def computeLabelStatistics(self, inputScan, inputLabelMapNode):
""" Use slicer core module to get the min/max intensity value inside the mask.
Returns tuple (min, max) with intensity values inside the mask. """
# Export lapel map node into a segmentation node
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(inputLabelMapNode, segmentationNode)
# Compute statistics (may take time)
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", inputScan.GetID())
# Disable all plugins
for plugin in segStatLogic.plugins:
pluginName = plugin.__class__.__name__
segStatLogic.getParameterNode().SetParameter(f"{pluginName}.enabled", str(False))
# Explicitly enable ScalarVolumeSegmentStatistics
segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.enabled", str(True))
segStatLogic.computeStatistics()
stats = segStatLogic.getStatistics()
# Remove temporary segmentation node
slicer.mrmlScene.RemoveNode(segmentationNode)
segmentId = stats["SegmentIDs"][0]
minIntensityValue = stats[segmentId, "ScalarVolumeSegmentStatisticsPlugin.min"]
maxIntensityValue = stats[segmentId, "ScalarVolumeSegmentStatisticsPlugin.max"]
return minIntensityValue, maxIntensityValue
def getCochleaSize(self):
import SegmentStatistics
# Update time label
lstm = time.time()
print(
"================= Begin Size Calculation ... ====================="
)
volInput = self.inputSelectorCoBx.currentNode()
volSeg = slicer.util.getNode((volInput.GetName() + "S"))
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
volSeg.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
volInput.GetID())
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled", "False")
segStatLogic.computeStatistics()
# Remove old table
nodes = slicer.util.getNodesByClass('vtkMRMLTableNode')
for f in nodes:
if ((f.GetName() == "CochleaStatistics")):
slicer.mrmlScene.RemoveNode(f)
#make a new table
self.resultsTableNode = slicer.vtkMRMLTableNode()
self.resultsTableNode.SetName(
self.inputFnm + "Tbl") #TODO: changet he name to the image+"_t"
segStatLogic.exportToTable(self.resultsTableNode)
for i in range(0, 7):
self.resultsTableNode.RemoveColumn(3)
self.resultsTableNode.GetTable().GetColumn(1).SetName("Size (mm^3)")
self.resultsTableNode.GetTable().GetColumn(2).SetName("Length (mm)")
self.resultsTableNode.SetCellText(0, 0, "Scala Tympani")
self.resultsTableNode.SetCellText(1, 0, "Scala Vestibuli")
self.resultsTableNode.SetCellText(0, 2, str(self.StLength))
self.resultsTableNode.SetCellText(1, 2, "0")
slicer.mrmlScene.AddNode(self.resultsTableNode)
segStatLogic.showTable(self.resultsTableNode)
# generate and show 3D model
volSeg.CreateClosedSurfaceRepresentation()
print("Calculation is done !!! ")
def getCochleaSize(self):
import SegmentStatistics
print("================= Begin Size Calculation ... =====================")
volInput = self.inputVolumeNode
volSeg = slicer.util.getNode((volInput.GetName()+"S"))
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", volSeg.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", volInput.GetID())
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.enabled","False")
segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled","False")
segStatLogic.computeStatistics()
# Remove old table
nodes = slicer.util.getNodesByClass('vtkMRMLTableNode')
for f in nodes:
if ((f.GetName() == "CochleaStatistics") ):
slicer.mrmlScene.RemoveNode(f)
#endif
#endfor
# compute the fiducial length
self.StLength = 0
self.StLength = self.getFiducilsDistance(self.markupsNode)
print(" length = " + str(self.StLength))
#make a new table with few columns
self.resultsTableNode = slicer.vtkMRMLTableNode()
self.resultsTableNode.SetName(self.inputFnm+"Tbl") #TODO: changet he name to the image+"_t"
segStatLogic.exportToTable(self.resultsTableNode)
for i in range (0,7):
self.resultsTableNode.RemoveColumn(3)
#endfor
self.resultsTableNode.GetTable().GetColumn(1).SetName("Size (mm^3)")
self.resultsTableNode.GetTable().GetColumn(2).SetName("Length (mm)")
self.resultsTableNode.SetCellText(0,0,"Scala Tympani")
self.resultsTableNode.SetCellText(1,0,"Scala Vestibuli")
self.resultsTableNode.SetCellText(0,2,str(self.StLength))
self.resultsTableNode.SetCellText(1,2,"0")
slicer.mrmlScene.AddNode(self.resultsTableNode)
segStatLogic.showTable(self.resultsTableNode)
# generate and show 3D model
volSeg.CreateClosedSurfaceRepresentation()
print("Measurements are completed !!! ")
def findVolume(self, segment):
# TODO: labelmap volume is more accurate: switch to labelmap based volume calculation
segStats = SegmentStatistics.SegmentStatisticsLogic()
#//params = segStats.getParameterNode()
table = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
segStats.getParameterNode().SetParameter(
"LabelMapSegmentStatisticsPlugin.enabled", str(False))
segStats.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.enabled", str(False))
segStats.getParameterNode().SetParameter("Segmentation", segment)
segStats.getParameterNode().SetParameter("MeasurementsTable",
table.GetID())
segStats.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.enabled", str(True))
segStats.getParameterNode().SetParameter("visibleSegmentsOnly",
str(False))
segStats.computeStatistics()
#//segStats.updateStatisticsForSegment(segment)
segStats.exportToTable(table)
segStats.showTable(table)
def onApplySButton(self):
""" This function takes advantage of the functions of the Segment Statistics module to assess the statistics of the segmentation"""
self.stats = {}
self.NofV = 1
self.logic = SegmentStatistics.SegmentStatisticsLogic()
self.parameterNode = self.logic.getParameterNode()
self.parameterNode.SetParameter(
"Segmentation",
self.segmentationSelector.currentNode().GetID())
self.parameterNode.SetParameter(
'ClosedSurfaceSegmentStatisticsPlugin.enabled', 'False')
self.parameterNode.SetParameter(
'LabelmapSegmentStatisticsPlugin.enabled', 'True')
self.parameterNode.SetParameter(
'LabelmapSegmentStatisticsPlugin.volume_cm3.enabled', 'False')
self.parameterNode.SetParameter(
'LabelmapSegmentStatisticsPlugin.volume_mm3.enabled', 'False')
self.parameterNode.SetParameter(
'LabelmapSegmentStatisticsPlugin.voxel_count.enabled', 'False')
self.parameterNode.SetParameter(
'LabelmapSegmentStatisticsPlugin.surface_area_mm2.enabled', 'True')
if self.scalarSelector.currentNode():
self.parameterNode.SetParameter(
"ScalarVolume",
self.scalarSelector.currentNode().GetID())
self.GetStats(self.scalarSelector.currentNode())
if self.scalarSelector2.currentNode():
self.parameterNode.SetParameter(
"ScalarVolume",
self.scalarSelector2.currentNode().GetID())
self.GetStats(self.scalarSelector2.currentNode())
try:
self.ROImean = np.array(self.stats['Mean'])
except:
self.ROImean = [0]
self.PopulateTableStats()
def computeImplantVolumeCc(self, inputVolume, segmentationNode,
implantSegmentId):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param inputVolume: volume to be thresholded
:param outputVolume: thresholding result
:param imageThreshold: values above/below this threshold will be set to 0
:param invert: if True then values above the threshold will be set to 0, otherwise values below are set to 0
:param showResult: show output volume in slice viewers
"""
if not inputVolume:
raise ValueError("Input volume is invalid")
masterVolumeNode = inputVolume
# Compute segment volumes
import SegmentStatistics
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.volume_mm3.enabled", "False")
segStatLogic.computeStatistics()
# print(segStatLogic.getStatistics()) # prints all computed metrics
implantVolumeCc = segStatLogic.getStatistics()[
implantSegmentId, "ScalarVolumeSegmentStatisticsPlugin.volume_cm3"]
logging.info("Processing result: " + str(implantVolumeCc))
return implantVolumeCc
"""
def run(self,
inputVolume,
imageThreshold_min,
imageThreshold_max,
minimumVoxelsize,
tls_per_min,
enableScreenshots=0):
"""
Run the actual algorithm
"""
if not self.isValidInputData(inputVolume):
slicer.util.errorDisplay('Input volume error.')
return False
logging.info('Processing started')
masterVolumeNode = inputVolume
# Create segmentation
SegmentationNodeCol = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLSegmentationNode")
SegmentationNodeCol.UnRegister(slicer.mrmlScene)
b = True
for SegmentationNode in SegmentationNodeCol:
if SegmentationNode.GetName() == "rc_seg":
SegmentationNode.GetSegmentation().RemoveAllSegments()
SegmentationNode.GetDisplayNode(
).ClearSegmentDisplayProperties()
print("segmantation rc_seg cleared ")
b = False
break
if b:
SegmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
SegmentationNode.UnRegister(slicer.mrmlScene)
SegmentationNode.SetName("rc_seg")
print("segmantation created : ", SegmentationNode.GetName())
SegmentationNode.CreateDefaultDisplayNodes(
) # only needed for display
SegmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
addedSegmentID = SegmentationNode.GetSegmentation().AddEmptySegment(
SegmentationNode.GetName() + "_")
# Create temporary segment editor to get access to effects
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorNode.SetSelectedSegmentID(addedSegmentID)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(SegmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
# Fill by thresholding
effect.setParameter("MinimumThreshold", str(imageThreshold_min))
effect.setParameter("MaximumThreshold", str(imageThreshold_max))
effect.self().onApply()
# Fill by thresholding
if minimumVoxelsize is not None:
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", "SPLIT_ISLANDS_TO_SEGMENTS")
effect.setParameter("MinimumSize", minimumVoxelsize)
effect.self().onApply()
# Compute segment volumes
resultsTableNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLTableNode')
resultsTableNode.UnRegister(slicer.mrmlScene)
import SegmentStatistics
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
SegmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.surface_mm2.enabled",
"False")
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.volume_cm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.volume_mm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.volume_cm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.volume_mm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.voxel_count.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.enabled", "True")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.max.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.mean.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.median.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.min.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.stdev.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.volume_mm3.enabled", "True")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.volume_cm3.enabled", "True")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled", "False")
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
col = resultsTableNode.AddColumn()
col.SetName("Time of lithotripsy [min:sec:1/100s]")
id_colone_vmm3 = resultsTableNode.GetColumnIndex("Volume [mm3]")
id_colone_Tl = resultsTableNode.GetColumnIndex(
"Time of lithotripsy [min:sec:1/100s]")
import math
for i in range(resultsTableNode.GetNumberOfRows()):
vol_i = float(resultsTableNode.GetCellText(i, id_colone_vmm3))
tl_i = math.modf(vol_i / tls_per_min)
tl_i_min = int(tl_i[1])
tli_1 = math.modf(60. * tl_i[0])
tli_sec = int(tli_1[1])
tli_cent = 100 * tli_1[0]
resultsTableNode.SetCellText(
i, id_colone_Tl,
"{:d}:{:d}:{:.0f}".format(tl_i_min, tli_sec, tli_cent))
segStatLogic.showTable(resultsTableNode)
logging.info('Processing completed !')
return True
#Turn mask range on
segmentEditorNode.MasterVolumeIntensityMaskOn()
#smoothing the cochlea
# Smoothing effect
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("SmoothingMethod", "MEDIAN")
effect.setParameter("KernelSizeMm", 0.3)
effect.self().onApply()
#Turn mask range off
segmentEditorNode.MasterVolumeIntensityMaskOff()
## Create table
resultsTableNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode')
## Use segmentStatistics to calculate the volume and export
import SegmentStatistics
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.enabled","False")
segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled","False")
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
#prepare and save the segmentation
seg = getNode('Segmentation')
##Get the segment vtk representation
segmentationNode = getNode("vtkMRMLSegmentationNode1")
cochlea_vtk = segmentationNode.GetSegmentation().GetSegment(cochlea)
##Create Model
modelNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode')
##Export segment to model