Navis

_Date: 23/11/20_

Additions
- new module: `models` for modelling networks and neurons
- new functions `navis.resample_along_axis`, `navis.insert_nodes`, `navis.remove_nodes`
- full rework of `navis.Dotprops`:
- make them a subclass of BaseNeuron
- implement `nat:dotprops` in `navis.make_dotprops`
- added `navis.read_nrrd` and `navis.write_nrrd`
- side-effect: renamed `navis.from_swc` :octicons-arrow-right-24: `read_swc` and `navis.to_swc` :octicons-arrow-right-24: `write_swc`
- improved conversion between nat and {{ navis }} `Dotprops`
- full rework of topology-related functions:
- `navis.strahler_index`, `navis.segregation_index`, `navis.bending_flow`, `navis.synapse_flow_centrality` and `navis.split_axon_dendrite` now work better, faster and more accurately. See their docs for details.
- new function: `navis.arbor_segregation_index`
- new `color_by` and `shade_by` parameters for `plot3d` and `plot2d` that lets you color/shade a
neuron by custom properties (e.g. by Strahler index or compartment)

Improvements
- neurons are now more memory efficient:
- pandas "categoricals" are used for connector and node "type" and "label" columns
- add a `.memory_usage` method analogous to that of `pandas.DataFrames`
- `navis.NeuronList` can now be pickled!
- made `navis.Viewer` faster
- `navis.prune_twigs` can now (optionally) prune by `exactly` the desired length
- improved `navis.NeuronList.apply`

Fixes
- small bugfixes and improvements

**Full Changelog**: [v0.3.2...v0.3.3](https://github.com/navis-org/navis/compare/v0.3.2...v0.3.3)

_Date: 18/10/20_

Improvements
- `navis.plot2d` and `navis.plot3d` now accept `trimesh.Trimesh` directly
- `navis.in_volume` now works with any mesh-like object, not just `navis.Volumes`

Fixes
- lots of small bugfixes and improvements

**Full Changelog**: [v0.3.1...v0.3.2](https://github.com/navis-org/navis/compare/v0.3.1...v0.3.2)

_Date: 07/10/20_

Additions
- new function `navis.rewire_skeleton`

Improvements
- `navis.heal_skeleton` and `navis.stitch_skeletons` are now much much faster
- `navis.reroot_skeleton` can now reroot to multiple roots in one go
- `navis.plot3d` now accepts a `soma` argument
- improved caching for neurons
- improved multiplication/division of neurons
- faster `r.nblast` and `r.nblast_allbyall`
- `r.xform_brain` now also adjusts the soma radius
- `neuprint.fetch_skeletons` now returns correct soma radius

Fixes
- lots of small bugfixes

**Full Changelog**: [v0.3.0...v0.3.1](https://github.com/navis-org/navis/compare/v0.3.0...v0.3.1)

_Date: 06/10/20_

Additions
- Started module to manipulate mesh data (see e.g. `navis.simplify_mesh`)

Improvements
- Improved interfaces with R NBLAST and `xform_brain`
- Improved attribute caching for neurons

**Full Changelog**: [v0.2.3...v0.3.0](https://github.com/navis-org/navis/compare/v0.2.3...v0.3.0)

_Date: 06/09/20_

Additions
- New Neuron property `.label` that if present will be used for plot legends
- New function for R interface: `navis.interfaces.r.load_rda`

Improvements
- Blender interface: improved scatter plot generation

_Date: 15/08/20_

Additions
- New `plot3d` parameter: with plotly backend, use `fig` to add data to existing plotly figure
- New `plot3d` parameter: with vispy backend, use `center=False` to not re-center camera on adding new data
- New `r.mirror_brain` parameter: use e.g. `via='FCWB'` if source space does not have mirror transform
- New `NeuronList` method: `append()` works like `list.append()`
- First implementation of smarter (re-)calculation of temporary Neuron properties using `.is_stale` property
- Neurons can now be multiplied/divided by array/list of x/y/z coordinates for non-isometric transforms

Fixes
- Fix issues with newer rpy2 versions
- Various improvements and bug fixes