/*
* Class: hdf_hdf5lib_H5
* Method: H5Aget_num_attrs
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Aget_1num_1attrs
(JNIEnv *env, jclass clss, jlong loc_id)
{
int retVal = -1;
retVal = H5Aget_num_attrs((hid_t)loc_id);
if (retVal < 0)
h5libraryError(env);
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Aget_1num_1attrs */
CPLErr HDF5Dataset::ReadGlobalAttributes(int bSUBDATASET)
{
HDF5GroupObjects *poRootGroup =
static_cast<HDF5GroupObjects *>(CPLCalloc(sizeof(HDF5GroupObjects), 1));
poH5RootGroup = poRootGroup;
poRootGroup->pszName = CPLStrdup("/");
poRootGroup->nType = H5G_GROUP;
poRootGroup->poHparent = nullptr;
poRootGroup->pszPath = nullptr;
poRootGroup->pszUnderscorePath = nullptr;
if( hHDF5 < 0 )
{
CPLError(CE_Failure, CPLE_AppDefined, "hHDF5 < 0!");
return CE_None;
}
H5G_stat_t oStatbuf = {{0, 0}, {0, 0}, 0, H5G_UNKNOWN, 0, 0, {0, 0, 0, 0}};
if( H5Gget_objinfo(hHDF5, "/", FALSE, &oStatbuf) < 0 )
return CE_Failure;
poRootGroup->objno[0] = oStatbuf.objno[0];
poRootGroup->objno[1] = oStatbuf.objno[1];
if( hGroupID > 0 )
H5Gclose(hGroupID);
hGroupID = H5Gopen(hHDF5, "/");
if( hGroupID < 0 )
{
CPLError(CE_Failure, CPLE_AppDefined, "hGroupId <0!");
return CE_None;
}
poRootGroup->nbAttrs = H5Aget_num_attrs(hGroupID);
H5Gget_num_objs(hGroupID, &(poRootGroup->nbObjs));
if( poRootGroup->nbObjs > 0 )
{
poRootGroup->poHchild = static_cast<HDF5GroupObjects *>(
CPLCalloc(static_cast<size_t>(poRootGroup->nbObjs),
sizeof(HDF5GroupObjects)));
H5Giterate(hGroupID, "/", nullptr, HDF5CreateGroupObjs, poRootGroup);
}
else
{
poRootGroup->poHchild = nullptr;
}
HDF5ListGroupObjects(poRootGroup, bSUBDATASET);
return CE_None;
}
/*----------------------------------------------------------------------------
* Name: h5aget_num_attrs_c
* Purpose: Call H5Aget_num_attrs to determine number of
* attributes of an object
* Inputs: obj_id - object identifier
* attr_num - number of attributes
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Thursday, August 12, 1999
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5aget_num_attrs_c (hid_t_f *obj_id, int_f *attr_num)
{
int_f ret_value=0; /* Return value */
/*
* Call H5Aget_num_attrs function.
*/
if ((*attr_num = (int_f)H5Aget_num_attrs((hid_t)*obj_id)) < 0)
HGOTO_DONE(FAIL);
done:
return ret_value;
}
CPLErr HDF5Dataset::ReadGlobalAttributes(int bSUBDATASET)
{
HDF5GroupObjects *poRootGroup;
poRootGroup = (HDF5GroupObjects*) CPLCalloc(sizeof(HDF5GroupObjects), 1);
poH5RootGroup=poRootGroup;
poRootGroup->pszName = CPLStrdup( "/" );
poRootGroup->nType = H5G_GROUP;
poRootGroup->poHparent = NULL;
poRootGroup->pszPath = NULL;
poRootGroup->pszUnderscorePath = NULL;
if( hHDF5 < 0 ) {
printf( "hHDF5 <0!!\n" );
return CE_None;
}
H5G_stat_t oStatbuf;
if( H5Gget_objinfo( hHDF5, "/", FALSE, &oStatbuf ) < 0 )
return CE_Failure;
poRootGroup->objno[0] = oStatbuf.objno[0];
poRootGroup->objno[1] = oStatbuf.objno[1];
if( hGroupID > 0 )
H5Gclose( hGroupID );
hGroupID = H5Gopen( hHDF5, "/" );
if( hGroupID < 0 ){
printf( "hGroupID <0!!\n" );
return CE_None;
}
poRootGroup->nbAttrs = H5Aget_num_attrs( hGroupID );
H5Gget_num_objs( hGroupID, &( poRootGroup->nbObjs ) );
if( poRootGroup->nbObjs > 0 ) {
poRootGroup->poHchild = ( HDF5GroupObjects * )
CPLCalloc( poRootGroup->nbObjs,
sizeof( HDF5GroupObjects ) );
H5Giterate( hGroupID, "/", NULL,
HDF5CreateGroupObjs, (void *)poRootGroup );
}
else poRootGroup->poHchild = NULL;
HDF5ListGroupObjects( poRootGroup, bSUBDATASET );
return CE_None;
}
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;
}
/* Open/close the file with HDF5. */
int
readfile_hdf5(char *file_name, long long *delta, int do_inq, int num_vars)
{
hid_t hdfid, hdf_grpid;
hid_t fapl_id;
struct timeval starttime, endtime;
long long startt, endt;
/* Start the clock. */
gettimeofday(&starttime, NULL);
/* Open and close the root group. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) ERR;
if ((hdfid = H5Fopen(file_name, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if ((hdf_grpid = H5Gopen2(hdfid, "/", H5P_DEFAULT)) < 0) ERR;
/* Do we want to do an inq? */
if (do_inq)
{
if (num_vars)
{
}
else /* global atts */
{
hsize_t num_obj;
/* Find out how many attributes. */
if ((num_obj = H5Aget_num_attrs(hdf_grpid)) < 0) ERR;
}
}
if (H5Gclose(hdf_grpid) < 0) ERR;
if (H5Fclose(hdfid) < 0) ERR;
gettimeofday(&endtime, NULL);
/* Compute the time delta */
startt = (1000000 * starttime.tv_sec) + starttime.tv_usec;
endt = (1000000 * endtime.tv_sec) + endtime.tv_usec;
*delta = endt - startt;
return 0;
}
int H5Dataset_read_attribute(H5Dataset* ind, H5Dataset* outd)
{
int ret_value=0, i=0, n=0;
hid_t did=-1;
if ( (did = H5Dopen(ind->fid, ind->fullpath)) < 0)
THROW_H5LIBRARY_ERROR(ind->error,ret_value, done);
if ( (n = H5Aget_num_attrs(did)) <=0 )
goto done;
ind->nattributes = n;
ind->attributes = (H5Attribute *)malloc(n*sizeof(H5Attribute));
for (i=0; i<n; i++) {
H5Attribute_ctor(&(ind->attributes[i]));
ind->attributes[i].fid = ind->fid;
ind->attributes[i].obj_path = (char *)malloc(strlen(ind->fullpath)+1);
strcpy(ind->attributes[i].obj_path, ind->fullpath);
ind->attributes[i].obj_type = H5OBJECT_DATASET;
}
/* read the attribute value into memory */
H5File_read_attribute(did, ind->attributes);
done:
if (did > 0 ) H5Dclose(did);
#ifndef HDF5_LOCAL
memset (outd, 0, sizeof (H5Dataset));
/* pass on the value */
outd->tclass = ind->tclass;
outd->error = ind->error;
outd->nattributes = ind->nattributes;
outd->attributes = ind->attributes;
ind->attributes = NULL;
ind->nattributes = 0;
#endif
return ret_value;
}
void Object::updateAttributes()
{
fAttributes.clear();
if (fObjectId < 0)
return;
// get attributes
int nAttrs = H5Aget_num_attrs(fObjectId);
if (nAttrs < 0) {
throw Exception("Could not retrieve number of attributes");
}
for (size_t iAttr = 0; iAttr < static_cast<size_t>(nAttrs); ++iAttr) {
char* attrName;
char objName[] = ".";
ssize_t nameLen = H5Aget_name_by_idx(fObjectId, objName, H5_INDEX_NAME, H5_ITER_INC, iAttr, 0, 0, H5P_DEFAULT);
if (nameLen > 0) {
// fetch name of this attribute
attrName = new char[++nameLen];
H5Aget_name_by_idx(fObjectId, objName, H5_INDEX_NAME, H5_ITER_INC, iAttr, attrName, nameLen, H5P_DEFAULT);
string sAttrName(attrName);
delete[] attrName;
// open attribute
hid_t attrId = H5Aopen_by_idx(fObjectId, objName, H5_INDEX_NAME, H5_ITER_INC, iAttr, H5P_DEFAULT, H5P_DEFAULT);
if (attrId < 0) {
cerr << "Could not open attribute '" << sAttrName << "'" << endl;
continue;
}
// parse type info
// cout << "Reading attribute: " << sAttrName << endl;
fAttributes[sAttrName] = llReadAttribute(attrId);
// close attribute
H5Aclose(attrId);
}
}
}
int HBase::numAttrs()
{
hsize_t nattr = H5Aget_num_attrs(fObjectId);
return (int)nattr;
}
herr_t HDF5CreateGroupObjs(hid_t hHDF5, const char *pszObjName,
void *poHObjParent)
{
herr_t ret; /* error return status */
hid_t hGroupID; /* identifier of group */
hid_t hDatasetID; /* identifier of dataset */
hsize_t nbObjs=0; /* number of objects in a group */
int nbAttrs=0; /* number of attributes in object */
int idx;
int n_dims;
H5G_stat_t oStatbuf;
hsize_t *dims=NULL;
hsize_t *maxdims=NULL;
hid_t datatype;
hid_t dataspace;
hid_t native;
herr_t status;
char *CreatePath( HDF5GroupObjects *poH5Object );
HDF5GroupObjects *poHchild;
HDF5GroupObjects *poHparent;
poHparent = ( HDF5GroupObjects * ) poHObjParent;
poHchild=poHparent->poHchild;
if( H5Gget_objinfo( hHDF5, pszObjName, FALSE, &oStatbuf ) < 0 )
return -1;
/* -------------------------------------------------------------------- */
/* Look for next child */
/* -------------------------------------------------------------------- */
for( idx=0; idx < poHparent->nbObjs; idx++ ) {
if( poHchild->pszName == NULL ) break;
poHchild++;
}
if( idx == poHparent->nbObjs )
return -1; // all children parsed
/* -------------------------------------------------------------------- */
/* Save child information */
/* -------------------------------------------------------------------- */
poHchild->pszName = CPLStrdup( pszObjName );
poHchild->nType = oStatbuf.type;
poHchild->nIndex = idx;
poHchild->poHparent = poHparent;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
poHchild->objno[0] = oStatbuf.objno[0];
poHchild->objno[1] = oStatbuf.objno[1];
if( poHchild->pszPath == NULL ) {
poHchild->pszPath = CreatePath( poHchild );
}
if( poHparent->pszPath == NULL ) {
poHparent->pszPath = CreatePath( poHparent );
}
switch ( oStatbuf.type )
{
case H5G_LINK:
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = NULL;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
break;
case H5G_GROUP:
if( ( hGroupID = H5Gopen( hHDF5, pszObjName ) ) == -1 ) {
printf( "Error: unable to access \"%s\" group.\n",
pszObjName );
return -1;
}
nbAttrs = H5Aget_num_attrs( hGroupID );
ret = H5Gget_num_objs( hGroupID, &nbObjs );
poHchild->nbAttrs= nbAttrs;
poHchild->nbObjs = (int) nbObjs;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
if( nbObjs > 0 ) {
poHchild->poHchild =( HDF5GroupObjects * )
CPLCalloc( (int)nbObjs, sizeof( HDF5GroupObjects ) );
memset( poHchild->poHchild,0,
(size_t) (sizeof( HDF5GroupObjects ) * nbObjs) );
}
else
poHchild->poHchild = NULL;
if( !HDF5GroupCheckDuplicate( poHparent, oStatbuf.objno ) )
H5Giterate( hHDF5, pszObjName, NULL,
HDF5CreateGroupObjs, (void*) poHchild );
else
CPLDebug( "HDF5", "avoiding link looping on node '%s'.",
pszObjName );
H5Gclose( hGroupID );
break;
case H5G_DATASET:
if( ( hDatasetID = H5Dopen( hHDF5, pszObjName ) ) == -1 ) {
printf( "Error: unable to access \"%s\" dataset.\n",
pszObjName );
return -1;
}
nbAttrs = H5Aget_num_attrs( hDatasetID );
datatype = H5Dget_type( hDatasetID );
dataspace = H5Dget_space( hDatasetID );
n_dims = H5Sget_simple_extent_ndims( dataspace );
native = H5Tget_native_type( datatype, H5T_DIR_ASCEND );
if( n_dims > 0 ) {
dims = (hsize_t *) CPLCalloc( n_dims,sizeof( hsize_t ) );
maxdims = (hsize_t *) CPLCalloc( n_dims,sizeof( hsize_t ) );
}
status = H5Sget_simple_extent_dims( dataspace, dims, maxdims );
if( maxdims != NULL )
CPLFree( maxdims );
if( n_dims > 0 ) {
poHchild->nRank = n_dims; // rank of the array
poHchild->paDims = dims; // dimmension of the array.
poHchild->HDatatype = datatype; // HDF5 datatype
}
else {
poHchild->nRank = -1;
poHchild->paDims = NULL;
poHchild->HDatatype = 0;
}
poHchild->nbAttrs = nbAttrs;
poHchild->nbObjs = 0;
poHchild->poHchild = NULL;
poHchild->native = native;
ret = H5Dclose( hDatasetID );
break;
case H5G_TYPE:
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = NULL;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
break;
default:
break;
}
return 0;
}
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");
}
herr_t HDF5CreateGroupObjs( hid_t hHDF5, const char *pszObjName,
void *poHObjParent)
{
HDF5GroupObjects *const poHparent =
static_cast<HDF5GroupObjects *>(poHObjParent);
HDF5GroupObjects *poHchild = poHparent->poHchild;
H5G_stat_t oStatbuf;
if( H5Gget_objinfo(hHDF5, pszObjName, FALSE, &oStatbuf) < 0 )
return -1;
// Look for next child.
unsigned idx = 0; // idx is used after the for loop.
for( ; idx < poHparent->nbObjs; idx++ )
{
if( poHchild->pszName == nullptr ) break;
poHchild++;
}
if( idx == poHparent->nbObjs )
return -1; // All children parsed.
// Save child information.
poHchild->pszName = CPLStrdup(pszObjName);
poHchild->nType = oStatbuf.type;
poHchild->nIndex = idx;
poHchild->poHparent = poHparent;
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
poHchild->objno[0] = oStatbuf.objno[0];
poHchild->objno[1] = oStatbuf.objno[1];
if( poHchild->pszPath == nullptr )
{
CreatePath(poHchild);
}
if( poHparent->pszPath == nullptr )
{
CreatePath(poHparent);
}
switch( oStatbuf.type )
{
case H5G_LINK:
{
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = nullptr;
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
break;
}
case H5G_GROUP:
{
hid_t hGroupID = H5I_INVALID_HID; // Identifier of group.
if( (hGroupID = H5Gopen(hHDF5, pszObjName)) == -1)
{
CPLError(CE_Failure, CPLE_AppDefined,
"unable to access \"%s\" group.", pszObjName);
return -1;
}
// Number of attributes in object.
const int nbAttrs = H5Aget_num_attrs(hGroupID);
hsize_t nbObjs = 0; // Number of objects in a group.
H5Gget_num_objs(hGroupID, &nbObjs);
poHchild->nbAttrs = nbAttrs;
poHchild->nbObjs = static_cast<int>(nbObjs);
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
if( nbObjs > 0 )
{
poHchild->poHchild = static_cast<HDF5GroupObjects *>(
CPLCalloc(static_cast<int>(nbObjs), sizeof(HDF5GroupObjects)));
memset(poHchild->poHchild, 0,
static_cast<size_t>(sizeof(HDF5GroupObjects) * nbObjs));
}
else
{
poHchild->poHchild = nullptr;
}
if( !HDF5GroupCheckDuplicate(poHparent, oStatbuf.objno) )
H5Giterate(hHDF5, pszObjName, nullptr, HDF5CreateGroupObjs, poHchild);
else
CPLDebug("HDF5", "avoiding link looping on node '%s'.", pszObjName);
H5Gclose(hGroupID);
break;
}
case H5G_DATASET:
{
hid_t hDatasetID = H5I_INVALID_HID; // Identifier of dataset.
if( (hDatasetID = H5Dopen(hHDF5, pszObjName)) == -1)
{
CPLError(CE_Failure, CPLE_AppDefined,
"unable to access \"%s\" dataset.", pszObjName);
return -1;
}
const int nbAttrs = H5Aget_num_attrs(hDatasetID);
const hid_t datatype = H5Dget_type(hDatasetID);
const hid_t dataspace = H5Dget_space(hDatasetID);
const int n_dims = H5Sget_simple_extent_ndims(dataspace);
const hid_t native = H5Tget_native_type(datatype, H5T_DIR_ASCEND);
hsize_t *maxdims = nullptr;
hsize_t *dims = nullptr;
if( n_dims > 0 )
{
dims = static_cast<hsize_t *>(CPLCalloc(n_dims, sizeof(hsize_t)));
maxdims =
static_cast<hsize_t *>(CPLCalloc(n_dims, sizeof(hsize_t)));
}
H5Sget_simple_extent_dims(dataspace, dims, maxdims);
if( maxdims != nullptr )
CPLFree(maxdims);
if( n_dims > 0 )
{
poHchild->nRank = n_dims; // rank of the array
poHchild->paDims = dims; // dimension of the array.
poHchild->HDatatype = datatype; // HDF5 datatype
}
else
{
poHchild->nRank = -1;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
}
poHchild->nbAttrs = nbAttrs;
poHchild->nbObjs = 0;
poHchild->poHchild = nullptr;
poHchild->native = native;
H5Tclose(datatype);
H5Sclose(dataspace);
H5Dclose(hDatasetID);
break;
}
case H5G_TYPE:
{
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = nullptr;
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
break;
}
default:
break;
}
return 0;
}
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 */
