Improve function parameters and reorganize modules

foa3d/__main__.py

@@ -1,29 +1,23 @@
 from foa3d.input import get_cli_parser, load_microscopy_image
-from foa3d.pipeline import (parallel_odf_at_scales, parallel_frangi_on_slices)
+from foa3d.pipeline import parallel_odf_at_scales, parallel_frangi_on_slices
 from foa3d.printing import print_pipeline_heading
 from foa3d.utils import delete_tmp_folder
 
 
 def foa3d(cli_args):
 
-    # load 3D microscopy image or 4D array of fiber orientation vectors
-    img, ts_msk, ch_ax, is_fovec, save_dir, tmp_dir, img_name = load_microscopy_image(cli_args)
+    # load 3D grayscale or RGB microscopy image or 4D array of fiber orientation vectors
+    in_img, save_dirs = load_microscopy_image(cli_args)
 
     # conduct parallel 3D Frangi-based fiber orientation analysis on batches of basic image slices
-    if not is_fovec:
-        fbr_vec_img, iso_fbr_img, px_sz \
-            = parallel_frangi_on_slices(img, ch_ax, cli_args, save_dir[0], tmp_dir, img_name, ts_msk=ts_msk)
-
-    # skip Frangi filter stage if orientation vectors were directly provided as input
-    else:
-        fbr_vec_img, iso_fbr_img, px_sz = (img, None, None)
+    out_img = parallel_frangi_on_slices(cli_args, save_dirs, in_img)
 
     # estimate 3D fiber ODF maps at the spatial scales of interest using concurrent workers
-    if cli_args.odf_res:
-        parallel_odf_at_scales(fbr_vec_img, iso_fbr_img, cli_args, px_sz, save_dir[1], tmp_dir, img_name)
+    parallel_odf_at_scales(cli_args, save_dirs, out_img['fbr_vec'], out_img['iso_fbr'],
+                           out_img['px_sz'], in_img['name'])
 
     # delete temporary folder
-    delete_tmp_folder(tmp_dir)
+    delete_tmp_folder(save_dirs['tmp'])
 
 
 def main():