From f6df368f937df2254d1ab40b12e7c878a4661ba8 Mon Sep 17 00:00:00 2001 From: ilan-gold Date: Tue, 18 Jan 2022 15:51:55 +0100 Subject: [PATCH 1/6] Clarify Docs on and Fix Extensions on `OverviewLayer` --- sites/docs/src/API_STRUCTURE.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/sites/docs/src/API_STRUCTURE.md b/sites/docs/src/API_STRUCTURE.md index 83af84108..3f83e5c6c 100644 --- a/sites/docs/src/API_STRUCTURE.md +++ b/sites/docs/src/API_STRUCTURE.md @@ -35,6 +35,8 @@ which accept `PixelSource` arguments for data fetching. These layers handle the and setting up the rendering by wrapping the `XRLayer`, `XR3DLayer` and `BitmapLayer`, which are the lower level rendering layers. The `XRLayer` (eXtended Range Layer) and `XR3DLayer` enable multi-channel additive blending of `Uint32`, `Uint16`, `Uint8` and `Float32` data on the GPU. +A crucial part of the layer is the `extensions` prop - these control the per-fragment (pixel) rendering. The default on all layers is `ColorPaletteExtension` and it will provide a default `colors` prop - thus all that is necessary for controlling rendering is the `contrastLimits`. But if you wish to do something different, for example to use a "colormap" like `viridis`, you will need to pass in `extensions: [new AdditiveColormapExtension()]` and `colormap: viridis`. Please see deck.gl's [documentation](https://deck.gl/docs/api-reference/extensions/overview) for more information. + #### Loader (Pixel Sources) Viv wraps both Tiff- and Zarr-based data sources in a unified `PixelSource` interface. A pixel From e29f774be3e0e30bfc2c5c1a809c7c8be07555cc Mon Sep 17 00:00:00 2001 From: ilan-gold Date: Tue, 18 Jan 2022 16:01:09 +0100 Subject: [PATCH 2/6] Fix docs. --- packages/layers/src/overview-layer.js | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/packages/layers/src/overview-layer.js b/packages/layers/src/overview-layer.js index a78986b82..fd6c4fab3 100644 --- a/packages/layers/src/overview-layer.js +++ b/packages/layers/src/overview-layer.js @@ -39,18 +39,15 @@ const defaultProps = { * @typedef LayerProps * @type {Object} * @property {Array.>} contrastLimits List of [begin, end] values to control each channel's ramp function. - * @property {Array.>} colors List of [r, g, b] values for each channel. * @property {Array.} channelsVisible List of boolean values for each channel for whether or not it is visible. * @property {Array} loader PixelSource[]. Assumes multiscale if loader.length > 1. * @property {Array} selections Selection to be used for fetching data. - * @property {number=} opacity Opacity of the layer. - * @property {string=} colormap String indicating a colormap (default: ''). The full list of options is here: https://github.com/glslify/glsl-colormap#glsl-colormap - * @property {Array.>=} domain Override for the possible max/min values (i.e something different than 65535 for uint16/'=} boundingBoxColor [r, g, b] color of the bounding box (default: [255, 0, 0]). * @property {number=} boundingBoxOutlineWidth Width of the bounding box in px (default: 1). * @property {Array.=} viewportOutlineColor [r, g, b] color of the outline (default: [255, 190, 0]). * @property {number=} viewportOutlineWidth Viewport outline width in px (default: 2). * @property {String=} id Unique identifier for this layer. + * @property {Array=} extensions [deck.gl extensions](https://deck.gl/docs/developer-guide/custom-layers/layer-extensions) to add to the layers. */ /** From 96e37fe3b7e74d6dc5e461f8994e249b88346f47 Mon Sep 17 00:00:00 2001 From: ilan-gold Date: Tue, 18 Jan 2022 16:05:43 +0100 Subject: [PATCH 3/6] Add comment to `SAMPLES.md` --- sites/docs/src/SAMPLES.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/sites/docs/src/SAMPLES.md b/sites/docs/src/SAMPLES.md index 87bfee63f..8206deac5 100644 --- a/sites/docs/src/SAMPLES.md +++ b/sites/docs/src/SAMPLES.md @@ -80,6 +80,8 @@ function App() { Date: Mon, 13 Nov 2023 09:02:19 -0500 Subject: [PATCH 4/6] add default extension --- packages/layers/src/overview-layer.js | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/layers/src/overview-layer.js b/packages/layers/src/overview-layer.js index fd6c4fab3..cf2392a3d 100644 --- a/packages/layers/src/overview-layer.js +++ b/packages/layers/src/overview-layer.js @@ -1,6 +1,7 @@ import { CompositeLayer, COORDINATE_SYSTEM } from '@deck.gl/core'; import { PolygonLayer } from '@deck.gl/layers'; import { getImageSize } from '@vivjs/loaders'; +import { ColorPaletteExtension } from '@vivjs/extensions'; import { Matrix4 } from '@math.gl/core'; import ImageLayer from './image-layer'; @@ -32,7 +33,12 @@ const defaultProps = { viewportOutlineColor: { type: 'array', value: [255, 190, 0], compare: true }, viewportOutlineWidth: { type: 'number', value: 2, compare: true }, overviewScale: { type: 'number', value: 1, compare: true }, - zoom: { type: 'number', value: 1, compare: true } + zoom: { type: 'number', value: 1, compare: true }, + extensions: { + type: 'array', + value: [new ColorPaletteExtension()], + compare: true + } }; /** From 25a92196ab9332d6fa205feadaabf33799db7bed Mon Sep 17 00:00:00 2001 From: Trevor Manz Date: Mon, 13 Nov 2023 09:09:03 -0500 Subject: [PATCH 5/6] fix zod --- packages/loaders/src/omexml.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/loaders/src/omexml.ts b/packages/loaders/src/omexml.ts index cfbc9cb5c..f3edf62d5 100644 --- a/packages/loaders/src/omexml.ts +++ b/packages/loaders/src/omexml.ts @@ -93,7 +93,7 @@ const UuidSchema = z .object({}) .extend({ attr: z.object({ - UUID: z.string() + FileName: z.string() }) }) .transform(flattenAttributes); From 60f108fec9045b70ff8956288b944c16634c2b4c Mon Sep 17 00:00:00 2001 From: Trevor Manz Date: Mon, 13 Nov 2023 09:09:45 -0500 Subject: [PATCH 6/6] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 769e3186d..8fb84c4e6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Update dev dependencies - Drop `fast-xml-parser` dependency in `@vivjs/loaders` - Validate expected OME-XML data-types +- Set default `extensions` in `OverviewLayer` ## 0.13.8