User talk:Haehn - Revision history

Haehn at 11:24, 29 April 2010

2010-04-29T11:24:01Z

Haehn: /* my notes.. */

2010-01-30T16:51:42Z

my notes..

Haehn: /* my notes.. */

2010-01-30T16:41:29Z

my notes..

Haehn: /* my notes.. */

2010-01-30T15:56:49Z

my notes..

Haehn: /* my notes.. */

2010-01-30T15:53:00Z

my notes..

Haehn: /* my notes.. */

2010-01-30T15:40:55Z

my notes..

Haehn: /* my notes.. */

2010-01-30T15:28:24Z

my notes..

Haehn at 15:25, 30 January 2010

2010-01-30T15:25:09Z

Haehn at 12:35, 30 January 2010

2010-01-30T12:35:53Z

Haehn at 12:17, 30 January 2010

2010-01-30T12:17:46Z

← Older revision		Revision as of 11:24, 29 April 2010
Line 1:		Line 1:
	==my notes..==		==my notes..==
		+
		+	* centerline prepare
		+	<pre>
		+	# new
		+	subdiv = slicer.vtkLinearSubdivisionFilter()
		+	subdiv.SetInput(surfaceTriangulator.GetOutput())
		+	subdiv.SetNumberOfSubdivisions(1)
		+	subdiv.Update()
		+
		+	smooth = slicer.vtkWindowedSincPolyDataFilter()
		+	smooth.SetInput(subdiv.GetOutput())
		+	smooth.SetNumberOfIterations(20)
		+	smooth.SetPassBand(0.1)
		+	smooth.SetBoundarySmoothing(1)
		+	smooth.Update()
		+
		+	normals = slicer.vtkPolyDataNormals()
		+	normals.SetInput(smooth.GetOutput())
		+	normals.SetAutoOrientNormals(1)
		+	normals.SetFlipNormals(0)
		+	normals.SetConsistency(1)
		+	normals.SplittingOff()
		+	normals.Update()
		+	</pre>

	* this code works locally:		* this code works locally:

@@ Line 175: / Line 175: @@
 ${INPUT_VESSELNESS}=$const(/Volumes/DATA2/dhaehn/gwe-results-snd/${FILE}-${TYPE}/${VESSELNESS_NAME}*.nrrd)
 ${VESSEL}=$const(0)
 ${LOW_THRESHOLD}=$range(0.4,0.6,0.1)
 ${HIGH_THRESHOLD}=$const(1.0)
@@ Line 236: / Line 224: @@
 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];
+f=open('/Volumes/DATA2/dhaehn/CTA_training_data/dataset${FILE}/vessel${VESSEL}/pointB.txt','r');
 ijkSeed2Pt = rasMatrix.MultiplyPoint(*seed2Pt);
@@ Line 263: / Line 268: @@
 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];
+f=open('/Volumes/DATA2/dhaehn/CTA_training_data/dataset${FILE}/vessel${VESSEL}/pointS.txt','r');
 pointLocator=slicer.vtkPointLocator();

@@ Line 175: / Line 175: @@
 ${INPUT_VESSELNESS}=$const(/Volumes/DATA2/dhaehn/gwe-results-snd/${FILE}-${TYPE}/${VESSELNESS_NAME}*.nrrd)
 ${VESSEL}=$const(0)
-${SEED1_X}=$const(-50.1738)
+${SEED1_X}=$const(-123.7)
-${SEED1_Y}=$const(-58.7432)
+${SEED1_Y}=$const(-85.6724)
-${SEED1_Z}=$const(77.2189)
+${SEED1_Z}=$const(22.4097)
-${SEED2_X}=$const(-50.1738)
+${SEED2_X}=$const(-57.3174)
-${SEED2_Y}=$const(-58.7432)
+${SEED2_Y}=$const(-42.0669)
-${SEED2_Z}=$const(77.2189)
+${SEED2_Z}=$const(73.0315)
-${CL_START_X}=$const(-61.3221)
+${CL_START_X}=$const(-68.6513)
-${CL_START_Y}=$const(-70.5911)
+${CL_START_Y}=$const(-57.758)
-${CL_START_Z}=$const(86.7588)
+${CL_START_Z}=$const(75.285)
-${CL_END_X}=$const(-110.032)
+${CL_END_X}=$const(-155.555)
-${CL_END_Y}=$const(-123.933)
+${CL_END_Y}=$const(-53.9931)
-${CL_END_Z}=$const(34.8108)
+${CL_END_Z}=$const(34.2092)
 ${LOW_THRESHOLD}=$range(0.4,0.6,0.1)
 ${HIGH_THRESHOLD}=$const(1.0)

@@ Line 281: / Line 281: @@
 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
+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>

@@ Line 193: / Line 193: @@
 ${ADVECTION}=$const(100)
 ${ITERATIONS}=$const(10)
-${OUTPUT_A}=$const(/Volumes/DATA2/dhaehn/gwe-results-centerlines-snd/${FILE}-${TYPE}/)
+${OUTPUT_A}=$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}--)

@@ Line 170: / Line 170: @@
 ${GAMMA}=$range(200.0,600.0,100.0)
 ${FILE}=$const(00)
-${TYPE}=$const(RCA,LCA)
+${TYPE}=$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})

@@ Line 189: / Line 189: @@
 ${LOW_THRESHOLD}=$range(0.4,0.6,0.1)
 ${HIGH_THRESHOLD}=$const(1.0)
-${PROPAGATION}=$range(-10,10,10)
+${PROPAGATION}=$range(-15,15,15)
-${CURVATURE}=$range(50,80,10)
+${CURVATURE}=$range(40,90,10)
 ${ADVECTION}=$const(100)
 ${ITERATIONS}=$const(10)

← Older revision		Revision as of 15:25, 30 January 2010
Line 159:		Line 159:

	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;		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;
		+	</pre>
		+
		+	* remote levelset plus centerlines and export 2nd run:
		+	<pre>
		+	${SIGMA_MIN}=$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)
		+	${VESSELNESS_NAME}=$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(-10,10,10)
		+	${CURVATURE}=$range(50,80,10)
		+	${ADVECTION}=$const(100)
		+	${ITERATIONS}=$const(10)
		+	${OUTPUT_A}=$const(/Volumes/DATA2/dhaehn/gwe-results-centerlines-snd/${FILE}-${TYPE}/)
		+	${OUTPUT_B}=$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
	</pre>		</pre>

@@ Line 142: / Line 142: @@
 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
 </pre>