#pandas is used for working with csv files import pandas as pd #nrrd just lets us open nrrd files import nrrd #import our function for converting a folder of segmentations to points from PyNutil import FolderToAtlasSpace, labelPoints #now we can use our function to convert the folder of segmentations to points points = FolderToAtlasSpace("test_data/oneSection15/", "test_data/C68_nonlinear.json", pixelID=[255, 0, 255], nonLinear=True) #first we need to find the label file for the volume label_path = "annotation_volumes//allen2022_colours.csv" #then the path to the volume volume_path = "annotation_volumes//annotation_10_reoriented.nrrd" #read the label file label_df = pd.read_csv(label_path) #read the annotation volume, it also has a header but we don't need it data, header = nrrd.read(volume_path) #now we can get the labels for each point