def check_data (subsfname, labelsfname, outdir, maskfname, outbase):
au.log.debug('Checking data')
nsubs = au.file_len(subsfname)
nlabs = au.file_len(labelsfname)
if (nsubs != nlabs):
err = 'Not same number of lines in input files\n'
err += labelsfname + ': ' + str(nlabs) + '\n'
err += (subsfname + ': ' + str(nsubs)) + '\n'
raise IOError(err)
if not outdir:
outdir = os.getcwd()
slicesdir = outdir + os.path.sep + au.slices_str()
if not os.path.exists (slicesdir):
os.mkdir (slicesdir)
tempdir = outdir + os.path.sep + au.temp_str()
if not os.path.exists (tempdir):
os.mkdir (tempdir)
au.log.info (slicesdir)
#check all files
subsfile = open(subsfname, 'r')
if maskfname:
for line in subsfile:
fpath = line.strip()
au.check_has_same_geometry (maskfname, fpath)
else:
path1 = ''
path2 = ''
for line in subsfile:
path1 = line.strip()
if not path2:
path2 = line.strip()
continue
else:
au.check_has_same_geometry (path1, path2)
subsfile.close()
if prefixes[m]:
ofname = prefixes[m] + '_' + ofname
oc = len(au.find(os.listdir(outdir), ofname))
nouts += oc
m += 1
if nouts >= nmasks:
au.log.debug('Nothing to do in ' + outdir + '. All files processed.')
return -1
else:
au.log.debug('Processing to output in: ' + outdir)
#number of subjects
subjsnum = au.file_len(subjsf)
#reading subjects list
subjlabels = np.zeros(subjsnum, dtype=int)
subjslist = {}
subjfile = open(subjsf, 'r')
c = 0
for s in subjfile:
line = s.strip().split(',')
subjlabels[c] = int(line[0])
subjfname = line[1].strip()
if not os.path.isabs(subjfname) and datadir:
subjslist[c] = datadir + os.path.sep + subjfname
else:
subjslist[c] = subjfname
c += 1
thrps = args.thresholdP.strip().split()
lthr = args.lthreshold.strip()
uthr = args.uthreshold.strip()
absolute = args.absolute
au.setup_logger(args.verbosity)
#checking number of files processed
if not os.path.exists(maskf):
err = 'Mask file not found: ' + maskf
au.log.error(err)
sys.exit(-1)
#number of subjects
subjsnum = au.file_len(subjsf)
#reading subjects list
subjlabels = np.zeros(subjsnum, dtype=int)
subjslist = {}
subjfile = open(subjsf, 'r')
c = 0
for s in subjfile:
line = s.strip().split(',')
subjlabels[c] = int(line[0])
subjfname = line[1].strip()
if not os.path.isabs(subjfname) and datadir:
subjslist[c] = datadir + os.path.sep + subjfname
else:
subjslist[c] = subjfname
foldno = args.foldno
cleanup = args.cleanup
leave = args.leave
absval = args.absolute
verbose = args.verbosity
chklst = args.checklist
au.setup_logger(verbose)
usemask = decide_whether_usemask(maskf)
foldno = get_fold_numberstr(foldno)
measure = get_measure_shortname(measure)
classnum = au.file_len(classf)
subjsnum = au.file_len(subjsf)
#reading label file
[labels, classnames] = parse_labels_file(classf)
#reading subjects list
[subjlabels, subjs] = parse_subjects_list(subjsf, datadir)
#if output dir does not exist, create
if not (os.path.exists(outdir)):
os.mkdir(outdir)
#checklist_fname
if chklst:
chkf = outdir + os.path.sep + au.checklist_str()
foldno = args.foldno
cleanup = args.cleanup
leave = args.leave
absval = args.absolute
verbose = args.verbosity
chklst = args.checklist
au.setup_logger(verbose)
usemask = decide_whether_usemask(maskf)
foldno = get_fold_numberstr (foldno)
measure = get_measure_shortname (measure)
classnum = au.file_len(classf)
subjsnum = au.file_len(subjsf)
#reading label file
[labels, classnames] = parse_labels_file (classf)
#reading subjects list
[subjlabels, subjs] = parse_subjects_list (subjsf, datadir)
#if output dir does not exist, create
if not(os.path.exists(outdir)):
os.mkdir(outdir)
#checklist_fname
if chklst:
chkf = outdir + os.path.sep + au.checklist_str()
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')