diff --git a/docs/changelog.md b/docs/changelog.md index b7ddb5e1..fd9e8068 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -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) @@ -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 @@ -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 @@ -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` @@ -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 @@ -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 @@ -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_