Releases: RatInABox-Lab/RatInABox
v1.14.1
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 therectified_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
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 toAgent.history
except for two things (same forNeurons
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 usingself.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 theAgent
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
tokwargs
to clean up the doctoring and some (previously fixed) constants have been exposed as via lettingkwargs
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 akwarg
) to set a differentAgent
from which you draw position data from. In case, say, you want to plot the spikes fromNeurons1
against the positions ofAgent2
.
New Contributors
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