def paratospharm(opts, config, data, outputDir):
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
pathParaToSPHARM = config["ParaToSPHARMMeshCLPPath"]
idlist = [id for id, l, g in data]
parafiles = ["%s/%s.para.vtk" % (workdir, id) for id, l, g in data]
surffiles = ["%s/%s.surf.vtk" % (workdir, id) for id, l, g in data]
lowresfiles = ["%s/%s.ip.SPHARM.vtk" % (workdir, id) for id, l, g in data]
highresfiles = [
"%s/%s.subj.SPHARM.vtk" % (workdir, id) for id, l, g in data
]
lowresparams = ["%s/%s.ip.Param.vtk" % (workdir, id) for id, l, g in data]
highresparams = [
"%s/%s.subj.Param.vtk" % (workdir, id) for id, l, g in data
]
dataset = zip(parafiles, surffiles, lowresfiles, lowresparams,
highresfiles, highresparams)
for idx, (pf, sf, lm, lp, hm, hp) in enumerate(dataset):
# check if the parafile is newer than lm-output
if system.is_file_newer(lm, pf, opts.overwrite):
if idx == 0:
id = idlist[idx]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 10 --spharmDegree 20 " +\
" {workdir}/{id}.ip. --paraOut"
else:
id = idlist[idx]
refid = idlist[0]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 10 --spharmDegree 20 " +\
"{workdir}/{id}.ip. --flipTemplateOn " +\
"--flipTemplate {workdir}/{refid}.ip.SPHARM.coef --paraOut"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=opts.verbose)
for idx, (pf, sf, lm, lp, hm, hp) in enumerate(dataset):
# check if the parafile is newer than hm-output
if system.is_file_newer(hm, pf, opts.overwrite):
if idx == 0:
id = idlist[idx]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 50 --spharmDegree 20 " +\
"{workdir}/{id}.subj. --paraOut"
else:
id = idlist[idx]
refid = idlist[0]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 50 --spharmDegree 20 " +\
"{workdir}/{id}.subj. --flipTemplateOn " +\
"--flipTemplate {workdir}/{refid}.subj.SPHARM.coef --paraOut"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=opts.verbose)
def paratospharm(opts, config, data, outputDir):
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
pathParaToSPHARM = config["ParaToSPHARMMeshCLPPath"]
idlist = [id for id,l,g in data]
parafiles = ["%s/%s.para.vtk"%(workdir,id) for id,l,g in data]
surffiles = ["%s/%s.surf.vtk"%(workdir,id) for id,l,g in data]
lowresfiles = ["%s/%s.ip.SPHARM.vtk"%(workdir,id) for id,l,g in data]
highresfiles = ["%s/%s.subj.SPHARM.vtk"%(workdir,id) for id,l,g in data]
lowresparams = ["%s/%s.ip.Param.vtk"%(workdir,id) for id,l,g in data]
highresparams = ["%s/%s.subj.Param.vtk"%(workdir,id) for id,l,g in data]
dataset = zip(parafiles, surffiles, lowresfiles, lowresparams, highresfiles, highresparams)
for idx,(pf,sf,lm,lp,hm,hp) in enumerate(dataset):
# check if the parafile is newer than lm-output
if system.is_file_newer(lm, pf, opts.overwrite):
if idx == 0:
id = idlist[idx]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 10 --spharmDegree 20 " +\
" {workdir}/{id}.ip. --paraOut"
else:
id = idlist[idx]
refid = idlist[0]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 10 --spharmDegree 20 " +\
"{workdir}/{id}.ip. --flipTemplateOn " +\
"--flipTemplate {workdir}/{refid}.ip.SPHARM.coef --paraOut"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=opts.verbose)
for idx,(pf,sf,lm,lp,hm,hp) in enumerate(dataset):
# check if the parafile is newer than hm-output
if system.is_file_newer(hm, pf, opts.overwrite):
if idx == 0:
id = idlist[idx]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 50 --spharmDegree 20 " +\
"{workdir}/{id}.subj. --paraOut"
else:
id = idlist[idx]
refid = idlist[0]
cmd = "{pathParaToSPHARM} {pf} {sf} --subdivLevel 50 --spharmDegree 20 " +\
"{workdir}/{id}.subj. --flipTemplateOn " +\
"--flipTemplate %s/%s.subj.SPHARM.coef --paraOut"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=opts.verbose)
def resample_segmentations(opts,config,data,outputdir):
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputdir)
refid = data[0][0]
reference_image = "{workdir}/{refid}.segpost.nii.gz".format(**locals())
pathResampleVolume = config["ResampleVolume2Path"]
for id,l,g in data:
segpost_image = "{workdir}/{id}.segpost.nii.gz".format(**locals())
labelMapNCResampled = "{workdir}/{id}.labelMapNCsegmentation.nrrd".format(**locals())
cmd = "{pathResampleVolume} {segpost_image} {labelMapNCResampled} -R {reference_image} -i nn"
if system.is_file_newer(labelMapNCResampled, segpost_image, opts.overwrite):
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
def compute_thickness(opts, config, data, outputdir, ids, idl, idh, idn):
pathThicknessTool = config["measureThicknessFilterPath"]
for (id, labelmap, group) in data:
labelmap = "{outputdir}/Processing/1.MeasurementandSPHARM/{id}.boundaryMap.mha".format(**locals())
# temporary
# workdir = "%s/Processing/1.MeasurementandSPHARM/%s_2" % (outputdir, id)
# measurementoutput = "%s/Processing/1.MeasurementandSPHARM/%s.thickness.mha" % (outputdir, id)
workdir = "{outputdir}/Processing/1.MeasurementandSPHARM/{id}".format(**locals())
measurementoutput = "{outputdir}/Processing/1.MeasurementandSPHARM/" +\
"{id}_measurementoutput.nrrd"
measurementoutput = measurementoutput.format(**locals())
if (not os.path.exists(workdir)):
os.makedirs(workdir)
if system.is_file_newer(measurementoutput, labelmap, opts.overwrite) or \
system.is_file_newer(measurementoutput, "{workdir}/laplacianCache.nii.gz".format(**locals()), opts.overwrite):
cmd = "{pathThicknessTool} --mr --sbt --ids {ids} --idl {idl} --idh {idh} --idn {idn} --ttrns 500 " +\
"--workdir {workdir} --cachedLaplacianOutput laplacianCache.nii.gz {labelmap} {measurementoutput}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
def resample_segmentations(opts,config,data,outputdir):
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputdir)
refid = data[0][0]
reference_image = "{workdir}/{refid}.segpost.nii.gz".format(**locals())
pathResampleVolume = config["ResampleVolume2Path"]
for id,l,g in data:
segpost_image = "{workdir}/{id}.segpost.nii.gz".format(**locals())
labelMapNCResampled = "{workdir}/{id}.labelMapNCsegmentation.nrrd".format(**locals())
cmd = "{pathResampleVolume} {segpost_image} {labelMapNCResampled} -R {reference_image} -i nn"
if system.is_file_newer(labelMapNCResampled, segpost_image, opts.overwrite):
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
def compute_thickness(opts, config, data, outputdir, ids, idl, idh):
pathThicknessTool = config["measureThicknessFilterPath"]
for (id, labelmap, group) in data:
labelmap = "{outputdir}/Processing/1.MeasurementandSPHARM/{id}.boundaryMap.mha".format(**locals())
# temporary
# workdir = "%s/Processing/1.MeasurementandSPHARM/%s_2" % (outputdir, id)
# measurementoutput = "%s/Processing/1.MeasurementandSPHARM/%s.thickness.mha" % (outputdir, id)
workdir = "{outputdir}/Processing/1.MeasurementandSPHARM/{id}".format(**locals())
measurementoutput = "{outputdir}/Processing/1.MeasurementandSPHARM/" +\
"{id}_measurementoutput.nrrd"
measurementoutput = measurementoutput.format(**locals())
if (not os.path.exists(workdir)):
os.makedirs(workdir)
if system.is_file_newer(measurementoutput, labelmap, opts.overwrite) or \
system.is_file_newer(measurementoutput, "{workdir}/laplacianCache.nii.gz".format(**locals()), opts.overwrite):
cmd = "{pathThicknessTool} --mr --sbt --ids {ids} --idl {idl} --idh {idh} --ttrns 500 " +\
"--workdir {workdir} --cachedLaplacianOutput laplacianCache.nii.gz {labelmap} {measurementoutput}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
def regenerate_segmentations(data, config, outputdir):
pathKmesh = config["kmeshPath"]
pathKcalc = config["kcalcPath"]
workdir = "{outputdir}/Processing/1.MeasurementandSPHARM".format(
**locals())
# before executing the boundary correction
# check if none of input is not generated.
testLabelMapsFail = False in [os.path.exists(x) for (t, x, g) in data]
if testLabelMapsFail:
raise RuntimeError("There are missing label maps")
surfaceInputList = [
"{workdir}/{id}.subj.SPHARM.vtk".format(**locals())
for (id, l, g) in data
]
testSurfaceInputsFail = False in [
os.path.exists(x) for x in surfaceInputList
]
if testSurfaceInputsFail:
raise RuntimeError(
"There are missing surface inputs. Check SPHARM results!")
if opts.nop1 is False:
for idx, (id, labelMap, group) in enumerate(data):
labelOutput = "{workdir}/{id}.zerocortex.nrrd".format(**locals())
surfaceInput = "{workdir}/{id}.subj.SPHARM.vtk".format(**locals())
#surfaceInput = "{workdir}/{id}.surf.vtk".format(**locals())
surfaceLabels = "{workdir}/{id}.labels.vtp".format(**locals())
if system.is_file_newer(labelOutput, labelMap, opts.overwrite):
cmd = "{pathKcalc} -e 'A==3?0:A' -o {labelOutput} {labelMap}"
cmd = cmd.format(**locals())
if system.run_process(cmd, verbose=True) != 0:
raise RuntimeError("fail to modify labelmap")
if system.is_file_newer(surfaceLabels, surfaceInput, opts.overwrite) or \
system.is_file_newer(surfaceLabels, labelOutput, opts.overwrite):
cmd = "{pathKmesh} -sampleImage -zrotate -outputScalarName labels " + \
"{labelOutput} {surfaceInput} {surfaceLabels}"
cmd = cmd.format(**locals())
if system.run_process(cmd, verbose=True) != 0:
raise RuntimError("fail to run kmesh")
# compute the average of labels scalar values to smooth out
if opts.nop2 is False:
cmd = "{pathKmesh} -averageScalars -threshold 1.8 " + \
"-scalarName labels -outputScalarName meanLabels"
cmd = cmd.format(**locals())
for (tag, labelmap, group) in data:
surfaceMeshWithLabels = "{workdir}/{tag}.labels.vtp".format(
**locals())
cmd += " " + surfaceMeshWithLabels
system.run_process(cmd, verbose=True)
if opts.nop3 is False:
for idx, (tag, labelMap, group) in enumerate(data):
labelOutput = "{workdir}/{tag}.zerocortex.nrrd".format(**locals())
surfaceLabels = "{workdir}/{tag}.labels.vtp".format(**locals())
voronoiImage = "{workdir}/{tag}.voronoi.mha".format(**locals())
surfaceImage = "{workdir}/{tag}.solution.mha".format(**locals())
boundaryMap = "{workdir}/{tag}.boundaryMap.mha".format(**locals())
if system.is_file_newer(labelOutput, voronoiImage, opts.overwrite) or \
system.is_file_newer(surfaceLabels, voronoiImage, opts.overwrite):
cmd = "{pathKmesh} -voronoiImage -zrotate -scalarName meanLabels " +\
"{labelOutput} {surfaceLabels} -o {voronoiImage}"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=True)
if system.is_file_newer(labelOutput, voronoiImage, opts.overwrite) or \
system.is_file_newer(surfaceLabels, voronoiImage, opts.overwrite):
cmd = "{pathKmesh} -scanConversion -zrotate " +\
"{surfaceLabels} {labelOutput} {surfaceImage}"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=True)
if system.is_file_newer(voronoiImage, boundaryMap, opts.overwrite) or \
system.is_file_newer(surfaceImage, boundaryMap, opts.overwrite):
cmd = "{pathKcalc} -e 'B>0?3:A' -o {boundaryMap} " +\
"{voronoiImage} {surfaceImage}"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=True)
def sample_thickness(opts, config, csvdata, outputDir, corr_opt):
meshDir = "{outputDir}/Processing/1.MeasurementandSPHARM".format(
**locals())
shapeworksDir = "{outputDir}/Processing/2.shapeworks".format(**locals())
sampleDir = "{outputDir}/Processing/3.sampling".format(**locals())
statDir = "{outputDir}/Statistics".format(**locals())
pathKmesh = config["kmeshPath"]
if (corr_opt == "initial_dense"):
extra_args = "--inputPointFlip"
else:
extra_args = ""
# depending on options, choose different meshes
# loop over ids
for id in [i for i, l, g in csvdata]:
distanceVector = "{sampleDir}/{id}.distanceVector.nrrd".format(
**locals())
inputMeasurement = "{meshDir}/{id}_measurementoutput.nrrd".format(
**locals())
# inputMeasurement = "%s/%s.thickness.mha" % (meshDir, id)
if (corr_opt == "initial_dense"):
samplingTxt = "%s/%s.initialDenseSampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothInitialDenseSampling.txt" % (
sampleDir, id)
samplingMeshOutput = "%s/%s.initialDenseSampling.vtk" % (sampleDir,
id)
originalMeshOutput = "%s/%s.initialDenseOriginal.vtk" % (sampleDir,
id)
inputMesh = "%s/%s.subj.SPHARM.vtk" % (meshDir, id)
elif (corr_opt == "correspondence"):
samplingTxt = "%s/%s.sampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothSampling.txt" % (sampleDir, id)
samplingMeshOutput = "%s/%s.sampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.original.vtk" % (sampleDir, id)
inputMesh = "%s/%s.correspondence.vtk" % (shapeworksDir, id)
elif (corr_opt == "dense_correspondence"):
samplingTxt = "%s/%s.denseSampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothDenseSampling.txt" % (sampleDir,
id)
samplingMeshOutput = "%s/%s.denseSampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.denseOriginal.vtk" % (sampleDir, id)
inputMesh = "%s/%s.dense_correspondence.vtk" % (shapeworksDir, id)
elif (corr_opt == "spharm_sampling"):
samplingTxt = "%s/%s.spharmSampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothSpharmSampling.txt" % (sampleDir,
id)
samplingMeshOutput = "%s/%s.spharmSampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.spharmOriginal.vtk" % (sampleDir, id)
inputMesh = "%s/%s.subj.SPHARM.vtk" % (meshDir, id)
#samplingCmd = "{MeshPointIntensitySamplingPath} --workDir {workdir} --inputAsPhysicalCoord {extra_args} --distanceVector {distanceVector} -i nn -a {samplingTxt} -m {samplingMeshOutput} --smoothedAttributeOutput {smoothSamplingTxt} --originalMeshOutput {originalMeshOutput} {inputMeasurement} {inputMesh}"
#exeCmd = samplingCmd.format(**locals())
# exeCmd = samplingCmd % (outputDir, distanceVector, samplingTxt, samplingMeshOutput, smoothSamplingTxt, originalMeshOutput, inputMeasurement, inputMesh)
#system.run_process(exeCmd,verbose=True)
if system.is_file_newer(smoothSamplingTxt, inputMeasurement, opts.overwrite) or \
system.is_file_newer(smoothSamplingTxt, samplingTxt, opts.overwrite) or \
system.is_file_newer(smoothSamplingTxt, samplingMeshOutput, opts.overwrite):
useStreamLine = corr_opt == "spharm_sampling"
if (not useStreamLine):
exeCmd = "{pathKmesh} -sampleImage {inputMeasurement} {inputMesh} {samplingMeshOutput} " +\
"-outputScalarName Thickness -zrotate"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
exeCmd = "{pathKmesh} -smoothScalars {samplingMeshOutput} {samplingMeshOutput} " +\
"-scalarName Thickness -outputScalarName smoothThickness -iter 3"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
exeCmd = "{pathKmesh} -exportScalars {samplingMeshOutput} {samplingTxt} -scalarName Thickness"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
exeCmd = "{pathKmesh} -exportScalars {samplingMeshOutput} {smoothSamplingTxt} " +\
"-scalarName smoothThickness "
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
else:
gradientFile = "{outputDir}/Processing/1.MeasurementandSPHARM/" +\
"{id}/laplacianGradient.nrrd".format(**locals())
gradientVTIFile = "{outputDir}/Processing/1.MeasurementandSPHARM/" +\
"{id}/laplacianGradient.vti".format(**locals())
streamLineFile = "{outputDir}/Processing/1.MeasurementandSPHARM/" +\
"{id}/stream_lines.vtp".format(**locals())
# vti image creation
exeCmd = "{pathKmesh} -vti {gradientFile} {gradientVTIFile} -attrDim 3"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
# RK45 integration
exeCmd = "{pathKmesh} -zrotate -traceDirection backward -traceStream " +\
"{gradientVTIFile} {inputMesh} {streamLineFile} {samplingMeshOutput}"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
# scalar export
exeCmd = "{pathKmesh} -scalarName Length -exportScalars " +\
"{samplingMeshOutput} {smoothSamplingTxt}"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd, verbose=True)
def regenerate_segmentations(data, config, outputdir):
pathKmesh = config["kmeshPath"]
pathKcalc = config["kcalcPath"]
workdir = "{outputdir}/Processing/1.MeasurementandSPHARM".format(**locals())
# before executing the boundary correction
# check if none of input is not generated.
testLabelMapsFail = False in [os.path.exists(x) for (t,x,g) in data]
if testLabelMapsFail:
raise RuntimeError("There are missing label maps")
surfaceInputList = ["{workdir}/{id}.subj.SPHARM.vtk".format(**locals()) for (id,l,g) in data]
testSurfaceInputsFail = False in [os.path.exists(x) for x in surfaceInputList]
if testSurfaceInputsFail:
raise RuntimeError("There are missing surface inputs. Check SPHARM results!")
if opts.nop1 is False:
for idx, (id,labelMap,group) in enumerate(data):
labelOutput = "{workdir}/{id}.zerocortex.nrrd".format(**locals())
surfaceInput = "{workdir}/{id}.subj.SPHARM.vtk".format(**locals())
#surfaceInput = "{workdir}/{id}.surf.vtk".format(**locals())
surfaceLabels = "{workdir}/{id}.labels.vtp".format(**locals())
if system.is_file_newer(labelOutput, labelMap, opts.overwrite):
cmd = "{pathKcalc} -e 'A==3?0:A' -o {labelOutput} {labelMap}"
cmd = cmd.format(**locals())
if system.run_process(cmd,verbose=True) != 0:
raise RuntimeError("fail to modify labelmap")
if system.is_file_newer(surfaceLabels, surfaceInput, opts.overwrite) or \
system.is_file_newer(surfaceLabels, labelOutput, opts.overwrite):
cmd = "{pathKmesh} -sampleImage -zrotate -outputScalarName labels " + \
"{labelOutput} {surfaceInput} {surfaceLabels}"
cmd = cmd.format(**locals())
if system.run_process(cmd,verbose=True) != 0:
raise RuntimError("fail to run kmesh")
# compute the average of labels scalar values to smooth out
if opts.nop2 is False:
cmd = "{pathKmesh} -averageScalars -threshold 1.8 " + \
"-scalarName labels -outputScalarName meanLabels"
cmd = cmd.format(**locals())
for (tag, labelmap, group) in data:
surfaceMeshWithLabels = "{workdir}/{tag}.labels.vtp".format(**locals())
cmd += " " + surfaceMeshWithLabels
system.run_process(cmd,verbose=True)
if opts.nop3 is False:
for idx,(tag,labelMap,group) in enumerate(data):
labelOutput = "{workdir}/{tag}.zerocortex.nrrd".format(**locals())
surfaceLabels = "{workdir}/{tag}.labels.vtp".format(**locals())
voronoiImage = "{workdir}/{tag}.voronoi.mha".format(**locals())
surfaceImage = "{workdir}/{tag}.solution.mha".format(**locals())
boundaryMap = "{workdir}/{tag}.boundaryMap.mha".format(**locals())
if system.is_file_newer(labelOutput, voronoiImage, opts.overwrite) or \
system.is_file_newer(surfaceLabels, voronoiImage, opts.overwrite):
cmd = "{pathKmesh} -voronoiImage -zrotate -scalarName meanLabels " +\
"{labelOutput} {surfaceLabels} -o {voronoiImage}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
if system.is_file_newer(labelOutput, voronoiImage, opts.overwrite) or \
system.is_file_newer(surfaceLabels, voronoiImage, opts.overwrite):
cmd = "{pathKmesh} -scanConversion -zrotate " +\
"{surfaceLabels} {labelOutput} {surfaceImage}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
if system.is_file_newer(voronoiImage, boundaryMap, opts.overwrite) or \
system.is_file_newer(surfaceImage, boundaryMap, opts.overwrite):
cmd = "{pathKcalc} -e 'B>0?3:A' -o {boundaryMap} " +\
"{voronoiImage} {surfaceImage}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
def sample_thickness(opts,config,csvdata,outputDir,corr_opt):
meshDir = "{outputDir}/Processing/1.MeasurementandSPHARM".format(**locals())
shapeworksDir = "{outputDir}/Processing/2.shapeworks".format(**locals())
sampleDir = "{outputDir}/Processing/3.sampling".format(**locals())
statDir = "{outputDir}/Statistics".format(**locals())
pathKmesh = config["kmeshPath"]
if (corr_opt == "initial_dense"):
extra_args = "--inputPointFlip"
else:
extra_args = ""
# depending on options, choose different meshes
# loop over ids
for id in [i for i,l,g in csvdata]:
distanceVector = "{sampleDir}/{id}.distanceVector.nrrd".format(**locals())
inputMeasurement = "{meshDir}/{id}_measurementoutput.nrrd".format(**locals())
# inputMeasurement = "%s/%s.thickness.mha" % (meshDir, id)
if (corr_opt == "initial_dense"):
samplingTxt = "%s/%s.initialDenseSampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothInitialDenseSampling.txt" % (sampleDir, id)
samplingMeshOutput = "%s/%s.initialDenseSampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.initialDenseOriginal.vtk" % (sampleDir, id)
inputMesh = "%s/%s.subj.SPHARM.vtk" % (meshDir, id)
elif (corr_opt == "correspondence"):
samplingTxt = "%s/%s.sampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothSampling.txt" % (sampleDir, id)
samplingMeshOutput = "%s/%s.sampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.original.vtk" % (sampleDir, id)
inputMesh = "%s/%s.correspondence.vtk" % (shapeworksDir, id)
elif (corr_opt == "dense_correspondence"):
samplingTxt = "%s/%s.denseSampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothDenseSampling.txt" % (sampleDir, id)
samplingMeshOutput = "%s/%s.denseSampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.denseOriginal.vtk" % (sampleDir, id)
inputMesh = "%s/%s.dense_correspondence.vtk" % (shapeworksDir, id)
elif (corr_opt == "spharm_sampling"):
samplingTxt = "%s/%s.spharmSampling.txt" % (sampleDir, id)
smoothSamplingTxt = "%s/%s.smoothSpharmSampling.txt" % (sampleDir, id)
samplingMeshOutput = "%s/%s.spharmSampling.vtk" % (sampleDir, id)
originalMeshOutput = "%s/%s.spharmOriginal.vtk" % (sampleDir, id)
inputMesh = "%s/%s.subj.SPHARM.vtk" % (meshDir, id)
#samplingCmd = "{MeshPointIntensitySamplingPath} --workDir {workdir} --inputAsPhysicalCoord {extra_args} --distanceVector {distanceVector} -i nn -a {samplingTxt} -m {samplingMeshOutput} --smoothedAttributeOutput {smoothSamplingTxt} --originalMeshOutput {originalMeshOutput} {inputMeasurement} {inputMesh}"
#exeCmd = samplingCmd.format(**locals())
# exeCmd = samplingCmd % (outputDir, distanceVector, samplingTxt, samplingMeshOutput, smoothSamplingTxt, originalMeshOutput, inputMeasurement, inputMesh)
#system.run_process(exeCmd,verbose=True)
if system.is_file_newer(smoothSamplingTxt, inputMeasurement, opts.overwrite) or \
system.is_file_newer(smoothSamplingTxt, samplingTxt, opts.overwrite) or \
system.is_file_newer(smoothSamplingTxt, samplingMeshOutput, opts.overwrite):
useStreamLine = corr_opt == "spharm_sampling"
if (not useStreamLine):
exeCmd = "{pathKmesh} -sampleImage {inputMeasurement} {inputMesh} {samplingMeshOutput} " +\
"-outputScalarName Thickness -zrotate"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
exeCmd = "{pathKmesh} -smoothScalars {samplingMeshOutput} {samplingMeshOutput} " +\
"-scalarName Thickness -outputScalarName smoothThickness -iter 3"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
exeCmd = "{pathKmesh} -exportScalars {samplingMeshOutput} {samplingTxt} -scalarName Thickness"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
exeCmd = "{pathKmesh} -exportScalars {samplingMeshOutput} {smoothSamplingTxt} " +\
"-scalarName smoothThickness "
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
else:
gradientFile = "{outputDir}/Processing/1.MeasurementandSPHARM/" +\
"{id}/laplacianGradient.nrrd".format(**locals())
gradientVTIFile = "{outputDir}/Processing/1.MeasurementandSPHARM/" +\
"{id}/laplacianGradient.vti".format(**locals())
streamLineFile = "{outputDir}/Processing/1.MeasurementandSPHARM/" +\
"{id}/stream_lines.vtp".format(**locals())
# vti image creation
exeCmd = "{pathKmesh} -vti {gradientFile} {gradientVTIFile} -attrDim 3"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
# RK45 integration
exeCmd = "{pathKmesh} -zrotate -traceDirection backward -traceStream " +\
"{gradientVTIFile} {inputMesh} {streamLineFile} {samplingMeshOutput}"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
# scalar export
exeCmd = "{pathKmesh} -scalarName Length -exportScalars " +\
"{samplingMeshOutput} {smoothSamplingTxt}"
exeCmd = exeCmd.format(**locals())
system.run_process(exeCmd,verbose=True)
