def test_report_session():
"""Generating a report for one session should mean that no other sessions
appear in any of the unique descriptions.
"""
report = BIDSReport(testlayout())
descriptions = report.generate(session='01')
assert 'session 02' not in ' '.join(descriptions.keys())
def test_report_gen():
"""Report generation should return a counter of unique descriptions in the
dataset.
"""
report = BIDSReport(testlayout())
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_report_subject():
"""Generating a report for one subject should only return one subject's
description (i.e., one pattern with a count of one).
"""
report = BIDSReport(testlayout())
descriptions = report.generate(subject='01')
assert sum(descriptions.values()) == 1
def test_report_session(testlayout):
"""Generating a report for one session should mean that no other sessions
appear in any of the unique descriptions.
"""
report = BIDSReport(testlayout)
descriptions = report.generate(session='01')
assert 'session 02' not in ' '.join(descriptions.keys())
def test_report_session(testlayout):
"""Generating a report for one session should mean that no other sessions
appear in any of the unique descriptions.
"""
report = BIDSReport(testlayout)
descriptions = report.generate(session="01")
assert "session 02" not in " ".join(descriptions.keys())
def test_report_subject(testlayout):
"""Generating a report for one subject should only return one subject's
description (i.e., one pattern with a count of one).
"""
report = BIDSReport(testlayout)
descriptions = report.generate(subject='01')
assert sum(descriptions.values()) == 1
def test_report_gen(testlayout):
"""Report generation should return a counter of unique descriptions in the
dataset.
"""
report = BIDSReport(testlayout)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_report_file_config():
"""Report initialization should take in a config file and use that if provided.
"""
config_file = abspath(
join(get_test_data_path(), '../../reports/config/converters.json'))
report = BIDSReport(testlayout(), config=config_file)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_report_gen_from_files(testlayout):
"""Report generation from file list should return a counter of unique
descriptions in the dataset.
"""
report = BIDSReport(testlayout)
files = testlayout.get(extension=['nii.gz', 'nii'])
descriptions = report.generate_from_files(files)
assert isinstance(descriptions, Counter)
def test_report_file_config(testlayout):
"""Report initialization should take in a config file and use that if
provided.
"""
config_file = abspath(join(get_test_data_path(),
'../../reports/config/converters.json'))
report = BIDSReport(testlayout, config=config_file)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_report_dict_config():
"""Report initialization should take in a config dict and use that if provided.
"""
config_file = abspath(
join(get_test_data_path(), '../../reports/config/converters.json'))
with open(config_file, 'r') as fobj:
config = json.load(fobj)
report = BIDSReport(testlayout(), config=config)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_report_dict_config(testlayout):
"""Report initialization should take in a config dict and use that if
provided.
"""
config_file = abspath(join(get_test_data_path(),
'../../reports/config/converters.json'))
with open(config_file, 'r') as fobj:
config = json.load(fobj)
report = BIDSReport(testlayout, config=config)
descriptions = report.generate()
assert isinstance(descriptions, Counter)
def test_report_init():
"""Report initialization should return a BIDSReport object.
"""
report = BIDSReport(testlayout())
assert isinstance(report, BIDSReport)
#!/usr/bin/env python
import sys
from pathlib import Path
from bids import BIDSLayout
from bids.reports import BIDSReport
cmd, bids_root, out_root, analysis_level, *opts = sys.argv
layout = BIDSLayout(bids_root)
reports = {}
for subject in layout.get_subjects():
rep = list(BIDSReport(layout).generate(subject=subject))[0]
reports.setdefault(rep, []).append(subject)
with open(Path(out_root) / "report.txt", "w") as out_file:
out_file.write(f"Scan parameter sets detected: {len(reports)}\n\n")
for rep, subs in reports.items():
rep = "\n".join(rep.splitlines()[:-2])
out_file.write(f"-----\nParameters for subjects: {', '.join(subs)}\n\n")
out_file.write(rep.replace("<deg>", "°") + "\n\n")