JSON Converter

This repository contains conversions mainly from json data type to xml and csv.

Conversion json to xml for whole slide image (./json_converter/json_to_xml.py)

To convert data from json to xml for whole slide image, you need to use json_to_xml.py with the following command lines:

• --input_files_folder: Path to the folder of json files.
• --output_folder: Path to the output folder (folder where the xml files will be written, if it doesn't exist it will create one).
• --hotspot_folder: Path to the hotspot annotations folder (folder of xml files containing coordinates of the hotspot).

Conversion json to xml for TMA (.(json_convert/json_csv_to_xml)

To convert data from json to xml for TMA, you need to use json_csv_to_xml.py with the following command lines:

• --input_files_folder: Path to the folder of json files.
• --output_folder: Path to the output folder (folder where the xml files will be written, if it doesn't exist it will create one).
• --coordinates_file: Path to the csv coordinates file (file containing the radius and coordinates of the center for each sample in the TMA).

Conversion json to csv (./json_converter/json_to_xml.py)

To convert data from json to csv you need to use json_to_csv.py with the following command lines:

• --input_files_folder: Path to the folder of json files.
• --output_folder: Path to the output folder (folder where the csv files will be written, if it doesn't exist it will create one).

Environment

You can set up the conda environment in the directory "./json_converter" by using the following command: conda env create -f environment.yml