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Fix deprecation warning of scipy.misc.imsave and greyscale seg masks #34

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@timmeinhardt timmeinhardt commented Jun 21, 2019

In the current version of the code the following line causes a deprecation warning:

sm.imsave(os.path.join(save_dir_res, os.path.basename(fname[jj]) + '.png'), pred)

As suggested by the warning, this PR replaces scipy.misc.imsave with imageio.imsave. In addition, this PR applies a little bit of refactoring to the corresponding code block and resolves a bug that previously the output probabilities of the sigmoid were saved as a greyscale segmentation mask. Now the saved segmentation mask will be the true predicted values, i.e., either 0 or 1.

Fixing this bug leads to a slight improvement in the final metric values. However, these are still lower than the reported values in the ablation study (Table 1) of the paper. Without contour snapping I am able to reproduce a mean J of 0.759 compared to the reported 77.4. Is there still something missing compared to the original TensorFlow version?

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