Update again.

src/fmripost_phase/interfaces/bids.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """BIDS-related interfaces for fMRIPost-Phase."""
 
 from json import loads

src/fmripost_phase/interfaces/confounds.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """Interfaces for miscellaneous confound extraction methods, including HighCor."""
 
 import os

src/fmripost_phase/interfaces/gift.py

@@ -1 +1,23 @@
+# 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 <[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/
+#
 """Interfaces for the GIFT toolbox."""

src/fmripost_phase/interfaces/laynii.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """LayNii is a C++ library for layer fMRI processing and analysis."""
 
 from nipype.interfaces.base import (

src/fmripost_phase/interfaces/regression.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """Interfaces for phase regression."""
 
 import numpy as np

src/fmripost_phase/interfaces/reportlets.py

@@ -0,0 +1,162 @@
+# 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 <[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/
+#
+"""ReportCapableInterfaces for segmentation tools."""
+
+import os
+import re
+import time
+from collections import Counter
+
+from nipype.interfaces.base import (
+    BaseInterfaceInputSpec,
+    File,
+    InputMultiObject,
+    SimpleInterface,
+    Str,
+    TraitedSpec,
+    isdefined,
+    traits,
+)
+
+SUBJECT_TEMPLATE = """\
+\t<ul class="elem-desc">
+\t\t<li>Subject ID: {subject_id}</li>
+\t\t<li>Functional series: {n_bold:d}</li>
+{tasks}
+\t\t<li>Standard output spaces: {std_spaces}</li>
+\t\t<li>Non-standard output spaces: {nstd_spaces}</li>
+\t</ul>
+"""
+
+FUNCTIONAL_TEMPLATE = """\
+\t\t<details open>
+\t\t<summary>Summary</summary>
+\t\t<ul class="elem-desc">
+\t\t\t<li>Original orientation: {ornt}</li>
+\t\t\t<li>Repetition time (TR): {tr:.03g}s</li>
+\t\t\t<li>Phase-encoding (PE) direction: {pedir}</li>
+\t\t\t<li>Slice timing correction: {stc}</li>
+\t\t\t<li>Susceptibility distortion correction: {sdc}</li>
+\t\t\t<li>Registration: {registration}</li>
+\t\t\t<li>Non-steady-state volumes: {dummy_scan_desc}</li>
+\t\t</ul>
+\t\t</details>
+"""
+
+ABOUT_TEMPLATE = """\t<ul>
+\t\t<li>fMRIPost-Phase version: {version}</li>
+\t\t<li>fMRIPost-Phase command: <code>{command}</code></li>
+\t\t<li>Date postprocessed: {date}</li>
+\t</ul>
+</div>
+"""
+
+
+class SummaryOutputSpec(TraitedSpec):
+    out_report = File(exists=True, desc='HTML segment containing summary')
+
+
+class SummaryInterface(SimpleInterface):
+    output_spec = SummaryOutputSpec
+
+    def _run_interface(self, runtime):
+        segment = self._generate_segment()
+        fname = os.path.join(runtime.cwd, 'report.html')
+        with open(fname, 'w') as fobj:
+            fobj.write(segment)
+        self._results['out_report'] = fname
+        return runtime
+
+    def _generate_segment(self):
+        raise NotImplementedError
+
+
+class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
+    subject_id = Str(desc='Subject ID')
+    bold = InputMultiObject(
+        traits.Either(File(exists=True), traits.List(File(exists=True))),
+        desc='BOLD functional series',
+    )
+    std_spaces = traits.List(Str, desc='list of standard spaces')
+    nstd_spaces = traits.List(Str, desc='list of non-standard spaces')
+
+
+class SubjectSummary(SummaryInterface):
+    input_spec = SubjectSummaryInputSpec
+    output_spec = SummaryOutputSpec
+
+    def _generate_segment(self):
+        BIDS_NAME = re.compile(
+            r'^(.*\/)?'
+            '(?P<subject_id>sub-[a-zA-Z0-9]+)'
+            '(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
+            '(_(?P<task_id>task-[a-zA-Z0-9]+))?'
+            '(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
+            '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
+            '(_(?P<run_id>run-[a-zA-Z0-9]+))?'
+        )
+
+        # Add list of tasks with number of runs
+        bold_series = self.inputs.bold if isdefined(self.inputs.bold) else []
+        bold_series = [s[0] if isinstance(s, list) else s for s in bold_series]
+
+        counts = Counter(
+            BIDS_NAME.search(series).groupdict()['task_id'][5:] for series in bold_series
+        )
+
+        tasks = ''
+        if counts:
+            header = '\t\t<ul class="elem-desc">'
+            footer = '\t\t</ul>'
+            lines = [
+                '\t\t\t<li>Task: {task_id} ({n_runs:d} run{s})</li>'.format(
+                    task_id=task_id, n_runs=n_runs, s='' if n_runs == 1 else 's'
+                )
+                for task_id, n_runs in sorted(counts.items())
+            ]
+            tasks = '\n'.join([header] + lines + [footer])
+
+        return SUBJECT_TEMPLATE.format(
+            subject_id=self.inputs.subject_id,
+            n_bold=len(bold_series),
+            tasks=tasks,
+            std_spaces=', '.join(self.inputs.std_spaces),
+            nstd_spaces=', '.join(self.inputs.nstd_spaces),
+        )
+
+
+class AboutSummaryInputSpec(BaseInterfaceInputSpec):
+    version = Str(desc='FMRIPREP version')
+    command = Str(desc='FMRIPREP command')
+    # Date not included - update timestamp only if version or command changes
+
+
+class AboutSummary(SummaryInterface):
+    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'),
+        )

src/fmripost_phase/interfaces/warpkit.py

@@ -1 +1,23 @@
+# 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 <[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/
+#
 """Interfaces for the warpkit toolbox."""

src/fmripost_phase/utils/bids.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """Utilities to handle BIDS inputs."""
 
 from __future__ import annotations

src/fmripost_phase/utils/utils.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """Utility functions for fmriprep_phase."""
 
 from nipype.pipeline import engine as pe

src/fmripost_phase/workflows/__init__.py

@@ -1,3 +1,25 @@
+# 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 <[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/
+#
 """Workflow functions for fMRIPost-phase."""
 
 from fmripost_phase.workflows import base, regression