Tags: sct-pipeline/gm-challenge
Tags
Updated code for simulations (#66) * Minor PEP8 fixes * Cropped phantom and changed output default folder * Added tqdm progress bar * Fixed generation of cord and GM masks * Cleanup * Updated .gitignore * Refactoring to remove duplication * Cleanup * Updated README * Started refactoring to get rid of old code deps * Fixed CSV reading code * Fixed subprocess syntax * Output results in separate folder * Also output WM mask * Introduced WM mask * Implemented metrics computation * Cleanup * Fixed wrong dict usage; updated README * Cleanup * Updated TODO * Fixed xticklabels * Fixed Matplotlib warning Warning: <ipython-input-3-13658aa197ad>:1: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(yticklabels, fontsize=fontsize_axes) Solution: https://stackoverflow.com/questions/63723514/userwarning-fixedformatter-should-only-be-used-together-with-fixedlocator * Fixed TypeError: a bytes-like object is required, not 'str' Solution: https://stackoverflow.com/questions/34283178/typeerror-a-bytes-like-object-is-required-not-str-in-python-and-csv * Output in simu_results/ * Updated .gitignore * Need to uncache otherwise the nibabel object changes More info: https://nipy.org/nibabel/images_and_memory.html * Removed verbose * Added progress bar * Changed output location * Compute contrast in % * Fixed creation of WM mask It was waaay to big * Eroded GM and WM masks further To address the accuracy issue when computing metrics * Cosmetic changes on the figure * Cleanup * Fixed centering of xtick