@fideus-labs/ngff-zarr 0.2.5 → 0.2.6
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.
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"from_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAMtD,MAAM,WAAW,mBAAmB;IAClC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;CACzB;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,YAAY,CAEhC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,WAAW,CAAC,
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1
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+
{"version":3,"file":"from_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAMtD,MAAM,WAAW,mBAAmB;IAClC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;CACzB;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,YAAY,CAEhC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,WAAW,CAAC,CA+NtB;AAED,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,EACjB,SAAS,CAAC,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC,EAAE,GAC5B,OAAO,CAAC,OAAO,CAAC,CAmClB"}
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package/esm/io/from_ngff_zarr.js
CHANGED
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@@ -56,11 +56,26 @@ store, options = {}) {
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56
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kind: "group",
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});
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const attrs = root.attrs;
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59
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-
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59
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+
// Handle both 0.4 (multiscales at root) and 0.5 (multiscales under ome) formats
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60
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let multiscalesArray;
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61
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let detectedVersion;
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62
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if (attrs && typeof attrs === "object" && "ome" in attrs) {
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63
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// OME-Zarr 0.5 format: metadata is under the 'ome' property
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64
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const omeAttrs = attrs.ome;
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65
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if (!omeAttrs || !omeAttrs.multiscales) {
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66
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throw new Error("No multiscales metadata found in OME-Zarr 0.5 store");
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67
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}
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multiscalesArray = omeAttrs.multiscales;
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69
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detectedVersion = omeAttrs.version;
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70
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}
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71
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else if (attrs && typeof attrs === "object" && "multiscales" in attrs) {
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72
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// OME-Zarr 0.4 format: metadata is at root
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73
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multiscalesArray = attrs
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.multiscales;
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75
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}
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76
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else {
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throw new Error("No multiscales metadata found in Zarr store");
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}
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62
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-
const multiscalesArray = attrs
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63
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-
.multiscales;
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if (!Array.isArray(multiscalesArray) || multiscalesArray.length === 0) {
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80
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throw new Error("No multiscales metadata found in Zarr store");
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}
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@@ -73,8 +88,9 @@ store, options = {}) {
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// Check version compatibility if specified
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if (version) {
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const metadataWithVersion = multiscalesMetadata;
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76
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-
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77
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-
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const actualVersion = metadataWithVersion.version || detectedVersion;
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if (actualVersion !== version) {
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throw new Error(`Expected OME-Zarr version ${version}, but found ${actualVersion || "unknown"}`);
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}
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}
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}
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@@ -1 +1 @@
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1
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-
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1
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+
{"version":3,"file":"from_ngff_zarr.js","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAU7D,MAAM,CAAC,KAAK,UAAU,YAAY;AAChC,qEAAqE;AACrE,KAA6C,EAC7C,UAA+B,EAAE;IAEjC,MAAM,QAAQ,GAAG,OAAO,CAAC,QAAQ,IAAI,KAAK,CAAC;IAC3C,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC;IAEhC,IAAI,CAAC;QACH,yDAAyD;QACzD,IAAI,aAA4C,CAAC;QACjD,IAAI,KAAK,YAAY,GAAG,IAAI,KAAK,YAAY,IAAI,CAAC,UAAU,EAAE,CAAC;YAC7D,aAAa,GAAG,KAAK,CAAC;QACxB,CAAC;aAAM,IAAI,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC,IAAI,KAAK,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;YACvE,qCAAqC;YACrC,aAAa,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QAC7C,CAAC;aAAM,CAAC;YACN,2DAA2D;YAC3D,IAAI,OAAO,MAAM,KAAK,WAAW,EAAE,CAAC;gBAClC,MAAM,IAAI,KAAK,CACb,0FAA0F,CAC3F,CAAC;YACJ,CAAC;YAED,oFAAoF;YACpF,IAAI,CAAC;gBACH,MAAM,EAAE,eAAe,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CACpD,kBAAkB,CACnB,CAAC;gBACF,mCAAmC;gBACnC,IAAI,KAAK,YAAY,eAAe,IAAI,KAAK,YAAY,YAAY,EAAE,CAAC;oBACtE,mCAAmC;oBACnC,aAAa,GAAG,KAAK,CAAC;gBACxB,CAAC;qBAAM,CAAC;oBACN,sDAAsD;oBACtD,MAAM,cAAc,GAAG,KAAK,CAAC,OAAO,CAAC,gBAAgB,EAAE,IAAI,CAAC,CAAC;oBAC7D,mCAAmC;oBACnC,aAAa,GAAG,IAAI,eAAe,CAAC,cAAc,CAAC,CAAC;gBACtD,CAAC;YACH,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,mCAAmC,KAAK,kDAAkD,CAC3F,CAAC;YACJ,CAAC;QACH,CAAC;QAED,0DAA0D;QAC1D,IAAI,cAAc,CAAC;QACnB,IAAI,CAAC;YACH,yCAAyC;YACzC,cAAc,GAAG,MAAM,IAAI,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC;QACjE,CAAC;QAAC,MAAM,CAAC;YACP,cAAc,GAAG,aAAa,CAAC;QACjC,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,cAA+B,EAAE;YAC5D,IAAI,EAAE,OAAO;SACd,CAAC,CAAC;QACH,MAAM,KAAK,GAAG,IAAI,CAAC,KAAgB,CAAC;QAEpC,gFAAgF;QAChF,IAAI,gBAA2B,CAAC;QAChC,IAAI,eAAmC,CAAC;QAExC,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,IAAI,KAAK,EAAE,CAAC;YACzD,4DAA4D;YAC5D,MAAM,QAAQ,GAAI,KAAiC,CAAC,GAGnD,CAAC;YACF,IAAI,CAAC,QAAQ,IAAI,CAAC,QAAQ,CAAC,WAAW,EAAE,CAAC;gBACvC,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;YACzE,CAAC;YACD,gBAAgB,GAAG,QAAQ,CAAC,WAAwB,CAAC;YACrD,eAAe,GAAG,QAAQ,CAAC,OAA6B,CAAC;QAC3D,CAAC;aAAM,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,aAAa,IAAI,KAAK,EAAE,CAAC;YACxE,2CAA2C;YAC3C,gBAAgB,GAAI,KAAiC;iBAClD,WAAwB,CAAC;QAC9B,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC,CAAC;QACjE,CAAC;QAED,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,gBAAgB,CAAC,IAAI,gBAAgB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtE,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC,CAAC;QACjE,CAAC;QACD,MAAM,mBAAmB,GAAG,gBAAgB,CAAC,CAAC,CAAY,CAAC;QAE3D,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,MAAM,GAAG,cAAc,CAAC,SAAS,CAAC,mBAAmB,CAAC,CAAC;YAC7D,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;gBACpB,MAAM,IAAI,KAAK,CAAC,8BAA8B,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC;YACxE,CAAC;YAED,2CAA2C;YAC3C,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,mBAAmB,GAAG,mBAA2C,CAAC;gBACxE,MAAM,aAAa,GAAG,mBAAmB,CAAC,OAAO,IAAI,eAAe,CAAC;gBACrE,IAAI,aAAa,KAAK,OAAO,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CACb,6BAA6B,OAAO,eAClC,aAAa,IAAI,SACnB,EAAE,CACH,CAAC;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,QAAQ,GAAG,mBAA+B,CAAC;QAEjD,yDAAyD;QACzD,IAAK,KAAiC,CAAC,KAAK,EAAE,CAAC;YAC7C,MAAM,SAAS,GAAI,KAAiC,CAAC,KAGpD,CAAC;YAEF,0DAA0D;YAC1D,IAAI,SAAS,CAAC,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC;gBAC5D,KACE,MAAM,OAAO,IAAI,SAAS,CAAC,QAE1B,EACD,CAAC;oBACD,IAAI,OAAO,CAAC,MAAM,IAAI,OAAO,OAAO,CAAC,MAAM,KAAK,QAAQ,EAAE,CAAC;wBACzD,MAAM,MAAM,GAAG,OAAO,CAAC,MAA4C,CAAC;wBAEpE,kEAAkE;wBAClE,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;4BACzD,kDAAkD;4BAClD,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;gCAC/B,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC;4BAC5B,CAAC;4BACD,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gCAC7B,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC;4BAC1B,CAAC;wBACH,CAAC;6BAAM,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;4BAClE,kDAAkD;4BAClD,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gCAC7B,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC;4BAC5B,CAAC;4BACD,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gCAC7B,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC;4BAC1B,CAAC;wBACH,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;YAED,QAAQ,CAAC,KAAK,GAAG,SAA6B,CAAC;QACjD,CAAC;QAED,MAAM,MAAM,GAAgB,EAAE,CAAC;QAE/B,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACxC,MAAM,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;YAE/B,MAAM,SAAS,GAAG,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE;gBAC1D,IAAI,EAAE,OAAO;aACd,CAAC,CAA6C,CAAC;YAEhD,uDAAuD;YACvD,IACE,CAAC,SAAS;gBACV,CAAC,CAAC,OAAO,IAAI,SAAS,CAAC;gBACvB,CAAC,CAAC,OAAO,IAAI,SAAS,CAAC;gBACvB,CAAC,CAAC,QAAQ,IAAI,SAAS,CAAC,EACxB,CAAC;gBACD,MAAM,IAAI,KAAK,CACb,8BAA8B,SAAS,0BAA0B,CAClE,CAAC;YACJ,CAAC;YAED,MAAM,KAAK,GAA2B,EAAE,CAAC;YACzC,MAAM,WAAW,GAA2B,EAAE,CAAC;YAE/C,KAAK,MAAM,SAAS,IAAI,OAAO,CAAC,yBAAyB,EAAE,CAAC;gBAC1D,IAAI,SAAS,CAAC,IAAI,KAAK,OAAO,EAAE,CAAC;oBAC/B,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE;wBAChC,IAAI,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;4BAC/B,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;wBACxC,CAAC;oBACH,CAAC,CAAC,CAAC;gBACL,CAAC;qBAAM,IAAI,SAAS,CAAC,IAAI,KAAK,a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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAE3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAGvD,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7D;AAED,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,
|
|
1
|
+
{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAE3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAGvD,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7D;AAED,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,CAsGf"}
|
package/esm/io/to_ngff_zarr.js
CHANGED
|
@@ -35,31 +35,40 @@ export async function toNgffZarr(store, multiscales, options = {}) {
|
|
|
35
35
|
}
|
|
36
36
|
// Create root location and group with zarrita v0.5.2 API
|
|
37
37
|
const root = zarr.root(_resolvedStore);
|
|
38
|
+
// Prepare multiscales metadata
|
|
39
|
+
const multiscalesMetadata = {
|
|
40
|
+
version: _version,
|
|
41
|
+
name: multiscales.metadata.name,
|
|
42
|
+
axes: multiscales.metadata.axes,
|
|
43
|
+
datasets: multiscales.metadata.datasets,
|
|
44
|
+
...(multiscales.metadata.coordinateTransformations && {
|
|
45
|
+
coordinateTransformations: multiscales.metadata.coordinateTransformations,
|
|
46
|
+
}),
|
|
47
|
+
...(multiscales.metadata.type && {
|
|
48
|
+
type: multiscales.metadata.type,
|
|
49
|
+
}),
|
|
50
|
+
...(multiscales.metadata.metadata && {
|
|
51
|
+
metadata: multiscales.metadata.metadata,
|
|
52
|
+
}),
|
|
53
|
+
};
|
|
38
54
|
// Create the root group with OME-Zarr metadata
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
|
|
56
|
-
},
|
|
57
|
-
],
|
|
58
|
-
...(multiscales.metadata.omero && {
|
|
59
|
-
omero: multiscales.metadata.omero,
|
|
60
|
-
}),
|
|
61
|
-
},
|
|
62
|
-
});
|
|
55
|
+
// For version 0.5, wrap metadata under "ome" property
|
|
56
|
+
// For version 0.4, place multiscales directly at root
|
|
57
|
+
const attributes = _version === "0.5"
|
|
58
|
+
? {
|
|
59
|
+
ome: {
|
|
60
|
+
version: _version,
|
|
61
|
+
multiscales: [multiscalesMetadata],
|
|
62
|
+
},
|
|
63
|
+
}
|
|
64
|
+
: {
|
|
65
|
+
multiscales: [multiscalesMetadata],
|
|
66
|
+
};
|
|
67
|
+
// Add OMERO metadata at root level if present (both versions)
|
|
68
|
+
if (multiscales.metadata.omero) {
|
|
69
|
+
attributes.omero = multiscales.metadata.omero;
|
|
70
|
+
}
|
|
71
|
+
const rootGroup = await zarr.create(root, { attributes });
|
|
63
72
|
// Write each image in the multiscales
|
|
64
73
|
for (let i = 0; i < multiscales.images.length; i++) {
|
|
65
74
|
const image = multiscales.images[i];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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