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Diffstat (limited to 'hl/src/H5LD.c')
| -rw-r--r-- | hl/src/H5LD.c | 639 |
1 files changed, 639 insertions, 0 deletions
diff --git a/hl/src/H5LD.c b/hl/src/H5LD.c new file mode 100644 index 0000000..4abd740 --- /dev/null +++ b/hl/src/H5LD.c @@ -0,0 +1,639 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * +* Copyright by The HDF Group. * +* Copyright by the Board of Trustees of the University of Illinois. * +* All rights reserved. * +* * +* This file is part of HDF5. The full HDF5 copyright notice, including * +* terms governing use, modification, and redistribution, is contained in * +* the files COPYING and Copyright.html. COPYING can be found at the root * +* of the source code distribution tree; Copyright.html can be found at the * +* root level of an installed copy of the electronic HDF5 document set and * +* is linked from the top-level documents page. It can also be found at * +* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * +* access to either file, you may request a copy from help@hdfgroup.org. * +* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +#include <string.h> +#include <stdlib.h> +#include <assert.h> +#include <stdio.h> +#include "H5LDprivate.h" + +/*------------------------------------------------------------------------- + * + * internal functions + * + *------------------------------------------------------------------------- + */ +static herr_t H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid); +static herr_t H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims); +static size_t H5LD_get_dset_type_size(hid_t did, const char *fields); +static herr_t H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, + const hsize_t *cur_dims, const char *fields, void *buf); + + +/*------------------------------------------------------------------------- + * Function: H5LD_clean_vector + * + * Purpose: Process the vector of info: + * 1) free the array of pointers to member names in listv[n] + * 2) close the type id of the last member in listv[n] + * 3) free the H5LD_memb_t structure itself as pointed to by listv[n] + * + * Return: void + * + * Programmer: Vailin Choi; Aug 2010 + * + *------------------------------------------------------------------------- + */ +void +H5LD_clean_vector(H5LD_memb_t *listv[]) +{ + unsigned n; /* Local index variable */ + + HDassert(listv); + + /* Go through info for each field stored in listv[] */ + for(n = 0; listv[n] != NULL; n++) { + if(listv[n]->names) { + HDfree(listv[n]->names); + listv[n]->names = NULL; + } /* end if */ + + /* Close the type id of the last member in the field */ + if(!(listv[n]->last_tid < 0)) { + H5Tclose(listv[n]->last_tid); + listv[n]->last_tid = -1; + } /* end if */ + + /* Free the H5LD_memb_t structure for the field */ + HDfree(listv[n]); + listv[n] = NULL; + } /* end for */ +} /* H5LD_clean_vector() */ + + +/*------------------------------------------------------------------------- + * Function: H5LD_construct_info() + * + * Purpose: Get the remaining info for a field: + * 1) Get the type id of the last member in the field + * 2) Get the total offset of all the members in the field + * 3) Get the type size of the last member in the field + * + * Return: Success: 0 + * Failure: negative + * + * Programmer: Vailin Choi; Aug 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid) +{ + hid_t tmp_tid = -1; /* Dataset type id */ + unsigned i; /* Local index variable */ + herr_t ret_value = FAIL; /* Return value */ + + /* Make a copy of the incoming datatype */ + tmp_tid = H5Tcopy(par_tid); + + /* Validate all the members in a field */ + for(i = 0; memb->names[i] != NULL; i++) { + hid_t memb_tid; /* Type id for a member in a field */ + int idx; /* Index # of a member in a compound datatype */ + + /* Get the member index and member type id */ + if((idx = H5Tget_member_index(tmp_tid, memb->names[i])) < 0) + goto done; + if((memb_tid = H5Tget_member_type(tmp_tid, (unsigned)idx)) < 0) + goto done; + + /* Sum up the offset of all the members in the field */ + memb->tot_offset += H5Tget_member_offset(tmp_tid, (unsigned)idx); + if(H5Tclose(tmp_tid) < 0) + goto done; + tmp_tid = memb_tid; + } /* end for */ + + /* Get the type size of the last member in the field */ + memb->last_tsize = H5Tget_size(tmp_tid); + + /* Save the type id of the last member in the field */ + memb->last_tid = H5Tcopy(tmp_tid); + + /* Indicate success */ + ret_value = SUCCEED; + +done: + H5E_BEGIN_TRY + H5Tclose(tmp_tid); + H5E_END_TRY + + return(ret_value); +} /* H5LD_construct_info() */ + + +/*------------------------------------------------------------------------- + * Function: H5LD_construct_vector + * + * Purpose: Process the comma-separated list of fields in "fields" as follows: + * Example: + * "fields": "a.b.c,d" + * listv[0]->tot_offset = total offset of "a" & "b" & "c" + * listv[0]->last_tid = type id of "c" + * listv[0]->last_tsize = type size of "c" + * listv[0]->names[0] = "a" + * listv[0]->names[1] = "b" + * listv[0]->names[2] = "c" + * listv[0]->names[3] = NULL + * + * listv[1]->tot_offset = offset of "d" + * listv[1]->last_tid = type id of "d" + * listv[1]->last_tsize = type size of "d" + * listv[1]->names[0] = "d" + * listv[1]->names[1] = NULL + * + * Return: Success: # of comma-separated fields in "fields" + * Failure: negative value + * + * Programmer: Vailin Choi; Aug 2010 + * +*------------------------------------------------------------------------- +*/ +int +H5LD_construct_vector(char *fields, H5LD_memb_t *listv[]/*OUT*/, hid_t par_tid) +{ + int nfields; /* The # of comma-separated fields in "fields" */ + hbool_t end_of_fields = FALSE; /* end of "fields" */ + char *fields_ptr; /* Pointer to "fields" */ + int ret_value = FAIL; /* Return value */ + + HDassert(listv); + HDassert(fields); + + fields_ptr = fields; + nfields = 0; + + /* Process till end of "fields" */ + while(!end_of_fields) { + H5LD_memb_t *memb = NULL; /* Pointer to structure for storing a field's info */ + char *cur; /* Pointer to a member in a field */ + size_t len; /* Estimated # of members in a field */ + hbool_t gotcomma = FALSE; /* A comma encountered */ + hbool_t gotmember = FALSE; /* Getting member in a field */ + hbool_t valid = TRUE; /* Whether a field being processed is valid or not */ + int j = 0; /* The # of members in a field */ + + len = (HDstrlen(fields_ptr) / 2) + 2; + + /* Allocate memory for an H5LD_memb_t for storing a field's info */ + if(NULL == (memb = (H5LD_memb_t *)HDcalloc((size_t)1, sizeof(H5LD_memb_t)))) + goto done; + + /* Allocate memory for an array of pointers to member names */ + if(NULL == (memb->names = (char **)HDcalloc(len, sizeof(char *)))) + goto done; + + memb->names[j] = fields_ptr; + memb->last_tid = -1; + cur = fields_ptr; + + /* Continue processing till: not valid or comma encountered or "fields" ended */ + while(valid && !gotcomma && !end_of_fields) { + switch(*fields_ptr) { + case '\0': /* end of list */ + if(gotmember) { /* getting something and end of "fields" */ + *cur++ = '\0';; + memb->names[++j] = NULL; + } /* end if */ + else /* getting nothing but end of list */ + valid = FALSE; + end_of_fields = TRUE; + break; + + case '\\': /* escape character */ + ++fields_ptr; /* skip it */ + if(*fields_ptr == '\0') + valid = FALSE; + else { + *cur++ = *fields_ptr++; + gotmember = TRUE; + } /* end else */ + break; + + case '.': /* nested field separator */ + *fields_ptr++ = *cur++ = '\0';; + if(gotmember) { + memb->names[++j] = cur; + gotmember = FALSE; + } /* end if */ + else + valid = FALSE; + break; + + case ',': /* field separator */ + *fields_ptr++ = *cur++ = '\0';; + if(gotmember) { + memb->names[++j] = NULL; + gotmember = FALSE; + } /* end if */ + else + valid = FALSE; + gotcomma = TRUE; + break; + + default: + *cur++ = *fields_ptr++; + gotmember = TRUE; + break; + } /* end switch */ + } /* while (valid && !gotcomma && !end_of_fields) */ + + /* If valid, put into listv and continue processing further info */ + if(valid) { + listv[nfields++] = memb; + if(H5LD_construct_info(memb, par_tid) < 0) + goto done; + } /* end if */ + else { + if(memb) + HDfree(memb); + goto done; + } /* end else */ + } /* while !end_of_fields */ + + /* Indicate success */ + ret_value = nfields; + +done: + listv[nfields] = NULL; + if(ret_value == FAIL) + H5LD_clean_vector(listv); + + return(ret_value); +} /* H5LD_construct_vector() */ + + +/*------------------------------------------------------------------------- + * Function: H5LD_get_dset_dims + * + * Purpose: To return the current size for each dimension of the + * dataset's dataspace + * + * Return: Success: 0 + * Failure: negative value + * + * Programmer: Vailin Choi; March 2010 + * +*------------------------------------------------------------------------- +*/ +static herr_t +H5LD_get_dset_dims(hid_t did, hsize_t *cur_dims) +{ + hid_t sid = -1; /* Dataspace ID */ + herr_t ret_value = FAIL; /* Return Value */ + + /* Verify parameter */ + if(cur_dims == NULL) + goto done; + + /* Get the dataset's dataspace */ + if((sid = H5Dget_space(did)) < 0) + goto done; + + /* Get the current dimension size */ + if(H5Sget_simple_extent_dims(sid, cur_dims, NULL) < 0) + goto done; + + /* Indicate success */ + ret_value = SUCCEED; + +done: + H5E_BEGIN_TRY { + H5Sclose(sid); + } H5E_END_TRY; + + return(ret_value); +} /* H5LD_get_dset_dims() */ + + +/*------------------------------------------------------------------------- + * Function: H5LD_get_dset_type_size + * + * Purpose: To return the size of the dataset's datatype in bytes + * null "fields": return the size of the dataset's datatype + * non-null "fields": return the size of the dataset's datatype + * with respect to the selection in "fields" + * + * Return: Success: size of the dataset's datatype + * Failure: 0 (valid datatypes are never zero size) + * + * Programmer: Vailin Choi; March 2010 + * + *------------------------------------------------------------------------- + */ +static size_t +H5LD_get_dset_type_size(hid_t did, const char *fields) +{ + hid_t dset_tid = -1; /* Dataset's type identifier */ + hid_t tid = -1; /* Native Type identifier */ + H5LD_memb_t **listv = NULL; /* Vector for storing information in "fields" */ + char *dup_fields = NULL; /* A copy of "fields" */ + size_t ret_value = 0; /* Return value */ + + /* Get the datatype of the dataset */ + if((dset_tid = H5Dget_type(did)) < 0) + goto done; + if((tid = H5Tget_native_type(dset_tid, H5T_DIR_DEFAULT)) < 0) + goto done; + + if(fields == NULL) /* If no "fields" is specified */ + ret_value = H5Tget_size(tid); + else { /* "fields" are specified */ + size_t len; /* Estimate the number of comma-separated fields in "fields" */ + size_t tot = 0; /* Data type size of all the fields in "fields" */ + int n = 0, num = 0; /* Local index variables */ + + HDassert(fields && *fields); + + /* Should be a compound datatype if "fields" exists */ + if(H5Tget_class(dset_tid) != H5T_COMPOUND) + goto done; + + /* Get a copy of "fields" */ + if(NULL == (dup_fields = HDstrdup(fields))) + goto done; + + /* Allocate memory for a list of H5LD_memb_t pointers to store "fields" info */ + len = (HDstrlen(fields) / 2) + 2; + if(NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *)))) + goto done; + + /* Process and store info for "fields" */ + if((num = H5LD_construct_vector(dup_fields, listv/*OUT*/, tid)) < 0) + goto done; + + /* Sum up the size of all the datatypes in "fields" */ + for(n = 0; n < num; n++) + tot += listv[n]->last_tsize; + + /* Clean up the vector of H5LD_memb_t structures */ + H5LD_clean_vector(listv); + + /* Return the total size */ + ret_value = tot; + } /* end else */ + +done: + H5E_BEGIN_TRY + H5Tclose(tid); + H5Tclose(dset_tid); + H5E_END_TRY + + /* Free the array of H5LD_memb_t pointers */ + if(listv) + HDfree(listv); + + /* Free memory */ + if(dup_fields) + HDfree(dup_fields); + + return(ret_value); +} /* H5LD_get_dset_type_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5LD_get_dset_elmts + * + * Purpose: To retrieve selected data from the dataset + * + * Return: Success: 0 + * Failure: negative + * + * Programmer: Vailin Choi; August 2010 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5LD_get_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, + const char *fields, void *buf) +{ + hid_t dtid = -1, tid = -1; /* Dataset type id */ + hid_t sid = -1, mid = -1; /* Dataspace and memory space id */ + hssize_t snum_elmts; /* Number of dataset elements in the selection (signed) */ + hsize_t num_elmts; /* Number of dataset elements in the selection */ + hsize_t start[H5S_MAX_RANK];/* Starting offset */ + hsize_t count[H5S_MAX_RANK];/* ??offset */ + H5LD_memb_t **listv = NULL; /* Vector for storing information in "fields" */ + char *dup_fields = NULL; /* A copy of "fields" */ + char *sav_buf = NULL; /* Saved pointer temporary buffer */ + unsigned ctr; /* Counter for # of curr_dims > prev_dims */ + int ndims; /* Number of dimensions for the dataset */ + int i; /* Local index variable */ + herr_t ret_value = FAIL; /* Return value */ + + /* Verify parameters */ + if(prev_dims == NULL || cur_dims == NULL || buf == NULL) + goto done; + + /* Get dataset's dataspace */ + if((sid = H5Dget_space(did)) < 0) + goto done; + + /* Get the number of dimensions */ + if((ndims = H5Sget_simple_extent_ndims(sid)) < 0) + goto done; + + /* Verify that cur_dims must have one dimension whose size is greater than prev_dims */ + HDmemset(start, 0, sizeof start); + HDmemset(count, 0, sizeof count); + ctr = 0; + for(i = 0; i < ndims; i++) + if(cur_dims[i] > prev_dims[i]) { + ++ctr; + count[i] = cur_dims[i] - prev_dims[i]; + start[i] = prev_dims[i]; + } /* end if */ + else { /* < or = */ + start[i] = 0; + count[i] = MIN(prev_dims[i], cur_dims[i]); + } /* end else */ + if(!ctr) + goto done; + + if(ctr == 1) { /* changes for only one dimension */ + /* Make the selection in the dataset based on "cur_dims" and "prev_dims" */ + if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0) + goto done; + } /* end if */ + else { /* changes for more than one dimensions */ + HDmemset(start, 0, sizeof start); + + /* Make the selection in the dataset based on "cur_dims" and "prev_dims" */ + if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, NULL, cur_dims, NULL) < 0) + goto done; + if(H5Sselect_hyperslab(sid, H5S_SELECT_NOTB, start, NULL, prev_dims, NULL) < 0) + goto done; + } /* end else */ + + /* Get the number of elements in the selection */ + if(0 == (snum_elmts = H5Sget_select_npoints(sid))) + goto done; + num_elmts = (hsize_t)snum_elmts; + + /* Create the memory space for the selection */ + if((mid = H5Screate_simple(1, &num_elmts, NULL)) < 0) + goto done; + + /* Get the native datatype size */ + if((dtid = H5Dget_type(did)) < 0) + goto done; + if((tid = H5Tget_native_type(dtid, H5T_DIR_DEFAULT)) < 0) + goto done; + + if(fields == NULL) { /* nothing in "fields" */ + /* Read and store all the elements in "buf" */ + if(H5Dread(did, tid, mid, sid, H5P_DEFAULT, buf) < 0) + goto done; + } /* end if */ + else { /* "fields" is specified */ + unsigned char *buf_p = (unsigned char *)buf; /* Pointer to the destination buffer */ + char *tmp_buf; /* Temporary buffer for data read */ + size_t tot_tsize; /* Total datatype size */ + size_t len; /* Estimate the number of comma-separated fields in "fields" */ + + /* should be a compound datatype if "fields" exists */ + if(H5Tget_class(tid) != H5T_COMPOUND) + goto done; + + /* Get the total size of the dataset's datatypes */ + if(0 == (tot_tsize = H5LD_get_dset_type_size(did, NULL))) + goto done; + + /* Allocate memory for reading in the elements in the dataset selection */ + if(NULL == (sav_buf = tmp_buf = (char *)HDcalloc((size_t)num_elmts, tot_tsize))) + goto done; + + /* Read the dataset elements in the selection */ + if(H5Dread(did, tid, mid, sid, H5P_DEFAULT, tmp_buf) < 0) + goto done; + + /* Make a copy of "fields" */ + if(NULL == (dup_fields = HDstrdup(fields))) + goto done; + + /* Allocate memory for the vector of H5LD_memb_t pointers */ + len = (HDstrlen(fields) / 2) + 2; + if(NULL == (listv = (H5LD_memb_t **)HDcalloc(len, sizeof(H5LD_memb_t *)))) + goto done; + + /* Process and store information for "fields" */ + if(H5LD_construct_vector(dup_fields, listv, tid) < 0) + goto done; + + /* Copy data for each dataset element in the selection */ + for(i = 0; i < (int)num_elmts; i++) { + int j; /* Local index variable */ + + /* Copy data for "fields" to the input buffer */ + for(j = 0; listv[j] != NULL; j++) { + HDmemcpy(buf_p, tmp_buf + listv[j]->tot_offset, listv[j]->last_tsize); + buf_p += listv[j]->last_tsize; + } /* end for */ + tmp_buf += tot_tsize; + } /* end for */ + + /* Clean up the vector of H5LD_memb_t structures */ + H5LD_clean_vector(listv); + } /* end else */ + + /* Indicate success */ + ret_value = SUCCEED; + +done: + H5E_BEGIN_TRY + H5Tclose(dtid); + H5Tclose(tid); + H5Sclose(sid); + H5Sclose(mid); + H5E_END_TRY + + /* Free the array of H5LD_memb_t pointers */ + if(listv) + HDfree(listv); + + /* Free memory */ + if(dup_fields) + HDfree(dup_fields); + if(sav_buf) + HDfree(sav_buf); + + return(ret_value); +} /* H5LD_get_dset_elmts() */ + +/*------------------------------------------------------------------------- + * + * Public functions + * + *------------------------------------------------------------------------- + */ + + +/*------------------------------------------------------------------------- + * Function: H5LDget_dset_dims + * + * Purpose: To retrieve the current dimension sizes for a dataset + * + * Return: Success: 0 + * Failure: negative value + * + * Programmer: Vailin Choi; March 2010 + * + *------------------------------------------------------------------------- + */ +herr_t +H5LDget_dset_dims(hid_t did, hsize_t *cur_dims) +{ + return(H5LD_get_dset_dims(did, cur_dims)); +} /* H5LDget_dset_dims() */ + + + +/*------------------------------------------------------------------------- + * Function: H5LDget_dset_type_size + * + * Purpose: To return the size in bytes of the datatype for the dataset + * + * Return: Success: size in bytes of the dataset's datatype + * Failure: 0 (valid datatypes are never zero size) + * + * Programmer: Vailin Choi; March 2010 + * + *------------------------------------------------------------------------- + */ +size_t +H5LDget_dset_type_size(hid_t did, const char *fields) +{ + return(H5LD_get_dset_type_size(did, fields)); +} /* H5LDget_dset_type_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5LDget_dset_elmts + * + * Purpose: To retrieve selected data from the dataset + * + * Return: Success: 0 + * Failure: negative value + * + * Programmer: Vailin Choi; March 2010 + * + *------------------------------------------------------------------------- + */ +herr_t +H5LDget_dset_elmts(hid_t did, const hsize_t *prev_dims, const hsize_t *cur_dims, const char *fields, void *buf) +{ + return(H5LD_get_dset_elmts(did, prev_dims, cur_dims, fields, buf) ); +} /* H5LDget_dset_elmts() */ + |