Warning: This document is for an old version of niworkflows. The main version is master.

niworkflows.reports.core module

Reports builder for BIDS-Apps.

Generalizes report generation across BIDS-Apps

class niworkflows.reports.core.Element(name, title=None)

Bases: object

Just a basic component of a report

class niworkflows.reports.core.Report(out_dir, run_uuid, config=None, out_filename='report.html', packagename=None, reportlets_dir=None, subject_id=None)

Bases: object

The full report object. This object maintains a BIDSLayout to index all reportlets.

>>> cwd = os.getcwd()
>>> os.chdir(tmpdir)

>>> from pkg_resources import resource_filename
>>> from shutil import copytree
>>> from bids.layout import BIDSLayout
>>> test_data_path = resource_filename('niworkflows', 'data/tests/work')
>>> testdir = Path(tmpdir)
>>> data_dir = copytree(test_data_path, str(testdir / 'work'))
>>> out_figs = testdir / 'out' / 'fmriprep'

>>> robj = Report(testdir / 'out', 'madeoutuuid', subject_id='01', packagename='fmriprep',
...               reportlets_dir=testdir / 'work' / 'reportlets')
>>> robj.layout.get(subject='01', desc='reconall')  
[<BIDSFile filename='.../figures/sub-01_desc-reconall_T1w.svg'>]

>>> robj.generate_report()
0
>>> len((testdir / 'out' / 'fmriprep' / 'sub-01.html').read_text())
36693

>>> os.chdir(cwd)

generate_report()

Once the Report has been indexed, the final HTML can be generated

index(config)

Traverse the reports config definition and instantiate reportlets.

This method also places figures in their final location.

init_layout()

class niworkflows.reports.core.Reportlet(layout, out_dir, config=None)

Bases: niworkflows.reports.core.Element

A reportlet has title, description and a list of components with either an HTML fragment or a path to an SVG file, and possibly a caption. This is a factory class to generate Reportlets reusing the layout from a Report object.

>>> cwd = os.getcwd()
>>> os.chdir(tmpdir)

>>> from pkg_resources import resource_filename
>>> from shutil import copytree
>>> from bids.layout import BIDSLayout
>>> test_data_path = resource_filename('niworkflows', 'data/tests/work')
>>> testdir = Path(tmpdir)
>>> data_dir = copytree(test_data_path, str(testdir / 'work'))
>>> out_figs = testdir / 'out' / 'fmriprep'
>>> bl = BIDSLayout(str(testdir / 'work' / 'reportlets'),
...                 config='figures', validate=False)

>>> bl.get(subject='01', desc='reconall') 
[<BIDSFile filename='.../fmriprep/sub-01/figures/sub-01_desc-reconall_T1w.svg'>]

>>> len(bl.get(subject='01', space='.*', regex_search=True))
2

>>> r = Reportlet(bl, out_figs, config={
...     'title': 'Some Title', 'bids': {'datatype': 'figures', 'desc': 'reconall'},
...     'description': 'Some description'})
>>> r.name
'datatype-figures_desc-reconall'

>>> r.components[0][0].startswith('<img')
True

>>> r = Reportlet(bl, out_figs, config={
...     'title': 'Some Title', 'bids': {'datatype': 'figures', 'desc': 'reconall'},
...     'description': 'Some description', 'static': False})
>>> r.name
'datatype-figures_desc-reconall'

>>> r.components[0][0].startswith('<object')
True

>>> r = Reportlet(bl, out_figs, config={
...     'title': 'Some Title', 'bids': {'datatype': 'figures', 'desc': 'summary'},
...     'description': 'Some description'})

>>> r.components[0][0].startswith('<h3')
True

>>> r.components[0][1] is None
True

>>> r = Reportlet(bl, out_figs, config={
...     'title': 'Some Title',
...     'bids': {'datatype': 'figures', 'space': '.*', 'regex_search': True},
...     'caption': 'Some description {space}'})
>>> sorted(r.components)[0][1]
'Some description MNI152NLin2009cAsym'

>>> sorted(r.components)[1][1]
'Some description MNI152NLin6Asym'

>>> r = Reportlet(bl, out_figs, config={
...     'title': 'Some Title',
...     'bids': {'datatype': 'fmap', 'space': '.*', 'regex_search': True},
...     'caption': 'Some description {space}'})
>>> r.is_empty()
True

>>> os.chdir(cwd)

is_empty()

class niworkflows.reports.core.SubReport(name, isnested=False, reportlets=None, title='')

Bases: niworkflows.reports.core.Element

SubReports are sections within a Report.

niworkflows.reports.core.generate_reports(subject_list, output_dir, run_uuid, config=None, work_dir=None, packagename=None)

Execute run_reports on a list of subjects.

niworkflows.reports.core.run_reports(out_dir, subject_label, run_uuid, config=None, reportlets_dir=None, packagename=None)

Run the reports.

>>> cwd = os.getcwd()
>>> os.chdir(tmpdir)

>>> from pkg_resources import resource_filename
>>> from shutil import copytree
>>> test_data_path = resource_filename('niworkflows', 'data/tests/work')
>>> testdir = Path(tmpdir)
>>> data_dir = copytree(test_data_path, str(testdir / 'work'))
>>> (testdir / 'fmriprep').mkdir(parents=True, exist_ok=True)

>>> run_reports(testdir / 'out', '01', 'madeoutuuid', packagename='fmriprep',
...             reportlets_dir=testdir / 'work' / 'reportlets')
0

>>> os.chdir(cwd)