Merge pull request #1077 from CHrlS98/bf-visualize-fodf

BF for asymmetric peaks

scilpy/viz/backends/fury.py

@@ -162,7 +162,7 @@ def set_viewport(scene, orientation, slice_index, volume_shape, aspect_ratio):
 
 
 def create_scene(actors, orientation, slice_index, volume_shape, aspect_ratio,
-                 bg_color=(0, 0, 0)):
+                 *, bg_color=(0, 0, 0)):
     """
     Create a 3D scene containing actors fitting inside a grid. The camera is
     placed based on the orientation supplied by the user. The projection mode
@@ -201,7 +201,7 @@ def create_scene(actors, orientation, slice_index, volume_shape, aspect_ratio,
     return scene
 
 
-def create_interactive_window(scene, window_size, interactor,
+def create_interactive_window(scene, window_size, interactor, *,
                               title="Viewer", open_window=True):
     """
     Create a 3D window with the content of scene, equiped with an interactor.
@@ -226,7 +226,7 @@ def create_interactive_window(scene, window_size, interactor,
         Object from Fury containing the 3D scene interactor.
     """
 
-    showm = window.ShowManager(scene, title=title,
+    showm = window.ShowManager(scene=scene, title=title,
                                size=window_size,
                                reset_camera=False,
                                interactor_style=interactor)

scilpy/viz/screenshot.py

@@ -127,7 +127,7 @@ def screenshot_peaks(img, orientation, slice_ids, size, mask_img=None):
                            img.shape, size)
 
 
-def compose_image(img_scene, img_size, slice_number, corner_position=(0, 0),
+def compose_image(img_scene, img_size, slice_number, *, corner_position=(0, 0),
                   transparency_scene=None, image_alpha=1.0,
                   labelmap_scene=None, labelmap_overlay_alpha=0.7,
                   overlays_scene=None, overlays_alpha=0.7,

scilpy/viz/slice.py

@@ -14,7 +14,7 @@
 from scilpy.viz.utils import affine_from_offset
 
 
-def create_texture_slicer(texture, orientation, slice_index, mask=None,
+def create_texture_slicer(texture, orientation, slice_index, *, mask=None,
                           value_range=None, opacity=1.0, offset=0.5,
                           lut=None, interpolation='nearest'):
     """
@@ -126,7 +126,7 @@ def create_contours_slicer(data, contour_values, orientation, slice_index,
     return contours_slicer
 
 
-def create_peaks_slicer(data, orientation, slice_index, peak_values=None,
+def create_peaks_slicer(data, orientation, slice_index, *, peak_values=None,
                         mask=None, color=None, peaks_width=1.0,
                         opacity=1.0, symmetric=False):
     """

scripts/scil_viz_fodf.py

@@ -156,6 +156,10 @@ def _build_arg_parser():
     peaks.add_argument('--peaks_width', default=1.0, type=float,
                        help='Width of peaks segments. [%(default)s]')
 
+    peaks.add_argument('--peaks_opacity', type=float, default=1.0,
+                       help='Peaks opacity. 1 is opaque, 0 is transparent '
+                            '[%(default)s].')
+
     peaks_scale = p.add_argument_group('Peaks scaling arguments', 'Choose '
                                        'between peaks values and arbitrary '
                                        'length.')
@@ -325,11 +329,12 @@ def main():
         peaks_actor = create_peaks_slicer(data['peaks'],
                                           args.axis_name,
                                           args.slice_index,
-                                          peaks_values,
-                                          mask,
-                                          args.peaks_color,
-                                          args.peaks_width,
-                                          not full_basis)
+                                          peak_values=peaks_values,
+                                          mask=mask,
+                                          color=args.peaks_color,
+                                          peaks_width=args.peaks_width,
+                                          opacity=args.peaks_opacity,
+                                          symmetric=not full_basis)
 
         actors.append(peaks_actor)