XML2DCM-ECG 1.1.10

Python-based solution for converting ECG data from XML format to the DICOM(Digital Imaging and Communications in Medicine) format

XML2DCM-ECG

Description

This repository contains a Python-based solution for converting ECG data from XML format to the DICOM (Digital Imaging and Communications in Medicine) format. The goal of this project is to facilitate the process of transforming clinical ECG data stored in XML files into a standardized, widely-used DICOM format, which is essential for healthcare systems, medical imaging devices, and Electronic Health Record (EHR) systems.

The solution handles the extraction and conversion of ECG information, including patient details, acquisition context, and waveform data, from XML files into the DICOM format. The project also integrates essential metadata such as the type of ECG lead (e.g., Lead I, Lead II), device information (e.g., acquisition device, software versions), and patient demographics.

Installation

You can install XML2DCM-ECG directly from PyPI:

pip install XML2DCM-ECG

Alternatively, you can use uv, a faster Python package manager with built-in script runner:

pip install uv

Usage

After installation, you can run the ECG XML-to-DICOM converter using either of the following methods.

1. Using standard CLI command

Run the following command:

   xml2dcm-ecg --debug True --debug_n 5 --project_root /path/to/project --data_root /path/to/data --ecg_xml_dir /path/to/xml_files --output_dir /path/to/save_dicom --filename_pattern "MUSE_(?P<examination_date>\d{8})_(\d{6})_(\d{5})" --out_filename_pattern "ECG_DICOM_{examination_date}_{seq}" 

2. Using uvx for fast execution

With uv installed, you can use uvx for faster execution:

   uvx xml2dcm-ecg --debug True --debug_n 5 --project_root /path/to/project --data_root /path/to/data --ecg_xml_dir /path/to/xml_files --output_dir /path/to/save_dicom --filename_pattern "MUSE_(?P<examination_date>\d{8})_(\d{6})_(\d{5})" --out_filename_pattern "ECG_DICOM_{examination_date}_{seq}"

CLI Options

Argument	Type	Required	Default	Description
--debug	bool	No	False	Enable debug mode to process a limited number of files
--debug_n	int	No	5	Number of files to process when debug is enabled
--project_root	str	Yes	—	Root directory of the project
--data_root	str	Yes	—	Root path for input data
--ecg_xml_dir	str	Yes	—	Relative path to the directory containing ECG XML files
--output_dir	str	No	ecg_dcm	Directory (under project_root) where converted DICOM files will be saved
--filename_pattern	str	Yes	—	Regex pattern to extract metadata from filenames
--out_filename_pattern	str	Yes	—	Format for naming output DICOM files using named groups from the regex

Pattern Requirements

To ensure consistent anonymization and file management, the following pattern requirements must be satisfied.

1. Filename Pattern (--filename_pattern)

   • Must include a named group that extracts a date value from the XML filename.
     Example: (?P<examination_date>\d{8})
   • The ECG XML files must have filenames that contain this date value, so the pattern can correctly extract it.

2. Output Filename Pattern (--out_filename_pattern)

   • Must contain:
     • Exactly one date-related key (e.g., {examination_date})
     • A sequence number key (e.g., {seq}) to differentiate multiple files with the same date

This is crucial for maintaining uniqueness among converted DICOM files, especially when multiple ECGs share the same date.

If seq is not included in the --out_filename_pattern, a warning will be printed and _{seq} will be automatically appended to ensure file uniqueness:

Warning: No sequence number in output filename pattern. Sequence numbers will not be used to differentiate files with the same date.
Add "seq" to the output filename pattern to enable sequence differentiation.

If more than one {...date...} key is found in the output filename pattern, the script will raise an error to enforce a single date field:

AssertionError: Expected one date key in the output filename pattern, found 2.

Make sure that:

• Your --filename_pattern includes the group(s) matching the required keys (e.g., (?P<examination_date>...))
• Your ECG XML filenames include a date string that matches this pattern
• Your --out_filename_pattern uses the same group names as placeholders (e.g., {examination_date}, {seq})

Example

• Input filename: MUSE_20250711_153012_00001.xml
• Extracted:
  • examination_date = 20250711
• Output filename: ECG_DICOM_20250711_00001.dcm

Example results

The following are examples of the ECG data converted from XML to DICOM format: