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yaml generator comment fixes #65

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merged 1 commit into from
Sep 2, 2025
Merged

yaml generator comment fixes #65

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17 changes: 13 additions & 4 deletions httomo_backends/scripts/yaml_pipelines_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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,
Expand Down Expand Up @@ -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.",
Expand Down
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