Fix Interleaved RGB Image Handling. #399

ilan-gold · 2021-03-29T20:42:48Z

Our current handling of RGB interleaved images doesn't work at all, partially because Avivator tries sending in an array of channel selections (whereas an interleaved RGB loader only has one selection available to it) and partially because isInterleaved was always passed in the PixelSource instead of its shape.

Background

After #358 I don't think we tested this (or if we did, we did not do it well enough). I will slack you a test URL @manzt - thanks @NHPatterson for bringing this to our attention.

Change List

Make sure isInterleaved is passed in a shape not the PixelSource itself.
Don't make extra selections in Avivator that an interleaved loader cannot handle.

Checklist

Update JSdoc types if there is any API change.
Make sure Avivator works as expected with your change.

manzt

Looks great! I experimented with interleaved data for zarr a couple weeks ago an ran into a similar issue. One thing I vaguely remember from that is the BitmapLayer failing with no default value... can you test this if you don't provide a photometric interpretation?

manzt · 2021-03-30T23:06:05Z

src/layers/ImageLayer.js

+      const {
+        meta: { photometricInterpretation }
+      } = loader;


What happens if no photometricInterpretation is provided? Is there a default? This is not included in Zarr, so it would be good to have a default:

const { photometricInterpretation = ?? } = loader.meta;

Good call, I'll add a default.

manzt · 2021-03-30T23:06:16Z

src/layers/MultiscaleImageLayer/utils.js

+  if (isInterleaved(base.shape)) {
+    const {
+      meta: { photometricInterpretation }
+    } = base;


same question here.

* Add test for BitmapLayer * Add more stringent requirement for layer. * Fix slicing bug. * Fix tests better. * Small fixes. * ImageLayer too.

* 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> 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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Trevor Manz <[email protected]> Co-authored-by: Andreas Girgensohn <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

ilan-gold added 2 commits March 29, 2021 16:39

Fix Interleaved RGB Image Handling.

84d848d

Prettier.

9d818df

ilan-gold requested a review from manzt March 29, 2021 20:50

ilan-gold mentioned this pull request Mar 29, 2021

Add test for Interleaved BitmapLayer #400

Merged

manzt reviewed Mar 30, 2021

View reviewed changes

ilan-gold added 3 commits March 31, 2021 12:02

Defaults for photometricInterpretation

7c7ca02

Merge branch 'master' into ilan-gold/fix_interleaved_rgb_bugs

11a71be

Add test for Interleaved BitmapLayer (#400)

d752d0d

* Add test for BitmapLayer * Add more stringent requirement for layer. * Fix slicing bug. * Fix tests better. * Small fixes. * ImageLayer too.

ilan-gold merged commit b912f55 into master Mar 31, 2021

ilan-gold deleted the ilan-gold/fix_interleaved_rgb_bugs branch March 31, 2021 16:33

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Fix Interleaved RGB Image Handling. #399

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ilan-gold commented Mar 29, 2021 •

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Fix Interleaved RGB Image Handling. #399

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ilan-gold commented Mar 29, 2021 •

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