@vitessce/all 3.3.2 → 3.3.3

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.
Files changed (19) hide show
  1. package/dist/{deflate-71cf29f7.js → deflate-ff8e0389.js} +1 -1
  2. package/dist/{hglib-872ad77b.js → hglib-6e6aad2d.js} +1 -1
  3. package/dist/{index-e1f3ff32.js → index-e7182d2c.js} +662 -92
  4. package/dist/index.js +1 -1
  5. package/dist/{jpeg-b2781c48.js → jpeg-dc640134.js} +1 -1
  6. package/dist/{lerc-69270d36.js → lerc-42f701c0.js} +1 -1
  7. package/dist/{lzw-3f41da4f.js → lzw-846a70ec.js} +1 -1
  8. package/dist/{packbits-19b767c9.js → packbits-8a313c48.js} +1 -1
  9. package/dist/{raw-bd484be0.js → raw-81ed6601.js} +1 -1
  10. package/dist/{webimage-c810ada2.js → webimage-72021080.js} +1 -1
  11. package/dist-tsc/base-plugins.d.ts +187 -0
  12. package/dist-tsc/base-plugins.d.ts.map +1 -1
  13. package/dist-tsc/base-plugins.js +7 -6
  14. package/dist-tsc/joint-file-types.d.ts +27 -0
  15. package/dist-tsc/joint-file-types.d.ts.map +1 -1
  16. package/dist-tsc/joint-file-types.js +77 -0
  17. package/package.json +22 -22
  18. package/src/base-plugins.ts +9 -3
  19. package/src/joint-file-types.ts +78 -0
package/dist/index.js CHANGED
@@ -1,4 +1,4 @@
1
- import { f, P, h, d, V, z } from "./index-e1f3ff32.js";
1
+ import { f, P, h, d, V, z } from "./index-e7182d2c.js";
2
2
  import "react";
3
3
  import "@vitessce/vit-s";
4
4
  import "react-dom";
package/dist/{jpeg-b2781c48.js → jpeg-dc640134.js} RENAMED
@@ -1,4 +1,4 @@
1
- import { B as BaseDecoder } from "./index-e1f3ff32.js";
1
+ import { B as BaseDecoder } from "./index-e7182d2c.js";
2
2
  import "react";
3
3
  import "@vitessce/vit-s";
4
4
  import "react-dom";
package/dist/{lerc-69270d36.js → lerc-42f701c0.js} RENAMED
@@ -1,5 +1,5 @@
1
1
  import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
2
- import { g as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, a as LercAddCompression } from "./index-e1f3ff32.js";
2
+ import { g as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, a as LercAddCompression } from "./index-e7182d2c.js";
3
3
  import "react";
4
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  import "@vitessce/vit-s";
5
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  import "react-dom";
package/dist/{lzw-3f41da4f.js → lzw-846a70ec.js} RENAMED
@@ -1,4 +1,4 @@
1
- import { B as BaseDecoder } from "./index-e1f3ff32.js";
1
+ import { B as BaseDecoder } from "./index-e7182d2c.js";
2
2
  import "react";
3
3
  import "@vitessce/vit-s";
4
4
  import "react-dom";
package/dist/{packbits-19b767c9.js → packbits-8a313c48.js} RENAMED
@@ -1,4 +1,4 @@
1
- import { B as BaseDecoder } from "./index-e1f3ff32.js";
1
+ import { B as BaseDecoder } from "./index-e7182d2c.js";
2
2
  import "react";
3
3
  import "@vitessce/vit-s";
4
4
  import "react-dom";
package/dist/{raw-bd484be0.js → raw-81ed6601.js} RENAMED
@@ -1,4 +1,4 @@
1
- import { B as BaseDecoder } from "./index-e1f3ff32.js";
1
+ import { B as BaseDecoder } from "./index-e7182d2c.js";
2
2
  import "react";
3
3
  import "@vitessce/vit-s";
4
4
  import "react-dom";
package/dist/{webimage-c810ada2.js → webimage-72021080.js} RENAMED
@@ -1,4 +1,4 @@
1
- import { B as BaseDecoder } from "./index-e1f3ff32.js";
1
+ import { B as BaseDecoder } from "./index-e7182d2c.js";
2
2
  import "react";
3
3
  import "@vitessce/vit-s";
4
4
  import "react-dom";
package/dist-tsc/base-plugins.d.ts CHANGED
@@ -213,6 +213,193 @@ export declare const baseJointFileTypes: (PluginJointFileType<z.ZodObject<{
213
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  embeddingType: string;
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  dims?: number[] | undefined;
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  }[] | undefined;
216
+ }>> | PluginJointFileType<z.ZodObject<{
217
+ image: z.ZodOptional<z.ZodObject<{
218
+ coordinateTransformations: z.ZodOptional<z.ZodArray<z.ZodUnion<[z.ZodObject<{
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+ type: z.ZodLiteral<"identity">;
220
+ }, "strip", z.ZodTypeAny, {
221
+ type: "identity";
222
+ }, {
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+ type: "identity";
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+ }>, z.ZodObject<{
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+ type: z.ZodLiteral<"translation">;
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+ translation: z.ZodArray<z.ZodNumber, "many">;
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+ }, "strip", z.ZodTypeAny, {
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+ type: "translation";
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+ translation: number[];
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+ }, {
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+ type: "translation";
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+ translation: number[];
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+ }>, z.ZodObject<{
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+ type: z.ZodLiteral<"scale">;
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+ scale: z.ZodArray<z.ZodNumber, "many">;
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+ }, "strip", z.ZodTypeAny, {
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+ type: "scale";
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+ scale: number[];
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+ }, {
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+ type: "scale";
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+ scale: number[];
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+ }>]>, "many">>;
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+ path: z.ZodString;
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+ }, "strip", z.ZodTypeAny, {
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+ path: string;
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+ coordinateTransformations?: ({
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+ type: "identity";
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+ } | {
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+ type: "translation";
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+ translation: number[];
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+ } | {
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+ type: "scale";
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+ scale: number[];
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+ })[] | undefined;
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+ }, {
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+ path: string;
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+ coordinateTransformations?: ({
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+ type: "identity";
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+ } | {
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+ type: "translation";
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+ translation: number[];
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+ } | {
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+ type: "scale";
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+ scale: number[];
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+ })[] | undefined;
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+ }>>;
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+ labels: z.ZodOptional<z.ZodObject<{
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+ path: z.ZodString;
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+ }, "strip", z.ZodTypeAny, {
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+ path: string;
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+ }, {
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+ path: string;
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+ }>>;
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+ obsFeatureMatrix: z.ZodOptional<z.ZodObject<{
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+ path: z.ZodString;
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+ featureFilterPath: z.ZodOptional<z.ZodString>;
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+ initialFeatureFilterPath: z.ZodOptional<z.ZodString>;
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+ region: z.ZodOptional<z.ZodString>;
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+ }, "strip", z.ZodTypeAny, {
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+ path: string;
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+ featureFilterPath?: string | undefined;
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+ initialFeatureFilterPath?: string | undefined;
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+ region?: string | undefined;
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+ }, {
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+ path: string;
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+ featureFilterPath?: string | undefined;
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+ initialFeatureFilterPath?: string | undefined;
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+ region?: string | undefined;
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+ }>>;
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+ obsSpots: z.ZodOptional<z.ZodObject<{
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+ path: z.ZodString;
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+ tablePath: z.ZodOptional<z.ZodString>;
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+ }, "strip", z.ZodTypeAny, {
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+ path: string;
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+ tablePath?: string | undefined;
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+ }, {
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+ path: string;
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+ tablePath?: string | undefined;
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+ }>>;
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+ obsSets: z.ZodOptional<z.ZodObject<{
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+ region: z.ZodOptional<z.ZodString>;
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+ tablePath: z.ZodOptional<z.ZodString>;
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+ obsSets: z.ZodArray<z.ZodObject<{
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+ name: z.ZodString;
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+ path: z.ZodUnion<[z.ZodString, z.ZodArray<z.ZodString, "many">]>;
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+ scorePath: z.ZodOptional<z.ZodString>;
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+ }, "strip", z.ZodTypeAny, {
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+ path: (string | string[]) & (string | string[] | undefined);
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+ name: string;
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+ scorePath?: string | undefined;
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+ }, {
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+ path: (string | string[]) & (string | string[] | undefined);
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+ name: string;
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+ scorePath?: string | undefined;
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+ }>, "many">;
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+ }, "strip", z.ZodTypeAny, {
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+ obsSets: {
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+ path: (string | string[]) & (string | string[] | undefined);
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+ name: string;
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+ scorePath?: string | undefined;
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+ }[];
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+ region?: string | undefined;
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+ tablePath?: string | undefined;
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+ }, {
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+ obsSets: {
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+ path: (string | string[]) & (string | string[] | undefined);
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+ name: string;
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+ scorePath?: string | undefined;
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+ }[];
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+ region?: string | undefined;
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+ tablePath?: string | undefined;
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+ }>>;
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+ }, "strip", z.ZodTypeAny, {
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+ image?: {
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+ path: string;
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+ coordinateTransformations?: ({
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+ type: "identity";
338
+ } | {
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+ type: "translation";
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+ translation: number[];
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+ } | {
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+ type: "scale";
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+ scale: number[];
344
+ })[] | undefined;
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+ } | undefined;
346
+ labels?: {
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+ path: string;
348
+ } | undefined;
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+ obsFeatureMatrix?: {
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+ path: string;
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+ featureFilterPath?: string | undefined;
352
+ initialFeatureFilterPath?: string | undefined;
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+ region?: string | undefined;
354
+ } | undefined;
355
+ obsSpots?: {
356
+ path: string;
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+ tablePath?: string | undefined;
358
+ } | undefined;
359
+ obsSets?: {
360
+ obsSets: {
361
+ path: (string | string[]) & (string | string[] | undefined);
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+ name: string;
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+ scorePath?: string | undefined;
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+ }[];
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+ region?: string | undefined;
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+ tablePath?: string | undefined;
367
+ } | undefined;
368
+ }, {
369
+ image?: {
370
+ path: string;
371
+ coordinateTransformations?: ({
372
+ type: "identity";
373
+ } | {
374
+ type: "translation";
375
+ translation: number[];
376
+ } | {
377
+ type: "scale";
378
+ scale: number[];
379
+ })[] | undefined;
380
+ } | undefined;
381
+ labels?: {
382
+ path: string;
383
+ } | undefined;
384
+ obsFeatureMatrix?: {
385
+ path: string;
386
+ featureFilterPath?: string | undefined;
387
+ initialFeatureFilterPath?: string | undefined;
388
+ region?: string | undefined;
389
+ } | undefined;
390
+ obsSpots?: {
391
+ path: string;
392
+ tablePath?: string | undefined;
393
+ } | undefined;
394
+ obsSets?: {
395
+ obsSets: {
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+ path: (string | string[]) & (string | string[] | undefined);
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+ name: string;
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+ scorePath?: string | undefined;
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+ }[];
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+ region?: string | undefined;
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+ tablePath?: string | undefined;
402
+ } | undefined;
216
403
  }>> | PluginJointFileType<z.ZodObject<{
217
404
  xy: z.ZodOptional<z.ZodString>;
218
405
  poly: z.ZodOptional<z.ZodString>;
package/dist-tsc/base-plugins.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AASA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EAqCF,MAAM,mBAAmB,CAAC;AAiH3B,eAAO,MAAM,aAAa,kBAiBzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA8DzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAe9B,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;4WAmLjC,CAAC"}
1
+ {"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AASA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EAwCF,MAAM,mBAAmB,CAAC;AAmH3B,eAAO,MAAM,aAAa,kBAiBzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA+DzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAe9B,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;4WAmLjC,CAAC"}
package/dist-tsc/base-plugins.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import { FileType, DataType, ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, } from '@vitessce/constants-internal';
2
2
  import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, } from '@vitessce/plugins';
3
- import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, imageSpatialdataSchema, obsSegmentationsSpatialdataSchema, obsFeatureMatrixSpatialdataSchema, obsSpotsSpatialdataSchema, obsSetsSpatialdataSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
3
+ import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, spatialdataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, imageSpatialdataSchema, obsSegmentationsOmeTiffSchema, obsSegmentationsOmeZarrSchema, obsSegmentationsSpatialdataSchema, obsFeatureMatrixSpatialdataSchema, obsSpotsSpatialdataSchema, obsSetsSpatialdataSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
4
4
  // Register view type plugins
5
5
  import { DescriptionSubscriber } from '@vitessce/description';
6
6
  import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
@@ -30,14 +30,14 @@ AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsSpot
30
30
  // MuData
31
31
  MuDataSource,
32
32
  // OME
33
- OmeZarrLoader,
33
+ OmeZarrLoader, OmeZarrAsObsSegmentationsLoader,
34
34
  // SpatialData
35
35
  SpatialDataTableSource, SpatialDataShapesSource, SpatialDataImageLoader, SpatialDataLabelsLoader, SpatialDataObsSpotsLoader, SpatialDataObsSetsLoader,
36
36
  // Legacy
37
37
  ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
38
38
  import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
39
39
  // Joint file types
40
- import { expandAnndataZarr, } from './joint-file-types.js';
40
+ import { expandAnndataZarr, expandSpatialdataZarr, } from './joint-file-types.js';
41
41
  import { expandAnndataCellSetsZarr, expandAnndataCellsZarr, expandAnndataExpressionMatrixZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandExpressionMatrixZarr, expandGenesJson, expandMoleculesJson, expandRasterJson, expandRasterOmeZarr, } from './joint-file-types-legacy.js';
42
42
  // Helper function to use COMPONENT_COORDINATION_TYPES.
43
43
  function makeViewType(name, component) {
@@ -100,7 +100,8 @@ export const baseFileTypes = [
100
100
  // All OME file types
101
101
  makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
102
102
  makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
103
- makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
103
+ makeFileType(FileType.OBS_SEGMENTATIONS_OME_ZARR, DataType.OBS_SEGMENTATIONS, OmeZarrAsObsSegmentationsLoader, ZarrDataSource, obsSegmentationsOmeZarrSchema),
104
+ makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, obsSegmentationsOmeTiffSchema),
104
105
  // SpatialData file types
105
106
  makeFileType(FileType.IMAGE_SPATIALDATA_ZARR, DataType.IMAGE, SpatialDataImageLoader, ZarrDataSource, imageSpatialdataSchema),
106
107
  // TODO: create a new loader for labels that returns obsSegmentations with obsSegmentationsType: 'bitmask'
@@ -129,7 +130,7 @@ export const baseFileTypes = [
129
130
  ];
130
131
  export const baseJointFileTypes = [
131
132
  new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
132
- // new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
133
+ new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
133
134
  // For legacy file types:
134
135
  new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
135
136
  new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
@@ -229,7 +230,7 @@ export const baseCoordinationTypes = [
229
230
  new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_VISIBLE, true, z.boolean()),
230
231
  new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_OPACITY, 1.0, z.number()),
231
232
  new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_WINDOW, null, z.array(z.number()).length(2).nullable()),
232
- new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_COLOR, null, z.array(z.number()).length(3).nullable()),
233
+ new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_COLOR, [255, 255, 255], z.array(z.number()).length(3).nullable()),
233
234
  new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_FILLED, true, z.boolean()),
234
235
  new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_STROKE_WIDTH, 1.0, z.number()),
235
236
  // Reference: https://www.awaresystems.be/imaging/tiff/tifftags/photometricinterpretation.html
package/dist-tsc/joint-file-types.d.ts CHANGED
@@ -1,4 +1,31 @@
1
1
  import type { z } from 'zod';
2
2
  import type { latestFileDefSchema } from '@vitessce/schemas';
3
3
  export declare function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>): any[];
4
+ export declare function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchema>): ({
5
+ fileType: string;
6
+ options: any;
7
+ coordinationValues: {
8
+ obsType: string;
9
+ featureType: string;
10
+ featureValueType: string;
11
+ };
12
+ url?: string | undefined;
13
+ requestInit?: any;
14
+ } | {
15
+ fileType: string;
16
+ options: any;
17
+ coordinationValues: {
18
+ obsType: string;
19
+ };
20
+ url?: string | undefined;
21
+ requestInit?: any;
22
+ } | {
23
+ fileType: string;
24
+ options: any;
25
+ coordinationValues: {
26
+ featureType: string;
27
+ };
28
+ url?: string | undefined;
29
+ requestInit?: any;
30
+ })[];
4
31
  //# sourceMappingURL=joint-file-types.d.ts.map
package/dist-tsc/joint-file-types.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"joint-file-types.d.ts","sourceRoot":"","sources":["../src/joint-file-types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAe7D,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,SAuK7E"}
1
+ {"version":3,"file":"joint-file-types.d.ts","sourceRoot":"","sources":["../src/joint-file-types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAe7D,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,SAuK7E;AAED,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;KA4EjF"}
package/dist-tsc/joint-file-types.js CHANGED
@@ -166,3 +166,80 @@ export function expandAnndataZarr(fileDef) {
166
166
  }]) : []),
167
167
  ];
168
168
  }
169
+ export function expandSpatialdataZarr(fileDef) {
170
+ const baseFileDef = {
171
+ url: fileDef.url,
172
+ requestInit: fileDef.requestInit,
173
+ coordinationValues: {
174
+ ...fileDef.coordinationValues,
175
+ obsType: fileDef.coordinationValues?.obsType || 'cell',
176
+ featureType: fileDef.coordinationValues?.featureType || 'gene',
177
+ featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
178
+ },
179
+ };
180
+ const extraCoordinationValues = {};
181
+ Object.entries(baseFileDef.coordinationValues).forEach(([key, value]) => {
182
+ if (!expectedCoordinationTypes.includes(key)) {
183
+ extraCoordinationValues[key] = value;
184
+ }
185
+ });
186
+ const { options = {} } = fileDef;
187
+ return [
188
+ // obsFeatureMatrix
189
+ ...(options.obsFeatureMatrix ? [{
190
+ ...baseFileDef,
191
+ fileType: FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR,
192
+ options: options.obsFeatureMatrix,
193
+ coordinationValues: {
194
+ ...extraCoordinationValues,
195
+ obsType: baseFileDef.coordinationValues.obsType,
196
+ featureType: baseFileDef.coordinationValues.featureType,
197
+ featureValueType: baseFileDef.coordinationValues.featureValueType,
198
+ },
199
+ }] : []),
200
+ // obsSets
201
+ ...(options.obsSets ? [{
202
+ ...baseFileDef,
203
+ fileType: FileType.OBS_SETS_SPATIALDATA_ZARR,
204
+ options: options.obsSets,
205
+ coordinationValues: {
206
+ ...extraCoordinationValues,
207
+ obsType: baseFileDef.coordinationValues.obsType,
208
+ },
209
+ }] : []),
210
+ // obsSpots
211
+ ...(options.obsSpots ? [{
212
+ ...baseFileDef,
213
+ fileType: FileType.OBS_SPOTS_SPATIALDATA_ZARR,
214
+ options: options.obsSpots,
215
+ coordinationValues: {
216
+ ...extraCoordinationValues,
217
+ obsType: baseFileDef.coordinationValues.obsType,
218
+ },
219
+ }] : []),
220
+ // TODO: obsPoints?
221
+ // TODO: obsLocations?
222
+ // image
223
+ ...(options.image ? [{
224
+ ...baseFileDef,
225
+ fileType: FileType.IMAGE_SPATIALDATA_ZARR,
226
+ options: options.image,
227
+ coordinationValues: {
228
+ ...extraCoordinationValues,
229
+ featureType: baseFileDef.coordinationValues.featureType,
230
+ // TODO: fileUid?
231
+ },
232
+ }] : []),
233
+ // labels
234
+ ...(options.labels ? [{
235
+ ...baseFileDef,
236
+ fileType: FileType.LABELS_SPATIALDATA_ZARR,
237
+ options: options.labels,
238
+ coordinationValues: {
239
+ ...extraCoordinationValues,
240
+ obsType: baseFileDef.coordinationValues.obsType,
241
+ // TODO: fileUid?
242
+ },
243
+ }] : []),
244
+ ];
245
+ }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@vitessce/all",
3
- "version": "3.3.2",
3
+ "version": "3.3.3",
4
4
  "author": "Gehlenborg Lab",
5
5
  "homepage": "http://vitessce.io",
6
6
  "repository": {
@@ -18,27 +18,27 @@
18
18
  "dependencies": {
19
19
  "@material-ui/core": "~4.12.3",
20
20
  "zod": "^3.21.4",
21
- "@vitessce/constants-internal": "3.3.2",
22
- "@vitessce/csv": "3.3.2",
23
- "@vitessce/description": "3.3.2",
24
- "@vitessce/feature-list": "3.3.2",
25
- "@vitessce/genomic-profiles": "3.3.2",
26
- "@vitessce/heatmap": "3.3.2",
27
- "@vitessce/json": "3.3.2",
28
- "@vitessce/layer-controller": "3.3.2",
29
- "@vitessce/layer-controller-beta": "3.3.2",
30
- "@vitessce/obs-sets-manager": "3.3.2",
31
- "@vitessce/ome-tiff": "3.3.2",
32
- "@vitessce/plugins": "3.3.2",
33
- "@vitessce/scatterplot-embedding": "3.3.2",
34
- "@vitessce/scatterplot-gating": "3.3.2",
35
- "@vitessce/schemas": "3.3.2",
36
- "@vitessce/spatial": "3.3.2",
37
- "@vitessce/spatial-beta": "3.3.2",
38
- "@vitessce/statistical-plots": "3.3.2",
39
- "@vitessce/status": "3.3.2",
40
- "@vitessce/vit-s": "3.3.2",
41
- "@vitessce/zarr": "3.3.2"
21
+ "@vitessce/csv": "3.3.3",
22
+ "@vitessce/description": "3.3.3",
23
+ "@vitessce/genomic-profiles": "3.3.3",
24
+ "@vitessce/feature-list": "3.3.3",
25
+ "@vitessce/heatmap": "3.3.3",
26
+ "@vitessce/json": "3.3.3",
27
+ "@vitessce/layer-controller": "3.3.3",
28
+ "@vitessce/layer-controller-beta": "3.3.3",
29
+ "@vitessce/obs-sets-manager": "3.3.3",
30
+ "@vitessce/ome-tiff": "3.3.3",
31
+ "@vitessce/scatterplot-embedding": "3.3.3",
32
+ "@vitessce/plugins": "3.3.3",
33
+ "@vitessce/constants-internal": "3.3.3",
34
+ "@vitessce/scatterplot-gating": "3.3.3",
35
+ "@vitessce/schemas": "3.3.3",
36
+ "@vitessce/spatial-beta": "3.3.3",
37
+ "@vitessce/statistical-plots": "3.3.3",
38
+ "@vitessce/spatial": "3.3.3",
39
+ "@vitessce/status": "3.3.3",
40
+ "@vitessce/vit-s": "3.3.3",
41
+ "@vitessce/zarr": "3.3.3"
42
42
  },
43
43
  "devDependencies": {
44
44
  "@types/react": "^18.0.28",
package/src/base-plugins.ts CHANGED
@@ -37,6 +37,7 @@ import {
37
37
  featureLabelsAnndataSchema,
38
38
  rasterJsonSchema,
39
39
  anndataZarrSchema,
40
+ spatialdataZarrSchema,
40
41
  anndataCellsZarrSchema,
41
42
  anndataCellSetsZarrSchema,
42
43
  anndataExpressionMatrixZarrSchema,
@@ -44,6 +45,8 @@ import {
44
45
  imageOmeZarrSchema,
45
46
  imageOmeTiffSchema,
46
47
  imageSpatialdataSchema,
48
+ obsSegmentationsOmeTiffSchema,
49
+ obsSegmentationsOmeZarrSchema,
47
50
  obsSegmentationsSpatialdataSchema,
48
51
  obsFeatureMatrixSpatialdataSchema,
49
52
  obsSpotsSpatialdataSchema,
@@ -123,6 +126,7 @@ import {
123
126
  MuDataSource,
124
127
  // OME
125
128
  OmeZarrLoader,
129
+ OmeZarrAsObsSegmentationsLoader,
126
130
  // SpatialData
127
131
  SpatialDataTableSource,
128
132
  SpatialDataShapesSource,
@@ -144,6 +148,7 @@ import {
144
148
  // Joint file types
145
149
  import {
146
150
  expandAnndataZarr,
151
+ expandSpatialdataZarr,
147
152
  } from './joint-file-types.js';
148
153
  import {
149
154
  expandAnndataCellSetsZarr,
@@ -223,7 +228,8 @@ export const baseFileTypes = [
223
228
  // All OME file types
224
229
  makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
225
230
  makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
226
- makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
231
+ makeFileType(FileType.OBS_SEGMENTATIONS_OME_ZARR, DataType.OBS_SEGMENTATIONS, OmeZarrAsObsSegmentationsLoader, ZarrDataSource, obsSegmentationsOmeZarrSchema),
232
+ makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, obsSegmentationsOmeTiffSchema),
227
233
  // SpatialData file types
228
234
  makeFileType(FileType.IMAGE_SPATIALDATA_ZARR, DataType.IMAGE, SpatialDataImageLoader, ZarrDataSource, imageSpatialdataSchema),
229
235
  // TODO: create a new loader for labels that returns obsSegmentations with obsSegmentationsType: 'bitmask'
@@ -253,7 +259,7 @@ export const baseFileTypes = [
253
259
 
254
260
  export const baseJointFileTypes = [
255
261
  new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
256
- // new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
262
+ new PluginJointFileType(FileType.SPATIALDATA_ZARR, expandSpatialdataZarr, spatialdataZarrSchema),
257
263
  // For legacy file types:
258
264
  new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
259
265
  new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
@@ -426,7 +432,7 @@ export const baseCoordinationTypes = [
426
432
  new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_VISIBLE, true, z.boolean()),
427
433
  new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_OPACITY, 1.0, z.number()),
428
434
  new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_WINDOW, null, z.array(z.number()).length(2).nullable()),
429
- new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_COLOR, null, z.array(z.number()).length(3).nullable()),
435
+ new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_COLOR, [255, 255, 255], z.array(z.number()).length(3).nullable()),
430
436
  new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_FILLED, true, z.boolean()),
431
437
  new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_STROKE_WIDTH, 1.0, z.number()),
432
438
  // Reference: https://www.awaresystems.be/imaging/tiff/tifftags/photometricinterpretation.html
package/src/joint-file-types.ts CHANGED
@@ -182,3 +182,81 @@ export function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>)
182
182
  ) : []),
183
183
  ];
184
184
  }
185
+
186
+ export function expandSpatialdataZarr(fileDef: z.infer<typeof latestFileDefSchema>) {
187
+ const baseFileDef: BaseFileDef = {
188
+ url: fileDef.url,
189
+ requestInit: fileDef.requestInit,
190
+ coordinationValues: {
191
+ ...fileDef.coordinationValues,
192
+ obsType: fileDef.coordinationValues?.obsType || 'cell',
193
+ featureType: fileDef.coordinationValues?.featureType || 'gene',
194
+ featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
195
+ },
196
+ };
197
+ const extraCoordinationValues: Record<string, any> = {};
198
+ Object.entries(baseFileDef.coordinationValues).forEach(([key, value]) => {
199
+ if (!expectedCoordinationTypes.includes(key)) {
200
+ extraCoordinationValues[key] = value;
201
+ }
202
+ });
203
+ const { options = {} } = fileDef;
204
+ return [
205
+ // obsFeatureMatrix
206
+ ...(options.obsFeatureMatrix ? [{
207
+ ...baseFileDef,
208
+ fileType: FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR,
209
+ options: options.obsFeatureMatrix,
210
+ coordinationValues: {
211
+ ...extraCoordinationValues,
212
+ obsType: baseFileDef.coordinationValues.obsType,
213
+ featureType: baseFileDef.coordinationValues.featureType,
214
+ featureValueType: baseFileDef.coordinationValues.featureValueType,
215
+ },
216
+ }] : []),
217
+ // obsSets
218
+ ...(options.obsSets ? [{
219
+ ...baseFileDef,
220
+ fileType: FileType.OBS_SETS_SPATIALDATA_ZARR,
221
+ options: options.obsSets,
222
+ coordinationValues: {
223
+ ...extraCoordinationValues,
224
+ obsType: baseFileDef.coordinationValues.obsType,
225
+ },
226
+ }] : []),
227
+ // obsSpots
228
+ ...(options.obsSpots ? [{
229
+ ...baseFileDef,
230
+ fileType: FileType.OBS_SPOTS_SPATIALDATA_ZARR,
231
+ options: options.obsSpots,
232
+ coordinationValues: {
233
+ ...extraCoordinationValues,
234
+ obsType: baseFileDef.coordinationValues.obsType,
235
+ },
236
+ }] : []),
237
+ // TODO: obsPoints?
238
+ // TODO: obsLocations?
239
+ // image
240
+ ...(options.image ? [{
241
+ ...baseFileDef,
242
+ fileType: FileType.IMAGE_SPATIALDATA_ZARR,
243
+ options: options.image,
244
+ coordinationValues: {
245
+ ...extraCoordinationValues,
246
+ featureType: baseFileDef.coordinationValues.featureType,
247
+ // TODO: fileUid?
248
+ },
249
+ }] : []),
250
+ // labels
251
+ ...(options.labels ? [{
252
+ ...baseFileDef,
253
+ fileType: FileType.LABELS_SPATIALDATA_ZARR,
254
+ options: options.labels,
255
+ coordinationValues: {
256
+ ...extraCoordinationValues,
257
+ obsType: baseFileDef.coordinationValues.obsType,
258
+ // TODO: fileUid?
259
+ },
260
+ }] : []),
261
+ ];
262
+ }