ENH: optionally only produce non-plot QC outputs

gyral_structure/qc/surface.py

@@ -25,7 +25,7 @@ def faces_to_vertices(arr, surface: CorticalMesh):
 
 
 def plot_all(surface: CorticalMesh, mask, nstream, basis: BasisFunc,
-             params=(), directory='.', skip_nsplit=False):
+             params=(), directory='.', skip_nsplit=False, skip_plots=False):
     """
     Plots all the QC plots on the surface
 
@@ -36,6 +36,7 @@ def plot_all(surface: CorticalMesh, mask, nstream, basis: BasisFunc,
     :param params: parameters
     :param directory: directory to store the plots
     :param skip_nsplit: skip the (slow) nsplit plot if True
+    :param skip_plots: skip all plots if True
     """
     masked_surface = surface[mask]
     request = read_surface(masked_surface, nsplit=1)
@@ -47,7 +48,7 @@ def plot_all(surface: CorticalMesh, mask, nstream, basis: BasisFunc,
 
     expected = nstream / masked_surface.size_faces()
 
-    if not skip_nsplit:
+    if not (skip_nsplit or skip_plots):
         import matplotlib.pyplot as plt
         fig, axes = plt.subplots(1, 1)
         nsplit.plot_offset(request, basis, params, axes=axes)
@@ -64,12 +65,13 @@ def plot_all(surface: CorticalMesh, mask, nstream, basis: BasisFunc,
         header=cifti2.Cifti2Header.from_axes((scl, bm))
     ).to_filename(op.join(directory, 'field.dscalar.nii'))
 
-    for toplot, name, label in [
-        (ncrossing / expected, 'density_crossing', r'$\rho$(streamlines crossing)'),
-        (density / expected, 'density_total',  r'$\rho$(streamlines)'),
-        (radiality, 'radiality',  'radial alignment'),
-    ]:
-        plot_array(surface, mask, toplot, op.join(directory, name), label)
+    if not skip_plots:
+        for toplot, name, label in [
+            (ncrossing / expected, 'density_crossing', r'$\rho$(streamlines crossing)'),
+            (density / expected, 'density_total',  r'$\rho$(streamlines)'),
+            (radiality, 'radiality',  'radial alignment'),
+        ]:
+            plot_array(surface, mask, toplot, op.join(directory, name), label)
 
 
 def plot_array(surface: CorticalMesh, mask, arr_faces, name, label):

gyral_structure/qc/volume.py

@@ -12,7 +12,7 @@ import nibabel as nib
 
 
 def plot_all(mask_img: nib.Nifti1Image, dyads: nib.Nifti1Image, basis: BasisFunc,
-             params=(), directory='.', skip_nsplit=False):
+             params=(), directory='.', skip_nsplit=False, skip_plots=False):
     """
     Plots all the QC plots on the surface
 
@@ -22,6 +22,7 @@ def plot_all(mask_img: nib.Nifti1Image, dyads: nib.Nifti1Image, basis: BasisFunc
     :param params: parameters
     :param directory: directory to store the plots
     :param skip_nsplit: skip the (slow) nsplit plot if True
+    :param skip_plots: skip all plots if True
     """
     mask = mask_img.get_data() > 0
     request = read_volume(mask_img, nsplit=1)
@@ -30,7 +31,7 @@ def plot_all(mask_img: nib.Nifti1Image, dyads: nib.Nifti1Image, basis: BasisFunc
     density = np.sqrt((field_voxels ** 2).sum(-1))
     alignment = abs(np.sum(dyad_to_mm(dyads.get_fdata()[mask], mask_img.affine) * field_voxels, -1)) / density
 
-    if not skip_nsplit:
+    if not (skip_nsplit or skip_plots):
         import matplotlib.pyplot as plt
         fig, axes = plt.subplots(1, 1)
         nsplit.plot_offset(request, basis, params, axes=axes, nsplit_ref=3)
@@ -40,10 +41,10 @@ def plot_all(mask_img: nib.Nifti1Image, dyads: nib.Nifti1Image, basis: BasisFunc
         (density, 'density',  'N(streamlines)'),
         (alignment, 'alignment',  'V1 alignment'),
     ]:
-        plot_array(mask_img, toplot, op.join(directory, name), label)
+        plot_array(mask_img, toplot, op.join(directory, name), label, skip_plots=skip_plots)
 
 
-def plot_array(img, arr, name, label):
+def plot_array(img, arr, name, label, skip_plots=False):
     """
     Produces QC plots for array on surface
 
@@ -51,14 +52,16 @@ def plot_array(img, arr, name, label):
     :param arr: array evaluated on the faces of the surface
     :param name: basename of the output file
     :param label: text describing the array
+    :param skip_plots: skip all plots if True
     """
     full_arr = np.zeros(img.shape, dtype=arr.dtype)
     full_arr[img.get_fdata() > 0] = arr
     nib.Nifti1Image(full_arr, None, header=img.header).to_filename(f'{name}.nii.gz')
 
-    import matplotlib.pyplot as plt
-    fig, axes = plt.subplots(1, 1)
-    axes.hist(arr, bins=51)
-    axes.set_xlabel(label)
-    axes.set_ylabel('N(voxels)')
-    fig.savefig(f'{name}_hist.png')
+    if not skip_plots:
+        import matplotlib.pyplot as plt
+        fig, axes = plt.subplots(1, 1)
+        axes.hist(arr, bins=51)
+        axes.set_xlabel(label)
+        axes.set_ylabel('N(voxels)')
+        fig.savefig(f'{name}_hist.png')

gyral_structure/scripts/gs_qc

@@ -19,6 +19,8 @@ parser.add_argument("-v", '--volume', nargs=2, action='append', help=(
 parser.add_argument("-d", '--dyads', help='Dyads to compare with in the volumetric masks')
 parser.add_argument("-sn", "--skip_nsplit", action='store_true',
                     help='Skip producing the relatively slow `npslit` plot if set')
+parser.add_argument("-sp", "--skip_plots", action='store_true',
+                    help='Skip producing any plots')
 args = parser.parse_args()
 
 from gyral_structure.basis import read
@@ -53,6 +55,7 @@ for surf_name in ('white', 'midthickness', 'pial'):
         bf, params,
         out_directory,
         skip_nsplit=args.skip_nsplit,
+        skip_plots=args.skip_plots,
     )
 
 if args.volume is not None:
@@ -65,4 +68,5 @@ if args.volume is not None:
             bf, params,
             out_directory,
             skip_nsplit=args.skip_nsplit,
+            skip_plots=args.skip_plots,
         )