Navis

_Date: 11/11/21_

Breaking
- `navis.MeshNeuron`: `__getattr__` does not search `trimesh` representation anymore
- NBLASTs: queries/targets now MUST be `navis.Dotprops` (no more automatic conversion, use `navis.make_dotprops`)
- Renamed functions to make it clear they work only on `TreeNeurons`:
- `smooth_neuron` :octicons-arrow-right-24: `navis.smooth_skeleton`
- `reroot_neuron` :octicons-arrow-right-24: `navis.reroot_skeleton`
- `rewire_neuron` :octicons-arrow-right-24: `navis.rewire_skeleton`
- `despike_neuron` :octicons-arrow-right-24: `navis.despike_skeleton`
- `average_neurons` :octicons-arrow-right-24: `navis.average_skeletons`
- `heal_fragmented_neuron` :octicons-arrow-right-24: `navis.heal_skeleton`
- `stitch_neurons` :octicons-arrow-right-24: `navis.stitch_skeletons`
- `cut_neuron` :octicons-arrow-right-24: `navis.cut_skeleton`
- Removals and other renamings:
- `navis.clustering` module was removed and with it `navis.cluster_xyz` and `ClustResult` class
- renamed `cluster_by_synapse_placement` :octicons-arrow-right-24: `navis.synapse_similarity`
- renamed `cluster_by_connectivity` :octicons-arrow-right-24: `navis.connectivity_similarity`
- renamed `sparseness` :octicons-arrow-right-24: `navis.connectivity_sparseness`
- renamed `navis.write_google_binary` :octicons-arrow-right-24: `navis.write_precomputed`
- `navis.geodesic_matrix` renamed parameter `tn_ids` :octicons-arrow-right-24: `from_`

Additions & Improvements
- `navis.NeuronList.apply()` now allows omitting failures
- `navis.VoxelNeuron`:
- new class representing neurons as voxels
- new (experimental) class representing neurons as voxels
- `navis.read_nrrd` now returns `VoxelNeuron` instead of `Dotprops` by default
- currently works with only a selection of functions
- `navis.TreeNeuron`:
- can now be initialized directly with `skeletor.Skeleton`
- new method: `navis.TreeNeuron.snap`
- `navis.MeshNeuron`:
- `navis.in_volume`, `navis.subset_neuron` and `navis.break_fragments` now work on `MeshNeurons`
- new properties: `.skeleton`, `.graph` and `.igraph`
- new methods: `navis.MeshNeuron.skeletonize` and `navis.MeshNeuron.snap`
- can now be initialized with `skeletor.Skeleton` and `(vertices, faces)` tuple
- plotting: `color_by` parameter now works with `MeshNeurons`
- `navis.Dotprops`:
- new property: `.sampling_resolution` (used e.g. for scaling vectors for plotting)
- new method: `navis.Dotprops.snap`
- Experimental support for non-isometric `.units` for neurons
- NBLASTs:
- new parameter `limit_dist` allows speeding up NBLASTs with minor precision loss
- new experimental parameter `batch_size` to NBLAST neurons in batches
- overall faster initialization with large lists of neurons
- SWC I/O (`navis.read_swc` & `navis.write_swc`):
- by default we will now deposit neuron meta data (name, id, units) in the SWC header (see `write_meta` parameter)
- meta data in SWC header can also be read back (see `read_meta` parameter)
- filenames can now be parsed into specific neuron properties (see `fmt` parameter)
- node IDs now start with 0 instead of 1 when writing SWC files
- I/O to/from Google neuroglancer's precomputed format:
- total rework of this module
- renamed `navis.write_google_binary` :octicons-arrow-right-24: `navis.write_precomputed`
- new function: `navis.read_precomputed`
- Plotting:
- new function `navis.plot_flat` plots neurons as dendrograms
- `navis.plot3d` with plotly backend now returns a plotly `Figure` instead of a figure dictionary
- new [k3d](https://k3d-jupyter.org) backend for plotting in Jupyter environments: try `navis.plot3d(x, backend='k3d')`
- new parameter for `navis.plot2d` and `navis.plot3d`: use `clusters=[0, 0, 0, 1, 1, ...]` to assigns clusters and have them automatically coloured accordingly
- `navis.plot2d` now allows `radius=True` parameter
- Transforms:
- support for elastix (`navis.transforms.ElastixTransform`)
- whether transforms are invertible is now determined by existence of `__neg__` method
- Most functions that work with `TreeNeurons` now also work with `MeshNeurons`
- New high-level wrappers to convert neurons: `navis.voxelize`, `navis.mesh` and `navis.skeletonize`
- `navis.make_dotprops` now accepts `parallel=True` parameter for parallel processing
- `navis.smooth_skeleton` can now be used to smooth arbitrary numeric columns in the node table
- New function `navis.drop_fluff` removes small disconnected bits and pieces from neurons
- New function `navis.patch_cloudvolume` monkey-patches `cloudvolume` (see the new tutorial)
- New function `navis.write_nrrd` writes `VoxelNeurons` to NRRD files
- New functions to read/write `MeshNeurons`: `navis.read_mesh` and `navis.write_mesh`
- New function `navis.read_nmx` reads pyKNOSSOS files
- New function `navis.smooth_mesh` smoothes meshes and `MeshNeurons`
- Improved/updated the InsectBrain DB interface (see the tutorial)
- Under-the-hood fixes and improvements to: `navis.plot2d`, `navis.split_axon_dendrite`, `navis.tortuosity`, `navis.resample_skeleton`, `navis.mirror_brain`
- First pass at a `NEURON` interface (see the new tutorial)
- First pass at interface with the Allen's MICrONS datasets (see the new tutorial)
- `NAVIS_SKIP_LOG_SETUP` environment variable prevents default log setup for library use
- Improved `navis.cable_overlap`

Fixes
- Under-the-hood fixes and improvements

**Full Changelog**: [v0.6.0...v1.0.0](https://github.com/navis-org/navis/compare/v0.6.0...v1.0.0)

_Date: 12/05/21_

Additions
- new functions: `navis.prune_at_depth`, `navis.read_rda`, `navis.cell_body_fiber`
- new functions to map units into neuron space: `BaseNeuron.map_units` and `navis.to_neuron_space`

Improvements
- many spatial parameters (e.g. in `navis.resample_skeleton`) can now be passed as unit string, e.g. `"5 microns"`
- many functions now accept a `parallel=True` parameter to use multiple cores (depends on `pathos`)
- `navis.read_swc` and `navis.write_swc` can now read/write directly from/to zip files
- reworked `navis.read_json`, and `navis.write_json`
- `nblast` functions now let you use your own scoring function (thanks to Ben Pedigo!)
- added `threshold` parameter to `navis.read_nrrd`
- `navis.nblast_smart`: drop `quantile` and add `score` criterion
- functions that manipulate neurons will now always return something (even if `inplace=True`)
- `navis.cut_skeleton` now always returns a single `NeuronList`
- `navis.mirror_brain` now works with `k=0/None` Dotprops
- all `reroot_to_soma` parameters have been renamed to `reroot_soma`
- `navis.TreeNeuron` now has a `soma_pos` property that can also be used to set the soma by position
- made transforms more robust against points outside deformation fields
- better deal if node ID of soma is `0` (e.g. during plotting)
- `navis.neuron2tangents` now drops zero-length vectors

Fixes
- fixed `navis.guess_radius`
- fixed NBLAST progress bars in notebook environments
- fixed a couple bugs with `CMTK` transforms

**Full Changelog**: [v0.5.3...v0.6.0](https://github.com/navis-org/navis/compare/v0.5.3...v0.6.0)

_Date: 10/04/21_

Additions
- new functions: `navis.nblast_smart`, `navis.synblast`, `navis.symmetrize_brain`
- `navis.plot2d`: `rasterize=True` will rasterize neurons (but not axes or labels) to help keep file sizes low
- `navis.plot3d` (plotly): `hover_name=True` will show neuron names on hover

Improvements
- `navis.simplify_mesh` now supports 3 backends: Blender3D, `open3d` or `pymeshlab`
- `navis.make_dotprops` can now produce `Dotprops` purely from skeleton edges (set `k=None`)
- reworked `navis.write_swc` (faster, easier to work with)
- a new type of landmark-based transform: moving least square transforms (thanks to Chris Barnes)
- vispy `navis.Viewer`: press B to show a bounding box
- moved tests from Travis to Github Actions (this now also includes testing tutorial notebooks)

Fixes
- a great many small and big bug fixes

**Full Changelog**: [v0.5.2...v0.5.3](https://github.com/navis-org/navis/compare/v0.5.2...v0.5.3)

_Date: 02/02/21_

Additions
- new functions: `navis.xform`, `navis.write_precomputed`

Improvements
- `navis.downsample_neuron` now also works on `Dotprops`
- Neurons: connectors are now included in bounding box calculations
- NeuronLists: added progress bar for division / multiplication

**Full Changelog**: [v0.5.1...v0.5.2](https://github.com/navis-org/navis/compare/v0.5.1...v0.5.2)

_Date: 10/01/21_

Fixes
- Various under-the-hood improvements and bugfixes

**Full Changelog**: [v0.5.0...v0.5.1](https://github.com/navis-org/navis/compare/v0.5.0...v0.5.1)

_Date: 05/01/21_

Additions
- new functions for transforming spatial data (locations, neurons, etc) between brain spaces:
- `navis.xform_brain` transforms data from one space to another
- `navis.mirror_brain` mirrors data about given axis
- see the new tutorials for explanations
- low-level interfaces to work with affine, H5-, CMTK- and thin plate spline transforms

Improvements
- de-cluttered top level namespace: some more obscure functions are now only available through modules

**Full Changelog**: [v0.4.3...v0.5.0](https://github.com/navis-org/navis/compare/v0.4.3...v0.5.0)