def _report_subject(self, subject, **kwargs):
"""Write a report for a single subject.
Parameters
----------
subject : :obj:`str`
Subject ID.
Attributes
----------
layout : :obj:`bids.grabbids.BIDSLayout`
Layout object for a BIDS dataset.
config : :obj:`dict`
Configuration info for methods generation.
Returns
-------
description : :obj:`str`
A publication-ready report of the dataset's data acquisition
information. Each scan type is given its own paragraph.
"""
description_list = []
# Remove session from kwargs if provided, else set sessions as all available
sessions = kwargs.pop(
'session', self.layout.get_sessions(subject=subject, **kwargs))
if not sessions:
sessions = [None]
elif not isinstance(sessions, list):
sessions = [sessions]
for ses in sessions:
niftis = self.layout.get(subject=subject,
extensions='nii.gz',
**kwargs)
if niftis:
description_list.append('For session {0}:'.format(ses))
description_list += parsing.parse_niftis(self.layout,
niftis,
subject,
self.config,
session=ses)
metadata = self.layout.get_metadata(niftis[0].filename)
else:
raise Exception('No niftis for subject {0}'.format(subject))
# Assume all data were converted the same way and use the last nifti file's
# json for conversion information.
if 'metadata' not in vars():
raise Exception(
'No valid jsons found. Cannot generate final paragraph.')
description = '\n\t'.join(description_list)
description = description.replace('\tFor session', '\nFor session')
description += '\n\n{0}'.format(parsing.final_paragraph(metadata))
return description
def test_parsing_parse(testlayout, testconfig):
"""
parsing.parse_niftis should return a list of strings, with each string
containing the description for a single nifti file (except functional data,
which is combined within task, across runs)
"""
subj = '01'
niftis = testlayout.get(subject=subj, extensions='nii.gz')
desc = parsing.parse_niftis(testlayout, niftis, subj, testconfig)
assert isinstance(desc, list)
assert isinstance(desc[0], str)
def _report_subject(self, subject, **kwargs):
"""Write a report for a single subject.
Parameters
----------
subject : :obj:`str`
Subject ID.
Attributes
----------
layout : :obj:`bids.layout.BIDSLayout`
Layout object for a BIDS dataset.
config : :obj:`dict`
Configuration info for methods generation.
Returns
-------
description : :obj:`str`
A publication-ready report of the dataset's data acquisition
information. Each scan type is given its own paragraph.
"""
description_list = []
# Remove sess from kwargs if provided, else set sess as all available
sessions = kwargs.pop('session',
self.layout.get_sessions(subject=subject,
**kwargs))
if not sessions:
sessions = [None]
elif not isinstance(sessions, list):
sessions = [sessions]
for ses in sessions:
niftis = self.layout.get(subject=subject, extensions='nii.gz',
**kwargs)
if niftis:
description_list.append('For session {0}:'.format(ses))
description_list += parsing.parse_niftis(self.layout, niftis,
subject, self.config,
session=ses)
metadata = self.layout.get_metadata(niftis[0].path)
else:
raise Exception('No niftis for subject {0}'.format(subject))
# Assume all data were converted the same way and use the last nifti
# file's json for conversion information.
if 'metadata' not in vars():
raise Exception('No valid jsons found. Cannot generate final '
'paragraph.')
description = '\n\t'.join(description_list)
description = description.replace('\tFor session', '\nFor session')
description += '\n\n{0}'.format(parsing.final_paragraph(metadata))
return description
def test_parsing_parse(testlayout, testconfig):
"""
parsing.parse_niftis should return a list of strings, with each string
containing the description for a single nifti file (except functional data,
which is combined within task, across runs)
"""
subj = '01'
niftis = testlayout.get(subject=subj, extensions='nii.gz')
desc = parsing.parse_niftis(testlayout, niftis, subj, testconfig)
assert isinstance(desc, list)
assert isinstance(desc[0], str)
def generate_from_files(self, files):
r"""Generate a methods section from a list of files.
Parameters
----------
files : list of BIDSImageFile objects
List of files from which to generate methods description.
Returns
-------
counter : :obj:`collections.Counter`
A dictionary of unique descriptions across subjects in the file list,
along with the number of times each pattern occurred. In cases
where all subjects underwent the same protocol, the most common
pattern is most likely the most complete. In cases where the
file list contains multiple protocols, each pattern will need to be
inspected manually.
Examples
--------
>>> from os.path import join
>>> from bids.layout import BIDSLayout
>>> from bids.reports import BIDSReport
>>> from bids.tests import get_test_data_path
>>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
>>> report = BIDSReport(layout)
>>> files = layout.get(session='01', extension=['nii.gz', 'nii'])
>>> counter = report.generate_from_files(files)
Number of patterns detected: 1
Remember to double-check everything and to replace <deg> with a degree symbol.
>>> counter.most_common()[0][0] # doctest: +ELLIPSIS
'For session 01:\n\tMR data were...'
"""
descriptions = []
subjs = sorted(
list(set([f.get_entities().get('subject') for f in files])))
sessions = sorted(
list(set([f.get_entities().get('session') for f in files])))
for sid in subjs:
subject_files = [
f for f in files if f.get_entities().get('subject') == sid
]
description_list = []
for ses in sessions:
niftis = [
f for f in subject_files
if f.get_entities().get('session') == ses
]
if niftis:
description_list.append('For session {0}:'.format(ses))
description_list += parsing.parse_niftis(self.layout,
niftis,
sid,
self.config,
session=ses)
metadata = self.layout.get_metadata(niftis[0].path)
else:
raise Exception(
'No niftis for subject {0}'.format(subject))
# Assume all data were converted the same way and use the last nifti
# file's json for conversion information.
if 'metadata' not in vars():
raise Exception('No valid jsons found. Cannot generate final '
'paragraph.')
description = '\n\t'.join(description_list)
description = description.replace('\tFor session', '\nFor session')
description += '\n\n{0}'.format(parsing.final_paragraph(metadata))
descriptions.append(description)
counter = Counter(descriptions)
print('Number of patterns detected: {0}'.format(len(counter.keys())))
print(utils.reminder())
return counter