Skip to content

Latest commit

 

History

History
812 lines (506 loc) · 19.8 KB

CHANGELOG.md

File metadata and controls

812 lines (506 loc) · 19.8 KB
Raw

Changelog

In Progress

Added

Changed

0.13.3

Added

  • @pnpm/meta-updater added to project
  • Added support for loading stacked TIFFs to the Multi TIFF loader.
  • Added 10x Xenium to the "In Action" page

Changed

  • Fix visualization of interpolation at highest level to be pixelated in MultiscaleImageLayer after breaking in deck.gl 8.8

0.13.2

Added

Changed

  • Upgrade deck.gl to 8.8
  • Use correct deck.gl 8.8 getTileData args.
  • Replace postversion script with version script for CI release.
  • Remove package-lock.json from root (since we use pnpm)
  • Update HTTP response check to !==200 in avivator/utils.js, and changed variable name isOffsets404 to isOffsetsNot200
  • Fix onHover function in VivViewer after deck.gl 8.8 upgrade.

0.13.1

Added

  • Added support for loading multiple single channel TIFFs.

Changed

  • Update doc strings for loadMultiTiff
  • Update release notes in README.md

0.13.0

Added

Changed

  • Migrate to pnpm monorepo
  • Fix all image URLs in README
  • Only run CHANGELOG action on pull_requests
  • fix(main): image URLs in README
  • test release (v0.13.0-alpha.0)
  • add postversion script to package.json

0.12.9

Added

  • See documentation for a description of the newly added 3D extensions and how they work.

Changed

  • Refactor 3D rendering to use extensions just like 2D.

0.12.9

Added

  • Support passing in additional layers to VivViewer through deckProps

Changed

0.12.8

Added

Changed

  • Log errors for loading in Avivator
  • Fix casting bug for Float64
  • Disable Pool usage temporarily in Avivator due to broken Worker module
  • Also disable Pool temporarily in Avivator for File OME-TIFF sources
  • Update ciatation in README
  • Add CITATION.cff
  • Separate Journal and Software citation information.

0.12.7

Added

Changed

0.12.6

Added

Changed

  • Bump deck.gl to 8.6.7
  • Fix custom BitmapLayer compilation issue by providing extensions: []

0.12.5

Added

Changed

  • Fix geotiff file size check, implemented when fixing 416 issue. Not all servers return file size as part of response.

0.12.4

Added

Changed

  • Upgrade geotiff fork to viv-0.0.3 to resolve 416 issue
  • Disable @vite/plugin-react for ESM build

0.12.3

Added

Changed

  • Fix multi-image tiff indexing.
  • Change ScaleBarLayer to use toPrecision instead of string cutoff.

0.12.2

Added

Changed

  • Fix "Add Channel" and "Show Volume" buttons in Avivator

0.12.1

Added

  • New note about port-forwarding to visualize remote data in the tutorial README
  • Setup workflow to deploy Avivator via GitHub Pages.
  • Support multiple images within an OME-TIFF file
  • Add note about Safari not working with localhost connections.

Changed

  • Fix image links in README.md.
  • Add extensions to docs.
  • Fix broken GH-pages workflow.
  • Fix exported types for Viv v0.12.
  • Fix selection callbacks.

0.12.0

Added

  • New LensExtension for controlling lensing on layers as a deck.gl extension
    • props like lensBorderRadius no longer used directly by the layer in favor of using the extensions prop with new LensExtension in connjunction with these props. So, to be able to use the lens feature, you must pass in the old props as well as the LensExtension to extensions.
  • Expose DECKGL_FILTER_COLOR, DECKGL_PROCESS_INTENSITY, AND DECKGL_MUTATE_COLOR hooks and document them.
  • Upgrade deck.gl to 8.6
  • extensions are now the main way for controlling how shaders render the image
    • LensExtension, ColorPaletteExtension, and AdditiveColormapExtension are exported from viv to be used mutually exclusively for controlling how the fragment shader renders. The ColorPaletteExtension is used by default and provides the normal one color per channel pseudo-coloring. AdditiveColormapExtension provides colormaps like viridis, jet and more. There have been slight changes to the props so please see the docs for more infomation.
    • These extensions are mutually exclusive and only available for 2D layers - for example you will need to add something like the following to your 2D layers for compatibility
    extensions: (colormap ? [
  new AdditiveColormapExtension(),
] : [
  new ColorPaletteExtension(),
])
  • Add @data alias for serving local data during development
  • Add Avivator video tutorial to README.md
  • Support basic OME-NGFF in Avivator
  • Add support for the multiscales[].axes field introduced in OME-NGFF v0.3
  • Bump zarr.js to get support for both / and . dimension separators
  • Add onResolutionChange callback and resolution indicator in Avivator

Changed

  • Remove special selection mechanism in Viewers/Views by using deck.gl's fixed TileLayer capabilities for caching the tileset.
  • Fix SAMPLES.md demo
  • Update tutorial
  • Clean up README.md with latest additions to Viv
  • Bold format names in README
  • Add description of "Indexed TIFF" to Avivator snackbar warning when offsets are missing
  • Refactor zustand stores to follow best practice in Avivator.
  • Fix onViewportLoad callback for MultiscaleImageLayer
  • There has been a small change to how transparentColor is handled - useTransparentColor is now necessary for AdditiveColormapExtension and ColorPaletteExtension to use the feature in addition to transparentColor for ColorPaletteExtension. The truthiness of transparentColor is no longer relied on.

0.11.0

Added

Changed

  • Change API for all public props
    • sliderValues -> contrastLimits
    • colorValues -> colors
    • channelIsOn -> channelsVisible
    • loaderSelection -> selections
    • MAX_SLIDERS_AND_CHANNELS -> MAX_CHANNELS
  • Upgrade Vite to ~2.5.4
  • Fix value-picking for VivViewer.
  • glOptions is removed in favor of a general deckProps for Viewer components for all props that can be passed to the DeckGL component.

0.10.6

Added

Changed

  • Upgrade deck.gl to 8.5
  • Update fork of geotiff.js
  • Fix changelog check in bash.
  • Update README to note Node version restrictions.
  • Maintain the value of the channel color in HSV when applying intensity (3D + 2D)
  • Fix documentation for React Components.
  • Fix documentation for TypeScript exports.
  • Fix channel stats for thin 3D volumes in Avivator.
  • Better checking for viewable volumes at certain resolutions.
  • Don't do RGB-HSV conversion on shaders. Instead, scale RGB linearly.
  • Consistent shader floats n.0 -> n.
  • Pin deck.gl to minor versions

0.10.5

Added

Changed

  • Fix Galaxy note in the README.md.
  • Fix interleaved RGB issue in Avivator when setting up viewer initially.

0.10.4

Added

Changed

  • Make OME-TIFF loader use a guessTileSize function just like the zarr loaders in order to handle pyramids that are not tiled, just downsampled.
  • Don't use changeFlags for updateState prop diffing.
  • Fix broken decoder Pool. Remove pool proxy.
  • Replace Webpack & Rollup with Vite for development & build.

0.10.3

Added

  • Add in-layer warning about WebGL1 to VolumeLayer.

Changed

  • Remove unneeeded VolumeButton.js file.
  • Make sure loading message reappears if the resolution changes.
  • Pass glOptions from the viewers to DeckGL

0.10.2

Added

Changed

  • Fix WebGL1 Float + LINEAR combination in XRLayer

0.10.1

Added

  • Log metadata for current file in Avivator.

Changed

  • Fix viewer props docs.
  • Fix lens in Avivator + ImageLayer.

0.10.0

Added

  • Add VolumeView, VolumeViewer, VolumeLayer, and XR3DLayer classes for volumetric ray casting.
  • Add screenshots to README.md
  • Allow users to choose LINEAR or NEAREST interpolation filtering for XRLayer.

Changed

  • Fix bug in getChannelStats where we only considered values over 1 for the sliders
  • Fix bug in getChannelStats where array of zeros passed in causes undefined slider settings
  • Check all properties in onHover to avoid crashes
  • Check for dependabot before running CHANGELOG checks
  • Make default setting for MutliscaleImageLayer for interpolation to be NEAREST at highest resolution, LINEAR otherwise.

0.9.5

Added

Changed

  • Fix VivViewer and VivView types.
  • Fix ImageLayer loader type.
  • Refine LayerProps JSDoc annotations for more precise emitted types.
  • Fix Avivator and getImageLyaers utility for loaderSelection that is empty array.

0.9.4

Added

  • Refactor JSDoc comments to properly annotate Layer classes with constructor signatures.
  • getChannelStats in snippet to show how to use it.

Changed

  • Fix interleaved RGB image handling.
  • Add test for interleaved RGB images.
  • Upgrade geotiff.js to fix geotiffjs/geotiff.js#214

0.9.3

Added

  • Support Float64 (OME double) datatype by casting array data to Float32.
  • onHover prop for VivViewer, PictureInPictureViewer, SideBySideViewer for deck.gl callback.
  • Add handleCoordnate hoverHook for PIP.

Changed

  • Make deck.gl a peer dependency (similar to React).

0.9.2

Added

Changed

  • Remove trimPyramid and require declaration of tileSize in ZarrPixelSource.

0.9.1

Added

Changed

  • Export defaults from tiff/pixel-source.ts and zarr/pixel-source.ts as TiffPixelSource and ZarrPixelSource.
  • Copy array-like selection for ZarrPixelSource rather than mutating.
  • Fix scale bar bug in View to match new loaders.

0.9.0

Added

  • onViewportLoad prop for ImageLayer for handling when the data for the viewport has loaded.

Changed

  • Fix z-slider broken by transition fields.
  • Upgrade deck.gl to 8.4.0-beta.1 to handle aborting tiles after selection better.
  • Rewrite data loaders as PixelSource | PixelSource[]. Introduce ZarrPixelSource and TiffPixelSource to support other types of images. Migrate src/loaders to TypeScript.
  • Add loadBioforamtsZarr, loadOmeZarr, and loadOmeTiff utilities.
  • Add predictive, fully typed OME-XML response from fast-xml-parser.
  • Upgrade Zarr.js to v0.4.
  • Remove casting of Int8Array, Int16Array, and Int32Array to Uint. Support texture on shader.

0.8.3

Added

  • Document support for bfconvert as a cli tool for generating image pyramids as well as the new pyramidal tiff spec.
  • Issue templates for Github.
  • Add transparentColor to allow the layer to set a color to be "transparent" (or use the automatically calculated one when colormaps are set).

Changed

  • Adjust the zoom level for tile layer if scaled.
  • Update getDefaultInitialViewState to return floating point zoom that fills the screen by default.
  • Upgrade geotiff to fix out-of-range requests issue.
  • Changed initialViewState to viewState in PictureInPictureViewer and to viewStates in the other viewers. The new properties control the deck.gl view state at any time and not just when the components are created.
  • Fix maxZoom bug.
  • Smooth transitions for global selection changes.
  • GH actions allow for running on PR as well as push (so that forked repos run tests).

0.8.2

Added

Changed

  • Fix opacity with photometric interpretations.
  • Only show background image when opacity is 1 (and viewport id prop matches that of the current viewport).
  • Fix minZoom calculation bug in MultiscaleImageLayer.

0.8.1

Added

  • Property onViewStateChange of all viewers accepts a callback for deck.gl view state changes.
  • Add a click handler to the overview that centers the detail view on the click position. The handler can be turned off by setting the PictureInPictureViewer property clickCenter to false.
  • Support interleaved RGB OME-TIFF files.

Changed

  • Fix documentation of instances where spreading is used in the arguments for a function.
  • Fix link to bioformats in README

0.8.0

Added

  • Export a getDefaultInitialViewState function for getting a default initial view state given a loader and desired size of view.
  • Added a README file for Avivator at avivator/README.md.

Changed

  • Fix default component args API.
  • Change WebGL setting so that textures of non-multiple-of-4 length bind and display.
  • Update preprint title in README.md
  • Use readRasters for TIFF for fetching tiles so that we are robust to non-uniformly sized tiles - thus we no longer need to "pad tiles."
  • Switch to Github Actions
  • Don't show snackbar if image provided is one of our demos.

0.7.0

Added

  • Support arbitrary affine transformations of MultiscaleImageLayer.

Changed

  • Clean up docs for OME-TIFF creation.
  • Remove OMETIFF_LOADING.md docs.
  • Upgrade deck.gl to 8.4.0-alpha.2.
  • Remove scale and translate from ImageLayer and its usages in favor of modelMatrix.

0.6.0

Added

Changed

  • Fix snackbars for errors and initial image.
  • Export custom zarr HTTPStore with abort controller signal support.
  • Modularize shaders using deck.gl shader modules.
  • Provide pure ESM export of Viv and use separate build for Avivator
  • Downgrade react back to 16.8

0.5.0

Added

  • Support local tiff files.
  • Support local zarr directories.
  • onClick callbacks for layers.

Changed

  • Removed greedy matching of dimension order in Bio-Formats Zarr output. Just check if OME-Zarr.
  • Upgrade to deck.gl 8.3.0
  • Use WASM LZW decoder from manzt/geotiff.js
  • Bundle UMD build with deps.

0.4.2

Added

  • Add snackbar for included images when no url provided.

Changed

  • Fix snackbar placement.
  • Fix small range, float sliders.
  • Clean up dependencies from migration.
  • Fix small dif between sliders in shaders.

0.4.1

Added

Changed

  • Fix lens and PIP.

0.4.0

Added

  • Lens view built into layers.
  • Add avivator.

Changed

  • Update docs for avivator.

0.3.3

Added

Changed

  • Upgrade geotiff.js to Ilan's branch for large string fix.

0.3.2

Added

Changed

  • Updated the font family for the ScaleBarLayer's internal TextLayer.
  • Guarantee that OverviewLayer shows an image by forcing it to be a power of 2.

0.3.1

Added

Changed

  • Pad OME-TIFF tiles using both height and width in the calculation.

0.3.0

Added

  • Thanks to deck.gl 8.2, we have a request scheduler which makes fetching tiles more efficient.

Changed

  • Use WebGL context to detect what shaders and textures to use, not whether WebGL2 is available on environment document.
  • Fix link in IMAGE_RENDERING.md and remove img2zarr reference since it has been depricated.
  • Upgrade deck.gl to 8.2.
  • Export XRLayer.
  • Fix OMEXML 32 bit float parse error.

0.2.11

Added

Changed

  • Move back on to geotiff full releases.

0.2.10

Added

Changed

  • Change geotiff fork branch to work with downstream installations.
  • Fix shaders divisor for intensity.

0.2.9

Added

  • Support Safari in 2D raster imagery.
  • Support height as primary dimension for sizing OverviewView.
  • Add preliminary RGB check.
  • Add doc giving an overview of our API structure.

Changed

  • Project overview boundary sizes instead of hardcoding.
  • Default demo color is now magenta and not red.
  • Remove Safari browser warning in docs.

0.2.8

Added

  • Export constants for loader type and max channels.

Changed

0.2.7

Added

  • Min/max, mean, standard deviation, median, IQR calculations directly from loaders.

Changed

0.2.6

Added

Changed

  • Don't minify es bundle.
  • Remove bioformats hack and update docs for container version.
  • Update zarr with new decoders.
  • Add tile-padding utility function for consistently sized tiles from Loader.getTile.
  • Fix #144 by padding uneven length tiles in StaticImageLayer.

0.2.5

Added

Changed

  • Address OMEXML discrepancy on StructuredAnnotations.

0.2.4

Added

Changed

  • Clean up dependencies.

0.2.3

Added

Changed

  • Add OME-TIFF to Covid-19 data description.
  • Clean up the docs.
  • Allow numeric indexing on OME-TIFF loader.

0.2.2

Added

  • Allow for headers with OME-TIFF.
  • Add COVID-19 Image to public demo.
  • Added getMetadata function to ZarrLoader and OMETiffLoader classes to enable Vitessce to obtain human-readable image layer metadata.

Changed

  • Change bioformats padding check.
  • Pad based on textures and not channel props.

0.2.1

Added

Changed

  • Allow for offsets in OMETiffLoader for bioformats6 pyramids.
  • Update geotiff off from Ilan's for to the official release.

0.2.0

Added

  • Remove threads.js and use WebWorkers for tiff decompression.
  • Add a dimension builder onto the tiff loader.
  • Add hover values for PictureInPictureViewer

Changed

  • Removed loader.serializeSelection and standardized loaderSelection for getTile and getRaster
  • Fix loaderSelection fetching on StaticImageLayer

0.1.7

Added

  • OMETiffLoader for reading ome-tiff files directly
  • Add scale bar (only for OMEXML for now)

Changed

0.1.6

Added

  • New classes for views/viewers
  • Zoom/pan lock buttons and linked views in demo

Changed

  • Refactored VivViewer to take in arbitrary views/layers
  • Check for loader.getRaster in VivViewerLayer before rendering StaticImageLayer base

0.1.5

Added

  • Add loaderSelection as prop for VivViewerLayer. This parameter is passed to loader.getTile and loader.getRaster in addtion to x, y and z.
  • Display warning for Safari users

Changed

  • Refactored demo to allow various channels and change selection
  • Use reducer for handling channel state in Demo
  • Use Material UI for demo components, and showcase all viv features
  • Update the IMAGE_RENDERING doc

0.1.4

Added

  • Add background image for nicer loading and temporary fix for minZoom issue
  • Add getRaster to TiffPyramidLoader
  • Picture-in-picture overview layer

Changed

  • Generalize colormaps to multichannel maps.
  • Add flags to check for loader change and rerender.
  • Remove minZoom from loaders and make loaders provide onTileError.
  • Wrap channelData in StaticImageLayer in Promise.
  • Allow no viewportId parameter

0.1.3

Added

Changed

0.1.2

Changed

  • Fixed shaders' if-then
  • Changed UMD build name to be valid
  • Provide default args for scale and isRgb in createZarrPyramid.
  • Remove unneeded attributes from TiffPyramidLoader.

0.1.1

Changed

  • Update deck.gl build
  • Bump zarr.js to v0.2.3
  • Set raster selection on data loader class

Added

  • Add test:watch to npm scripts.

0.1.0

Changed

  • Clean up shaders
  • Extracted data utils to loaders and refactored demo

Added

  • StaticImageLayer added and exported for viewing non-tiled images
  • Single channel colormaps for tiled and static
  • Expose opacity and visibility
  • Testing for layers added
  • More automated build process

0.0.8

Changed

  • Update build process to use rollup

0.0.7

Changed

  • Remove sort

0.0.6

Added

  • New zarr API and standardize data utilities

Changed

  • Fix brightness from channel toggling
  • Removed Microscopy from export names
  • Consolidated data access logic to data-utils
  • Refactored microscopy-viewer-layer-base.js
  • Fix toggling defaults for sliders and colors when channels are off.

0.0.5

Added

  • Resolve linting
  • Update demo switching
  • Add channel-toggling
  • Simplify API for TIFF by inferring metadata from file
  • Clean up vertex shader

Changed

  • Fixed no-unused-expressions

v0.0.4

Added

  • Anti-aliasing for the borders implemented.

Changed

  • Prettier on CI will now actually scan all files.

v0.0.3

Added

  • Automate Deployment
  • Add slider names corresponding to metadata in demo
  • Linting and Travis integration. Apply prettier to everything. (Ignore most ESLint errors for now

Changed

  • Fix no-extraneous-dependencies
  • Fix global-require