making it python 3 compatible_REVISED #194
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…mpatibility, adding the future imports to keep others clean and behavior particularly division consistent
…, adding a new notebook for simple tests, fixing typo in safe_xrange, most tests pass now, but still differences, probably because SimpleITK, numpy, and PyWavelets have changed.
In python 3, the zip function returns a 'zip' object, similar to python generators. This does not change it's implementation in python for loops, but it is not evaluated if it is used to generate a numpy array. Therefore, add a cast to list, which evaluates the object, before assigning it to the numpy array. Also, use relative imports in tests. Finally, fix some print-function bugs in the 'bin' and 'batchexamples' folder and rerun the python notebooks, so the output reflects the changes made.
Some functions expect string types (such as in nose-testing), but python 3.5 by default provides unicode strings. Add forced casts where necessary. Also, 'wb' mode requires strings to be encoded as bytes, not string in python 3.5. The fix did not work in this case. Change mode to 'w', which accepts regular strings. Additionally, safe_cmp produced errors for dictionary comparison in python 3.5, replace by `==` comparison. Finally, update layout in testing files (such as replace `!=` by `is not` in comparisons to `None`). Update feature name in testing output to also reflect the feature class.
In python 3.5 GLRLM results differed from baseline. This due to the different implementation of the `filter()` function, which returns an iterator instead of a list. In GLRLM calculation, there where 2 iterations over this iter-object (one for flat-angle check, one for matrix calculation), causing it to break in python 3.5. Fix by merging the 2 iterations into one loop. Additionally, simplify the filter function.
Reverts 1fa906e
Ensures python 3 compatibility.
In python 3, `xrange` and `basestring` are undefined names (python 2 specific). Therefore, these will produce an F821 flake8 error on testing in python 3 environment. Add this error to the ignore list to let it pass the flake 8 test. Alternative: add `radiomics/__init__.py` to the excluded files (`xrange` and `basestring` only used here).
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@JoostJM I ended up working on this earlier tonight. I will push the topic shortly. |
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Let's also note that my topic is based on the current master |
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@jcfr Great! Also, currently the python 3 tests are failing for python 3.3, python 3.4 and higher work. The error is that the test try to install the latest version of numpy (as the requirement is >=1.9.2). However, numpy 1.12.0 requires python 2.7 or python >= 3.4. |
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superseded by #196 |
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supersedes #188
Additional changes to previous PR:
cc @Radiomics/developers, @kmader