v1.14.1

Minor interpolation bug fix as pointed out by #114. Also changed save_to_history() from using list(array) to array.tolist()

v1.14.0

numpy-2.0.0 compatibility

No substantial changes, I just fixed a few bugs to make compatible with numpy>=2.0.0

v1.13.0

Grids cell

• Grid cells work in 1D
• Grid cells have a width_ratio parameter which sets the ration of the width of the receptive field to the grid scale. It mist be between 0 (very sharp grid fields) and 1 (very diffuse grid fields) and only works for the rectified_cosines models.

• Minor api change (warning thrown, will not break) three_shifted_cosines --> shifted_cosines
• Default grid cells have been changed to 30 grid cells in three increasingly slightly rotated modules.

• Grid cell documentation on the readme has been improved

Plotting:

• Plotting the rate map of a single neuron in 1D can now be optimised using optimise_plot_for_single_neuron (without this it just does a mountain plot with a single line, which isn't ideal.

numpy pinned to versions <2.0.0

This will be unpinned as a soon as important associated packages (matplotlib, scipy etc.) support 2.0.0.

v1.12.6

BVC scaling bug fix

Thanks @colleenjg for minor bug fix relating to BVC firing rate scaling (see PR #109 and issue #108)

v1.12.5

Teeny tiny bug fixes....

Full Changelog: v1.12.3...v1.12.5

v1.12.3

Bug fix to maintain compatibility with python<=3.8.

We had been using list[str] (works in python>=3.9 only) and so have reverted back to from typing import List then List[str]. This fixes issue #105

v1.12.2

Bug fixes and very minor changes from 1.12.1

v1.12.1

Faster animations and bug fixes

• New Agent._history_arrays dataframe. This is identical to Agent.history except for two things (same for Neurons too):
  • It is dictionary of arrays, not lists.
  • It should only be accessed via its getter-function _history_arrays = self.get_history_arrays()
    For now this API is intended to be mostly internal. We don't recommend users use this and instead should stuck to using self.history as before. But it speeds up animation internally a lot because it checks a cache to see if the list-->array conversion has been done recently and only repeats it if it hasn't.
• Plotting rate maps via the history method now shows the regions where the Agent never went as grey rather than black (i.e. zero firing rate). This is more realistic, shows the data more honestly and closer to how experimentalists do it (i.e. by shooting spikes and dividing by position occupancy).
  • Additionally users can specify the discretisation of the rate mat smoothing

PlaceCells.plot_rate_map(method="history", bin_size=0.06) #defaults of 0.04, i.e. 4 cm

• Bug fixes relating to #104 and some other minor stuff I hadn't spotted in 1.12.

Full Changelog: 1.12.0...v1.12.1

v1.12.0

Main charges include:

• Significantly modularised Agent.update() function. It is now more readable. This should be fully backwards compatible for conventional users of RiaB. For power users a few internal variables were renamed e.g. save_velocity-->measured_velocity but really very few. It also accepts (but doesn't recommend) users just forcing the next position of the Agent via

Agent.update(forced_next_position = <next_pos>)

This should be fully backwards compatible for conventional users of RiaB. For power users a few internal variables were renamed e.g. save_velocity-->measured_velocity but really very few.

• Small bug fixes for @colleenjg to do with warning when params['n']` is incompatible with the specific class.
• Bug fix from @gsivori to make position sampling acknowledge and account for the existence of holes in the Environment more naturally than was done before.
• Minor changes to some plotting functions. More params have been moved from args to kwargs to clean up the doctoring and some (previously fixed) constants have been exposed as via letting kwargs define them. This both simplifies and improves plotting.

What's Changed

• Position sampling in Environments with holes. by @gsivori in #100
• Small fixes and new warning for Neurons classes. by @colleenjg in #101
• Fixes spurious warning raised when initializing VectorCells objects. by @colleenjg in #103
• For spike rasters, or rate maps plotted via the 'history' method there is a hidden option (via a kwarg) to set a different Agent from which you draw position data from. In case, say, you want to plot the spikes from Neurons1 against the positions of Agent2.

New Contributors

• @gsivori made their first contribution in #100

Full Changelog: v1.11.4...v1.12.0

v1.11.4

1D Objects (thanks @colleenjg) and minor bug fix for place cell distributions relating to #96