@vitessce/spatial-utils 3.6.11 → 3.6.12
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/{deflate-CBbIkiez.js → deflate-TxuAgoYJ.js} +1 -1
- package/dist/{index-SrBFQLfa.js → index-B7UQn9SL.js} +168 -51
- package/dist/index.js +17 -16
- package/dist/{jpeg-CPDP-GQ7.js → jpeg-C55SiNtf.js} +1 -1
- package/dist/{lerc-DqLmboAn.js → lerc-cC8m0WBJ.js} +1 -1
- package/dist/{lzw-m-7_MlEr.js → lzw-CEZtZPvs.js} +1 -1
- package/dist/{packbits-D2Yz8IY3.js → packbits-BDxIgeb9.js} +1 -1
- package/dist/{raw-C8msAWCy.js → raw-NP8gx4mT.js} +1 -1
- package/dist/{webimage-CBuzuQEe.js → webimage-BMtq3qgy.js} +1 -1
- package/dist-tsc/dag.d.ts +35 -0
- package/dist-tsc/dag.d.ts.map +1 -0
- package/dist-tsc/dag.js +75 -0
- package/dist-tsc/dag.test.d.ts +2 -0
- package/dist-tsc/dag.test.d.ts.map +1 -0
- package/dist-tsc/dag.test.js +29 -0
- package/dist-tsc/index.d.ts +1 -1
- package/dist-tsc/index.js +1 -1
- package/dist-tsc/spatial.d.ts +25 -0
- package/dist-tsc/spatial.d.ts.map +1 -1
- package/dist-tsc/spatial.js +71 -29
- package/dist-tsc/spatial.test.js +544 -1
- package/package.json +8 -7
- package/src/dag.js +83 -0
- package/src/dag.test.js +34 -0
- package/src/index.js +1 -0
- package/src/spatial.js +85 -30
- package/src/spatial.test.js +547 -0
package/dist-tsc/spatial.test.js
CHANGED
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@@ -1,5 +1,5 @@
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import { describe, it, expect } from 'vitest';
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-
import { coordinateTransformationsToMatrix, normalizeCoordinateTransformations, getSwapAxesMatrix, } from './spatial.js';
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import { coordinateTransformationsToMatrix, normalizeCoordinateTransformations, getSwapAxesMatrix, coordinateTransformationsToMatrixForSpatialData, } from './spatial.js';
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const defaultAxes = [
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{ type: 'time', name: 't' },
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{ type: 'channel', name: 'c' },
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@@ -300,6 +300,44 @@ describe('Spatial.js', () => {
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// the user to specify this somehow and use that information to filter which transforms
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// are included here.
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{
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input: {
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axes: [
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{
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name: 'c',
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type: 'channel',
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},
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'cyx',
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},
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output: {
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axes: [
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{
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name: 'c',
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type: 'channel',
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},
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'ST8059048',
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},
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scale: [
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1.0,
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8.670500183814605,
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@@ -310,4 +348,509 @@ describe('Spatial.js', () => {
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]);
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});
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});
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describe('coordinateTransformationsToMatrixForSpatialData', () => {
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it('supports transformations from visium_hd_3.0.0_io.zip labels/rasterized_016um element', () => {
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const zattrs = {
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'image-label': {
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version: '0.4-dev-spatialdata',
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},
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multiscales: [
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{
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axes: [
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{
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name: 'y',
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type: 'space',
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},
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{
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name: 'x',
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type: 'space',
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},
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],
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coordinateTransformations: [
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{
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input: {
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axes: [
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'yx',
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},
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output: {
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axes: [
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'Visium_HD_Mouse_Small_Intestine',
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},
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transformations: [
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{
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input: {
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axes: [
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'yx',
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},
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output: {
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axes: [
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'global',
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},
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transformations: [
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{
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affine: [
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[
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-0.38,
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257.07,
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],
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[
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-0.38,
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24102.79,
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],
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],
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input: {
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axes: [
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{
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name: 'y',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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],
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name: 'yx',
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},
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output: {
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axes: [
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name: 'x',
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type: 'space',
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unit: 'unit',
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},
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{
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name: 'y',
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unit: 'unit',
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},
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],
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name: 'global',
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},
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type: 'affine',
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},
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],
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name: 'xy',
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output: {
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name: 'y',
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unit: 'unit',
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name: 'global',
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type: 'identity',
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unit: 'unit',
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},
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],
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name: 'Visium_HD_Mouse_Small_Intestine_downscaled_hires',
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},
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transformations: [
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input: {
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axes: [
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},
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name: 'yx',
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unit: 'unit',
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name: 'global',
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transformations: [
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],
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output: {
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name: 'global',
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name: 'xy',
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output: {
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axes: [
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name: 'x',
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type: 'space',
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unit: 'unit',
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name: 'y',
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type: 'space',
|
|
656
|
+
unit: 'unit',
|
|
657
|
+
},
|
|
658
|
+
],
|
|
659
|
+
name: 'global',
|
|
660
|
+
},
|
|
661
|
+
scale: [
|
|
662
|
+
0.25,
|
|
663
|
+
0.25,
|
|
664
|
+
],
|
|
665
|
+
type: 'scale',
|
|
666
|
+
},
|
|
667
|
+
],
|
|
668
|
+
type: 'sequence',
|
|
669
|
+
},
|
|
670
|
+
{
|
|
671
|
+
input: {
|
|
672
|
+
axes: [
|
|
673
|
+
{
|
|
674
|
+
name: 'y',
|
|
675
|
+
type: 'space',
|
|
676
|
+
unit: 'unit',
|
|
677
|
+
},
|
|
678
|
+
{
|
|
679
|
+
name: 'x',
|
|
680
|
+
type: 'space',
|
|
681
|
+
unit: 'unit',
|
|
682
|
+
},
|
|
683
|
+
],
|
|
684
|
+
name: 'yx',
|
|
685
|
+
},
|
|
686
|
+
output: {
|
|
687
|
+
axes: [
|
|
688
|
+
{
|
|
689
|
+
name: 'x',
|
|
690
|
+
type: 'space',
|
|
691
|
+
unit: 'unit',
|
|
692
|
+
},
|
|
693
|
+
{
|
|
694
|
+
name: 'y',
|
|
695
|
+
type: 'space',
|
|
696
|
+
unit: 'unit',
|
|
697
|
+
},
|
|
698
|
+
],
|
|
699
|
+
name: 'Visium_HD_Mouse_Small_Intestine_downscaled_lowres',
|
|
700
|
+
},
|
|
701
|
+
transformations: [
|
|
702
|
+
{
|
|
703
|
+
input: {
|
|
704
|
+
axes: [
|
|
705
|
+
{
|
|
706
|
+
name: 'y',
|
|
707
|
+
type: 'space',
|
|
708
|
+
unit: 'unit',
|
|
709
|
+
},
|
|
710
|
+
{
|
|
711
|
+
name: 'x',
|
|
712
|
+
type: 'space',
|
|
713
|
+
unit: 'unit',
|
|
714
|
+
},
|
|
715
|
+
],
|
|
716
|
+
name: 'yx',
|
|
717
|
+
},
|
|
718
|
+
output: {
|
|
719
|
+
axes: [
|
|
720
|
+
{
|
|
721
|
+
name: 'x',
|
|
722
|
+
type: 'space',
|
|
723
|
+
unit: 'unit',
|
|
724
|
+
},
|
|
725
|
+
{
|
|
726
|
+
name: 'y',
|
|
727
|
+
type: 'space',
|
|
728
|
+
unit: 'unit',
|
|
729
|
+
},
|
|
730
|
+
],
|
|
731
|
+
name: 'global',
|
|
732
|
+
},
|
|
733
|
+
transformations: [
|
|
734
|
+
{
|
|
735
|
+
affine: [
|
|
736
|
+
[
|
|
737
|
+
-0.38,
|
|
738
|
+
58.43,
|
|
739
|
+
257.07,
|
|
740
|
+
],
|
|
741
|
+
[
|
|
742
|
+
-58.42,
|
|
743
|
+
-0.38,
|
|
744
|
+
24102.79,
|
|
745
|
+
],
|
|
746
|
+
],
|
|
747
|
+
input: {
|
|
748
|
+
axes: [
|
|
749
|
+
{
|
|
750
|
+
name: 'y',
|
|
751
|
+
type: 'space',
|
|
752
|
+
unit: 'unit',
|
|
753
|
+
},
|
|
754
|
+
{
|
|
755
|
+
name: 'x',
|
|
756
|
+
type: 'space',
|
|
757
|
+
unit: 'unit',
|
|
758
|
+
},
|
|
759
|
+
],
|
|
760
|
+
name: 'yx',
|
|
761
|
+
},
|
|
762
|
+
output: {
|
|
763
|
+
axes: [
|
|
764
|
+
{
|
|
765
|
+
name: 'x',
|
|
766
|
+
type: 'space',
|
|
767
|
+
unit: 'unit',
|
|
768
|
+
},
|
|
769
|
+
{
|
|
770
|
+
name: 'y',
|
|
771
|
+
type: 'space',
|
|
772
|
+
unit: 'unit',
|
|
773
|
+
},
|
|
774
|
+
],
|
|
775
|
+
name: 'global',
|
|
776
|
+
},
|
|
777
|
+
type: 'affine',
|
|
778
|
+
},
|
|
779
|
+
],
|
|
780
|
+
type: 'sequence',
|
|
781
|
+
},
|
|
782
|
+
{
|
|
783
|
+
input: {
|
|
784
|
+
axes: [
|
|
785
|
+
{
|
|
786
|
+
name: 'x',
|
|
787
|
+
type: 'space',
|
|
788
|
+
unit: 'unit',
|
|
789
|
+
},
|
|
790
|
+
{
|
|
791
|
+
name: 'y',
|
|
792
|
+
type: 'space',
|
|
793
|
+
unit: 'unit',
|
|
794
|
+
},
|
|
795
|
+
],
|
|
796
|
+
name: 'xy',
|
|
797
|
+
},
|
|
798
|
+
output: {
|
|
799
|
+
axes: [
|
|
800
|
+
{
|
|
801
|
+
name: 'x',
|
|
802
|
+
type: 'space',
|
|
803
|
+
unit: 'unit',
|
|
804
|
+
},
|
|
805
|
+
{
|
|
806
|
+
name: 'y',
|
|
807
|
+
type: 'space',
|
|
808
|
+
unit: 'unit',
|
|
809
|
+
},
|
|
810
|
+
],
|
|
811
|
+
name: 'global',
|
|
812
|
+
},
|
|
813
|
+
scale: [
|
|
814
|
+
0.025,
|
|
815
|
+
0.025,
|
|
816
|
+
],
|
|
817
|
+
type: 'scale',
|
|
818
|
+
},
|
|
819
|
+
],
|
|
820
|
+
type: 'sequence',
|
|
821
|
+
},
|
|
822
|
+
],
|
|
823
|
+
datasets: [
|
|
824
|
+
{
|
|
825
|
+
coordinateTransformations: [
|
|
826
|
+
{
|
|
827
|
+
scale: [
|
|
828
|
+
1.0,
|
|
829
|
+
1.0,
|
|
830
|
+
],
|
|
831
|
+
type: 'scale',
|
|
832
|
+
},
|
|
833
|
+
],
|
|
834
|
+
path: '0',
|
|
835
|
+
},
|
|
836
|
+
],
|
|
837
|
+
name: 'rasterized_016um',
|
|
838
|
+
version: '0.4-dev-spatialdata',
|
|
839
|
+
},
|
|
840
|
+
],
|
|
841
|
+
spatialdata_attrs: {
|
|
842
|
+
version: '0.2',
|
|
843
|
+
},
|
|
844
|
+
};
|
|
845
|
+
const firstMultiscales = zattrs.multiscales[0];
|
|
846
|
+
const targetCoordinateSystem = 'Visium_HD_Mouse_Small_Intestine';
|
|
847
|
+
const matrix = coordinateTransformationsToMatrixForSpatialData(firstMultiscales, targetCoordinateSystem);
|
|
848
|
+
expect(matrix).toEqual([
|
|
849
|
+
58.43, -0.38, 0, 0,
|
|
850
|
+
-0.38, -58.42, 0, 0,
|
|
851
|
+
0, 0, 1, 0,
|
|
852
|
+
257.07, 24102.79, 0, 1,
|
|
853
|
+
]);
|
|
854
|
+
});
|
|
855
|
+
});
|
|
313
856
|
});
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@vitessce/spatial-utils",
|
|
3
|
-
"version": "3.6.
|
|
3
|
+
"version": "3.6.12",
|
|
4
4
|
"author": "HIDIVE Lab at HMS",
|
|
5
5
|
"homepage": "http://vitessce.io",
|
|
6
6
|
"repository": {
|
|
@@ -20,12 +20,13 @@
|
|
|
20
20
|
"zarrita": "0.5.2",
|
|
21
21
|
"math.gl": "^3.5.6",
|
|
22
22
|
"mathjs": "^9.2.0",
|
|
23
|
-
"
|
|
24
|
-
"@vitessce/
|
|
25
|
-
"@vitessce/
|
|
26
|
-
"@vitessce/
|
|
27
|
-
"@vitessce/
|
|
28
|
-
"@vitessce/
|
|
23
|
+
"internmap": "^2.0.3",
|
|
24
|
+
"@vitessce/gl": "3.6.12",
|
|
25
|
+
"@vitessce/utils": "3.6.12",
|
|
26
|
+
"@vitessce/zarr-utils": "3.6.12",
|
|
27
|
+
"@vitessce/constants-internal": "3.6.12",
|
|
28
|
+
"@vitessce/globals": "3.6.12",
|
|
29
|
+
"@vitessce/error": "3.6.12"
|
|
29
30
|
},
|
|
30
31
|
"scripts": {
|
|
31
32
|
"bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",
|
package/src/dag.js
ADDED
|
@@ -0,0 +1,83 @@
|
|
|
1
|
+
import { InternMap } from 'internmap';
|
|
2
|
+
|
|
3
|
+
|
|
4
|
+
// Simple DAG class, with minimum functionality:
|
|
5
|
+
// to find a path from targetInput-to-targetOutput.
|
|
6
|
+
// Edges can have arbitrary attributes.
|
|
7
|
+
export class DAG {
|
|
8
|
+
/**
|
|
9
|
+
* DAG constructor.
|
|
10
|
+
* @param {{ from: string, to: string, attributes: any}[]} edges
|
|
11
|
+
*/
|
|
12
|
+
constructor(edges) {
|
|
13
|
+
/**
|
|
14
|
+
* Adjacency list representation of the DAG.
|
|
15
|
+
* Maps each input to an array of outputs.
|
|
16
|
+
* @type {Map<string, string[]>}
|
|
17
|
+
*/
|
|
18
|
+
this.graph = new Map();
|
|
19
|
+
/**
|
|
20
|
+
* Mapping from [from, to] pairs to edge data.
|
|
21
|
+
* @type {InternMap<[string, string], any>}
|
|
22
|
+
*/
|
|
23
|
+
this.edgeData = new InternMap([], JSON.stringify);
|
|
24
|
+
|
|
25
|
+
// Build adjacency list
|
|
26
|
+
edges.forEach((edge) => {
|
|
27
|
+
const { from, to } = edge;
|
|
28
|
+
if (!this.graph.has(from)) {
|
|
29
|
+
this.graph.set(from, []);
|
|
30
|
+
}
|
|
31
|
+
this.graph.get(from).push(to);
|
|
32
|
+
this.edgeData.set([from, to], edge.attributes);
|
|
33
|
+
});
|
|
34
|
+
}
|
|
35
|
+
|
|
36
|
+
/**
|
|
37
|
+
* Find a path from start to end using DFS.
|
|
38
|
+
* @param {string} start
|
|
39
|
+
* @param {string} end
|
|
40
|
+
* @returns {{ from: string, to: string, attributes: any }[] | null} Returns
|
|
41
|
+
* the path as an array of edges or null if no path exists.
|
|
42
|
+
*/
|
|
43
|
+
findPath(start, end) {
|
|
44
|
+
const path = [];
|
|
45
|
+
const visited = new Set();
|
|
46
|
+
|
|
47
|
+
// Depth-first search (DFS) to find a path from start to end.
|
|
48
|
+
const dfs = (node) => {
|
|
49
|
+
if (node === end) {
|
|
50
|
+
return true;
|
|
51
|
+
}
|
|
52
|
+
visited.add(node);
|
|
53
|
+
|
|
54
|
+
const neighbors = this.graph.get(node) || [];
|
|
55
|
+
// Do not use forEach to allow early exit (returning).
|
|
56
|
+
// eslint-disable-next-line no-restricted-syntax
|
|
57
|
+
for (const neighbor of neighbors) {
|
|
58
|
+
if (!visited.has(neighbor)) {
|
|
59
|
+
path.push([node, neighbor]);
|
|
60
|
+
if (dfs(neighbor)) {
|
|
61
|
+
return true;
|
|
62
|
+
}
|
|
63
|
+
path.pop(); // backtrack
|
|
64
|
+
}
|
|
65
|
+
}
|
|
66
|
+
|
|
67
|
+
return false;
|
|
68
|
+
};
|
|
69
|
+
|
|
70
|
+
// Start DFS from the start node.
|
|
71
|
+
const found = dfs(start);
|
|
72
|
+
if (found) {
|
|
73
|
+
// Convert path to a list of edge objects with info
|
|
74
|
+
return path.map(([from, to]) => ({
|
|
75
|
+
from,
|
|
76
|
+
to,
|
|
77
|
+
attributes: this.edgeData.get([from, to]),
|
|
78
|
+
}));
|
|
79
|
+
}
|
|
80
|
+
// If no path is found, return null.
|
|
81
|
+
return null;
|
|
82
|
+
}
|
|
83
|
+
}
|