Fixed the bug in plot_coefs + changes in calc_shimmed_anat_orient

make sure that the program doesn't crash if the slices dimension is different than 1
shimming-toolbox · Dec 14, 2022 · ab5e5e9 · ab5e5e9
1 parent 0993d52
commit ab5e5e9
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Showing 2 changed files with 6 additions and 10 deletions.
diff --git a/shimmingtoolbox/cli/b0shim.py b/shimmingtoolbox/cli/b0shim.py
@@ -1031,15 +1031,14 @@ def _plot_coefs(coil, slices, static_coefs, path_output, coil_number, rt_coefs=N
         temp_max = np.array(static_coefs).max()
         if max_y is None or max_y < temp_max:
             max_y = np.array(static_coefs).max()
-    nb_slices = 0
     for nb_slices, i_shim in enumerate(shimmed_slice):
         i_slice = slices[i_shim]
-        _add_sub_figure(i_shim, fig, number_slices_shimmed, nb_slices, rt_coefs, pres_probe_min,
+        _add_sub_figure(i_shim, fig, number_slices_shimmed, nb_slices+1, rt_coefs, pres_probe_min,
                         pres_probe_max, bounds, min_y, max_y,
                         units, static_coefs, i_slice)
     # Print a subplot for all the non shimmed slices
     nb_slices = nb_slices + 1
-    _add_sub_figure(last_i, fig, number_slices_shimmed, nb_slices, rt_coefs, pres_probe_min,
+    _add_sub_figure(last_i, fig, number_slices_shimmed, nb_slices+1, rt_coefs, pres_probe_min,
                     pres_probe_max, bounds, min_y, max_y,
                     units, static_coefs, list_slice_wo_shimmed)
     # Save the figure

diff --git a/shimmingtoolbox/shim/sequencer.py b/shimmingtoolbox/shim/sequencer.py
@@ -281,14 +281,11 @@ def _cal_shimmed_anat_orient(coefs, coils, nii_mask_anat, nii_fieldmap, slices,
                                      mode='grid-constant',
                                      cval=0).get_fdata()
     shimmed_anat_orient = fieldmap_anat
-    nb_channel = np.shape(coefs)[1]
-    dimx = np.shape(coils_anat)[0]
-    dimy = np.shape(coils_anat)[1]
+
     for i_shim in list_shim_slice:
-        # We want to do the np.sum with a 2D matrix so that it is faster
-        coils_anat_reduced = np.reshape(coils_anat[:, :, slices[i_shim], :], (-1, nb_channel))
-        corr = np.sum(coefs[i_shim] * coils_anat_reduced, axis=1, keepdims=False)
-        shimmed_anat_orient[..., slices[i_shim]] += np.reshape(corr, (dimx, dimy, 1))
+        # We want to do the np.sum with a 3D matrix if possible
+        corr = np.sum(coefs[i_shim] * coils_anat[:,:, slices[i_shim], :], axis=3, keepdims=False)
+        shimmed_anat_orient[..., slices[i_shim]] += corr
     fname_shimmed_anat_orient = os.path.join(path_output, 'fig_shimmed_anat_orient.nii.gz')
     nii_shimmed_anat_orient = nib.Nifti1Image(shimmed_anat_orient * nii_mask_anat.get_fdata(), nii_mask_anat.affine,
                                               header=nii_mask_anat.header)