# 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/
#
"""class mixin and utilities for enabling reports for nipype interfaces."""
from nipype.interfaces.base import File, traits
from nipype.interfaces.mixins import reporting
from ... import NIWORKFLOWS_LOG
from ...viz.utils import cuts_from_bbox, compose_view
class _SVGReportCapableInputSpec(reporting.ReportCapableInputSpec):
out_report = File(
"report.svg", usedefault=True, desc="filename for the visual report"
)
compress_report = traits.Enum(
"auto",
True,
False,
usedefault=True,
desc="Compress the reportlet using SVGO or"
"WEBP. 'auto' - compress if relevant "
"software is installed, True = force,"
"False - don't attempt to compress",
)
[docs]
class RegistrationRC(reporting.ReportCapableInterface):
"""An abstract mixin to registration nipype interfaces."""
_fixed_image = None
_moving_image = None
_fixed_image_mask = None
_fixed_image_label = "fixed"
_moving_image_label = "moving"
_contour = None
_dismiss_affine = False
def _generate_report(self):
"""Generate the visual report."""
from nilearn.image import threshold_img, load_img
from nilearn.masking import apply_mask, unmask
from niworkflows.viz.utils import plot_registration
NIWORKFLOWS_LOG.info("Generating visual report")
fixed_image_nii = load_img(self._fixed_image)
moving_image_nii = load_img(self._moving_image)
contour_nii = load_img(self._contour) if self._contour is not None else None
if self._fixed_image_mask:
fixed_image_nii = unmask(
apply_mask(fixed_image_nii, self._fixed_image_mask),
self._fixed_image_mask,
)
# since the moving image is already in the fixed image space we
# should apply the same mask
moving_image_nii = unmask(
apply_mask(moving_image_nii, self._fixed_image_mask),
self._fixed_image_mask,
)
mask_nii = load_img(self._fixed_image_mask)
else:
mask_nii = threshold_img(fixed_image_nii, 1e-3)
n_cuts = 7
if not self._fixed_image_mask and contour_nii:
cuts = cuts_from_bbox(contour_nii, cuts=n_cuts)
else:
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
# Call composer
compose_view(
plot_registration(
fixed_image_nii,
"fixed-image",
estimate_brightness=True,
cuts=cuts,
label=self._fixed_image_label,
contour=contour_nii,
compress=self.inputs.compress_report,
dismiss_affine=self._dismiss_affine,
),
plot_registration(
moving_image_nii,
"moving-image",
estimate_brightness=True,
cuts=cuts,
label=self._moving_image_label,
contour=contour_nii,
compress=self.inputs.compress_report,
dismiss_affine=self._dismiss_affine,
),
out_file=self._out_report,
)
[docs]
class SegmentationRC(reporting.ReportCapableInterface):
"""An abstract mixin to segmentation nipype interfaces."""
def _generate_report(self):
from niworkflows.viz.utils import plot_segs
compose_view(
plot_segs(
image_nii=self._anat_file,
seg_niis=self._seg_files,
bbox_nii=self._mask_file,
out_file=self.inputs.out_report,
masked=self._masked,
compress=self.inputs.compress_report,
),
fg_svgs=None,
out_file=self._out_report,
)
[docs]
class SurfaceSegmentationRC(reporting.ReportCapableInterface):
"""An abstract mixin to registration nipype interfaces."""
_anat_file = None
_mask_file = None
_contour = None
def _generate_report(self):
"""Generate the visual report."""
from nilearn.image import threshold_img, load_img
from nilearn.masking import apply_mask, unmask
from niworkflows.viz.utils import plot_registration
NIWORKFLOWS_LOG.info("Generating visual report")
anat = load_img(self._anat_file)
contour_nii = load_img(self._contour) if self._contour is not None else None
if self._mask_file:
anat = unmask(apply_mask(anat, self._mask_file), self._mask_file)
mask_nii = load_img(self._mask_file)
else:
mask_nii = threshold_img(anat, 1e-3)
n_cuts = 7
if not self._mask_file and contour_nii:
cuts = cuts_from_bbox(contour_nii, cuts=n_cuts)
else:
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
# 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._out_report,
)
[docs]
class ReportingInterface(reporting.ReportCapableInterface):
"""
Interface that always generates a report.
A subclass must define an ``input_spec`` and override ``_generate_report``.
"""
output_spec = reporting.ReportCapableOutputSpec
def __init__(self, generate_report=True, **kwargs):
super().__init__(
generate_report=generate_report, **kwargs
)
def _run_interface(self, runtime):
return runtime