def mergeStructures(self,label="all"):
"""merge the named or all structure labels into the master label"""
merge = self.mergeVolume()
if not merge:
return
rows = self.structures.rowCount()
# check that structures are all the same size as the merge volume
dims = merge.GetImageData().GetDimensions()
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName )
if not structureVolume:
mergeName = merge.GetName()
self.errorDialog( "Merge Aborted: No image data for volume node %s."%(structureName) )
return
if structureVolume.GetImageData().GetDimensions() != dims:
mergeName = merge.GetName()
self.errorDialog( "Merge Aborted: Volume %s does not have the same dimensions as the target merge volume. Use the Resample Scalar/Vector/DWI module to resample. Use %s as the Reference Volume and select Nearest Neighbor (nn) Interpolation Type."%(structureName,mergeName) )
return
# check that user really wants to merge
rows = self.structures.rowCount()
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName)
if structureVolume.GetImageData().GetMTime() < merge.GetImageData().GetMTime():
mergeName = merge.GetName()
self.errorDialog( "Note: Merge volume has been modified more recently than structure volumes.\nCreating backup copy as %s-backup"%mergeName )
self.volumesLogic.CloneVolume( slicer.mrmlScene, merge, mergeName+"-backup" )
#
# find the Image Label Combine
# - call Enter to be sure GUI has been built
#
combiner = slicer.vtkImageLabelCombine()
#
# iterate through structures merging into merge volume
#
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName )
if row == 0:
# first row, just copy into merge volume
merge.GetImageData().DeepCopy( structureVolume.GetImageData() )
continue
combiner.SetInput1( merge.GetImageData() )
combiner.SetInput2( structureVolume.GetImageData() )
self.statusText( "Merging $structureName..." )
combiner.Update()
merge.GetImageData().DeepCopy( combiner.GetOutput() )
# mark all volumes as modified so we will be able to tell if the
# merged volume gets edited after these
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName )
structureVolume.GetImageData().Modified()
selectionNode = self.applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( self.master.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID( merge.GetID() )
self.applicationLogic.PropagateVolumeSelection()
self.statusText( "Finished merging." )
def mergeStructures(self, label="all"):
"""merge the named or all structure labels into the master label"""
merge = self.mergeVolume()
if not merge:
return
rows = self.structures.rowCount()
# check that structures are all the same size as the merge volume
dims = merge.GetImageData().GetDimensions()
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
if not structureVolume:
mergeName = merge.GetName()
self.errorDialog(
"Merge Aborted: No image data for volume node %s." %
(structureName))
return
if structureVolume.GetImageData().GetDimensions() != dims:
mergeName = merge.GetName()
self.errorDialog(
"Merge Aborted: Volume %s does not have the same dimensions as the target merge volume. Use the Resample Scalar/Vector/DWI module to resample. Use %s as the Reference Volume and select Nearest Neighbor (nn) Interpolation Type."
% (structureName, mergeName))
return
# check that user really wants to merge
rows = self.structures.rowCount()
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
if structureVolume.GetImageData().GetMTime() < merge.GetImageData(
).GetMTime():
mergeName = merge.GetName()
self.errorDialog(
"Note: Merge volume has been modified more recently than structure volumes.\nCreating backup copy as %s-backup"
% mergeName)
self.volumesLogic.CloneVolume(slicer.mrmlScene, merge,
mergeName + "-backup")
#
# find the Image Label Combine
# - call Enter to be sure GUI has been built
#
combiner = slicer.vtkImageLabelCombine()
#
# iterate through structures merging into merge volume
#
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
if row == 0:
# first row, just copy into merge volume
merge.GetImageData().DeepCopy(structureVolume.GetImageData())
continue
combiner.SetInput1(merge.GetImageData())
combiner.SetInput2(structureVolume.GetImageData())
self.statusText("Merging $structureName...")
combiner.Update()
merge.GetImageData().DeepCopy(combiner.GetOutput())
# mark all volumes as modified so we will be able to tell if the
# merged volume gets edited after these
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
structureVolume.GetImageData().Modified()
selectionNode = self.applicationLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(self.master.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(merge.GetID())
self.applicationLogic.PropagateVolumeSelection(0)
self.statusText("Finished merging.")