@vitessce/spatial-utils 3.6.10 → 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-D50eseYg.js → deflate-TxuAgoYJ.js} +1 -1
- package/dist/{index-RMBcVNTZ.js → index-B7UQn9SL.js} +170 -52
- package/dist/index.js +17 -16
- package/dist/{jpeg-Dp762_Sy.js → jpeg-C55SiNtf.js} +1 -1
- package/dist/{lerc-R19D-u1d.js → lerc-cC8m0WBJ.js} +1 -1
- package/dist/{lzw-CS9qpOLK.js → lzw-CEZtZPvs.js} +1 -1
- package/dist/{packbits-smBOUAP8.js → packbits-BDxIgeb9.js} +1 -1
- package/dist/{raw-B-RRtlid.js → raw-NP8gx4mT.js} +1 -1
- package/dist/{webimage-CZyj01Qe.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/src/spatial.test.js
CHANGED
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@@ -3,6 +3,7 @@ import {
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coordinateTransformationsToMatrix,
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normalizeCoordinateTransformations,
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getSwapAxesMatrix,
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coordinateTransformationsToMatrixForSpatialData,
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} from './spatial.js';
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const defaultAxes = [
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@@ -308,6 +309,44 @@ 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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@@ -318,4 +357,512 @@ 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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58.43,
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257.07,
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],
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[
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-58.42,
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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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{
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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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type: 'affine',
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},
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],
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type: 'sequence',
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input: {
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unit: 'unit',
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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: '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',
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unit: 'unit',
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],
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name: 'global',
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type: 'identity',
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type: 'sequence',
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input: {
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axes: [
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name: 'y',
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unit: 'unit',
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name: 'x',
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unit: 'unit',
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name: 'yx',
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output: {
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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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name: 'y',
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unit: 'unit',
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name: 'yx',
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output: {
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unit: 'unit',
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name: 'global',
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transformations: [
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affine: [
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],
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input: {
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name: 'yx',
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name: 'global',
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type: 'affine',
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name: 'xy',
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output: {
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unit: 'unit',
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},
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+
],
|
|
668
|
+
name: 'global',
|
|
669
|
+
},
|
|
670
|
+
scale: [
|
|
671
|
+
0.25,
|
|
672
|
+
0.25,
|
|
673
|
+
],
|
|
674
|
+
type: 'scale',
|
|
675
|
+
},
|
|
676
|
+
],
|
|
677
|
+
type: 'sequence',
|
|
678
|
+
},
|
|
679
|
+
{
|
|
680
|
+
input: {
|
|
681
|
+
axes: [
|
|
682
|
+
{
|
|
683
|
+
name: 'y',
|
|
684
|
+
type: 'space',
|
|
685
|
+
unit: 'unit',
|
|
686
|
+
},
|
|
687
|
+
{
|
|
688
|
+
name: 'x',
|
|
689
|
+
type: 'space',
|
|
690
|
+
unit: 'unit',
|
|
691
|
+
},
|
|
692
|
+
],
|
|
693
|
+
name: 'yx',
|
|
694
|
+
},
|
|
695
|
+
output: {
|
|
696
|
+
axes: [
|
|
697
|
+
{
|
|
698
|
+
name: 'x',
|
|
699
|
+
type: 'space',
|
|
700
|
+
unit: 'unit',
|
|
701
|
+
},
|
|
702
|
+
{
|
|
703
|
+
name: 'y',
|
|
704
|
+
type: 'space',
|
|
705
|
+
unit: 'unit',
|
|
706
|
+
},
|
|
707
|
+
],
|
|
708
|
+
name: 'Visium_HD_Mouse_Small_Intestine_downscaled_lowres',
|
|
709
|
+
},
|
|
710
|
+
transformations: [
|
|
711
|
+
{
|
|
712
|
+
input: {
|
|
713
|
+
axes: [
|
|
714
|
+
{
|
|
715
|
+
name: 'y',
|
|
716
|
+
type: 'space',
|
|
717
|
+
unit: 'unit',
|
|
718
|
+
},
|
|
719
|
+
{
|
|
720
|
+
name: 'x',
|
|
721
|
+
type: 'space',
|
|
722
|
+
unit: 'unit',
|
|
723
|
+
},
|
|
724
|
+
],
|
|
725
|
+
name: 'yx',
|
|
726
|
+
},
|
|
727
|
+
output: {
|
|
728
|
+
axes: [
|
|
729
|
+
{
|
|
730
|
+
name: 'x',
|
|
731
|
+
type: 'space',
|
|
732
|
+
unit: 'unit',
|
|
733
|
+
},
|
|
734
|
+
{
|
|
735
|
+
name: 'y',
|
|
736
|
+
type: 'space',
|
|
737
|
+
unit: 'unit',
|
|
738
|
+
},
|
|
739
|
+
],
|
|
740
|
+
name: 'global',
|
|
741
|
+
},
|
|
742
|
+
transformations: [
|
|
743
|
+
{
|
|
744
|
+
affine: [
|
|
745
|
+
[
|
|
746
|
+
-0.38,
|
|
747
|
+
58.43,
|
|
748
|
+
257.07,
|
|
749
|
+
],
|
|
750
|
+
[
|
|
751
|
+
-58.42,
|
|
752
|
+
-0.38,
|
|
753
|
+
24102.79,
|
|
754
|
+
],
|
|
755
|
+
],
|
|
756
|
+
input: {
|
|
757
|
+
axes: [
|
|
758
|
+
{
|
|
759
|
+
name: 'y',
|
|
760
|
+
type: 'space',
|
|
761
|
+
unit: 'unit',
|
|
762
|
+
},
|
|
763
|
+
{
|
|
764
|
+
name: 'x',
|
|
765
|
+
type: 'space',
|
|
766
|
+
unit: 'unit',
|
|
767
|
+
},
|
|
768
|
+
],
|
|
769
|
+
name: 'yx',
|
|
770
|
+
},
|
|
771
|
+
output: {
|
|
772
|
+
axes: [
|
|
773
|
+
{
|
|
774
|
+
name: 'x',
|
|
775
|
+
type: 'space',
|
|
776
|
+
unit: 'unit',
|
|
777
|
+
},
|
|
778
|
+
{
|
|
779
|
+
name: 'y',
|
|
780
|
+
type: 'space',
|
|
781
|
+
unit: 'unit',
|
|
782
|
+
},
|
|
783
|
+
],
|
|
784
|
+
name: 'global',
|
|
785
|
+
},
|
|
786
|
+
type: 'affine',
|
|
787
|
+
},
|
|
788
|
+
],
|
|
789
|
+
type: 'sequence',
|
|
790
|
+
},
|
|
791
|
+
{
|
|
792
|
+
input: {
|
|
793
|
+
axes: [
|
|
794
|
+
{
|
|
795
|
+
name: 'x',
|
|
796
|
+
type: 'space',
|
|
797
|
+
unit: 'unit',
|
|
798
|
+
},
|
|
799
|
+
{
|
|
800
|
+
name: 'y',
|
|
801
|
+
type: 'space',
|
|
802
|
+
unit: 'unit',
|
|
803
|
+
},
|
|
804
|
+
],
|
|
805
|
+
name: 'xy',
|
|
806
|
+
},
|
|
807
|
+
output: {
|
|
808
|
+
axes: [
|
|
809
|
+
{
|
|
810
|
+
name: 'x',
|
|
811
|
+
type: 'space',
|
|
812
|
+
unit: 'unit',
|
|
813
|
+
},
|
|
814
|
+
{
|
|
815
|
+
name: 'y',
|
|
816
|
+
type: 'space',
|
|
817
|
+
unit: 'unit',
|
|
818
|
+
},
|
|
819
|
+
],
|
|
820
|
+
name: 'global',
|
|
821
|
+
},
|
|
822
|
+
scale: [
|
|
823
|
+
0.025,
|
|
824
|
+
0.025,
|
|
825
|
+
],
|
|
826
|
+
type: 'scale',
|
|
827
|
+
},
|
|
828
|
+
],
|
|
829
|
+
type: 'sequence',
|
|
830
|
+
},
|
|
831
|
+
],
|
|
832
|
+
datasets: [
|
|
833
|
+
{
|
|
834
|
+
coordinateTransformations: [
|
|
835
|
+
{
|
|
836
|
+
scale: [
|
|
837
|
+
1.0,
|
|
838
|
+
1.0,
|
|
839
|
+
],
|
|
840
|
+
type: 'scale',
|
|
841
|
+
},
|
|
842
|
+
],
|
|
843
|
+
path: '0',
|
|
844
|
+
},
|
|
845
|
+
],
|
|
846
|
+
name: 'rasterized_016um',
|
|
847
|
+
version: '0.4-dev-spatialdata',
|
|
848
|
+
},
|
|
849
|
+
],
|
|
850
|
+
spatialdata_attrs: {
|
|
851
|
+
version: '0.2',
|
|
852
|
+
},
|
|
853
|
+
};
|
|
854
|
+
const firstMultiscales = zattrs.multiscales[0];
|
|
855
|
+
const targetCoordinateSystem = 'Visium_HD_Mouse_Small_Intestine';
|
|
856
|
+
const matrix = coordinateTransformationsToMatrixForSpatialData(
|
|
857
|
+
firstMultiscales,
|
|
858
|
+
targetCoordinateSystem,
|
|
859
|
+
);
|
|
860
|
+
expect(matrix).toEqual([
|
|
861
|
+
58.43, -0.38, 0, 0,
|
|
862
|
+
-0.38, -58.42, 0, 0,
|
|
863
|
+
0, 0, 1, 0,
|
|
864
|
+
257.07, 24102.79, 0, 1,
|
|
865
|
+
]);
|
|
866
|
+
});
|
|
867
|
+
});
|
|
321
868
|
});
|