/*
* Class: hdf_hdf5lib_H5
* Method: H5Aopen_idx
* Signature: (JI)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Aopen_1idx
(JNIEnv *env, jclass clss, jlong loc_id, jint idx)
{
hid_t attr_id = H5Aopen_idx((hid_t)loc_id, (unsigned int) idx);
if (attr_id < 0)
h5libraryError(env);
return (jlong)attr_id;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen_1idx */
/*----------------------------------------------------------------------------
* Name: h5aopen_idx_c
* Purpose: Call H5Aopen_idx to open an attribute
* Inputs: obj_id - object identifier
* idx - attribute index ( zero based)
* Outputs: attr_id - attribute identifier
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Thursday, August 12, 1999
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5aopen_idx_c (hid_t_f *obj_id, int_f *idx, hid_t_f *attr_id)
{
int_f ret_value=0; /* Return value */
/*
* Call H5Aopen_idx function.
*/
if ((*attr_id = (hid_t_f)H5Aopen_idx((hid_t)*obj_id, (unsigned)*idx)) < 0)
HGOTO_DONE(FAIL);
done:
return ret_value;
}
char HBase::hasNamedAttr(const char * attrName)
{
hsize_t nattr = H5Aget_num_attrs(fObjectId);
//std::cout<<"\n "<<fObjectPath<<" has "<<nattr<<" attrs\n";
hsize_t i;
for(i = 0; i < nattr; i++) {
hid_t aid = H5Aopen_idx(fObjectId, (unsigned int)i );
//std::cout<<getAttrName(aid)<<"\n";
if(getAttrName(aid) == attrName) {
//std::cout<<"found "<<attrName;
H5Aclose(aid);
return 1;
}
H5Aclose(aid);
}
return 0;
}
std::vector<std::string> list_attributes(hdf5dataset& hdataset)
{
H5O_info_t info;
H5Oget_info(hdataset.handle(), &info);
std::size_t num_attr = info.num_attrs;
std::vector<std::string> result(num_attr);
const int MAX_LEN = 256;
char attr_name[MAX_LEN];
for(std::size_t i = 0; i < num_attr; ++i)
{
hid_t attribute_id = H5Aopen_idx(hdataset.handle(), i);
H5Aget_name(attribute_id, MAX_LEN, attr_name);
result[i] = std::string(attr_name);
H5Aclose(attribute_id);
}
return result;
}
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 read_amuse_hdf5_header(char *filename,
int *npart,
int *ncol,
int *ndim,
int *ndimV,
double *time,
int *ierr)
{
hid_t file_id;
hid_t group_id, group_id1, group_id2;
hid_t attrib_id;
herr_t status;
herr_t HDF5_error = -1;
*ierr = 0;
*ndim = 0;
*ndimV = 0;
if (debug) printf("DEBUG: opening %s \n",filename);
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if (file_id == HDF5_error)
{ printf("ERROR opening %s \n",filename); *ierr = 1; return; }
char *maingroup = "particles";
/*
* Open the "particles" dataset and read the number of particles attribute
*
*/
if (!checkfordataset(file_id,maingroup))
{
printf(" ERROR: \"%s\" dataset not found in AMUSE HDF5 file\n",maingroup);
*ierr = 2;
return;
}
#if H5_VERSION_GE(1,8,0)
group_id1 = H5Gopen2(file_id,maingroup,H5P_DEFAULT);
#else
group_id1 = H5Gopen(file_id,maingroup);
#endif
if (group_id1 == HDF5_error)
{ printf("ERROR opening %s data set \n",maingroup); *ierr = 2; return; }
#if H5_VERSION_GE(1,8,0)
group_id = H5Gopen2(group_id1,"0000000001",H5P_DEFAULT);
#else
group_id = H5Gopen(group_id1,"0000000001");
#endif
if (group_id == HDF5_error)
{ printf("ERROR opening 00000000001 data set \n"); *ierr = 2; return; }
int nattrib;
int i;
char name[256];
nattrib = H5Aget_num_attrs(group_id);
if (debug) printf("number of attributes found = %i\n",nattrib);
/*
* Read through all of the attributes in the header, so we
* can still spit out the values even if they are not used by SPLASH
*/
for(i=0; i < nattrib; i++) {
attrib_id = H5Aopen_idx(group_id,i);
ssize_t attr_status;
attr_status = H5Aget_name(attrib_id, 256, name);
hid_t type_id;
type_id = H5Aget_type(attrib_id);
/*type_class = H5Tget_native_type(type_id,H5T_DIR_ASCEND);*/
if (strcmp(name,"time")==0) {
status = H5Aread(attrib_id,H5T_NATIVE_DOUBLE,time);
} else if (strcmp(name,"number_of_particles")==0) {
status = H5Aread(attrib_id,H5T_NATIVE_INT,npart);
} else {
if (debug) printf("DEBUG: unknown attribute %s \n",name);
}
if (status==HDF5_error) {
printf(" ERROR reading attribute %s \n",name);
}
status = H5Aclose(attrib_id);
}
/*
* Now we need to get the number of data columns in the file
* (from the number of datasets in the "attributes" group)
*/
#if H5_VERSION_GE(1,8,0)
group_id2 = H5Gopen2(group_id,"attributes",H5P_DEFAULT);
#else
group_id2 = H5Gopen(group_id,"attributes");
#endif
if (group_id2 == HDF5_error)
{ printf("ERROR opening %s data set \n","attributes"); *ierr = 2; return; }
hsize_t ndatasets;
status = H5Gget_num_objs(group_id2, &ndatasets);
if (debug) printf("DEBUG: number of datasets = %i \n",(int)ndatasets);
*ncol = (int)ndatasets;
int idim;
/* check that coordinates are present in file */
idim = get_rank_by_name(group_id2,"x");
if (idim <= 0) { printf("ERROR: x positions not found\n"); *ierr = 3; }
idim = get_rank_by_name(group_id2,"y");
if (idim <= 0) { printf("ERROR: y positions not found\n"); *ierr = 3; }
idim = get_rank_by_name(group_id2,"z");
if (idim <= 0) {
printf("z positions not found, assuming file is 2D \n");
*ndim = 2;
*ndimV = 2;
} else {
*ndim = 3;
*ndimV = 3;
}
/* finish, close all open datasets and close file */
status = H5Gclose(group_id2);
if (status == HDF5_error)
{ printf("ERROR closing attributes data set \n"); *ierr = 3; return; }
status = H5Gclose(group_id);
if (status == HDF5_error)
{ printf("ERROR closing %s data set \n",maingroup); *ierr = 3; return; }
status = H5Gclose(group_id1);
if (status == HDF5_error)
{ printf("ERROR closing 0001 data set \n"); *ierr = 3; return; }
status = H5Fclose( file_id );
if (status == HDF5_error) { printf("ERROR closing file \n"); *ierr = 7; }
if (debug) printf("DEBUG: finished header read \n");
}
void rdiff(const char *name, hid_t f1, hid_t f2) {
hid_t g1 = H5Gopen(f1, name, H5P_DEFAULT);
hid_t g2 = H5Gopen(f2, name, H5P_DEFAULT);
if (g1 >= 0 && g2 >= 0) {
int n1 = H5Aget_num_attrs(g1);
for (int i = 0; i < n1; i++) {
char aname[MAXNAME];
hid_t a1 = H5Aopen_idx(g1, i);
assert(H5Aget_name(a1, MAXNAME, aname) < MAXNAME);
H5Aclose(a1);
if (!H5LTfind_attribute(g2, aname)) {
printf("Only in %s[%s%s]\n", file1, name, aname);
continue;
}
int d1, d2;
H5LTget_attribute_ndims(f1, name, aname, &d1);
H5LTget_attribute_ndims(f2, name, aname, &d2);
assert(d1 <= 1 && d2 <= 1);
hsize_t dims1, dims2;
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_attribute_info(f1, name, aname, &dims1, &t1, &ts1);
H5LTget_attribute_info(f2, name, aname, &dims2, &t2, &ts2);
assert(t1 == t2);
assert(t1 == H5T_INTEGER || t1 == H5T_FLOAT || t1 == H5T_STRING);
if (t1 == H5T_INTEGER) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
int v1, v2;
H5LTget_attribute_int(f1, name, aname, &v1);
H5LTget_attribute_int(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%d %s[%s%s]=%d\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_FLOAT) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
float v1, v2;
H5LTget_attribute_float(f1, name, aname, &v1);
H5LTget_attribute_float(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%g %s[%s%s]=%g\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_STRING) {
assert(ts1 < 256 && ts2 < 256);
char buf1[256];
char buf2[256];
H5LTget_attribute_string(f1, name, aname, buf1);
H5LTget_attribute_string(f2, name, aname, buf2);
if (strcmp(buf1, buf2)) {
printf("%s[%s%s]=%s %s[%s%s]=%s\n", file1, name, aname, buf1, file2, name, aname, buf2);
}
}
}
int n2 = H5Aget_num_attrs(g2);
for (int i = 0; i < n2; i++) {
char aname[MAXNAME];
hid_t a2 = H5Aopen_idx(g2, i);
assert(H5Aget_name(a2, MAXNAME, aname) < MAXNAME);
H5Aclose(a2);
if (!H5LTfind_attribute(g1, aname)) {
printf("Only in %s[%s%s]\n", file2, name, aname);
continue;
}
}
hsize_t nobj;
H5Gget_num_objs(g1, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g1, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g1, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g2, oname)) {
printf("Only in %s[%s%s]\n", file1, name, oname);
continue;
}
hsize_t dims1[2], dims2[2];
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_dataset_info(g1, oname, dims1, &t1, &ts1);
H5LTget_dataset_info(g2, oname, dims2, &t2, &ts2);
if (dims1[0] != dims2[0] || dims1[1] != dims2[1]) {
printf("%s[%s%s](%d,%d) != %s[%s%s](%d,%d)\n",
file1, name, oname, dims1[1], dims1[0],
file2, name, oname, dims2[1], dims2[0]);
continue;
}
float *data1 = malloc(dims1[0]*dims1[1]*sizeof(float));
float *data2 = malloc(dims1[0]*dims1[1]*sizeof(float));
H5LTread_dataset_float(g1, oname, data1);
H5LTread_dataset_float(g2, oname, data2);
float maxdiff = 0;
for (int i = dims1[0]*dims1[1]-1; i >= 0; i--) {
float d = data1[i] - data2[i];
if (d < 0) d = -d;
if (d > maxdiff) maxdiff = d;
}
printf("max |%s[%s%s] - %s[%s%s]| = %g\n",
file1, name, oname, file2, name, oname, maxdiff);
free(data1); free(data2);
}
H5Gget_num_objs(g2, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g2, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g2, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g1, oname)) {
printf("Only in %s[%s%s]\n", file2, name, oname);
continue;
}
}
H5Gclose(g1);
H5Gclose(g2);
} else if (g1 >= 0) {
printf("Only in %s:%s\n", file1, name);
H5Gclose(g1);
} else if (g2 >= 0) {
printf("Only in %s:%s\n", file2, name);
H5Gclose(g2);
} else {
printf("Group %s does not exist in either file.\n", name);
}
}
/* ****************************************************************************************************************************** */
int main(int argc, char *argv[]) {
hid_t fileID, dataSetID;
herr_t hErrVal;
int i;
hsize_t dims[1024], maxDims[1024];
H5T_class_t class;
char classStr[32];
hid_t dataTypeID;
size_t dataSize;
H5T_order_t order;
int rank; /* Note this is an int, not an hssize_t */
int intVal;
hid_t dataSpaceID;
hid_t rootGroupID;
hsize_t numInRootGrp, firstDataSetIdx, foundFirstDataSet;
char attrName[1024], firstDataSetName[1024];
ssize_t objectNameSize, attrNameSize;
H5G_stat_t objectStatInfo;
int numAttrs;
int curAttrIdx;
hid_t attrID;
hsize_t numDataPoints;
unsigned majnum, minnum, relnum;
/* Load the library -- not required most platforms. */
hErrVal = H5open();
mjrHDF5_chkError(hErrVal);
/* Get the library version */
hErrVal = H5get_libversion(&majnum, &minnum, &relnum);
mjrHDF5_chkError(hErrVal);
printf("Lib Version: v%lu.%lur%lu\n", (unsigned long)majnum, (unsigned long)minnum, (unsigned long)relnum);
/* Open an existing file. */
fileID = H5Fopen(TST_FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT);
mjrHDF5_chkError(fileID);
/* Get the ID for the "root" group -- every HDF5 has one */
rootGroupID = H5Gopen(fileID, "/", H5P_DEFAULT);
mjrHDF5_chkError(rootGroupID);
/* Get the number of objects in the root group. */
hErrVal = H5Gget_num_objs(rootGroupID, &numInRootGrp);
mjrHDF5_chkError(hErrVal);
printf("The root group contains %lu object%c\n", (unsigned long)numInRootGrp, (numInRootGrp==1?' ':'s'));
if(numInRootGrp < 1) {
printf("As the file contains NO objects, I have nothing left to do...\n");
exit(1);
} /* end if */
/* Find the first dataset in the root group. */
for(foundFirstDataSet=0,firstDataSetIdx=0; (!foundFirstDataSet)&&(firstDataSetIdx<numInRootGrp); firstDataSetIdx++) {
/* Get object name from the index. */
objectNameSize = H5Gget_objname_by_idx(rootGroupID, firstDataSetIdx, firstDataSetName, 1024);
mjrHDF5_chkError(objectNameSize);
if(objectNameSize == 0) { /* Need to check for zero return too */
printf("ERROR: Object with index %lu doesn't exist in root group!\n", (unsigned long)firstDataSetIdx);
exit(1);
} /* end if */
/* Now use the object name to get info about the object... */
hErrVal = H5Gget_objinfo(rootGroupID, firstDataSetName, 0, &objectStatInfo);
mjrHDF5_chkError(hErrVal);
/* If the object is a dataset, then print out some info. */
if(objectStatInfo.type == H5G_DATASET) {
printf("Object %luth (%s) is a dataset!\n", (unsigned long)firstDataSetIdx, firstDataSetName);
printf("The name of the %luth object of the root group is: %s\n", (unsigned long)firstDataSetIdx, firstDataSetName);
foundFirstDataSet = 1;
printf("Info for the %s dataset:\n", firstDataSetName);
printf(" Modify time: %lu\n", (unsigned long)objectStatInfo.mtime);
printf(" Type: %lu\n", (unsigned long)objectStatInfo.type);
printf(" Link count: %lu\n", (unsigned long)objectStatInfo.nlink);
} /* end if */
} /* end for */
/* Note: At this point index of the dataset will be: firstDataSetIdx-- */
if(!foundFirstDataSet) {
printf("ERROR: Could not find a dataset in the root group\n");
exit(1);
} /* end if */
/* Open the dataset we found -- we know it exists. */
dataSetID = H5Dopen(rootGroupID, firstDataSetName, H5P_DEFAULT);
mjrHDF5_chkError(dataSetID);
/* ****************************************************************************************************************************** */
/* Get some info regarding the TYPE of the dataset. */
dataTypeID = H5Dget_type(dataSetID);
mjrHDF5_chkError(dataTypeID);
/* Get the class of the data */
class = H5Tget_class(dataTypeID);
mjrHDF5_Tclass2str(class, classStr);
printf(" Object class: %s\n", classStr);
/* Get the size of the type */
dataSize = H5Tget_size(dataTypeID);
if(dataSize == 0) {
printf("ERROR: Failure in H5Tget_size().\n");
exit(1);
} /* end if */
printf(" Size of data type: %lu\n", (unsigned long)dataSize);
/* Get the byte order */
order = H5Tget_order(dataTypeID);
printf(" Byte Order: ");
switch(order) {
case H5T_ORDER_ERROR : printf("ERROR\n"); break;
case H5T_ORDER_LE : printf("Little Endian\n"); break;
case H5T_ORDER_BE : printf("Big Endian\n"); break;
case H5T_ORDER_VAX : printf("VAX mixed endian\n"); break;
case H5T_ORDER_MIXED : printf("Mixed endian\n"); break;
case H5T_ORDER_NONE : printf("particular order\n"); break;
} /* end switch */
/* We are done with the datatype. */
hErrVal = H5Tclose(dataTypeID);
mjrHDF5_chkError(hErrVal);
/* ****************************************************************************************************************************** */
/* Figure out the size of the dataset. */
dataSpaceID = H5Dget_space(dataSetID);
mjrHDF5_chkError(dataSpaceID);
/* Get the number of dims. */
rank = H5Sget_simple_extent_ndims(dataSpaceID);
mjrHDF5_chkError(rank);
if(rank > 1024) {
/* This can't really happen (limit is 32) */
printf("ERROR: rank too large.\n");
exit(1);
} /* end if */
/* Get the size of each dim. */
intVal = H5Sget_simple_extent_dims(dataSpaceID, dims, maxDims);
mjrHDF5_chkError(intVal);
printf(" Dataspace Rank %lu\n", (unsigned long)rank);
printf(" Dim Lengths: ");
for(i=0; i<rank; i++)
if(dims[i] == H5S_UNLIMITED) {
printf("%s ", "UNLIMITED");
} else {
printf("%ld ", (long)(dims[i]));
} /* end if/else */
printf("\n");
printf(" Max Dim Lengths: ");
for(i=0; i<rank; i++)
if(maxDims[i] == H5S_UNLIMITED) {
printf("%s ", "UNLIMITED");
} else {
printf("%ld ", (long)(maxDims[i]));
} /* end if/else */
printf("\n");
numDataPoints = H5Sget_simple_extent_npoints(dataSpaceID);
if(numDataPoints == 0) {
printf("ERROR: Call to H5Sget_simple_extent_npoints failed.\n");
exit(1);
} /* end if */
printf("Number of data points: %lu\n", (unsigned long)numDataPoints);
/* We are done with the dataSpaceID */
hErrVal = H5Sclose(dataSpaceID);
mjrHDF5_chkError(hErrVal);
/* Get the number of attributes for the dataSet. */
numAttrs = H5Aget_num_attrs(dataSetID);
mjrHDF5_chkError(numAttrs);
printf(" Number of attrs: %lu\n", (unsigned long)numAttrs);
/* If we have any attributes, we get info for them */
if(numAttrs > 0) {
printf(" Attribute info:\n");
for(curAttrIdx=0; curAttrIdx<numAttrs; curAttrIdx++) {
attrID = H5Aopen_idx(dataSetID, curAttrIdx);
mjrHDF5_chkError(attrID);
attrNameSize = H5Aget_name(attrID, 1024, attrName);
mjrHDF5_chkError(attrNameSize);
printf(" Number %3lu: ", (unsigned long)curAttrIdx);
dataTypeID = H5Aget_type(attrID);
mjrHDF5_chkError(dataTypeID);
/* Get the class for the type. */
class = H5Tget_class(dataTypeID);
mjrHDF5_Tclass2str(class, classStr);
printf(" Class: %-16s", classStr);
/* Get the size of the type */
dataSize = H5Tget_size(dataTypeID);
if(dataSize == 0) {
printf("ERROR: Failure in H5Tget_size().\n");
exit(1);
} /* end if */
printf(" Size: %3lu ", (unsigned long)dataSize);
hErrVal = H5Tclose(dataTypeID);
mjrHDF5_chkError(hErrVal);
printf(" Name: %s \n", attrName);
hErrVal = H5Aclose(attrID);
mjrHDF5_chkError(hErrVal);
} /* end for */
} /* end if */
