bca_survival.tools.bca_totalseg_extraction module

BOA Results extractor

This script processes BOA data by extracting measurements from the individual JSON files across a directory structure. It targets two types of measurement files: - total-measurements.json: Contains segmentation measurements for various organs - bca-measurements.json: Contains body composition analysis measurements

The script consolidates these measurements into Excel spreadsheets for further analysis.

Usage:

boa-extract base_path output_path python -m survival_analysis.boa_extractor base_path output_path

Author: Eric

bca_survival.tools.bca_totalseg_extraction.process_json_files(root_dir)[source]

Walks through the directory structure, identifies relevant JSON files, processes them, and compiles the data into pandas DataFrames.

Parameters:

root_dir (str) – The root directory to search for measurement files

Returns:

A tuple containing two DataFrames:

  • final_total_df: DataFrame with organ segmentation measurements

  • final_bca_df: DataFrame with body composition analysis measurements

Return type:

tuple

bca_survival.tools.bca_totalseg_extraction.process_totalseg_measurements(file_path, dirpath)[source]

Processes an individual total-measurements.json file to extract organ segmentation measurements.

Parameters:

  • file_path (str) – Path to the JSON file

  • dirpath (str) – Directory path containing the file (used to extract the study ID)

Returns:

A DataFrame with one row representing the measurements from the file

Return type:

pandas.DataFrame

bca_survival.tools.bca_totalseg_extraction.process_bca_measurements(folder_path)[source]

Processes the bca-measurements.json file in the given folder and extracts the measurement data.

Parameters:

folder_path (str) – The path to the folder containing the bca-measurements.json file.

Returns:

A DataFrame containing the measurement data with formatted

column names, or None if the file doesn’t exist.

Return type:

pandas.DataFrame or None

bca_survival.tools.bca_totalseg_extraction.main(root_path, output_path)[source]

Main function to iterate over folders, process the JSON files, and save the results to Excel files.

Parameters:

  • root_path (str) – The base directory containing the folders with JSON files

  • output_path (str) – Path to save the resulting Excel files

Return type:

None

bca_survival.tools.bca_totalseg_extraction.main_cli()[source]

Command-line interface entry point for the BOA extractor. This function is referenced in pyproject.toml to create the console script.

Return type:

None