qsiprep.viz.reports module

qsiprep reports builder

class qsiprep.viz.reports.Element(name, title=None)

Bases: object

Just a basic component of a report

class qsiprep.viz.reports.Report(path, viz_config, out_dir, run_uuid, out_filename='report.html', pipeline_type='qsiprep')

Bases: object

The full report object

generate_report()

index(viz_config)

index_error_dir(error_dir)

Crawl subjects crash directory for the corresponding run and return text for .pklz crash file found.

class qsiprep.viz.reports.Reportlet(name, imgtype=None, file_pattern=None, title=None, description=None, raw=False)

Bases: Element

A reportlet has title, description and a list of graphical components

class qsiprep.viz.reports.SubReport(name, reportlets=None, title='')

Bases: Element

SubReports are sections within a Report

qsiprep.viz.reports.generate_interactive_report_summary(output_dir)

Gather the dwiqc values from the outputs in a

qsiprep.viz.reports.generate_name_title(filename)

qsiprep.viz.reports.generate_reports(subject_list, pipeline_mode='qsiprep')

A wrapper to run_reports on a given subject_list

qsiprep.viz.reports.order_by_run(subreport)

qsiprep.viz.reports.run_reports(reportlets_dir, out_dir, subject_label, run_uuid, report_type='qsiprep')

Runs the reports

>>> import os
>>> from shutil import copytree
>>> from tempfile import TemporaryDirectory
>>> filepath = os.path.dirname(os.path.realpath(__file__))
>>> test_data_path = os.path.realpath(os.path.join(filepath,
...                                   '../data/tests/work'))
>>> curdir = os.getcwd()
>>> tmpdir = TemporaryDirectory()
>>> os.chdir(tmpdir.name)
>>> data_dir = copytree(test_data_path, os.path.abspath('work'))
>>> os.makedirs('out/qsiprep', exist_ok=True)
>>> run_reports(os.path.abspath('work/reportlets'),
...             os.path.abspath('out'),
...             '01', 'madeoutuuid')
0
>>> os.chdir(curdir)
>>> tmpdir.cleanup()