def run(input_fpath, output_fpath, input_node_name=None):
assert _recent_opr_nodes == []
input_node = None
if input_node_name is not None:
input_node = getNode(input_node_name)
if input_node is None:
input_node = _load_volume(input_fpath, input_node_name)
atlas_volume, atlas_mask = _get_atlas_nodes()
output_volume_node = slicer.vtkMRMLScalarVolumeNode()
output_mask_node = slicer.vtkMRMLScalarVolumeNode()
output_volume_node.SetName('{}-output'.format(input_node.GetName()))
output_mask_node.SetName('{}-mask'.format(input_node.GetName()))
slicer.mrmlScene.AddNode(output_volume_node)
slicer.mrmlScene.AddNode(output_mask_node)
output_mask_node.LabelMapOn()
params = {
'atlasMRIVolume': atlas_volume.GetID(),
'atlasMaskVolume': atlas_mask.GetID(),
'patientVolume': input_node.GetID(),
'patientOutputVolume': output_volume_node.GetID(),
'patientMaskLabel': output_mask_node.GetID()
}
cli_node = slicer.cli.run(slicer.modules.swissskullstripper,
None,
params,
wait_for_completion=True)
# cli_node.AddObserver('ModifiedEvent', _on_status_modified)
_recent_opr_nodes[:] = [
input_node, output_volume_node, output_mask_node, output_fpath
]
_on_finished()
def run(input_fpath, output_fpath, input_node_name=None):
assert _recent_opr_nodes == []
input_node = None
if input_node_name is not None:
input_node = getNode(input_node_name)
if input_node is None:
input_node = _load_volume(input_fpath, input_node_name)
atlas_volume, atlas_mask = _get_atlas_nodes()
output_volume_node = slicer.vtkMRMLScalarVolumeNode()
output_mask_node = slicer.vtkMRMLScalarVolumeNode()
output_volume_node.SetName('{}-output'.format(input_node.GetName()))
output_mask_node.SetName('{}-mask'.format(input_node.GetName()))
slicer.mrmlScene.AddNode(output_volume_node)
slicer.mrmlScene.AddNode(output_mask_node)
output_mask_node.LabelMapOn()
params = {
'atlasMRIVolume': atlas_volume.GetID(),
'atlasMaskVolume': atlas_mask.GetID(),
'patientVolume': input_node.GetID(),
'patientOutputVolume': output_volume_node.GetID(),
'patientMaskLabel': output_mask_node.GetID()
}
cli_node = slicer.cli.run(slicer.modules.swissskullstripper, None, params,
wait_for_completion=True)
# cli_node.AddObserver('ModifiedEvent', _on_status_modified)
_recent_opr_nodes[:] = [
input_node, output_volume_node, output_mask_node, output_fpath]
_on_finished()
def run(input_fpath, output_fpath, input_node_name=None):
assert _recent_opr_nodes == []
input_node = None
if input_node_name is not None:
input_node = getNode(input_node_name)
if input_node is None:
input_node = _load_volume(input_fpath, input_node_name)
slicer.util.saveNode(input_node, output_fpath + '.nii.gz')
def run(input_fpath, output_fpath, input_node_name=None):
assert _recent_opr_nodes == []
input_node = None
if input_node_name is not None:
input_node = getNode(input_node_name)
if input_node is None:
input_node = _load_volume(input_fpath, input_node_name)
slicer.util.saveNode(input_node, output_fpath + '.nii.gz')
def calculateNeedleToCoronalAngle(
self): #calculates angle between needle and coronal plane
needleModelToNeedleTipNode = getNode('NeedleModelToNeedleTip')
needleToRas = vtk.vtkMatrix4x4()
needleModelToNeedleTipNode.GetMatrixTransformToWorld(needleToRas)
directionVector = numpy.dot(self.arrayFromVtkMatrix(needleToRas),
numpy.array([0, 0, 1, 0]))
coronalPlane = numpy.array([0, 1, 0, 0])
self.calculateAngle(directionVector, coronalPlane)
def _get_atlas_nodes(volume_name='atlasImage',
mask_name='atlasMask',
volume_path='data/atlasImage.mha',
mask_path='data/atlasMask.mha'):
volume_node = getNode(volume_name)
mask_node = getNode(mask_name)
if volume_node is not None and mask_node is not None:
return volume_node, mask_node
fname = __file__
if fname.endswith('.pyc'):
fname = fname[:-1]
basedir = os.path.dirname(os.path.realpath(fname))
p = lambda v: os.path.join(basedir, v)
if volume_node is None:
volume_node = _load_volume(p(volume_path), volume_name)
if mask_node is None:
mask_node = _load_volume(p(mask_path), mask_name)
mask_node.LabelMapOn()
return volume_node, mask_node
def _get_atlas_nodes(volume_name='atlasImage',
mask_name='atlasMask',
volume_path='data/atlasImage.mha',
mask_path='data/atlasMask.mha'):
volume_node = getNode(volume_name)
mask_node = getNode(mask_name)
if volume_node is not None and mask_node is not None:
return volume_node, mask_node
fname = __file__
if fname.endswith('.pyc'):
fname = fname[:-1]
basedir = os.path.dirname(os.path.realpath(fname))
p = lambda v: os.path.join(basedir, v)
if volume_node is None:
volume_node = _load_volume(p(volume_path), volume_name)
if mask_node is None:
mask_node = _load_volume(p(mask_path), mask_name)
mask_node.LabelMapOn()
return volume_node, mask_node
def loadRecordingSequences(self, recordingFile):
logging.debug("loading \'recording\' sequences")
recordingFileBaseName = os.path.splitext(
os.path.basename(recordingFile))[0]
slicer.app.coreIOManager().loadNodes('Sequence Metafile',
{'fileName': recordingFile})
self.recordingData_browserNode = slicer.mrmlScene.GetFirstNodeByName(
recordingFileBaseName)
self.recordingData_trackerToReferenceNode = self.initializeLinearTransformNode(
recordingFileBaseName + "-TrackerToReference")
self.recordingData_needleToTrackerNode = self.initializeLinearTransformNode(
recordingFileBaseName + "-NeedleToTracker")
self.recordingData_cauteryToTrackerNode = self.initializeLinearTransformNode(
recordingFileBaseName + "-CauteryToTracker")
self.probeToTrackerNode = self.initializeLinearTransformNode(
recordingFileBaseName + "-ProbeToTracker")
self.imageToTransducerNode = self.initializeLinearTransformNode(
recordingFileBaseName + "-ImageToTransducer")
self.imageNode = getNode(recordingFileBaseName + "-Image")
self.trackerToReferenceNode = self.recordingData_trackerToReferenceNode
self.cauteryToTrackerNode = self.recordingData_cauteryToTrackerNode
self.needleToTrackerNode = self.recordingData_needleToTrackerNode
self.setupResliceDriver()
def showUltrasound(self, volumeNode):
resliceLogic = modules.volumereslicedriver.logic()
if resliceLogic == None:
logging.error(
"Volume reslice driver module not found! Install SlicerIGT extension."
)
return
redNode = getNode('vtkMRMLSliceNodeRed')
resliceLogic.SetDriverForSlice(volumeNode.GetID(), redNode)
resliceLogic.SetModeForSlice(6, redNode) # Transverse mode
resliceLogic.SetFlipForSlice(False, redNode)
resliceLogic.SetRotationForSlice(180, redNode)
redSliceLogic = self.layoutManager.sliceWidget('Red').sliceLogic()
redSliceLogic.GetSliceCompositeNode().SetBackgroundVolumeID(
volumeNode.GetID())
redSliceLogic.FitSliceToAll()
# Show red slice in 3D viewer
sliceWidget = app.layoutManager().sliceWidget('Red')
sliceLogic = sliceWidget.sliceLogic()
sliceNode = sliceLogic.GetSliceNode()
sliceNode.SetSliceVisible(True)
def setTransforms(self): #Run the actual algorithm
logging.info('Setting up data for evaluation')
# Get all nodes of models and transforms
trackerToReferenceNode = getNode('*TrackerToReferenceTransform [*')
probeToTrackerNode = getNode('*ProbeToTrackerTransform [*')
needleToTrackerNode = getNode('*NeedleToTrackerTransform [*')
imageToTransducerNode = getNode('*ImageToTransducerTransform [*')
imageNode = getNode('*Image [*')
referenceToRasNode = getNode('ReferenceToRas')
transducerToProbeNode = getNode('TransducerToProbe')
tumorModelNode = getNode('TumorModel')
needleModelToNeedleTipNode = getNode('NeedleModelToNeedleTip')
needleTipToNeedleNode = getNode('NeedleTipToNeedle')
# Create needle model
needleModelNode = modules.createmodels.logic().CreateNeedle(
80, 1.0, 2.5, 0)
needleModelNode.GetDisplayNode().SetColor(0, 1, 1)
needleModelNode.SetName("NeedleModel")
needleModelNode.GetDisplayNode().SliceIntersectionVisibilityOn()
# Set image to RAS hierarchy
imageNode.SetAndObserveTransformNodeID(imageToTransducerNode.GetID())
imageToTransducerNode.SetAndObserveTransformNodeID(
transducerToProbeNode.GetID())
transducerToProbeNode.SetAndObserveTransformNodeID(
probeToTrackerNode.GetID())
probeToTrackerNode.SetAndObserveTransformNodeID(
trackerToReferenceNode.GetID())
trackerToReferenceNode.SetAndObserveTransformNodeID(
referenceToRasNode.GetID())
# Set needle and tumor to RAS hierarchy
needleModelToNeedleTipNode.SetAndObserveTransformNodeID(
needleTipToNeedleNode.GetID())
needleModelNode.SetAndObserveTransformNodeID(
needleModelToNeedleTipNode.GetID())
needleToTrackerNode.SetAndObserveTransformNodeID(
trackerToReferenceNode.GetID())
needleTipToNeedleNode.SetAndObserveTransformNodeID(
needleToTrackerNode.GetID())
tumorModelNode.SetAndObserveTransformNodeID(
needleToTrackerNode.GetID())
needleModelNode.GetDisplayNode().SetColor(0, 1, 1)
needleModelNode.GetDisplayNode().SetSliceIntersectionVisibility(1)
tumorModelNode.GetDisplayNode().SetColor(0, 1, 0)
tumorModelNode.GetDisplayNode().SetOpacity(0.5)
tumorModelNode.GetDisplayNode().SetSliceIntersectionVisibility(1)
# Center 3D view
layoutManager = app.layoutManager()
threeDWidget = layoutManager.threeDWidget(0)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
self.showUltrasound(imageNode)
logging.info('Set up complete, data ready for evaluation')
return True