Draft resampling workflow (#16)

* Work on incorporating resampler.

* Something like this?

* Keep working.

* Update base.py

* Drop task_id from collect_derivatives.

* Run ruff.

* Address ruff's concerns.

* Update resampler.py

* Work on resampling workflow.

pyproject.toml

@@ -18,12 +18,13 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-  "fmriprep",
+  "fmriprep @ git+https://github.com/nipreps/fmriprep.git@master",
   "nipype >= 1.8.5",
-  "nireports",
-  "niworkflows",
+  "nireports @ git+https://github.com/nipreps/nireports.git@main",
+  "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
   "pybids >= 0.15.6",
-  "smriprep",
+  "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
+  "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
   "typer",
 ]
 dynamic = ["version"]

src/fmripost_aroma/interfaces/resampler.py

@@ -0,0 +1,62 @@
+"""Interfaces for resampling."""
+
+from nipype.interfaces.base import (
+    BaseInterfaceInputSpec,
+    File,
+    SimpleInterface,
+    TraitedSpec,
+    traits,
+)
+
+
+class _ResamplerInputSpec(BaseInterfaceInputSpec):
+    bold_file = File(exists=True, desc='BOLD file to resample.')
+    derivs_path = traits.Directory(
+        exists=True,
+        desc='Path to derivatives.',
+    )
+    output_dir = traits.Directory(
+        exists=True,
+        desc='Output directory.',
+    )
+    space = traits.Str(
+        'MNI152NLin6Asym',
+        usedefault=True,
+        desc='Output space.',
+    )
+    resolution = traits.Str(
+        '2',
+        usedefault=True,
+        desc='Output resolution.',
+    )
+
+
+class _ResamplerOutputSpec(TraitedSpec):
+    output_file = File(exists=True, desc='Resampled BOLD file.')
+
+
+class Resampler(SimpleInterface):
+    """Extract timeseries and compute connectivity matrices.
+
+    Write out time series using Nilearn's NiftiLabelMasker
+    Then write out functional correlation matrix of
+    timeseries using numpy.
+    """
+
+    input_spec = _ResamplerInputSpec
+    output_spec = _ResamplerOutputSpec
+
+    def _run_interface(self, runtime):
+        from fmripost_aroma.utils import resampler
+
+        output_file = resampler.main(
+            bold_file=self.inputs.bold_file,
+            derivs_path=self.inputs.derivs_path,
+            output_dir=self.inputs.output_dir,
+            space=self.inputs.space,
+            resolution=self.inputs.resolution,
+        )
+
+        self._results['output_file'] = output_file
+
+        return runtime