Difference between revisions of "User talk:Haehn"
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volumeNode.SetModifiedSinceRead(1); | volumeNode.SetModifiedSinceRead(1); | ||
slicer.VolumesGUI.GetLogic().SaveArchetypeVolume('/home/haehn/data/test.nrrd',volumeNode);" | slicer.VolumesGUI.GetLogic().SaveArchetypeVolume('/home/haehn/data/test.nrrd',volumeNode);" | ||
+ | |||
+ | * remote Frangi: | ||
+ | <pre> | ||
+ | ${SIGMA_MIN}=$const(1.0) | ||
+ | ${SIGMA_MAX}=$const(4.0) | ||
+ | ${SIGMA_STEPS}=$const(10) | ||
+ | ${ALPHA}=$range(0.1,0.5,0.1) | ||
+ | ${BETA}=$range(500.0,1500.0,500.0) | ||
+ | ${GAMMA}=$range(300.0,1500.0,100.0) | ||
+ | ${FILE}=$const(00) | ||
+ | ${TYPE}=$const{RCA} | ||
+ | ${OUTPUT}=$const(/Volumes/DATA2/gwe-results/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${ALPHA2}.nrrd) | ||
+ | |||
+ | ${SLICER_HOME}/Slicer3 --no_splash --evalpython | ||
+ | "import sys; | ||
+ | from Slicer import slicer; | ||
+ | sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); | ||
+ | from SlicerVMTKVesselEnhancementGUI import *; | ||
+ | hiddengui = VMTKVesselEnhancement(); | ||
+ | from SlicerVMTKVesselEnhancementLogic import *; | ||
+ | vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); | ||
+ | |||
+ | volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd','Vessels',0); | ||
+ | matrix = slicer.vtkMatrix4x4(); | ||
+ | volNode.GetIJKToRASMatrix(matrix); | ||
+ | |||
+ | outVolumeData = vesselness.ApplyFrangiVesselness(volNode.GetImageData(),${SIGMA_MIN},${SIGMA_MAX},${SIGMA_STEPS},${ALPHA},${BETA},${GAMMA}); | ||
+ | |||
+ | outputNode=slicer.MRMLScene.CreateNodeByClass('vtkMRMLScalarVolumeNode'); | ||
+ | volumeNode=slicer.MRMLScene.AddNode(outputNode); | ||
+ | volumeNode.SetAndObserveImageData(outVolumeData); | ||
+ | volumeNode.SetIJKToRASMatrix(matrix); | ||
+ | volumeNode.SetModifiedSinceRead(1); | ||
+ | slicer.VolumesGUI.GetLogic().SaveArchetypeVolume(${OUTPUT},volumeNode); | ||
+ | Slicer.tk.eval('exit 0');" | ||
+ | </pre> |
Revision as of 10:48, 19 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(4.0) ${SIGMA_STEPS}=$const(10) ${ALPHA}=$range(0.1,0.5,0.1) ${BETA}=$range(500.0,1500.0,500.0) ${GAMMA}=$range(300.0,1500.0,100.0) ${FILE}=$const(00) ${TYPE}=$const{RCA} ${OUTPUT}=$const(/Volumes/DATA2/gwe-results/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${ALPHA2}.nrrd) ${SLICER_HOME}/Slicer3 --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); from SlicerVMTKVesselEnhancementGUI import *; hiddengui = VMTKVesselEnhancement(); from SlicerVMTKVesselEnhancementLogic import *; vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd','Vessels',0); matrix = slicer.vtkMatrix4x4(); volNode.GetIJKToRASMatrix(matrix); outVolumeData = vesselness.ApplyFrangiVesselness(volNode.GetImageData(),${SIGMA_MIN},${SIGMA_MAX},${SIGMA_STEPS},${ALPHA},${BETA},${GAMMA}); outputNode=slicer.MRMLScene.CreateNodeByClass('vtkMRMLScalarVolumeNode'); volumeNode=slicer.MRMLScene.AddNode(outputNode); volumeNode.SetAndObserveImageData(outVolumeData); volumeNode.SetIJKToRASMatrix(matrix); volumeNode.SetModifiedSinceRead(1); slicer.VolumesGUI.GetLogic().SaveArchetypeVolume(${OUTPUT},volumeNode); Slicer.tk.eval('exit 0');"