merge (#445)

* Fix Interleaved RGB Image Handling. (#399) * Fix Interleaved RGB Image Handling. * Prettier. * Defaults for photometricInterpretation * Add test for Interleaved BitmapLayer (#400) * Add test for BitmapLayer * Add more stringent requirement for layer. * Fix slicing bug. * Fix tests better. * Small fixes. * ImageLayer too. * 0.9.4 (#405) * Fix type/docs for VivView(er) and Consumers. (#407) * Fix type/docs for VivViewer and VivView (and upstream users) * Use special jsdoc -> typescript syntax. * Small Fixes * Fix ImageLayer * Try functional component * Small fixes. * Small fixes. * Fix `ImageLayer` `loader` type. (#410) * Improve emitted TS types for layers (#413) * Create `Viv` utility type to refine emitted Layer constructor types. * Do not export VivProps type. * Fix Empty Loader Selection Bug. (#416) * 0.9.5 (#417) * Fix Bugs in `getChannelStats`. (#419) * Fix Bugs in `getChannelStats`. * Use > 0 instead of epsilon value. * Check all properties in onHover to avoid crashes (#426) * Bump url-parse from 1.4.7 to 1.5.1 in /avivator (#427) Bumps [url-parse](https://github.com/unshiftio/url-parse) from 1.4.7 to 1.5.1. - [Release notes](https://github.com/unshiftio/url-parse/releases) - [Commits](unshiftio/url-parse@1.4.7...1.5.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump hosted-git-info from 2.8.8 to 2.8.9 (#429) Bumps [hosted-git-info](https://github.com/npm/hosted-git-info) from 2.8.8 to 2.8.9. - [Release notes](https://github.com/npm/hosted-git-info/releases) - [Changelog](https://github.com/npm/hosted-git-info/blob/v2.8.9/CHANGELOG.md) - [Commits](npm/hosted-git-info@v2.8.8...v2.8.9) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump lodash from 4.17.20 to 4.17.21 in /avivator (#431) Bumps [lodash](https://github.com/lodash/lodash) from 4.17.20 to 4.17.21. - [Release notes](https://github.com/lodash/lodash/releases) - [Commits](lodash/lodash@4.17.20...4.17.21) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump postcss from 8.1.4 to 8.2.15 in /avivator (#432) Bumps [postcss](https://github.com/postcss/postcss) from 8.1.4 to 8.2.15. - [Release notes](https://github.com/postcss/postcss/releases) - [Changelog](https://github.com/postcss/postcss/blob/main/CHANGELOG.md) - [Commits](postcss/postcss@8.1.4...8.2.15) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump lodash from 4.17.20 to 4.17.21 (#428) Bumps [lodash](https://github.com/lodash/lodash) from 4.17.20 to 4.17.21. - [Release notes](https://github.com/lodash/lodash/releases) - [Commits](lodash/lodash@4.17.20...4.17.21) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Check for dependabot before running CHANGELOG checks (#433) * New README Screenshots (#435) * Add Screenshots for README * Change width. * Update URLs * Allow for LINEAR/NEAREST Filtering Interpolation Choice (#437) * Allow for LINEAR/NEAREST Filtering Interpolation Choice * Change variable name * Change filtering options. * Bump browserslist from 4.16.1 to 4.16.6 (#441) Bumps [browserslist](https://github.com/browserslist/browserslist) from 4.16.1 to 4.16.6. - [Release notes](https://github.com/browserslist/browserslist/releases) - [Changelog](https://github.com/browserslist/browserslist/blob/main/CHANGELOG.md) - [Commits](browserslist/browserslist@4.16.1...4.16.6) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump browserslist from 4.14.6 to 4.16.6 in /avivator (#442) Bumps [browserslist](https://github.com/browserslist/browserslist) from 4.14.6 to 4.16.6. - [Release notes](https://github.com/browserslist/browserslist/releases) - [Changelog](https://github.com/browserslist/browserslist/blob/main/CHANGELOG.md) - [Commits](browserslist/browserslist@4.14.6...4.16.6) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Trevor Manz <trevor.j.manz@gmail.com> Co-authored-by: Andreas Girgensohn <andreasg123@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
hms-dbmi · May 26, 2021 · d3e5bff · d3e5bff
1 parent 08e0f55
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,11 +4,38 @@
 
 ### Added
 
+- 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
+
+## 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 https://github.com/geotiffjs/geotiff.js/issues/214
 
 ## 0.9.3

diff --git a/README.md b/README.md
@@ -3,6 +3,8 @@
 A library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Bio-Formats-compatible Zarr and OME-TIFF.
 Written in JavaScript and built on Deck.gl with modern web technologies.
 
+<img src="https://github.com/hms-dbmi/viv/raw/master/docs/3d-slicing.gif" alt="drawing" width="400"/> <img src="https://github.com/hms-dbmi/viv/raw/master/docs/glomerular-lens.png" alt="drawing" width="400"/>
+
 ## About
 
 Viv is a JavaScript library providing utilities for rendering primary imaging data. Viv supports WebGL-based multi-channel rendering of both pyramidal and non-pyramidal images. The rendering components of Viv are provided as Deck.gl layers, making it easy to compose images with existing layers and efficiently update rendering properties within a reactive paradigm.
@@ -20,21 +22,25 @@ More details can be found in our preprint describing the Viv library and related
 ### Tools Built with Viv
 
 #### Vitessce
+
 - http://vitessce.io
 
 #### OME-NGFF:
+
 - https://blog.openmicroscopy.org/file-formats/community/2020/11/04/zarr-data/
-- https://blog.openmicroscopy.org/file-formats/community/2020/12/01/zarr-hcs/ 
+- https://blog.openmicroscopy.org/file-formats/community/2020/12/01/zarr-hcs/
 
 #### ImJoy:
-- https://imjoy.io/docs/#/i2k_tutorial?id=open-integration-with-imjoy  
+
+- https://imjoy.io/docs/#/i2k_tutorial?id=open-integration-with-imjoy
 
 #### Galaxy:
+
 - The Avivator image viewer will be included as the default visualization for OME-TIFF files: https://github.com/galaxyproject/galaxy/pull/10534
 
 #### HuBMAP CCF EUI:
-- https://github.com/hubmapconsortium/ccf-ui
 
+- https://github.com/hubmapconsortium/ccf-ui
 
 ## Supported Data Formats
 

diff --git a/avivator/package-lock.json b/avivator/package-lock.json
diff --git a/avivator/src/Avivator.js b/avivator/src/Avivator.js
@@ -262,7 +262,7 @@ export default function Avivator(props) {
       // Set new image to default selection for non-global selections (0)
       // and use current global selection otherwise.
       selection[field] = GLOBAL_SLIDER_DIMENSION_FIELDS.includes(field)
-        ? selections[0][field]
+        ? globalSelections[field]
         : 0;
     });
     const { domain, slider } = await getSingleSelectionStats({

diff --git a/avivator/src/utils.js b/avivator/src/utils.js
@@ -137,14 +137,22 @@ function getDefaultGlobalSelection({ labels, shape }) {
   return selection;
 }
 
+/**
+ * @param {Array.<number>} shape loader shape
+ */
+export function isInterleaved(shape) {
+  const lastDimSize = shape[shape.length - 1];
+  return lastDimSize === 3 || lastDimSize === 4;
+}
+
 // Create a default selection using the midpoint of the available global dimensions,
 // and then the first four available selections from the first selectable channel.
 /**
  * 
  * @param { import('../../src/types').PixelSource<['t', 'z', 'c']> } pixelSource 
  */
 export function buildDefaultSelection(pixelSource) {
-  const selection = [];
+  let selection = [];
   const globalSelection = getDefaultGlobalSelection(pixelSource);
   // First non-global dimension with some sort of selectable values.
 
@@ -163,6 +171,7 @@ export function buildDefaultSelection(pixelSource) {
     });
   }
 
+  selection = isInterleaved(pixelSource.shape) ? [{ ...selection[0], c: 0 }] : selection;
   return selection;
 }
 

diff --git a/docs/3d-slicing.gif b/docs/3d-slicing.gif
diff --git a/docs/glomerular-lens.png b/docs/glomerular-lens.png