Getting started

Install M3Resp

M3Resp works with Python 3.12, 3.13 and 3.14. In the M3Resp source folder, install the base package:

pip

python -m pip install -e .

uv

uv sync

Then install the integration for each modality that you use:

pip

python -m pip install -e ".[eit]"       # EIT processing
python -m pip install -e ".[emg]"       # EMG processing
python -m pip install -e ".[all]"       # EIT and EMG processing

uv

uv sync --extra eit  # EIT processing
uv sync --extra emg  # EMG processing
uv sync --extra all  # Both integrations

uv sync installs only the extras in the command and removes all other extras. So name each extra that you need, for example uv sync --extra all --extra dev.

The base package reads and checks workflow files, synchronizes recordings, makes synthetic EIT data and exports results.

Run a workflow

A workflow file is a YAML or JSON file with a list of processing steps. Run the example workflow from the M3Resp source folder:

pip

m3resp run examples/multimodal_example/multimodal.workflow.yaml

uv

uv run m3resp run examples/multimodal_example/multimodal.workflow.yaml

The example uses the synthetic recordings in tests/data and writes the results to output/multimodal-summary. M3Resp reads the file paths in a workflow file from the folder of that file.

To list all processing steps:

pip

m3resp steps

uv

uv run m3resp steps

Use Python

Run the same workflow from Python:

from m3resp import load_spec, run_spec

spec = load_spec("examples/multimodal_example/multimodal.workflow.yaml")
result = run_spec(spec)
print(result.status)               # succeeded
print(result.resolved_output_dir)  # the folder with the result files

To run each step yourself, use a session:

import os

from m3resp import M3Session

session = M3Session()
session.load_eit(os.path.join("tests", "data", "m3resp_multimodal_1_eit_draeger.bin"), vendor="draeger")
session.run_preset("eit")
print(len(session.events["eit_breaths"]))  # 13

Continue with the tutorials, or read how a workflow file is built.