Changelog

Version 3.2.3

  • Fix neurom.app.morph_stats.extract_dataframe for Population objects with several workers (#1080)

  • Update readthedocs config (#1077)

  • Can pass List[Population] args to neurom.app.morph_stats.extract_dataframe (#1076)

  • Fix compatibility with MorphIO>=3.3.6 (#1075)

  • Check that soma is not empty when features need it (#1073)

Version 3.2.2

  • Fix QhullError warning (#1063)

Version 3.2.1

  • Fix: extract_stats could not work on single neurite (#1060)

  • Fix view cli to use ‘equal’ axis when available (#1051)

  • Remove single point contour somas in h5 and asc tests (#1045)

  • Remove duplicated deps jinja, sphinx (#1043)

Version 3.2.0

  • Add neurom.features.morphology.length_fraction_above_soma feature.

  • List of multiple kwargs configurations are now allowed in``neurom.apps.morph_stats``.

  • neurom.features.neurite.principal_direction_extents directions correspond to extents ordered in a descending order.

  • Add features neurom.features.morphology.(aspect_ration, circularity, shape_factor)`

  • Fix neurom.morphmath.principal_direction_extent to calculate correctly the pca extent.

  • Fix neurom.features.neurite.segment_taper_rates to return signed taper rates.

  • Fix warning system so that it doesn’t change the pre-existing warnings configuration

  • Fix neurom.features.bifurcation.partition_asymmetry Uylings variant to not throw for bifurcations with leaves.

  • Fix neurom.features.neurite.principal_direction_extents to remove duplicate points when calculated.

  • Add neurom.features.morphology.volume_density feature so that it is calculated correctly when the entire morphology is taken into account instead of summing the per neurite volume densities.

  • Add support for py39 and py310 testing.

  • Fix neurom.features.morphology.sholl_frequency to return an empty list when a neurite_type that is not present in the morphology is specified.

  • Fix neurom.features.morphology.trunk_origin_radii to warn and use only the root section for the calculation of the path distances. Edge cases from the combination of min_length_filter and max_length_filter are addressed.

  • Fix neurom.features.morphology.sholl_frequency to use soma center in distance calculation, instead of using the origin.

  • Add neurom.features.morphology.trunk_angles_inter_types and neurom.features.morphology.trunk_angles_from_vector features, make neurom.features.morphology.trunk_angles more generic and add length filter to neurom.features.morphology.trunk_origin_radii.

  • Deprecate python3.6

  • Add doc on spherical coordinates.

Version 3.1.0

  • Add morphology features total_width, total_height and total_depth

Version 3.0.2

  • Fix ‘raw’ mode in neurom stats.

  • Add example astrocyte analysis notebook.

  • Fix readthedocs documentation build.

  • Delete all requirements txt files and update documentation accordingly.

  • Adding back unifurcation check

Version 3.0.1

  • Add method to Soma class to check wether it overlaps a point or not.

  • Ensure neurom.morphmath.angle_between_vectors always return 0 when the vectors are equal.

Version 3.0.0

  • Rename all ‘neuron’ names to ‘morphology’ names, including module and package names. Previous ‘neuron’ names still exist but deprecated. It is recommended to use new names:

    • neurom.check.neuron_checks => neurom.check.morphology_checks, replace neuron_checks with morphology_checks in configs for neurom check.

    • neurom.core.neuron => neurom.core.morphology

    • neurom.core.neuron.Neuron => neurom.core.morphology.Morphology

    • neurom.core.neuron.graft_neuron => neurom.core.morphology.graft_morphology

    • neurom.io.utils.load_neuron => neurom.io.utils.load_morphology

    • neurom.io.utils.load_neurons => neurom.io.utils.load_morphologies

    • neurom.core.Population.neurons => neurom.core.Population.morphologies

  • Refactor plotting functionality. Migration to v3 version.

    • deprecate neurom.view.viewer

    • rename neurom.view.view to neurom.view.matplotlib_impl

    • rename neurom.view.plotly to neurom.view.plotly_impl

    • rename neurom.view.common to neurom.view.matplotlib_utils

    • swap arguments ax and nrn of all plot functions in neurom.view.matplotlib_impl, also nrn arg is renamed to morph.

    • delete neurom.view.plotly.draw. Use instead neurom.view.plotly_impl.plot_morph and neurom.view.plotly_impl.plot_morph3d.

  • Refactor features.
    • Drop ‘func’ suffix of all module names within features package:

      • neurom.features.bifurcationfunc => neurom.features.bifurcation

      • neurom.features.sectionfunc => neurom.features.section

      • neurom.features.neuritefunc => neurom.features.neurite

      • neurom.features.neuronfunc => neurom.features.morphology

    • Rigid classification of features. neurite features must accept only a single neurite. morphology features must accept only a single morphology. population features must accept only a collection of neurons or a neuron population.

    • Some features were deleted, renamed, added. See Migration to v3 version.

    • Name consistency among private variables.

    • Delete deprecated neurom.features.register_neurite_feature.

  • Refactor morphology statistics, e.g. neurom stats command.

    • New config format. See Kwargs format (starting version 3.0.0). The old format is still supported. The only necessary change is replace ‘total’ with ‘sum’, ‘neuron’ with ‘morphology’.

    • Keep feature names as is. Don’t trim ‘s’ at the end of plurals.

  • Delete neurom.check.structural_checks, neurom.core.tree that were deprecated in v2.

  • Delete unused neurom.utils.memoize

Version 2.3.1

  • fix features.neuronfunc._neuron_population for ‘sholl_frequency’ feature over a neuron population.

  • use a tuple for subplot default value in view.common.get_figure.

Version 2.3.0

  • Introduce a new method to calculate partition asymmetry by Uylings. See docstring of neurom.features.neuritefunc.partition_asymmetries().

  • Follow the same morphology validation rules as in MorphIO. See the doc page about it.

  • Remove the cli command neurom features that listed all possible features. Instead a proper documentation is provided on that topic. See neurom.features.get().

  • Make neurom.features.neuronfunc.sholl_crossings private.

  • Remove NeuriteType.all from NEURITES

Version 2.2.1

  • Fix ‘section_path_lengths’ feature for Population

Version 2.2.0

  • Don’t force loading of neurons into memory for Population (#922). See new API of Population and load_neurons

  • Move total_length feature to from neuritefunc to neuronfunc. Use neurite_lengths feature for neurites

  • Include morphology filename extension into Neuron’s name

  • Extend tree_type_checker to accept a single tuple as an argument. Additionally validate function’s arguments (#912, #914)

  • Optimize Sholl analysis code (#905, #919)

Version 2.1.2

  • Allow for morphologies without soma (#900)

Version 2.1.1

  • Drop relative imports (keep backward compatibility) (#898)

  • Account for all custom neurite types in NeuriteType (#902)

  • Remove excessive pylint disables (#903)

Version 2.0.2

See a separate dedicated page for it.