diff --git a/content/posts/yt_napari_updates.md b/content/posts/yt_napari_updates.md new file mode 100644 index 0000000..e6afaee --- /dev/null +++ b/content/posts/yt_napari_updates.md @@ -0,0 +1,80 @@ +--- +title: Updates from yt-napari +date: 2023-10-06T11:27:24-05:00 +lastmod: 2023-10-06T11:27:24-05:00 +author: Chris Havlin +cover: /img/yt_napari_updates/path_3D_measurements.png +categories: + - tutorial + - development + - releases +tags: + - fun + - volume-rendering + - time-series + - documentation +draft: false +--- + +yt-napari has seen a number of new features, performance improvements and new documentation +in the past year or so. Read on to find out more! + + + +## Long form video walkthroughs + +One of the main efforts of the past year has been improving documentation. This included not just new +static documentation (e.g., new [example notebooks](https://yt-napari.readthedocs.io/en/latest/notebooks.html)), +but also the yt-napari Tutorial Series. The series starts with an introduction to napari for yt users, +moves on to how to use the yt-napari plugin to load data into napari from yt and ends with some videos showing +examples of using **other** napari plugins for analysis and visualization of yt data in napari. The final +videos are particularly fun as they apply image analysis methods used by the bio-imaging community to segment +yt-data. For example, here's a screenshot of using a watershed transformation via the `napari-simpleitk-image-processing` +plugin to identify 3D density voids in `enzo_tiny_cosmology` and then the `napari-clusters-plotter` to interactively +visualize mean field values within the domains: + +![](/img/yt_napari_updates/density_watershed.png) + +Or, check out [this short clip](https://www.youtube.com/watch?v=lBo8jI52BnM) from a longer video in which the +`napari-clusters-plotter` plugin is used to interactively visualize how field intensities relate spatially after having +used `napari-clusters-plotter` to run a kmeans classification. + +Additionally, you can also use standard napari shapes layers to interactively sample at points or along paths and +then use plugins like `napari-line-plot` or `napari-properties-plotter` to visualize how data data varies +along the path (screen shot from the [Introduction to other plugins video](https://www.youtube.com/watch?v=k1LdEQ_5Gfw)): + +![](/img/yt_napari_updates/path_3D_measurements.png) + +Check out either of the following to access all the videos: + +* [List of video titles and links](https://yt-napari.readthedocs.io/en/latest/tutorials.html) +* [Full YouTube Playlist](https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1) + + +## New Feature: Sampling Timeseries + +One of the more exciting new features of recent releases is the ability to sample and load +timeseries for both slices and 3D regions from the napari GUI, a jupyter notebook or via JSON file. +This allows you to interactively visualize time-dependent behavior. For example, the following +shows a small 3D region centered on the final max density of the `enzo_tiny_cosmology` dataset: + +![](/img/yt_napari_updates/yt_napari_timeseries_small.gif) + +For higher resolution sampling, you can work from a notebook and leverage dask to lazily-sample 3D +regions across a timeseries so that you can load the current timestep on demand: + +![](/img/yt_napari_updates/yt_napari_timeseries_regdask_vid.gif) + +Check out the sample notebooks and videos for loading timeseries ([notebook](https://yt-napari.readthedocs.io/en/latest/examples/ytnapari_scene_04_timeseries.html), +[video](https://youtu.be/uNK33C6nOZU)) and using dask with timeseries +([notebook](https://yt-napari.readthedocs.io/en/latest/examples/ytnapari_scene_05_timeseries_dask.html), +[video](https://www.youtube.com/watch?v=5eeOrcuqvH8)) + +## The future of yt-napari + +One of the exciting features in development upstream in napari is improved on-demand loading of +multi-resolution data. Once that work is completed, it will open up the possibility of progressive +sampling in yt-napari! Check out this video for a preview of what this might enable in yt-napari: +[progressive of the DeeplyNestedZoom dataset](https://www.youtube.com/watch?v=ofoURuz-Cbw). There's +also plenty to do with yt-napari as it is now, check out the [Issues page](https://github.com/data-exp-lab/yt-napari/issues) +to get involved! \ No newline at end of file diff --git a/static/img/yt_napari_updates/density_watershed.png b/static/img/yt_napari_updates/density_watershed.png new file mode 100644 index 0000000..52a1853 Binary files /dev/null and b/static/img/yt_napari_updates/density_watershed.png differ diff --git a/static/img/yt_napari_updates/path_3D_measurements.png b/static/img/yt_napari_updates/path_3D_measurements.png new file mode 100644 index 0000000..6836d26 Binary files /dev/null and b/static/img/yt_napari_updates/path_3D_measurements.png differ diff --git a/static/img/yt_napari_updates/yt_napari_timeseries_regdask_vid.gif b/static/img/yt_napari_updates/yt_napari_timeseries_regdask_vid.gif new file mode 100644 index 0000000..0d65c6d Binary files /dev/null and b/static/img/yt_napari_updates/yt_napari_timeseries_regdask_vid.gif differ diff --git a/static/img/yt_napari_updates/yt_napari_timeseries_small.gif b/static/img/yt_napari_updates/yt_napari_timeseries_small.gif new file mode 100644 index 0000000..b9e9c6c Binary files /dev/null and b/static/img/yt_napari_updates/yt_napari_timeseries_small.gif differ