This release includes most of the CBSTools package and migrates the code to python 3
New features:
- Python 3 integration: all runs with python 3 now, including JCC (note: because of the different ways python 2 and 3 coexist in different installations (regular Linux, Conda, Docker, etc) you have to be careful to explicitly use 'python3 -m pip', 'python3 -m jcc' etc rather than the shorthand versions. There's a naming convention problem with 'dir' in the init.py as generated by JCC for python 3.7, which we handled with post-hoc find&replace).
- New examples: now including registration and atlas-based segmentation examples. The registration tools require ANTs and Nipype (note: for these modules, the inputs must be file names, not directly Nifti1Image objects).
- New modules: a lot of additional CBSTools have been ported, including a clean port of the isosurface meshing tool. New modules from the IMCN-TK have been added as well (note: because we have multiple sources, now the java code from all external repositories is compiled into a single collection of jar files and wrapped as one "nighresjava" python package).
- Memory management: the JVM checks for available memory and recruits it accordingly.
- File i/o: the .vtk surface files can handle different mesh options (with or without data included, one or n-dimensional).