def makeModel(self,volumeNode, labelNumber, smoothValue,namenode):
#the volume need to present must valid
if not volumeNode:
return
# set up the model maker node
parameters = {}
parameters['Name'] = "EditorModel"
parameters["InputVolume"] = volumeNode.GetID()
parameters['FilterType'] = "Sinc"
# build only the currently selected model.
parameters['Labels'] = labelNumber #using default label, that can further improved by using label that user selected
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters['GenerateAll'] = False
parameters["JointSmoothing"] = False
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
parameters["Decimate"] = 0.25
parameters["Smooth"] = smoothValue #defaul smooth parameter
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelHierarchyNode" )
outHierarchy = None
for n in range(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLModelHierarchyNode" )
if node.GetName() == "Editor Models":
outHierarchy = node
break
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene( slicer.mrmlScene )
outHierarchy.SetName( namenode )
slicer.mrmlScene.AddNode( outHierarchy )
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
slicer.cli.run(modelMaker, None, parameters)
def makeModels(study, finding, colorTable):
if (study is None) | (finding is None) | (colorTable is None):
return
seg = finding.GetSegmentationMappedByStudyNodeID(study.GetID())
if seg:
labelVolume = seg.GetLabelVolumeNode()
#create a temporary model hierarchy for generating models
tempMH = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(tempMH)
if (labelVolume is not None) & (tempMH is not None):
parameters = {'InputVolume': labelVolume.GetID(), 'ColorTable': colorTable.GetID(),
'ModelSceneFile': tempMH.GetID(), 'GenerateAll': False, 'StartLabel': finding.GetColorID(),
'EndLabel': finding.GetColorID(), 'Name': labelVolume.GetName() + "_" + finding.GetName() + "_M"}
cliModelMaker = None
cliModelMaker = slicer.cli.run(slicer.modules.modelmaker, cliModelMaker, parameters, wait_for_completion = True)
genModelNodes = vtk.vtkCollection()
tempMH.GetChildrenModelNodes(genModelNodes)
if genModelNodes.GetNumberOfItems() > 0:
modelNode = genModelNodes.GetItemAsObject(0)
if modelNode:
if modelNode.IsA('vtkMRMLModelNode'):
hnode = slicer.vtkMRMLHierarchyNode.GetAssociatedHierarchyNode(modelNode.GetScene(), modelNode.GetID())
if hnode:
if seg.GetModelHierarchyNode():
SlicerLongitudinalPETCTModuleViewHelper.removeModelHierarchyAndChildModelNodesFromScene(seg.GetModelHierarchyNode())
hnode.SetName(seg.GetName()+"_Model")
seg.SetAndObserveModelHierarchyNodeID(hnode.GetID())
modelNode.SetName(labelVolume.GetName() + "_" + finding.GetName()+"_M")
if modelNode.GetDisplayNode():
modelNode.GetDisplayNode().SetName(labelVolume.GetName() + "_" + finding.GetName()+"_D")
modelNode.GetDisplayNode().AddViewNodeID(SlicerLongitudinalPETCTModuleViewHelper.getStandardViewNode().GetID())
hnode.SetName(labelVolume.GetName() + "_" + finding.GetName()+"_H")
modelNode.SetHideFromEditors(False)
else:
seg.SetAndObserveModelHierarchyNodeID("")
slicer.mrmlScene.RemoveNode(modelNode)
slicer.mrmlScene.RemoveNode(hnode)
slicer.mrmlScene.RemoveNode(tempMH.GetDisplayNode())
slicer.mrmlScene.RemoveNode(tempMH)
#return '#%02X%02X%02X' % (r,g,b)
def _internalTest():
# test loading of measurements file
logic = lapdMouseVisualizerLogic()
measurementsFile = '/home/christian/data/R01_lapdmousetest/m01/geometry_measurements.csv'
slicer.util.loadNodeFromFile(measurementsFile, 'TableFile')
measurementsTable = slicer.util.getFirstNodeByClassByName(
'vtkMRMLTableNode', 'geometry_measurements')
model = logic.measurementsTable2Model(measurementsTable)
model.SetScene(slicer.mrmlScene)
model.CreateDefaultDisplayNodes()
slicer.mrmlScene.AddNode(model)
# test loading of measurements file
logic = lapdMouseVisualizerLogic()
treeFilename = '/home/christian/data/R01_lapdmousetest/m01/m01_AirwayTree.meta'
tree = logic.readMetaTree(treeFilename)
modelHierarchy = slicer.vtkMRMLModelHierarchyNode()
model = logic.tree2Model(tree)
model.SetScene(slicer.mrmlScene)
model.CreateDefaultDisplayNodes()
slicer.mrmlScene.AddNode(model)
self.delayDisplay('Test passed!')
def test_sceneImport24281(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
self.delayDisplay("Getting Data")
import SampleData
head = SampleData.downloadSample("MRHead")
#
# create a label map and set it for editing
#
self.delayDisplay("Setting up LabelMap")
volumesLogic = slicer.modules.volumes.logic()
headLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, head, head.GetName() + '-label' )
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetActiveVolumeID( head.GetID() )
selectionNode.SetActiveLabelVolumeID( headLabel.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# got to the editor and do some drawing
#
import EditorLib
self.delayDisplay("Setting up Editor and drawing")
editUtil = EditorLib.EditUtil.EditUtil()
parameterNode = editUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffectOptions = EditorLib.PaintEffectOptions()
paintEffectOptions.setMRMLDefaults()
paintEffectOptions.__del__()
self.delayDisplay('Paint radius is %s' % parameterNode.GetParameter('PaintEffect,radius'))
sliceWidget = lm.sliceWidget('Red')
size = min(sliceWidget.width,sliceWidget.height)
step = size / 12
center = size / 2
parameterNode.SetParameter('PaintEffect,radius', '20')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.delayDisplay('Paint radius is %s, tool radius is %d' % (parameterNode.GetParameter('PaintEffect,radius'),paintTool.radius))
for label in xrange(1,5):
editUtil.setLabel(label)
pos = center - 2*step + (step * label)
self.delayDisplay('Painting %d, at (%d,%d)' % (label,pos,pos),200)
paintTool.paintAddPoint(pos,pos)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
#
# now build:
# create a model using the command line module
# based on the current editor parameters
# - make a new hierarchy node
#
self.delayDisplay( "Building..." )
parameters = {}
parameters["InputVolume"] = headLabel.GetID()
# create models for all labels
parameters["JointSmoothing"] = True
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene( slicer.mrmlScene )
outHierarchy.SetName( "sceneImport2428Hierachy" )
slicer.mrmlScene.AddNode( outHierarchy )
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
self.CLINode = None
self.CLINode = slicer.cli.runSync(modelMaker, self.CLINode, parameters, delete_temporary_files=False)
self.delayDisplay("Models built")
success = self.verifyModels()
success = success and (slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelNode" ) > 3)
self.delayDisplay("Test finished")
if success:
self.delayDisplay("Ahh... test passed.")
else:
self.delayDisplay("!$!$!#!@#!@!@$%! Test Failed!!")
self.assertTrue(success)
def build(self):
"""make models of current merge volume"""
#
# get the image data for the label layer
#
self.statusText( "Building..." )
merge = self.merge
if not merge:
return
#
# create a model using the command line module
# based on the current editor parameters
#
parameters = {}
parameters["InputVolume"] = merge.GetID()
parameters['FilterType'] = "Sinc"
parameters['GenerateAll'] = True
# not needed: setting StartLabel and EndLabel instead
#parameters['Labels'] = self.getPaintLabel()
parameters["JointSmoothing"] = True
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
# create models for all labels
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters["Decimate"] = 0.25
parameters["Smooth"] = 10
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelHierarchyNode" )
outHierarchy = None
for n in xrange(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLModelHierarchyNode" )
if node.GetName() == "Editor Models":
outHierarchy = node
break
if outHierarchy and self.replaceModels.checked and numNodes > 0:
# user wants to delete any existing models, so take down hierarchy and
# delete the model nodes
rr = range(numNodes)
rr.reverse()
for n in rr:
node = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLModelHierarchyNode" )
if node.GetParentNodeID() == outHierarchy.GetID():
slicer.mrmlScene.RemoveNode( node.GetModelNode() )
slicer.mrmlScene.RemoveNode( node )
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene( slicer.mrmlScene )
outHierarchy.SetName( "Editor Models" )
slicer.mrmlScene.AddNode( outHierarchy )
parameters["ModelSceneFile"] = outHierarchy
try:
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
self.CLINode = slicer.cli.run(modelMaker, self.CLINode, parameters)
self.statusText( "Model Making Started..." )
except AttributeError:
slicer.util.errorDisplay('The ModelMaker module is not available<p>Perhaps it was disabled in the application '
'settings or did not load correctly.', windowTitle='Editor')
def build(self):
"""make models of current merge volume"""
#
# get the image data for the label layer
#
self.statusText("Building...")
merge = self.merge
if not merge:
return
#
# create a model using the command line module
# based on the current editor parameters
#
parameters = {}
parameters["InputVolume"] = merge.GetID()
parameters['FilterType'] = "Sinc"
parameters['GenerateAll'] = True
# not needed: setting StartLabel and EndLabel instead
#parameters['Labels'] = self.getPaintLabel()
parameters["JointSmoothing"] = True
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
# create models for all labels
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters["Decimate"] = 0.25
parameters["Smooth"] = 10
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
"vtkMRMLModelHierarchyNode")
outHierarchy = None
for n in xrange(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass(
n, "vtkMRMLModelHierarchyNode")
if node.GetName() == "Editor Models":
outHierarchy = node
break
if outHierarchy and self.replaceModels.checked and numNodes > 0:
# user wants to delete any existing models, so take down hierarchy and
# delete the model nodes
rr = range(numNodes)
rr.reverse()
for n in rr:
node = slicer.mrmlScene.GetNthNodeByClass(
n, "vtkMRMLModelHierarchyNode")
if node.GetParentNodeID() == outHierarchy.GetID():
slicer.mrmlScene.RemoveNode(node.GetModelNode())
slicer.mrmlScene.RemoveNode(node)
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene(slicer.mrmlScene)
outHierarchy.SetName("Editor Models")
slicer.mrmlScene.AddNode(outHierarchy)
parameters["ModelSceneFile"] = outHierarchy
try:
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
self.CLINode = slicer.cli.run(modelMaker, self.CLINode, parameters)
self.statusText("Model Making Started...")
except AttributeError:
slicer.util.errorDisplay(
'The ModelMaker module is not available<p>Perhaps it was disabled in the application '
'settings or did not load correctly.',
windowTitle='Editor')
def TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0], [0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def test_sceneImport24281(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
self.delayDisplay("Getting Data")
import SampleData
head = SampleData.downloadSample("MRHead")
#
# create a label map and set it for editing
#
self.delayDisplay("Setting up LabelMap")
volumesLogic = slicer.modules.volumes.logic()
headLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, head, head.GetName() + '-label' )
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetActiveVolumeID( head.GetID() )
selectionNode.SetActiveLabelVolumeID( headLabel.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# got to the editor and do some drawing
#
self.delayDisplay("Setting up Editor and drawing")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffectOptions = EditorLib.PaintEffectOptions()
paintEffectOptions.setMRMLDefaults()
paintEffectOptions.__del__()
self.delayDisplay('Paint radius is %s' % parameterNode.GetParameter('PaintEffect,radius'))
sliceWidget = lm.sliceWidget('Red')
size = min(sliceWidget.width,sliceWidget.height)
step = int(size / 12)
center = int(size / 2)
parameterNode.SetParameter('PaintEffect,radius', '20')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
self.delayDisplay('Paint radius is %s, tool radius is %d' % (parameterNode.GetParameter('PaintEffect,radius'),paintTool.radius))
for label in range(1,5):
EditUtil.setLabel(label)
pos = center - 2*step + (step * label)
self.delayDisplay('Painting %d, at (%d,%d)' % (label,pos,pos),200)
paintTool.paintAddPoint(pos,pos)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
#
# now build:
# create a model using the command line module
# based on the current editor parameters
# - make a new hierarchy node
#
self.delayDisplay( "Building..." )
parameters = {}
parameters["InputVolume"] = headLabel.GetID()
# create models for all labels
parameters["JointSmoothing"] = True
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene( slicer.mrmlScene )
outHierarchy.SetName( "sceneImport2428Hierachy" )
slicer.mrmlScene.AddNode( outHierarchy )
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
self.CLINode = None
self.CLINode = slicer.cli.runSync(modelMaker, self.CLINode, parameters, delete_temporary_files=False)
self.delayDisplay("Models built")
success = self.verifyModels()
success = success and (slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelNode" ) > 3)
self.delayDisplay("Test finished")
if success:
self.delayDisplay("Ahh... test passed.")
else:
self.delayDisplay("!$!$!#!@#!@!@$%! Test Failed!!")
self.assertTrue(success)
def makeModel(self,modelName='EditorModel',smooth=True):
#
# create a model using the command line module
# based on the current editor parameters
#
volumeNode = EditUtil.getLabelVolume()
if not volumeNode:
return
#
# set up the model maker node
#
parameters = {}
parameters['Name'] = modelName
parameters["InputVolume"] = volumeNode.GetID()
parameters['FilterType'] = "Sinc"
# build only the currently selected model.
parameters['Labels'] = EditUtil.getLabel()
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters['GenerateAll'] = False
parameters["JointSmoothing"] = False
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
if smooth:
parameters["Decimate"] = 0.25
parameters["Smooth"] = 10
else:
parameters["Decimate"] = 0
parameters["Smooth"] = 0
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass( "vtkMRMLModelHierarchyNode" )
outHierarchy = None
for n in xrange(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLModelHierarchyNode" )
if node.GetName() == "Editor Models":
outHierarchy = node
break
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene( slicer.mrmlScene )
outHierarchy.SetName( "Editor Models" )
slicer.mrmlScene.AddNode( outHierarchy )
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
slicer.cli.run(modelMaker, None, parameters)
slicer.util.showStatusMessage( "Model Making Started...", 2000 )
def test_sceneImport24281(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
self.delayDisplay("Getting Data")
import SampleData
head = SampleData.downloadSample("MRHead")
# Create segmentation
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(head)
# Add a few segments
segments = [["Segment A", [0, 65, 32], 25, [1.0, 0.0, 0.0]],
["Segment B", [1, -14, 30], 30, [1.0, 1.0, 0.0]],
["Segment C", [0, 28, -7], 15, [0.0, 1.0, 1.0]],
["Segment D", [31, 33, 27], 25, [0.0, 0.0, 1.0]]]
for [name, position, radius, color] in segments:
seed = vtk.vtkSphereSource()
seed.SetCenter(position)
seed.SetRadius(radius)
seed.Update()
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
seed.GetOutput(), name, color)
# Export to labelmap volume
headLabel = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
slicer.modules.segmentations.logic(
).ExportVisibleSegmentsToLabelmapNode(segmentationNode, headLabel,
head)
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetActiveVolumeID(head.GetID())
selectionNode.SetActiveLabelVolumeID(headLabel.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# now build:
# create a model using the command line module
# based on the current editor parameters
# - make a new hierarchy node
#
self.delayDisplay("Building...")
parameters = {}
parameters["InputVolume"] = headLabel.GetID()
# create models for all labels
parameters["JointSmoothing"] = True
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene(slicer.mrmlScene)
outHierarchy.SetName("sceneImport2428Hierachy")
slicer.mrmlScene.AddNode(outHierarchy)
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
self.CLINode = None
self.CLINode = slicer.cli.runSync(modelMaker,
self.CLINode,
parameters,
delete_temporary_files=False)
self.delayDisplay("Models built")
success = self.verifyModels()
success = success and (
slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode") > 3)
self.delayDisplay("Test finished")
if success:
self.delayDisplay("Ahh... test passed.")
else:
self.delayDisplay("!$!$!#!@#!@!@$%! Test Failed!!")
self.assertTrue(success)
def TestSection_03_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName(
)
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName(
)
# Use MRHead and Tinypatient for testing
import SampleData
mrVolumeNode = SampleData.downloadSample("MRHead")
[tinyVolumeNode,
tinySegmentationNode] = SampleData.downloadSamples('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(
mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.GetSegmentation().SetMasterRepresentationName(
binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(
mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.
GetReferenceImageGeometryParameterName(), geometryStr)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0, 0.0, 1.0)
segment.AddRepresentation(binaryLabelmapReprName,
segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData(
) # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0, 3, 24.5)
translationTransformMatrix.SetElement(1, 3, 24.5)
translationTransformMatrix.SetElement(2, 3, 11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(
translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(
translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (23, 23, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (24.5, 24.5, 11.5),
(261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter(
'Smoothing factor', '0.0')
self.assertTrue(
tinySegmentationNode.GetSegmentation().CreateRepresentation(
closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(
closedSurfaceReprName)
tinySegmentationNode.Modified(
) # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy)
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(
rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0],
[0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0] * 3
center = [0] * 3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = [x / 2.0 for x in xyz]
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def makeModel(self, modelName='EditorModel', smooth=True):
#
# create a model using the command line module
# based on the current editor parameters
#
volumeNode = EditUtil.getLabelVolume()
if not volumeNode:
return
#
# set up the model maker node
#
parameters = {}
parameters['Name'] = modelName
parameters["InputVolume"] = volumeNode.GetID()
parameters['FilterType'] = "Sinc"
# build only the currently selected model.
parameters['Labels'] = EditUtil.getLabel()
parameters["StartLabel"] = -1
parameters["EndLabel"] = -1
parameters['GenerateAll'] = False
parameters["JointSmoothing"] = False
parameters["SplitNormals"] = True
parameters["PointNormals"] = True
parameters["SkipUnNamed"] = True
if smooth:
parameters["Decimate"] = 0.25
parameters["Smooth"] = 10
else:
parameters["Decimate"] = 0
parameters["Smooth"] = 0
#
# output
# - make a new hierarchy node if needed
#
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
"vtkMRMLModelHierarchyNode")
outHierarchy = None
for n in xrange(numNodes):
node = slicer.mrmlScene.GetNthNodeByClass(
n, "vtkMRMLModelHierarchyNode")
if node.GetName() == "Editor Models":
outHierarchy = node
break
if not outHierarchy:
outHierarchy = slicer.vtkMRMLModelHierarchyNode()
outHierarchy.SetScene(slicer.mrmlScene)
outHierarchy.SetName("Editor Models")
slicer.mrmlScene.AddNode(outHierarchy)
parameters["ModelSceneFile"] = outHierarchy
modelMaker = slicer.modules.modelmaker
#
# run the task (in the background)
# - use the GUI to provide progress feedback
# - use the GUI's Logic to invoke the task
# - model will show up when the processing is finished
#
slicer.cli.run(modelMaker, None, parameters)
slicer.util.showStatusMessage("Model Making Started...", 2000)
