diff --git a/httomo_backends/scripts/yaml_pipelines_generator.py b/httomo_backends/scripts/yaml_pipelines_generator.py index f8079700..ad982b09 100644 --- a/httomo_backends/scripts/yaml_pipelines_generator.py +++ b/httomo_backends/scripts/yaml_pipelines_generator.py @@ -149,7 +149,7 @@ def yaml_pipelines_generator( ) pipeline_full[i]["side_outputs"].yaml_add_eol_comment( key="cor", - comment="A side output of the method, here a CoR scalar value", + comment="An estimated CoR value provided as a side output", ) pipeline_full[i]["side_outputs"].yaml_add_eol_comment( key="overlap", @@ -158,17 +158,22 @@ def yaml_pipelines_generator( elif "corr" in module_name and "remove_outlier" in method_name: pipeline_full.yaml_set_comment_before_after_key( i, - "--- Removing dead pixels in the data, aka zingers. Use if sharp streaks are present in reconstruction. Please use before normalisation. ---", + "--- Removing unresponsive pixels in the data, aka zingers. Use if sharp streaks are present in the reconstruction. To be applied before normalisation. ---", indent=0, ) pipeline_full += yaml_template_method if pipeline_full[i]["parameters"]["dif"] == "REQUIRED": # fix for the absent parameter in TomoPy's algorithm pipeline_full[i]["parameters"]["dif"] = 0.1 + pipeline_full[i]["parameters"].yaml_add_eol_comment( + key="kernel_size", + comment="The size of the 3D neighbourhood surrounding the voxel. Odd integer.", + ) pipeline_full[i]["parameters"].yaml_add_eol_comment( key="dif", - comment="A difference between the outlier value and the median value of neighboring pixels.", + comment="A difference between the outlier value and the median value of neighbouring pixels.", ) + elif "distortion" in method_name: pipeline_full.yaml_set_comment_before_after_key( i, @@ -225,8 +230,12 @@ def yaml_pipelines_generator( pipeline_full += yaml_template_method pipeline_full[i]["parameters"].yaml_add_eol_comment( key="center", - comment="Reference to center of rotation side output OR an integer.", + comment="Reference to center of rotation side output above OR a float number.", ) + pipeline_full[i]["parameters"].yaml_add_eol_comment( + key="detector_pad", + comment="Horizontal detector padding to minimise circle/arc-type artifacts in the reconstruction", + ) pipeline_full[i]["parameters"].yaml_add_eol_comment( key="recon_mask_radius", comment="Zero pixels outside the mask-circle radius.",