def individual_html(in_iqms, in_plots=None):
import os.path as op #pylint: disable=W0404
import datetime
from mriqc import __version__ as ver
from mriqc.reports.utils import iqms2html
from mriqc.data import IndividualTemplate
from json import load
from io import open #pylint: disable=W0622
with open(in_iqms) as f:
iqms_dict = load(f)
if in_plots is None:
in_plots = []
svg_files = []
for pfile in in_plots:
with open(pfile) as f:
svg_files.append('\n'.join(f.read().split('\n')[1:]))
qctype = iqms_dict.pop('qc_type')
if qctype == 'anat':
qctype = 'anatomical'
sub_id = iqms_dict.pop('subject_id')
ses_id = iqms_dict.pop('session_id')
run_id = iqms_dict.pop('run_id')
out_file = op.abspath('sub-{}_ses-{}_run-{}_T1w-report.html'.format(
sub_id[4:] if sub_id.startswith('sub-') else sub_id,
ses_id, run_id))
tpl = IndividualTemplate()
tpl.generate_conf({
'qctype': qctype,
'sub_id': sub_id,
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict),
'svg_files': svg_files
}, out_file)
return out_file
def individual_html(in_iqms, in_plots=None, exclude_index=0, wf_details=None):
import os.path as op #pylint: disable=W0404
import datetime
from json import load
from mriqc import __version__ as ver
from mriqc.reports.utils import iqms2html, anat_flags, read_report_snippet
from mriqc.data import IndividualTemplate
from mriqc import logging
from io import open #pylint: disable=W0622
report_log = logging.getLogger('mriqc.report')
report_log.setLevel(logging.INFO)
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
if in_plots is None:
in_plots = []
if wf_details is None:
wf_details = []
# Extract and prune metadata
metadata = iqms_dict.pop('metadata', None)
qctype = metadata.pop('qc_type', None)
file_id = [
metadata.pop(k, None) for k in
['subject_id', 'session_id', 'task_id', 'acq_id', 'rec_id', 'run_id']
]
file_id = [comp for comp in file_id if comp is not None]
# Deal with special IQMs
if qctype.startswith('anat'):
qctype = 'anatomical'
flags = anat_flags(iqms_dict)
if flags:
wf_details.append(flags)
elif qctype.startswith('func'):
qctype = 'functional'
else:
RuntimeError('Unknown QC type "%s"' % qctype)
config = {
'qctype': qctype,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': [read_report_snippet(pfile) for pfile in in_plots],
'exclude_index': exclude_index,
'workflow_details': wf_details,
'metadata': iqms2html(metadata, 'metadata-table'),
}
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
def individual_html(in_iqms, in_plots=None):
import os.path as op #pylint: disable=W0404
import datetime
from json import load
from mriqc import logging, __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports.utils import iqms2html, read_report_snippet
from mriqc.data import IndividualTemplate
from io import open #pylint: disable=W0622
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
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
if in_plots is None:
in_plots = []
# 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]
pred_qa = None #metadata.pop('mriqc_pred', None)
config = {
'modality': mod,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': [read_report_snippet(pfile) for pfile in in_plots],
'workflow_details': wf_details,
'provenance': iqms2html(prov, 'provenance-table'),
'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
def individual_html(in_iqms, in_plots=None):
from os import path as op
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
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
# 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')
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,
'sub_id': '_'.join(file_id),
'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,
'provenance': iqms2html(prov, 'provenance-table'),
'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
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'))
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
def individual_html(in_iqms, in_plots=None, exclude_index=0, wf_details=None):
import os.path as op #pylint: disable=W0404
import datetime
from json import load
from mriqc import __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports.utils import iqms2html, anat_flags, read_report_snippet
from mriqc.data import IndividualTemplate
from mriqc import logging
from io import open #pylint: disable=W0622
report_log = logging.getLogger('mriqc.report')
report_log.setLevel(logging.INFO)
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
if in_plots is None:
in_plots = []
if wf_details is None:
wf_details = []
# Extract and prune metadata
metadata = iqms_dict.pop('metadata', None)
mod = metadata.pop('modality', None)
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]
pred_qa = None #metadata.pop('mriqc_pred', None)
# Deal with special IQMs
if mod in ('T1w', 'T2w'):
flags = anat_flags(iqms_dict)
if flags:
wf_details.append(flags)
elif mod == 'bold':
pass
else:
RuntimeError('Unknown modality "%s"' % mod)
config = {
'modality': mod,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': [read_report_snippet(pfile) for pfile in in_plots],
'exclude_index': exclude_index,
'workflow_details': wf_details,
'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