def run_particle_tools(config, data, outputdir, ids):
import sys,os
pathPython = sys.executable
pathShapeWorksScript = os.path.dirname(os.path.abspath(__file__)) + "/shapeworks.py"
pathShapeWorksRun = config["ShapeWorksRunPath"]
pathImageMath = config["ImageMathPath"]
pathShapeWorksGroom = config["ShapeWorksGroomPath"]
pathBinaryToDistanceMap = config["BinaryToDistanceMapPath"]
workdir = "%s/Processing/2.shapeworks" % (outputdir)
# generate binary distance map for each label map
# cmd = "%s %s %s/inputimage.txt %s/inputsurfacemodels.txt -c %s/outputCorrespondence.txt -w %s/outputWarped.txt --workingDir %s --pathShapeWorksRun %s --pathShapeWorksGroom %s --pathImageMath %s --pathBinaryToDistanceMap %s" % (pathPython, pathShapeWorksScript, workdir, workdir, workdir, workdir, workdir, pathShapeWorksRun, pathShapeWorksGroom, pathImageMath, pathBinaryToDistanceMap)
outputCorrespondence = "{workdir}/outputCorrespondence.txt"
outputCorrespondence = outputCorrespondence.format(**locals())
if (not system.is_file_exist(outputCorrespondence,opts.overwrite)):
cmd = "{pathPython} {pathShapeWorksScript} {workdir}/inputimage.txt " +\
"{workdir}/inputsurfacemodels.txt " + \
"-c {workdir}/outputCorrespondence.txt " +\
"-w {workdir}/outputWarped.txt " +\
"--workingDir {workdir}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
def run_particle_tools(config, data, outputdir, ids):
import sys,os
pathPython = sys.executable
pathShapeWorksScript = os.path.dirname(os.path.abspath(__file__)) + "/shapeworks.py"
pathShapeWorksRun = config["ShapeWorksRunPath"]
pathImageMath = config["ImageMathPath"]
pathShapeWorksGroom = config["ShapeWorksGroomPath"]
pathBinaryToDistanceMap = config["BinaryToDistanceMapPath"]
workdir = "%s/Processing/2.shapeworks" % (outputdir)
# generate binary distance map for each label map
# cmd = "%s %s %s/inputimage.txt %s/inputsurfacemodels.txt -c %s/outputCorrespondence.txt -w %s/outputWarped.txt --workingDir %s --pathShapeWorksRun %s --pathShapeWorksGroom %s --pathImageMath %s --pathBinaryToDistanceMap %s" % (pathPython, pathShapeWorksScript, workdir, workdir, workdir, workdir, workdir, pathShapeWorksRun, pathShapeWorksGroom, pathImageMath, pathBinaryToDistanceMap)
outputCorrespondence = "{workdir}/outputCorrespondence.txt"
outputCorrespondence = outputCorrespondence.format(**locals())
if (not system.is_file_exist(outputCorrespondence,opts.overwrite)):
cmd = "{pathPython} {pathShapeWorksScript} {workdir}/inputimage.txt " +\
"{workdir}/inputsurfacemodels.txt " + \
"-c {workdir}/outputCorrespondence.txt " +\
"-w {workdir}/outputWarped.txt " +\
"--workingDir {workdir}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=True)
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)
def file_exists(f):
return not opts.overwrite and os.path.isfile(f) and os.stat(f).st_size > 0
for idx,(pf,sf,lm,lp,hm,hp) in enumerate(dataset):
if not file_exists(lm):
if idx == 0:
cmd = "%s %s %s --subdivLevel 10 --spharmDegree 20 %s/%s.ip. --paraOut" % (pathParaToSPHARM, pf, sf, workdir, idlist[idx])
else:
cmd = "%s %s %s --subdivLevel 10 --spharmDegree 20 %s/%s.ip. --flipTemplateOn --flipTemplate %s/%s.ip.SPHARM.coef --paraOut" % (pathParaToSPHARM, pf, sf, workdir, idlist[idx], workdir, idlist[idx-1])
system.run_process(cmd,verbose=opts.verbose)
if not file_exists(hm):
if idx == 0:
cmd = "%s %s %s --subdivLevel 50 --spharmDegree 20 %s/%s.subj. --paraOut" % (pathParaToSPHARM, pf, sf, workdir, idlist[idx])
else:
cmd = "%s %s %s --subdivLevel 50 --spharmDegree 20 %s/%s.subj. --flipTemplateOn --flipTemplate %s/%s.subj.SPHARM.coef --paraOut" % (pathParaToSPHARM, pf, sf, workdir, idlist[idx], workdir, idlist[idx-1])
system.run_process(cmd,verbose=opts.verbose)
def resample_segmentations(config,data,outputdir):
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
reference_image = "%s/%s.segpost.nii.gz" % (workdir,data[0][0])
pathResampleVolume = config["ResampleVolume2Path"]
for id,l,g in data:
segpost_image = "%s/%s.segpost.nii.gz" % (workdir,id)
labelMapNCResampled = "%s/%s.labelMapNCsegmentation.nrrd" % (workdir,id)
cmd = "%s %s %s -R %s -i nn" % (pathResampleVolume, \
segpost_image, labelMapNCResampled, reference_image)
system.run_process(cmd,verbose=True)
def resample_segmentations(config, data, outputdir):
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
reference_image = "%s/%s.segpost.nii.gz" % (workdir, data[0][0])
pathResampleVolume = config["ResampleVolume2Path"]
for id, l, g in data:
segpost_image = "%s/%s.segpost.nii.gz" % (workdir, id)
labelMapNCResampled = "%s/%s.labelMapNCsegmentation.nrrd" % (workdir,
id)
cmd = "%s %s %s -R %s -i nn" % (pathResampleVolume, \
segpost_image, labelMapNCResampled, reference_image)
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 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 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 run_particle_tools(config, data, outputdir, ids):
pathPython = config["PythonPath"]
pathShapeWorksScript = config["ShapeWorksPythonScriptPath"]
pathShapeWorksRun = config["ShapeWorksRunPath"]
pathImageMath = config["ImageMathPath"]
pathShapeWorksGroom = config["ShapeWorksGroomPath"]
pathBinaryToDistanceMap = config["BinaryToDistanceMapPath"]
workdir = "%s/Processing/2.shapeworks" % (outputdir)
# generate binary distance map for each label map
# cmd = "%s %s %s/inputimage.txt %s/inputsurfacemodels.txt -c %s/outputCorrespondence.txt -w %s/outputWarped.txt --workingDir %s --pathShapeWorksRun %s --pathShapeWorksGroom %s --pathImageMath %s --pathBinaryToDistanceMap %s" % (pathPython, pathShapeWorksScript, workdir, workdir, workdir, workdir, workdir, pathShapeWorksRun, pathShapeWorksGroom, pathImageMath, pathBinaryToDistanceMap)
cmd = "%s %s %s/inputimage.txt %s/inputsurfacemodels.txt " + \
"-c %s/outputCorrespondence.txt -w %s/outputWarped.txt " +\
"--workingDir %s" % (pathPython, pathShapeWorksScript, \
workdir, workdir, workdir, workdir, workdir)
system.run_process(cmd,verbose=True)
def run_particle_tools(config, data, outputdir, ids):
pathPython = config["PythonPath"]
pathShapeWorksScript = config["ShapeWorksPythonScriptPath"]
pathShapeWorksRun = config["ShapeWorksRunPath"]
pathImageMath = config["ImageMathPath"]
pathShapeWorksGroom = config["ShapeWorksGroomPath"]
pathBinaryToDistanceMap = config["BinaryToDistanceMapPath"]
workdir = "%s/Processing/2.shapeworks" % (outputdir)
# generate binary distance map for each label map
# cmd = "%s %s %s/inputimage.txt %s/inputsurfacemodels.txt -c %s/outputCorrespondence.txt -w %s/outputWarped.txt --workingDir %s --pathShapeWorksRun %s --pathShapeWorksGroom %s --pathImageMath %s --pathBinaryToDistanceMap %s" % (pathPython, pathShapeWorksScript, workdir, workdir, workdir, workdir, workdir, pathShapeWorksRun, pathShapeWorksGroom, pathImageMath, pathBinaryToDistanceMap)
cmd = "%s %s %s/inputimage.txt %s/inputsurfacemodels.txt " + \
"-c %s/outputCorrespondence.txt -w %s/outputWarped.txt " +\
"--workingDir %s" % (pathPython, pathShapeWorksScript, \
workdir, workdir, workdir, workdir, workdir)
system.run_process(cmd, verbose=True)
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 compute_thickness(config, data, outputdir, ids, idl, idh):
pathTool = config["measureThicknessFilterPath"]
for (id, labelmap, group) in data:
workdir = "%s/Processing/1.MeasurementandSPHARM/%s" % (outputdir, id)
measurementoutput = "%s/Processing/1.MeasurementandSPHARM/%s_measurementoutput.nrrd" % (outputdir, id)
# temporary
# workdir = "%s/Processing/1.MeasurementandSPHARM/%s_2" % (outputdir, id)
labelmap = "%s/Processing/1.MeasurementandSPHARM/%s.boundaryMap.mha" % (outputdir, id)
# measurementoutput = "%s/Processing/1.MeasurementandSPHARM/%s.thickness.mha" % (outputdir, id)
if (not os.path.exists(workdir)):
os.makedirs(workdir)
if (not os.path.isfile(measurementoutput)):
cmd = "%s --mr --sbt --workdir %s --ids %s --idl %s --idh %s --ttrns 500 %s %s" % (pathTool, workdir, ids, idl, idh, labelmap, measurementoutput)
print cmd
system.run_process(cmd,verbose=True)
else:
print "Skipping", measurementoutput
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)
def file_exists(f):
return not opts.overwrite and os.path.isfile(
f) and os.stat(f).st_size > 0
for idx, (pf, sf, lm, lp, hm, hp) in enumerate(dataset):
if not file_exists(lm):
if idx == 0:
cmd = "%s %s %s --subdivLevel 10 --spharmDegree 20 %s/%s.ip. --paraOut" % (
pathParaToSPHARM, pf, sf, workdir, idlist[idx])
else:
cmd = "%s %s %s --subdivLevel 10 --spharmDegree 20 %s/%s.ip. --flipTemplateOn --flipTemplate %s/%s.ip.SPHARM.coef --paraOut" % (
pathParaToSPHARM, pf, sf, workdir, idlist[idx], workdir,
idlist[idx - 1])
system.run_process(cmd, verbose=opts.verbose)
if not file_exists(hm):
if idx == 0:
cmd = "%s %s %s --subdivLevel 50 --spharmDegree 20 %s/%s.subj. --paraOut" % (
pathParaToSPHARM, pf, sf, workdir, idlist[idx])
else:
cmd = "%s %s %s --subdivLevel 50 --spharmDegree 20 %s/%s.subj. --flipTemplateOn --flipTemplate %s/%s.subj.SPHARM.coef --paraOut" % (
pathParaToSPHARM, pf, sf, workdir, idlist[idx], workdir,
idlist[idx - 1])
system.run_process(cmd, verbose=opts.verbose)
def genparamesh(opts, config, data, outputDir):
pathGenParaMesh = config["GenParaMeshCLPPath"]
pathImageMath = config["ImageMathPath"]
pathSegPostProcess = config["SegPostProcessCLPPath"]
workdir = "{outputDir}/Processing/1.MeasurementandSPHARM".format(
**locals())
for (id, labelmap, group) in data:
eulerName = "{workdir}/{id}.euler.txt".format(**locals())
paraFile = "{workdir}/{id}.para.vtk".format(**locals())
surfFile = "{workdir}/{id}.surf.vtk".format(**locals())
surfaceLabel = "{workdir}/{id}.seg.nii.gz".format(**locals())
segpostLabel = "{workdir}/{id}.segpost.nii.gz".format(**locals())
if (not system.is_file_exist(surfaceLabel, opts.overwrite)):
ids = opts.ids
cmd = "{pathImageMath} {labelmap} -extractLabel {ids} -outfile {surfaceLabel}"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=opts.verbose)
if (not system.is_file_exist(segpostLabel, opts.overwrite)):
cmd = "{pathSegPostProcess} {surfaceLabel} {segpostLabel}"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=opts.verbose)
if (not system.is_file_exist(paraFile, opts.overwrite)):
num_iters = opts.genparamesh_iter
cmd = "{pathGenParaMesh} --EulerFile --outEulerName {eulerName} {segpostLabel} " +\
"--iter {num_iters} --label 1 {paraFile} {surfFile}"
cmd = cmd.format(**locals())
system.run_process(cmd, verbose=opts.verbose)
def genparamesh(opts, config, data, outputDir):
pathGenParaMesh = config["GenParaMeshCLPPath"]
pathImageMath = config["ImageMathPath"]
pathSegPostProcess = "SegPostProcess" #config["SegPostProcess"]
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
# check if executables exist
find_executables([pathGenParaMesh, pathImageMath, pathSegPostProcess])
def file_exists(f):
return not opts.overwrite and os.path.isfile(f) and os.stat(f).st_size > 0
for (id, labelmap, group) in data:
eulerName = "%s/%s.euler.txt" % (workdir, id)
paraFile = "%s/%s.para.vtk" % (workdir, id)
surfFile = "%s/%s.surf.vtk" % (workdir, id)
surfaceLabel = "%s/%s.seg.nii.gz" % (workdir, id)
segpostLabel = "%s/%s.segpost.nii.gz" % (workdir, id)
if (not file_exists(surfaceLabel)):
cmd = "%s %s -extractLabel %s -outfile %s" \
% (pathImageMath, labelmap, opts.ids, surfaceLabel)
system.run_process(cmd,verbose=opts.verbose)
if (not file_exists(segpostLabel)):
cmd = "%s %s -o %s" \
% (pathSegPostProcess, surfaceLabel, segpostLabel)
system.run_process(cmd,verbose=opts.verbose)
if (not file_exists(paraFile)):
num_iters = opts.genparamesh_iter
cmd = "%s --EulerFile --outEulerName %s %s --iter %d --label %s %s %s" \
% (pathGenParaMesh, eulerName, segpostLabel, num_iters, 1, paraFile, surfFile)
system.run_process(cmd,verbose=opts.verbose)
def genparamesh(opts, config, data, outputDir):
pathGenParaMesh = config["GenParaMeshCLPPath"]
pathImageMath = config["ImageMathPath"]
pathSegPostProcess = config["SegPostProcessCLPPath"]
workdir = "{outputDir}/Processing/1.MeasurementandSPHARM".format(**locals())
for (id, labelmap, group) in data:
eulerName = "{workdir}/{id}.euler.txt".format(**locals())
paraFile = "{workdir}/{id}.para.vtk".format(**locals())
surfFile = "{workdir}/{id}.surf.vtk".format(**locals())
surfaceLabel = "{workdir}/{id}.seg.nii.gz".format(**locals())
segpostLabel = "{workdir}/{id}.segpost.nii.gz".format(**locals())
if (not system.is_file_exist(surfaceLabel,opts.overwrite)):
ids = opts.ids
cmd = "{pathImageMath} {labelmap} -extractLabel {ids} -outfile {surfaceLabel}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=opts.verbose)
if (not system.is_file_exist(segpostLabel,opts.overwrite)):
cmd = "{pathSegPostProcess} {surfaceLabel} {segpostLabel}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=opts.verbose)
if (not system.is_file_exist(paraFile,opts.overwrite)):
num_iters = opts.genparamesh_iter
cmd = "{pathGenParaMesh} --EulerFile --outEulerName {eulerName} {segpostLabel} " +\
"--iter {num_iters} --label 1 {paraFile} {surfFile}"
cmd = cmd.format(**locals())
system.run_process(cmd,verbose=opts.verbose)
def genparamesh(opts, config, data, outputDir):
pathGenParaMesh = config["GenParaMeshCLPPath"]
pathImageMath = config["ImageMathPath"]
pathSegPostProcess = "SegPostProcess" #config["SegPostProcess"]
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
# check if executables exist
find_executables([pathGenParaMesh, pathImageMath, pathSegPostProcess])
def file_exists(f):
return not opts.overwrite and os.path.isfile(
f) and os.stat(f).st_size > 0
for (id, labelmap, group) in data:
eulerName = "%s/%s.euler.txt" % (workdir, id)
paraFile = "%s/%s.para.vtk" % (workdir, id)
surfFile = "%s/%s.surf.vtk" % (workdir, id)
surfaceLabel = "%s/%s.seg.nii.gz" % (workdir, id)
segpostLabel = "%s/%s.segpost.nii.gz" % (workdir, id)
if (not file_exists(surfaceLabel)):
cmd = "%s %s -extractLabel %s -outfile %s" \
% (pathImageMath, labelmap, opts.ids, surfaceLabel)
system.run_process(cmd, verbose=opts.verbose)
if (not file_exists(segpostLabel)):
cmd = "%s %s -o %s" \
% (pathSegPostProcess, surfaceLabel, segpostLabel)
system.run_process(cmd, verbose=opts.verbose)
if (not file_exists(paraFile)):
num_iters = opts.genparamesh_iter
cmd = "%s --EulerFile --outEulerName %s %s --iter %d --label %s %s %s" \
% (pathGenParaMesh, eulerName, segpostLabel, num_iters, 1, paraFile, surfFile)
system.run_process(cmd, verbose=opts.verbose)
def compute_thickness(config, data, outputdir, ids, idl, idh):
pathTool = config["measureThicknessFilterPath"]
for (id, labelmap, group) in data:
workdir = "%s/Processing/1.MeasurementandSPHARM/%s" % (outputdir, id)
measurementoutput = "%s/Processing/1.MeasurementandSPHARM/%s_measurementoutput.nrrd" % (
outputdir, id)
# temporary
# workdir = "%s/Processing/1.MeasurementandSPHARM/%s_2" % (outputdir, id)
labelmap = "%s/Processing/1.MeasurementandSPHARM/%s.boundaryMap.mha" % (
outputdir, id)
# measurementoutput = "%s/Processing/1.MeasurementandSPHARM/%s.thickness.mha" % (outputdir, id)
if (not os.path.exists(workdir)):
os.makedirs(workdir)
if (not os.path.isfile(measurementoutput)):
cmd = "%s --mr --sbt --workdir %s --ids %s --idl %s --idh %s --ttrns 500 %s %s" % (
pathTool, workdir, ids, idl, idh, labelmap, measurementoutput)
print cmd
system.run_process(cmd, verbose=True)
else:
print "Skipping", measurementoutput
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 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 perform_analysis(opts, config, csvdata, outputDir, corr_opt="initial_dense"):
ids = [i for i,l,g in csvdata]
groups = [g for i,l,g in csvdata]
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())
sample_thickness(opts,config,csvdata,outputDir,corr_opt)
# collect_attributes()
# compute_statistics()
# aggregate sampling files into a single file
groupSet = set(groups)
datafiles = []
tag = ""
for group in groupSet:
# setup output filename template
if (corr_opt == "initial_dense"):
tag = "_initialDenseSampling"
datafilename = "%s/data_initialDenseSampling_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_initialDenseSampling_%s.txt" % (statDir, group)
outfilename = "%s/list_initialDenseSampling_%s.txt" % (statDir, group)
elif (corr_opt == "correspondence"):
tag = ""
datafilename = "%s/data_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_%s.txt" % (statDir, group)
outfilename = "%s/list_%s.txt" % (statDir, group)
elif (corr_opt == "dense_correspondence"):
tag = "_dense"
datafilename = "%s/data_dense_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_dense_%s.txt" % (statDir, group)
outfilename = "%s/list_dense_%s.txt" % (statDir, group)
elif (corr_opt == "spharm_sampling"):
tag = "_spharm"
datafilename = "%s/data_spharm_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_spharm_%s.txt" % (statDir, group)
outfilename = "%s/list_spharm_%s.txt" % (statDir, group)
# process and write the aggregated data
outfile = open(outfilename, 'w')
for (id, g) in zip(ids, groups):
if (g != group):
continue
if (corr_opt == "initial_dense"):
samplingTxt = "%s/%s.smoothInitialDenseSampling.txt" % (sampleDir, id)
elif (corr_opt == "correspondence"):
samplingTxt = "%s/%s.smoothSampling.txt" % (sampleDir, id)
elif (corr_opt == "dense_correspondence"):
samplingTxt = "%s/%s.smoothDenseSampling.txt" % (sampleDir, id)
elif (corr_opt == "spharm_sampling"):
samplingTxt = "%s/%s.smoothSpharmSampling.txt" % (sampleDir, id)
if (os.path.isfile(samplingTxt)):
outfile.write(samplingTxt)
outfile.write("\n")
else:
print "can't find", samplingTxt
outfile.close()
# concatenate those attribute files into a file
concatColumnsToFile(outfilename, datafilename)
datafiles.append((group, datafilename))
# perform statistical analysis
rscriptExePath = config["RscriptPath"]
rscriptPath = os.path.dirname(os.path.abspath(__file__)) + "/rodentThicknessStats.r"
if (corr_opt == "initial_dense"):
outputfile = "%s/stats.initialDenseSampling.txt" % statDir
outputVTK = "%s/stats.initialDenseSampling.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
elif (corr_opt == "correspondence"):
outputfile = "%s/stats.correspondence.txt" % statDir
outputVTK = "%s/stats.correspondence.vtk" % (statDir)
inputVTK = "%s/%s.correspondence.vtk" % (shapeworksDir, ids[0])
elif (corr_opt == "dense_correspondence"):
outputfile = "%s/stats.denseCorrespondence.txt" % statDir
outputVTK = "%s/stats.denseCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.dense_correspondence.vtk" % (shapeworksDir, ids[0])
elif (corr_opt == "spharm_sampling"):
outputfile = "%s/stats.spharmCorrespondence.txt" % statDir
outputVTK = "%s/stats.spharmCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
#pythonScriptPath = config["vtkPointAttributesPythonScriptPath"]
pathKmesh = config["kmeshPath"]
datafilelist = ""
datagroups = ""
for (group, file) in datafiles:
datafilelist = datafilelist + " " + file
datagroups = datagroups + " " + group
# compute per-group statistics
cmd = "%s -computeVectorStats -scalarName %s -importVectors %s %s %s/%s_thickness.vtk" % (pathKmesh, group + "_Thickness", inputVTK, file, statDir, group)
system.run_process(cmd,verbose=True)
if (len(datafiles) > 1):
runCmd = "%s %s %s %s %s" % (rscriptExePath, rscriptPath, datafilelist, outputfile, datagroups)
system.run_process(runCmd,verbose=True)
#visCmd = "%s %s %s %s -i %s -t" % (pythonPath, pythonScriptPath, inputVTK, outputVTK, outputfile)
visCmd = "%s -use-header %s %s -importCSV %s" % (pathKmesh, inputVTK, outputVTK, outputfile)
system.run_process(visCmd,verbose=True)
# connected components for p-value
print "computing connected components with t.pvalue..."
runCmd = "%s -connectScalars %s -scalarName t.pvalue %s -thresholdMin 0 -thresholdMax 0.05" % (pathKmesh, outputVTK, outputVTK)
system.run_process(runCmd,verbose=True)
print "export scalars..."
runCmd = "%s -exportScalars -scalarName RegionIds %s %s/regionIds.txt" % (pathKmesh, outputVTK, statDir)
system.run_process(runCmd,verbose=True)
# create a combined data file with regions
regionIdFile = "%s/regionIds.txt" % (statDir)
if os.path.exists(regionIdFile):
for (group, file) in datafiles:
dataregionfilename = "%s/data_region%s_%s.txt" % (statDir, tag, group)
concatColumnsToFile([regionIdFile, "%s/data%s_%s.txt" % (statDir, tag, group)], dataregionfilename, inputIsList = True)
# perform splitting
performSplit([dataregionfilename], "%s/data_%s_region_" % (statDir, group) + "%02d.txt")
# boxplot
draw_boxplot = True
if draw_boxplot:
groupList = list(groupSet)
try:
print sys.path
import boxplot
gr1 = groupList[0]
gr2 = groupList[1]
boxplot.draw_boxplot(groupList[0], groupList[1], \
"{statDir}/data_{gr1}_region_*.txt".format(**locals()), \
"{statDir}/data_{gr2}_region_*.txt".format(**locals()), \
"{statDir}/{gr1}_{gr2}_regions.pdf".format(**locals()))
except BaseException as e:
print system.bcolors.WARNING + e.message + system.bcolors.ENDC
pass
def performAnalysis(cvsdata, config, outputDir, opt="initial_dense"):
ids = []
groups = []
for (id, labelmap, group) in cvsdata:
ids.append(id)
groups.append(group)
meshDir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
shapeworksDir = "%s/Processing/2.shapeworks" % (outputDir)
sampleDir = "%s/Processing/3.meshintensity" % (outputDir)
statDir = "%s/Statistical" % (outputDir)
pathKmesh = config["kmeshPath"]
if (opt == "initial_dense"):
samplingCmd = config[
"MeshPointIntensitySamplingPath"] + " --workDir %s --inputAsPhysicalCoord --inputPointFlip --distanceVector %s -i nn -a %s -m %s --smoothedAttributeOutput %s --originalMeshOutput %s %s %s"
else:
samplingCmd = config[
"MeshPointIntensitySamplingPath"] + " --workDir %s --inputAsPhysicalCoord --distanceVector %s -i nn -a %s -m %s --smoothedAttributeOutput %s --originalMeshOutput %s %s %s"
# depending on options, choose different meshes
# loop over ids
for id in ids:
distanceVector = "%s/%s.distanceVector.nrrd" % (sampleDir, id)
inputMeasurement = "%s/%s_measurementoutput.nrrd" % (meshDir, id)
# inputMeasurement = "%s/%s.thickness.mha" % (meshDir, id)
if (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 (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 (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 (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)
# execute sampling
# exeCmd = samplingCmd % (outputDir, distanceVector, samplingTxt, samplingMeshOutput, smoothSamplingTxt, originalMeshOutput, inputMeasurement, inputMesh)
# new sampling command
useStreamLine = True and opt == "spharm_sampling"
if (not useStreamLine):
exeCmd = "%s -sampleImage %s %s %s -outputScalarName Thickness -zrotate" % (
pathKmesh, inputMeasurement, inputMesh, samplingMeshOutput)
system.run_process(exeCmd, verbose=True)
exeCmd = "%s -smoothScalars %s %s -scalarName Thickness -outputScalarName smoothThickness -iter 3" % (
pathKmesh, samplingMeshOutput, samplingMeshOutput)
system.run_process(exeCmd, verbose=True)
exeCmd = "%s -exportScalars %s %s -scalarName Thickness " % (
pathKmesh, samplingMeshOutput, samplingTxt)
system.run_process(exeCmd, verbose=True)
exeCmd = "%s -exportScalars %s %s -scalarName smoothThickness " % (
pathKmesh, samplingMeshOutput, smoothSamplingTxt)
system.run_process(exeCmd, verbose=True)
else:
gradientFile = "%s/Processing/1.MeasurementandSPHARM/%s/laplacianGradient.nrrd" % (
outputDir, id)
gradientVTIFile = "%s/Processing/1.MeasurementandSPHARM/%s/laplacianGradient.vti" % (
outputDir, id)
streamLineFile = "%s/Processing/1.MeasurementandSPHARM/%s/stream_lines.vtp" % (
outputDir, id)
# vti image creation
exeCmd = "%s -vti %s %s -attrDim 3" % (pathKmesh, gradientFile,
gradientVTIFile)
system.run_process(exeCmd, verbose=True)
# RK45 integration
exeCmd = "%s -traceStream %s %s %s %s -zrotate -traceDirection backward" % (
pathKmesh, gradientVTIFile, inputMesh, streamLineFile,
samplingMeshOutput)
system.run_process(exeCmd, verbose=True)
# scalar export
exeCmd = "%s -exportScalars %s %s -scalarName Length " % (
pathKmesh, samplingMeshOutput, smoothSamplingTxt)
system.run_process(exeCmd, verbose=True)
# aggregate sampling files into a single file
groupSet = set(groups)
datafiles = []
tag = ""
for group in groupSet:
# setup output filename template
if (opt == "initial_dense"):
tag = "_initialDenseSampling"
datafilename = "%s/data_initialDenseSampling_%s.txt" % (statDir,
group)
dataregionfilename = "%s/data_region_initialDenseSampling_%s.txt" % (
statDir, group)
outfilename = "%s/list_initialDenseSampling_%s.txt" % (statDir,
group)
elif (opt == "correspondence"):
tag = ""
datafilename = "%s/data_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_%s.txt" % (statDir, group)
outfilename = "%s/list_%s.txt" % (statDir, group)
elif (opt == "dense_correspondence"):
tag = "_dense"
datafilename = "%s/data_dense_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_dense_%s.txt" % (statDir,
group)
outfilename = "%s/list_dense_%s.txt" % (statDir, group)
elif (opt == "spharm_sampling"):
tag = "_spharm"
datafilename = "%s/data_spharm_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_spharm_%s.txt" % (statDir,
group)
outfilename = "%s/list_spharm_%s.txt" % (statDir, group)
# process and write the aggregated data
outfile = open(outfilename, 'w')
for (id, g) in zip(ids, groups):
if (g != group):
continue
if (opt == "initial_dense"):
samplingTxt = "%s/%s.smoothInitialDenseSampling.txt" % (
sampleDir, id)
elif (opt == "correspondence"):
samplingTxt = "%s/%s.smoothSampling.txt" % (sampleDir, id)
elif (opt == "dense_correspondence"):
samplingTxt = "%s/%s.smoothDenseSampling.txt" % (sampleDir, id)
elif (opt == "spharm_sampling"):
samplingTxt = "%s/%s.smoothSpharmSampling.txt" % (sampleDir,
id)
if (os.path.isfile(samplingTxt)):
outfile.write(samplingTxt)
outfile.write("\n")
else:
print "can't find", samplingTxt
outfile.close()
# concatenate those attribute files into a file
concatColumnsToFile(outfilename, datafilename)
datafiles.append((group, datafilename))
# perform statistical analysis
rscriptExePath = config["RScriptPath"]
rscriptPath = config["RScriptRodentThicknessPath"]
if (opt == "initial_dense"):
outputfile = "%s/stats.initialDenseSampling.txt" % statDir
outputVTK = "%s/stats.initialDenseSampling.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
elif (opt == "correspondence"):
outputfile = "%s/stats.correspondence.txt" % statDir
outputVTK = "%s/stats.correspondence.vtk" % (statDir)
inputVTK = "%s/%s.correspondence.vtk" % (shapeworksDir, ids[0])
elif (opt == "dense_correspondence"):
outputfile = "%s/stats.denseCorrespondence.txt" % statDir
outputVTK = "%s/stats.denseCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.dense_correspondence.vtk" % (shapeworksDir, ids[0])
elif (opt == "spharm_sampling"):
outputfile = "%s/stats.spharmCorrespondence.txt" % statDir
outputVTK = "%s/stats.spharmCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
pythonPath = config["PythonPath"]
pythonScriptPath = config["vtkPointAttributesPythonScriptPath"]
datafilelist = ""
datagroups = ""
for (group, file) in datafiles:
datafilelist = datafilelist + " " + file
datagroups = datagroups + " " + group
# compute per-group statistics
cmd = "%s -computeVectorStats -scalarName %s -importVectors %s %s %s/%s_thickness.vtk" % (
pathKmesh, group + "_Thickness", inputVTK, file, statDir, group)
print cmd
system.run_process(cmd, verbose=True)
if (len(datafiles) > 1):
runCmd = "%s %s %s %s %s" % (rscriptExePath, rscriptPath, datafilelist,
outputfile, datagroups)
system.run_process(runCmd, verbose=True)
visCmd = "%s %s %s %s -i %s -t" % (pythonPath, pythonScriptPath,
inputVTK, outputVTK, outputfile)
system.run_process(visCmd, verbose=True)
# connected components for p-value
print "computing connected components with t.pvalue..."
runCmd = "%s -connectScalars %s -scalarName t.pvalue %s -thresholdMin 0 -thresholdMax 0.05" % (
pathKmesh, outputVTK, outputVTK)
system.run_process(runCmd, verbose=True)
print "export scalars..."
runCmd = "%s -exportScalars -scalarName RegionIds %s %s/regionIds.txt" % (
pathKmesh, outputVTK, statDir)
system.run_process(runCmd, verbose=True)
# create a combined data file with regions
regionIdFile = "%s/regionIds.txt" % (statDir)
if os.path.exists(regionIdFile):
for (group, file) in datafiles:
dataregionfilename = "%s/data_region%s_%s.txt" % (statDir, tag,
group)
concatColumnsToFile(
[regionIdFile,
"%s/data%s_%s.txt" % (statDir, tag, group)],
dataregionfilename,
inputIsList=True)
# perform splitting
performSplit([dataregionfilename], "%s/data_%s_region_" %
(statDir, group) + "%02d.txt")
# boxplot
groupList = list(groupSet)
runCmd = "%s %s '%s' '%s' %s/%s_%s_regions.pdf --label1 %s --label2 %s" % (
pythonPath,
pythonScriptPath.replace(
"vtkPointAttributes.py",
"boxplot.py"), "%s/data_%s_region_*.txt" %
(statDir, groupList[0]), "%s/data_%s_region_*.txt" %
(statDir, groupList[1]), statDir, groupList[0], groupList[1],
groupList[0], groupList[1])
print runCmd
system.run_process(runCmd, 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)
import system
import sys
import logging
system.setup_logger(logfilename="test.log")
retcode = system.run_process("/devel/linux/SPHARM-PDM/spharm-pdm-build-joowhi/bin/GenParaMeshCLP %s %s %s" % (sys.argv[1], sys.argv[2], sys.argv[3]), verbose=True)
print "Return Code = ", retcode
def regenerate_segmentations(data, config, outputdir):
pathKmesh = config["kmeshPath"]
pathKcalc = config["kcalcPath"]
workdir = "%s/Processing/1.MeasurementandSPHARM" % (outputdir)
# before executing the boundary correction
# check if none of input is not generated.
labelMapList = [labelMap for (tag, labelMap, group) in data]
testLabelMapsFail = False in [os.path.exists(x) for x in labelMapList]
if testLabelMapsFail:
raise RuntimeError("There are missing label maps")
surfaceInputList = [
"%s/%s.subj.SPHARM.vtk" % (workdir, tag)
for (tag, labelMap, group) 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!")
for (idx, item) in enumerate(data):
tag = item[0]
labelMap = item[1]
group = item[2]
labelOutput = workdir + "/" + tag + "/labelmap_zeroSolution.nrrd"
surfaceInput = workdir + "/" + tag + ".subj.SPHARM.vtk"
surfaceLabels = workdir + "/" + tag + ".labels.vtp"
voronoiImage = workdir + "/" + tag + ".voronoi.mha"
surfaceImage = workdir + "/" + tag + ".solution.mha"
boundaryMap = workdir + "/" + tag + ".boundaryMap.mha"
cmd = "%s -e 'A==3?0:A' -o %s %s" % (pathKcalc, labelOutput, labelMap)
system.run_process(cmd, verbose=True)
cmd = "%s -sampleImage -zrotate %s %s %s -outputScalarName labels" % (
pathKmesh, labelOutput, surfaceInput, surfaceLabels)
system.run_process(cmd, verbose=True)
cmd = "%s -averageScalars -threshold 1.8 -scalarName labels -outputScalarName meanLabels" % (
pathKmesh)
for (tag, labelmap, group) in data:
cmd += " " + workdir + "/" + tag + ".labels.vtp"
print cmd
system.run_process(cmd, verbose=True)
for (idx, item) in enumerate(data):
tag = item[0]
labelMap = item[1]
group = item[2]
labelOutput = workdir + "/" + tag + "/labelmap_zeroSolution.nrrd"
surfaceInput = workdir + "/" + tag + ".subj.SPHARM.vtk"
surfaceLabels = workdir + "/" + tag + ".labels.vtp"
voronoiImage = workdir + "/" + tag + ".voronoi.mha"
surfaceImage = workdir + "/" + tag + ".solution.mha"
boundaryMap = workdir + "/" + tag + ".boundaryMap.mha"
cmd = "%s -voronoiImage -zrotate %s %s %s -scalarName meanLabels" % (
pathKmesh, labelOutput, surfaceLabels, voronoiImage)
print cmd
system.run_process(cmd, verbose=True)
cmd = "%s -scanConversion -zrotate %s %s %s" % (
pathKmesh, surfaceLabels, labelOutput, surfaceImage)
print cmd
system.run_process(cmd, verbose=True)
cmd = "%s -e 'B>0?3:A' -o %s %s %s" % (pathKcalc, boundaryMap,
voronoiImage, surfaceImage)
print cmd
system.run_process(cmd, verbose=True)
def perform_analysis(opts,
config,
csvdata,
outputDir,
corr_opt="initial_dense"):
ids = [i for i, l, g in csvdata]
groups = [g for i, l, g in csvdata]
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())
sample_thickness(opts, config, csvdata, outputDir, corr_opt)
# collect_attributes()
# compute_statistics()
# aggregate sampling files into a single file
groupSet = set(groups)
datafiles = []
tag = ""
for group in groupSet:
# setup output filename template
if (corr_opt == "initial_dense"):
tag = "_initialDenseSampling"
datafilename = "%s/data_initialDenseSampling_%s.txt" % (statDir,
group)
dataregionfilename = "%s/data_region_initialDenseSampling_%s.txt" % (
statDir, group)
outfilename = "%s/list_initialDenseSampling_%s.txt" % (statDir,
group)
elif (corr_opt == "correspondence"):
tag = ""
datafilename = "%s/data_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_%s.txt" % (statDir, group)
outfilename = "%s/list_%s.txt" % (statDir, group)
elif (corr_opt == "dense_correspondence"):
tag = "_dense"
datafilename = "%s/data_dense_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_dense_%s.txt" % (statDir,
group)
outfilename = "%s/list_dense_%s.txt" % (statDir, group)
elif (corr_opt == "spharm_sampling"):
tag = "_spharm"
datafilename = "%s/data_spharm_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_spharm_%s.txt" % (statDir,
group)
outfilename = "%s/list_spharm_%s.txt" % (statDir, group)
# process and write the aggregated data
outfile = open(outfilename, 'w')
for (id, g) in zip(ids, groups):
if (g != group):
continue
if (corr_opt == "initial_dense"):
samplingTxt = "%s/%s.smoothInitialDenseSampling.txt" % (
sampleDir, id)
elif (corr_opt == "correspondence"):
samplingTxt = "%s/%s.smoothSampling.txt" % (sampleDir, id)
elif (corr_opt == "dense_correspondence"):
samplingTxt = "%s/%s.smoothDenseSampling.txt" % (sampleDir, id)
elif (corr_opt == "spharm_sampling"):
samplingTxt = "%s/%s.smoothSpharmSampling.txt" % (sampleDir,
id)
if (os.path.isfile(samplingTxt)):
outfile.write(samplingTxt)
outfile.write("\n")
else:
print "can't find", samplingTxt
outfile.close()
# concatenate those attribute files into a file
concatColumnsToFile(outfilename, datafilename)
datafiles.append((group, datafilename))
# perform statistical analysis
rscriptExePath = config["RscriptPath"]
rscriptPath = os.path.dirname(
os.path.abspath(__file__)) + "/rodentThicknessStats.r"
if (corr_opt == "initial_dense"):
outputfile = "%s/stats.initialDenseSampling.txt" % statDir
outputVTK = "%s/stats.initialDenseSampling.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
elif (corr_opt == "correspondence"):
outputfile = "%s/stats.correspondence.txt" % statDir
outputVTK = "%s/stats.correspondence.vtk" % (statDir)
inputVTK = "%s/%s.correspondence.vtk" % (shapeworksDir, ids[0])
elif (corr_opt == "dense_correspondence"):
outputfile = "%s/stats.denseCorrespondence.txt" % statDir
outputVTK = "%s/stats.denseCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.dense_correspondence.vtk" % (shapeworksDir, ids[0])
elif (corr_opt == "spharm_sampling"):
outputfile = "%s/stats.spharmCorrespondence.txt" % statDir
outputVTK = "%s/stats.spharmCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
#pythonScriptPath = config["vtkPointAttributesPythonScriptPath"]
pathKmesh = config["kmeshPath"]
datafilelist = ""
datagroups = ""
for (group, file) in datafiles:
datafilelist = datafilelist + " " + file
datagroups = datagroups + " " + group
# compute per-group statistics
cmd = "%s -computeVectorStats -scalarName %s -importVectors %s %s %s/%s_thickness.vtk" % (
pathKmesh, group + "_Thickness", inputVTK, file, statDir, group)
system.run_process(cmd, verbose=True)
if (len(datafiles) > 1):
runCmd = "%s %s %s %s %s" % (rscriptExePath, rscriptPath, datafilelist,
outputfile, datagroups)
system.run_process(runCmd, verbose=True)
#visCmd = "%s %s %s %s -i %s -t" % (pythonPath, pythonScriptPath, inputVTK, outputVTK, outputfile)
visCmd = "%s -use-header %s %s -importCSV %s" % (pathKmesh, inputVTK,
outputVTK, outputfile)
system.run_process(visCmd, verbose=True)
# connected components for p-value
print "computing connected components with t.pvalue..."
runCmd = "%s -connectScalars %s -scalarName t.pvalue %s -thresholdMin 0 -thresholdMax 0.05" % (
pathKmesh, outputVTK, outputVTK)
system.run_process(runCmd, verbose=True)
print "export scalars..."
runCmd = "%s -exportScalars -scalarName RegionIds %s %s/regionIds.txt" % (
pathKmesh, outputVTK, statDir)
system.run_process(runCmd, verbose=True)
# create a combined data file with regions
regionIdFile = "%s/regionIds.txt" % (statDir)
if os.path.exists(regionIdFile):
for (group, file) in datafiles:
dataregionfilename = "%s/data_region%s_%s.txt" % (statDir, tag,
group)
concatColumnsToFile(
[regionIdFile,
"%s/data%s_%s.txt" % (statDir, tag, group)],
dataregionfilename,
inputIsList=True)
# perform splitting
performSplit([dataregionfilename], "%s/data_%s_region_" %
(statDir, group) + "%02d.txt")
# boxplot
draw_boxplot = True
if draw_boxplot:
groupList = list(groupSet)
try:
print sys.path
import boxplot
gr1 = groupList[0]
gr2 = groupList[1]
boxplot.draw_boxplot(groupList[0], groupList[1], \
"{statDir}/data_{gr1}_region_*.txt".format(**locals()), \
"{statDir}/data_{gr2}_region_*.txt".format(**locals()), \
"{statDir}/{gr1}_{gr2}_regions.pdf".format(**locals()))
except BaseException as e:
print system.bcolors.WARNING + e.message + system.bcolors.ENDC
pass
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 = "%s/Processing/1.MeasurementandSPHARM" % (outputdir)
# before executing the boundary correction
# check if none of input is not generated.
labelMapList = [labelMap for (tag, labelMap, group) in data]
testLabelMapsFail = False in [os.path.exists(x) for x in labelMapList]
if testLabelMapsFail:
raise RuntimeError("There are missing label maps")
surfaceInputList = ["%s/%s.subj.SPHARM.vtk" % (workdir, tag) for (tag,labelMap,group) 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!")
for (idx, item) in enumerate(data):
tag = item[0]
labelMap = item[1]
group = item[2]
labelOutput = workdir + "/" + tag + "/labelmap_zeroSolution.nrrd"
surfaceInput = workdir + "/" + tag + ".subj.SPHARM.vtk"
surfaceLabels = workdir + "/" + tag + ".labels.vtp"
voronoiImage = workdir + "/" + tag + ".voronoi.mha"
surfaceImage = workdir + "/" + tag + ".solution.mha"
boundaryMap = workdir + "/" + tag + ".boundaryMap.mha"
cmd = "%s -e 'A==3?0:A' -o %s %s" % (pathKcalc, labelOutput, labelMap)
system.run_process(cmd,verbose=True)
cmd = "%s -sampleImage -zrotate %s %s %s -outputScalarName labels" % (pathKmesh, labelOutput, surfaceInput, surfaceLabels)
system.run_process(cmd,verbose=True)
cmd = "%s -averageScalars -threshold 1.8 -scalarName labels -outputScalarName meanLabels" % (pathKmesh)
for (tag, labelmap, group) in data:
cmd += " " + workdir + "/" + tag + ".labels.vtp"
print cmd
system.run_process(cmd,verbose=True)
for (idx, item) in enumerate(data):
tag = item[0]
labelMap = item[1]
group = item[2]
labelOutput = workdir + "/" + tag + "/labelmap_zeroSolution.nrrd"
surfaceInput = workdir + "/" + tag + ".subj.SPHARM.vtk"
surfaceLabels = workdir + "/" + tag + ".labels.vtp"
voronoiImage = workdir + "/" + tag + ".voronoi.mha"
surfaceImage = workdir + "/" + tag + ".solution.mha"
boundaryMap = workdir + "/" + tag + ".boundaryMap.mha"
cmd = "%s -voronoiImage -zrotate %s %s %s -scalarName meanLabels" % (pathKmesh, labelOutput, surfaceLabels, voronoiImage)
print cmd
system.run_process(cmd,verbose=True)
cmd = "%s -scanConversion -zrotate %s %s %s" % (pathKmesh, surfaceLabels, labelOutput, surfaceImage)
print cmd
system.run_process(cmd,verbose=True)
cmd = "%s -e 'B>0?3:A' -o %s %s %s" % (pathKcalc, boundaryMap, voronoiImage, surfaceImage)
print cmd
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 performAnalysis(cvsdata, config, outputDir, opt="initial_dense"):
ids = []
groups = []
for (id, labelmap, group) in cvsdata:
ids.append(id)
groups.append(group)
meshDir = "%s/Processing/1.MeasurementandSPHARM" % (outputDir)
shapeworksDir = "%s/Processing/2.shapeworks" % (outputDir)
sampleDir = "%s/Processing/3.meshintensity" % (outputDir)
statDir = "%s/Statistical" % (outputDir)
pathKmesh = config["kmeshPath"]
if (opt == "initial_dense"):
samplingCmd = config["MeshPointIntensitySamplingPath"] + " --workDir %s --inputAsPhysicalCoord --inputPointFlip --distanceVector %s -i nn -a %s -m %s --smoothedAttributeOutput %s --originalMeshOutput %s %s %s"
else:
samplingCmd = config["MeshPointIntensitySamplingPath"] + " --workDir %s --inputAsPhysicalCoord --distanceVector %s -i nn -a %s -m %s --smoothedAttributeOutput %s --originalMeshOutput %s %s %s"
# depending on options, choose different meshes
# loop over ids
for id in ids:
distanceVector = "%s/%s.distanceVector.nrrd" % (sampleDir, id)
inputMeasurement = "%s/%s_measurementoutput.nrrd" % (meshDir, id)
# inputMeasurement = "%s/%s.thickness.mha" % (meshDir, id)
if (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 (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 (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 (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)
# execute sampling
# exeCmd = samplingCmd % (outputDir, distanceVector, samplingTxt, samplingMeshOutput, smoothSamplingTxt, originalMeshOutput, inputMeasurement, inputMesh)
# new sampling command
useStreamLine = True and opt == "spharm_sampling"
if (not useStreamLine):
exeCmd = "%s -sampleImage %s %s %s -outputScalarName Thickness -zrotate" % (pathKmesh, inputMeasurement, inputMesh, samplingMeshOutput)
system.run_process(exeCmd,verbose=True)
exeCmd = "%s -smoothScalars %s %s -scalarName Thickness -outputScalarName smoothThickness -iter 3" % (pathKmesh, samplingMeshOutput, samplingMeshOutput)
system.run_process(exeCmd,verbose=True)
exeCmd = "%s -exportScalars %s %s -scalarName Thickness " % (pathKmesh, samplingMeshOutput, samplingTxt)
system.run_process(exeCmd,verbose=True)
exeCmd = "%s -exportScalars %s %s -scalarName smoothThickness " % (pathKmesh, samplingMeshOutput, smoothSamplingTxt)
system.run_process(exeCmd,verbose=True)
else:
gradientFile = "%s/Processing/1.MeasurementandSPHARM/%s/laplacianGradient.nrrd" % (outputDir, id)
gradientVTIFile = "%s/Processing/1.MeasurementandSPHARM/%s/laplacianGradient.vti" % (outputDir, id)
streamLineFile = "%s/Processing/1.MeasurementandSPHARM/%s/stream_lines.vtp" % (outputDir, id)
# vti image creation
exeCmd = "%s -vti %s %s -attrDim 3" % (pathKmesh, gradientFile, gradientVTIFile)
system.run_process(exeCmd,verbose=True)
# RK45 integration
exeCmd = "%s -traceStream %s %s %s %s -zrotate -traceDirection backward" % (pathKmesh, gradientVTIFile, inputMesh, streamLineFile, samplingMeshOutput)
system.run_process(exeCmd,verbose=True)
# scalar export
exeCmd = "%s -exportScalars %s %s -scalarName Length " % (pathKmesh, samplingMeshOutput, smoothSamplingTxt)
system.run_process(exeCmd,verbose=True)
# aggregate sampling files into a single file
groupSet = set(groups)
datafiles = []
tag = ""
for group in groupSet:
# setup output filename template
if (opt == "initial_dense"):
tag = "_initialDenseSampling"
datafilename = "%s/data_initialDenseSampling_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_initialDenseSampling_%s.txt" % (statDir, group)
outfilename = "%s/list_initialDenseSampling_%s.txt" % (statDir, group)
elif (opt == "correspondence"):
tag = ""
datafilename = "%s/data_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_%s.txt" % (statDir, group)
outfilename = "%s/list_%s.txt" % (statDir, group)
elif (opt == "dense_correspondence"):
tag = "_dense"
datafilename = "%s/data_dense_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_dense_%s.txt" % (statDir, group)
outfilename = "%s/list_dense_%s.txt" % (statDir, group)
elif (opt == "spharm_sampling"):
tag = "_spharm"
datafilename = "%s/data_spharm_%s.txt" % (statDir, group)
dataregionfilename = "%s/data_region_spharm_%s.txt" % (statDir, group)
outfilename = "%s/list_spharm_%s.txt" % (statDir, group)
# process and write the aggregated data
outfile = open(outfilename, 'w')
for (id, g) in zip(ids, groups):
if (g != group):
continue
if (opt == "initial_dense"):
samplingTxt = "%s/%s.smoothInitialDenseSampling.txt" % (sampleDir, id)
elif (opt == "correspondence"):
samplingTxt = "%s/%s.smoothSampling.txt" % (sampleDir, id)
elif (opt == "dense_correspondence"):
samplingTxt = "%s/%s.smoothDenseSampling.txt" % (sampleDir, id)
elif (opt == "spharm_sampling"):
samplingTxt = "%s/%s.smoothSpharmSampling.txt" % (sampleDir, id)
if (os.path.isfile(samplingTxt)):
outfile.write(samplingTxt)
outfile.write("\n")
else:
print "can't find", samplingTxt
outfile.close()
# concatenate those attribute files into a file
concatColumnsToFile(outfilename, datafilename)
datafiles.append((group, datafilename))
# perform statistical analysis
rscriptExePath = config["RScriptPath"]
rscriptPath = config["RScriptRodentThicknessPath"]
if (opt == "initial_dense"):
outputfile = "%s/stats.initialDenseSampling.txt" % statDir
outputVTK = "%s/stats.initialDenseSampling.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
elif (opt == "correspondence"):
outputfile = "%s/stats.correspondence.txt" % statDir
outputVTK = "%s/stats.correspondence.vtk" % (statDir)
inputVTK = "%s/%s.correspondence.vtk" % (shapeworksDir, ids[0])
elif (opt == "dense_correspondence"):
outputfile = "%s/stats.denseCorrespondence.txt" % statDir
outputVTK = "%s/stats.denseCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.dense_correspondence.vtk" % (shapeworksDir, ids[0])
elif (opt == "spharm_sampling"):
outputfile = "%s/stats.spharmCorrespondence.txt" % statDir
outputVTK = "%s/stats.spharmCorrespondence.vtk" % (statDir)
inputVTK = "%s/%s.subj.SPHARM.vtk" % (meshDir, ids[0])
pythonPath = config["PythonPath"]
pythonScriptPath = config["vtkPointAttributesPythonScriptPath"]
datafilelist = ""
datagroups = ""
for (group, file) in datafiles:
datafilelist = datafilelist + " " + file
datagroups = datagroups + " " + group
# compute per-group statistics
cmd = "%s -computeVectorStats -scalarName %s -importVectors %s %s %s/%s_thickness.vtk" % (pathKmesh, group + "_Thickness", inputVTK, file, statDir, group)
print cmd
system.run_process(cmd,verbose=True)
if (len(datafiles) > 1):
runCmd = "%s %s %s %s %s" % (rscriptExePath, rscriptPath, datafilelist, outputfile, datagroups)
system.run_process(runCmd,verbose=True)
visCmd = "%s %s %s %s -i %s -t" % (pythonPath, pythonScriptPath, inputVTK, outputVTK, outputfile)
system.run_process(visCmd,verbose=True)
# connected components for p-value
print "computing connected components with t.pvalue..."
runCmd = "%s -connectScalars %s -scalarName t.pvalue %s -thresholdMin 0 -thresholdMax 0.05" % (pathKmesh, outputVTK, outputVTK)
system.run_process(runCmd,verbose=True)
print "export scalars..."
runCmd = "%s -exportScalars -scalarName RegionIds %s %s/regionIds.txt" % (pathKmesh, outputVTK, statDir)
system.run_process(runCmd,verbose=True)
# create a combined data file with regions
regionIdFile = "%s/regionIds.txt" % (statDir)
if os.path.exists(regionIdFile):
for (group, file) in datafiles:
dataregionfilename = "%s/data_region%s_%s.txt" % (statDir, tag, group)
concatColumnsToFile([regionIdFile, "%s/data%s_%s.txt" % (statDir, tag, group)], dataregionfilename, inputIsList = True)
# perform splitting
performSplit([dataregionfilename], "%s/data_%s_region_" % (statDir, group) + "%02d.txt")
# boxplot
groupList = list(groupSet)
runCmd = "%s %s '%s' '%s' %s/%s_%s_regions.pdf --label1 %s --label2 %s" % (pythonPath, pythonScriptPath.replace("vtkPointAttributes.py", "boxplot.py"), "%s/data_%s_region_*.txt" % (statDir, groupList[0]), "%s/data_%s_region_*.txt" % (statDir, groupList[1]), statDir, groupList[0], groupList[1], groupList[0], groupList[1])
print runCmd
system.run_process(runCmd,verbose=True)
import system
import sys
import logging
system.setup_logger(logfilename="test.log")
retcode = system.run_process(
"/devel/linux/SPHARM-PDM/spharm-pdm-build-joowhi/bin/GenParaMeshCLP %s %s %s"
% (sys.argv[1], sys.argv[2], sys.argv[3]),
verbose=True)
print "Return Code = ", retcode
