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docs: update API docs
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@schlegelp
schlegelp committed Oct 5, 2024
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Expand Up @@ -124,9 +124,12 @@ In addition, a [`navis.TreeNeuron`][] has a range of different properties:

| Method | Description |
|--------|-------------|
| [`TreeNeuron.adjacency_matrix`][navis.TreeNeuron.adjacency_matrix] | {{ autosummary("navis.TreeNeuron.adjacency_matrix") }} |
| [`TreeNeuron.cable_length`][navis.TreeNeuron.cable_length] | {{ autosummary("navis.TreeNeuron.cable_length") }} |
| [`TreeNeuron.cycles`][navis.TreeNeuron.cycles] | {{ autosummary("navis.TreeNeuron.cycles") }} |
| [`TreeNeuron.downsample`][navis.TreeNeuron.downsample] | {{ autosummary("navis.TreeNeuron.downsample") }} |
| [`TreeNeuron.edges`][navis.TreeNeuron.edges] | {{ autosummary("navis.TreeNeuron.edges") }} |
| [`TreeNeuron.edge_coords`][navis.TreeNeuron.edge_coords] | {{ autosummary("navis.TreeNeuron.edge_coords") }} |
| [`TreeNeuron.igraph`][navis.TreeNeuron.igraph] | {{ autosummary("navis.TreeNeuron.igraph") }} |
| [`TreeNeuron.is_tree`][navis.TreeNeuron.is_tree] | {{ autosummary("navis.TreeNeuron.is_tree") }} |
| [`TreeNeuron.n_branches`][navis.TreeNeuron.n_branches] | {{ autosummary("navis.TreeNeuron.n_branches") }} |
Expand All @@ -140,9 +143,22 @@ In addition, a [`navis.TreeNeuron`][] has a range of different properties:
| [`TreeNeuron.simple`][navis.TreeNeuron.simple] | {{ autosummary("navis.TreeNeuron.simple") }} |
| [`TreeNeuron.soma_pos`][navis.TreeNeuron.soma_pos] | {{ autosummary("navis.TreeNeuron.soma_pos") }} |
| [`TreeNeuron.subtrees`][navis.TreeNeuron.subtrees] | {{ autosummary("navis.TreeNeuron.subtrees") }} |
| [`TreeNeuron.vertices`][navis.TreeNeuron.vertices] | {{ autosummary("navis.TreeNeuron.vertices") }} |
| [`TreeNeuron.volume`][navis.TreeNeuron.volume] | {{ autosummary("navis.TreeNeuron.volume") }} |


#### Skeleton utility functions

| Function | Description |
|----------|-------------|
| [`navis.rewire_skeleton()`][navis.rewire_skeleton] | {{ autosummary("navis.rewire_skeleton") }} |
| [`navis.insert_nodes()`][navis.insert_nodes] | {{ autosummary("navis.insert_nodes") }} |
| [`navis.remove_nodes()`][navis.remove_nodes] | {{ autosummary("navis.remove_nodes") }} |
| [`navis.graph.simplify_graph()`][navis.graph.simplify_graph] | {{ autosummary("navis.graph.simplify_graph") }} |
| [`navis.graph.skeleton_adjacency_matrix()`][navis.graph.skeleton_adjacency_matrix] | {{ autosummary("navis.graph.skeleton_adjacency_matrix") }} |



### Mesh neurons

Properties specific to [`navis.MeshNeuron`][]:
Expand Down Expand Up @@ -173,10 +189,16 @@ These are methods and properties specific to [VoxelNeurons][navis.VoxelNeuron]:

| Property | Description |
|------|------|
| [`VoxelNeuron.density`][navis.VoxelNeuron.density] | {{ autosummary("navis.VoxelNeuron.density") }} |
| [`VoxelNeuron.grid`][navis.VoxelNeuron.grid] | {{ autosummary("navis.VoxelNeuron.grid") }} |
| [`VoxelNeuron.voxels`][navis.VoxelNeuron.voxels] | {{ autosummary("navis.VoxelNeuron.voxels") }} |
| [`VoxelNeuron.max`][navis.VoxelNeuron.max] | {{ autosummary("navis.VoxelNeuron.max") }} |
| [`VoxelNeuron.min`][navis.VoxelNeuron.min] | {{ autosummary("navis.VoxelNeuron.min") }} |
| [`VoxelNeuron.nnz`][navis.VoxelNeuron.nnz] | {{ autosummary("navis.VoxelNeuron.nnz") }} |
| [`VoxelNeuron.offset`][navis.VoxelNeuron.offset] | {{ autosummary("navis.VoxelNeuron.offset") }} |
| [`VoxelNeuron.shape`][navis.VoxelNeuron.shape] | {{ autosummary("navis.VoxelNeuron.shape") }} |
| [`VoxelNeuron.strip()`][navis.VoxelNeuron.strip] | {{ autosummary("navis.VoxelNeuron.strip") }} |
| [`VoxelNeuron.threshold()`][navis.VoxelNeuron.threshold] | {{ autosummary("navis.VoxelNeuron.threshold") }} |
| [`VoxelNeuron.voxels`][navis.VoxelNeuron.voxels] | {{ autosummary("navis.VoxelNeuron.voxels") }} |


### Dotprops
Expand Down Expand Up @@ -207,6 +229,8 @@ These functions will let you convert between neuron types:
| [`navis.conversion.voxels2mesh()`][navis.conversion.voxels2mesh] | {{ autosummary("navis.conversion.voxels2mesh") }} |
| [`navis.conversion.tree2meshneuron()`][navis.conversion.tree2meshneuron] | {{ autosummary("navis.conversion.tree2meshneuron") }} |

See also [Utility](#utility) for functions to convert to/from basic data types.

### NeuronList methods

[`NeuronLists`][navis.NeuronList] let you access all the properties and methods of the neurons
Expand Down Expand Up @@ -346,6 +370,7 @@ Functions to edit morphology:
| [`navis.smooth_skeleton()`][navis.smooth_skeleton] | {{ autosummary("navis.smooth_skeleton") }} |
| [`navis.smooth_mesh()`][navis.smooth_mesh] | {{ autosummary("navis.smooth_mesh") }} |
| [`navis.smooth_voxels()`][navis.smooth_voxels] | {{ autosummary("navis.smooth_voxels") }} |
| [`navis.thin_voxels()`][navis.thin_voxels] | {{ autosummary("navis.thin_voxels") }} |


### Resampling
Expand Down Expand Up @@ -508,22 +533,6 @@ Collection of functions to work with graphs and adjacency matrices.
|----------|-------------|
| [`navis.NeuronConnector`][] | {{ autosummary("navis.NeuronConnector") }} |

### Graphs

Functions to convert between neurons graph representation (networkx or iGraph).

| Function | Description |
|----------|-------------|
| [`navis.neuron2nx()`][navis.neuron2nx] | {{ autosummary("navis.neuron2nx") }} |
| [`navis.neuron2igraph()`][navis.neuron2igraph] | {{ autosummary("navis.neuron2igraph") }} |
| [`navis.neuron2KDTree()`][navis.neuron2KDTree] | {{ autosummary("navis.neuron2KDTree") }} |
| [`navis.network2nx()`][navis.network2nx] | {{ autosummary("navis.network2nx") }} |
| [`navis.network2igraph()`][navis.network2igraph] | {{ autosummary("navis.network2igraph") }} |
| [`navis.rewire_skeleton()`][navis.rewire_skeleton] | {{ autosummary("navis.rewire_skeleton") }} |
| [`navis.insert_nodes()`][navis.insert_nodes] | {{ autosummary("navis.insert_nodes") }} |
| [`navis.remove_nodes()`][navis.remove_nodes] | {{ autosummary("navis.remove_nodes") }} |
| [`navis.graph.simplify_graph()`][navis.graph.simplify_graph] | {{ autosummary("navis.graph.simplify_graph") }} |

### Connectivity metrics

Functions to analyse/cluster neurons based on connectivity.
Expand Down Expand Up @@ -581,6 +590,21 @@ Various utility functions.
| [`navis.example_neurons()`][navis.example_neurons] | {{ autosummary("navis.example_neurons") }} |
| [`navis.example_volume()`][navis.example_volume] | {{ autosummary("navis.example_volume") }} |

### Conversion

Functions to convert between data types.

| Function | Description |
|----------|-------------|
| [`navis.neuron2nx()`][navis.neuron2nx] | {{ autosummary("navis.neuron2nx") }} |
| [`navis.neuron2igraph()`][navis.neuron2igraph] | {{ autosummary("navis.neuron2igraph") }} |
| [`navis.neuron2KDTree()`][navis.neuron2KDTree] | {{ autosummary("navis.neuron2KDTree") }} |
| [`navis.neuron2tangents()`][navis.neuron2tangents] | {{ autosummary("navis.neuron2tangents") }} |
| [`navis.network2nx()`][navis.network2nx] | {{ autosummary("navis.network2nx") }} |
| [`navis.network2igraph()`][navis.network2igraph] | {{ autosummary("navis.network2igraph") }} |
| [`navis.nx2neuron()`][navis.nx2neuron] | {{ autosummary("navis.nx2neuron") }} |
| [`navis.ve2neuron()`][navis.ve2neuron] | {{ autosummary("navis.ve2neuron") }} |

## Network Models

{{ navis }} comes with a simple network traversal model (used in [Schlegel, Bates et al., 2021](https://elifesciences.org/articles/66018)).
Expand Down

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