Change Notes

Changed in Version 2.2.1

• Added:

  • ll keyword arguments to EM_H2MM_C(), h2mm_model.optimize(), H2MM_arr(), and h2mm_model.evaluate(). Setting ll=True results in function returning as second return value (in tuple) the loglik of each burst.

• Internal changes (no change in results)

  • Better allocation of arrays in viterbi_sort()

• Fixed:

  • Previous version of H2MM_arr() had misallocation resulting in rare segfault. The mistake has been resolved

  • Previous versions had bug in C function viterbi_burst (in H2MM_C/viterbi.c) where a running sum varaible was not reset at the beginning of each iteration. This resulted in incorrect (although still very close) computation of omega and loglik. This bug has been fixed.

Changed in Version 2.1.2

• Fixed: issue Issue 4 where viterbi_sort() failed when run from ipython __main__.

Changed in Version 2.1.1

• Added loglikpath keyword argument to path_loglik(), if True, the loglikelihood of each photon is return in an array of arrays.

• Fixed

  • Setting of h2mm_model.prior, h2mm_model.trans h2mm_model.obs, and h2mm_model.niter after model is sorted now raises an error.

  • h2mm_model.optimize() after models sorted with option inplace=True now raises error and prevents modification of model.

Changed in version 2.0.6

• Added h2mm_model.tobytes() and h2mm_model.frombytes() methods enabling serializing/loading h2mm_model

Changed in version 2.0.5

• Added beta IPyPlot class, for plotting with matplotlib

  • This class is not considered “official”, and is not guaranteed to be backwards compatible with minor revision changes

Note

When H2MM_C was first introduced, different version numbers were given in Zenodo and pip repositories, creating confusion, as one stated at 1.x.x, the other at 0.x.x. Version 2.0.5 marks the unification of these versioning systems. All version in Documentation refrence the pip versioning.

Changed in version 2.0.0

• Interface changes

  • max_iter default now 2046 ( \(2^{11} - 2\), so that output includeing initial and last non-calculated modelof size \(2^{11} = 2048\))

  • inplace of EM_H2MM_C(), h2mm_model.optimize(), and h2mm_model.evaluate() now defaults to False

  • Introduction of Printer and subclasses StdPrinter and IPyPrinter to handle formatting of output through print_formatter in EM_H2MM_C()

    • New print_func

    • print_args no longer used to set update frequency and keep

      • Use print_freq and print_fmt_kwargs instead (see further notes)

  • print_func as a function now takes signature (niter, new, current, old, iter_time, total_time, *print_args, **print_kwargs)

  • print_func no longer called before optimization to check output type etc.

  • bounds_func now takes signature (niter, new, current, old, *bounds, **bounds_kwargs)

  • bounds_func no longer called before optimization

• Internal Changes

  • Improved memory handling, indexes arrays no longer copied

  • Switched types of most C variables to fixed width <stdint.h> defined types

    • indexes from unsigned long to uint8_t

    • deltas (times) from unsigned long to int32_t

    • h2mm_mod.nstate/ndet to int64_t