Add files via upload

Author: jzeyl

functions_baffle planner.py

@@ -0,0 +1,97 @@
+
+def subtract():
+  """
+  Subtracts the skull (first segment) from the baffle (second segment)
+  """
+  masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')
+  segmentationNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLSegmentationNode')
+  segmentationNode.CreateDefaultDisplayNodes() # only needed for display
+  segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
+  # Create segment editor to get access to effects
+  segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
+  segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
+  segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
+  segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
+  segmentEditorWidget.setSegmentationNode(segmentationNode)
+  segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
+  #getnames
+  bafflename = segmentationNode.GetSegmentation().GetNthSegment(1).GetName()#get name of baffle
+  skullname = segmentationNode.GetSegmentation().GetNthSegment(0).GetName()#get name of skull
+  ##run subtaction
+  segmentEditorWidget.setActiveEffectByName('Logical operators')
+  effect = segmentEditorWidget.activeEffect()
+  segmentEditorNode.SetSelectedSegmentID(bafflename)######perform operations
+  effect.setParameter("Operation", "SUBTRACT")
+  effect.setParameter("ModifierSegmentID", skullname)#subtract this selection
+  effect.self().onApply()
+  #remove segment editor connection
+  segmentEditorWidget = None
+  slicer.mrmlScene.RemoveNode(segmentEditorNode)
+
+
+def smooth(mm):
+  """
+  Smooth the baffle (the second segment) using median smoothing. Takes an argument in mm.
+  """
+  masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')
+  segmentationNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLSegmentationNode')
+  segmentationNode.CreateDefaultDisplayNodes() # only needed for display
+  segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
+  # Create segment editor to get access to effects
+  segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
+  segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
+  segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
+  segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
+  segmentEditorWidget.setSegmentationNode(segmentationNode)
+  segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
+  #getnames of segments in segmentation
+  bafflename = segmentationNode.GetSegmentation().GetNthSegment(1).GetName()#get name of baffle
+  skullname = segmentationNode.GetSegmentation().GetNthSegment(0).GetName()#get name of skull
+  ##run Smoothing
+  segmentEditorWidget.setActiveEffectByName("Smoothing")
+  effect = segmentEditorWidget.activeEffect()
+  segmentEditorNode.SetSelectedSegmentID(bafflename)
+  effect.setParameter("SmoothingMethod", "MEDIAN")
+  effect.setParameter("KernelSizeMm", mm)
+  effect.self().onApply()
+  #remove segment editor connection
+  segmentEditorWidget = None
+  slicer.mrmlScene.RemoveNode(segmentEditorNode)
+
+
+def connect():
+  """
+  Connects the segmentation and volume nodes together in preparation for subsequent functions. Adds a segmentation node to the scene
+  """
+  global masterVolumeNode
+  #Connect the volumes and segmentation to allow programatic access to model-segmentation conversion and segmentation effects
+  masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')#detects the first scalar volume
+  global segmentationNode
+  segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
+  segmentationNode.CreateDefaultDisplayNodes() # only needed for display
+  segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
+
+def modelToSeg():
+  """
+  Converts model and baffle to segmentations. Takes the first and second models in the scene (besides from the 3 slice models already present in the 
+  scene by default). Skull should be the first model, baffle the second.
+  """
+  modelskull = slicer.mrmlScene.GetNthNodeByClass(3, 'vtkMRMLModelNode')
+  modelbaffle = slicer.mrmlScene.GetNthNodeByClass(4, 'vtkMRMLModelNode')
+  # Import the model into the segmentation node
+  slicer.modules.segmentations.logic().ImportModelToSegmentationNode(modelskull, segmentationNode)
+  slicer.modules.segmentations.logic().ImportModelToSegmentationNode(modelbaffle, segmentationNode)
+
+
+def seg_to_obj(path, segmentationNode):
+  """
+  Convert baffle to obj. Converts the second segmentation. Takes as arguments the name of the segmentation("Segmentation" by default), and saves an obj file as the name of the segmentation .
+  Example usage: seg_to_obj("c:/tmp", "Segmentation")
+  """
+  segmentationNode = getNode(segmentationNode)
+  bafflename = segmentationNode.GetSegmentation().GetNthSegment(1).GetName()#get name of baffle
+  segmentIds = vtk.vtkStringArray()
+  segmentIds.InsertNextValue(bafflename)
+  # Write to STL file
+  slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsClosedSurfaceRepresentationToFiles(path, segmentationNode, segmentIds, "OBJ")
+

load_dicom_modified_otsu.py

@@ -0,0 +1,73 @@
+loadedNodeIDs = []  # this list will contain the list of all loaded node IDs
+
+
+#Imports the necessary libraries and modules for loading DICOM files and creating a surface mesh from a volume node using CLI module.
+import argparse
+import DICOMLib.DICOMUtils as utils
+import DICOMScalarVolumePlugin
+
+
+#Create command line arguments using argparse module and then parses them using parse_args() method.
+parser = argparse.ArgumentParser(description='Load dicom')
+parser.add_argument('-f', '--folder', type=str, help='DICOM FOLDER PATH', required=True)
+args = parser.parse_args()
+
+#Use DICOMScalarVolumePlugin module to load the scalar volume reader.
+from DICOMLib import DICOMUtils
+with DICOMUtils.TemporaryDICOMDatabase() as db:
+  DICOMUtils.importDicom(args.folder, db)
+  patientUIDs = db.patients()
+  for patientUID in patientUIDs:
+    loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
+
+
+
+#Creates a surface mesh from volume node using CLI module grayscale model maker. Threshold is set as a parameter
+#Adds ' skull' to the name of the volume as name of model
+def modelFromVolume(thresh):
+  """Create surface mesh from volume node using CLI module"""
+  global volumeNode
+  volumeNode = slicer.mrmlScene.GetNthNodeByClass(0,"vtkMRMLScalarVolumeNode")
+  # Set parameters
+  parameters = {}
+  parameters["InputVolume"] = volumeNode
+  parameters["Threshold"] = thresh
+  global outputModelNode
+  outputModelNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelNode")
+  outputModelNode.SetName(volumeNode.GetName()+' skull')
+  volumeNode.GetName()
+  parameters["OutputGeometry"] = outputModelNode
+  # Execute
+  grayMaker = slicer.modules.grayscalemodelmaker
+  cliNode = slicer.cli.runSync(grayMaker, None, parameters)
+  # Process results
+  if cliNode.GetStatus() & cliNode.ErrorsMask:
+    # error
+    errorText = cliNode.GetErrorText()
+    slicer.mrmlScene.RemoveNode(cliNode)
+    raise ValueError("CLI execution failed: " + errorText)
+  # success
+  slicer.mrmlScene.RemoveNode(cliNode)
+  return outputModelNode
+
+
+#get otsu threshold
+masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')
+import vtkITK
+Otsu_thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
+Otsu_thresholdCalculator.SetInputData(masterVolumeNode.GetImageData())
+Otsu_thresholdCalculator.SetMethodToOtsu()
+Otsu_thresholdCalculator.Update()
+Otsuval = Otsu_thresholdCalculator.GetThreshold()
+#print('Otsu threshold is: ' + Otsuval)
+#get max value in volume
+otsu_int = int(Otsuval)
+print("Otsu threshold is:")
+print(otsu_int)
+
+try:
+  modelFromVolume(otsu_int)
+except:
+  print("failed to create model")
+
+