seperated all scripts into seperate directories

PyNutil/main.py

@@ -2,10 +2,10 @@ import json
 import os
 
 from .io.atlas_loader import load_atlas_data, load_custom_atlas
-from .data_analysis import quantify_labeled_points
+from .processing.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
+from .processing.coordinate_extraction import folder_to_atlas_space
+from .processing.counting_and_load import label_points
 
 
 class PyNutil:

PyNutil/processing/__init__.py

+from . import *

PyNutil/coordinate_extraction.py → PyNutil/processing/coordinate_extraction.py

 import numpy as np
 import pandas as pd
-from .io.read_and_write import load_visualign_json
+from ..io.read_and_write import load_visualign_json
 from .counting_and_load import flat_to_dataframe
 from .visualign_deformations import triangulate, transform_vec
 from glob import glob
@@ -8,7 +8,7 @@ import cv2
 from skimage import measure
 import threading
 import re
-from .io.reconstruct_dzi import reconstruct_dzi
+from ..io.reconstruct_dzi import reconstruct_dzi
 
 
 def number_sections(filenames, legacy=False):