adding getters for region reference data

src/hdf5_hl.d.ts

@@ -154,6 +154,8 @@ export declare class DatasetRegion {
     private _metadata?;
     constructor(source_dataset: Dataset, region_reference: RegionReference);
     get metadata(): Metadata;
+    get value(): OutputData;
+    _value_getter(json_compatible?: boolean): OutputData;
 }
 export declare const h5wasm: {
     File: typeof File;

src/hdf5_hl.ts

@@ -1050,6 +1050,29 @@ export class DatasetRegion {
     }
     return this._metadata;
   }
+
+  get value() {
+    return this._value_getter(false);
+  }
+
+  _value_getter(json_compatible=false) {
+    let metadata = this.metadata;
+    // if auto_refresh is on, getting the metadata has triggered a refresh of the dataset_id;
+    let nbytes = metadata.size * metadata.total_size;
+    let data_ptr = Module._malloc(nbytes);
+    let processed: OutputData;
+    try {
+      Module.get_region_data(this.source_dataset.file_id, this.region_reference.ref_data, BigInt(data_ptr));
+      let data = Module.HEAPU8.slice(data_ptr, data_ptr + nbytes);
+      processed = process_data(data, metadata, json_compatible);
+    } finally {
+      if (metadata.vlen) {
+        Module.reclaim_vlen_memory(this.source_dataset.file_id, this.source_dataset.path, "", BigInt(data_ptr));
+      }
+      Module._free(data_ptr);
+    }
+    return processed;
+  }
 }
 
 function create_nested_array(value: JSONCompatibleOutputData[], shape: number[]) {

src/hdf5_util.cc

@@ -1114,7 +1114,7 @@ val get_region_metadata(hid_t loc_id, const val ref_data_in)
     hid_t dcpl;
     herr_t status;
     const std::vector<uint8_t> ref_data_vec = convertJSArrayToNumberVector<uint8_t>(ref_data_in);
-    const hobj_ref_t *ref_ptr = (hobj_ref_t *)ref_data_vec.data();
+    const hdset_reg_ref_t *ref_ptr = (hdset_reg_ref_t *)ref_data_vec.data();
     hid_t ds_id = H5Rdereference2(loc_id, H5P_DEFAULT, H5R_DATASET_REGION, ref_ptr);
 
     dtype = H5Dget_type(ds_id);
@@ -1150,6 +1150,57 @@ val get_region_metadata(hid_t loc_id, const val ref_data_in)
     return metadata;
 }
 
+int get_region_data(hid_t loc_id, val ref_data_in, uint64_t rdata_uint64)
+{
+    hid_t ds_id;
+    hid_t dspace;
+    hid_t dtype;
+    hid_t memtype;
+    hid_t memspace;
+    herr_t status;
+    void *rdata = (void *)rdata_uint64;
+    const std::vector<uint8_t> ref_data_vec = convertJSArrayToNumberVector<uint8_t>(ref_data_in);
+    const hdset_reg_ref_t *ref_ptr = (hdset_reg_ref_t *)ref_data_vec.data();
+    ds_id = H5Rdereference2(loc_id, H5P_DEFAULT, H5R_DATASET_REGION, ref_ptr);
+    dspace = H5Rget_region(ds_id, H5R_DATASET_REGION, ref_ptr);
+    dtype = H5Dget_type(ds_id);
+    // assumes that data to write will match type of dataset (exept endianness)
+    memtype = H5Tcopy(dtype);
+    // inputs and outputs from javascript will always be little-endian
+    H5T_order_t dorder = H5Tget_order(dtype);
+    if (dorder == H5T_ORDER_BE || dorder == H5T_ORDER_VAX)
+    {
+        status = H5Tset_order(memtype, H5T_ORDER_LE);
+    }
+    int rank = H5Sget_simple_extent_ndims(dspace);
+    htri_t is_regular = H5Sis_regular_hyperslab(dspace);
+    if (is_regular > 0)
+    {
+        std::vector<hsize_t> count(rank);
+        std::vector<hsize_t> block(rank);
+        std::vector<hsize_t> shape_out(rank);
+        htri_t success = H5Sget_regular_hyperslab(dspace, nullptr, nullptr, count.data(), block.data());
+        for (int d = 0; d < rank; d++)
+        {
+            int blocksize = (block.at(d) == NULL) ? 1 : block.at(d); 
+            shape_out.at(d) = (count.at(d) * blocksize);
+        }
+        memspace = H5Screate_simple(shape_out.size(), &shape_out[0], nullptr);
+    }
+    else
+    {
+        hsize_t total_size = H5Sget_select_npoints(dspace);
+        memspace = H5Screate_simple(1, &total_size, nullptr);
+    }
+    status = H5Dread(ds_id, memtype, memspace, dspace, H5P_DEFAULT, rdata);
+    H5Dclose(ds_id);
+    H5Sclose(dspace);
+    H5Sclose(memspace);
+    H5Tclose(dtype);
+    H5Tclose(memtype);
+    return (int)status;
+}
+
 EMSCRIPTEN_BINDINGS(hdf5)
 {
     function("get_keys", &get_keys_vector);
@@ -1192,6 +1243,7 @@ EMSCRIPTEN_BINDINGS(hdf5)
     function("create_region_reference", &create_region_reference);
     function("get_referenced_name", &get_referenced_name);
     function("get_region_metadata", &get_region_metadata);
+    function("get_region_data", &get_region_data);
 
     class_<H5L_info2_t>("H5L_info2_t")
         .constructor<>()

src/hdf5_util_helpers.d.ts

@@ -121,6 +121,7 @@ export interface H5Module extends EmscriptenModule {
     create_region_reference(file_id: bigint, path: string, count: bigint[] | null, offset: bigint[] | null, strides: bigint[] | null): Uint8Array,
     get_referenced_name(loc_id: bigint, ref_ptr: Uint8Array, is_object: boolean): string;
     get_region_metadata(loc_id: bigint, ref_ptr: Uint8Array): Metadata;
+    get_region_data(loc_id: bigint, ref_data: Uint8Array, rdata_ptr: bigint): number;
 }
 
 export declare type Filter = {