Merge pull request #189 from jhlegarreta/CallNireportsDWIPlot

ENH: Call the DWI plot method from nireports

src/eddymotion/data/dmri.py

@@ -160,7 +160,7 @@ def to_nifti(self, filename, **kwargs):
 
     def plot_mosaic(self, index=None, **kwargs):
         """Visualize one direction of the dMRI dataset."""
-        from eddymotion.viz import plot_dwi
+        from nireports.reportlets.modality.dwi import plot_dwi
 
         return plot_dwi(
             self.bzero if index is None else self.dataobj[..., index],

src/eddymotion/viz.py

@@ -22,45 +22,10 @@
 #
 """Visualization utilities."""
 
-import nibabel as nb
 import numpy as np
 from nireports.reportlets.nuisance import plot_carpet as nw_plot_carpet
 
 
-def plot_dwi(dataobj, affine, gradient=None, **kwargs):
-    """Plot a DW map."""
-    import matplotlib.pyplot as plt
-    from nilearn.plotting import plot_anat
-
-    plt.rcParams.update(
-        {
-            "text.usetex": True,
-            "font.family": "sans-serif",
-            "font.sans-serif": ["Helvetica"],
-        }
-    )
-
-    affine = np.diag(nb.affines.voxel_sizes(affine).tolist() + [1])
-    affine[:3, 3] = -1.0 * (affine[:3, :3] @ ((np.array(dataobj.shape) - 1) * 0.5))
-
-    vmax = kwargs.pop("vmax", None) or np.percentile(dataobj, 98)
-    cut_coords = kwargs.pop("cut_coords", None) or (0, 0, 0)
-
-    return plot_anat(
-        nb.Nifti1Image(dataobj, affine, None),
-        vmax=vmax,
-        cut_coords=cut_coords,
-        title=(
-            r"Reference $b$=0"
-            if gradient is None
-            else f"""\
-$b$={gradient[3].astype(int)}, \
-$\\vec{{b}}$ = ({', '.join(str(v) for v in gradient[:3])})"""
-        ),
-        **kwargs,
-    )
-
-
 def rotation_matrix(u, v):
     r"""
     Calculate the rotation matrix *R* such that :math:`R \cdot \mathbf{u} = \mathbf{v}`.