add script to convert annotations to csv

data-preprocessing/extract_annotations.py

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+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)
+
+    

data-preprocessing/requirements.txt

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+python-dotenv