Changelog

Version 3.1.5

  • Fix outer value lookup with vector data (#19)

  • Fix compatibility with groupby from pandas 2.0

Version 3.1.4

  • switch hemisphere constants to be in line with Allen Institute

Version 3.1.3

  • Add a RegionMap conversion to Pandas DataFrame (#6)

  • Add a function to compute the spatial intersection of a line-segment with a VoxelData object (#11)

Version 3.1.1

  • Add documentation for ROI Mask, Orientation and scalar file formats

  • CellCollection::save_sonata allows for a mode; output file can be appended to, or overwritten.

  • CellCollection can now read multiple SONATA popluations.

Version 3.1.0

  • Add str/repr to CellCollection.

  • CellCollection.save_sonata learned how to force_library so that the user can control the behavior of @library creation.

  • Use Rotation.from_euler from scipy in angles_to_matrices (fix rotation around x and z axis).

  • Add values_to_region_attribute and values_to_hemisphere to convert values returned by VoxelData.lookup().

Version 3.0.2

  • Set the dtype of the default zero offset of VoxelData to np.float32 (consistent with the other assignments)

  • Use pytest for tests instead of nosetests

  • Cleanup deprecation warnings emitted by numpy/pandas

Version 3.0.1

Improvements

  • Use sphinx-bluebrain-theme for documentation

  • Add missing API to documentation

Version 3.0.0

Python 2 compatibility

  • Dropped Python 2 support

Bug Fixes

  • Fixed issue with H5PY >= 3.0.0 string type behavior. Changes in H5py >= 3.0.0 API affected the reading of h5 files by returning string fields as bytes fields. The recommended use of the method Dataset.asstr() to return string field is implemented in this version.

Removed modules

  • Removed deprecated module voxcell.positions

  • Removed deprecated module voxcell.build

  • Removed deprecated module voxcell.core

  • Removed deprecated module voxcell.voxell_data

  • Removed deprecated function voxcell.vector_field.generate_homogeneous_field:

  • Removed deprecated function voxcell.vector_field.calculate_fields_by_distance_from:

  • Removed deprecated function voxcell.vector_field.calculate_fields_by_distance_to:

  • Removed deprecated function voxcell.vector_field.calculate_fields_by_distance_between:

  • Removed deprecated function voxcell.vector_field.compute_cylindrical_tangent_vectors:

  • Removed deprecated function voxcell.vector_field.compute_hemispheric_spherical_tangent_fields:

Version 2.7.4

Improvements

  • Remove the NodePopulation implementation and hard deprecate the class. Deprecate the node_population.py module itself.

Version 2.7.3

New Features

  • Add a function to retrieve the region ids of layers in a brain region

Version 2.7.2

Bug Fixes

  • Force the version of h5py to h5py<3.0.0. h5py==3.0.0 dropped the python2 support and changed the string behaviors.

Version 2.7.1

  • Set the nrrd header field kinds with the value [‘vector’, ‘domain’, ‘domain’, domain’] when saving an nrrd file which holds a non-scalar vector field over a volume. This change enables visualization of direction vectors (3D vector field) and orientations (quaternions, 4D) with ITK-SNAP and 3D Slicer.

  • Changed processing of properties of CellCollection that are pandas.Categorical. A special rule for string properties is applied. If unique values of a property make less than half of its all values then it is loaded as pandas.Categorical.

  • Deprecated the Hierarchy class in profit of the RegionMap. The Hierarchy class should be removed in 2.8.0. Redo the docs for the RegionMap object.

  • Changed saving of CellCollection. Raise an error if there is a None or np.NaN in CellCollection.

  • Fixed the orientation loading for sonata files in CellCollection. Two different formats exist : the euler’s angles and the quaternions.

    • use quaternions if all “orientation_[x|y|z]” are present

    • if some of the “orientation_[x|y|z]” fields are here but not all. Raise.

    • if orientations and rotation_angles are present use quaternions

    • if no quaternions and some of the rotation_angles use the eulers angles and assign 0 to the missing ones.

  • Added a orientation_format property to the CellCollection class. This allows the user to choose which sonata orientation format she/he wants to use.

  • Added a size function to CellCollection.

  • Check the sizes of the orientations/positions/properties before saving.

Version 2.7.0

  • Introduce serialization of CellCollection to SONATA format. It is the preferred choice. MVD3 can be saved/loaded only when the direct file extension .mvd3 is used.