From 4b1e981738e0c3b8fb6ad56e4ee35b81beb480c0 Mon Sep 17 00:00:00 2001 From: AliceJoubert Date: Wed, 12 Mar 2025 10:44:46 +0100 Subject: [PATCH] Update cli --- clinica/pipelines/cli_param/option.py | 13 +++++++++++++ clinica/pipelines/dwi/preprocessing/fmap/cli.py | 2 +- clinica/pipelines/dwi/preprocessing/t1/cli.py | 9 +++++---- clinica/pipelines/pet/linear/cli.py | 8 ++------ clinica/pipelines/t1_linear/flair_linear_cli.py | 15 +++------------ clinica/pipelines/t1_linear/t1_linear_cli.py | 15 +++------------ clinica/pipelines/t1_volume/t1_volume_cli.py | 2 +- .../t1_volume_create_dartel_cli.py | 2 +- .../t1_volume_dartel2mni_cli.py | 2 +- .../t1_volume_parcellation_cli.py | 2 +- .../t1_volume_register_dartel_cli.py | 2 +- .../t1_volume_tissue_segmentation_cli.py | 2 +- 12 files changed, 33 insertions(+), 41 deletions(-) diff --git a/clinica/pipelines/cli_param/option.py b/clinica/pipelines/cli_param/option.py index e0b08d1c3..082404834 100644 --- a/clinica/pipelines/cli_param/option.py +++ b/clinica/pipelines/cli_param/option.py @@ -220,3 +220,16 @@ is_flag=True, help="If True, large intermediary files will be deleted before the end of the pipeline.", ) + +antspy = option( + "--use-antspy", + is_flag=True, + help="Use ANTsPy instead of ANTs.", +) + +uncropped = option( + "-ui", + "--uncropped_image", + is_flag=True, + help="Do not crop the image with template (cropped image are suggested for using with DL models)", +) diff --git a/clinica/pipelines/dwi/preprocessing/fmap/cli.py b/clinica/pipelines/dwi/preprocessing/fmap/cli.py index 32e8cd19d..c86509070 100644 --- a/clinica/pipelines/dwi/preprocessing/fmap/cli.py +++ b/clinica/pipelines/dwi/preprocessing/fmap/cli.py @@ -15,6 +15,7 @@ @cli_param.argument.caps_directory @cli_param.option_group.pipeline_specific_options @cli_param.option.low_bval +@cli_param.option.caps_name @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory @@ -23,7 +24,6 @@ @cli_param.option_group.advanced_pipeline_options @cli_param.option.use_cuda @cli_param.option.initrand -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/dwi/preprocessing/t1/cli.py b/clinica/pipelines/dwi/preprocessing/t1/cli.py index f59aa3e32..ec1033b21 100644 --- a/clinica/pipelines/dwi/preprocessing/t1/cli.py +++ b/clinica/pipelines/dwi/preprocessing/t1/cli.py @@ -9,23 +9,24 @@ pipeline_name = "dwi-preprocessing-using-t1" +# todo :rq random seed and initrand same principle ?? @clinica_pipeline @click.command(name=pipeline_name) @cli_param.argument.bids_directory @cli_param.argument.caps_directory @cli_param.option_group.pipeline_specific_options +@cli_param.option.delete_cache @cli_param.option.low_bval +@cli_param.option.initrand +@cli_param.option.random_seed @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs @cli_param.option_group.advanced_pipeline_options @cli_param.option.use_cuda -@cli_param.option.initrand -@cli_param.option.delete_cache -@cli_param.option.random_seed -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/pet/linear/cli.py b/clinica/pipelines/pet/linear/cli.py index cb7d8a7dd..fd9cee443 100644 --- a/clinica/pipelines/pet/linear/cli.py +++ b/clinica/pipelines/pet/linear/cli.py @@ -9,6 +9,7 @@ pipeline_name = "pet-linear" +# todo : no caps name ? @clinica_pipeline @click.command(name=pipeline_name) @cli_param.argument.bids_directory @@ -17,12 +18,7 @@ @cli_param.argument.suvr_reference_region @cli_param.option_group.pipeline_specific_options @cli_param.option.reconstruction_method -@cli_param.option.option( - "-ui", - "--uncropped_image", - is_flag=True, - help="Do not crop the image with template (cropped image are suggested for using with DL models)", -) +@cli_param.option.uncropped @cli_param.option.option( "--save_pet_in_t1w_space", is_flag=True, diff --git a/clinica/pipelines/t1_linear/flair_linear_cli.py b/clinica/pipelines/t1_linear/flair_linear_cli.py index 621fccb08..456d43d0e 100644 --- a/clinica/pipelines/t1_linear/flair_linear_cli.py +++ b/clinica/pipelines/t1_linear/flair_linear_cli.py @@ -14,24 +14,15 @@ @cli_param.argument.bids_directory @cli_param.argument.caps_directory @cli_param.option_group.pipeline_specific_options -@cli_param.option_group.option( - "-ui", - "--uncropped_image", - is_flag=True, - help="Do not crop the image with template (cropped image are suggested for using with DL models)", -) +@cli_param.option.uncropped @cli_param.option.random_seed +@cli_param.option.antspy @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs -@cli_param.option.option( - "--use-antspy", - is_flag=True, - help="Use ANTsPy instead of ANTs.", -) -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/t1_linear/t1_linear_cli.py b/clinica/pipelines/t1_linear/t1_linear_cli.py index 422ee3c57..fd1a622a6 100644 --- a/clinica/pipelines/t1_linear/t1_linear_cli.py +++ b/clinica/pipelines/t1_linear/t1_linear_cli.py @@ -14,24 +14,15 @@ @cli_param.argument.bids_directory @cli_param.argument.caps_directory @cli_param.option_group.pipeline_specific_options -@cli_param.option.option( - "-ui", - "--uncropped_image", - is_flag=True, - help="Do not crop the image with template (cropped image are suggested for using with DL models)", -) +@cli_param.option.uncropped @cli_param.option.random_seed +@cli_param.option.antspy @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs -@cli_param.option.option( - "--use-antspy", - is_flag=True, - help="Use ANTsPy instead of ANTs.", -) -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/t1_volume/t1_volume_cli.py b/clinica/pipelines/t1_volume/t1_volume_cli.py index 5956e6a7b..b244a43c3 100644 --- a/clinica/pipelines/t1_volume/t1_volume_cli.py +++ b/clinica/pipelines/t1_volume/t1_volume_cli.py @@ -19,6 +19,7 @@ @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @cli_param.option.yes @cli_param.option_group.advanced_pipeline_options @cli_param.option.tissue_classes @@ -32,7 +33,6 @@ @option.global_option_group @option.n_procs @click.pass_context -@cli_param.option.caps_name def cli( ctx: click.Context, bids_directory: str, diff --git a/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py b/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py index 0ae3d4306..b7e881906 100644 --- a/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py +++ b/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py @@ -17,11 +17,11 @@ @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs @cli_param.option_group.advanced_pipeline_options @cli_param.option.dartel_tissues -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py b/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py index ce890d910..ae4d3a6f8 100644 --- a/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py +++ b/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py @@ -19,13 +19,13 @@ @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs @cli_param.option_group.advanced_pipeline_options @cli_param.option.tissues @cli_param.option.modulate @cli_param.option.voxel_size -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py b/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py index 7c0f3832c..2e4e1e994 100644 --- a/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py +++ b/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py @@ -16,11 +16,11 @@ @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs @cli_param.option_group.advanced_pipeline_options @cli_param.option.modulate -@cli_param.option.caps_name def cli( caps_directory: str, group_label: str, diff --git a/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_cli.py b/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_cli.py index 5c1de84e8..fe638a722 100644 --- a/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_cli.py +++ b/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_cli.py @@ -17,11 +17,11 @@ @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs @cli_param.option_group.advanced_pipeline_options @cli_param.option.tissues -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str, diff --git a/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py b/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py index f1aa00e3f..705712f12 100644 --- a/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py +++ b/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py @@ -16,6 +16,7 @@ @cli_param.option_group.common_pipelines_options @cli_param.option.subjects_sessions_tsv @cli_param.option.working_directory +@cli_param.option.caps_name @option.global_option_group @option.n_procs @cli_param.option_group.advanced_pipeline_options @@ -24,7 +25,6 @@ @cli_param.option.tissue_probability_maps @cli_param.option.dont_save_warped_unmodulated @cli_param.option.save_warped_modulated -@cli_param.option.caps_name def cli( bids_directory: str, caps_directory: str,