ENH: Refactor CLI scripts #347
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Combine the `pyradiomics` and `pyradiomicsbatch` entry point into 1 joint entry point `pyradiomics`. This new entry point operates in batch mode when input to `Image|Batch` has `.csv` extension. In batch mode, `Mask` argument is ignored. In single mode `Mask` inputs is required. Additionally, enables easy multi-threaded extraction by specifying `--jobs` / `-j` argument (with integer indicating number of parallel threads to use. Will only work in batch mode, as extraction is multi-threaded at the case level (1 thread per case). Removes argument `--label` / `-l`, specifying an override label to use is now achieved through specifying `-s "label:N"`, with N being the label value. Also includes a small update to initialization of the feature extractor: - In addition to a string pointing to a parameter file, feature extractor now also accepts a dictionary (top level specifies customization types 'setting', 'imageType' and 'featureClass') as 1st positional argument - Regardless of initialization with or without a customization file/dictionary, `kwargs` passed to the constructor are used to override settings.
JoostJM
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Maybe for now include a stub entrypoint for pyradiomicsbatch that issues an error and pointer to the documentation for switching to the new style. |
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Additionally, re-add the `pyradiomicsbatch` as a deprecated entry point to preserve legacy functionality. Also re-add the `--label` argument as a deprecated argument in the `pyradiomics` entry point.
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lgtm 👍 |
This was referenced Mar 13, 2018
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Mar 21, 2018
Recently a [PR](AIM-Harvard/pyradiomics#347) was merged in PyRadiomics, refactoring the commandline interface. Update the SlicerRadiomics module to work with the new functionality. Additionally, fix a bug when requesting the XML from the SlicerRadiomicsScript (due to a name change, it is now necessary to cut off "Script").
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Remove use .bat and .sh wrapper script, and instead define the CLI entry point as a python script. This makes use of the new Slicer functionality described in Slicer/Slicer#894 and implemented in r27143-r27145. This fixes #43. Additionally, check if a `--label <label>` argument is present, and if so, update it to the new-style: `--setting=label:<label>`. Parameter `--label` is deprecated by PR AIM-Harvard/pyradiomics#347.
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Combine the
pyradiomicsandpyradiomicsbatchentry point into 1 joint entry pointpyradiomics.This new entry point operates in batch mode when input to
Image|Batchhas.csvextension.In batch mode,
Maskargument is ignored. In single modeMaskinputs is required.Additionally, enables easy multi-threaded extraction by specifying
--jobs/-jargument (with integer indicating number of parallel threads to use.Will only work in batch mode, as extraction is multi-threaded at the case level (1 thread per case).
Removes argument
--label/-l, specifying an override label to use is now achieved through specifying-s "label:N", with N being the label value.Also includes a small update to initialization of the feature extractor:
kwargspassed to the constructor are used to override settings.cc @Radiomics/developers