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docs: fix some formatting issues in changelog
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@schlegelp
schlegelp committed Oct 17, 2024
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Expand Up @@ -31,20 +31,20 @@ and various other quality of life improvements.
when visualizing large numbers of skeletons while using the defaults

##### Additions
- New interface to the [H01](https://h01-release.storage.googleapis.com/landing.html) dataset by Jinhan Choi and Jakob Troidl (Lichtman lab); see the new tutorial for details
- New interface to the [H01](https://h01-release.storage.googleapis.com/landing.html) dataset by Jinhan Choi and Jakob Troidl; see the new tutorial for details

##### Improvements
- I/O:
- [`read_nrrd`][navis.read_nrrd], [`read_tiff`][navis.read_tiff] and [`read_mesh`][navis.read_mesh] now use the same backend as e.g. [`read_swc`][navis.read_swc] which enables some niceties such as reading directly from URLs and archives, parallel processing, etc
- all `read_*` functions now have an `error` parameter that can be used to skip errors
- [`read_nrrd`][navis.read_nrrd], [`read_tiff`][navis.read_tiff] and [`read_mesh`][navis.read_mesh] now use the same backend as e.g. [`read_swc`][navis.read_swc] which enables some niceties such as reading directly from URLs and archives, parallel processing, etc
- all `read_*` functions now have an `error` parameter that can be used to skip errors
- Image data:
- new function: [`navis.thin_voxels`][] can be used to thin images and `VoxelNeurons` to single-pixel width (see also below)
- new `thin` parameter for [`read_nrrd`][navis.read_nrrd], [`read_tiff`][navis.read_tiff]
- new function: [`navis.thin_voxels`][] can be used to thin images and `VoxelNeurons` to single-pixel width (see also below)
- new `thin` parameter for [`read_nrrd`][navis.read_nrrd], [`read_tiff`][navis.read_tiff]
- [`TreeNeurons`][navis.TreeNeuron]:
- skeletons can now be initialized from a `(vertices, edges)` tuple (see also [`navis.edges2neuron`])
- new property: `TreeNeuron.vertices` gives read-only to node (vertex) coordinates
- skeletons can now be initialized from a `(vertices, edges)` tuple - see also [`navis.edges2neuron`][]
- new property: `TreeNeuron.vertices` gives read-only to node (vertex) coordinates
- [`VoxelNeurons`][navis.VoxelNeuron]:
- New properties: `VoxelNeuron.nnz` and `VoxelNeuron.density`
- ew properties: `VoxelNeuron.nnz` and `VoxelNeuron.density`
- [`navis.drop_fluff`][] and [`navis.neuron2nx`][] now also works with [`Dotprops`][navis.Dotprops]

**Full Changelog**: [v1.8.0...v1.9.0](https://github.com/navis-org/navis/compare/v1.8.0...v1.9.0)
Expand Down Expand Up @@ -79,25 +79,25 @@ more consistent and easier to use.

##### Improvements
- Plotting:
- [`navis.plot3d`][]:
- `legendgroup` parameter (plotly backend) now also sets the legend group's title
- new parameters for the plotly backend:
- `legend` (default `True`): determines whether legends is shown
- `legend_orientation` (default `v`): determines whether legend is aranged vertically (`v`) or horizontally (`h`)
- `linestyle` (default `-`): determines line style for skeletons
- default for `radius` is now `"auto"`
- [`navis.plot2d`][]:
- the `view` parameter now also works with `methods` `3d` and `3d_complex`
- the `color_by` and `shade_by` parameters now also work when plotting skeletons with `radius=True`
- new defaults: `radius="auto"`, `alpha=1`, `figsize=None` (use matplotlib defaults)
- new parameters for methods `3d` and `3d_complex`: `mesh_shade=False` and `non_view_axes3d`
- the `scalebar` and `soma` parameters can now also be dictionaries to style (color, width, etc) the scalebar/soma
- the `connectors` parameter can now be used to show specific connector types (e.g. `connectors="pre"`)
- [`navis.plot3d`][]:
- `legendgroup` parameter (plotly backend) now also sets the legend group's title
- new parameters for the plotly backend:
- `legend` (default `True`): determines whether legends is shown
- `legend_orientation` (default `v`): determines whether legend is aranged vertically (`v`) or horizontally (`h`)
- `linestyle` (default `-`): determines line style for skeletons
- default for `radius` is now `"auto"`
- [`navis.plot2d`][]:
- the `view` parameter now also works with `methods` `3d` and `3d_complex`
- the `color_by` and `shade_by` parameters now also work when plotting skeletons with `radius=True`
- new defaults: `radius="auto"`, `alpha=1`, `figsize=None` (use matplotlib defaults)
- new parameters for methods `3d` and `3d_complex`: `mesh_shade=False` and `non_view_axes3d`
- the `scalebar` and `soma` parameters can now also be dictionaries to style (color, width, etc) the scalebar/soma
- the `connectors` parameter can now be used to show specific connector types (e.g. `connectors="pre"`)
- I/O:
- `read_*` functions are now able to read from FTP servers (`ftp://...`)
- the `limit` parameter used in many `read_*` functions can now also be a regex pattern or a `slice`
- New parameter in [`navis.resample_skeleton`][]: use `map_column` to include arbitrary columns in the resampling
- [`navis.prune_twigs`][] and [`navis.cable_length`][] now accept a `mask` parameter
- [`navis.prune_twigs`][] and [`navis.morpho.cable_length`][] now accept a `mask` parameter
- General improvements to docs and tutorials

##### Fixes
Expand Down Expand Up @@ -158,8 +158,8 @@ _Date: 07/04/24_
##### Fixes
- Fixed interface to InsectBrainDB
- `navis.read_precomputed`:
- now correctly parses the `info` file depending on the source
- reading large files (i.e. meshes) directly from a URL should not break anymore
- now correctly parses the `info` file depending on the source
- reading large files (i.e. meshes) directly from a URL should not break anymore
- Fixed writing vertex properties in `navis.write_precomputed`
- Fixed a bug in `navis.resample_skeleton`
- Fixed an occasional issue when plotting skeletons with radii
Expand Down Expand Up @@ -313,13 +313,13 @@ _Date: 11/11/21_
##### 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
- 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`
- 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`
Expand Down Expand Up @@ -452,9 +452,9 @@ _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
- `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
Expand Down Expand Up @@ -526,8 +526,8 @@ 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`
- 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
Expand Down Expand Up @@ -646,9 +646,9 @@ _Date: 26/05/20_
_Date: 15/05/20_

##### Improvements
- improvements to R and Blender interface
- improved loading from SWCs (up to 2x faster)
- TreeNeurons: allow rerooting by setting the `.root` attribute
- Improvements to R and Blender interface
- Improved loading from SWCs (up to 2x faster)
- `TreeNeurons`: allow rerooting by setting the `.root` attribute

## Version `0.1.14` { data-toc-label="0.1.14" }
_Date: 05/05/20_
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