# opexebo
[](https://travis-ci.com/kavli-ntnu/opexebo)
[](https://codecov.io/gh/kavli-ntnu/opexebo)
[](https://opexebo.readthedocs.io/en/latest/?badge=latest)
This library provides various analysis tools written by and for the Moser group at the [Kavli Institute](https://www.ntnu.edu/kavli) in Trondheim.
The package contains a mixture of translations of the older MatLab based [Behavioural Neurology Toolbox](https://bitbucket.org/cnc-ntnu/bnt), and other functions written only in Python 3, as part of the transition towards providing open access to research code.
### Documentation
Specifications and documentation for `opexebo` are available on [Read the Docs](https://opexebo.readthedocs.io/en/latest/).
### Installation
Install with pip:
```
pip install opexebo
```
Opexebo has an optional dependency, `sep`, that is not installed by default. To be able to install it, you require a C++ compiler installed on your system. On Linux, `gcc` will do the job. On Windows, the the Microsoft Visual C++ Build Tools fulfil the same role (https://www.microsoft.com/en-us/download/details.aspx?id=48159). To force installation of all optional dependencies, append `[full]` to the install command, for example:
pip install opexebo[full]
### Tests
Tests are implemented with `pytest`. Ensure that the various development tools are installed via
```python
pip install -r dev-requirements.txt
```
And then run tests with `pytest .`
# History
## 0.7.0
* Update dependencies for more modern versions (particularly `numpy`, `scipy` and `pytest`)
* Switch supported Python versions for 3.8+
## 0.6.1
* Fix some docstrings that were not updated to reflect changes in 0.6.0
* Fix the default limit behaviour of `accumulate_spatial` for bin width specification.
## 0.6.0
* Rewrite `spatial_occupancy` and `rate_map` to remove the walk filter (signature breaking)
* The individual analysis functions should be single purpose, and the walk-filter breaks this rule.
* Ideally, the walk-filter should be applied to spikes/tracking data _first_, and the resulting data then used for further analysis.
* A dedicated function has been provided to replace this: `general.walk_filter`
* Rewrite `shuffle` to better handle edge cases (including 1-spike-only) (signature breaking)
* Added `general.walk_filter` to provide replace the specific filtering implemented in each of `spatial_occupancy` and `rate_map`
* Fix a bug where `accumulate_spatial` can't handle cases where a single spike is present
* Fix an error in the LFP power spectrum calculation with fft
* Removed support for providing 1D position data as a 2d array with length 1
* Caused frustrating circular issues in cases where only a single data point was provided.
* Fairly low value addition, so support removed.
## 0.5.5 (2021-06-01)
* Publish to PyPi
## 0.5.2 (2021-04-19)
* Support 1D data in spatial occupancy and ratemap
* Add Opexebo-specific errors
* Add automated testing prior to release
* Add `calculate_speed`
* Add `egocentric_occupancy`
* Fixed an edge case error in `accumulate_spatial`
## 0.4.3 (2020-02-19)
* Substantial cleanup to `accumulate_spatial`
- Function was mathematically correct but confusing, due to the difference between opexebo's standard of `(x, y)` and NumPy's standard of `(y, x)`
* Added `upsampling`
* Added `circular_mask`
* Mandatory keyword arguments have been made positional
* `peak_search` updated to handle issues with MaskedArrays containing negative values
* Dcumentation expanded, made Sphinx compatible, and published on ReadTheDocs
* Further work on BorderScore, still experimental though
- Functional for Rectangular arenas
- Circular arenas are still WIP, should not be relied upon yet.
## 0.4.2 (2020-02-05)
* Speedscore modified substantially
- Adaptive filtering added, allowing the user to specify an upper speed as a bandwidth
- Adaptive filtering adjusted to behave more sensibly in the case of small bin sizes
- Speeds are smoothed before correlating
* Spatial cross correlation added
* General `bin_number` to `bin_size` code refactored to make future development more consistent
* Assorted unit tests added, including run-once code removed for speed
* Fix errors associated with `>` where applied to MaskedArrays (which, unlike ndarrays, do not correctly obey the symbol)
## 0.4.0 (2019-12-10)
* Ratemaps updated to handle walk filter (signature now requires providing animal speeds)
* Angular occupancy coverage calculation corrected
* circular arenas now handled in Spatial Occupancy
* Population Vector Correlation added
## 0.3.5 (2019-11-18)
* Assorted bugfixes to HDtuning
* Gridscore to handle NaNs more gracefully
## 0.3.4 (2019-20-25)
* `sep` made an optional dependency
* Alternative, non `sep` based code uses `skimage`
* Attempting to use `sep` if not installed with raise an error
## 0.3.2 (2019-09-20)
* Consistent calculating of bin numbers when histogramming
## 0.3.0 (2019-08-27)
* Third development release
* Improve NaN handling throughout by moving to MaskedArrays
* Fix Angular handling to function in seconds instead of frames
* Remove matplotlib from requirements
## 0.2.0
* Second development release
- Implementation of time-map -> rate-map -> (acorr, gridness score)
- Implementation of rate-map stats, grid stats
- Implementation of angular-map -> tuning-curve -> head direction score, stats.
- Non-production-ready implementation of border-score, speed-score.
## 0.1.0 (2018-08-30)
* First development release
- Implementation of gridness score, autocorrelogram, place-field detection
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