Difference between revisions of "User talk:Haehn"
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delta_cl=cl_e-cl_s; | delta_cl=cl_e-cl_s; | ||
vesselnessFile=str(vesselnessFile[0]).replace('.nrrd','').split('/'); | vesselnessFile=str(vesselnessFile[0]).replace('.nrrd','').split('/'); | ||
− | outputFile='${OUTPUT_A}${SYSTEM_JOB_NUM}_'+vesselnessFile[len(vesselnessFile)-1]+'${OUTPUT_B}'+str(delta_fm).replace(':','-')+'${OUTPUT_C}'+str(delta_gac).replace(':','-')+'-MC--'+str(delta_mc).replace(':','-')+'-CL--'+str(delta_cl).replace(':','-')+'.dat'; centerlines.Export(centerline,outputFile,0,0,1);"; fi; echo "ended" > ${OUTPUT_A}ended_${VESSELNESS_NAME}${OUTPUT_B}${OUTPUT_C}.txt fi | + | outputFile='${OUTPUT_A}${SYSTEM_JOB_NUM}_'+vesselnessFile[len(vesselnessFile)-1]+'${OUTPUT_B}'+str(delta_fm).replace(':','-')+'${OUTPUT_C}'+str(delta_gac).replace(':','-')+'-MC--'+str(delta_mc).replace(':','-')+'-CL--'+str(delta_cl).replace(':','-')+'.dat'; centerlines.Export(centerline,outputFile,0,0,1);"; fi; echo "ended" > ${OUTPUT_A}ended_${VESSELNESS_NAME}${OUTPUT_B}${OUTPUT_C}.txt; fi |
</pre> | </pre> |
Revision as of 15:56, 30 January 2010
Home < User talk:Haehnmy 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}) if [ -e ${OUTPUT}*.nrrd ]; then echo '${OUTPUT}*.nrrd exists!'; else ${SLICER_HOME}/bin/Slicer3-real --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); from SlicerVMTKVesselEnhancementGUI import *; hiddengui = VMTKVesselEnhancement(); from SlicerVMTKVesselEnhancementLogic import *; vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${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);"; fi;
- 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(01) ${TYPE}=$const(RCA) ${INPUT}=$const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd) ${VESSELNESS_NAME}=$const(${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}) ${INPUT_VESSELNESS}=$const(/Volumes/DATA2/dhaehn/gwe-results/${FILE}-${TYPE}/${VESSELNESS_NAME}*.nrrd) ${VESSEL}=$const(0) ${SEED_X}=$const(-50.1738) ${SEED_Y}=$const(-58.7432) ${SEED_Z}=$const(77.2189) ${CL_START_X}=$const(-61.3221) ${CL_START_Y}=$const(-70.5911) ${CL_START_Z}=$const(86.7588) ${CL_END_X}=$const(-110.032) ${CL_END_Y}=$const(-123.933) ${CL_END_Z}=$const(34.8108) ${LOW_THRESHOLD}=$range(0.4,0.6,0.1) ${HIGH_THRESHOLD}=$const(1.0) ${PROPAGATION}=$range(-10,10,10) ${CURVATURE}=$range(50,80,10) ${ADVECTION}=$const(100) ${ITERATIONS}=$const(10) ${OUTPUT_A}=$const(/Volumes/DATA2/dhaehn/gwe-results-centerlines/${FILE}-${TYPE}/) ${OUTPUT_B}=$const(-V${VESSEL}-FM-${LOW_THRESHOLD}-${HIGH_THRESHOLD}--) ${OUTPUT_C}=$const(-GAC-${PROPAGATION}-${CURVATURE}-${ADVECTION}-N${ITERATIONS}--) if [ -e ${OUTPUT_A}${VESSELNESS_NAME}*${OUTPUT_B}*${OUTPUT_C}*.dat ]; then echo '${OUTPUT_A}${VESSELNESS_NAME}*${OUTPUT_B}*${OUTPUT_C}*.dat exists!'; else ${SLICER_HOME}/bin/Slicer3-real --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKEasyLevelSetSegmentation/VMTKEasyLevelSetSegmentation'); sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKCenterlines/VMTKCenterlines'); from VMTKEasyLevelSetSegmentationGUI import *; hiddengui = VMTKEasyLevelSetSegmentationGUI(); from VMTKEasyLevelSetSegmentationLogic import *; levelset = VMTKEasyLevelSetSegmentationLogic(hiddengui); from VMTKCenterlinesGUI import *; hidden2gui = VMTKCenterlinesGUI(); from VMTKCenterlinesLogic import *; centerlines = VMTKCenterlinesLogic(hidden2gui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${INPUT}','Original',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; vesselnessFile=str(vesselnessFile[0]).replace('.nrrd','').split('/'); outputFile='${OUTPUT_A}'+vesselnessFile[len(vesselnessFile)-1]+'${OUTPUT_B}'+str(delta_fm).replace(':','-')+'${OUTPUT_C}'+str(delta_gac).replace(':','-')+'-MC--'+str(delta_mc).replace(':','-')+'-CL--'+str(delta_cl).replace(':','-')+'.dat'; centerlines.Export(centerline,outputFile,0,0,1);"; fi
- remote Frangi 2nd Run
${SIGMA_MIN}=$const(1.0) ${SIGMA_MAX}=$const(5.0) ${SIGMA_STEPS}=$const(10) ${ALPHA}=$range(0.1,0.3,0.1) ${BETA}=$const(500.0) ${GAMMA}=$range(200.0,600.0,100.0) ${FILE}=$const(00) ${TYPE}=$const(RCA,LCA) ${INPUT}=$const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd) ${OUTPUT}=$const(/Volumes/DATA2/dhaehn/gwe-results-snd/${FILE}-${TYPE}/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}) ${SLICER}=$const(/Users/dhaehn/current_slicer) if [ -e ${OUTPUT}*.nrrd ]; then echo '${OUTPUT}*.nrrd exists!'; else ${SLICER}/bin/Slicer3-real --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); from SlicerVMTKVesselEnhancementGUI import *; hiddengui = VMTKVesselEnhancement(); from SlicerVMTKVesselEnhancementLogic import *; vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${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);"; fi;
- remote levelset plus centerlines and export 2nd run:
${SIGMA_MIN}=$const(1.0) ${SIGMA_MAX}=$const(5.0) ${SIGMA_STEPS}=$const(10) ${ALPHA}=$range(0.1,0.3,0.1) ${BETA}=$const(500.0) ${GAMMA}=$range(200.0,600.0,100.0) ${FILE}=$const(00) ${TYPE}=$const(RCA) ${INPUT}=$const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd) ${VESSELNESS_NAME}=$const(${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}) ${INPUT_VESSELNESS}=$const(/Volumes/DATA2/dhaehn/gwe-results-snd/${FILE}-${TYPE}/${VESSELNESS_NAME}*.nrrd) ${VESSEL}=$const(0) ${SEED1_X}=$const(-50.1738) ${SEED1_Y}=$const(-58.7432) ${SEED1_Z}=$const(77.2189) ${SEED2_X}=$const(-50.1738) ${SEED2_Y}=$const(-58.7432) ${SEED2_Z}=$const(77.2189) ${CL_START_X}=$const(-61.3221) ${CL_START_Y}=$const(-70.5911) ${CL_START_Z}=$const(86.7588) ${CL_END_X}=$const(-110.032) ${CL_END_Y}=$const(-123.933) ${CL_END_Z}=$const(34.8108) ${LOW_THRESHOLD}=$range(0.4,0.6,0.1) ${HIGH_THRESHOLD}=$const(1.0) ${PROPAGATION}=$range(-15,15,15) ${CURVATURE}=$range(40,90,10) ${ADVECTION}=$const(100) ${ITERATIONS}=$const(10) ${OUTPUT_A}=$const(/Volumes/DATA2/dhaehn/gwe-results-centerlines-snd/${FILE}-${TYPE}${VESSEL}/) ${OUTPUT_B}=$const(-V${VESSEL}-FM-${LOW_THRESHOLD}-${HIGH_THRESHOLD}--) ${OUTPUT_C}=$const(-GAC-${PROPAGATION}-${CURVATURE}-${ADVECTION}-N${ITERATIONS}--) ${SLICER}=$const(/Users/dhaehn/current_slicer) if [ -e ${OUTPUT_A}${VESSELNESS_NAME}*${OUTPUT_B}*${OUTPUT_C}*.dat ]; then echo '${OUTPUT_A}${VESSELNESS_NAME}*${OUTPUT_B}*${OUTPUT_C}*.dat exists!'; else if [ -e ${OUTPUT_A}ended_${VESSELNESS_NAME}${OUTPUT_B}${OUTPUT_C}.txt ]; then echo '${OUTPUT_A}ended_${VESSELNESS_NAME}${OUTPUT_B}${OUTPUT_C}.dat exists!'; else ${SLICER}/bin/Slicer3-real --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKEasyLevelSetSegmentation/VMTKEasyLevelSetSegmentation'); sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKCenterlines/VMTKCenterlines'); from VMTKEasyLevelSetSegmentationGUI import *; hiddengui = VMTKEasyLevelSetSegmentationGUI(); from VMTKEasyLevelSetSegmentationLogic import *; levelset = VMTKEasyLevelSetSegmentationLogic(hiddengui); from VMTKCenterlinesGUI import *; hidden2gui = VMTKCenterlinesGUI(); from VMTKCenterlinesLogic import *; centerlines = VMTKCenterlinesLogic(hidden2gui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${INPUT}','Original',0); import glob; vesselnessFile=glob.glob('${INPUT_VESSELNESS}'); vesselnessNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume(vesselnessFile[0],'Vessels',0); matrix = slicer.vtkMatrix4x4(); volNode.GetIJKToRASMatrix(matrix); rasMatrix = slicer.vtkMatrix4x4(); volNode.GetRASToIJKMatrix(rasMatrix); image = volNode.GetImageData(); vesselImage = vesselnessNode.GetImageData(); seedList = slicer.vtkIdList(); targetList = slicer.vtkIdList(); seedPt = [${SEED1_X},${SEED1_Y},${SEED1_Z},1]; ijkSeedPt = rasMatrix.MultiplyPoint(*seedPt); seedList.InsertNextId(vesselImage.ComputePointId(int(ijkSeedPt[0]),int(ijkSeedPt[1]),int(ijkSeedPt[2]))); seed2Pt = [${SEED2_X},${SEED2_Y},${SEED2_Z},1]; ijkSeed2Pt = rasMatrix.MultiplyPoint(*seed2Pt); seedList.InsertNextId(vesselImage.ComputePointId(int(ijkSeed2Pt[0]),int(ijkSeed2Pt[1]),int(ijkSeed2Pt[2]))); from datetime import *; fm_s = datetime.now(); fm = levelset.ExecuteFM(vesselImage,${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},${CL_END_Z},1]; pointLocator=slicer.vtkPointLocator(); pointLocator.SetDataSet(mc); pointLocator.BuildLocator(); id=pointLocator.FindClosestPoint(int(clSeedPt[0]),int(clSeedPt[1]),int(clSeedPt[2])); clSeeds.InsertNextId(id); id=pointLocator.FindClosestPoint(int(clTargetPt[0]),int(clTargetPt[1]),int(clTargetPt[2])); clTargets.InsertNextId(id); cl_s=datetime.now(); prepared = centerlines.prepareModel(mc); centerline = centerlines.computeCenterlines(prepared,clSeeds,clTargets); cl_e=datetime.now(); delta_cl=cl_e-cl_s; vesselnessFile=str(vesselnessFile[0]).replace('.nrrd','').split('/'); outputFile='${OUTPUT_A}${SYSTEM_JOB_NUM}_'+vesselnessFile[len(vesselnessFile)-1]+'${OUTPUT_B}'+str(delta_fm).replace(':','-')+'${OUTPUT_C}'+str(delta_gac).replace(':','-')+'-MC--'+str(delta_mc).replace(':','-')+'-CL--'+str(delta_cl).replace(':','-')+'.dat'; centerlines.Export(centerline,outputFile,0,0,1);"; fi; echo "ended" > ${OUTPUT_A}ended_${VESSELNESS_NAME}${OUTPUT_B}${OUTPUT_C}.txt; fi