/*------------------------------------------------------------------------- * Function: H5PTcreate_vl * * Purpose: Creates a dataset containing a table of variable length records * and returns the Identifier of the table. * * Return: Success: table ID, Failure: Negative * * Programmer: Nat Furrer, [email protected] * James Laird, [email protected] * * Date: April 12, 2004 * * Comments: This function does not handle compression or fill data * currently. Fill data is not necessary because the * table is initially of size 0. * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5PTcreate_vl ( hid_t loc_id, const char*dset_name, hsize_t chunk_size) { hid_t ret_value=H5I_BADID; hid_t vltype; /* Create a variable length type that uses single bytes as its base type */ vltype = H5Tvlen_create(H5T_NATIVE_UCHAR); if(vltype < 0) goto out; if((ret_value=H5PTcreate_fl(loc_id, dset_name, vltype, chunk_size, 0)) < 0) goto out; /* close the vltype */ if(H5Tclose(vltype) < 0) goto out; return ret_value; out: if(ret_value != H5I_BADID) H5PTclose(ret_value); return H5I_BADID; }
/*-------------------------------------------------------------------------
* Function: gent_nested_vl
*
* Purpose: Generate a nested variable length dataset in LOC_ID
*
*-------------------------------------------------------------------------
*/
static void gent_nested_vl(hid_t loc_id)
{
hid_t sid, did, tid1, tid2;
hsize_t dims[1] = {2};
hvl_t buf[2];
hvl_t *tvl;
/* allocate and initialize VL dataset to write */
buf[0].len = 1;
buf[0].p = HDmalloc( 1 * sizeof(hvl_t));
tvl = (hvl_t *)buf[0].p;
tvl->p = HDmalloc( 1 * sizeof(int) );
tvl->len = 1;
((int *)tvl->p)[0]=1;
buf[1].len = 1;
buf[1].p = HDmalloc( 1 * sizeof(hvl_t));
tvl = (hvl_t *)buf[1].p;
tvl->p = HDmalloc( 2 * sizeof(int) );
tvl->len = 2;
((int *)tvl->p)[0]=2;
((int *)tvl->p)[1]=3;
/* create dataspace */
sid = H5Screate_simple(1, dims, NULL);
/* create datatype */
tid1 = H5Tvlen_create(H5T_NATIVE_INT);
/* create nested VL datatype */
tid2 = H5Tvlen_create(tid1);
/* create dataset */
did = H5Dcreate2(loc_id, DATASET_NESTED_VL, tid2, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* write */
H5Dwrite(did, tid2, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
/* close */
H5Dvlen_reclaim(tid2,sid,H5P_DEFAULT,buf);
H5Sclose(sid);
H5Dclose(did);
H5Tclose(tid1);
H5Tclose(tid2);
}
//--------------------------------------------------------------------------
// Function: VarLenType overloaded constructor
///\brief Creates a new variable-length datatype based on the specified
/// \a base_type.
///\param base_type - IN: Pointer to existing datatype
///\exception H5::DataTypeIException
// Description
// DataType passed by pointer to avoid clashing with copy
// constructor.
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
VarLenType::VarLenType(const DataType* base_type) : DataType()
{
id = H5Tvlen_create(base_type->getId());
if (id < 0)
{
throw DataTypeIException("VarLenType constructor",
"H5Tvlen_create returns negative value");
}
}
/*-------------------------------------------------------------------------
* Function: gent_named_vl
*
* Purpose: Generate a variable lenght named datatype for a dataset in
LOC_ID
*
*-------------------------------------------------------------------------
*/
static void gent_named_vl(hid_t loc_id)
{
hid_t sid, did, tid;
hsize_t dims[1] = {2};
hvl_t buf[2];
/* allocate and initialize VL dataset to write */
buf[0].len = 1;
buf[0].p = HDmalloc( 1 * sizeof(int));
((int *)buf[0].p)[0]=1;
buf[1].len = 2;
buf[1].p = HDmalloc( 2 * sizeof(int));
((int *)buf[1].p)[0]=2;
((int *)buf[1].p)[1]=3;
/* create dataspace */
sid = H5Screate_simple(1, dims, NULL);
/* create datatype */
tid = H5Tvlen_create(H5T_NATIVE_INT);
/* create named datatype */
H5Tcommit2(loc_id, "vl", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* create dataset */
did = H5Dcreate2(loc_id, DATASET_NAMED_VL, tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* write */
H5Dwrite(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
/* close */
H5Dvlen_reclaim(tid,sid,H5P_DEFAULT,buf);
H5Sclose(sid);
H5Dclose(did);
H5Tclose(tid);
}
/*
adds different types of attributes to an object.
returns the number of attributes added to the objects.
*/
int add_attrs(hid_t oid, int idx)
{
char name[32];
int i0, i1, i2, j, nattrs=0;
hid_t aid, tid, tid1, sid;
hvl_t i_vlen[4];
hobj_ref_t ref;
zipcode_t cmp_data[4];
unsigned int i = 0xffffffff;
long long l = -2147483647;
float f = 123456789.987654321;
double d = 987654321.123456789;
char *s[7] = {"Parting", "is such", "sweeter", "sorrow."};
float f_array[4] = {1.0, 2.22, 3.333, 4.444};
char *s_vlen[4] = {"Parting", "is such", "sweet", "sorrow."};
hsize_t dims1[1]={1}, dims2[1]={4}, dims3[2]={3,5};
int int3d[4][3][5];
size_t offset = 0;
for (i0=0; i0<4; i0++) {
i_vlen[i0].len = (i0+1);
i_vlen[i0].p = (int *)calloc(i_vlen[i0].len, sizeof(int));
for (j=0; j<i_vlen[i0].len; j++)
((int *)i_vlen[i0].p)[j] = i0*100+j;
for (i1=0; i1<3; i1++) {
for (i2=0; i2<5; i2++)
int3d[i0][i1][i2] = i0*i1-i1*i2+i0*i2;
}
}
cmp_data[0].zipcode = 01001;
cmp_data[0].city = "Agawam, Massachusetts";
cmp_data[1].zipcode = 99950;
cmp_data[1].city = "Ketchikan, Alaska";
cmp_data[2].zipcode = 00501;
cmp_data[2].city = "Holtsville, New York";
cmp_data[3].zipcode = 61820;
cmp_data[3].city = "Champaign, Illinois";
/* 1 scalar point */
sid = H5Screate (H5S_SCALAR);
sprintf(name, "%05d scalar int", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_UINT, sid, &i);
sprintf(name, "%05d scalar ulong", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_INT64, sid, &l);
sprintf(name, "%05d scalar str", idx);
tid = H5Tcopy (H5T_C_S1);
H5Tset_size (tid, H5T_VARIABLE);
nattrs += add_attr(oid, name, tid, sid, &s[2]);
H5Tclose(tid);
H5Sclose(sid);
/* 4 single point */
sid = H5Screate_simple (1, dims1, NULL);
H5Rcreate(&ref, oid, ".", H5R_OBJECT, -1);
sprintf(name, "%05d single float", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_FLOAT, sid, &f);
sprintf(name, "%05d single double", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_DOUBLE, sid, &d);
sprintf(name, "%05d single obj_ref", idx);
nattrs += add_attr(oid, name, H5T_STD_REF_OBJ, sid, &ref);
H5Sclose(sid);
/* 7 fixed length 1D array */
sid = H5Screate_simple (1, dims1, NULL);
tid = H5Tarray_create (H5T_NATIVE_FLOAT, 1, dims2);
sprintf(name, "%05d array float", idx);
nattrs += add_attr(oid, name, tid, sid, &f_array[0]);
H5Tclose(tid);
tid = H5Tcopy (H5T_C_S1);
H5Tset_size (tid, strlen(s[0])+1);
tid1 = H5Tarray_create (tid, 1, dims2);
sprintf(name, "%05d array str", idx);
nattrs += add_attr(oid, name, tid1, sid, s);
H5Tclose(tid1);
H5Tclose(tid);
H5Sclose(sid);
/* 9 fixed length 2D int arrays */
sid = H5Screate_simple (1, dims2, NULL);
tid = H5Tarray_create (H5T_NATIVE_INT, 2, dims3);
sprintf(name, "%05d array int 2D", idx);
nattrs += add_attr(oid, name, tid, sid, int3d[0][0]);
H5Tclose(tid);
H5Sclose(sid);
/* 10 variable length arrays */
sid = H5Screate_simple (1, dims2, NULL);
tid = H5Tcopy (H5T_C_S1);
H5Tset_size (tid, H5T_VARIABLE);
sprintf(name, "%05d vlen strings", idx);
nattrs += add_attr(oid, name, tid, sid, s_vlen);
H5Tclose(tid);
tid = H5Tvlen_create (H5T_NATIVE_INT);;
sprintf(name, "%05d vlen int array", idx);
nattrs += add_attr(oid, name, tid, sid, i_vlen);
H5Tclose(tid);
H5Sclose(sid);
/* 12 compound data */
sid = H5Screate_simple (1, dims2, NULL);
tid = H5Tcreate (H5T_COMPOUND, sizeof (zipcode_t));
tid1 = H5Tcopy (H5T_C_S1);
H5Tset_size (tid1, H5T_VARIABLE);
H5Tinsert (tid, "zip code", 0, H5T_NATIVE_INT); offset += sizeof(H5T_NATIVE_INT);
H5Tinsert (tid, "City", offset, tid1); offset += sizeof(char *);
sprintf(name, "%05d compound data", idx);
nattrs += add_attr(oid, name, tid, sid, cmp_data);
H5Tclose(tid1);
H5Tclose(tid);
H5Sclose(sid);
for (i0=0; i0<4; i0++)
free(i_vlen[i0].p);
return nattrs;
}
/*****************************************************************************
This function generates attributes, groups, and datasets of many types.
Parameters:
fname: file_name.
ngrps: number of top level groups.
ndsets: number of datasets.
attrs: number of attributes.
nrow: number of rows in a dataset.
chunk: chunk size (single number).
vlen: max vlen size.
comp: use latest format.
latest: use gzip comnpression.
Return: Non-negative on success/Negative on failure
Programmer: Peter Cao <*****@*****.**>, Jan. 2013
****************************************************************************/
herr_t create_perf_test_file(const char *fname, int ngrps, int ndsets,
int nattrs, hsize_t nrows, hsize_t dim0, hsize_t chunk, int vlen,
int compressed, int latest)
{
int i, j, k;
hid_t fid, sid_null, sid_scalar, sid_1d, sid_2d, did, aid, sid_2, sid_large,
fapl=H5P_DEFAULT, dcpl=H5P_DEFAULT, gid1, gid2, cmp_tid, tid_str,
tid_enum, tid_array_f, tid_vlen_i, tid_vlen_s;
char name[32], tmp_name1[32], tmp_name2[32], tmp_name3[32];
hsize_t dims[1]={dim0}, dims2d[2]={dim0, (dim0/4+1)}, dims_array[1]={FIXED_LEN},
dim1[1]={2};
char *enum_names[4] = {"SOLID", "LIQUID", "GAS", "PLASMA"};
test_comp_t *buf_comp=NULL, *buf_comp_large=NULL;
int *buf_int=NULL;
float (*buf_float_a)[FIXED_LEN]=NULL;
double **buf_double2d=NULL;
hvl_t *buf_vlen_i=NULL;
char (*buf_str)[FIXED_LEN];
char **buf_vlen_s=NULL;
hobj_ref_t buf_ref[2];
hdset_reg_ref_t buf_reg_ref[2];
size_t offset, len;
herr_t status;
char *names[NTYPES] = { "int", "ulong", "float", "double", "fixed string",
"enum", "fixed float array", "vlen int array", "vlen strings"};
hid_t types[NTYPES] = { H5T_NATIVE_INT, H5T_NATIVE_UINT64, H5T_NATIVE_FLOAT,
H5T_NATIVE_DOUBLE, tid_str, tid_enum, tid_array_f, tid_vlen_i, tid_vlen_s};
hsize_t coords[4][2] = { {0, 1}, {3, 5}, {1, 0}, {2, 4}}, start=0, stride=1, count=1;
if (nrows < NROWS) nrows = NROWS;
if (ngrps<NGROUPS) ngrps=NGROUPS;
if (ndsets<NDSETS) ndsets=NDSETS;
if (nattrs<NATTRS) nattrs=NATTRS;
if (dim0<DIM0) dim0=DIM0;
if (chunk>dim0) chunk=dim0/4;
if (chunk<1) chunk = 1;
if (vlen<1) vlen = MAXVLEN;
/* create fixed string datatype */
types[4] = tid_str = H5Tcopy (H5T_C_S1);
H5Tset_size (tid_str, FIXED_LEN);
/* create enum datatype */
types[5] = tid_enum = H5Tenum_create(H5T_NATIVE_INT);
for (i = (int) SOLID; i <= (int) PLASMA; i++) {
phase_t val = (phase_t) i;
status = H5Tenum_insert (tid_enum, enum_names[i], &val);
}
/* create float array datatype */
types[6] = tid_array_f = H5Tarray_create (H5T_NATIVE_FLOAT, 1, dims_array);
/* create variable length integer datatypes */
types[7] = tid_vlen_i = H5Tvlen_create (H5T_NATIVE_INT);
/* create variable length string datatype */
types[8] = tid_vlen_s = H5Tcopy (H5T_C_S1);
H5Tset_size (tid_vlen_s, H5T_VARIABLE);
/* create compound datatypes */
cmp_tid = H5Tcreate (H5T_COMPOUND, sizeof (test_comp_t));
offset = 0;
for (i=0; i<NTYPES-2; i++) {
H5Tinsert(cmp_tid, names[i], offset, types[i]);
offset += H5Tget_size(types[i]);
}
H5Tinsert(cmp_tid, names[7], offset, types[7]);
offset += sizeof (hvl_t);
H5Tinsert(cmp_tid, names[8], offset, types[8]);
/* create dataspace */
sid_1d = H5Screate_simple (1, dims, NULL);
sid_2d = H5Screate_simple (2, dims2d, NULL);
sid_2 = H5Screate_simple (1, dim1, NULL);
sid_large = H5Screate_simple (1, &nrows, NULL);
sid_null = H5Screate (H5S_NULL);
sid_scalar = H5Screate (H5S_SCALAR);
/* create fid access property */
fapl = H5Pcreate (H5P_FILE_ACCESS);
H5Pset_libver_bounds (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
/* create dataset creation property */
dcpl = H5Pcreate (H5P_DATASET_CREATE);
/* set dataset chunk */
if (chunk>0) {
H5Pset_chunk (dcpl, 1, &chunk);
}
/* set dataset compression */
if (compressed) {
if (chunk<=0) {
chunk = dim0/10+1;;
H5Pset_chunk (dcpl, 1, &chunk);
}
H5Pset_shuffle (dcpl);
H5Pset_deflate (dcpl, 6);
}
/* allocate buffers */
buf_comp = (test_comp_t *)calloc(dim0, sizeof(test_comp_t));
buf_comp_large = (test_comp_t *)calloc(nrows, sizeof(test_comp_t));
buf_int = (int *)calloc(dim0, sizeof(int));
buf_float_a = malloc(dim0*sizeof(*buf_float_a));
buf_vlen_i = (hvl_t *)calloc(dim0, sizeof (hvl_t));
buf_vlen_s = (char **)calloc(dim0, sizeof(char *));
buf_str = malloc(dim0*sizeof (*buf_str));
/* allocate array of doulbe pointers */
buf_double2d = (double **)calloc(dims2d[0],sizeof(double *));
/* allocate a contigous chunk of memory for the data */
buf_double2d[0] = (double *)calloc( dims2d[0]*dims2d[1],sizeof(double) );
/* assign memory city to pointer array */
for (i=1; i <dims2d[0]; i++) buf_double2d[i] = buf_double2d[0]+i*dims2d[1];
/* fill buffer values */
len = 1;
for (i=0; i<dims[0]; i++) {
buf_comp[i].i = buf_int[i] = i-2147483648;
buf_comp[i].l = 0xffffffffffffffff-i;
buf_comp[i].f = 1.0/(i+1.0);
buf_comp[i].d = 987654321.0*i+1.0/(i+1.0);
buf_comp[i].e = (phase_t) (i % (int) (PLASMA + 1));
for (j=0; j<FIXED_LEN; j++) {
buf_comp[i].f_array[j] = buf_float_a[i][j] = i*100+j;
buf_str[i][j] = 'a' + (i%26);
}
buf_str[i][FIXED_LEN-1] = 0;
strcpy(buf_comp[i].s, buf_str[i]);
len = (1-cos(i/8.0))/2*vlen+1;
if (!i) len = vlen;
buf_vlen_i[i].len = len;
buf_vlen_i[i].p = (int *)calloc(len, sizeof(int));
for (j=0; j<len; j++) ((int*)(buf_vlen_i[i].p))[j] = i*100+j;
buf_comp[i].i_vlen = buf_vlen_i[i];
buf_vlen_s[i] = (char *)calloc(len, sizeof(char));
for (j=0; j<len-1; j++)
buf_vlen_s[i][j] = j%26+'A';
buf_comp[i].s_vlen = buf_vlen_s[i];
for (j=0; j<dims2d[1]; j++)
buf_double2d[i][j] = i+j/10000.0;
}
for (i=0; i<nrows; i++) {
buf_comp_large[i].i = i-2147483648;
buf_comp_large[i].l = 0xffffffffffffffff-i;
buf_comp_large[i].f = 1.0/(i+1.0);
buf_comp_large[i].d = 987654321.0*i+1.0/(i+1.0);
buf_comp_large[i].e = (phase_t) (i % (int) (PLASMA + 1));
for (j=0; j<FIXED_LEN-1; j++) {
buf_comp_large[i].f_array[j] = i*100+j;
buf_comp_large[i].s[j] = 'a' + (i%26);
}
len = i%vlen+1;
buf_comp_large[i].i_vlen.len = len;
buf_comp_large[i].i_vlen.p = (int *)calloc(len, sizeof(int));
for (j=0; j<len; j++) ((int*)(buf_comp_large[i].i_vlen.p))[j] = i*100+j;
buf_comp_large[i].s_vlen = (char *)calloc(i+2, sizeof(char));
for (j=0; j<i+1; j++) (buf_comp_large[i].s_vlen)[j] = j%26+'A';
}
/* create file */
if (latest)
fid = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
else
fid = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
add_attrs(fid, 0);
sprintf(name, "a cmp ds of %d rows", nrows);
did = H5Dcreate (fid, name, cmp_tid, sid_large, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, cmp_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_comp_large);
add_attrs(did, 0);
H5Dclose(did);
// /* add attributes*/
gid1 = H5Gcreate (fid, "attributes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (nattrs<1) nattrs = 1;
i=0;
while (i<nattrs) i += add_attrs(gid1, i);
H5Gclose(gid1);
/* add many sub groups to a group*/
gid1 = H5Gcreate (fid, "groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
add_attrs(gid1, 0);
for (i=0; i<ngrps; i++) {
/* create sub groups */
sprintf(name, "g%02d", i);
gid2 = H5Gcreate (gid1, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (i<10) add_attrs(gid2, 0);
H5Gclose(gid2);
}
H5Gclose(gid1);
/* add many datasets to a group */
gid1 = H5Gcreate (fid, "datasets", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
add_attrs(gid1, 0);
for (j=0; j<ndsets; j+=12) {
/* 1 add a null dataset */
sprintf(name, "%05d null dataset", j);
did = H5Dcreate (gid1, name, H5T_STD_I32LE, sid_null, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 2 add scalar int point */
sprintf(name, "%05d scalar int point", j);
did = H5Dcreate (gid1, name, H5T_NATIVE_INT, sid_scalar, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &j);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 3 scalar vlen string */
sprintf(name, "%05d scalar vlen string", j);
did = H5Dcreate (gid1, name, tid_vlen_s, sid_scalar, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, tid_vlen_s, H5S_ALL, H5S_ALL, H5P_DEFAULT, &buf_vlen_s[0]);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 4 add fixed-length float array */
sprintf(name, "%05d fixed-length float array", j);
did = H5Dcreate (gid1, name, tid_array_f, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_array_f, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_float_a);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 5 add fixed-length strings */
sprintf(name, "%05d fixed-length strings", j);
did = H5Dcreate (gid1, name, tid_str, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_str, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_str);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 6 add compound data */
sprintf(name, "%05d compund data", j);
did = H5Dcreate (gid1, name, cmp_tid, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, cmp_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_comp);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 7 add 2D double */
sprintf(name, "%05d 2D double", j);
strcpy (tmp_name1, name);
did = H5Dcreate (gid1, name, H5T_NATIVE_DOUBLE, sid_2d, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_double2d[0]);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 8 add 1D int array */
sprintf(name, "%05d 1D int array", j);
did = H5Dcreate (gid1, name, H5T_NATIVE_INT, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_int);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 9 add vlen int array */
sprintf(name, "%05d vlen int array", j);
strcpy (tmp_name2, name);
did = H5Dcreate (gid1, name, tid_vlen_i, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_vlen_i, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_vlen_i);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 10 add vlen strings */
sprintf(name, "%05d vlen strings", j);
strcpy (tmp_name3, name);
did = H5Dcreate (gid1, name, tid_vlen_s, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_vlen_s, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_vlen_s);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 11 add object refs */
H5Rcreate(&buf_ref[0],gid1, ".", H5R_OBJECT, -1);
H5Rcreate(&buf_ref[1],gid1, tmp_name3, H5R_OBJECT, -1);
sprintf(name, "%05d obj refs", j);
did = H5Dcreate (gid1, name, H5T_STD_REF_OBJ, sid_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_ref);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 12 add region refs */
H5Sselect_elements (sid_2d, H5S_SELECT_SET, 4, coords[0]);
H5Rcreate(&buf_reg_ref[0],gid1, tmp_name1, H5R_DATASET_REGION, sid_2d);
H5Sselect_none(sid_2d);
count = dims[0]/2+1;
H5Sselect_hyperslab (sid_1d, H5S_SELECT_SET, &start, &stride, &count,NULL);
H5Rcreate(&buf_reg_ref[1],gid1, tmp_name2, H5R_DATASET_REGION, sid_1d);
H5Sselect_none(sid_1d);
sprintf(name, "%05d region refs", j);
did = H5Dcreate (gid1, name, H5T_STD_REF_DSETREG, sid_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_reg_ref);
if (!j) add_attrs(did, j);
H5Dclose(did);
}
H5Gclose(gid1);
H5Tclose (tid_array_f);
H5Tclose (tid_vlen_i);
H5Tclose (tid_vlen_s);
H5Tclose (tid_enum);
H5Tclose (tid_str);
H5Tclose (cmp_tid);
H5Pclose (dcpl);
H5Pclose (fapl);
H5Sclose (sid_1d);
H5Sclose (sid_2d);
H5Sclose (sid_2);
H5Sclose (sid_large);
H5Sclose (sid_null);
H5Sclose (sid_scalar);
H5Fclose (fid);
for (i=0; i<dims[0]; i++) {
if (buf_vlen_i[i].p) free(buf_vlen_i[i].p);
if (buf_vlen_s[i]) free(buf_vlen_s[i]);
}
for (i=0; i<nrows; i++) {
if (buf_comp_large[i].i_vlen.p) free(buf_comp_large[i].i_vlen.p);
if (buf_comp_large[i].s_vlen) free(buf_comp_large[i].s_vlen);
}
free (buf_comp);
free (buf_comp_large);
free (buf_int);
free (buf_float_a);
free (buf_double2d[0]);
free (buf_double2d);
free (buf_str);
free(buf_vlen_i);
free(buf_vlen_s);
return 0;
}
int
main (void)
{
hid_t file, filetype, memtype, space, dset, attr;
/* Handles */
herr_t status;
hvl_t wdata[2], /* Array of vlen structures */
*rdata; /* Pointer to vlen structures */
hsize_t dims[1] = {2};
int *ptr,
ndims,
i, j;
/*
* Initialize variable-length data. wdata[0] is a countdown of
* length LEN0, wdata[1] is a Fibonacci sequence of length LEN1.
*/
wdata[0].len = LEN0;
ptr = (int *) malloc (wdata[0].len * sizeof (int));
for (i=0; i<wdata[0].len; i++)
ptr[i] = wdata[0].len - i; /* 3 2 1 */
wdata[0].p = (void *) ptr;
wdata[1].len = LEN1;
ptr = (int *) malloc (wdata[1].len * sizeof (int));
ptr[0] = 1;
ptr[1] = 1;
for (i=2; i<wdata[1].len; i++)
ptr[i] = ptr[i-1] + ptr[i-2]; /* 1 1 2 3 5 8 etc. */
wdata[1].p = (void *) ptr;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create variable-length datatype for file and memory.
*/
filetype = H5Tvlen_create (H5T_STD_I32LE);
memtype = H5Tvlen_create (H5T_NATIVE_INT);
/*
* Create dataset with a scalar dataspace.
*/
space = H5Screate (H5S_SCALAR);
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT);
status = H5Sclose (space);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the attribute and write the variable-length data to it
*/
attr = H5Acreate (dset, ATTRIBUTE, filetype, space, H5P_DEFAULT);
status = H5Awrite (attr, memtype, wdata);
/*
* Close and release resources. Note the use of H5Dvlen_reclaim
* removes the need to manually free() the previously malloc'ed
* data.
*/
status = H5Dvlen_reclaim (memtype, space, H5P_DEFAULT, wdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (filetype);
status = H5Tclose (memtype);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the attribute has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file, dataset, and attribute.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET);
attr = H5Aopen_name (dset, ATTRIBUTE);
/*
* Get dataspace and allocate memory for array of vlen structures.
* This does not actually allocate memory for the vlen data, that
* will be done by the library.
*/
space = H5Aget_space (attr);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (hvl_t *) malloc (dims[0] * sizeof (hvl_t));
/*
* Create the memory datatype.
*/
memtype = H5Tvlen_create (H5T_NATIVE_INT);
/*
* Read the data.
*/
status = H5Aread (attr, memtype, rdata);
/*
* Output the variable-length data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%u]:\n {",ATTRIBUTE,i);
ptr = rdata[i].p;
for (j=0; j<rdata[i].len; j++) {
printf (" %d", ptr[j]);
if ( (j+1) < rdata[i].len )
printf (",");
}
printf (" }\n");
}
/*
* Close and release resources. Note we must still free the
* top-level pointer "rdata", as H5Dvlen_reclaim only frees the
* actual variable-length data, and not the structures themselves.
*/
status = H5Dvlen_reclaim (memtype, space, H5P_DEFAULT, rdata);
free (rdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (memtype);
status = H5Fclose (file);
return 0;
}
int
main()
{
printf("\n*** Checking HDF5 attribute functions some more.\n");
printf("*** Creating tst_xplatform2_3.nc with HDF only...");
{
hid_t fapl_id, fcpl_id;
size_t chunk_cache_size = MY_CHUNK_CACHE_SIZE;
size_t chunk_cache_nelems = CHUNK_CACHE_NELEMS;
float chunk_cache_preemption = CHUNK_CACHE_PREEMPTION;
hid_t fileid, grpid, attid, spaceid;
hid_t s1_typeid, vlen_typeid, s3_typeid;
hid_t file_typeid1[NUM_OBJ], native_typeid1[NUM_OBJ];
hid_t file_typeid2, native_typeid2;
hsize_t num_obj;
H5O_info_t obj_info;
char obj_name[STR_LEN + 1];
hsize_t dims[1] = {ATT_LEN}; /* netcdf attributes always 1-D. */
struct s1
{
float x;
double y;
};
struct s3
{
hvl_t data[NUM_VL];
};
/* cvc stands for "Compound with Vlen of Compound." */
struct s3 cvc_out[ATT_LEN];
int i, j, k;
/* Create some output data: a struct s3 array (length ATT_LEN)
* which holds an array of vlen (length NUM_VL) of struct s1. */
for (i = 0; i < ATT_LEN; i++)
for (j = 0; j < NUM_VL; j++)
{
cvc_out[i].data[j].len = i + 1;
if (!(cvc_out[i].data[j].p = calloc(sizeof(struct s1), cvc_out[i].data[j].len))) ERR;
for (k = 0; k < cvc_out[i].data[j].len; k++)
{
((struct s1 *)cvc_out[i].data[j].p)[k].x = 42.42;
((struct s1 *)cvc_out[i].data[j].p)[k].y = 2.0;
}
}
/* Create the HDF5 file, with cache control, creation order, and
* all the timmings. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, chunk_cache_nelems, chunk_cache_size,
chunk_cache_preemption) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST,
H5F_LIBVER_LATEST) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create the compound type for struct s1. */
if ((s1_typeid = H5Tcreate(H5T_COMPOUND, sizeof(struct s1))) < 0) ERR;
if (H5Tinsert(s1_typeid, X_NAME, offsetof(struct s1, x),
H5T_NATIVE_FLOAT) < 0) ERR;
if (H5Tinsert(s1_typeid, Y_NAME, offsetof(struct s1, y),
H5T_NATIVE_DOUBLE) < 0) ERR;
if (H5Tcommit(grpid, S1_TYPE_NAME, s1_typeid) < 0) ERR;
/* Create a vlen type. Its a vlen of struct s1. */
if ((vlen_typeid = H5Tvlen_create(s1_typeid)) < 0) ERR;
if (H5Tcommit(grpid, VLEN_TYPE_NAME, vlen_typeid) < 0) ERR;
/* Create the struct s3 type, which contains the vlen. */
if ((s3_typeid = H5Tcreate(H5T_COMPOUND, sizeof(struct s3))) < 0) ERR;
if (H5Tinsert(s3_typeid, VL_NAME, offsetof(struct s3, data),
vlen_typeid) < 0) ERR;
if (H5Tcommit(grpid, S3_TYPE_NAME, s3_typeid) < 0) ERR;
/* Create an attribute of this new type. */
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
if ((attid = H5Acreate(grpid, S3_ATT_NAME, s3_typeid, spaceid,
H5P_DEFAULT)) < 0) ERR;
if (H5Awrite(attid, s3_typeid, cvc_out) < 0) ERR;
/* Close the types. */
if (H5Tclose(s1_typeid) < 0 ||
H5Tclose(vlen_typeid) < 0 ||
H5Tclose(s3_typeid) < 0) ERR;
/* Close the att. */
if (H5Aclose(attid) < 0) ERR;
/* Close the space. */
if (H5Sclose(spaceid) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* How many objects in this group? (There should be 3, the
* types. Atts don't count as objects to HDF5.) */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
if (num_obj != NUM_OBJ) ERR;
/* For each object in the group... */
for (i = 0; i < num_obj; i++)
{
/* Get the name, and make sure this is a type. */
if (H5Oget_info_by_idx(grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT) < 0) ERR;
if (H5Lget_name_by_idx(grpid, ".", H5_INDEX_NAME, H5_ITER_INC, i,
obj_name, STR_LEN + 1, H5P_DEFAULT) < 0) ERR;
if (obj_info.type != H5O_TYPE_NAMED_DATATYPE) ERR;
/* Get the typeid and native typeid. */
if ((file_typeid1[i] = H5Topen2(grpid, obj_name, H5P_DEFAULT)) < 0) ERR;
if ((native_typeid1[i] = H5Tget_native_type(file_typeid1[i],
H5T_DIR_DEFAULT)) < 0) ERR;
}
/* There is one att: open it by index. */
if ((attid = H5Aopen_idx(grpid, 0)) < 0) ERR;
/* Get file and native typeids of the att. */
if ((file_typeid2 = H5Aget_type(attid)) < 0) ERR;
if ((native_typeid2 = H5Tget_native_type(file_typeid2, H5T_DIR_DEFAULT)) < 0) ERR;
/* Close the attribute. */
if (H5Aclose(attid) < 0) ERR;
/* Close the typeids. */
for (i = 0; i < NUM_OBJ; i++)
{
if (H5Tclose(file_typeid1[i]) < 0) ERR;
if (H5Tclose(native_typeid1[i]) < 0) ERR;
}
if (H5Tclose(file_typeid2) < 0) ERR;
if (H5Tclose(native_typeid2) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Deallocate our vlens. */
for (i = 0; i < ATT_LEN; i++)
for (j = 0; j < NUM_VL; j++)
free(cvc_out[i].data[j].p);
}
SUMMARIZE_ERR;
printf("*** Checking vlen of compound file...");
{
#define NUM_OBJ_1 1
#define ATT_NAME "Poseidon"
hid_t fapl_id, fcpl_id;
hid_t fileid, grpid, attid, spaceid;
hid_t vlen_typeid;
hid_t file_typeid1[NUM_OBJ_1], native_typeid1[NUM_OBJ_1];
hid_t file_typeid2, native_typeid2;
hsize_t num_obj;
H5O_info_t obj_info;
char obj_name[STR_LEN + 1];
hsize_t dims[1] = {ATT_LEN}; /* netcdf attributes always 1-D. */
/* vc stands for "Vlen of Compound." */
hvl_t vc_out[ATT_LEN];
int i, k;
/* Create some output data: an array of vlen (length ATT_LEN) of
* int. */
for (i = 0; i < ATT_LEN; i++)
{
vc_out[i].len = i + 1;
if (!(vc_out[i].p = calloc(sizeof(int), vc_out[i].len))) ERR;
for (k = 0; k < vc_out[i].len; k++)
((int *)vc_out[i].p)[k] = 42;
}
/* Create the HDF5 file with creation order. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create a vlen type. Its a vlen of int. */
if ((vlen_typeid = H5Tvlen_create(H5T_NATIVE_INT)) < 0) ERR;
if (H5Tcommit(grpid, VLEN_TYPE_NAME, vlen_typeid) < 0) ERR;
/* Create an attribute of this new type. */
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
if ((attid = H5Acreate(grpid, ATT_NAME, vlen_typeid, spaceid,
H5P_DEFAULT)) < 0) ERR;
if (H5Awrite(attid, vlen_typeid, vc_out) < 0) ERR;
/* Close the type. */
if (H5Tclose(vlen_typeid) < 0) ERR;
/* Close the att. */
if (H5Aclose(attid) < 0) ERR;
/* Close the space. */
if (H5Sclose(spaceid) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* How many objects in this group? (There should be 2, the
* types. Atts don't count as objects to HDF5.) */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
if (num_obj != NUM_OBJ_1) ERR;
/* For each object in the group... */
for (i = 0; i < num_obj; i++)
{
/* Get the name, and make sure this is a type. */
if (H5Oget_info_by_idx(grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT) < 0) ERR;
if (H5Lget_name_by_idx(grpid, ".", H5_INDEX_NAME, H5_ITER_INC, i,
obj_name, STR_LEN + 1, H5P_DEFAULT) < 0) ERR;
if (obj_info.type != H5O_TYPE_NAMED_DATATYPE) ERR;
/* Get the typeid and native typeid. */
if ((file_typeid1[i] = H5Topen2(grpid, obj_name, H5P_DEFAULT)) < 0) ERR;
if ((native_typeid1[i] = H5Tget_native_type(file_typeid1[i],
H5T_DIR_DEFAULT)) < 0) ERR;
}
/* There is one att: open it by index. */
if ((attid = H5Aopen_idx(grpid, 0)) < 0) ERR;
/* Get file and native typeids of the att. */
if ((file_typeid2 = H5Aget_type(attid)) < 0) ERR;
if ((native_typeid2 = H5Tget_native_type(file_typeid2, H5T_DIR_DEFAULT)) < 0) ERR;
/* Close the attribute. */
if (H5Aclose(attid) < 0) ERR;
/* Close the typeids. */
for (i = 0; i < NUM_OBJ_1; i++)
{
if (H5Tclose(file_typeid1[i]) < 0) ERR;
if (H5Tclose(native_typeid1[i]) < 0) ERR;
}
if (H5Tclose(file_typeid2) < 0) ERR;
if (H5Tclose(native_typeid2) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Deallocate our vlens. */
for (i = 0; i < ATT_LEN; i++)
free(vc_out[i].p);
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
void pyne::Material::_load_comp_protocol1(hid_t db, std::string datapath, int row) {
std::string nucpath;
hid_t data_set = H5Dopen2(db, datapath.c_str(), H5P_DEFAULT);
hsize_t data_offset[1] = {row};
if (row < 0) {
// Handle negative row indices
hid_t data_space = H5Dget_space(data_set);
hsize_t data_dims[1];
H5Sget_simple_extent_dims(data_space, data_dims, NULL);
data_offset[0] += data_dims[0];
};
// Grab the nucpath
hid_t nuc_attr = H5Aopen(data_set, "nucpath", H5P_DEFAULT);
H5A_info_t nuc_info;
H5Aget_info(nuc_attr, &nuc_info);
hsize_t nuc_attr_len = nuc_info.data_size;
hid_t str_attr = H5Tcopy(H5T_C_S1);
H5Tset_size(str_attr, nuc_attr_len);
char * nucpathbuf = new char [nuc_attr_len];
H5Aread(nuc_attr, str_attr, nucpathbuf);
nucpath = std::string(nucpathbuf, nuc_attr_len);
delete[] nucpathbuf;
// Grab the nuclides
std::vector<int> nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(db, nucpath, H5T_NATIVE_INT);
int nuc_size = nuclides.size();
hsize_t nuc_dims[1] = {nuc_size};
// Get the data hyperslab
hid_t data_hyperslab = H5Dget_space(data_set);
hsize_t data_count[1] = {1};
H5Sselect_hyperslab(data_hyperslab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
// Get memory space for writing
hid_t mem_space = H5Screate_simple(1, data_count, NULL);
// Get material type
size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*nuc_size;
hid_t desc = H5Tcreate(H5T_COMPOUND, material_struct_size);
hid_t comp_values_array_type = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, nuc_dims);
// make the data table type
H5Tinsert(desc, "mass", HOFFSET(pyne::material_struct, mass), H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "density", HOFFSET(pyne::material_struct, density),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "atoms_per_molecule", HOFFSET(pyne::material_struct, atoms_per_mol),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "comp", HOFFSET(pyne::material_struct, comp), comp_values_array_type);
// make the data array, have to over-allocate
material_struct * mat_data = new material_struct [material_struct_size];
// Finally, get data and put in on this instance
H5Dread(data_set, desc, mem_space, data_hyperslab, H5P_DEFAULT, mat_data);
mass = (*mat_data).mass;
density = (*mat_data).density;
atoms_per_molecule = (*mat_data).atoms_per_mol;
for (int i = 0; i < nuc_size; i++)
comp[nuclides[i]] = (double) (*mat_data).comp[i];
delete[] mat_data;
H5Tclose(str_attr);
//
// Get metadata from associated dataset, if available
//
std::string attrpath = datapath + "_metadata";
bool attrpath_exists = h5wrap::path_exists(db, attrpath);
if (!attrpath_exists)
return;
hid_t metadatapace, attrtype, metadataet, metadatalab, attrmemspace;
int attrrank;
hvl_t attrdata [1];
attrtype = H5Tvlen_create(H5T_NATIVE_CHAR);
// Get the metadata from the file
metadataet = H5Dopen2(db, attrpath.c_str(), H5P_DEFAULT);
metadatalab = H5Dget_space(metadataet);
H5Sselect_hyperslab(metadatalab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
attrmemspace = H5Screate_simple(1, data_count, NULL);
H5Dread(metadataet, attrtype, attrmemspace, metadatalab, H5P_DEFAULT, attrdata);
// convert to in-memory JSON
Json::Reader reader;
reader.parse((char *) attrdata[0].p, (char *) attrdata[0].p+attrdata[0].len, metadata, false);
// close attr data objects
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(metadataet);
H5Sclose(metadatapace);
H5Tclose(attrtype);
// Close out the HDF5 file
H5Fclose(db);
};
void pyne::Material::write_hdf5(std::string filename, std::string datapath,
std::string nucpath, float row, int chunksize) {
int row_num = (int) row;
// Turn off annoying HDF5 errors
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
//Set file access properties so it closes cleanly
hid_t fapl;
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
// Create new/open datafile.
hid_t db;
if (pyne::file_exists(filename)) {
bool ish5 = H5Fis_hdf5(filename.c_str());
if (!ish5)
throw h5wrap::FileNotHDF5(filename);
db = H5Fopen(filename.c_str(), H5F_ACC_RDWR, fapl);
}
else
db = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
//
// Read in nuclist if available, write it out if not
//
bool nucpath_exists = h5wrap::path_exists(db, nucpath);
std::vector<int> nuclides;
int nuc_size;
hsize_t nuc_dims[1];
if (nucpath_exists) {
nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(db, nucpath, H5T_NATIVE_INT);
nuc_size = nuclides.size();
nuc_dims[0] = nuc_size;
} else {
nuclides = std::vector<int>();
for (pyne::comp_iter i = comp.begin(); i != comp.end(); i++)
nuclides.push_back(i->first);
nuc_size = nuclides.size();
// Create the data if it doesn't exist
int nuc_data [nuc_size];
for (int n = 0; n != nuc_size; n++)
nuc_data[n] = nuclides[n];
nuc_dims[0] = nuc_size;
hid_t nuc_space = H5Screate_simple(1, nuc_dims, NULL);
hid_t nuc_set = H5Dcreate2(db, nucpath.c_str(), H5T_NATIVE_INT, nuc_space,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(nuc_set, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, nuc_data);
H5Fflush(db, H5F_SCOPE_GLOBAL);
};
//
// Write out the data itself to the file
//
hid_t data_set, data_space, data_hyperslab;
int data_rank = 1;
hsize_t data_dims[1] = {1};
hsize_t data_max_dims[1] = {H5S_UNLIMITED};
hsize_t data_offset[1] = {0};
size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*nuc_size;
hid_t desc = H5Tcreate(H5T_COMPOUND, material_struct_size);
hid_t comp_values_array_type = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, nuc_dims);
// make the data table type
H5Tinsert(desc, "mass", HOFFSET(pyne::material_struct, mass), H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "density", HOFFSET(pyne::material_struct, density),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "atoms_per_molecule", HOFFSET(pyne::material_struct, atoms_per_mol),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "comp", HOFFSET(pyne::material_struct, comp),
comp_values_array_type);
material_struct * mat_data = new material_struct[material_struct_size];
(*mat_data).mass = mass;
(*mat_data).density = density;
(*mat_data).atoms_per_mol = atoms_per_molecule;
for (int n = 0; n != nuc_size; n++) {
if (0 < comp.count(nuclides[n]))
(*mat_data).comp[n] = comp[nuclides[n]];
else
(*mat_data).comp[n] = 0.0;
};
// get / make the data set
bool datapath_exists = h5wrap::path_exists(db, datapath);
if (datapath_exists) {
data_set = H5Dopen2(db, datapath.c_str(), H5P_DEFAULT);
data_space = H5Dget_space(data_set);
data_rank = H5Sget_simple_extent_dims(data_space, data_dims, data_max_dims);
// Determine the row size.
if (std::signbit(row))
row_num = data_dims[0] + row; // careful, row is negative
if (data_dims[0] <= row_num) {
// row == -0, extend to data set so that we can append, or
// row_num is larger than current dimension, resize to accomodate.
data_dims[0] = row_num + 1;
H5Dset_extent(data_set, data_dims);
}
data_offset[0] = row_num;
} else {
// Get full space
data_space = H5Screate_simple(1, data_dims, data_max_dims);
// Make data set properties to enable chunking
hid_t data_set_params = H5Pcreate(H5P_DATASET_CREATE);
hsize_t chunk_dims[1] ={chunksize};
H5Pset_chunk(data_set_params, 1, chunk_dims);
H5Pset_deflate(data_set_params, 1);
material_struct * data_fill_value = new material_struct[material_struct_size];
(*data_fill_value).mass = -1.0;
(*data_fill_value).density= -1.0;
(*data_fill_value).atoms_per_mol = -1.0;
for (int n = 0; n != nuc_size; n++)
(*data_fill_value).comp[n] = 0.0;
H5Pset_fill_value(data_set_params, desc, &data_fill_value);
// Create the data set
data_set = H5Dcreate2(db, datapath.c_str(), desc, data_space, H5P_DEFAULT,
data_set_params, H5P_DEFAULT);
H5Dset_extent(data_set, data_dims);
// Add attribute pointing to nuc path
hid_t nuc_attr_type = H5Tcopy(H5T_C_S1);
H5Tset_size(nuc_attr_type, nucpath.length());
hid_t nuc_attr_space = H5Screate(H5S_SCALAR);
hid_t nuc_attr = H5Acreate2(data_set, "nucpath", nuc_attr_type, nuc_attr_space,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(nuc_attr, nuc_attr_type, nucpath.c_str());
H5Fflush(db, H5F_SCOPE_GLOBAL);
// Remember to de-allocate
delete[] data_fill_value;
};
// Get the data hyperslab
data_hyperslab = H5Dget_space(data_set);
hsize_t data_count[1] = {1};
H5Sselect_hyperslab(data_hyperslab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
// Get a memory space for writing
hid_t mem_space = H5Screate_simple(1, data_count, data_max_dims);
// Write the row...
H5Dwrite(data_set, desc, mem_space, data_hyperslab, H5P_DEFAULT, mat_data);
// Close out the Dataset
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(data_set);
H5Sclose(data_space);
H5Tclose(desc);
//
// Write out the metadata to the file
//
std::string attrpath = datapath + "_metadata";
hid_t metadatapace, attrtype, metadataet, metadatalab, attrmemspace;
int attrrank;
attrtype = H5Tvlen_create(H5T_NATIVE_CHAR);
// get / make the data set
bool attrpath_exists = h5wrap::path_exists(db, attrpath);
if (attrpath_exists) {
metadataet = H5Dopen2(db, attrpath.c_str(), H5P_DEFAULT);
metadatapace = H5Dget_space(metadataet);
attrrank = H5Sget_simple_extent_dims(metadatapace, data_dims, data_max_dims);
if (data_dims[0] <= row_num) {
// row == -0, extend to data set so that we can append, or
// row_num is larger than current dimension, resize to accomodate.
data_dims[0] = row_num + 1;
H5Dset_extent(metadataet, data_dims);
}
data_offset[0] = row_num;
} else {
hid_t metadataetparams;
hsize_t attrchunkdims [1];
// Make data set properties to enable chunking
metadataetparams = H5Pcreate(H5P_DATASET_CREATE);
attrchunkdims[0] = chunksize;
H5Pset_chunk(metadataetparams, 1, attrchunkdims);
H5Pset_deflate(metadataetparams, 1);
hvl_t attrfillvalue [1];
attrfillvalue[0].len = 3;
attrfillvalue[0].p = (char *) "{}\n";
H5Pset_fill_value(metadataetparams, attrtype, &attrfillvalue);
// make dataset
metadatapace = H5Screate_simple(1, data_dims, data_max_dims);
metadataet = H5Dcreate2(db, attrpath.c_str(), attrtype, metadatapace,
H5P_DEFAULT, metadataetparams, H5P_DEFAULT);
H5Dset_extent(metadataet, data_dims);
};
// set the attr string
hvl_t attrdata [1];
Json::FastWriter writer;
std::string metadatatr = writer.write(metadata);
attrdata[0].p = (char *) metadatatr.c_str();
attrdata[0].len = metadatatr.length();
// write the attr
metadatalab = H5Dget_space(metadataet);
H5Sselect_hyperslab(metadatalab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
attrmemspace = H5Screate_simple(1, data_count, data_max_dims);
H5Dwrite(metadataet, attrtype, attrmemspace, metadatalab, H5P_DEFAULT, attrdata);
// close attr data objects
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(metadataet);
H5Sclose(metadatapace);
H5Tclose(attrtype);
// Close out the HDF5 file
H5Fclose(db);
// Remember the milk!
// ...by which I mean to deallocate
delete[] mat_data;
};
herr_t H5VLARRAYmake( hid_t loc_id,
const char *dset_name,
const char *obversion,
const int rank,
const hsize_t *dims,
hid_t type_id,
hsize_t chunk_size,
void *fill_data,
int compress,
char *complib,
int shuffle,
int fletcher32,
const void *data)
{
hvl_t vldata;
hid_t dataset_id, space_id, datatype, tid1;
hsize_t dataset_dims[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
hsize_t dims_chunk[1];
hid_t plist_id;
unsigned int cd_values[6];
if (data)
/* if data, one row will be filled initially */
dataset_dims[0] = 1;
else
/* no data, so no rows on dataset initally */
dataset_dims[0] = 0;
dims_chunk[0] = chunk_size;
/* Fill the vldata estructure with the data to write */
/* This is currectly not used */
vldata.p = (void *)data;
vldata.len = 1; /* Only one array type to save */
/* Create a VL datatype */
if (rank == 0) {
datatype = H5Tvlen_create(type_id);
}
else {
tid1 = H5Tarray_create(type_id, rank, dims);
datatype = H5Tvlen_create(tid1);
H5Tclose( tid1 ); /* Release resources */
}
/* The dataspace */
space_id = H5Screate_simple( 1, dataset_dims, maxdims );
/* Modify dataset creation properties, i.e. enable chunking */
plist_id = H5Pcreate (H5P_DATASET_CREATE);
if ( H5Pset_chunk ( plist_id, 1, dims_chunk ) < 0 )
return -1;
/*
Dataset creation property list is modified to use
*/
/* Fletcher must be first */
if (fletcher32) {
if ( H5Pset_fletcher32( plist_id) < 0 )
return -1;
}
/* Then shuffle (blosc shuffles inplace) */
if (shuffle && (strcmp(complib, "blosc") != 0)) {
if ( H5Pset_shuffle( plist_id) < 0 )
return -1;
}
/* Finally compression */
if (compress) {
cd_values[0] = compress;
cd_values[1] = (int)(atof(obversion) * 10);
cd_values[2] = VLArray;
/* The default compressor in HDF5 (zlib) */
if (strcmp(complib, "zlib") == 0) {
if ( H5Pset_deflate( plist_id, compress) < 0 )
return -1;
}
/* The Blosc compressor does accept parameters */
else if (strcmp(complib, "blosc") == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 6, cd_values) < 0 )
return -1;
}
/* The LZO compressor does accept parameters */
else if (strcmp(complib, "lzo") == 0) {
if ( H5Pset_filter( plist_id, FILTER_LZO, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
/* The bzip2 compress does accept parameters */
else if (strcmp(complib, "bzip2") == 0) {
if ( H5Pset_filter( plist_id, FILTER_BZIP2, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
else {
/* Compression library not supported */
fprintf(stderr, "Compression library not supported\n");
return -1;
}
}
/* Create the dataset. */
if ((dataset_id = H5Dcreate(loc_id, dset_name, datatype, space_id,
H5P_DEFAULT, plist_id, H5P_DEFAULT )) < 0 )
goto out;
/* Write the dataset only if there is data to write */
if (data)
if ( H5Dwrite( dataset_id, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &vldata ) < 0 )
goto out;
/* Terminate access to the data space. */
if ( H5Sclose( space_id ) < 0 )
return -1;
/* Release the datatype in the case that it is not an atomic type */
if ( H5Tclose( datatype ) < 0 )
return -1;
/* End access to the property list */
if ( H5Pclose( plist_id ) < 0 )
goto out;
return dataset_id;
out:
return -1;
}
