Source code for mriqc.reports.individual

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
# pylint: disable=no-member
#
# @Author: oesteban
# @Date:   2016-01-05 11:33:39
# @Email:  code@oscaresteban.es
# @Last modified by:   oesteban
""" Encapsulates report generation functions """
from __future__ import print_function, division, absolute_import, unicode_literals


[docs]def individual_html(in_iqms, in_plots=None, api_id=None): from pathlib import Path import datetime from json import load from mriqc import logging, __version__ as ver from mriqc.utils.misc import BIDS_COMP from mriqc.reports import REPORT_TITLES from mriqc.reports.utils import iqms2html, read_report_snippet from mriqc.data import IndividualTemplate report_log = logging.getLogger('mriqc.report') def _get_details(in_iqms, modality): in_prov = in_iqms.pop('provenance', {}) warn_dict = in_prov.pop('warnings', None) sett_dict = in_prov.pop('settings', None) wf_details = [] if modality == 'bold': bold_exclude_index = in_iqms.get('dumb_trs') if bold_exclude_index is None: report_log.warning('Building bold report: no exclude index was found') elif bold_exclude_index > 0: msg = """\ <span class="problematic">Non-steady state (strong T1 contrast) has been detected in the \ first {} volumes</span>. They were excluded before generating any QC measures and plots.""" wf_details.append(msg.format(bold_exclude_index)) hmc_fsl = sett_dict.pop('hmc_fsl') if hmc_fsl is not None: msg = 'Framewise Displacement was computed using ' if hmc_fsl: msg += 'FSL <code>mcflirt</code>' else: msg += 'AFNI <code>3dvolreg</code>' wf_details.append(msg) fd_thres = sett_dict.pop('fd_thres') if fd_thres is not None: wf_details.append( 'Framewise Displacement threshold was defined at %f mm' % fd_thres) elif modality in ('T1w', 'T2w'): if warn_dict.pop('small_air_mask', False): wf_details.append( '<span class="problematic">Detected hat mask was too small</span>') if warn_dict.pop('large_rot_frame', False): wf_details.append( '<span class="problematic">Detected a zero-filled frame, has the original ' 'image been rotated?</span>') return in_prov, wf_details, sett_dict in_iqms = Path(in_iqms) with in_iqms.open() as jsonfile: iqms_dict = load(jsonfile) # Now, the in_iqms file should be correctly named out_file = str(Path(in_iqms.with_suffix(".html").name).resolve()) # Extract and prune metadata metadata = iqms_dict.pop('bids_meta', None) mod = metadata.pop('modality', None) prov, wf_details, _ = _get_details(iqms_dict, mod) file_id = [metadata.pop(k, None) for k in list(BIDS_COMP.keys())] file_id = [comp for comp in file_id if comp is not None] if in_plots is None: in_plots = [] else: if any(('melodic_reportlet' in k for k in in_plots)): REPORT_TITLES['bold'].insert(3, ('ICA components', 'ica-comps')) if any(('plot_spikes' in k for k in in_plots)): REPORT_TITLES['bold'].insert(3, ('Spikes', 'spikes')) in_plots = [(REPORT_TITLES[mod][i] + (read_report_snippet(v), )) for i, v in enumerate(in_plots)] pred_qa = None # metadata.pop('mriqc_pred', None) config = { 'modality': mod, 'dataset': metadata.pop('dataset', None), 'bids_name': in_iqms.with_suffix("").name, 'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"), 'version': ver, 'imparams': iqms2html(iqms_dict, 'iqms-table'), 'svg_files': in_plots, 'workflow_details': wf_details, 'webapi_url': prov.pop('webapi_url'), 'webapi_port': prov.pop('webapi_port'), '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) report_log.info('Generated individual log (%s)', out_file) return out_file