REF: Refactor gradient data checks in DWI data class

Refactor gradient data checks in DWI data class: PR
#325 introduced the row-major
convention for gradient data in NiFreeze. However, gradient loading was
not tested thoroughly. This resulted in some execution flows that would
not guarantee a row-major internal convention or would crash under some
circumstances.

This commit refactors the gradient data checks and adds thorough
testing:
- Define all error or warning messages as global variables so that they
  can be checked exactly in tests.
- Ensure that gradients conform to the row-major convention when
  instantiating the DWI class directly. This allows to separate the
  gradient reformatting from the dimensionality check with the DWI
  volume sequence. This simplifies the flow, as the gradient
  reformatting to the row-major convention does not depend on the number
  of volumes in the DWI sequence. Also, this makes the flow more
  consistent with the refactored checks of the NIfTI file-based loading
  utility function (`from_nii`).
- Ensure that the gradients conform to the row-major convention
  immediately after loading the gradients file in the NIfTI file-based
  loading utility function (`from_nii`). As opposed to the previous
  implementation, this allows to load the gradients from a file where
  data follows either column-major or row-major convention. e.g. In the
  previous implementation the `if grad.shape[1] < 2:` was making an
  assumption about the layout and/or one that was wrong because we
  require 4 columns (direction (x,y,z) + b-value) or rows (if in
  column-major). The new implementation simplifies the execution flow.

Author: jhlegarreta

src/nifreeze/data/dmri.py

@@ -63,6 +63,25 @@
 DTI_MIN_ORIENTATIONS = 6
 """Minimum number of nonzero b-values in a DWI dataset."""
 
+GRADIENT_VOLUME_DIMENSIONALITY_MISMATCH_MISSING_ERROR = "Gradient table shape does not match the number of diffusion volumes: expected {n_volumes} rows, found {n_gradients}."
+"""dMRI volume count vs. gradient count mismatch error message."""
+
+GRADIENT_BVAL_BVEC_PRIORITY_WARN_MSG = "Both a gradients table file and b-vec/val files are defined; ignoring b-vec/val files in favor of the gradients_file."
+""""dMRI gradient file priority warning message."""
+
+GRADIENT_NDIM_ERROR_MSG = "Gradient table must be a 2D array"
+"""dMRI gradient dimensionality error message."""
+
+GRADIENT_DATA_MISSING_ERROR = (
+    "No gradient data provided. Please specify either a gradients_file or (bvec_file & bval_file)."
+)
+"""dMRI missing gradient data error message."""
+
+GRADIENT_EXPECTED_COLUMNS_ERROR_MSG = (
+    "Gradient table must have four columns (3 direction components and one b-value)."
+)
+"""dMRI gradient expected columns error message."""
+
 
 @attrs.define(slots=True)
 class DWI(BaseDataset[np.ndarray]):
@@ -84,7 +103,13 @@ def _normalize_gradients(self) -> None:
 
         gradients = np.asarray(self.gradients)
         if gradients.ndim != 2:
-            raise ValueError("Gradient table must be a 2D array")
+            raise ValueError(GRADIENT_NDIM_ERROR_MSG)
+        if gradients.shape[1] == 4:
+            pass
+        elif gradients.shape[0] == 4:
+            gradients = gradients.T
+        else:
+            raise ValueError(GRADIENT_EXPECTED_COLUMNS_ERROR_MSG)
 
         n_volumes = None
         if self.dataobj is not None:
@@ -94,15 +119,11 @@ def _normalize_gradients(self) -> None:
                 n_volumes = None
 
         if n_volumes is not None and gradients.shape[0] != n_volumes:
-            if gradients.shape[1] == n_volumes:
-                gradients = gradients.T
-            else:
-                raise ValueError(
-                    "Gradient table shape does not match the number of diffusion volumes: "
-                    f"expected {n_volumes} rows, found {gradients.shape[0]}"
+            raise ValueError(
+                GRADIENT_VOLUME_DIMENSIONALITY_MISMATCH_MISSING_ERROR.format(
+                    n_volumes=n_volumes, n_gradients=gradients.shape[0]
                 )
-        elif n_volumes is None and gradients.shape[1] > gradients.shape[0]:
-            gradients = gradients.T
+            )
 
         self.gradients = gradients
 
@@ -381,11 +402,15 @@ def from_nii(
     if gradients_file:
         grad = np.loadtxt(gradients_file, dtype="float32")
         if bvec_file and bval_file:
-            warn(
-                "Both a gradients table file and b-vec/val files are defined; "
-                "ignoring b-vec/val files in favor of the gradients_file.",
-                stacklevel=2,
-            )
+            warn(GRADIENT_BVAL_BVEC_PRIORITY_WARN_MSG, stacklevel=2)
+        if grad.ndim != 2:
+            raise ValueError(GRADIENT_NDIM_ERROR_MSG)
+        if grad.shape[1] == 4:
+            pass
+        elif grad.shape[0] == 4:
+            grad = grad.T
+        else:
+            raise ValueError(GRADIENT_EXPECTED_COLUMNS_ERROR_MSG)
     elif bvec_file and bval_file:
         bvecs = np.loadtxt(bvec_file, dtype="float32")
         if bvecs.ndim == 1:
@@ -398,24 +423,7 @@ def from_nii(
             bvals = np.squeeze(bvals)
         grad = np.column_stack((bvecs, bvals))
     else:
-        raise RuntimeError(
-            "No gradient data provided. "
-            "Please specify either a gradients_file or (bvec_file & bval_file)."
-        )
-
-    if grad.ndim == 1:
-        grad = grad[np.newaxis, :]
-
-    if grad.shape[1] < 2:
-        raise ValueError("Gradient table must have at least two columns (direction + b-value).")
-
-    if grad.shape[1] != 4:
-        if grad.shape[0] == 4:
-            grad = grad.T
-        else:
-            raise ValueError(
-                "Gradient table must have four columns (3 direction components and one b-value)."
-            )
+        raise RuntimeError(GRADIENT_DATA_MISSING_ERROR)
 
     # 3) Create the DWI instance. We'll filter out volumes where b-value > b0_thres
     #    as "DW volumes" if the user wants to store only the high-b volumes here