FIX/RF: Nipype interfaces

nipreps/synthstrip/wrappers/nipype.py

@@ -22,6 +22,7 @@
 #
 """SynthStrip interface."""
 
+import logging
 import os
 from pathlib import Path
 
@@ -30,15 +31,11 @@
     CommandLineInputSpec,
     File,
     TraitedSpec,
-    Undefined,
+    isdefined,
     traits,
 )
 
-_fs_home = os.getenv('FREESURFER_HOME', None)
-_default_model_path = Path(_fs_home) / 'models' / 'synthstrip.1.pt' if _fs_home else Undefined
-
-if _fs_home and not _default_model_path.exists():
-    _default_model_path = Undefined
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class _SynthStripInputSpec(CommandLineInputSpec):
@@ -50,8 +47,6 @@ class _SynthStripInputSpec(CommandLineInputSpec):
     )
     use_gpu = traits.Bool(False, usedefault=True, argstr='-g', desc='Use GPU', nohash=True)
     model = File(
-        str(_default_model_path),
-        usedefault=True,
         exists=True,
         argstr='--model %s',
         desc="file containing model's weights",
@@ -78,6 +73,26 @@ class _SynthStripOutputSpec(TraitedSpec):
 
 
 class SynthStrip(CommandLine):
+    """NiPrep implementation of FreeSurfer's SynthStrip."""
+
     _cmd = 'nipreps-synthstrip'
     input_spec = _SynthStripInputSpec
     output_spec = _SynthStripOutputSpec
+
+    def _parse_inputs(self, skip=None):
+        if not isdefined(self.inputs.model):
+            self._set_default_model()
+        return super()._parse_inputs(skip or [])
+
+    def _set_default_model(self):
+        model = None
+        fs_home = os.getenv('FREESURFER_HOME', None)
+        if fs_home and Path(fs_home).exists():
+            model = Path(fs_home) / 'models' / 'synthstrip.1.pt'
+
+        if not model or not model.exists():
+            IFLOGGER.warning('No SynthStrip model was found.')
+            return
+
+        IFLOGGER.info('Using default SynthStrip model: %s', model.name)
+        self.inputs.model = model

nipreps/synthstrip/wrappers/tests/test_nipype.py

@@ -0,0 +1,45 @@
+from pathlib import Path
+
+import pytest
+
+try:
+    from nipreps.synthstrip.wrappers.nipype import SynthStrip
+except ImportError:
+    pytest.skip('Nipype not installed.')
+
+
+@pytest.fixture
+def t1w(tmp_path):
+    t1w = tmp_path / 'T1w.nii.gz'
+    t1w.touch()
+    return t1w
+
+
+@pytest.fixture
+def fsdir(tmp_path):
+    fs = tmp_path / 'freesurfer'
+    (fs / 'models').mkdir(parents=True)
+    (fs / 'models' / 'synthstrip.1.pt').touch()
+    return fs
+
+
+def test_nipype_synthstrip_fs(t1w, fsdir, monkeypatch):
+    # First with FS environment
+    monkeypatch.setenv('FREESURFER_HOME', str(fsdir))
+    syn = SynthStrip(in_file=t1w)
+    assert 'synthstrip.1.pt' in syn.cmdline
+
+    # now remove the default file
+    (fsdir / 'models' / 'synthstrip.1.pt').unlink()
+    syn = SynthStrip(in_file=t1w)
+    assert 'synthstrip.1.pt' not in syn.cmdline
+
+    monkeypatch.delenv('FREESURFER_HOME')
+    syn = SynthStrip(in_file=t1w)
+    assert 'synthstrip.1.pt' not in syn.cmdline
+
+    model = Path('model.pt')
+    model.touch()
+    syn = SynthStrip(in_file=t1w, model=model)
+    assert 'model.pt' in syn.cmdline
+    model.unlink()

pyproject.toml

@@ -99,6 +99,7 @@ ignore = [
   "S311",  # We are not using random for cryptographic purposes
   "ISC001",
   "S603",
+  "S101",
 ]
 
 [tool.ruff.lint.flake8-quotes]