CHANGELOG.rst

Changelog

Version 4.0.0

• Morphology class accepts only morphio objects, not files anymore. (#1120)
• Replace iter_* methods by properties in core objects and improve iter_segments. (#1054)
• NeuriteType extended to allow mixed type declarations as tuple of ints. (#1071)
• All features return built-in types (#1064)
• Morphology class also allows mutable morphio objects to be passed explicitly. (#1049)
• Morphology class uses morphio immutable class by composition, istead of inheritance. (#979)
• Morphology level radial distance features use the soma as reference point. (#1030)
• Make neurom.core.Population resolve paths. Symlinks are not resolved. (#1047)
• Mixed subtree processing can be used in morph_stats app via the use_subtrees flag. (#1034)
• neurom.view.[plot_tree|plot_tree3d|plot_soma|plot_soma3D] were hidden from the neurom.view module. They can still be imported from neurom.view.matplotlib_impl. (#1032)
• Mixed subtree processing. (#981)
• Deprecated modules and classes were removed. (#1026)

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. :ref:`migration-v3.0.0`.

  • 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 :ref:`migration-v3.0.0`.
  • Name consistency among private variables.
  • Delete deprecated neurom.features.register_neurite_feature.

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

  • New config format. See :ref:`morph-stats-new-config`. 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 :ref:`doc page<validation>` about it.
• Remove the cli command neurom features that listed all possible features. Instead a proper documentation is provided on that topic. See :func:`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 :class:`Population<neurom.core.population.Population>` and load_neurons<neurom.io.utils.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 :ref:`page<migration-v2>` for it.