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updates to the generator, version update ruamel
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@dkazanc
dkazanc committed Jan 27, 2025
1 parent 04bac64 commit 68275ab
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Showing 2 changed files with 59 additions and 26 deletions.
2 changes: 1 addition & 1 deletion docs/source/doc-conda-requirements.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,5 +17,5 @@ dependencies:
- loguru
- graypy
- tqdm
- ruamel.yaml
- ruamel.yaml>=0.18
- pip
83 changes: 58 additions & 25 deletions docs/source/scripts/yaml_pipelines_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ def yaml_pipelines_generator(
returns zero if the processing is successful
"""

yaml = ruamel.yaml.YAML(typ="rt")
yaml = ruamel.yaml.YAML(typ="rt", pure=True)

# open YAML file to inspect
with open(path_to_pipelines, "r") as file:
Expand All @@ -61,7 +61,7 @@ def yaml_pipelines_generator(
print("loading yaml file with methods failed", e)

with open(path_to_output_file, "w") as f:
# a loop over methods in the high-level pipeline file
# a loop over methods in the high-level pipeline file (directive)
methods_no = len(pipeline_file_content)
pipeline_full = CS()
for i in range(methods_no):
Expand Down Expand Up @@ -90,79 +90,112 @@ def yaml_pipelines_generator(
# should be the first method in the list
pipeline_full.yaml_set_comment_before_after_key(
i,
"Standard tomography loader for NeXus files",
"--- Standard tomography loader for NeXus files. ---",
indent=0,
)
pipeline_full += yaml_template_method
elif "rotation" in module_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Center of Rotation method for automatic center finding. Required for reconstruction",
"--- Center of Rotation auto-finding. Required for reconstruction bellow. ---",
indent=0,
)
pipeline_full += yaml_template_method
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="ind",
comment="A vertical slice (sinogram) index to calculate CoR, `mid` can be used for middle",
)
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="cor_initialisation_value",
comment="Use if an approximate CoR is known",
)
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="average_radius",
comment="Average several sinograms to improve SNR, one can try 3-5 range",
)
pipeline_full[i]["side_outputs"].yaml_add_eol_comment(
key="cor",
comment="A side output of the method, here a CoR scalar value",
)
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. Only required if there are sharp streaks in the reconstruction.",
"--- Removing dead pixels in the data, aka zingers. Use if sharp streaks are present in reconstruction. ---",
indent=0,
)
pipeline_full += yaml_template_method
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="dif",
comment="A difference between the outlier value and the median value of neighbouring pixels.",
)
elif "normalize" in module_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Normalisation of projection data using collected flats/darks and taking negative log (not needed with Paganin). ",
"--- Normalisation of projection data using collected flats/darks images. --- ",
indent=0,
)
pipeline_full += yaml_template_method
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="minus_log",
comment="If Paganin method is used bellow, set it to false.",
)
elif "stripe" in module_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Method to remove stripe artefacts in the data that lead to ring artefacts in the reconstruction. ",
"--- Method to remove stripe artefacts in the data that lead to ring artefacts in the reconstruction. --- ",
indent=0,
)
pipeline_full += yaml_template_method
elif "algorithm" in module_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Reconstruction method. Use a reference to the center or set to an integer.",
"--- Reconstruction method. ---",
indent=0,
)
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.",
)
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="recon_mask_radius",
comment="Zero pixels outside the mask-circle radius.",
)
elif "calculate_stats" in method_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Calculate global statistics on the reconstructed volume (min/max needed specifically for data rescaling) ",
"--- Calculate global statistics on the reconstructed volume, required for data rescaling. ---",
indent=0,
)
pipeline_full += yaml_template_method
elif "rescale_to_int" in method_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Rescaling the data using min/max obtained from calculate_stats",
"--- Rescaling the data using min/max obtained from `calculate_stats`. ---",
indent=0,
)
pipeline_full += yaml_template_method
elif "images" in module_name:
pipeline_full.yaml_set_comment_before_after_key(
i,
"Saving data into images",
"--- Saving data into images. ---",
indent=0,
)
pipeline_full += yaml_template_method
pipeline_full[i]["parameters"].yaml_add_eol_comment(
key="file_format",
comment="`tif` or `jpeg` can be used.",
)
else:
pipeline_full.yaml_set_comment_before_after_key(
i,
"--------------------------------------------------------#",
indent=0,
)
pipeline_full += yaml_template_method
pipeline_full += yaml_template_method

# tried inline comments here, doesn't work for some reason
# pipeline_full[5]["parameters"].yaml_add_eol_comment(
# key="center",
# comment="Some inline comment",
# )
yaml.representer.add_representer(type(None), __represent_none)
ruamel.yaml.dump(
pipeline_full,
f,
Dumper=ruamel.yaml.RoundTripDumper,
default_flow_style=None,
width=50,
indent=0,
)
yaml.dump(pipeline_full, f)

return 0

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