Merge pull request #7 from smeisler/pydra-synthstrip

[ENH] Pydra version of synthstrip

README.md

@@ -10,6 +10,9 @@ pip install nipreps-synthstrip
 
 # For the nipype interface
 pip install nipreps-synthstrip[nipype]
+
+# For the pydra interface
+pip install nipreps-synthstrip[pydra]
 ```
 
 ### Command Line Tool
@@ -24,8 +27,14 @@ $ nipreps-synthstrip
 from nipreps.synthstrip.wrappers.nipype import SynthStrip
 ```
 
+### Pydra Interface
+
+```python
+from nipreps.synthstrip.wrappers.pydra import SynthStrip
+```
+
 ## Citation
 
 > A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann.
 > SynthStrip: Skull-Stripping for Any Brain Image.
-> https://arxiv.org/abs/2203.09974
+> https://arxiv.org/abs/2203.09974

nipreps/synthstrip/wrappers/pydra.py

@@ -0,0 +1,119 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2022 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/
+#
+"""SynthStrip interface."""
+
+import os
+import attr
+from pathlib import Path
+import pydra
+
+_fs_home = os.getenv("FREESURFER_HOME", None)
+_default_model_path = Path(_fs_home) / "models" / "synthstrip.1.pt" if _fs_home else None
+
+if _fs_home and not _default_model_path.exists():
+    _default_model_path = None
+
+SynthStripInputSpec = pydra.specs.SpecInfo(
+    name='SynthStripInputSpec',
+    fields=[
+        (
+            'in_file',
+            attr.ib(
+                type=str,
+                metadata={
+                    'argstr': "-i",
+                    'help_string': 'Input image to skullstrip',
+                    'mandatory': True,
+                },
+            ),
+        ),
+        (
+            'out_file',
+            str,
+            {
+                'argstr': "-o",
+                "help_string": "Save stripped image to path",
+                "output_file_template": "{in_file}_desc-brain.nii.gz",
+            },
+        ),
+        (
+            'out_mask',
+            str,
+            {
+                'argstr': "-m",
+                "help_string": "Save binary brain mask to path",
+                "output_file_template": "{in_file}_desc-brain_mask.nii.gz",
+            },
+        ),
+        (
+            'use_gpu',
+            bool,
+            False,
+            {
+                'argstr': "-g",
+                'help_string': 'Use the GPU',
+            },
+        ),
+        (
+            'border_mm',
+            int,
+            1,
+            {
+                'argstr': "-b",
+                "help_string": "Mask border threshold in mm",
+            },
+        ),
+        (
+            'no_csf',
+            bool,
+            False,
+            {
+                'argstr': "--no-csf",
+                'help_string': 'Exclude CSF from brain border',
+            },
+        ),
+        (
+            'model',
+            pydra.specs.File,
+            str(_default_model_path),
+            {
+                'argstr': "--model",
+                "help_string": "File containing model's weights",
+            },
+        ),
+        (
+            'num_threads',
+            int,
+            {
+                'argstr': "-n",
+                "help_string": "Number of threads",
+            },
+        ),
+    ],
+    bases=(pydra.specs.ShellSpec,),
+)
+
+SynthStrip = pydra.ShellCommandTask(
+    executable="nipreps-synthstrip",
+    input_spec = SynthStripInputSpec
+)

pyproject.toml

@@ -43,6 +43,9 @@ dev = [
 nipype = [
     "nipype",
 ]
+pydra = [
+    "pydra",
+]
 test = [
     "pytest",
 ]
@@ -65,4 +68,4 @@ target-version = ['py310']
 skip-string-normalization = true
 
 [tool.isort]
-profile = 'black'
+profile = 'black'