/* * Copyright © 1998 NCSA * All rights reserved. * * Programmer: Robb Matzke * 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 #include #include #include #include #include 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 { 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 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_entry_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_entry_t *loc, const char *name, H5T_t *type, const H5D_create_t *dcpl) { H5R_t *ra = 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==(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(H5R_meta_type_g)); if (NULL==(ra->meta=H5D_create(H5G_entof(ra->group), "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; 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: 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_entry_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_entry_t *loc, const char *name) { H5R_t *ra = NULL; H5R_t *ret_value = 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==(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: 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->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(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; i0 && !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_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 (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_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 (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; iraw_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; iraw_cur_size[1]) { H5R_fix_overflow(ra, type, meta+i, size[i]-raw_cur_size[1], (uint8*)(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"); } } 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 (nelmtsnover) { /* 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"); } #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"); } } /* 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 */ 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 *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(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); /* * 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. */ if (NULL==(buf_out=H5MM_calloc(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"); } if (NULL==(raw_buf=H5MM_malloc(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, &H5D_xfer_dflt, raw_buf)<0) { HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL, "unable to read raw dataset"); } HDmemset(raw_buf+raw_read_size[0]*raw_read_size[1]*type_size, 0, (nrows-raw_read_size[0])*raw_read_size[1]*type_size); /* 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_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, 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)); /* Copy data into output buffers */ for (i=0; i0 && NULL==(buf_out[i]=H5MM_malloc(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, 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, &H5D_xfer_dflt, 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; igroup); }