fix: interface internal streamlining toward getting tests to pass

fix: interface internal streamlining toward getting tests to pass

Author: oesteban

sdcflows/interfaces/bspline.py

@@ -378,20 +378,30 @@ def _run_interface(self, runtime):
         )
 
         # We can now write out the fieldmap
-        # unwarp.mapped.to_filename(out_field)
-        # self._results["out_field"] = out_field
+        self._results["out_field"] = fname_presuffix(
+            self.inputs.in_data,
+            suffix="_field",
+            newpath=runtime.cwd,
+        )
+        unwarp.mapped.to_filename(self._results["out_field"])
 
         # HMC matrices are only necessary when reslicing the data (i.e., apply())
         # Check the length of in_xfms matches that of in_data
-        self._results["out_corrected"] = unwarp.apply(
+        self._results["out_corrected"] = fname_presuffix(
+            self.inputs.in_data,
+            suffix="_sdc",
+            newpath=runtime.cwd,
+        )
+
+        unwarp.apply(
             self.inputs.in_data,
             self.inputs.pe_dir,
             self.inputs.ro_time,
-            xfms=self.inputs.in_xfms,
+            xfms=self.inputs.in_xfms if isdefined(self.inputs.in_xfms) else None,
             num_threads=(
                 None if not isdefined(self.inputs.num_threads) else self.inputs.num_threads
             ),
-        )
+        ).to_filename(self._results["out_corrected"])
         return runtime
 
 

sdcflows/transform.py

@@ -261,7 +261,7 @@ def apply(
         cval: float = 0.0,
         prefilter: bool = True,
         output_dtype: Union[str, np.dtype] = None,
-        num_threads: int = os.cpu_count(),
+        num_threads: int = None,
         allow_negative: bool = False,
     ):
         """
@@ -329,12 +329,13 @@ def apply(
 
         # Prepare data
         data = np.squeeze(np.asanyarray(moving.dataobj))
+        ndim = min(data.ndim, 3)
         output_dtype = output_dtype or moving.header.get_data_dtype()
 
         # Reference image's voxel coordinates (in voxel units)
         voxcoords = nt.linear.Affine(
             reference=moving
-        ).reference.ndindex.reshape((data.ndim - 1, *data.shape[:-1])).astype("float32")
+        ).reference.ndindex.reshape((ndim, *data.shape[:ndim])).astype("float32")
 
         # The VSM is just the displacements field given in index coordinates
         # voxcoords is the deformation field, i.e., the target position of each voxel
@@ -358,7 +359,7 @@ def apply(
             mode=mode,
             cval=cval,
             prefilter=prefilter,
-            max_concurrent=num_threads,
+            max_concurrent=num_threads or min(os.cpu_count(), 12),
         ))
 
         if not allow_negative: