Remove dependency for tqdm
#232
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Remove dependency for the tqdm package, as this is rarely used (only for GLCM and GLSZM in full-python mode). Instead provide 3 variables which can hold function definitions used for instantiating and interacting with a progress bar. In the helloRadiomics script and notebook, this changed functionality is illustrated with a commented out section in the script and a separate cell in the notebook. This section and cell assume the `tqdm` package is installed and use it to show a progressbar during calculation of the glcm matrix in full-python mode.
jcfr
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Mar 29, 2017
radiomics/glszm.py
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| else: | ||
| # Ensure that even if progress functions are defined, progress is only given if 'verbose' is True | ||
| self.initProgress = None | ||
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This code should probably be moved to the base class.
jcfr
reviewed
Mar 29, 2017
radiomics/__init__.py
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| @@ -161,6 +161,18 @@ def getInputImageTypes(): | |||
| return _inputImages | |||
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| def getProgressFunctions(): | |||
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should that function be private: _getProgressFunctions() ? Or should the variable (init|report|close)progress be private global ?
Either way we need to document the signature of the functions too.
As @jcfr showed in AIM-Harvard#230, the progress reporting can be simplified, requiring the user only to specify one variable that holds a progress reporter. Update PyRadiomics to this implementation and add examples for both use with `tqdm.tqdm` (which can be used directly) or `click.progressbar` (which requires a simple wrapper class). Examples are provided in both the helloRadiomics script and notebook. Progress reporting in full-python mode in GLCM and GLSZM now uses a progress reporter that is instantiated with an interator (as opposed to a length) and uses this progress reporter in the loop to iterate over the gray levels. This is encapsulated in a `with` statement to ensure correct closure. Finally, a dummy progress reporter is provided for the cases where no progressbar is needed (none specified or verbosity level > INFO). In those cases the `_dummyProgressReporter` (defined in `__init__.py`) is used, which accepts the arguments from PyRadiomics and iterates over the gray levels passed in the iterable, but does not report any progress back to the user.
Add documentation on how to add a progress reporter in the developers section of the documentation. The `_DummyProgressReporter` class and `_getProgressReporter` function also have documentation, but these are not included in the sphinx-generated documentation.
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Remove dependency for the tqdm package, as this is rarely used (only for GLCM and GLSZM in full-python mode).
Instead provide 3 variables which can hold function definitions used for instantiating and interacting with a progress bar.
In the helloRadiomics script and notebook, this changed functionality is illustrated with a commented out section in the script and a separate cell in the notebook. This section and cell assume the
tqdmpackage is installed and use it to show a progressbar during calculation of the glcm matrix in full-python mode.TODO before merge:
_getProgressReporterfunction in__init__.py