enh: finalize migration of reporting interfaces

Resolves: #54.

.circleci/config.yml

@@ -17,6 +17,12 @@ jobs:
     steps:
       - checkout
 
+      - run:
+          name: Git config - pacify datalad
+          command: |
+            git config --global user.name 'NiPreps Bot'
+            git config --global user.email '[email protected]'
+
       - restore_cache:
           keys:
             - tf-v0-{{ .Branch }}-{{ .Revision }}
@@ -32,12 +38,46 @@ jobs:
           command: |
             python -c "from templateflow.api import get; get('Fischer344', desc=None, suffix='T2w')"
             python -c "from templateflow.api import get; get('MNI152NLin6Asym', resolution=2, desc='LR', suffix='T1w')"
+            python -c "from templateflow.api import get; get('OASIS30ANTs', resolution=1, desc=None, suffix='T1w')"
+            python -c "from templateflow.api import get; get('OASIS30ANTs', resolution=1, desc='brain', suffix='mask')"
+            python -c "from templateflow.api import get; get('OASIS30ANTs', resolution=1, label='brain', suffix='probseg')"
+            python -c "from templateflow.api import get; get('OASIS30ANTs', resolution=1, desc='BrainCerebellumRegistration', suffix='mask')"
+            python -c "from templateflow.api import get; get('OASIS30ANTs', resolution=1, desc='4', suffix='dseg')"
 
       - save_cache:
          key: tf-v0-{{ .Branch }}-{{ .Revision }}
          paths:
             - /tmp/templateflow
 
+      - restore_cache:
+          keys:
+            - data-v1-{{ .Branch }}-
+            - data-v1-master-
+            - data-v1-
+      - run:
+          name: Get test data from ds000003
+          command: |
+            mkdir -p /tmp/data
+            pushd /tmp/data
+            if [[ ! -d ds000003 ]]; then
+              datalad install -r https://github.com/nipreps-data/ds000003.git
+            fi
+            datalad update -r --merge -d ds000003/
+            datalad get -J 2 -r -d ds000003/ ds000003/*
+            popd
+
+      - save_cache:
+         key: data-v1-{{ .Branch }}-{{ epoch }}
+         paths:
+            - /tmp/data/ds000003
+
+      - run:
+          name: Store FreeSurfer license file
+          command: |
+            mkdir -p /tmp/fslicense
+            cd /tmp/fslicense
+            echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
+
       - run:
           name: Run unit tests
           no_output_timeout: 2h

nireports/conftest.py

@@ -30,13 +30,14 @@
 import pytest
 import tempfile
 
+
 # disable ET
 os.environ['NO_ET'] = '1'
 
 _datadir = (Path(__file__).parent / "tests" / "data").resolve(strict=True)
-niprepsdev_path = os.getenv(
+niprepsdev_path = Path(os.getenv(
     "TEST_DATA_HOME", str(Path.home() / ".cache" / "nipreps-dev")
-)
+))
 test_output_dir = os.getenv("TEST_OUTPUT_DIR")
 test_workdir = os.getenv("TEST_WORK_DIR")
 
@@ -50,8 +51,8 @@ def expand_namespace(doctest_namespace):
     doctest_namespace["os"] = os
     doctest_namespace["pytest"] = pytest
     doctest_namespace["Path"] = Path
-    doctest_namespace["testdata_path"] = _datadir
-    doctest_namespace["niprepsdev_path"] = niprepsdev_path
+    doctest_namespace["test_data_package"] = _datadir
+    doctest_namespace["test_data_home"] = niprepsdev_path
 
     doctest_namespace["os"] = os
     doctest_namespace["Path"] = Path
@@ -72,10 +73,15 @@ def expand_namespace(doctest_namespace):
 
 
 @pytest.fixture
-def testdata_path():
+def test_data_package():
     return _datadir
 
 
+@pytest.fixture
+def test_data_home():
+    return niprepsdev_path
+
+
 @pytest.fixture
 def workdir():
     return None if test_workdir is None else Path(test_workdir)

nireports/interfaces/reporting/base.py

@@ -0,0 +1,199 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2023 The NiPreps Developers <[email protected]>
+#
+# 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 nipype import logging
+from nireports.reportlets.utils import cuts_from_bbox, compose_view
+
+_LOGGER = logging.getLogger("nipype.interface")
+
+
+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",
+    )
+
+
+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 nireports.reportlets.mosaic import plot_registration
+
+        _LOGGER.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,
+        )
+
+
+class SegmentationRC(reporting.ReportCapableInterface):
+    """An abstract mixin to segmentation nipype interfaces."""
+
+    def _generate_report(self):
+        from nireports.reportlets.mosaic 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,
+        )
+
+
+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 nireports.reportlets.mosaic import plot_registration
+
+        _LOGGER.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,
+        )
+
+
+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(ReportingInterface, self).__init__(
+            generate_report=generate_report, **kwargs
+        )
+
+    def _run_interface(self, runtime):
+        return runtime