From 57c4ea40470d303adc7cf1126cd1914432017e33 Mon Sep 17 00:00:00 2001 From: Reza Eghbali Date: Wed, 3 Jul 2024 19:06:01 -0700 Subject: [PATCH] removed dicom_dir from run --- pyalfe/main.py | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/pyalfe/main.py b/pyalfe/main.py index b1e5ea4..313a765 100644 --- a/pyalfe/main.py +++ b/pyalfe/main.py @@ -90,11 +90,6 @@ def download(assets): '--data-dir-structure', type=click.Choice(['alfe', 'bids'], case_sensitive=False), ) -@click.option( - '-dcm', - '--dicom-dir', - type=click.Path(), default=None -) def run( accession: str, config: str, @@ -261,17 +256,17 @@ def process_dicom( nifti_dir: str, data_dir_structure: str, overwrite: bool, - ): +): from pyalfe.containers import DicomProcessingContianer container = DicomProcessingContianer() container.config.from_ini(config, required=True, envs_required=True) - + options = container.config.options() options['dicom_dir'] = dicom_dir - if nifti_dir: + if nifti_dir: options['nifti_dir'] = nifti_dir else: options['nifti_dir'] = options['input_dir'] @@ -285,7 +280,5 @@ def process_dicom( pipeline_runner.run(accession) - - if __name__ == '__main__': main()