Difference between revisions of "User talk:Haehn"
From NAMIC Wiki
| Line 24: | Line 24: | ||
${GAMMA}=$range(300.0,1500.0,100.0) | ${GAMMA}=$range(300.0,1500.0,100.0) | ||
${FILE}=$const(00) | ${FILE}=$const(00) | ||
| − | ${TYPE}=$const{ | + | ${TYPE}=$const(RCA) |
| − | ${OUTPUT}=$const(/Volumes/DATA2/gwe-results/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${ | + | ${INPUT}=const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd) |
| + | ${OUTPUT}=$const(/Volumes/DATA2/dhaehn/gwe-results/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}.nrrd) | ||
| − | ${SLICER_HOME}/Slicer3 --no_splash --evalpython | + | ${SLICER_HOME}/Slicer3 --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); from SlicerVMTKVesselEnhancementGUI import *; hiddengui = VMTKVesselEnhancement(); from SlicerVMTKVesselEnhancementLogic import *; vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${INPUT}','Vessels',0); matrix = slicer.vtkMatrix4x4(); volNode.GetIJKToRASMatrix(matrix); 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('${OUTPUT}',volumeNode); Slicer.tk.eval('exit 0');" |
| − | "import sys; | ||
| − | from Slicer import slicer; | ||
| − | sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); | ||
| − | from SlicerVMTKVesselEnhancementGUI import *; | ||
| − | hiddengui = VMTKVesselEnhancement(); | ||
| − | from SlicerVMTKVesselEnhancementLogic import *; | ||
| − | vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); | ||
| − | |||
| − | volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume(' | ||
| − | matrix = slicer.vtkMatrix4x4(); | ||
| − | volNode.GetIJKToRASMatrix(matrix); | ||
| − | |||
| − | outVolumeData = vesselness.ApplyFrangiVesselness(volNode.GetImageData(),${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> | </pre> | ||
Revision as of 11:15, 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)
${INPUT}=const(/Volumes/DATA2/dhaehn/cutted/Image${FILE}_${TYPE}.nrrd)
${OUTPUT}=$const(/Volumes/DATA2/dhaehn/gwe-results/${FILE}-${TYPE}-out-${SIGMA_MIN}-${SIGMA_MAX}-N${SIGMA_STEPS}-${ALPHA}-${BETA}-${GAMMA}.nrrd)
${SLICER_HOME}/Slicer3 --no_splash --evalpython "import sys; from Slicer import slicer; sys.path.append(str(slicer.Application.GetExtensionsInstallPath())+'/'+str(slicer.Application.GetSvnRevision())+'/VMTKVesselEnhancement/VMTKVesselEnhancement'); from SlicerVMTKVesselEnhancementGUI import *; hiddengui = VMTKVesselEnhancement(); from SlicerVMTKVesselEnhancementLogic import *; vesselness=SlicerVMTKVesselEnhancementLogic(hiddengui); volNode=slicer.VolumesGUI.GetLogic().AddArchetypeVolume('${INPUT}','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');"
