[ENH] Update options in client for pipelines

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)",
+)

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,