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CHANGELOG.md

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Version updates

All notable changes to NRV are sumed up in this file.

[1.1.2] - 2024-09-12

Added

  • 'ui', a subpackage for user interface to separate from utils which are ment to stay internal.
  • Help restructuration to have a API description more user friendly.
  • nrv.CONFIG as a singleton object gathering configuration related data, parameters and methods.

Fixed

  • small fix in filter_freq to avoid filtering artifact

Removed

  • methods such as load_any_axon, load_any_electrode... (load_any_ + something) are deprecated, though not removed for backward compatibility. Please only use load_any function.

[1.1.1] - 2024-08-05

Added

  • Updated the way axons post-processing is handled during fascicle and nerve simulation:
    • These must now be defined as functions instead of external Python scripts.
    • For backward compatibility, some built-in postprocessing functions can be called using str (see builtin_postproc_functions).
    • The postproc_script attribute has been retained to set the postprocessing as either str or function regardless of the type.
    • The postproc function must at least take an axon_results as argument and return an axon_results, evantual key arguments can be added to the postproc_kwargs attribute.
  • Add block_summary method in axons_results which returns axon block characteristics: blocked, onset response, number of onset APs.
  • Add getAPspeed and get_avg_AP_speed methods in axons_results to measure AP propagation velocity. Should be used instead of speed (deprecated method)
  • Add is_blocked method in axons_results to detect AP propagation block. Should be used instead of block (deprecated method)
  • Add is_recruited method in axons_results to detect AP in an axon.
  • Add optional normalize bool parameter in get_recruited_axons, get_recruited_axons_greater_than, get_recruited_axons_lesser_than methods from fascicle_results
  • Action potential (AP) analysis methods added in axons_results (split_APs, count_APs, get_start_APs, detect_AP_collisions, etc). See usage in example 18
  • Several plot functions added in axons_results (raster_plot, colormap_plot and plot_x_t)
  • self.save_path from fascicle and nerve is passed to postprocessing_function/scripts if specified and used to save data from postprocessing_function/scripts.
  • Fascicles and Nerve return nerve_results and fascicle_results by default (self.return_parameters_only and self.save_results are false at init)
  • Updated tutorials and examples with newest features, removed use of deprecated methods/functions
  • Add NRV_examples.py and NRV_tutorials.py to run all examples/tutorials
  • Reorganized Example folder
  • reworked rasterize method of the axon_result class
  • deprecated functions of CL_postprocessing
  • Add the axon_block_threshold function in CL_simulations to evaluate block thresholds with arbitrary stimulation settings
  • deprecated block_threshold_point_source and block_threshold_from_axonfrom CL_simulations as they are replaced by the more generalized version axon_block_threshold.
  • Add the axon_AP_threshold function in CL_simulations to evaluate activation thresholds with arbitrary stimulation settings (see Example 16)
  • deprecated firing_threshold_point_source and firing_threshold_from_axonfrom CL_simulations as they are replaced by the more generalized version axon_AP_threshold.
  • Added CL simulation documentation.
  • Added the search_threshold_dispatcher function to parallelize the exploration to parameter effect on threshold + doc & example (see Example 17)
  • Doc gallery for examples. Examples have been relocated to docs/examples

Fixed

  • issues with mcore optimization
  • Fix duplicate node count in node_index of myelinated axons
  • fit_to_size parameter in fill_with_population is not considered if fascicle diameter is None
  • remove_outliers parameter in fill_with_population is not called if fascicle diameter is None

Removed

[1.1.0] - 2024-05-27

Added

  • Significant improvement in the documentation
  • first simulations for nerve EIT direct models -> not documented yet, technical tests pass, still under scientific tests and development
  • classes for results and more
  • modification of post-processing architecture
  • progress bar for parallel computing with process specific toolbars
  • decorator for single-core function definition

Fixed

  • issues with type hints on documentation generation
  • code troubles with DOLFINx v0.8.0 now resolved, versions below are not supported anymore
  • most of the parameters of fascicles (and nerve) can now also be set at the instantiation. (see doc)

[1.0.1] - 2024-01-26

Fixed

  • issue #38:
    • Now FEMSimulation results are saved in a folder ending in .bp which can also be opened in ParaView (-5.12.0 or higher).
    • DOLFINx v0.6.0 and v0.8.0 are now suported

[1.0.0] - 2024-01-12

[0.9.16] - 2023-12-12

Added

  • Automatic versioning for dev team
  • this tracking file

Fixed

  • automated releases,
  • automatic push on pypi