@vitessce/spatial-utils 3.3.6 → 3.3.7

package/dist/chunk-INHXZS53-bee20a28.js

@@ -0,0 +1,19 @@
+var __toBinary = /* @__PURE__ */ (() => {
+  var table = new Uint8Array(128);
+  for (var i = 0; i < 64; i++)
+    table[i < 26 ? i + 65 : i < 52 ? i + 71 : i < 62 ? i - 4 : i * 4 - 205] = i;
+  return (base64) => {
+    var n = base64.length, bytes = new Uint8Array((n - (base64[n - 1] == "=") - (base64[n - 2] == "=")) * 3 / 4 | 0);
+    for (var i2 = 0, j = 0; i2 < n; ) {
+      var c0 = table[base64.charCodeAt(i2++)], c1 = table[base64.charCodeAt(i2++)];
+      var c2 = table[base64.charCodeAt(i2++)], c3 = table[base64.charCodeAt(i2++)];
+      bytes[j++] = c0 << 2 | c1 >> 4;
+      bytes[j++] = c1 << 4 | c2 >> 2;
+      bytes[j++] = c2 << 6 | c3;
+    }
+    return bytes;
+  };
+})();
+export {
+  __toBinary as _
+};

package/dist/{deflate-91360e96.js → deflate-88edcce0.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-ecfc14b5.js";
+import { B as BaseDecoder } from "./index-2e60bcd0.js";
 import "react";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {

package/dist/gzip-6a24f0fe.js

@@ -0,0 +1,30 @@
+var __defProp = Object.defineProperty;
+var __defNormalProp = (obj, key, value) => key in obj ? __defProp(obj, key, { enumerable: true, configurable: true, writable: true, value }) : obj[key] = value;
+var __publicField = (obj, key, value) => {
+  __defNormalProp(obj, typeof key !== "symbol" ? key + "" : key, value);
+  return value;
+};
+var _a;
+import { g as gzipSync, a as gunzipSync } from "./browser-122c4c35.js";
+var GZip = (_a = class {
+  constructor(level = 1) {
+    __publicField(this, "level");
+    if (level < 0 || level > 9) {
+      throw new Error("Invalid gzip compression level, it should be between 0 and 9");
+    }
+    this.level = level;
+  }
+  static fromConfig({ level }) {
+    return new _a(level);
+  }
+  encode(data) {
+    return gzipSync(data, { level: this.level });
+  }
+  decode(data) {
+    return gunzipSync(data);
+  }
+}, __publicField(_a, "codecId", "gzip"), _a);
+var gzip_default = GZip;
+export {
+  gzip_default as default
+};

package/dist/{index-ecfc14b5.js → index-2e60bcd0.js}

@@ -22,7 +22,7 @@ var __privateSet = (obj, member, value, setter2) => {
   setter2 ? setter2.call(obj, value) : member.set(obj, value);
   return value;
 };
-var _bytes, _encoder, _encode_buffer, _strides, _TypedArray, _BYTES_PER_ELEMENT, _shape, _endian, _shape2, _strides2, _metadata, _metadata2, _a2, _b;
+var _bytes, _encoder, _data, _encode_buffer, _strides, _TypedArray, _BYTES_PER_ELEMENT, _shape, _endian, _shape2, _strides2, _encoder_config, _decoder_config, _metadata, _metadata2, _a2, _b;
 import "react";
 function _mergeNamespaces(n3, m) {
   for (var i2 = 0; i2 < m.length; i2++) {
@@ -119066,16 +119066,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c) => registry$2.set(c, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-862c78b4.js").then((m) => m.default));
-addDecoder(5, () => import("./lzw-a029f738.js").then((m) => m.default));
+addDecoder([void 0, 1], () => import("./raw-56a83d25.js").then((m) => m.default));
+addDecoder(5, () => import("./lzw-19c945c0.js").then((m) => m.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-8a56f635.js").then((m) => m.default));
-addDecoder([8, 32946], () => import("./deflate-91360e96.js").then((m) => m.default));
-addDecoder(32773, () => import("./packbits-1048f7af.js").then((m) => m.default));
-addDecoder(34887, () => import("./lerc-cafe8298.js").then((m) => m.default));
-addDecoder(50001, () => import("./webimage-452cf0ca.js").then((m) => m.default));
+addDecoder(7, () => import("./jpeg-36de5225.js").then((m) => m.default));
+addDecoder([8, 32946], () => import("./deflate-88edcce0.js").then((m) => m.default));
+addDecoder(32773, () => import("./packbits-1b575957.js").then((m) => m.default));
+addDecoder(34887, () => import("./lerc-cecad635.js").then((m) => m.default));
+addDecoder(50001, () => import("./webimage-0c15a0b7.js").then((m) => m.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset = 0;
@@ -131266,14 +131266,14 @@ function normalizeCoordinateTransformations(coordinateTransformations, datasets)
   return result;
 }
 class NodeNotFoundError extends Error {
-  constructor(msg) {
-    super(msg);
+  constructor(context, options = {}) {
+    super(`Node not found: ${context}`, options);
     this.name = "NodeNotFoundError";
   }
 }
 class KeyError extends Error {
-  constructor(msg) {
-    super(msg);
+  constructor(path) {
+    super(`Missing key: ${path}`);
     this.name = "KeyError";
   }
 }
@@ -131384,56 +131384,56 @@ class ByteStringArray {
 _encoder = new WeakMap();
 const _UnicodeStringArray = class {
   constructor(chars, x2, byteOffset, length2) {
-    __publicField(this, "_data");
+    __privateAdd(this, _data, void 0);
     __publicField(this, "chars");
     __privateAdd(this, _encode_buffer, void 0);
     this.chars = chars;
     if (typeof x2 === "number") {
-      this._data = new Int32Array(x2 * chars);
+      __privateSet(this, _data, new Int32Array(x2 * chars));
     } else if (x2 instanceof ArrayBuffer) {
       if (length2)
         length2 *= chars;
-      this._data = new Int32Array(x2, byteOffset, length2);
+      __privateSet(this, _data, new Int32Array(x2, byteOffset, length2));
     } else {
       const values = x2;
       const d = new _UnicodeStringArray(chars, 1);
-      this._data = new Int32Array(function* () {
+      __privateSet(this, _data, new Int32Array(function* () {
         for (let str of values) {
           d.set(0, str);
-          yield* d._data;
+          yield* __privateGet(d, _data);
         }
-      }());
+      }()));
     }
     __privateSet(this, _encode_buffer, new Int32Array(chars));
   }
   get BYTES_PER_ELEMENT() {
-    return this._data.BYTES_PER_ELEMENT * this.chars;
+    return __privateGet(this, _data).BYTES_PER_ELEMENT * this.chars;
   }
   get byteLength() {
-    return this._data.byteLength;
+    return __privateGet(this, _data).byteLength;
   }
   get byteOffset() {
-    return this._data.byteOffset;
+    return __privateGet(this, _data).byteOffset;
   }
   /** @type {ArrayBuffer} */
   get buffer() {
-    return this._data.buffer;
+    return __privateGet(this, _data).buffer;
   }
   /** @type {number} */
   get length() {
-    return this._data.length / this.chars;
+    return __privateGet(this, _data).length / this.chars;
   }
   get(idx) {
     const offset = this.chars * idx;
     let result = "";
     for (let i2 = 0; i2 < this.chars; i2++) {
-      result += String.fromCodePoint(this._data[offset + i2]);
+      result += String.fromCodePoint(__privateGet(this, _data)[offset + i2]);
     }
     return result.replace(/\u0000/g, "");
   }
   set(idx, value) {
     const offset = this.chars * idx;
-    const view = this._data.subarray(offset, offset + this.chars);
+    const view = __privateGet(this, _data).subarray(offset, offset + this.chars);
     view.fill(0);
     for (let i2 = 0; i2 < this.chars; i2++) {
       view[i2] = value.codePointAt(i2) ?? 0;
@@ -131441,9 +131441,9 @@ const _UnicodeStringArray = class {
   }
   fill(value) {
     this.set(0, value);
-    let encoded = this._data.subarray(0, this.chars);
+    let encoded = __privateGet(this, _data).subarray(0, this.chars);
     for (let i2 = 1; i2 < this.length; i2++) {
-      this._data.set(encoded, i2 * this.chars);
+      __privateGet(this, _data).set(encoded, i2 * this.chars);
     }
   }
   *[Symbol.iterator]() {
@@ -131453,6 +131453,7 @@ const _UnicodeStringArray = class {
   }
 };
 let UnicodeStringArray = _UnicodeStringArray;
+_data = new WeakMap();
 _encode_buffer = new WeakMap();
 function json_decode_object(bytes) {
   const str = new TextDecoder().decode(bytes);
@@ -131818,8 +131819,115 @@ const _VLenUTF8 = class {
 let VLenUTF8 = _VLenUTF8;
 _shape2 = new WeakMap();
 _strides2 = new WeakMap();
+function throw_on_nan_replacer(_key, value) {
+  if (value !== value) {
+    throw new Error("JsonCodec allow_nan is false but NaN was encountered during encoding.");
+  }
+  if (value === Infinity) {
+    throw new Error("JsonCodec allow_nan is false but Infinity was encountered during encoding.");
+  }
+  if (value === -Infinity) {
+    throw new Error("JsonCodec allow_nan is false but -Infinity was encountered during encoding.");
+  }
+  return value;
+}
+function sort_keys_replacer(_key, value) {
+  return value instanceof Object && !(value instanceof Array) ? Object.keys(value).sort().reduce((sorted, key) => {
+    sorted[key] = value[key];
+    return sorted;
+  }, {}) : value;
+}
+const _JsonCodec = class {
+  constructor(configuration) {
+    __publicField(this, "configuration");
+    __publicField(this, "kind", "array_to_bytes");
+    __privateAdd(this, _encoder_config, void 0);
+    __privateAdd(this, _decoder_config, void 0);
+    this.configuration = configuration;
+    const { encoding = "utf-8", skipkeys = false, ensure_ascii = true, check_circular = true, allow_nan = true, sort_keys = true, indent, strict = true } = configuration;
+    let separators = configuration.separators;
+    if (!separators) {
+      if (!indent) {
+        separators = [",", ":"];
+      } else {
+        separators = [", ", ": "];
+      }
+    }
+    __privateSet(this, _encoder_config, {
+      encoding,
+      skipkeys,
+      ensure_ascii,
+      check_circular,
+      allow_nan,
+      indent,
+      separators,
+      sort_keys
+    });
+    __privateSet(this, _decoder_config, { strict });
+  }
+  static fromConfig(configuration) {
+    return new _JsonCodec(configuration);
+  }
+  encode(buf) {
+    const { indent, encoding, ensure_ascii, check_circular, allow_nan, sort_keys } = __privateGet(this, _encoder_config);
+    if (encoding !== "utf-8") {
+      throw new Error("JsonCodec does not yet support non-utf-8 encoding.");
+    }
+    const replacer_functions = [];
+    if (!check_circular) {
+      throw new Error("JsonCodec does not yet support skipping the check for circular references during encoding.");
+    }
+    if (!allow_nan) {
+      replacer_functions.push(throw_on_nan_replacer);
+    }
+    if (sort_keys) {
+      replacer_functions.push(sort_keys_replacer);
+    }
+    const items = Array.from(buf.data);
+    items.push("|O");
+    items.push(buf.shape);
+    let replacer = void 0;
+    if (replacer_functions.length) {
+      replacer = function(key, value) {
+        let new_value = value;
+        replacer_functions.forEach((sub_replacer) => {
+          new_value = sub_replacer(key, new_value);
+        });
+        return new_value;
+      };
+    }
+    let json_str = JSON.stringify(items, replacer, indent);
+    if (ensure_ascii) {
+      json_str = json_str.replace(/[\u007F-\uFFFF]/g, function(chr) {
+        const full_str = "0000" + chr.charCodeAt(0).toString(16);
+        const sub_str = full_str.substring(full_str.length - 4);
+        return "\\u" + sub_str;
+      });
+    }
+    return new TextEncoder().encode(json_str);
+  }
+  decode(bytes) {
+    const { strict } = __privateGet(this, _decoder_config);
+    if (!strict) {
+      throw new Error("JsonCodec does not yet support non-strict decoding.");
+    }
+    const items = json_decode_object(bytes);
+    const shape = items.pop();
+    items.pop();
+    if (!shape) {
+      throw new Error("0D not implemented for JsonCodec.");
+    } else {
+      const stride = get_strides(shape, "C");
+      const data = items;
+      return { data, shape, stride };
+    }
+  }
+};
+let JsonCodec = _JsonCodec;
+_encoder_config = new WeakMap();
+_decoder_config = new WeakMap();
 function create_default_registry() {
-  return (/* @__PURE__ */ new Map()).set("blosc", () => import("./blosc-0acfcf7e.js").then((m) => m.default)).set("gzip", () => import("./gzip-dd5ab7c8.js").then((m) => m.default)).set("lz4", () => import("./lz4-abb4416a.js").then((m) => m.default)).set("zlib", () => import("./zlib-cd823c38.js").then((m) => m.default)).set("zstd", () => import("./zstd-4072ca78.js").then((m) => m.default)).set("transpose", () => TransposeCodec).set("bytes", () => BytesCodec).set("crc32c", () => Crc32cCodec).set("vlen-utf8", () => VLenUTF8);
+  return (/* @__PURE__ */ new Map()).set("blosc", () => import("./blosc-537fd004.js").then((m) => m.default)).set("gzip", () => import("./gzip-6a24f0fe.js").then((m) => m.default)).set("lz4", () => import("./lz4-bbd18009.js").then((m) => m.default)).set("zlib", () => import("./zlib-175cd38d.js").then((m) => m.default)).set("zstd", () => import("./zstd-ec5a40b8.js").then((m) => m.default)).set("transpose", () => TransposeCodec).set("bytes", () => BytesCodec).set("crc32c", () => Crc32cCodec).set("vlen-utf8", () => VLenUTF8).set("json2", () => JsonCodec);
 }
 const registry = create_default_registry();
 function create_codec_pipeline(chunk_metadata) {
@@ -132062,6 +132170,7 @@ let Array$1 = (_b = class extends Location {
     return is_dtype(this.dtype, query);
   }
 }, _a2 = CONTEXT_MARKER, _metadata2 = new WeakMap(), _b);
+let VERSION_COUNTER = create_version_counter();
 function create_version_counter() {
   let version_counts = /* @__PURE__ */ new WeakMap();
   function get_counts(store) {
@@ -132079,7 +132188,6 @@ function create_version_counter() {
     }
   };
 }
-let VERSION_COUNTER = create_version_counter();
 async function load_attrs(location) {
   let meta_bytes = await location.store.get(location.resolve(".zattrs").path);
   if (!meta_bytes)
@@ -132105,7 +132213,9 @@ async function open_array_v2(location, attrs) {
   let { path } = location.resolve(".zarray");
   let meta2 = await location.store.get(path);
   if (!meta2) {
-    throw new NodeNotFoundError(path);
+    throw new NodeNotFoundError("v2 array", {
+      cause: new KeyError(path)
+    });
   }
   VERSION_COUNTER.increment(location.store, "v2");
   return new Array$1(location.store, location.path, v2_to_v3_array_metadata(json_decode_object(meta2), attrs));
@@ -132114,7 +132224,9 @@ async function open_group_v2(location, attrs) {
   let { path } = location.resolve(".zgroup");
   let meta2 = await location.store.get(path);
   if (!meta2) {
-    throw new NodeNotFoundError(path);
+    throw new NodeNotFoundError("v2 group", {
+      cause: new KeyError(path)
+    });
   }
   VERSION_COUNTER.increment(location.store, "v2");
   return new Group(location.store, location.path, v2_to_v3_group_metadata(json_decode_object(meta2), attrs));
@@ -132123,7 +132235,9 @@ async function _open_v3(location) {
   let { store, path } = location.resolve("zarr.json");
   let meta2 = await location.store.get(path);
   if (!meta2) {
-    throw new NodeNotFoundError(path);
+    throw new NodeNotFoundError("v3 array or group", {
+      cause: new KeyError(path)
+    });
   }
   let meta_doc = json_decode_object(meta2);
   if (meta_doc.node_type === "array" && (meta_doc.data_type === "uint64" || meta_doc.data_type === "int64") && meta_doc.fill_value != void 0) {
@@ -132145,8 +132259,8 @@ async function open_v3(location, options = {}) {
   throw new Error(`Expected node of kind ${options.kind}, found ${kind}.`);
 }
 async function open(location, options = {}) {
-  const store = "store" in location ? location.store : location;
-  const version_max = VERSION_COUNTER.version_max(store);
+  let store = "store" in location ? location.store : location;
+  let version_max = VERSION_COUNTER.version_max(store);
   let open_primary = version_max === "v2" ? open.v2 : open.v3;
   let open_secondary = version_max === "v2" ? open.v3 : open.v2;
   return open_primary(location, options).catch((err2) => {
@@ -132190,7 +132304,7 @@ function* product(...iterables) {
     results[i2] = iterators[i2].next();
   }
 }
-function slice_indices(start, stop, step, length2) {
+function slice_indices({ start, stop, step }, length2) {
   if (step === 0) {
     throw new Error("slice step cannot be zero");
   }
@@ -132231,10 +132345,7 @@ function slice(start, stop, step = null) {
   return {
     start,
     stop,
-    step,
-    indices(length2) {
-      return slice_indices(this.start, this.stop, this.step, length2);
-    }
+    step
   };
 }
 function create_queue() {
@@ -132302,7 +132413,7 @@ class SliceDimIndexer {
     __publicField(this, "dim_chunk_len");
     __publicField(this, "nitems");
     __publicField(this, "nchunks");
-    const [start, stop, step] = dim_sel.indices(dim_len);
+    const [start, stop, step] = slice_indices(dim_sel, dim_len);
     this.start = start;
     this.stop = stop;
     this.step = step;
@@ -132388,25 +132499,20 @@ function unwrap(arr, idx) {
 }
 async function get$1(arr, selection, opts, setter2) {
   var _a3;
-  const context = get_context(arr);
-  const indexer = new BasicIndexer({
+  let context = get_context(arr);
+  let indexer = new BasicIndexer({
     selection,
     shape: arr.shape,
     chunk_shape: arr.chunks
   });
-  const out = setter2.prepare(new context.TypedArray(indexer.shape.reduce((a2, b) => a2 * b, 1)), indexer.shape, context.get_strides(indexer.shape, opts.order));
-  const queue = ((_a3 = opts.create_queue) == null ? void 0 : _a3.call(opts)) ?? create_queue();
+  let out = setter2.prepare(new context.TypedArray(indexer.shape.reduce((a2, b) => a2 * b, 1)), indexer.shape, context.get_strides(indexer.shape, opts.order));
+  let queue = ((_a3 = opts.create_queue) == null ? void 0 : _a3.call(opts)) ?? create_queue();
   for (const { chunk_coords, mapping } of indexer) {
-    queue.add(() => arr.getChunk(chunk_coords, opts.opts).then(({ data, shape, stride }) => {
-      const chunk = setter2.prepare(data, shape, stride);
+    queue.add(async () => {
+      let { data, shape, stride } = await arr.getChunk(chunk_coords, opts.opts);
+      let chunk = setter2.prepare(data, shape, stride);
       setter2.set_from_chunk(out, chunk, mapping);
-    }).catch((err2) => {
-      if (!(err2 instanceof KeyError))
-        throw err2;
-      if (context.fill_value) {
-        setter2.set_scalar(out, mapping.map((m) => m.to).filter((s2) => s2 !== null), context.fill_value);
-      }
-    }));
+    });
   }
   await queue.onIdle();
   return indexer.shape.length === 0 ? unwrap(out.data, 0) : out;

package/dist/index.js

@@ -1,4 +1,4 @@
-import { D, e, a, b, c, d, F, G, Z, C, r, n, E, A, y, l, m, z, x, h, q, v, o, i, f, j, k, u, t, p, s, w } from "./index-ecfc14b5.js";
+import { D, e, a, b, c, d, F, G, Z, C, r, n, E, A, y, l, m, z, x, h, q, v, o, i, f, j, k, u, t, p, s, w } from "./index-2e60bcd0.js";
 import "react";
 export {
   D as DEFAULT_CELLS_LAYER,

package/dist/{jpeg-8a56f635.js → jpeg-36de5225.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ecfc14b5.js";
+import { B as BaseDecoder } from "./index-2e60bcd0.js";
 import "react";
 const dctZigZag = new Int32Array([
   0,

package/dist/{lerc-cafe8298.js → lerc-cecad635.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ecfc14b5.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-2e60bcd0.js";
 import "react";
 const LercParameters = {
   Version: 0,