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

@@ -0,0 +1 @@
+python-dotenv