data-preprocessing/extract_annotations.py

import json
import os
from itertools import chain
from dotenv import load_dotenv
import pandas as pd

def to_relative_focus(stack):
 best_index = stack["best_index"]
 images = stack["images"]

 best_value = images[best_index]["focus_value"]
 for i in range(len(images)):
 images[i]["focus_value"] = images[i]["focus_value"] - best_value
 return stack


def flatten_stack(stack):
 images = stack["images"]

 def f(image):
 del image["neighbours"]
 image["stack_id"] = stack["stack_id"]
 image["obj_name"] = stack["obj_name"]
 return image

 images = list(map(f, images))
 return images


if __name__ == "__main__":
 load_dotenv()
 data_file = os.getenv('DATA_FILE')
 out_file = os.getenv('OUT_FILE')

 with open(data_file) as f:
 content = json.load(f)

 annotated = filter(lambda x: x["best_index"], content)
 relative_focus = map(to_relative_focus, annotated)
 flattened = chain(*map(flatten_stack,relative_focus))
 
 dataframe = pd.DataFrame(flattened)
 dataframe.to_csv(out_file)