test_report.py

"""Testing automatic BIDS report."""

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause

import os.path as op
import textwrap

import mne
import pytest
from mne.datasets import testing

from mne_bids import BIDSPath, make_report
from mne_bids.config import BIDS_VERSION
from mne_bids.write import write_raw_bids

subject_id = "01"
session_id = "01"
run = "01"
acq = "01"
task = "testing"

_bids_path = BIDSPath(
    subject=subject_id, session=session_id, run=run, acquisition=acq, task=task
)

# Get the MNE testing sample data
data_path = testing.data_path(download=False)
raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_trunc_raw.fif")

warning_str = dict(
    channel_unit_changed="ignore:The unit for chann*.:RuntimeWarning:mne",
)


@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
@testing.requires_testing_data
def test_report(tmp_path):
    """Test that report generated works as intended."""
    bids_root = str(tmp_path)
    raw = mne.io.read_raw_fif(raw_fname, verbose=False)
    raw.info["line_freq"] = 60
    bids_path = _bids_path.copy().update(root=bids_root)
    write_raw_bids(raw, bids_path, overwrite=True, verbose=False)

    report = make_report(bids_root)

    expected_report = f""" The [Unspecified] dataset was created by [Unspecified1], and [Unspecified2] and
conforms to BIDS version {BIDS_VERSION}.
This report was generated with MNE-BIDS (https://doi.org/10.21105/joss.01896).
The dataset consists of 1 participants (sex were all unknown; handedness were
all unknown; ages all unknown) and 1 recording sessions: 01. Data was recorded
using an MEG system (Elekta) sampled at 300.31 Hz with line noise at
60.0 Hz. The following software filters were applied during recording:
SpatialCompensation. There was 1 scan in total. Recording durations ranged from
20.0 to 20.0 seconds (mean = 20.0, std = 0.0), for a total of 20.0 seconds of
data recorded over all scans. For each dataset, there were on average 376.0 (std
= 0.0) recording channels per scan, out of which 374.0 (std = 0.0) were used in
analysis (2.0 +/- 0.0 were removed from analysis)."""  # noqa: E501

    expected_report = "\n".join(textwrap.wrap(expected_report, width=80))
    assert report == expected_report


@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
@testing.requires_testing_data
def test_report_no_participant_information(tmp_path):
    """Test report with participants.tsv with participant_id column only."""
    bids_root = tmp_path
    raw = mne.io.read_raw_fif(raw_fname, verbose=False)
    raw.info["line_freq"] = 60
    bids_path = _bids_path.copy().update(root=bids_root)
    write_raw_bids(raw, bids_path, overwrite=True, verbose=False)

    # remove all information and check if report still runs
    (bids_root / "participants.json").unlink()

    # overwrite participant information to see if report still runs
    (bids_root / "participants.tsv").write_text("participant_id\nsub-001")

    report = make_report(bids_root)

    expected_report = f""" The [Unspecified] dataset was created by [Unspecified1], and [Unspecified2] and
conforms to BIDS version {BIDS_VERSION}.
This report was generated with MNE-BIDS (https://doi.org/10.21105/joss.01896).
The dataset consists of 1 participants (sex were all unknown; handedness were
all unknown; ages all unknown) and 1 recording sessions: 01. Data was recorded
using an MEG system (Elekta) sampled at 300.31 Hz with line noise at
60.0 Hz. The following software filters were applied during recording:
SpatialCompensation. There was 1 scan in total. Recording durations ranged from
20.0 to 20.0 seconds (mean = 20.0, std = 0.0), for a total of 20.0 seconds of
data recorded over all scans. For each dataset, there were on average 376.0 (std
= 0.0) recording channels per scan, out of which 374.0 (std = 0.0) were used in
analysis (2.0 +/- 0.0 were removed from analysis)."""  # noqa: E501

    expected_report = "\n".join(textwrap.wrap(expected_report, width=80))
    assert report == expected_report