This repository show some sample python scripts for some convenience functions such as exporting to LMs to obscure format. You can use these examples to modify develop your own scripts for specific functions.
import os, glob, numpy
def convertMorphoJLM(inputFileDirectory, outputLandmarkFile)
extensionInput = ".mrk.json"
fileList = glob.glob(inputDirectory+"*.json")
success, currentLMNode = slicer.util.loadMarkupsFiducialList(fileList[0])
subjectNumber = len(fileList)
landmarkNumber = currentLMNode.GetNumberOfFiducials()
LMArray=numpy.zeros(shape=(subjectNumber,landmarkNumber,3))
fileIndex=0
fileStems=[];
headerLM = ["Subject"]
for pointIndex in range(currentLMNode.GetNumberOfMarkups()):
headerLM.append(currentLMNode.GetNthControlPointLabel(pointIndex)+'_X')
headerLM.append(currentLMNode.GetNthControlPointLabel(pointIndex)+'_Y')
headerLM.append(currentLMNode.GetNthControlPointLabel(pointIndex)+'_Z')
LPS = [-1,-1,1]
point = [0,0,0]
for file in fileList:
if fileIndex>0:
success, currentLMNode = slicer.util.loadMarkupsFiducialList(file)
fileStems.append(os.path.basename(file.split(extensionInput)[0]))
for pointIndex in range(currentLMNode.GetNumberOfMarkups()):
point=currentLMNode.GetNthControlPointPositionVector(pointIndex)
point.Set(point[0]*LPS[0],point[1]*LPS[1],point[2]*LPS[2])
LMArray[fileIndex, pointIndex,:]=point
slicer.mrmlScene.RemoveNode(currentLMNode)
fileIndex+=1
temp = numpy.column_stack((numpy.array(fileStems), LMArray.reshape(subjectNumber, int(3 * landmarkNumber))))
temp = numpy.vstack((numpy.array(headerLM), temp))
numpy.savetxt(outputLandmarkFile, temp, fmt="%s", delimiter=",")This example shows how to interact with a variety of Slicer modules via Python to create an automated imaging pipeline. The function takes a folder of volumes (NRRD or NII.GZ) extension) and for each volume will:
- Auto-threshold (OTSU)
- Run connected components (selecting the largest component)
- Create a model from the segmentation
- Use surface toolbox to decimate the model 80%
- Save the resultant model in OBJ format to the input folder
def slicerScriptingExampleFunction(inputPath):
import os
# Setup the SurfaceToolboxWidget to access logic functions
try:
slicer.modules.SurfaceToolboxWidget
except:
currentModule = slicer.util.selectedModule()
slicer.util.selectModule('SurfaceToolbox')
slicer.util.selectModule(currentModule)
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
# Loop over and process each file in the inputPath
for inputFilename in os.listdir(inputPath):
# Check for valid extensions
fn, ext = os.path.splitext(inputFilename)
if (ext.lower() != '.nrrd'):
fn2, ext2 = os.path.splitext(fn)
if (ext2+ext.lower() != '.nii.gz'):
print("skipping ", inputFilename)
continue
# Load volume and set up segmentation
inputFilePath = os.path.join(inputPath, inputFilename)
volumeNode = slicer.util.loadVolume(inputFilePath)
segNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segNode.SetReferenceImageGeometryParameterFromVolumeNode(volumeNode)
addedSegmentID = segNode.GetSegmentation().AddEmptySegment("total")
segmentEditorWidget.setSegmentationNode(segNode)
segmentEditorWidget.setMasterVolumeNode(volumeNode)
# Compute OTSU threshold
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(volumeNode.GetImageData())
thresholdCalculator.SetMethodToOtsu()
thresholdCalculator.Update()
OTSUThresholdValue = thresholdCalculator.GetThreshold()
volumeScalarRange = volumeNode.GetImageData().GetScalarRange()
# Thresholding with OTSU level
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(OTSUThresholdValue))
effect.setParameter("MaximumThreshold",str(volumeScalarRange[1]))
effect.self().onApply()
# Connected components to extract largest component
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", "KEEP_LARGEST_ISLAND")
effect.self().onApply()
# Export segment to a model
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
exportFolderItemId = shNode.CreateFolderItem(shNode.GetSceneItemID(), "Segments")
slicer.modules.segmentations.logic().ExportAllSegmentsToModels(segNode, exportFolderItemId)
itemList=[]
shNode.GetItemChildren(exportFolderItemId,itemList)
if itemList is []:
print("Error: no model node exported for ", volumeNode.GetName())
continue
modelNode = shNode.GetItemDataNode(itemList[0])
# Decimate the model 80%
slicer.modules.SurfaceToolboxWidget.logic.decimate(modelNode, modelNode, 0.8)
# Save the resultant model as OBJ to the folder
outputModelName = os.path.join(inputPath, volumeNode.GetName() + ".obj")
slicer.util.saveNode(modelNode, outputModelName)
# Clean up
slicer.mrmlScene.RemoveNode(volumeNode)
slicer.mrmlScene.RemoveNode(segNode)
slicer.mrmlScene.RemoveNode(modelNode)
shNode.RemoveItem(exportFolderItemId)After defining this function, run it on a folder containing volumes using:
slicerScriptingExampleFunction('/path/to/my/data')