Merge pull request #39 from jhlegarreta/CallDIPYFuncsWithKeywordArgs

ENH: Use keyword arguments when calling  DIPY keyword arg functions

Author: effigies

scripts/dwi_gp_estimation_signal_plot.py

@@ -115,7 +115,7 @@ def main() -> None:
     y_pred = load_api(args.dwi_pred_data_fname, nb.Nifti1Image).get_fdata()
 
     bvals, bvecs = read_bvals_bvecs(str(args.bval_data_fname), str(args.bvec_data_fname))
-    gtab = gradient_table(bvals, bvecs)
+    gtab = gradient_table(bvals, bvecs=bvecs)
 
     # Pick one voxel randomly
     rng = np.random.default_rng(1234)

src/nifreeze/model/_dipy.py

@@ -286,5 +286,5 @@ def _rasb2dipy(gradient):
         from dipy.core.gradients import gradient_table
 
         warnings.filterwarnings("ignore", category=UserWarning)
-        retval = gradient_table(gradient[3, :], gradient[:3, :].T)
+        retval = gradient_table(gradient[3, :], bvecs=gradient[:3, :].T)
     return retval

src/nifreeze/testing/simulations.py

@@ -178,7 +178,7 @@ def create_single_shell_gradient_table(
 
     # Add a b0 value to the gradient table
     bvals, bvecs = add_b0(bvals, bvecs)
-    return gradient_table(bvals, bvecs)
+    return gradient_table(bvals, bvecs=bvecs)
 
 
 def get_query_vectors(