Warning: This document is for the development version of smriprep.

Source code for smriprep.interfaces.reports

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# We support and encourage derived works from this project, please read
# about our expectations at
#
#     https://www.nipreps.org/community/licensing/
#
"""Interfaces to generate reportlets."""

import time
from pathlib import Path

from nipype.interfaces import freesurfer as fs
from nipype.interfaces.base import (
    BaseInterfaceInputSpec,
    Directory,
    File,
    InputMultiObject,
    SimpleInterface,
    Str,
    TraitedSpec,
    isdefined,
)
from nipype.interfaces.io import FSSourceInputSpec as _FSSourceInputSpec
from nipype.interfaces.mixins import reporting
from niworkflows.interfaces.reportlets.base import _SVGReportCapableInputSpec

SUBJECT_TEMPLATE = """\
\t<ul class="elem-desc">
\t\t<li>Subject ID: {subject_id}</li>
\t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
\t\t<li>Standard spaces: {output_spaces}</li>
\t\t<li>FreeSurfer reconstruction: {freesurfer_status}</li>
\t</ul>
"""

ABOUT_TEMPLATE = """\t<ul>
\t\t<li>sMRIPrep version: {version}</li>
\t\t<li>sMRIPrep command: <code>{command}</code></li>
\t\t<li>Date preprocessed: {date}</li>
\t</ul>
</div>
"""


class _SummaryOutputSpec(TraitedSpec):
    out_report = File(exists=True, desc='HTML segment containing summary')


[docs] class SummaryInterface(SimpleInterface): """Base Nipype interface for html summaries.""" output_spec = _SummaryOutputSpec def _run_interface(self, runtime): segment = self._generate_segment() path = Path(runtime.cwd) / 'report.html' path.write_text(segment) self._results['out_report'] = str(path) return runtime def _generate_segment(self): raise NotImplementedError
class _SubjectSummaryInputSpec(BaseInterfaceInputSpec): t1w = InputMultiObject(File(exists=True), desc='T1w structural images') t2w = InputMultiObject(File(exists=True), desc='T2w structural images') subjects_dir = Directory(desc='FreeSurfer subjects directory') subject_id = Str(desc='Subject ID') output_spaces = InputMultiObject(Str, desc='list of standard spaces') class _SubjectSummaryOutputSpec(_SummaryOutputSpec): # This exists to ensure that the summary is run prior to the first ReconAll # call, allowing a determination whether there is a pre-existing directory subject_id = Str(desc='FreeSurfer subject ID')
[docs] class SubjectSummary(SummaryInterface): """Subject html summary reportlet.""" input_spec = _SubjectSummaryInputSpec output_spec = _SubjectSummaryOutputSpec def _run_interface(self, runtime): if isdefined(self.inputs.subject_id): self._results['subject_id'] = self.inputs.subject_id return super()._run_interface(runtime) def _generate_segment(self): if not isdefined(self.inputs.subjects_dir): freesurfer_status = 'Not run' else: recon = fs.ReconAll( subjects_dir=self.inputs.subjects_dir, subject_id=self.inputs.subject_id, T1_files=self.inputs.t1w, flags='-noskullstrip', ) if recon.cmdline.startswith('echo'): freesurfer_status = 'Pre-existing directory' else: freesurfer_status = 'Run by sMRIPrep' t2w_seg = '' if self.inputs.t2w: t2w_seg = f'(+ {len(self.inputs.t2w):d} T2-weighted)' output_spaces = self.inputs.output_spaces if not isdefined(output_spaces): output_spaces = '&lt;none given&gt;' else: output_spaces = ', '.join(output_spaces) return SUBJECT_TEMPLATE.format( subject_id=self.inputs.subject_id, n_t1s=len(self.inputs.t1w), t2w=t2w_seg, output_spaces=output_spaces, freesurfer_status=freesurfer_status, )
class _AboutSummaryInputSpec(BaseInterfaceInputSpec): version = Str(desc='sMRIPrep version') command = Str(desc='sMRIPrep command') # Date not included - update timestamp only if version or command changes
[docs] class AboutSummary(SummaryInterface): """About section reportlet.""" input_spec = _AboutSummaryInputSpec def _generate_segment(self): return ABOUT_TEMPLATE.format( version=self.inputs.version, command=self.inputs.command, date=time.strftime('%Y-%m-%d %H:%M:%S %z'), )
class _FSSurfaceReportInputSpec(_SVGReportCapableInputSpec, _FSSourceInputSpec): pass class _FSSurfaceReportOutputSpec(reporting.ReportCapableOutputSpec): pass
[docs] class FSSurfaceReport(SimpleInterface): """Replaces ``ReconAllRPT``, without need of calling recon-all.""" input_spec = _FSSurfaceReportInputSpec output_spec = _FSSurfaceReportOutputSpec def _run_interface(self, runtime): from nibabel import load from niworkflows.viz.utils import ( compose_view, cuts_from_bbox, plot_registration, ) rootdir = Path(self.inputs.subjects_dir) / self.inputs.subject_id _anat_file = str(rootdir / 'mri' / 'brain.mgz') _contour_file = str(rootdir / 'mri' / 'ribbon.mgz') anat = load(_anat_file) contour_nii = load(_contour_file) n_cuts = 7 cuts = cuts_from_bbox(contour_nii, cuts=n_cuts) self._results['out_report'] = str(Path(runtime.cwd) / self.inputs.out_report) # Call composer compose_view( plot_registration( anat, 'fixed-image', estimate_brightness=True, cuts=cuts, contour=contour_nii, compress=self.inputs.compress_report, ), [], out_file=self._results['out_report'], ) return runtime