def glob_matfiles(pattern, subject_getter, ignore=None, restrict=None):
if ignore is None:
ignore = []
i = 1
doc = {}
for mat_file in sorted(glob.glob(pattern)):
sid = parse_path(mat_file, subject_id=subject_getter)['subject_id']
if (restrict is None and sid not in ignore) or (
restrict is not None and sid in restrict):
doc.setdefault('mat_files', []).append(mat_file)
doc.setdefault('subjects', []).append('sub%03i' % i)
doc.setdefault('original_subjects', []).append(sid)
i += 1
else:
doc.setdefault('ignored_subjects', []).append(sid)
return doc
def glob_matfiles(pattern, subject_getter, ignore=None, restrict=None):
if ignore is None:
ignore = []
i = 1
doc = {}
for mat_file in sorted(glob.glob(pattern)):
sid = parse_path(mat_file, subject_id=subject_getter)['subject_id']
if (restrict is None and sid not in ignore) or (restrict is not None
and sid in restrict):
doc.setdefault('mat_files', []).append(mat_file)
doc.setdefault('subjects', []).append('sub%03i' % i)
doc.setdefault('original_subjects', []).append(sid)
i += 1
else:
doc.setdefault('ignored_subjects', []).append(sid)
return doc
def load_intra(mat_file, memory=Memory(None), **kwargs):
doc = {}
mat_file = os.path.realpath(mat_file)
doc.update(parse_path(mat_file, **kwargs))
work_dir = os.path.split(mat_file)[0]
mat_file = memory.cache(load_matfile)(mat_file)
mat = mat_file['SPM']
doc.update(get_intra_infos(mat_file, memory))
doc['mask'] = check_path(os.path.join(work_dir, str(mat.VM.fname)))
doc['onsets'], doc['conditions'] = get_intra_onsets(mat_file, memory)
doc.update(get_intra_preproc(mat_file, work_dir, doc['n_scans'], memory))
doc.update(get_intra_images(mat_file, work_dir, memory))
doc.update(get_intra_design(
mat_file, doc['n_scans'], doc['contrasts'], memory))
return doc
def load_intra(mat_file, memory=Memory(None), **kwargs):
doc = {}
mat_file = os.path.realpath(mat_file)
doc.update(parse_path(mat_file, **kwargs))
work_dir = os.path.split(mat_file)[0]
mat_file = memory.cache(load_matfile)(mat_file)
mat = mat_file['SPM']
doc.update(get_intra_infos(mat_file, memory))
doc['mask'] = check_path(os.path.join(work_dir, str(mat.VM.fname)))
doc['onsets'], doc['conditions'] = get_intra_onsets(mat_file, memory)
doc.update(get_intra_preproc(mat_file, work_dir, doc['n_scans'], memory))
doc.update(get_intra_images(mat_file, work_dir, memory))
doc.update(
get_intra_design(mat_file, doc['n_scans'], doc['contrasts'], memory))
return doc
def load_preproc(mat_file, memory=Memory(None), **kwargs):
doc = {}
mat_file = os.path.realpath(mat_file)
doc.update(parse_path(mat_file, **kwargs))
work_dir = os.path.split(mat_file)[0]
mat_file = memory.cache(load_matfile)(mat_file)
if 'jobs' in mat_file:
mat = mat_file['jobs']
elif 'matlabbatch' in mat_file:
mat = mat_file['matlabbatch']
else:
raise Exception("mat_file type not known.")
if not hasattr(mat, '__iter__'):
return doc
for step in mat:
if hasattr(step, 'spm'):
step = step.spm
doc.update(parse_spm8_preproc(work_dir, step))
else:
doc.update(parse_spm5_preproc(work_dir, step))
return doc
def load_preproc(mat_file, memory=Memory(None), **kwargs):
doc = {}
mat_file = os.path.realpath(mat_file)
doc.update(parse_path(mat_file, **kwargs))
work_dir = os.path.split(mat_file)[0]
mat_file = memory.cache(load_matfile)(mat_file)
if 'jobs' in mat_file:
mat = mat_file['jobs']
elif 'matlabbatch' in mat_file:
mat = mat_file['matlabbatch']
else:
raise Exception("mat_file type not known.")
if not hasattr(mat, '__iter__'):
return doc
for step in mat:
if hasattr(step, 'spm'):
step = step.spm
doc.update(parse_spm8_preproc(work_dir, step))
else:
doc.update(parse_spm5_preproc(work_dir, step))
return doc