User talk:Haehn
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my notes..
- this code works locally:
"import sys; from Slicer import slicer; volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('/home/haehn/data/Image00_LCA.nrrd','Liver',0); matrix = slicer.vtkMatrix4x4(); volNode.GetIJKToRASMatrix(matrix);
outputNode=slicer.MRMLScene.CreateNodeByClass('vtkMRMLScalarVolumeNode'); volumeNode=slicer.MRMLScene.AddNode(outputNode); volumeNode.SetAndObserveImageData(volNode.GetImageData()); volumeNode.SetIJKToRASMatrix(matrix); volumeNode.SetModifiedSinceRead(1); slicer.VolumesGUI.GetLogic().SaveArchetypeVolume('/home/haehn/data/test.nrrd',volumeNode);"
- remote Frangi:
${SIGMA_MIN}=$const(1.0) ${SIGMA_MAX}=$const(5.0) ${SIGMA_STEPS}=$const(10) ${ALPHA}=$range(0.1,0.5,0.1) ${BETA}=$range(500.0,1500.0,500.0) ${GAMMA}=$range(300.0,1000.0,100.0) ${FILE}=$const(00) ${TYPE}=$const(RCA) ${INPUT}=$const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd) ${OUTPUT}=$const(/Volumes/DATA2/dhaehn/gwe-results/${FILE}-${TYPE}/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}) ${SLICER_HOME}/Slicer3 --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); from SlicerVMTKVesselEnhancementGUI import *; hiddengui = VMTKVesselEnhancement(); from SlicerVMTKVesselEnhancementLogic import *; vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${INPUT}','Vessels',0); matrix = slicer.vtkMatrix4x4(); volNode.GetIJKToRASMatrix(matrix); from datetime import *; s=datetime.now(); outVolumeData = vesselness.ApplyFrangiVesselness(volNode.GetImageData(),${SIGMA_MIN},${SIGMA_MAX},${SIGMA_STEPS},${ALPHA},${BETA},${GAMMA}); e=datetime.now(); delta=e-s; outputNode=slicer.MRMLScene.CreateNodeByClass('vtkMRMLScalarVolumeNode'); volumeNode=slicer.MRMLScene.AddNode(outputNode); volumeNode.SetAndObserveImageData(outVolumeData); volumeNode.SetIJKToRASMatrix(matrix); volumeNode.SetModifiedSinceRead(1); slicer.VolumesGUI.GetLogic().SaveArchetypeVolume('${OUTPUT}--'+str(delta).replace(':','-')+'.nrrd',volumeNode);Slicer.tk.eval('exit 0');"
- remote levelset plus centerlines and export:
${SIGMA_MIN}=$const(1.0) ${SIGMA_MAX}=$const(5.0) ${SIGMA_STEPS}=$const(10) ${ALPHA}=$range(0.1,0.5,0.1) ${BETA}=$range(500.0,1500.0,500.0) ${GAMMA}=$range(300.0,1000.0,100.0) ${FILE}=$const(00) ${TYPE}=$const(RCA) ${INPUT}=$const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd) ${VESSELNESS_NAME}=$const(${FILE}-${TYPE}/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}) ${INPUT_VESSELNESS}=$const(/Volumes/DATA2/dhaehn/gwe-results/${VESSELNESS_NAME}*.nrrd) ${VESSEL}=$const(0) ${SEED_X}=$const(1) ${SEED_Y}=$const(1) ${SEED_Z}=$const(1) ${CL_START_X}=$const(1) ${CL_START_Y}=$const(1) ${CL_START_Z}=$const(1) ${CL_END_X}=$const(1) ${CL_END_Y}=$const(1) ${CL_END_Z}=$const(1) ${LOW_THRESHOLD}=$const(0.1) ${HIGH_THRESHOLD}=$const(1.0) ${PROPAGATION}=$range(-20,20,10) ${CURVATURE}=$range(50,90,10) ${ADVECTION}=$const(100) ${ITERATIONS}=$const(10) ${OUTPUT_A}=$const(/Volumes/DATA2/dhaehn/gwe-results-centerlines/${VESSELNESS_NAME}-${VESSEL}-FM-${LOW_THRESHOLD}-${HIGH_THRESHOLD}--) ${OUTPUT_B}=$const(-GAC-${PROPAGATION}-${CURVATURE}-${ADVECTION}-N${ITERATIONS}--) ${SLICER_HOME}/bin/Slicer3-real --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKEasyLevelSetSegmentation/VMTKEasyLevelSetSegmentation'); sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKCenterlines/VMTKCenterlines'); from VMTKEasyLevelSetSegmentationGUI import *; hiddengui = VMTKEasyLevelSetSegmentationGUI(); from VMTKEasyLevelSetSegmentationLogic import *; levelset = VMTKEasyLevelSetSegmentationLogic(hiddengui); from VMTKCenterlinesGUI import *; hidden2gui = VMTKCenterlinesGUI(); from VMTKCenterlinesLogic import *; centerlines = VMTKCenterlinesLogic(hidden2gui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${INPUT}','Originals',0); import glob; vesselnessFile=glob.glob('${INPUT_VESSELNESS}'); vesselnessNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume(vesselnessFile[0],'Vessels',0); matrix = slicer.vtkMatrix4x4(); volNode.GetIJKToRASMatrix(matrix); rasMatrix = slicer.vtkMatrix4x4(); volNode.GetRASToIJKMatrix(rasMatrix); image = volNode.GetImageData(); vesselImage = vesselnessNode.GetImageData(); seedList = slicer.vtkIdList(); targetList = slicer.vtkIdList(); seedPt = [${SEED_X},${SEED_Y},${SEED_Z},1]; ijkSeedPt = rasMatrix.MultiplyPoint(*seedPt); seedList.InsertNextId(vesselImage.ComputePointId(int(ijkSeedPt[0]),int(ijkSeedPt[1]),int(ijkSeedPt[2]))); from datetime import *; fm_s = datetime.now(); fm = levelset.ExecuteFM(vesselImage,${LOW_THRESHOLD},${HIGH_THRESHOLD},seedList,targetList); fm_e = datetime.now(); delta_fm=fm_e-fm_s; gac_s=datetime.now(); gac = levelset.ExecuteGAC(image,fm,${ITERATIONS},${PROPAGATION},${CURVATURE},${ADVECTION},'geodesic'); gac_e=datetime.now(); delta_gac=gac_e-gac_s; mc_s=datetime.now(); mc = levelset.MarchingCubes(gac,matrix,0.0); mc_e=datetime.now(); delta_mc=mc_e-mc_s; clSeeds = slicer.vtkIdList(); clTargets = slicer.vtkIdList(); clSeedPt = [${CL_START_X},${CL_START_Y},${CL_START_Z},1]; clTargetPt = [${CL_END_X},${CL_END_Y},${CL_END_Z},1]; pointLocator=slicer.vtkPointLocator(); pointLocator.SetDataSet(mc); pointLocator.BuildLocator(); id=pointLocator.FindClosestPoint(int(clSeedPt[0]),int(clSeedPt[1]),int(clSeedPt[2])); clSeeds.InsertNextId(id); id=pointLocator.FindClosestPoint(int(clTargetPt[0]),int(clTargetPt[1]),int(clTargetPt[2])); clTargets.InsertNextId(id); cl_s=datetime.now(); prepared = centerlines.prepareModel(mc); centerline = centerlines.computeCenterlines(prepared,clSeeds,clTargets); cl_e=datetime.now(); delta_cl=cl_e-cl_s; outputFile='${OUTPUT_A}'+str(delta_fm).replace(':','-')+'${OUTPUT_B}'+str(delta_gac).replace(':','-')+'-MC--'+str(delta_mc).replace(':','-')+'-CL--'+str(delta_cl).replace(':','-')+'.dat';"