def _run_interface(self, runtime):
mask = None
if isdefined(self.inputs.in_mask):
mask = self.inputs.in_mask
title = self.inputs.title
if isdefined(self.inputs.subject):
title += ', subject %s' % self.inputs.subject
if isdefined(self.inputs.metadata):
title += ' (' + '_'.join(self.inputs.metadata) + ')'
if isdefined(self.inputs.figsize):
fig = plot_mosaic(
self.inputs.in_file,
title=title,
overlay_mask=mask,
figsize=self.inputs.figsize)
else:
fig = plot_mosaic(
self.inputs.in_file,
title=title,
overlay_mask=mask)
fig.savefig(self.inputs.out_file, dpi=self.inputs.dpi)
return runtime
def plot_anat_mosaic_helper(in_file, subject_id, session_id,
run_id, out_name, bbox_mask_file=None,
title='T1w session: {session_id} run: {run_id}',
only_plot_noise=False):
from mriqc.interfaces.viz_utils import plot_mosaic
import os
title = title.format(**{"session_id": session_id,
"run_id": run_id})
fig = plot_mosaic(in_file, bbox_mask_file=bbox_mask_file, title=title,
only_plot_noise=only_plot_noise)
fig.savefig(out_name, format=out_name.split('.')[-1], dpi=300)
return os.path.abspath(out_name)
def _subject_plots(self, subid):
# Get subject-specific info
subdf = self.dataframe.loc[self.dataframe['subject_id'] == subid]
sessions = sorted(pd.unique(subdf.session_id.ravel()))
subject_plots = []
# Create figure here to avoid too many figures
fig = plt.Figure(figsize=DINA4_LANDSCAPE)
# Re-build mosaic location
for sesid in sessions:
sesdf = subdf.loc[subdf['session_id'] == sesid]
scans = sorted(pd.unique(sesdf.run_id.ravel()))
# Each scan has a volume and (optional) fd plot
for scanid in scans:
nii_paths = op.join(self.report_dir, self.qctype[:4],
'{}_ses-{}_{}/mosaic*.nii.gz'.format(subid, sesid, scanid))
nii_files = sorted(glob(nii_paths))
log.info('Found mosaic files: %s', nii_files)
for mosaic in nii_files:
fname, ext = op.splitext(op.basename(mosaic))
if ext == '.gz':
fname, _ = op.splitext(fname)
fname = fname[7:]
out_mosaic = op.join(
self.work_dir, 'mosaic_{}_{}_ses-{}_run-{}_{}.pdf'.format(
self.qctype[:4], subid, sesid, scanid, fname))
title = 'Filename: {}, session: {}, other: {}'.format(fname, sesid, scanid)
fig = plot_mosaic(mosaic, fig=fig, title=title)
fig.savefig(out_mosaic, dpi=self.dpi)
fig.clf()
subject_plots.append(out_mosaic)
plots = op.join(self.report_dir, self.qctype[:4],
'{}_ses-{}_{}/plot_*.pdf'.format(subid, sesid, scanid))
for fname in sorted(glob(plots)):
if op.isfile(fname):
subject_plots.append(fname)
plt.close()
# Summary cover
sfailed = []
if self.failed:
sfailed = ['%s (%s)' % (s[1], s[2])
for s in self.failed if subid == s[0]]
out_sum = op.join(self.work_dir, '%s_summary_%s.pdf' % (self.qctype, subid))
self.summary_cover(sub_id=subid, out_file=out_sum)
subject_plots.insert(0, out_sum)
# Summary (violinplots) of QC measures
qc_ms = op.join(self.work_dir, '%s_measures_%s.pdf' % (self.qctype, subid))
func = getattr(self, '_report_' + self.qctype)
func(subject=subid, out_file=qc_ms)
subject_plots.append(qc_ms)
sub_path = None
if len(subject_plots) > 0:
# Generate final report with collected pdfs in plots
sub_path = op.join(self.out_dir, '{}_{}.pdf'.format(self.qctype, subid))
concat_pdf(subject_plots, sub_path)
self.result[subid] = {'success': True, 'path': sub_path}
return sub_path
def _subject_plots(self, subid):
# Get subject-specific info
subdf = self.dataframe.loc[self.dataframe['subject_id'] == subid]
sessions = sorted(pd.unique(subdf.session_id.ravel()))
subject_plots = []
# Create figure here to avoid too many figures
fig = plt.Figure(figsize=DINA4_LANDSCAPE)
# Re-build mosaic location
for sesid in sessions:
sesdf = subdf.loc[subdf['session_id'] == sesid]
scans = sorted(pd.unique(sesdf.run_id.ravel()))
# Each scan has a volume and (optional) fd plot
for scanid in scans:
nii_paths = op.join(self.report_dir, self.qctype[:4],
'{}_ses-{}_{}/mosaic*.nii.gz'.format(subid, sesid, scanid))
nii_files = sorted(glob(nii_paths))
if not nii_files:
nii_paths = op.join(
self.report_dir, self.qctype[:4], '{}_ses-[u]{}_[u]{}/mosaic*.nii.gz'.format(
subid, sesid, scanid))
nii_files = sorted(glob(nii_paths))
if not nii_files:
MRIQC_REPORT_LOG.warning(
'No mosaic files were found for subject %s, session %s',
subid, sesid)
for mosaic in nii_files:
fname, ext = op.splitext(op.basename(mosaic))
if ext == '.gz':
fname, _ = op.splitext(fname)
fname = fname[7:]
out_mosaic = op.join(
self.work_dir, 'mosaic_{}_{}_ses-{}_run-{}_{}.pdf'.format(
self.qctype[:4], subid, sesid, scanid, fname))
title = 'Filename: {}, session: {}, other: {}'.format(fname, sesid, scanid)
fig = plot_mosaic(mosaic, fig=fig, title=title)
fig.savefig(out_mosaic, dpi=self.dpi)
fig.clf()
subject_plots.append(out_mosaic)
plots = op.join(self.report_dir, self.qctype[:4],
'{}_ses-{}_{}/plot_*.pdf'.format(subid, sesid, scanid))
pdf_plots = sorted(glob(plots))
if not pdf_plots:
plots = op.join(
self.report_dir, self.qctype[:4],
'{}_ses-[u]{}_[u]{}/plot_*.pdf'.format(subid, sesid, scanid))
pdf_plots = sorted(glob(plots))
if not pdf_plots:
MRIQC_REPORT_LOG.warning(
'No PDF plots were found for subject %s, session %s', subid, sesid)
for fname in sorted(pdf_plots):
if op.isfile(fname):
subject_plots.append(fname)
plt.close()
# Summary cover
# sfailed = []
# if self.failed:
# sfailed = ['%s (%s)' % (s[1], s[2])
# for s in self.failed if subid == s[0]]
out_sum = op.join(self.work_dir, '%s_summary_%s.pdf' % (self.qctype, subid))
self.summary_cover(sub_id=subid, out_file=out_sum)
subject_plots.insert(0, out_sum)
# Summary (violinplots) of QC measures
qc_ms = op.join(self.work_dir, '%s_measures_%s.pdf' % (self.qctype, subid))
func = getattr(self, '_report_' + self.qctype)
func(subject=subid, out_file=qc_ms)
subject_plots.append(qc_ms)
sub_path = None
if len(subject_plots) > 0:
# Generate final report with collected pdfs in plots
sub_path = op.join(self.out_dir, '{}_{}.pdf'.format(self.qctype, subid))
concat_pdf(subject_plots, sub_path)
self.result[subid] = {'success': True, 'path': sub_path}
MRIQC_REPORT_LOG.info(
'Generated individual %s report (%s) for subject %s',
self.qctype, sub_path, subid)
return sub_path
