removing redundant script files

Author: jzeyl

.Rhistory

@@ -4,6 +4,10 @@
 # Load dry bone CT of skull into the scene and run this script to automatically segment endocranium
 #slicer.util.loadVolume("C:\\Users\\jeffzeyl\\Desktop\\RD01r2_2019\\pigeon0000.tif", returnNode=True)
 
+slicer.util.loadVolume(r"C:\Users\jeffz\Desktop\copyoutput\Jun5 batch\Pcrow\crowbetter0000.tif", returnNode=True)
+spacing = 0.021875#set resolution
+ID = "PCrow"
+
 masterVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
 #or can get the volume node by the name slicer.util.getNode('pigeon0000')
 #print(mastervolumeNode)
@@ -75,173 +79,3 @@
 Otsu_thresholdCalculator.Update()
 Otsuval = Otsu_thresholdCalculator.GetThreshold()
 
-#MAX ENTROPY THRESHOLD OF COLUMELLA
-#OverwriteMode: OverwriteNone
-#SelectedSegmentID: threshcol
-#ActiveEffectName: "Threshold"
-#MaskMode: PaintAllowedInsideSingleSegment #segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideVisibleSegments)
-#MaskSegmentID: paintcol
-threshcol = segmentationNode.GetSegmentation().AddEmptySegment(ID+" thresh col")
-segmentEditorWidget.setActiveEffectByName("Threshold")
-segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteNone)
-segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideSingleSegment)
-segmentEditorNode.SetSelectedSegmentID(ID+" thresh col")
-segmentEditorNode.SetMaskSegmentID(ID+" paint col")
-effect = segmentEditorWidget.activeEffect()
-effect.setParameter("MinimumThreshold", str(Maxentval))
-effect.setParameter("MaximumThreshold",str(volumeScalarRange[1]))
-effect.self().onApply()#apply separate
-
-#run keep largest island on thresholded columella
-segmentEditorWidget.setActiveEffectByName("Islands")
-effect = segmentEditorWidget.activeEffect()
-segmentEditorNode.SetSelectedSegmentID(ID+" thresh col")
-effect.setParameterDefault("Operation", "KEEP_LARGEST_ISLAND")
-
-effect.self().onApply()#apply separate
-
-#quantification table
-#resultsTableNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode')# create table node
-#import SegmentStatistics
-#segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
-#segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
-#segStatLogic.getParameterNode().SetParameter("ScalarVolume", os.listdir(folder)[0].replace('.tif',''))############change here to the named volume
-#segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.enabled","False")
-#segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled","False")
-#segStatLogic.computeStatistics()
-#segStatLogic.exportToTable(resultsTableNode)
-#segStatLogic.showTable(resultsTableNode)
-
-#OR STORE STATS AS DICTIONARY:
-import SegmentStatistics
-segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
-segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
-#segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_origin_ras.enabled",str(True))
-#segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_diameter_mm.enabled",str(True))
-#segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_direction_ras_x.enabled",str(True))
-#segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_direction_ras_y.enabled",str(True))
-#segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_direction_ras_z.enabled",str(True))
-segStatLogic.computeStatistics()
-stats = segStatLogic.getStatistics()
-#x = thisdict["model"]
-#stats['BS01-2019 thresh col']
-#colvol = stats[ID+" thresh col", 'ClosedSurfaceSegmentStatisticsPlugin.volume_mm3']
-colvol = stats[ID+" thresh col",'LabelmapSegmentStatisticsPlugin.volume_mm3']
-'KW01 thresh col', 'LabelmapSegmentStatisticsPlugin.volume_mm3'
-'KW01 thresh col', 'LabelmapSegmentStatisticsPlugin.volume_mm3'
-
-#Write to text file
-# with is like your try .. finally block in this case
-with open('C:\\Users\\jeffzeyl\\Desktop\\Volumes.txt', 'r') as file:
-    # read a list of lines into data
-    data = file.readlines()
-
-data.append(ID+', '+str(colvol)+'\n')
-
-# and write everything back
-with open('C:\\Users\\jeffzeyl\\Desktop\\Volumes.txt', 'w') as file:
-    file.writelines( data )
-#
-#
-
-
-#MAX ENTROPY THRESHOLD OF ECD
-segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteNone)
-segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideSingleSegment)
-segmentEditorNode.SetSelectedSegmentID(ID+" thresh ECD")
-segmentEditorNode.SetMaskSegmentID(ID+" paint ECD")
-segmentEditorWidget.setActiveEffectByName("Threshold")
-effect = segmentEditorWidget.activeEffect()
-#effect.setParameter("AutoThresholdMode",'SET_MIN_UPPER')
-#effect.setParameter("AutoThresholdMethod","MAXIMUM_ENTROPY")#maximum entropy algorithm
-effect.setParameter("MinimumThreshold", str(0))
-effect.setParameter("MaximumThreshold",str(Maxentval))
-
-effect.self().onApply()#apply separate
-
-#run KEEP LARGEST ISLAND on ECD tip
-segmentEditorWidget.setActiveEffectByName("Islands")
-effect = segmentEditorWidget.activeEffect()
-segmentEditorNode.SetSelectedSegmentID(ID+" thresh ECD")
-effect.setParameterDefault("Operation", "KEEP_LARGEST_ISLAND")
-
-effect.self().onApply()#apply separate
-
-#moments/ISODATA-MAXENT THRESHOLD FOR UMBO
-segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteNone)
-effect = segmentEditorWidget.activeEffect()
-segmentEditorNode.SetMaskMode(slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideSingleSegment)
-segmentEditorNode.SetSelectedSegmentID(ID+" thresh umbo")
-segmentEditorNode.SetMaskSegmentID(ID+" paint umbo")
-segmentEditorWidget.setActiveEffectByName("Threshold")
-effect.setParameter("MinimumThreshold", str(ISOval))#//str(Momentsval),str(ISOval)
-effect.setParameter("MaximumThreshold",str(Maxentval))
-
-effect.self().onApply()#apply separate
-
-#remove visibility of painted segments
-segmentationNodedisplaynode = segmentationNode.GetDisplayNode()#make display node
-
-segmentationNodedisplaynode.SetSegmentVisibility2DFill(ID+" paint col", 0)
-segmentationNodedisplaynode.SetSegmentVisibility2DOutline(ID+" paint col", 0)
-segmentationNodedisplaynode.SetSegmentVisibility3D(ID+" paint col", 0)
-
-segmentationNodedisplaynode.SetSegmentVisibility2DFill(ID+" paint umbo", 0)
-segmentationNodedisplaynode.SetSegmentVisibility2DOutline(ID+" paint umbo", 0)
-segmentationNodedisplaynode.SetSegmentVisibility3D(ID+" paint umbo", 0)
-
-segmentationNodedisplaynode.SetSegmentVisibility2DFill(ID+" paint ECD", 0)
-segmentationNodedisplaynode.SetSegmentVisibility2DOutline(ID+" paint ECD", 0)
-segmentationNodedisplaynode.SetSegmentVisibility3D(ID+" paint ECD", 0)
-
-segmentationNodedisplaynode.SetSegmentVisibility2DFill(ID+" thresh ECD", 1)
-
-#TO DO - default settings paint for umbo. - 3d sphere
-#TO DO - threshold Umbo - lower iso
-
-#show segmentation in 3D
-segmentationNode.CreateClosedSurfaceRepresentation()
-
-#OTHER FIDUCIAL CODE< MAY BE USEFUL:
-# Get point positions as numpy array
-#import numpy as np
-#nOfFiduciallPoints = FIDNode5.GetNumberOfFiducials()
-#points = np.zeros([nOfFiduciallPoints,3])
-#for i in range(0, nOfFiduciallPoints):
-#  FIDNode5.GetNthFiducialPosition(i, points[i,:])
-#
-#points[2][1]
-#points[2][1]
-
-#Change markup fiducial display properties
-#Display properties are stored in display node(s) associated with the fiducial node.
-#defaultMarkupsDisplayNode = slicer.vtkMRMLMarkupsDisplayNode()
-#defaultMarkupsDisplayNode.SetGlyphScale(0.3)
-#defaultMarkupsDisplayNode.SetTextScale(0.3)
-#slicer.mrmlScene.AddDefaultNode(defaultMarkupsDisplayNode)
-#
-#fiducialNode = getNode('F')
-#fiducialDisplayNode = fiducialNode.GetDisplayNode()
-#fiducialDisplayNode.SetSelectedColor(1,1,0) # Set color to yellow
-#
-#fiducialDisplayNode.SetVisibility(False) # Hide all points
-#fiducialDisplayNode.SetVisibility(True) # Show all points
-#fiducialDisplayNode.SetViewNodeIDs(["vtkMRMLSliceNodeRed", "vtkMRMLViewNode1"]) # Only show in red slice view and first 3D view
-##################################################################################333
-
-##fidNode = getNode("vtkMRMLMarkupsFiducialNode1")
-##n = fidNode.AddFiducial(4.0, 5.5, -6.0)
-##fidNode.SetNthFiducialLabel(n, "new label")
-### each markup is given a unique id which can be accessed from the superclass level
-##id1 = fidNode.GetNthMarkupID(n)
-### manually set the position
-##fidNode.SetNthFiducialPosition(n, 6.0, 7.0, 8.0)
-### set the label
-##fidNode.SetNthFiducialLabel(n, "New label")
-### set the selected flag, only selected = 1 fiducials will be passed to CLIs
-##fidNode.SetNthFiducialSelected(n, 1)
-### set the visibility flag
-##fidNode.SetNthFiducialVisibility(n, 0)  
-
-# Make segmentation results visible in 3D
-#segmentationNode.CreateClosedSurfaceRepresentation()