Internal:PODM CNF

Things TODO

1. Create scripts to run the image easily. ✔
2. Test:
   1. Linux ✔
   2. Windows ✔
   3. MacOS
3. Add Linear Interpolation Code as default output ✔
   1. Code is ready need to be integrated with PODM ✔
4. Segment automatically nrrd data ✔
   1. i.e. iterate with ITK Gajik's image and convert values !=0 -> 1 ✔
   2. Should be done as preproceccing step in PODM and it should be ON by default ✔
5. add Volume grading command line option (ON and OFF for now) ( right now there is a macro, convert it to input flag OFF by default) ✔
6. nrrd images do not visualize well in paraview -> add convert_image tool in the docker image. ( available at /RC/group/RC_NIKOS/Christos/convert_image.git ) so that the users can convert their raw data and visualize them in paraview, add runscript (or option in runscript) for that✔
7. Add memory limit flag for docker inside the python script
   1. The command --memory for docker =limits only physical memory not swap , using it make PODM to use swap. Constraning swap does not seem to work.
8. No (easy) way to kill the script and the docker instance (system signals ?)
9. Set up version tracking (on docker images ? , in code embed git sha in a header during compilation and print it during execution)
10. Create User Documentation ✔
11. explain better delta ?
12. Clean up text output ✔
13. segmentation can be easily be implemented in parallel just by using the Multithreaded ITK template [1] (maybe also linear interpolation ?) (low priority)