def merge_slices(datadir, fileregex, outfname, outdir='', cleanup=True):
if not outdir:
outdir = datadir
au.log.info('Merging the ' + fileregex + ' files in ' + outdir)
fregex = datadir + os.path.sep + fileregex
imglob = ''
imglob = au.exec_comm(['imglob', fregex])
imglob = imglob.strip()
outdata = ''
if imglob:
if os.path.isabs(outfname): outdata = outfname
else: outdata = outdir + os.path.sep + outfname
os.system('fslmerge -z ' + outdata + ' ' + imglob)
if cleanup:
au.imrm(fregex)
else:
au.log.error('aizkolari_postproc: Error: could not find ' + fregex +
' in ' + datadir)
return outdata
def merge_slices (datadir, fileregex, outfname, outdir='', cleanup=True):
if not outdir:
outdir = datadir
au.log.info ('Merging the ' + fileregex + ' files in ' + outdir)
fregex = datadir + os.path.sep + fileregex
imglob = ''
imglob = au.exec_comm(['imglob', fregex])
imglob = imglob.strip()
outdata = ''
if imglob:
if os.path.isabs (outfname): outdata = outfname
else: outdata = outdir + os.path.sep + outfname
os.system('fslmerge -z ' + outdata + ' ' + imglob)
if cleanup:
au.imrm(fregex)
else:
au.log.error ('aizkolari_postproc: Error: could not find ' + fregex + ' in ' + datadir)
return outdata
def merge_stats_slices (datadir, group):
slice_str = au.slice_str()
groupfregex = group + 's_' + slice_str + '_????' + '.'
#This is a 4D volume with all subjects, it can be a big file, so I'm not creating it
#merge_slices (datadir, groupfregex, group + 's')
au.imrm(datadir + os.path.sep + groupfregex)
[statfnames, mnames] = get_stats_fnames (group, outdir='')
statfnames = statfnames[0]
out = []
for i in np.arange(len(statfnames)):
fname = statfnames[i]
m = mnames[i]
regex = group + 's_' + slice_str + '_????' + '_' + m
o = merge_slices (datadir, regex , fname, datadir, cleanup=False)
au.imrm(datadir + os.path.sep + regex)
out.append(o)
return out
def merge_stats_slices(datadir, group):
slice_str = au.slice_str()
groupfregex = group + 's_' + slice_str + '_????' + '.'
#This is a 4D volume with all subjects, it can be a big file, so I'm not creating it
#merge_slices (datadir, groupfregex, group + 's')
au.imrm(datadir + os.path.sep + groupfregex)
[statfnames, mnames] = get_stats_fnames(group, outdir='')
statfnames = statfnames[0]
out = []
for i in np.arange(len(statfnames)):
fname = statfnames[i]
m = mnames[i]
regex = group + 's_' + slice_str + '_????' + '_' + m
o = merge_slices(datadir, regex, fname, datadir, cleanup=False)
au.imrm(datadir + os.path.sep + regex)
out.append(o)
return out
def slice_and_merge (subsfname, labelsfname, checkfname, outdir='', maskfname='', outbase=''):
check_data (subsfname, labelsfname, outdir, maskfname, outbase)
nsubs = au.file_len(subsfname)
nlabs = au.file_len(labelsfname)
if not outdir:
outdir = os.getcwd()
slicesdir = outdir + os.path.sep + au.slices_str()
tempdir = outdir + os.path.sep + au.temp_str()
tmpdirlst = os.listdir(tempdir)
fpath = ''
olddir = os.getcwd()
if not au.is_done (checkfname, au.preslicingdata_str()):
#slicing subjects
au.log.info ('Slicing all subjects: takes a while')
subsfile = open(subsfname, 'r')
for line in subsfile:
fpath = line.strip()
isfile = os.path.basename(fpath)
osfile = tempdir + os.path.sep + isfile
#test if file has been sliced
fdim3 = au.fslval(fpath, 'dim3')
regex = au.remove_ext(isfile) + '*'
nslices = au.count_match (tmpdirlst, regex)
if fdim3 != nslices:
#if not, then slice it in tempdir
au.log.debug('Slicing ' + isfile)
os.chdir (tempdir)
shutil.copy (fpath, tempdir)
au.fslslice (osfile)
os.remove(osfile)
os.chdir (olddir)
else:
au.log.debug(isfile + ' previously sliced')
subsfile.close()
au.checklist_add (checkfname, au.preslicingdata_str())
if not au.is_done (checkfname, au.premergingdata_str()):
#merging each slice
if not outbase:
outbase = au.data_str()
if not fpath:
subsfile = open(subsfname, 'r')
for line in subsfile:
fpath = line.strip()
break
au.log.info ('Merging all subject slices: takes a while')
nslices = int(au.fslval(fpath,'dim3'))
for slice in range(nslices):
slicezp = au.zeropad(slice)
mergeout = outbase + '_slice_' + slicezp
outdata = slicesdir + os.path.sep + mergeout
#check if data file exists
if not au.imtest(outdata):
#if not, then create it, merging all the corresponding slices
au.log.debug('Merging slice ' + slicezp)
imglob = ''
subsfile = open(subsfname, 'r')
for line in subsfile:
fpath = line.strip()
isfile = au.remove_ext(os.path.basename(fpath)).strip()
isfile = tempdir + os.path.sep + isfile + '_slice_' + slicezp
imglob += isfile + ' '
os.system('fslmerge -t ' + outdata + ' ' + imglob)
for f in imglob.split():
au.imrm(f)
else:
au.log.debug('Slice ' + slicezp + ' previously done')
au.checklist_add (checkfname, au.premergingdata_str())
#slicing mask
if maskfname:
if os.path.exists(maskfname) and not au.is_done (checkfname, au.preslicingmask_str()):
au.log.info('Slicing mask ' + maskfname)
au.imcp (maskfname, slicesdir + os.path.sep + au.mask_str())
os.chdir (slicesdir)
au.fslslice (au.mask_str())
au.imrm (au.mask_str())
au.checklist_add (checkfname, au.preslicingmask_str())
os.chdir (olddir)
au.log.debug('Done preprocessing')