Remove unused code and refactor (#79)

* Remove unused code

* Move code to brainglobe-utils

* Simplify test structure

brainglobe_workflows/brainmapper/analyse/analyse.py → brainglobe_workflows/brainmapper/analyse.py

@@ -20,49 +20,17 @@ def run(args, cells, atlas, downsampled_space):
         cell_list.append([cell.z, cell.y, cell.x])
     cells = np.array(cell_list)
 
-    run_analysis(
+    logging.info("Transforming points to atlas space")
+    transformed_cells, points_out_of_bounds = transform_points_to_atlas_space(
         cells,
         args.signal_planes_paths[0],
         args.orientation,
         args.voxel_sizes,
-        atlas,
-        deformation_field_paths,
-        downsampled_space,
-        args.paths.downsampled_points,
-        args.paths.atlas_points,
-        args.paths.brainrender_points,
-        args.brainreg_paths.volume_csv_path,
-        args.paths.all_points_csv,
-        args.paths.summary_csv,
-    )
-
-
-def run_analysis(
-    cells,
-    signal_planes,
-    orientation,
-    voxel_sizes,
-    atlas,
-    deformation_field_paths,
-    downsampled_space,
-    downsampled_points_path,
-    atlas_points_path,
-    brainrender_points_path,
-    volume_csv_path,
-    all_points_csv_path,
-    summary_csv_path,
-):
-    logging.info("Transforming points to atlas space")
-    transformed_cells, points_out_of_bounds = transform_points_to_atlas_space(
-        cells,
-        signal_planes,
-        orientation,
-        voxel_sizes,
         downsampled_space,
         atlas,
         deformation_field_paths,
-        downsampled_points_path=downsampled_points_path,
-        atlas_points_path=atlas_points_path,
+        downsampled_points_path=args.paths.downsampled_points,
+        atlas_points_path=args.paths.atlas_points,
     )
     logging.warning(
         f"{len(points_out_of_bounds)} points ignored due to falling outside "
@@ -75,11 +43,11 @@ def run_analysis(
         cells,
         transformed_cells,
         atlas,
-        volume_csv_path,
-        all_points_csv_path,
-        summary_csv_path,
+        args.brainreg_paths.volume_csv_path,
+        args.paths.all_points_csv,
+        args.paths.summary_csv,
     )
     logging.info("Exporting data to brainrender")
     export_points_to_brainrender(
-        transformed_cells, atlas.resolution[0], brainrender_points_path
+        transformed_cells, atlas.resolution[0], args.paths.brainrender_points
     )