Extract properties from JSON file and write to CSV

json_to_csv_flatter.py

import math
import sys
import ijson
import csv
import argparse

def extract_to_csv(json_filename, new_json_filename, csv_filename):
  # ijson's parser chokes on NaNs, so let's get rid of them
  # NaN containing fields not needed for Adam's analysis?
  # if Circularity and Pixel area are NaN, we're in trouble!!!
  json_file = open(json_filename, "r")
  with open(new_json_filename, "w") as new_json_file:
     for line in json_file:
        if "NaN" in line:
          line = line.replace("NaN", "0")
          #print(line)
        new_json_file.write(line)

  columns = []
  with open(new_json_filename, "rb") as input_file:
      # load json iteratively
      parser = ijson.parse(input_file)
      particle_property_column = []
      for prefix, event, value in parser:
        # structured, so Circularity always before Pixel area...
        if "Circularity" in prefix or "circularity" in prefix:
          particle_property_column.append(prefix)
          particle_property_column.append(value)
        elif "Pixel area (um^2)" in prefix:
          particle_property_column.append(prefix)
          particle_property_column.append(value)
          columns.append(particle_property_column)
          particle_property_column = []

  with open(csv_filename, "w+") as output_file:
    csv_file = csv.writer(output_file)
    for c in columns:
      csv_file.writerow(c)

if __name__ == "__main__":
  parser = argparse.ArgumentParser(description="Extract relevent data from aggregate.py JSON output and write to CSV file. A second JSON file is output where NaNs are converted to 0 (JSON_mod).")
  parser.add_argument("JSON")
  parser.add_argument("JSON_mod")
  parser.add_argument("CSV")
  args = parser.parse_args()
  extract_to_csv(args.JSON, args.JSON_mod, args.CSV)