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update changelog
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mgeplf committed May 17, 2024
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30 changes: 30 additions & 0 deletions CHANGELOG.rst
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Changelog
=========

Version 0.2.6
-------------
* Updating regression requirements, teach
`atlas-densities cell-densities fit-average-densities` to have `--min-data-points` (#81)

Version 0.2.5
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* Fix nans in compute_region_volumes (#80)

Version 0.2.4
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* Add r_square values to the results of the fitting. (#68)
* Add check to the region filter in case the input dataset is all equal to 0 for the region of interest. (#74)
* Fix fitting and optimization steps (#75)
* Faster _compute_region_cell_counts (#72)
* Cleanup app tests (#78)
* Faster compute average intensities (#73)
* Speedup mtype density creation from probability maps using voxcell's ValueToIndexVoxels (#79)

Version 0.2.3
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* remove pkg_resources, use importlib (#62)
* Drop literature values from regions that are not in hierarchy or not in the annotation volume (#61)

Version 0.2.2
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* add ``atlas-densities combination manipulate``

Version 0.2.1
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* The following *cell-density* sub-commands can now optionally take a ``--group-ids-config-path``:
*cell-density*, *glia-cell-densities*, *inhibitory-and-excitatory-neuron-densities*, *fit-average-densities*

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1 change: 1 addition & 0 deletions README.rst
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Expand Up @@ -286,6 +286,7 @@ respective standard deviation and `coefficient of determination`_ (`r_square`).
--fitted-densities-output-path=data/ccfv2/first_estimates/first_estimates.csv \
--fitting-maps-output-path=data/ccfv2/first_estimates/fitting.json
Note: One can use the ``--min-data-points`` to require a minimum of points for the linear regression; the default is 1.

Compute inhibitory/excitatory neuron densities
----------------------------------------------
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1 change: 0 additions & 1 deletion atlas_densities/densities/fitting.py
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Expand Up @@ -396,7 +396,6 @@ def linear_fitting_xy(
Raises:
AtlasDensitiesError if some of the `sigma`values are negative.
"""

if len(xdata) < min_data_points:
return {"coefficient": np.nan, "standard_deviation": np.nan, "r_square": np.nan}

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