Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
"provenance": iqms2html(prov, "provenance-table"),
"md5sum": prov["md5sum"],
"metadata": iqms2html(metadata, "metadata-table"),
"pred_qa": pred_qa,
}
if _config["metadata"] is None:
_config["workflow_details"].append(
'<span class="warning">File has no metadata</span> '
"<span>(sidecar JSON file missing or empty)</span>"
)
tpl = IndividualTemplate()
tpl.generate_conf(_config, out_file)
config.loggers.cli.info("Generated individual log (%s)", out_file)
return out_file
from ..utils.bids import DEFAULT_TYPES
from ..reports import group_html
from ..utils.misc import generate_tsv # , generate_pred
config.loggers.cli.info("Group level started...")
# Generate reports
mod_group_reports = []
for mod in config.execution.modalities or DEFAULT_TYPES:
output_dir = config.execution.output_dir
dataframe, out_tsv = generate_tsv(output_dir, mod)
# If there are no iqm.json files, nothing to do.
if dataframe is None:
continue
config.loggers.cli.info(
f"Generated summary TSV table for the {mod} data ({out_tsv})"
)
# out_pred = generate_pred(derivatives_dir, settings['output_dir'], mod)
# if out_pred is not None:
# log.info('Predicted QA CSV table for the %s data generated (%s)',
# mod, out_pred)
out_html = output_dir / f"group_{mod}.html"
group_html(
out_tsv,
mod,
csv_failed=output_dir / f"group_variant-failed_{mod}.csv",
out_file=out_html,
)
config.loggers.cli.info(f"Group-{mod} report generated ({out_html})")
# run MRIQC
mriqc_wf.run(**config.nipype.get_plugin())
# Warn about submitting measures AFTER
if not config.execution.no_sub:
config.loggers.cli.warning(config.DSA_MESSAGE)
config.loggers.cli.log(25, "Participant level finished successfully.")
# Set up group level
if "group" in config.workflow.analysis_level:
from ..utils.bids import DEFAULT_TYPES
from ..reports import group_html
from ..utils.misc import generate_tsv # , generate_pred
config.loggers.cli.info("Group level started...")
# Generate reports
mod_group_reports = []
for mod in config.execution.modalities or DEFAULT_TYPES:
output_dir = config.execution.output_dir
dataframe, out_tsv = generate_tsv(output_dir, mod)
# If there are no iqm.json files, nothing to do.
if dataframe is None:
continue
config.loggers.cli.info(
f"Generated summary TSV table for the {mod} data ({out_tsv})"
)
# out_pred = generate_pred(derivatives_dir, settings['output_dir'], mod)
# if out_pred is not None:
# mod, out_pred)
out_html = output_dir / f"group_{mod}.html"
group_html(
out_tsv,
mod,
csv_failed=output_dir / f"group_variant-failed_{mod}.csv",
out_file=out_html,
)
config.loggers.cli.info(f"Group-{mod} report generated ({out_html})")
mod_group_reports.append(mod)
if not mod_group_reports:
raise Exception("No data found. No group level reports were generated.")
config.loggers.cli.info("Group level finished successfully.")
f"Generated summary TSV table for the {mod} data ({out_tsv})"
)
# out_pred = generate_pred(derivatives_dir, settings['output_dir'], mod)
# if out_pred is not None:
# log.info('Predicted QA CSV table for the %s data generated (%s)',
# mod, out_pred)
out_html = output_dir / f"group_{mod}.html"
group_html(
out_tsv,
mod,
csv_failed=output_dir / f"group_variant-failed_{mod}.csv",
out_file=out_html,
)
config.loggers.cli.info(f"Group-{mod} report generated ({out_html})")
mod_group_reports.append(mod)
if not mod_group_reports:
raise Exception("No data found. No group level reports were generated.")
config.loggers.cli.info("Group level finished successfully.")