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Diffstat (limited to 'src/H5RA.c')
| -rw-r--r-- | src/H5RA.c | 1290 |
1 files changed, 0 insertions, 1290 deletions
diff --git a/src/H5RA.c b/src/H5RA.c deleted file mode 100644 index 71b7eb5..0000000 --- a/src/H5RA.c +++ /dev/null @@ -1,1290 +0,0 @@ -/* - * Copyright © 1998 NCSA - * All rights reserved. - * - * Programmer: Robb Matzke <matzke@llnl.gov> - * Tuesday, August 25, 1998 - * - * Purpose: A ragged array package layered on top of other HDF5 objects. - * This was originally implemented on the HDF5 API but has been - * moved under the API so it meshes better with other objects, - * is somewhat faster, and has better debugging support. - * - * Note: This file implementes a two dimensional array where each row - * of the array is a different length (a.k.a., ragged array). It - * is intended for applications where the distribution of row - * lengths is such that most rows near an average length with - * only a few rows that are significantly shorter or longer. The - * raw data is split among two datasets `raw' and `over': the - * `raw' dataset is a 2d chunked dataset whose width is large - * enough to hold most of the rows and the `over' dataset is a - * heap that stores the end of rows that overflow the first - * dataset. A third dataset called `meta' contains one record - * for each row and describes what elements (if any) overflow - * the `raw' dataset and where they are stored in the `over' - * dataset. All three datasets are contained in a single group - * whose name is the name of the ragged array. - */ -#include <H5RAprivate.h> - -#include <H5private.h> -#include <H5Eprivate.h> -#include <H5Iprivate.h> -#include <H5MMprivate.h> -#include <H5Pprivate.h> - -typedef struct H5RA_meta_t { - hsize_t nelmts; /*num elements in row */ - hssize_t offset; /*offset into overflow array */ - hsize_t nover; /*allocated size in overflow array */ -} H5RA_meta_t; - -struct H5RA_t { - H5G_t *group; /*the group containing everything */ - H5D_t *meta; /*ragged meta data array */ - H5D_t *raw; /*fixed-width raw data */ - H5D_t *over; /*overflow data */ -}; - -#define PABLO_MASK H5RA_mask -static intn interface_initialize_g = 0; -#define INTERFACE_INIT H5RA_init_interface -static herr_t H5RA_init_interface(void); -static H5T_t *H5RA_meta_type_g = NULL; - -static herr_t H5RA_fix_overflow(H5RA_t *ra, H5T_t *type, H5RA_meta_t *meta, - hsize_t nelmts, void *buf); - - -/*------------------------------------------------------------------------- - * Function: H5RA_init_interface - * - * Purpose: Initialize the interface. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5RA_init_interface(void) -{ - H5T_t *type = NULL; - - FUNC_ENTER(H5RA_init_interface, FAIL); - - /* The atom group */ - if (H5I_init_group(H5I_RAGGED, H5I_RAGGED_HASHSIZE, 0, - (H5I_free_t)H5RA_close)<0) { - HRETURN_ERROR (H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to initialize interface"); - } - - /* The meta dataset type */ - if (NULL==(type=H5T_create(H5T_COMPOUND, sizeof(H5RA_meta_t))) || - H5T_insert(type, "nelmts", HOFFSET(H5RA_meta_t, nelmts), H5I_object(H5T_NATIVE_HSIZE_g))<0 || - H5T_insert(type, "offset", HOFFSET(H5RA_meta_t, offset), H5I_object(H5T_NATIVE_HSSIZE_g))<0 || - H5T_insert(type, "nover", HOFFSET(H5RA_meta_t, nover), H5I_object(H5T_NATIVE_HSIZE_g))) { - HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to define ragged array meta type"); - } - H5RA_meta_type_g = type; - - FUNC_LEAVE(SUCCEED); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_term_interface - * - * Purpose: Terminate the ragged array interface. - * - * Return: Success: Positive if anything was done that might - * affect some other interface. Zero otherwise. - * - * Failure: Negaitive - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -intn -H5RA_term_interface(void) -{ - intn n=0; - - if (interface_initialize_g) { - if ((n=H5I_nmembers(H5I_RAGGED))) { - H5I_clear_group(H5I_RAGGED, FALSE); - } else { - H5T_close(H5RA_meta_type_g); - H5RA_meta_type_g = NULL; - H5I_destroy_group(H5I_RAGGED); - interface_initialize_g = 0; - n = 1; /*H5T,H5I*/ - } - } - return n; -} - - -/*------------------------------------------------------------------------- - * Function: H5RAcreate - * - * Purpose: Create a new ragged array with the specified name. A ragged - * array is implemented as a group containing three datasets. - * The dataset `raw' is a fixed width dataset which will hold - * the majority of the data. The dataset `over' is a one - * dimensional heap which will hold the end of rows which are - * too long to fit in `raw'. Finally, the `meta' dataset - * contains information about the `over' array. All elements of - * the ragged array are stored with the same data type. - * - * The property list PLIST_ID should contain information about - * chunking. The chunk width will determine the width of the - * `raw' dataset while the chunk length should be such that the - * total chunk size is reasonably large (I/O will be performed - * in units of chunks). If the PLIST_ID doesn't have a chunk - * size defined (e.g., H5P_DEFAULT) then this function will fail. - * - * Return: Success: A ragged array ID. - * - * Failure: Negative - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -hid_t -H5RAcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t plist_id) -{ - H5RA_t *ra=NULL; - H5G_entry_t *loc=NULL; - H5T_t *type=NULL; - const H5D_create_t *plist=NULL; - hid_t ret_value=FAIL; - - FUNC_ENTER(H5RAcreate, FAIL); - H5TRACE4("i","isii",loc_id,name,type_id,plist_id); - - /* Check args */ - if (NULL==(loc=H5G_loc(loc_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location"); - } - if (!name || !*name) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name given"); - } - if (H5I_DATATYPE!=H5I_get_type(type_id) || - NULL==(type=H5I_object(type_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); - } - if (H5P_DEFAULT==plist_id) { - plist = &H5D_create_dflt; - } else if (H5P_DATASET_CREATE!=H5P_get_class(plist_id) || - NULL==(plist=H5I_object(plist_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, - "not a dataset creation property list"); - } - if (H5D_CHUNKED!=plist->layout) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "property list must define a chunked storage layout"); - } - if (2!=plist->layout) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "chunked storage is not two dimensional"); - } - - /* Do the real work */ - if (NULL==(ra=H5RA_create(loc, name, type, plist))) { - HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to create ragged array"); - } - - /* Register the new dataset to get an ID for it */ - if ((ret_value=H5I_register(H5I_RAGGED, ra))<0) { - H5RA_close(ra); - HRETURN_ERROR(H5E_RAGGED, H5E_CANTREGISTER, FAIL, - "unable to register ragged array"); - } - - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_create - * - * Purpose: Create a new ragged array implemented as a group. - * - * Return: Success: Pointer to the new ragged array. - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -H5RA_t * -H5RA_create(H5G_entry_t *loc, const char *name, H5T_t *type, - const H5D_create_t *dcpl) -{ - H5RA_t *ra = NULL; - H5S_t *space = NULL; - hsize_t cur_dims[2]; - hsize_t max_dims[2]; - H5RA_t *ret_value=NULL; - H5D_create_t d1_dcpl; - - FUNC_ENTER(H5RA_create, NULL); - - /* Check args */ - assert(loc); - assert(name && *name); - assert(type); - assert(dcpl); - assert(H5D_CHUNKED==dcpl->layout); - - /* Create the data struct */ - if (NULL==(ra=H5MM_calloc(sizeof(H5RA_t)))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, - "memory allocation failed for ragged array struct"); - } - - /* Create the group to contain the arrays */ - if (NULL==(ra->group=H5G_create(loc, name, 0))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to create container group"); - } - - /* The raw data array */ - cur_dims[0] = 0; - max_dims[0] = H5S_UNLIMITED; - cur_dims[1] = max_dims[1] = dcpl->chunk_size[1]; - if (NULL==(space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(space, 2, cur_dims, max_dims)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to define raw dataset extents"); - } - if (NULL==(ra->raw=H5D_create(H5G_entof(ra->group), "raw", type, space, - dcpl))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to create raw dataset"); - } - if (H5S_close(space)<0) { - space = NULL; - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to close raw dataset extents"); - } - space = NULL; - - /* The overflow data array */ - cur_dims[0] = 0; - max_dims[0] = H5S_UNLIMITED; - if (NULL==(space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(space, 1, cur_dims, max_dims)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to define overflow dataset extents"); - } - d1_dcpl = *dcpl; - d1_dcpl.chunk_ndims = 1; - d1_dcpl.chunk_size[0] = dcpl->chunk_size[0]*dcpl->chunk_size[1]; - if (NULL==(ra->over=H5D_create(H5G_entof(ra->group), "over", type, space, - &d1_dcpl))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to create overflow dataset"); - } - if (H5S_close(space)<0) { - space = NULL; - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to close overflow dataset extents"); - } - space = NULL; - - /* The meta data array */ - cur_dims[0] = 0; - max_dims[0] = H5S_UNLIMITED; - if (NULL==(space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(space, 1, cur_dims, max_dims)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to define meta dataset extents"); - } - d1_dcpl.chunk_size[0] = MAX(1, - (dcpl->chunk_size[0]*dcpl->chunk_size[1]* - H5T_get_size(type))/ - H5T_get_size(H5RA_meta_type_g)); - if (NULL==(ra->meta=H5D_create(H5G_entof(ra->group), "meta", - H5RA_meta_type_g, space, &d1_dcpl))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to create meta dataset"); - } - if (H5S_close(space)<0) { - space = NULL; - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, - "unable to close meta dataset extents"); - } - space = NULL; - - ret_value = ra; - - done: - if (!ret_value) { - if (space) H5S_close(space); - if (ra) { - if (ra->group) H5G_close(ra->group); - if (ra->raw) H5D_close(ra->raw); - if (ra->over) H5D_close(ra->over); - if (ra->meta) H5D_close(ra->meta); - H5MM_xfree(ra); - } - } - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RAopen - * - * Purpose: Opens an existing ragged array. The name of the array should - * be the same that was used when the array was created; that is, - * the name of the group which implements the array. - * - * Return: Success: An array ID - * - * Failure: Negative - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -hid_t -H5RAopen(hid_t loc_id, const char *name) -{ - H5G_entry_t *loc=NULL; - H5RA_t *ra=NULL; - hid_t ret_value=FAIL; - - FUNC_ENTER(H5RAopen, FAIL); - H5TRACE2("i","is",loc_id,name); - - /* Check args */ - if (NULL==(loc=H5G_loc(loc_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location"); - } - if (!name || !*name) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name given"); - } - - /* The real work */ - if (NULL==(ra=H5RA_open(loc, name))) { - HRETURN_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, FAIL, - "unable to open ragged array"); - } - - /* Turn it into an atom */ - if ((ret_value=H5I_register(H5I_RAGGED, ra))<0) { - H5RA_close(ra); - HRETURN_ERROR(H5E_RAGGED, H5E_CANTREGISTER, FAIL, - "unable to register ragged array"); - } - - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_isa - * - * Purpose: Determines if an object is a ragged array. - * - * Return: Success: TRUE if the object is a ragged array; FALSE - * otherwise. - * - * Failure: Negative - * - * Programmer: Robb Matzke - * Wednesday, November 4, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -htri_t -H5RA_isa(H5G_entry_t *ent) -{ - htri_t exists; - H5G_entry_t d_ent; - - FUNC_ENTER(H5RA_isa, FAIL); - - /* Open the container group */ - if ((exists=H5G_isa(ent))<0) { - HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to read object header"); - } else if (!exists) { - HRETURN(FALSE); - } - - /* Is `raw' a dataset? */ - if (H5G_find(ent, "raw", NULL, &d_ent)<0) HRETURN(FALSE); - if ((exists=H5D_isa(&d_ent))<0) { - HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found"); - } else if (!exists) { - HRETURN(FALSE); - } - - /* Is `over' a dataset? */ - if (H5G_find(ent, "over", NULL, &d_ent)<0 || - (exists=H5D_isa(&d_ent))<0) { - HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found"); - } else if (!exists) { - HRETURN(FALSE); - } - - /* Is `meta' a dataset? */ - if (H5G_find(ent, "meta", NULL, &d_ent)<0 || - (exists=H5D_isa(&d_ent))<0) { - HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found"); - } else if (!exists) { - HRETURN(FALSE); - } - - FUNC_LEAVE(TRUE); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_open - * - * Purpose: Open a ragged array. The name of the array is the same as - * the group that implements the array. - * - * Return: Success: Ptr to a new ragged array object. - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -H5RA_t * -H5RA_open(H5G_entry_t *loc, const char *name) -{ - H5RA_t *ra = NULL; - H5RA_t *ret_value = NULL; - - FUNC_ENTER(H5RA_open, NULL); - - /* Check arguments */ - assert(loc); - assert(name && *name); - - /* Create the struct */ - if (NULL==(ra=H5MM_calloc(sizeof(H5RA_t)))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, - "memory allocation failed for ragged array struct"); - } - - /* Open the containing group */ - if (NULL==(ra->group=H5G_open(loc, name))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, NULL, - "unable to open container group"); - } - - /* Open the datasets */ - if (NULL==(ra->raw=H5D_open(H5G_entof(ra->group), "raw")) || - NULL==(ra->over=H5D_open(H5G_entof(ra->group), "over")) || - NULL==(ra->meta=H5D_open(H5G_entof(ra->group), "meta"))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, NULL, - "unable to open one or more component datasets"); - } - - ret_value = ra; - - done: - if (!ret_value) { - if (ra) { - if (ra->group) H5G_close(ra->group); - if (ra->raw) H5D_close(ra->raw); - if (ra->over) H5D_close(ra->over); - if (ra->meta) H5D_close(ra->meta); - H5MM_xfree(ra); - } - } - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RAclose - * - * Purpose: Close a ragged array. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5RAclose(hid_t array_id) -{ - FUNC_ENTER(H5RAclose, FAIL); - H5TRACE1("e","i",array_id); - - /* Check args */ - if (H5I_RAGGED!=H5I_get_type(array_id) || - NULL==H5I_object(array_id)) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array"); - } - - /* - * Decrement the counter on the array. It will be freed if the count - * reaches zero. - */ - if (H5I_dec_ref(array_id) < 0) { - HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to free"); - } - - FUNC_LEAVE(SUCCEED); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_close - * - * Purpose: Close a ragged array - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5RA_close(H5RA_t *ra) -{ - FUNC_ENTER(H5RA_close, FAIL); - - assert(ra); - if ((ra->group && H5G_close(ra->group)<0) || - (ra->raw && H5D_close(ra->raw)<0) || - (ra->over && H5D_close(ra->over)<0) || - (ra->meta && H5D_close(ra->meta)<0)) { - HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to close one or more component datasets"); - } - HDmemset(ra, 0, sizeof(H5RA_t)); - H5MM_xfree(ra); - - FUNC_LEAVE(SUCCEED); -} - - -/*------------------------------------------------------------------------- - * Function: H5RAwrite - * - * Purpose: Write a contiguous set of rows to a ragged array beginning at - * row number START_ROW and continuing for NROWS rows. Each row - * of the ragged array contains SIZE[] elements of type TYPE_ID - * and each row is stored in a buffer pointed to by BUF[]. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5RAwrite(hid_t array_id, hssize_t start_row, hsize_t nrows, - hid_t type_id, hsize_t size[/*nrows*/], void *buf[/*nrows*/]) -{ - H5RA_t *ra=NULL; - H5T_t *type=NULL; - hsize_t i; - - FUNC_ENTER(H5RAwrite, FAIL); - H5TRACE6("e","iHshi*[a2]h*[a2]x",array_id,start_row,nrows,type_id,size, - buf); - - /* Check args */ - if (H5I_RAGGED!=H5I_get_type(array_id) || - NULL==(ra=H5I_object(array_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array"); - } - if (H5I_DATATYPE!=H5I_get_type(type_id) || - NULL==(type=H5I_object(type_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); - } - if (nrows>0 && !size) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size array"); - } - if (nrows>0 && !buf) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer array"); - } - for (i=0; i<nrows; i++) { - if (size[i]>0 && !buf[i]) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "one or more buffer points are null"); - } - } - - /* Do the work */ - if (H5RA_write(ra, start_row, nrows, type, size, buf)<0) { - HRETURN_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL, - "unable to write to ragged array"); - } - - FUNC_LEAVE(SUCCEED); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_write - * - * Purpose: Write a contiguous set of rows to a ragged array beginning at - * row number START_ROW and continuing for NROWS rows. Each row - * of the ragged array contains SIZE[] elements of type TYPE_ID - * and each row is stored in a buffer pointed to by BUF[]. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5RA_write(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type, - hsize_t size[], void *buf[]) -{ - herr_t ret_value=FAIL; - H5RA_meta_t *meta = NULL; - H5S_t *mf_space=NULL; /*meta file data space */ - H5S_t *mm_space=NULL; /*meta memory data space */ - H5S_t *rf_space=NULL; /*raw data file space */ - H5S_t *rm_space=NULL; /*raw data memory space */ - hsize_t meta_cur_size; /*current meta data nelmts */ - hsize_t meta_read_size; /*amount to read */ - hsize_t raw_cur_size[2]; /*raw data current size */ - hssize_t hs_offset[2]; /*hyperslab offset */ - hsize_t hs_size[2]; /*hyperslab size */ - uint8_t *raw_buf=NULL; /*raw buffer */ - size_t type_size; /*size of the TYPE argument */ - hsize_t i; - - FUNC_ENTER(H5RA_write, FAIL); - - /* Check args */ - assert(ra); - assert(type); - assert(0==nrows || size); - assert(0==nrows || buf); - if (0==nrows) HRETURN(SUCCEED); - type_size = H5T_get_size(type); - - /* Get the meta data */ - if (NULL==(mf_space=H5D_get_space(ra->meta)) || - H5S_get_simple_extent_dims(mf_space, &meta_cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to get current meta data extents"); - } - if ((hsize_t)start_row>=meta_cur_size) { - meta_read_size = 0; - } else { - meta_read_size = MIN(nrows, meta_cur_size-(hsize_t)start_row); - } - if (NULL==(mm_space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(mm_space, 1, &meta_read_size, NULL)<0 || - H5S_select_hyperslab(mf_space, H5S_SELECT_SET, &start_row, NULL, - &meta_read_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set meta data selection"); - } - assert((nrows*sizeof(H5RA_meta_t))==(hsize_t)((size_t)(nrows*sizeof(H5RA_meta_t)))); /*check for overflow*/ - if (NULL==(meta=H5MM_malloc((size_t)(nrows*sizeof(H5RA_meta_t))))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for meta data"); - } - if (H5D_read(ra->meta, H5RA_meta_type_g, mm_space, mf_space, - H5P_DEFAULT, meta)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, - "unable to read meta data"); - } - assert(((nrows-meta_read_size)*sizeof(H5RA_meta_t))==(hsize_t)((size_t)((nrows-meta_read_size)*sizeof(H5RA_meta_t)))); /*check for overflow*/ - HDmemset(meta+meta_read_size, 0, - (size_t)((nrows-meta_read_size)*sizeof(H5RA_meta_t))); - - /* Write the part of the data that will fit in the raw dataset */ - if (NULL==(rf_space=H5D_get_space(ra->raw)) || - H5S_get_simple_extent_dims(rf_space, raw_cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to determine current raw data extents"); - } - assert((nrows*raw_cur_size[1]*type_size)==(hsize_t)((size_t)(nrows*raw_cur_size[1]*type_size))); /*check for overflow*/ - if (NULL==(raw_buf=H5MM_malloc((size_t)(nrows*raw_cur_size[1]*type_size)))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, - "unable to allocate buffer for raw data"); - } - for (i=0; i<nrows; i++) { - size_t nbytes = MIN(size[i], raw_cur_size[1])*type_size; - HDmemcpy(raw_buf+i*raw_cur_size[1]*type_size, buf[i], nbytes); - assert((raw_cur_size[1]*type_size-nbytes)==(hsize_t)((size_t)(raw_cur_size[1]*type_size-nbytes))); /*check for overflow*/ - HDmemset(raw_buf+i*raw_cur_size[1]*type_size+nbytes, 0, - (size_t)(raw_cur_size[1]*type_size-nbytes)); - } - if ((hsize_t)start_row+nrows>raw_cur_size[0]) { - raw_cur_size[0] = (hsize_t)start_row + nrows; - if (H5D_extend(ra->raw, raw_cur_size)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to extend raw dataset"); - } - /* Throw away previous raw file dataspace */ - H5S_close(rf_space); - - /* Retrieve newly extended raw file dataspace */ - if (NULL==(rf_space=H5D_get_space(ra->raw)) || - H5S_get_simple_extent_dims(rf_space, raw_cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to determine current raw data extents"); - } - } - hs_offset[0] = start_row; - hs_offset[1] = 0; - hs_size[0] = nrows; - hs_size[1] = raw_cur_size[1]; - if (NULL==(rm_space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(rm_space, 2, hs_size, NULL)<0 || - H5S_select_hyperslab(rf_space, H5S_SELECT_SET, - hs_offset, NULL, hs_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set meta data selection"); - } - if (H5D_write(ra->raw, type, rm_space, rf_space, H5P_DEFAULT, - raw_buf)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL, - "unable to write raw data"); - } - - /* Update the meta data */ - for (i=0; i<nrows; i++) { - if (size[i]>raw_cur_size[1]) { - H5RA_fix_overflow(ra, type, meta+i, size[i]-raw_cur_size[1], - (uint8_t*)(buf[i])+raw_cur_size[1]*type_size); - } - meta[i].nelmts = size[i]; - } - - /* Extend and write the new meta data */ - if ((hsize_t)start_row+nrows>meta_cur_size) { - meta_cur_size = (hsize_t)start_row+nrows; - if (H5D_extend(ra->meta, &meta_cur_size)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to extend meta dataset"); - } - /* Throw away previous meta file dataspace */ - H5S_close(mf_space); - - /* Retrieve newly extended meta file dataspace */ - if (NULL==(mf_space=H5D_get_space(ra->meta)) || - H5S_get_simple_extent_dims(mf_space, &meta_cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to determine current raw data extents"); - } - } - if (H5S_set_extent_simple(mm_space, 1, &nrows, NULL)<0 || - H5S_select_hyperslab(mf_space, H5S_SELECT_SET, &start_row, NULL, - &nrows, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set meta data selection"); - } - if (H5D_write(ra->meta, H5RA_meta_type_g, mm_space, mf_space, - H5P_DEFAULT, meta)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL, - "unable to write meta data"); - } - - ret_value = SUCCEED; - done: - H5MM_xfree(meta); - H5MM_xfree(raw_buf); - if (mm_space) H5S_close(mm_space); - if (mf_space) H5S_close(mf_space); - if (rm_space) H5S_close(rm_space); - if (rf_space) H5S_close(rf_space); - - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_fix_overflow - * - * Purpose: Updates the overflow information for a row. This is where - * the heap management comes into play. The NELMTS is the - * number of elements that overflow into the heap and BUF is a - * pointer to those elements. The first part of the row has - * already been written to the raw dataset. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Wednesday, August 26, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5RA_fix_overflow(H5RA_t *ra, H5T_t *type, H5RA_meta_t *meta, hsize_t nelmts, - void *buf) -{ - H5S_t *of_space=NULL; /*overflow file space */ - H5S_t *om_space=NULL; /*overflow memory space */ - hsize_t cur_size; /*num elmts in overflow dataset */ - herr_t ret_value=FAIL; /*return value */ - - FUNC_ENTER(H5RA_fix_overflow, FAIL); - - assert(ra); - assert(meta); - assert(buf); - - if (nelmts==meta->nover) { - /* The space is already allocated -- do nothing */ - - } else if (nelmts<meta->nover) { - /* Too much space is allocated -- free the extra */ -#ifndef LATER - /* - * For now we don't worry about reclaiming space. But we remember - * the original amount allocated to allow the row to grow again up to - * that amount. - */ -#endif - - } else if (meta->nover>0) { - /* Space is allocated but we need more */ -#ifndef LATER - /* - * For now we'll just reallocate space at the end of the overflow - * dataset, but eventually we'll want to move the smallest of the - * current overflow, the previous overflow, or the following overflow - * region to the end of the file and be careful to reclaim space. - */ - if (NULL==(of_space=H5D_get_space(ra->over)) || - H5S_get_simple_extent_dims(of_space, &cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to get overflow dataset extents"); - } - meta->offset = (hssize_t)cur_size; - meta->nover = nelmts; - cur_size += nelmts; - if (H5D_extend(ra->over, &cur_size)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to extend overflow dataset"); - } - /* Throw away previous overflow file dataspace */ - H5S_close(of_space); - - /* Retrieve newly extended overflow file dataspace */ - if (NULL==(of_space=H5D_get_space(ra->over)) || - H5S_get_simple_extent_dims(of_space, &cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to determine current overflow data extents"); - } -#endif - - } else { - /* No space is allocated */ - assert(nelmts>0); - if (NULL==(of_space=H5D_get_space(ra->over)) || - H5S_get_simple_extent_dims(of_space, &cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to get overflow dataset extents"); - } - meta->offset = (hssize_t)cur_size; - meta->nover = nelmts; - cur_size += nelmts; - if (H5D_extend(ra->over, &cur_size)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to extend overflow dataset"); - } - /* Throw away previous overflow file dataspace */ - H5S_close(of_space); - - /* Retrieve newly extended overflow file dataspace */ - if (NULL==(of_space=H5D_get_space(ra->over)) || - H5S_get_simple_extent_dims(of_space, &cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to determine current overflow data extents"); - } - } - - /* Write the data */ - if (nelmts>0) { - if (!of_space && NULL==(of_space=H5D_get_space(ra->over))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to get overflow dataset extents"); - } - if (NULL==(om_space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(om_space, 1, &nelmts, NULL)<0 || - H5S_select_hyperslab(of_space, H5S_SELECT_SET, &(meta->offset), - NULL, &nelmts, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set overflow selection"); - } - if (H5D_write(ra->over, type, om_space, of_space, H5P_DEFAULT, - buf)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL, - "unable to write to overflow dataset"); - } - } - - ret_value = SUCCEED; - - done: - if (of_space) H5S_close(of_space); - if (om_space) H5S_close(om_space); - if (ret_value<0) { - meta->offset = 0; - meta->nover = 0; - } - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RAread - * - * Purpose: Reads the contents of one or more rows of a ragged array - * pointed to by ARRAY_ID. The rows to read begin at row - * START_ROW and continue for NROWS rows with all raw data - * converted to type TYPE_ID. - * - * The caller must allocate the SIZE[] and BUF[] arrays but - * memory for the data can be allocated by either the caller or - * the library. In the former case the caller should initialize - * the BUF[] array with pointers to valid memory and the SIZE[] - * array with the lengths of the buffers. In the latter case - * the caller should initialize BUF[] with null pointers (the - * input value of SIZE[] is irrelevant in this case) and the - * library will allocate memory for each row by calling malloc(). - * - * Return: Success: Non-negative. The values of the SIZE[] array will - * be the true length of each row. If a row is - * longer than the caller-allocated length then - * SIZE[] will contain the true length of the - * row although not all elements of that row - * will be stored in the buffer. - * - * Failure: Negative. The BUF[] array will contain it's - * original pointers (null or otherwise) - * although the caller-supplied buffers may have - * been modified. The SIZE[] array may also be - * modified. - * - * Programmer: Robb Matzke - * Tuesday, August 25, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5RAread(hid_t array_id, hssize_t start_row, hsize_t nrows, - hid_t type_id, hsize_t size[/*nrows*/], void *buf[/*nrows*/]) -{ - H5RA_t *ra=NULL; - H5T_t *type=NULL; - - FUNC_ENTER(H5RAread, FAIL); - H5TRACE6("e","iHshi*[a2]h*[a2]x",array_id,start_row,nrows,type_id,size, - buf); - - /* Check args */ - if (H5I_RAGGED!=H5I_get_type(array_id) || - NULL==(ra=H5I_object(array_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array"); - } - if (H5I_DATATYPE!=H5I_get_type(type_id) || - NULL==(type=H5I_object(type_id))) { - HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); - } - if (nrows>0 && !size) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size array"); - } - if (nrows>0 && !buf) { - HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer array"); - } - - /* Do the work */ - if (H5RA_read(ra, start_row, nrows, type, size, buf)<0) { - HRETURN_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, - "unable to read ragged array"); - } - - FUNC_LEAVE(SUCCEED); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_read - * - * Purpose: Reads (part of) a ragged array. See H5RAread() for details. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Wednesday, August 26, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5RA_read(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type, - hsize_t size[], void *buf[]) -{ - herr_t ret_value=FAIL; - H5RA_meta_t *meta = NULL; - H5S_t *mf_space=NULL; /*meta file data space */ - H5S_t *mm_space=NULL; /*meta memory data space */ - H5S_t *rf_space=NULL; /*raw data file space */ - H5S_t *rm_space=NULL; /*raw data memory space */ - H5S_t *of_space=NULL; /*overflow data file space */ - H5S_t *om_space=NULL; /*overflow data memory space */ - hsize_t meta_cur_size; /*current meta data nelmts */ - hsize_t meta_read_size; /*amount of meta data to read */ - hsize_t raw_cur_size[2]; /*raw data current size */ - hsize_t raw_read_size[2]; /*amount of raw data to read */ - hssize_t hs_offset[2]; /*hyperslab offset */ - hsize_t hs_size[2]; /*hyperslab size */ - uint8_t *raw_buf=NULL; /*raw buffer */ - size_t type_size; /*size of the TYPE argument */ - void **buf_out=NULL; /*output BUF values */ - hsize_t i; /*counter */ - - FUNC_ENTER(H5RA_read, FAIL); - - /* Check args */ - assert(ra); - assert(type); - assert(0==nrows || size); - assert(0==nrows || buf); - if (0==nrows) HRETURN(SUCCEED); - type_size = H5T_get_size(type); - - /* - * Malloc `buf_out' to hold the output values for `buf'. We have to do - * this because if we return failure we want `buf' to have the original - * values. - */ - assert((nrows*sizeof(void*))==(hsize_t)((size_t)(nrows*sizeof(void*)))); /*check for overflow*/ - if (NULL==(buf_out=H5MM_calloc((size_t)(nrows*sizeof(void*))))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for BUF output values"); - } - - /* Read from the raw dataset */ - if (NULL==(rf_space=H5D_get_space(ra->raw)) || - H5S_get_simple_extent_dims(rf_space, raw_cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to determine current raw data extents"); - } - if ((hsize_t)start_row>=raw_cur_size[0]) { - raw_read_size[0] = 0; - raw_read_size[1] = raw_cur_size[1]; - } else { - raw_read_size[0] = MIN(nrows, raw_cur_size[0]-(hsize_t)start_row); - raw_read_size[1] = raw_cur_size[1]; - } - hs_offset[0] = start_row; - hs_offset[1] = 0; - if (NULL==(rm_space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(rm_space, 2, raw_read_size, NULL)<0 || - H5S_select_hyperslab(rf_space, H5S_SELECT_SET, hs_offset, NULL, - raw_read_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set raw dataset selection"); - } - assert((nrows*raw_read_size[1]*type_size)==(hsize_t)((size_t)(nrows*raw_read_size[1]*type_size))); /*check for overflow*/ - if (NULL==(raw_buf=H5MM_malloc((size_t)(nrows*raw_read_size[1]*type_size)))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for raw dataset"); - } - if (H5D_read(ra->raw, type, rm_space, rf_space, H5P_DEFAULT, - raw_buf)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, - "unable to read raw dataset"); - } - assert(((nrows-raw_read_size[0])*raw_read_size[1]*type_size)==(hsize_t)((size_t)((nrows-raw_read_size[0])*raw_read_size[1]*type_size))); /*check for overflow*/ - HDmemset(raw_buf+raw_read_size[0]*raw_read_size[1]*type_size, 0, - (size_t)((nrows-raw_read_size[0])*raw_read_size[1]*type_size)); - - /* Get the meta data */ - assert((nrows*sizeof(H5RA_meta_t))==(hsize_t)((size_t)(nrows*sizeof(H5RA_meta_t)))); /*check for overflow*/ - if (NULL==(meta=H5MM_malloc((size_t)(nrows*sizeof(H5RA_meta_t))))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for meta data"); - } - if (NULL==(mf_space=H5D_get_space(ra->meta)) || - H5S_get_simple_extent_dims(mf_space, &meta_cur_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to get current meta data extents"); - } - if ((hsize_t)start_row>=meta_cur_size) { - meta_read_size = 0; - } else { - meta_read_size = MIN(nrows, meta_cur_size-(hsize_t)start_row); - } - if (NULL==(mm_space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(mm_space, 1, &meta_read_size, NULL)<0 || - H5S_select_hyperslab(mf_space, H5S_SELECT_SET, &start_row, NULL, - &meta_read_size, NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set meta data selection"); - } - if (H5D_read(ra->meta, H5RA_meta_type_g, mm_space, mf_space, - H5P_DEFAULT, meta)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, - "unable to read meta data"); - } - assert(((nrows-meta_read_size)*sizeof(H5RA_meta_t))==(hsize_t)((size_t)((nrows-meta_read_size)*sizeof(H5RA_meta_t)))); /*check for overflow*/ - HDmemset(meta+meta_read_size, 0, - (size_t)((nrows-meta_read_size)*sizeof(H5RA_meta_t))); - - /* Copy data into output buffers */ - for (i=0; i<nrows; i++) { - /* - * If the caller didn't supply a buffer then allocate a buffer large - * enough to hold the entire row. Ignore the input value for the - * size and request the entire row. - */ - if (NULL==(buf_out[i]=buf[i])) { - assert((meta[i].nelmts*type_size)==(hsize_t)((size_t)(meta[i].nelmts*type_size))); /*check for overflow*/ - if (meta[i].nelmts>0 && - NULL==(buf_out[i]=H5MM_malloc((size_t)(meta[i].nelmts*type_size)))) { - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for result"); - } - size[i] = meta[i].nelmts; - } else { - size[i] = MIN(size[i], meta[i].nelmts); - } - if (0==size[i]) continue; - - /* Copy the part of the row from the raw dataset */ - HDmemcpy(buf_out[i], raw_buf+i*raw_read_size[1]*type_size, - (size_t)(MIN(size[i], raw_read_size[1])*type_size)); - - /* Copy the part of the row from the overflow dataset */ - if (size[i]>raw_read_size[1]) { - if (!of_space && NULL==(of_space=H5D_get_space(ra->over))) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to get overflow extents"); - } - hs_size[0] = size[i]-raw_read_size[1]; - if (NULL==(om_space=H5S_create(H5S_SIMPLE)) || - H5S_set_extent_simple(om_space, 1, size+i, NULL)<0 || - H5S_select_hyperslab(om_space, H5S_SELECT_SET, - (hssize_t*)(raw_read_size+1), NULL, - hs_size, NULL)<0 || - H5S_select_hyperslab(of_space, H5S_SELECT_SET, - &(meta[i].offset), NULL, hs_size, - NULL)<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to set overflow selection"); - } - if (H5D_read(ra->over, type, om_space, of_space, H5P_DEFAULT, - buf_out[i])<0) { - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to read overflow dataset"); - } - if (H5S_close(om_space)<0) { - om_space = NULL; - HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, - "unable to close overflow memory space"); - } - om_space = NULL; - } - - /* Actual row size */ - size[i] = meta[i].nelmts; - } - - /* Copy output buffers into BUF argument */ - for (i=0; i<nrows; i++) buf[i] = buf_out[i]; - ret_value = SUCCEED; - - done: - if (rf_space) H5S_close(rf_space); - if (rm_space) H5S_close(rm_space); - if (mf_space) H5S_close(mf_space); - if (mm_space) H5S_close(mm_space); - if (of_space) H5S_close(of_space); - if (om_space) H5S_close(om_space); - H5MM_xfree(meta); - H5MM_xfree(raw_buf); - if (buf_out) { - for (i=0; i<nrows; i++) { - if (!buf[i]) H5MM_xfree(buf_out[i]); - } - H5MM_xfree(buf_out); - } - - FUNC_LEAVE(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5RA_entof - * - * Purpose: Return a pointer to the ragged arrays symbol table entry. - * - * Return: Success: Ptr to symbol table entry - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Friday, August 28, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -H5G_entry_t * -H5RA_entof(H5RA_t *ra) -{ - assert(ra); - return H5G_entof(ra->group); -} |