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fluidimage.util subpackage and script to launch topologies in bulk

Bitbucket Importer requested to merge bitbucket/merged-pr-6 into branch/default

Created originally on Bitbucket by avmo (Ashwin Vishnu)

Was already merged in Bitbucket before import, marked as merged by the import user

Updates synced with changes in cornic/fluidimage

  • ParamsList classes to launch topologies in bulk. Try to fix preproc complete mode.

  • Reorganize paramlist module and other functions in fluidimage/init.py to util subpackage

  • More robust preproc saving compatible with double index images

  • Fix a small bug in paramslist. Add sequential mode

  • Memory improvements and saving bugs fixed

    • Bug in saving proprocessed images: wrong index of middle image
    • Remove serie attr from PreprocResults class - not required
    • Memory efficient decorator in fluidimage/pre_proc/io.py
    • Memory OSError workaround in fluidimage/topologies/base.py
    • cprint and cstring for coloured standard output

  • Solve bug waiting queues affecting the loading of images.

  • Solve bug logger + multiprocessing. Improve logging.

  • Better logging.

  • Try if memory increases with image loading/saving

  • Try to solve the problem of memory.

  • Log + params files saved. loggin_level argument for topologies.

  • Log parser.

  • More logging parsing.

  • Improve logging and topology.

  • Try to improve topology for better speedup.

  • Minor changes to fluidimage/util/util.py and its imports

  • Add test for TopologyPreproc

  • Minor changes to make LogTopology work

  • Try to improve topography.

  • More logging.

  • Add plot of nb of workers.

  • Change topology with profiling.

  • Update workers in a thread.

  • New function display in PreprocBase class

  • Small clean up in example preproc_simple

  • Improve speedup.

  • Extend display function of pre_proc to TopologyPreproc

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