diff options
Diffstat (limited to 'src/H5R.c')
| -rw-r--r-- | src/H5R.c | 1075 |
1 files changed, 1075 insertions, 0 deletions
diff --git a/src/H5R.c b/src/H5R.c new file mode 100644 index 0000000..02c4e25 --- /dev/null +++ b/src/H5R.c @@ -0,0 +1,1075 @@ +/* + * 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 <H5Rprivate.h> + +#include <H5private.h> +#include <H5Eprivate.h> +#include <H5Iprivate.h> +#include <H5MMprivate.h> +#include <H5Pprivate.h> + +typedef struct H5R_meta_t { + hsize_t nelmts; /*num elements in row */ + hssize_t offset; /*offset into overflow array */ + hsize_t nover; /*allocated size in overflow array */ +} H5R_meta_t; + +struct H5R_t { + H5D_t *meta; /*ragged meta data array */ + H5D_t *raw; /*fixed-width raw data */ + H5D_t *over; /*overflow data */ +}; + +#define PABLO_MASK H5R_mask +static hbool_t interface_initialize_g = FALSE; +#define INTERFACE_INIT H5R_init_interface +static herr_t H5R_init_interface(void); +static void H5R_term_interface(void); +static H5T_t *H5R_meta_type_g = NULL; + +static herr_t H5R_fix_overflow(H5R_t *ra, H5T_t *type, H5R_meta_t *meta, + hsize_t nelmts, void *buf); + + +/*------------------------------------------------------------------------- + * Function: H5R_init_interface + * + * Purpose: Initialize the interface. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5R_init_interface(void) +{ + herr_t ret_value = SUCCEED; + H5T_t *type = NULL; + + FUNC_ENTER(H5R_init_interface, FAIL); + + /* The atom group */ + if ((ret_value=H5I_init_group(H5_RAGGED, H5I_RAGGED_HASHSIZE, 0, + (herr_t(*)(void*))H5R_close))>=0) { + ret_value = H5_add_exit(H5R_term_interface); + } + + /* The meta dataset type */ + if (NULL==(type=H5T_create(H5T_COMPOUND, sizeof(H5R_meta_t))) || + H5T_insert(type, "nelmts", HOFFSET(H5R_meta_t, nelmts), + 0, NULL, NULL, H5I_object(H5T_NATIVE_HSIZE_g))<0 || + H5T_insert(type, "offset", HOFFSET(H5R_meta_t, offset), + 0, NULL, NULL, H5I_object(H5T_NATIVE_HSSIZE_g))<0 || + H5T_insert(type, "nover", HOFFSET(H5R_meta_t, nover), + 0, NULL, NULL, H5I_object(H5T_NATIVE_HSIZE_g))) { + HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, + "unable to define ragged array meta type"); + } + H5R_meta_type_g = type; + + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5R_term_interface + * + * Purpose: Terminate the ragged array interface. + * + * Return: void + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static void +H5R_term_interface(void) +{ + H5I_destroy_group(H5_RAGGED); + H5T_close(H5R_meta_type_g); + H5R_meta_type_g = NULL; +} + + +/*------------------------------------------------------------------------- + * Function: H5Rcreate + * + * 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: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +hid_t +H5Rcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t plist_id) +{ + H5R_t *ra=NULL; + H5G_t *loc=NULL; + H5T_t *type=NULL; + const H5D_create_t *plist=NULL; + hid_t ret_value=FAIL; + + FUNC_ENTER(H5Rcreate, 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 (H5_DATATYPE!=H5I_group(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=H5R_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(H5_RAGGED, ra))<0) { + H5R_close(ra); + HRETURN_ERROR(H5E_RAGGED, H5E_CANTREGISTER, FAIL, + "unable to register ragged array"); + } + + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5R_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: + * + *------------------------------------------------------------------------- + */ +H5R_t * +H5R_create(H5G_t *loc, const char *name, H5T_t *type, const H5D_create_t *dcpl) +{ + H5R_t *ra = NULL; + H5G_t *grp = NULL; + H5S_t *space = NULL; + hsize_t cur_dims[2]; + hsize_t max_dims[2]; + H5R_t *ret_value=NULL; + H5D_create_t d1_dcpl; + + FUNC_ENTER(H5R_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(H5R_t)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for ragged array struct"); + } + + /* Create the group to contain the arrays */ + if (NULL==(grp=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(grp, "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(grp, "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(H5R_meta_type_g)); + if (NULL==(ra->meta=H5D_create(grp, "meta", H5R_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; + + /* Close the group -- we no longer need it */ + if (H5G_close(grp)<0) { + grp = NULL; + HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, + "unable to close ragged array group"); + } + grp = NULL; + ret_value = ra; + + done: + if (!ret_value) { + if (grp) H5G_close(grp); + if (space) H5S_close(space); + if (ra) { + 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: H5Ropen + * + * 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: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +hid_t +H5Ropen(hid_t loc_id, const char *name) +{ + H5G_t *loc=NULL; + H5R_t *ra=NULL; + hid_t ret_value=FAIL; + + FUNC_ENTER(H5Ropen, 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=H5R_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(H5_RAGGED, ra))<0) { + H5R_close(ra); + HRETURN_ERROR(H5E_RAGGED, H5E_CANTREGISTER, FAIL, + "unable to register ragged array"); + } + + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5R_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: + * + *------------------------------------------------------------------------- + */ +H5R_t * +H5R_open(H5G_t *loc, const char *name) +{ + H5R_t *ra = NULL; + H5R_t *ret_value = NULL; + H5G_t *grp=NULL; + + FUNC_ENTER(H5R_open, NULL); + + /* Check arguments */ + assert(loc); + assert(name && *name); + + /* Create the struct */ + if (NULL==(ra=H5MM_calloc(sizeof(H5R_t)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for ragged array struct"); + } + + /* Open the containing group */ + if (NULL==(grp=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(grp, "raw")) || + NULL==(ra->over=H5D_open(grp, "over")) || + NULL==(ra->meta=H5D_open(grp, "meta"))) { + HGOTO_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, NULL, + "unable to open one or more component datasets"); + } + + /* Close group */ + if (H5G_close(grp)<0) { + grp = NULL; + HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL, + "unable to close container group"); + } + grp = NULL; + ret_value = ra; + + done: + if (!ret_value) { + if (grp) H5G_close(grp); + if (ra) { + 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: H5Rclose + * + * Purpose: Close a ragged array. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Rclose(hid_t array_id) +{ + H5R_t *ra=NULL; + + FUNC_ENTER(H5Rclose, FAIL); + H5TRACE1("e","i",array_id); + + /* Check args */ + if (H5_RAGGED!=H5I_group(array_id) || + NULL==(ra=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: H5R_close + * + * Purpose: Close a ragged array + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5R_close(H5R_t *ra) +{ + FUNC_ENTER(H5R_close, FAIL); + + assert(ra); + if ((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(H5R_t)); + H5MM_xfree(ra); + + FUNC_LEAVE(SUCCEED); +} + + +/*------------------------------------------------------------------------- + * Function: H5Rwrite + * + * 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: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Rwrite(hid_t array_id, hssize_t start_row, hsize_t nrows, + hid_t type_id, hsize_t size[/*nrows*/], void *buf[/*nrows*/]) +{ + H5R_t *ra=NULL; + H5T_t *type=NULL; + hsize_t i; + + FUNC_ENTER(H5Rwrite, FAIL); + H5TRACE6("e","iHshi*[a2]h*[a2]x",array_id,start_row,nrows,type_id,size, + buf); + + /* Check args */ + if (H5_RAGGED!=H5I_group(array_id) || + NULL==(ra=H5I_object(array_id))) { + HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array"); + } + if (H5_DATATYPE!=H5I_group(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 (H5R_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: H5R_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: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Tuesday, August 25, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5R_write(H5R_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type, + hsize_t size[], void *buf[]) +{ + herr_t ret_value=FAIL; + H5R_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 *raw_buf=NULL; /*raw buffer */ + size_t type_size; /*size of the TYPE argument */ + hsize_t i; + + FUNC_ENTER(H5R_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_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 (NULL==(meta=H5MM_malloc(nrows*sizeof(H5R_meta_t)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for meta data"); + } + if (H5D_read(ra->meta, H5R_meta_type_g, mm_space, mf_space, + &H5D_xfer_dflt, meta)<0) { + HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, + "unable to read meta data"); + } + HDmemset(meta+meta_read_size, 0, + (nrows-meta_read_size)*sizeof(H5R_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_extent_dims(rf_space, raw_cur_size, NULL)<0) { + HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL, + "unable to determine current raw data extents"); + } + if (NULL==(raw_buf=H5MM_malloc(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); + HDmemset(raw_buf+i*raw_cur_size[1]*type_size+nbytes, 0, + 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"); + } + } + 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, &H5D_xfer_dflt, + 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]) { + H5R_fix_overflow(ra, type, meta+i, size[i]-raw_cur_size[1], + (uint8*)(buf[i])+raw_cur_size[1]); + } + 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"); + } + } + 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, H5R_meta_type_g, mm_space, mf_space, + &H5D_xfer_dflt, 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: H5R_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: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Wednesday, August 26, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5R_fix_overflow(H5R_t *ra, H5T_t *type, H5R_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(H5R_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_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"); + } +#endif + + } else { + /* No space is allocated */ + assert(nelmts>0); + if (NULL==(of_space=H5D_get_space(ra->over)) || + H5S_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"); + } + } + + /* 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, &H5D_xfer_dflt, + 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: H5Rread + * + * 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: SUCCEED. 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: FAIL. 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 +H5Rread(hid_t array_id, hssize_t start_row, hsize_t nrows, + hid_t type_id, hsize_t size[/*nrows*/], void *buf[/*nrows*/]) +{ + H5R_t *ra=NULL; + H5T_t *type=NULL; + + FUNC_ENTER(H5Rread, FAIL); + H5TRACE6("e","iHshi*[a2]h*[a2]x",array_id,start_row,nrows,type_id,size, + buf); + + /* Check args */ + if (H5_RAGGED!=H5I_group(array_id) || + NULL==(ra=H5I_object(array_id))) { + HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array"); + } + if (H5_DATATYPE!=H5I_group(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 (H5R_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: H5R_read + * + * Purpose: Reads (part of) a ragged array. See H5Rread() for details. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Wednesday, August 26, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5R_read(H5R_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type, + hsize_t size[], void *buf[]) +{ + herr_t ret_value=FAIL; + H5R_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 of meta data to read */ + hsize_t raw_cur_size[2]; /*raw data current size */ + hsize_t raw_read_size; /*amount of raw data to read */ + hssize_t hs_offset[2]; /*hyperslab offset */ + hsize_t hs_size[2]; /*hyperslab size */ + uint8 *raw_buf=NULL; /*raw buffer */ + size_t type_size; /*size of the TYPE argument */ + hsize_t i; + + FUNC_ENTER(H5R_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); + + /* Read from the raw dataset */ + if (NULL==(rf_space=H5D_get_space(ra->raw)) || + H5S_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; + } else { + raw_read_size = MIN(nrows, raw_cur_size[0]-(hsize_t)start_row); + } + + + + + + + + /* Get the meta data */ + if (NULL==(meta=H5MM_malloc(nrows*sizeof(H5R_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_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, H5R_meta_type_g, mm_space, mf_space, + &H5D_xfer_dflt, meta)<0) { + HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, + "unable to read meta data"); + } + HDmemset(meta+meta_read_size, 0, + (nrows-meta_read_size)*sizeof(H5R_meta_t)); + + + HGOTO_ERROR(H5E_RAGGED, H5E_UNSUPPORTED, FAIL, + "not implemented yet"); + + done: + FUNC_LEAVE(ret_value); +} + |