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Noah/fix omezarr tile math mistake #45

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merged 4 commits into from
Dec 2, 2024
Merged

Noah/fix omezarr tile math mistake #45

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06a9f2f
fix a small mistake that would "visit" tiles that could extend past t…
froyo-np Dec 2, 2024
d70d164
use original versa demo image
froyo-np Dec 2, 2024
2d4bc13
add a super basic regression test for this bug
froyo-np Dec 2, 2024
b4d62c7
formatting
froyo-np Dec 2, 2024
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1 change: 0 additions & 1 deletion examples/src/omezarr/app.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ import { SliceView } from './sliceview';
import { type OmeZarrDataset, loadOmeZarr } from '@alleninstitute/vis-omezarr';

const demo_versa = 'https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/';

export function AppUi() {
return <DataPlease />;
}
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16 changes: 14 additions & 2 deletions examples/src/omezarr/sliceview.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ import {
type RenderSettings,
} from '@alleninstitute/vis-omezarr';
import type { RenderFrameFn } from '@alleninstitute/vis-scatterbrain';
import React, { useState } from 'react';
import React, { useCallback, useState } from 'react';
import { useContext, useEffect, useRef } from 'react';
import { renderServerContext } from '~/common/react/render-server-provider';
type Props = {
Expand All @@ -21,7 +21,7 @@ const settings: RenderSettings = {
B: { gamut: { min: 0, max: 100 }, index: 2 },
},
plane: 'xy',
planeIndex: 0,
planeIndex: 3,
camera: {
view: Box2D.create([0, 0], [250, 120]),
screenSize: [500, 500],
Expand Down Expand Up @@ -82,10 +82,22 @@ export function SliceView(props: Props) {
);
}
}, [server, renderer.current, cnvs.current, omezarr, view]);
const pan = useCallback(
(e: React.MouseEvent<HTMLCanvasElement>) => {
if (e.ctrlKey) {
const pos = Vec2.div([-e.movementX, -e.movementY], settings.camera.screenSize);
const scaledOffset = Vec2.mul(pos, Box2D.size(view));
const v = Box2D.translate(view, scaledOffset);
setView(v);
}
},
[view]
);
return (
<canvas
id={'hey there'}
ref={cnvs}
onMouseMove={pan}
onWheel={(e) => {
const scale = e.deltaY > 0 ? 1.1 : 0.9;
const m = Box2D.midpoint(view);
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2 changes: 1 addition & 1 deletion packages/omezarr/package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "@alleninstitute/vis-omezarr",
"version": "0.0.1",
"version": "0.0.2",
"contributors": [
{
"name": "Lane Sawyer",
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195 changes: 195 additions & 0 deletions packages/omezarr/src/sliceview/loader.test.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,195 @@
import type { ZarrDataset } from '../zarr-data';
import { describe, expect, it } from 'vitest';
import { Box2D, box2D } from '@alleninstitute/vis-geometry';
import { getVisibleTiles } from './loader';
const exampleOmeZarr: ZarrDataset = {
url: 'https://allen-genetic-tools.s3.us-west-2.amazonaws.com/tissuecyte/1263343692/ome-zarr/',
multiscales: [
{
axes: [
{
name: 'c',
type: 'channel',
unit: 'millimeter',
},
{
name: 'z',
type: 'space',
unit: 'millimeter',
},
{
name: 'y',
type: 'space',
unit: 'millimeter',
},
{
name: 'x',
type: 'space',
unit: 'millimeter',
},
],
datasets: [
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.00035, 0.00035],
type: 'scale',
},
{
translation: [0, 0, 0, 0],
type: 'translation',
},
],
path: '0',
shape: [3, 142, 29998, 39998],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0007, 0.0007],
type: 'scale',
},
{
translation: [0, 0, 0.00035, 0.00035],
type: 'translation',
},
],
path: '1',
shape: [3, 142, 14999, 19999],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0014, 0.0014],
type: 'scale',
},
{
translation: [0, 0, 0.00105, 0.00105],
type: 'translation',
},
],
path: '2',
shape: [3, 142, 7499, 9999],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0028, 0.0028],
type: 'scale',
},
{
translation: [0, 0, 0.00245, 0.00245],
type: 'translation',
},
],
path: '3',
shape: [3, 142, 3749, 4999],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0056, 0.0056],
type: 'scale',
},
{
translation: [0, 0, 0.00525, 0.00525],
type: 'translation',
},
],
path: '4',
shape: [3, 142, 1874, 2499],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0112, 0.0112],
type: 'scale',
},
{
translation: [0, 0, 0.01085, 0.01085],
type: 'translation',
},
],
path: '5',
shape: [3, 142, 937, 1249],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0224, 0.0224],
type: 'scale',
},
{
translation: [0, 0, 0.02205, 0.02205],
type: 'translation',
},
],
path: '6',
shape: [3, 142, 468, 624],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0448, 0.0448],
type: 'scale',
},
{
translation: [0, 0, 0.044449999999999996, 0.044449999999999996],
type: 'translation',
},
],
path: '7',
shape: [3, 142, 234, 312],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.0896, 0.0896],
type: 'scale',
},
{
translation: [0, 0, 0.08925, 0.08925],
type: 'translation',
},
],
path: '8',
shape: [3, 142, 117, 156],
},
{
coordinateTransformations: [
{
scale: [1, 0.1, 0.1792, 0.1792],
type: 'scale',
},
{
translation: [0, 0, 0.17885, 0.17885],
type: 'translation',
},
],
path: '9',
shape: [3, 142, 58, 78],
},
],
},
],
};

describe('omezarr basic tiled loading', () => {
describe('getVisibleTiles', () => {
it('visible tiles cannot extend beyond the bounds of their layer', () => {
const view: box2D = {
minCorner: [-7, -11],
maxCorner: [28, 35],
};
const camera = { view, screenSize: [210, 210] as const };
const visible = getVisibleTiles(camera, 'xy', 2, exampleOmeZarr, 256);
// this is a basic regression test: we had a bug which would result in
// tiles from the image being larger than the image itself (they would be the given tile size)
expect(visible.length).toBe(1);
const expectedLayer = exampleOmeZarr.multiscales[0].datasets[9];
// we expect to be seeing the lowest resolution layer with our very zoomed out, low res camera
const [_c, _z, y, x] = expectedLayer.shape;
expect(visible[0].bounds).toEqual(Box2D.create([0, 0], [x, y]));
});
});
});
2 changes: 1 addition & 1 deletion packages/omezarr/src/sliceview/loader.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ function visitTilesWithin(idealTilePx: vec2, size: vec2, bounds: box2D, visit: (
for (let y = Math.floor(boundsInTiles.minCorner[1]); y < Math.ceil(boundsInTiles.maxCorner[1]); y += 1) {
// all tiles visited are always within both the bounds, and the image itself
const lo = Vec2.mul([x, y], idealTilePx);
const hi = Vec2.add(lo, idealTilePx);
const hi = Vec2.min(size, Vec2.add(lo, idealTilePx));
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this is the fix - it limits the visited tiles by the total size of the image. The bug here caused a bunch of math later in the process to be incorrect, because the tiles extended past what was actually possible.

visit(Box2D.create(lo, hi));
}
}
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