Programmatic Execution (Python)

MEGqc exposes dispatchers in meg_qc.test that are also used by CLI and GUI.

Step 0 (recommended): export editable config first

Create an editable settings.ini using the same CLI utility used in shell workflows:

mkdir -p /path/to/configs
get-megqc-config --target_directory /path/to/configs --filename settings_global.ini

Then edit /path/to/configs/settings_global.ini for your run.

Import dispatchers

from meg_qc.test import (
    run_calculation_dispatch,
    run_plotting_dispatch,
    run_gqi_dispatch,
    run_all_dispatch,
)

Resolve package internal config path

run_calculation_dispatch requires the package internal config path.

from pathlib import Path
import meg_qc

pkg_root = Path(meg_qc.__file__).resolve().parent
internal_cfg = str(pkg_root / "settings" / "settings_internal.ini")

1) Calculation example

run_calculation_dispatch(
    dataset_paths=["/path/ds1", "/path/ds2"],
    config_file_path="/path/to/configs/settings_global.ini",
    internal_config_file_path=internal_cfg,
    sub_list="all",
    n_jobs=4,
    analysis_mode="new",
    analysis_id="qa_pass_01",
    existing_config_policy="provided",
    processed_subjects_policy="skip",
)

2) Plotting example

run_plotting_dispatch(
    dataset_paths=["/path/ds1", "/path/ds2"],
    qa_subject=True,
    qa_group=True,
    qa_multisample=True,
    qc_group=True,
    qc_multisample=True,
    analysis_mode="reuse",
    analysis_id="qa_pass_01",
    njobs=4,
)

3) GQI recomputation example

run_gqi_dispatch(
    dataset_paths=["/path/ds1", "/path/ds2"],
    default_config_file_path="/path/to/configs/settings_global.ini",
    analysis_mode="reuse",
    analysis_id="qa_pass_01",
)

4) Run ALL orchestration example

run_all_dispatch(
    dataset_paths=["/path/ds1", "/path/ds2"],
    config_file_path="/path/to/configs/settings_global.ini",
    internal_config_file_path=internal_cfg,
    sub_list="all",
    calc_n_jobs=4,
    plot_njobs=4,
    analysis_mode="new",
    analysis_id="qa_pass_02",
    qa_subject=True,
    qa_group=True,
    qa_multisample=True,
    qc_group=True,
    qc_multisample=True,
)

Notes

• analysis_mode='reuse' requires analysis_id.

• in analysis_mode='new', calculation can auto-generate IDs if omitted; providing explicit IDs is recommended for reproducibility.

• multisample plotting modes require at least two datasets.