removed redundant functions

PyNutil/coordinate_processing.py

-from .coordinate_extraction import folder_to_atlas_space
-from .counting_and_load import label_points
-
-
-def extract_coordinates(segmentation_folder, alignment_json, atlas_labels, pixel_id, non_linear, object_cutoff, atlas_volume, use_flat):
-    return folder_to_atlas_space(
-        segmentation_folder,
-        alignment_json,
-        atlas_labels,
-        pixel_id,
-        non_linear,
-        object_cutoff,
-        atlas_volume,
-        use_flat,
-    )
-
-
-def label_points_group(points, atlas_volume):
-    return label_points(points, atlas_volume, scale_factor=1)

PyNutil/data_analysis.py

 import pandas as pd
-from .counting_and_load import pixel_count_per_region
-from .coordinate_processing import label_points_group
+from .counting_and_load import pixel_count_per_region, label_points
  
 
 def quantify_labeled_points(
@@ -12,8 +11,8 @@ def quantify_labeled_points(
     atlas_labels,
     atlas_volume
 ):
-    labeled_points_centroids = label_points_group(centroids, atlas_volume)
-    labeled_points = label_points_group(pixel_points, atlas_volume)
+    labeled_points_centroids = label_points(centroids, atlas_volume)
+    labeled_points = label_points(pixel_points, atlas_volume, scale_factor=1)
 
     per_section_df = _quantify_per_section(
         labeled_points,

PyNutil/main.py

@@ -2,9 +2,10 @@ import json
 import os
 
 from .io.atlas_loader import load_atlas_data, load_custom_atlas
-from .coordinate_processing import extract_coordinates, label_points_group
 from .data_analysis import quantify_labeled_points
 from .io.file_operations import save_analysis_output
+from .coordinate_extraction import folder_to_atlas_space
+from .counting_and_load import label_points
 
 
 class PyNutil:
@@ -64,7 +65,7 @@ class PyNutil:
             self.points_len,
             self.centroids_len,
             self.segmentation_filenames,
-        ) = extract_coordinates(
+        ) = folder_to_atlas_space(
             self.segmentation_folder,
             self.alignment_json,
             self.atlas_labels,