Backport to 1.12: H5Dchunk_iter now passes offsets in units of datase…

…t elements, fix HDFGroup#1419 (HDFGroup#1969)

* H5Dchunk_iter now passes chunk dimension scaled offsets, fix HDFGroup#1419

* Update docs for H5Dchunk_iter, H5Dget_chunk_info*

Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following

 * offset          Logical position of the chunk’s first element in units of dataset elements
 * filter_mask  Bitmask indicating the filters used when the chunk was written
 * size             Chunk size in bytes, 0 if the chunk does not exist

src/H5Dchunk.c

@@ -252,6 +252,7 @@ typedef struct H5D_chunk_coll_fill_info_t {
 typedef struct H5D_chunk_iter_ud_t {
     H5D_chunk_iter_op_t op;      /* User defined callback */
     void               *op_data; /* User data for user defined callback */
+    H5O_layout_chunk_t *chunk;   /* Chunk layout */
 } H5D_chunk_iter_ud_t;
 
 /********************/
@@ -7675,13 +7676,20 @@ static int
 H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
 {
     const H5D_chunk_iter_ud_t *data      = (H5D_chunk_iter_ud_t *)udata;
+    const H5O_layout_chunk_t  *chunk     = data->chunk;
     int                        ret_value = H5_ITER_CONT;
+    hsize_t                    offset[H5O_LAYOUT_NDIMS];
+    unsigned                   ii; /* Match H5O_layout_chunk_t.ndims */
+
+    /* Similar to H5D__get_chunk_info */
+    for (ii = 0; ii < chunk->ndims; ii++)
+        offset[ii] = chunk_rec->scaled[ii] * chunk->dim[ii];
 
     FUNC_ENTER_PACKAGE_NOERR
 
     /* Check for callback failure and pass along return value */
-    if ((ret_value = (data->op)(chunk_rec->scaled, chunk_rec->filter_mask, chunk_rec->chunk_addr,
-                                chunk_rec->nbytes, data->op_data)) < 0)
+    if ((ret_value = (data->op)(offset, chunk_rec->filter_mask, chunk_rec->chunk_addr, chunk_rec->nbytes,
+                                data->op_data)) < 0)
         HERROR(H5E_DATASET, H5E_CANTNEXT, "iteration operator failed");
 
     FUNC_LEAVE_NOAPI(ret_value)
@@ -7741,6 +7749,7 @@ H5D__chunk_iter(H5D_t *dset, H5D_chunk_iter_op_t op, void *op_data)
         /* Set up info for iteration callback */
         ud.op      = op;
         ud.op_data = op_data;
+        ud.chunk   = &dset->shared->layout.u.chunk;
 
         /* Iterate over the allocated chunks calling the iterator callback */
         if ((ret_value = (layout->storage.u.chunk.ops->iterate)(&idx_info, H5D__chunk_iter_cb, &ud)) < 0)

src/H5Dpublic.h

@@ -224,11 +224,24 @@ typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_us
 
 //! <!-- [H5D_chunk_iter_op_t_snip] -->
 /**
- * Define the operator function pointer for H5Dchunk_iter()
+ * \brief Callback for H5Dchunk_iter()
+ *
+ * \param[in]     offset      Logical position of the chunk’s first element in units of dataset elements
+ * \param[in]     filter_mask Bitmask indicating the filters used when the chunk was written
+ * \param[in]     addr        Chunk address in the file
+ * \param[in]     size        Chunk size in bytes, 0 if the chunk does not exist
+ * \param[in,out] op_data     Pointer to any user-defined data associated with
+ *                            the operation.
+ * \returns \li Zero (#H5_ITER_CONT) causes the iterator to continue, returning
+ *              zero when all elements have been processed.
+ *          \li A positive value (#H5_ITER_STOP) causes the iterator to
+ *              immediately return that value, indicating short-circuit success.
+ *          \li A negative (#H5_ITER_ERROR) causes the iterator to immediately
+ *              return that value, indicating failure.
  */
-//! <!-- [H5D_chunk_iter_op_t_snip] -->
-typedef int (*H5D_chunk_iter_op_t)(const hsize_t *offset, uint32_t filter_mask, haddr_t addr, uint32_t nbytes,
+typedef int (*H5D_chunk_iter_op_t)(const hsize_t *offset, uint32_t filter_mask, haddr_t addr, uint32_t size,
                                    void *op_data);
+//! <!-- [H5D_chunk_iter_op_t_snip] -->
 
 /********************/
 /* Public Variables */
@@ -596,10 +609,10 @@ H5_DLL herr_t H5Dget_num_chunks(hid_t dset_id, hid_t fspace_id, hsize_t *nchunks
  * \brief Retrieves information about a chunk specified by its coordinates
  *
  * \dset_id
- * \param[in]  offset      Logical position of the chunk’s first element
- * \param[out] filter_mask Indicating filters used with the chunk when written
+ * \param[in]  offset      Logical position of the chunk’s first element in units of dataset elements
+ * \param[out] filter_mask Bitmask indicating the filters used when the chunk was written
  * \param[out] addr        Chunk address in the file
- * \param[out] size        Chunk size in bytes, 0 if chunk doesn’t exist
+ * \param[out] size        Chunk size in bytes, 0 if the chunk does not exist
  *
  * \return \herr_t
  *
@@ -633,7 +646,7 @@ H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, u
  *
  * \return \herr_t
  *
- * \details H5Dget_chunk_iter iterates over all chunks in the dataset, calling the
+ * \details H5Dchunk_iter iterates over all chunks in the dataset, calling the
  *          user supplied callback with the details of the chunk and the supplied
  *          \p op_data.
  *
@@ -677,10 +690,10 @@ H5_DLL herr_t H5Dchunk_iter(hid_t dset_id, H5D_chunk_iter_op_t cb, void *op_data
  * \dset_id
  * \param[in]  fspace_id File dataspace selection identifier (See Note below)
  * \param[in]  chk_idx   Index of the chunk
- * \param[out] offset    Logical position of the chunk’s first element
- * \param[out] filter_mask Indicating filters used with the chunk when written
+ * \param[out] offset    Logical position of the chunk’s first element in units of dataset elements
+ * \param[out] filter_mask Bitmask indicating the filters used when the chunk was written
  * \param[out] addr      Chunk address in the file
- * \param[out] size      Chunk size in bytes, 0 if chunk doesn’t exist
+ * \param[out] size      Chunk size in bytes, 0 if the chunk does not exist
  *
  * \return \herr_t
  *

test/chunk_info.c

@@ -1721,9 +1721,9 @@ test_basic_query(hid_t fapl)
     if (chunk_infos[0].nbytes != 96)
         FAIL_PUTS_ERROR("size mismatch");
 
-    if (chunk_infos[1].offset[0] != 1)
+    if (chunk_infos[1].offset[0] != CHUNK_NX)
         FAIL_PUTS_ERROR("offset[0] mismatch");
-    if (chunk_infos[1].offset[1] != 1)
+    if (chunk_infos[1].offset[1] != CHUNK_NY)
         FAIL_PUTS_ERROR("offset[1] mismatch");
 
     /* Iterate and stop after one iteration */