segmentation.GetSegmentIDs(segmentIDs)
for segmentIndex in xrange(0,segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(segmentIndex)
segment = segmentation.GetSegment(segmentID)
binaryLabelmap = segment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
if not binaryLabelmap:
logging.error('Failed to retrieve binary labelmap from segment ' + segmentID + ' in segmentation ' + segmentationNode.GetName())
continue
labelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(labelmapNode)
labelmapName = segmentationNode.GetName() + "_" + segmentID
labelmapNode.SetName(labelmapName)
if not vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateLabelmapVolumeFromOrientedImageData(binaryLabelmap,labelmapNode):
logging.error('Failed to create labelmap from segment ' + segmentID + ' in segmentation ' + segmentationNode.GetName())
continue
# Append volume to list
labelmapsToSave.append(labelmapNode)
return labelmapsToSave
def loadFiles(self,files=None,name=None):
if not files:
files = self.files
if not name:
name = self.name
fileList = vtk.vtkStringArray()
for f in files:
fileList.InsertNextValue(f)
vl = slicer.modules.volumes.logic()
# TODO: pass in fileList once it is known to be in the right order
self.volumeNode = vl.AddArchetypeVolume( files[0], name, 0 )
# automatically select the volume to display
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
if self.volumeNode:
selNode.SetReferenceActiveVolumeID(self.volumeNode.GetID())
appLogic.PropagateVolumeSelection()
def copyNodeContentToNewScriptedModuleNode(oldDataNode, shNode):
newDataNode = slicer.vtkMRMLScriptedModuleNode()
newDataNode.HideFromEditorsOff()
# Copy node attributes
attributeNames = vtk.vtkStringArray()
oldDataNode.GetAttributeNames(attributeNames)
for index in range(attributeNames.GetNumberOfValues()):
attributeName = attributeNames.GetValue(index)
newDataNode.SetAttribute(attributeName,
oldDataNode.GetAttribute(attributeName))
slicer.mrmlScene.AddNode(newDataNode)
newDataNode.SetName(oldDataNode.GetName())
# Copy node references
newDataNode.CopyReferences(oldDataNode)
# Move children
childItemIDs = vtk.vtkIdList()
#shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
shNode.GetItemChildren(shNode.GetItemByDataNode(oldDataNode), childItemIDs)
for index in range(childItemIDs.GetNumberOfIds()):
childItemID = childItemIDs.GetId(index)
shNode.ReparentItemByDataNode(childItemID, newDataNode)
return newDataNode
