New function to create violin plots from sct_pipeline results #1759
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zougloub
approved these changes
May 21, 2018
scripts/sct_pipeline_makefig.py
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| def get_parser(): | ||
| parser = argparse.ArgumentParser( | ||
| description='Generate figure from the output of sct_pipeline.') | ||
| parser.add_argument("-i", |
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When using argparse for new code, suggest to use short/long arguments:
"-i", "--input",
"-l", "--label",
"-v", "--verbose",
scripts/sct_pipeline_makefig.py
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| sct.start_stream_logger() | ||
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| # fs = 10 # font size | ||
| nb_plots = args.i.__len__() |
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This way, the long argument name will be used as default attribute name (args.input if above was used).
scripts/sct_pipeline_makefig.py
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| list_data = [] | ||
| text_results = [] # numerical results to display inside the figure | ||
| for fname_pickle in args.i: | ||
| df = pickle.load(open(fname_pickle, "rb")) |
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Could be changed to io.open() (more explanatory IMO, but it's a question of taste/habits)
scripts/sct_pipeline_makefig.py
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| # | ||
| # Generate figure from the output of sct_pipeline. | ||
| # | ||
| # Copyright (c) 2013 Polytechnique Montreal <www.neuro.polymtl.ca> |
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| if __name__ == '__main__': | ||
| parser = get_parser() | ||
| arguments = parser.parse_args() |
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Although you can invoke the program with -i file_1 -label A -i file_2 -label B you will invariably have users who end up doing -i file_1 file_2 -label A B and end up with -i file_1 file_2 -label A.
if len(arguments.i) != len(arguments.label):
raise RuntimeError("Mismatch between # of files and labels")
Perhaps the labels should be the file names, if not provided.
jcohenadad
added a commit
that referenced
this pull request
Dec 18, 2019
* New function to create violin plots from sct_pipeline results * Various fixes and improvements Former-commit-id: d40444e
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Description of the Change
Implements a new function to generate visual results from
sct_pipeline.Example usage:
Generated figure:
Future improvements:
sct_pipelineresults and use them in this function (notably to get rid of the flaglabel)