From a347f8863d0c56bce769d885e65c671e8ff17765 Mon Sep 17 00:00:00 2001 From: Philipp Schlegel Date: Mon, 23 Sep 2024 10:01:04 +0100 Subject: [PATCH] docs: various small fixes --- README.md | 8 ++++---- docs/api.md | 15 ++++++++++----- docs/changelog.md | 4 ++-- docs/index.md | 6 +++--- 4 files changed, 19 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 9930c033..166919b9 100644 --- a/README.md +++ b/README.md @@ -8,13 +8,13 @@ NAVis is a Python 3 library for **N**euron **A**nalysis and **Vis**ualization. Visit our documentation [here](https://navis-org.github.io/navis/ "NAVis Documentation")! ## Features -* **polyglot**: work and convert between neuron skeletons, meshes, dotprops and images -* **visualize**: 2D (matplotlib) and 3D (vispy, plotly or k3d) +* **polyglot**: work with and convert between neuron skeletons, meshes, dotprops and images +* **visualize**: 2D (matplotlib) and 3D (octarine, vispy, plotly or k3d) plots * **process**: skeletonization, meshing, smoothing, repair, downsampling, etc. * **morphometrics**: Strahler analysis, cable length, volume, tortuosity and more * **similarity**: compare & cluster by morphology (e.g. NBLAST, persistence or form factor) or connectivity metrics * **transform**: move data between template brains (built-in support for HDF5, CMTK, Elastix and landmark-based transforms) -* **interface**: load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and other data sources +* **interface**: load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and other remote data repositories * **model** neurons and networks using the *NEURON* simulator * **render**: use Blender 3D for high quality [visualizations](https://youtu.be/wl3sFG7WQJc) * **R** neuron libraries: interfaces with [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr) and more @@ -27,7 +27,7 @@ Visit our documentation [here](https://navis-org.github.io/navis/ "NAVis Documen See the [documentation](http://navis.readthedocs.io/ "NAVis ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient: ```sh -pip3 install 'navis[all]' +pip3 install "navis[all]" ``` which includes all optional extras providing features and/or performance improvements. diff --git a/docs/api.md b/docs/api.md index 97d05f64..b97ced7e 100644 --- a/docs/api.md +++ b/docs/api.md @@ -20,7 +20,7 @@ This API reference is a more or less complete account of the primary functions: 1. [Neuron- and NeuronList functions and methods](#neurons-neuronlists) 2. [Functions for visualization](#visualization) -3. [Manipulate or analyze neuron morphology](#morphometrics) +3. [Manipulate or analyze neuron morphology](#neuron-morphology) 4. [Transforming and mirroring data](#transforming-and-mirroring) 5. [Analyze connectivity](#connectivity) 6. [Import/Export](#importexport) @@ -233,8 +233,8 @@ Properties: |----------|-------------| | [`NeuronList.bbox`][navis.NeuronList.bbox] | {{ autosummary("navis.NeuronList.bbox") }} | | [`NeuronList.empty`][navis.NeuronList.empty] | {{ autosummary("navis.NeuronList.empty") }} | -| [`NeuronList.id`] | An array with the IDs of the neurons contained in the list. | -| [`NeuronList.idx`] | An indexer similar to pandas' `iloc` that accepts neuron IDs. | +| [`NeuronList.id`][navis.NeuronList.id] | An array with the IDs of the neurons contained in the list. | +| [`NeuronList.idx`][navis.NeuronList.idx] | An indexer similar to pandas' `iloc` that accepts neuron IDs. | | [`NeuronList.is_degenerated`][navis.NeuronList.is_degenerated] | {{ autosummary("navis.NeuronList.is_degenerated") }} | | [`NeuronList.is_mixed`][navis.NeuronList.is_mixed] | {{ autosummary("navis.NeuronList.is_mixed") }} | | [`NeuronList.shape`][navis.NeuronList.shape] | {{ autosummary("navis.NeuronList.shape") }} | @@ -370,7 +370,6 @@ NBLAST and related functions: | [`navis.nblast_smart`][navis.nblast_smart] | {{ autosummary("navis.nblast_smart") }} | | [`navis.nblast_allbyall`][navis.nblast_allbyall] | {{ autosummary("navis.nblast_allbyall") }} | | [`navis.nblast_align`][navis.nblast_align] | {{ autosummary("navis.nblast_align") }} | -| [`navis.vxnblast`][navis.vxnblast] | {{ autosummary("navis.vxnblast") }} | | [`navis.synblast`][navis.synblast] | {{ autosummary("navis.synblast") }} | | [`navis.persistence_distances`][navis.persistence_distances] | {{ autosummary("navis.persistence_distances") }} | @@ -476,6 +475,12 @@ So to register and use a new transform you would look something like this: >>> xf = navis.xform_brain(data, 'brainA', 'brainB') ``` +You can check which transforms are registered like so: + +``` python +>>> navis.transforms.registry.summary() # this outputs a dataframe +``` + These are the methods and properties of ``registry``: | Method | Description | @@ -758,7 +763,7 @@ from navis.interfaces import insectbrain_db Functions to be run inside [Blender 3D](https://www.blender.org/) and import CATMAID data (see Examples). Please note that this requires Blender >2.8 as earlier versions are shipped with older Python versions not supported by {{ navis }}. -See the [tutorials](../generated/gallery/3_interfaces/plot_01_interfaces_blender/) for an introduction of how to use {{ navis }} in +See the [tutorials](../generated/gallery/3_interfaces/plot_02_interfaces_blender/) for an introduction of how to use {{ navis }} in Blender. _Not imported at top level! Must be imported explicitly:_ diff --git a/docs/changelog.md b/docs/changelog.md index f0a69a77..62eb06a5 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -62,8 +62,8 @@ more consistent and easier to use. - 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` + - `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 - General improvements to docs and tutorials diff --git a/docs/index.md b/docs/index.md index 84730788..bc1752ff 100644 --- a/docs/index.md +++ b/docs/index.md @@ -48,7 +48,7 @@ morphology. It stands on the shoulders of the excellent --- - Generate beautiful publication-ready 2D (matplotlib) and 3D (octarine, + Generate beautiful, publication-ready 2D (matplotlib) and 3D (octarine, vispy or plotly) [figures](generated/gallery/#plotting). - :material-progress-wrench:{ .lg .middle } __Processing__ @@ -61,7 +61,7 @@ morphology. It stands on the shoulders of the excellent --- - Uses compiled Rust code under-the-hood. Also scale thanks to + Uses compiled Rust code under-the-hood and out-of-the-box support for [multiprocessing](generated/gallery/6_misc/plot_00_misc_multiprocess). - :material-lightbulb-group:{ .lg .middle } __Clustering__ @@ -75,7 +75,7 @@ morphology. It stands on the shoulders of the excellent --- Fully featured [transform system](generated/gallery/5_transforms/plot_00_transforms) to move neurons between brain spaces. - We support e.g. CMTK or Elastix. + We support CMTK, Elastix, landmark-based transforms and more! - :octicons-file-directory-symlink-24:{ .lg .middle } __Import/Export__