dcm2niix/run.py at master · flywheel-apps/dcm2niix · GitHub

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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Main script for dcm2niix gear."""

import flywheel_gear_toolkit

from dcm2niix_gear.dcm2niix import prepare
from dcm2niix_gear.dcm2niix import dcm2niix_utils
from dcm2niix_gear.dcm2niix import dcm2niix_run
from dcm2niix_gear.pydeface import pydeface_run
from dcm2niix_gear.utils import parse_config
from dcm2niix_gear.utils import resolve


def main(gear_context):
    """Orchestrate dcm2niix gear."""

    # Prepare dcm2niix input, which is a directory of dicom or parrec images
    gear_args = parse_config.generate_gear_args(gear_context, "prepare")
    dcm2niix_input_dir = prepare.setup(**gear_args)

    # Run dcm2niix
    gear_args = parse_config.generate_gear_args(gear_context, "dcm2niix")
    output = dcm2niix_run.convert_directory(
        dcm2niix_input_dir, gear_context.work_dir, **gear_args
    )

    # Nipype interface output from dcm2niix can be a string or list (desired)
    try:

        output_image_files = output.outputs.converted_files
        if isinstance(output_image_files, str):
            output_image_files = [output_image_files]

        output_sidecar_files = output.outputs.bids
        if isinstance(output_sidecar_files, str):
            output_sidecar_files = [output_sidecar_files]

    except AttributeError:
        log.info("No outputs were produced from dcm2niix tool.")
        output_image_files = None

    # NIfTI files are assumed to be expected for coil combined and pydeface
    if not gear_context.config["output_nrrd"] and output_image_files is not None:

        # Apply coil combined method
        if gear_context.config["coil_combine"]:
            dcm2niix_utils.coil_combine(output_image_files)

        # Run pydeface
        if gear_context.config["pydeface"]:
            gear_args = parse_config.generate_gear_args(gear_context, "pydeface")
            pydeface_run.deface_multiple_niftis(output_image_files, **gear_args)

    # If bvals or bvecs defined, then add to the list of output image files
    if isinstance(output.outputs.bvals, str):
        output_image_files.append(output.outputs.bvals)

    if isinstance(output.outputs.bvals, list):
        output_image_files.extend(output.outputs.bvals)

    if isinstance(output.outputs.bvecs, str):
        output_image_files.append(output.outputs.bvecs)

    if isinstance(output.outputs.bvecs, list):
        output_image_files.extend(output.outputs.bvecs)

    # Resolve gear outputs, including metadata capture
    gear_args = parse_config.generate_gear_args(gear_context, "resolve")
    resolve.setup(
        output_image_files,
        output_sidecar_files,
        str(gear_context.work_dir),
        dcm2niix_input_dir,
        gear_context.output_dir,
        **gear_args,
    )

    exit_status = 0

    return exit_status


if __name__ == "__main__":

    with flywheel_gear_toolkit.GearToolkitContext() as gear_context:
        gear_context.init_logging()
        log = gear_context.log
        exit_status = main(gear_context)

    log.info(f"Successful dcm2niix gear execution with exit status {exit_status}.")