From 304b307c29d5130634082054fb3aeb98070b216f Mon Sep 17 00:00:00 2001 From: jidicula Date: Sun, 8 Nov 2020 14:32:54 -0500 Subject: [PATCH 1/2] Add documentation stub for dicom_to_nifti.py Resolves #165 **Why this change was necessary** `dicom_to_nifti.py` wasn't added to the `api.rst` document, but should be in there in the `misc` section. **What this change does** See title. **Any side-effects?** Re-compile docs locally to see it update locally. --- docs/source/6_api_reference/api.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/6_api_reference/api.rst b/docs/source/6_api_reference/api.rst index 639fd09bd..c85eb4285 100644 --- a/docs/source/6_api_reference/api.rst +++ b/docs/source/6_api_reference/api.rst @@ -50,3 +50,6 @@ misc .. automodule:: shimmingtoolbox.cli.download_data :members: + +.. automodule:: shimmingtoolbox.cli.dicom_to_nifti + :members: From 8e514c35bfb2c8b3c2fae46d72db3113e121b8a4 Mon Sep 17 00:00:00 2001 From: jidicula Date: Sun, 8 Nov 2020 14:38:41 -0500 Subject: [PATCH 2/2] Add src code formatting to CLI docstring --- shimmingtoolbox/cli/dicom_to_nifti.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shimmingtoolbox/cli/dicom_to_nifti.py b/shimmingtoolbox/cli/dicom_to_nifti.py index 3b032a92c..3cf9c5186 100644 --- a/shimmingtoolbox/cli/dicom_to_nifti.py +++ b/shimmingtoolbox/cli/dicom_to_nifti.py @@ -21,7 +21,7 @@ @click.option('-remove_tmp/-dont_remove_tmp', default=False, help="Specifies if tmp folder will be deleted after processing") def dicom_to_nifti_cli(path_dicoms, path_nifti, subject, fname_config, remove_tmp): - """Converts dicom files into nifti files by calling dcm2bids.""" + """Converts dicom files into nifti files by calling ``dcm2bids``.""" dicom_to_nifti(path_dicoms, path_nifti, subject_id=subject, path_config_dcm2bids=fname_config, remove_tmp=remove_tmp)