Clean up

PyNutil/load_workflow.py

+"""Create workflow for calculating load based on atlas maps and segmentations"""
+
 import struct
 import matplotlib.pyplot as plt
 import pandas as pd
@@ -22,6 +24,20 @@ allen_id_image = lbidx[values.astype(int)] # assign allen IDs into image array
 
 plt.imshow(allen_id_image)
 
+"""count pixels for unique idx"""
+unique_ids, counts = np.unique(allen_id_image, return_counts=True)
+
+area_per_label = list(zip(unique_ids,counts))
+# create a list of unique regions and pixel counts per region
+
+df_area_per_label = pd.DataFrame(area_per_label, columns=["idx","area_count"])
+# create a pandas df with regions and pixel counts
+
+print(df_area_per_label)
+df_area_per_label.to_csv("../outputs/s037_area_per_idx.csv", sep=";", na_rep='', index= False)
+
+
+
 
 # Count area per unique label
 # Scale up to size of corresponding segmentation

PyNutil/pyflat.py

+   
+"""This is Gergely Csusc's code from VisuAlign MediaWiki NITRC page,
+this was a test, not used elsewhere in PyNutil"""   
+   
    import sys
    for arg in sys.argv:
        if arg.startswith("flat="):