fix: update to new Estimator object and dw mentions

Author: oesteban

src/nifreeze/cli/run.py

@@ -25,7 +25,7 @@
 from pathlib import Path
 
 from nifreeze.cli.parser import parse_args
-from nifreeze.data.dmri import DWI
+from nifreeze.data.base import BaseDataset
 from nifreeze.estimator import Estimator
 
 
@@ -40,12 +40,12 @@ def main(argv=None) -> None:
     args = parse_args(argv)
 
     # Open the data with the given file path
-    dwi_dataset: DWI = DWI.from_filename(args.input_file)
+    dataset: BaseDataset = BaseDataset.from_filename(args.input_file)
 
     estimator: Estimator = Estimator()
 
-    _ = estimator.estimate(
-        dwi_dataset,
+    _ = estimator.run(
+        dataset,
         align_kwargs=args.align_config,
         models=args.models,
         omp_nthreads=args.nthreads,
@@ -58,7 +58,7 @@ def main(argv=None) -> None:
     output_path: Path = Path(args.output_dir) / output_filename
 
     # Save the DWI dataset to the output path
-    dwi_dataset.to_filename(output_path)
+    dataset.to_filename(output_path)
 
 
 if __name__ == "__main__":

test/test_integration.py

@@ -70,26 +70,25 @@ def test_proximity_estimator_trivial_model(datadir, tmp_path):
         brainmask=dwdata.brainmask,
     )
 
-    estimator = Estimator()
-    em_affines = estimator.estimate(
+    estimator = Estimator(dwi_motion, model="b0")
+    estimator.run(
         data=dwi_motion,
         models=("b0",),
         seed=None,
         align_kwargs={
-            "fixed_modality": "b0",
-            "moving_modality": "b0",
+            "config_file": "b0-to-b0_level0.json",
             "num_threads": min(cpu_count(), 8),
         },
     )
 
     # Uncomment to see the realigned dataset
     nt.linear.LinearTransformsMapping(
-        em_affines,
+        dwi_motion.motion_affines,
         reference=b0nii,
     ).apply(moved_nii).to_filename(tmp_path / "realigned.nii.gz")
 
     # For each moved b0 volume
-    for i, est in enumerate(em_affines):
+    for i, est in enumerate(dwi_motion.motion_affines):
         assert (
             displacements_within_mask(
                 masknii,