Rename variables

foa3d/__main__.py

@@ -6,31 +6,30 @@
 
 def foa3d(cli_args):
 
-    # load microscopy volume image or array of fiber orientation vectors
+    # load 3D microscopy image or 4D array of fiber orientation vectors
     img, ts_msk, is_tiled, is_fiber, save_dir, tmp_dir, img_name = load_microscopy_image(cli_args)
 
     # get resources configuration
     ram, jobs = get_resource_config(cli_args)
 
     # conduct parallel 3D Frangi-based fiber orientation analysis on batches of basic image slices
     if not is_fiber:
-        fiber_vec_img, iso_fiber_img, px_sz, img_name \
+        fbr_vec_img, iso_fbr_img, px_sz, img_name \
             = parallel_frangi_on_slices(img, cli_args, save_dir[0], tmp_dir, img_name,
                                         ts_msk=ts_msk, ram=ram, jobs=jobs, is_tiled=is_tiled)
-
     else:
-        fiber_vec_img, iso_fiber_img, px_sz = (img, None, None)
+        fbr_vec_img, iso_fbr_img, px_sz = (img, None, None)
 
     # estimate 3D fiber ODF maps at the spatial scales of interest using concurrent workers
     if cli_args.odf_res:
-        parallel_odf_at_scales(fiber_vec_img, iso_fiber_img, cli_args, px_sz, save_dir[1], tmp_dir, img_name, ram=ram)
+        parallel_odf_at_scales(fbr_vec_img, iso_fbr_img, cli_args, px_sz, save_dir[1], tmp_dir, img_name, ram=ram)
 
     # delete temporary folder
     delete_tmp_folder(tmp_dir)
 
 
 def main():
-    # start Foa3D pipeline by terminal
+    # start Foa3D by terminal
     print_pipeline_heading()
     foa3d(cli_args=get_cli_parser())
 

foa3d/frangi.py

@@ -214,7 +214,7 @@ def compute_scaled_orientation(scale_px, img, alpha=0.001, beta=1, gamma=None, d
     vesselness = compute_scaled_vesselness(eigen1, eigen2, eigen3, alpha=alpha, beta=beta, gamma=gamma)
 
     # reject vesselness background
-    enhanced_img = reject_vesselness_background(vesselness, eigen2, eigen3, dark)
+    enhanced_img = reject_fiber_background(vesselness, eigen2, eigen3, dark)
 
     # stack eigenvalues list
     eigenval = np.stack(eigenval, axis=-1)
@@ -332,7 +332,7 @@ def frangi_filter(img, scales_px=1, alpha=0.001, beta=1.0, gamma=None, dark=True
     return enhanced_img, fiber_vec, eigenval
 
 
-def reject_vesselness_background(vesselness, eigen2, eigen3, dark):
+def reject_fiber_background(vesselness, eigen2, eigen3, dark):
     """
     Reject the fiber background, exploiting the sign of the "secondary"
     eigenvalues λ2 and λ3.