int AMRreader::
readAMRmesh()
{
//if( blkxs_!=NULL ) return 0;
hid_t file_id = H5Fopen( filename_.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
if( file_id<0 ) {
debug1 << "Failed to open AMR file: " << filename_ << " when read in mesh.\n";
return -1;
}
hid_t gid = H5Gopen1( file_id, amr_grpname );
if( gid<0 ) {
debug1 << "Failed to open AMR group in " << filename_ << " when read in mesh.\n";
return -2;
}
blkxs_ = new float[3*nblks_];
blkdx_ = new float[3*nblks_];
if( blkxs_==NULL || blkdx_==NULL ) {
debug1 << "Failed to allocate blkxs_ or blkddx_ for " << filename_ << ".\n";
return -3;
}
hid_t xsid = H5Dopen1( gid, amr_crdname );
if( xsid<0 ) {
debug1 << "Failed to open block coordinates in " << filename_ << ".\n";
return -4;
}
herr_t herr = H5Dread( xsid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, blkxs_ );
H5Dclose(xsid);
if( herr<0 ) {
debug1 << "Failed to read block coordinates in " << filename_ << ".\n";
return -5;
}
hid_t dxid = H5Dopen1( gid, amr_stpname );
if( dxid<0 ) {
debug1 << "Failed to open block steps in " << filename_ << ".\n";
return -6;
}
herr = H5Dread( dxid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, blkdx_ );
H5Dclose(dxid);
if( herr<0 ) {
debug1 << "Failed to read block steps in " << filename_ << ".\n";
return -7;
}
H5Gclose( gid );
H5Fclose( file_id );
return 0;
}
/** Select a different resolution from a multi-resolution image.
* \ingroup mi2VPrp
*/
int miselect_resolution(mihandle_t volume, int depth)
{
hid_t grp_id;
char path[MI2_MAX_PATH];
if ( volume->hdf_id < 0 || depth > MI2_MAX_RESOLUTION_GROUP || depth < 0) {
return (MI_ERROR);
}
grp_id = H5Gopen1(volume->hdf_id, MI_ROOT_PATH "/image");
if (grp_id < 0) {
return (MI_ERROR);
}
/* Check given depth with the available depth in file.
Make sure the selected resolution does exist.
*/
if (depth > volume->create_props->depth) {
return (MI_ERROR);
}
else if (depth != 0) {
if (minc_update_thumbnail(volume, grp_id, 0, depth) < 0) {
return (MI_ERROR);
}
}
volume->selected_resolution = depth;
if (volume->image_id >= 0) {
H5Dclose(volume->image_id);
}
sprintf(path, "%d/image", depth);
volume->image_id = H5Dopen1(grp_id, path);
if (volume->volume_class == MI_CLASS_REAL) {
if (volume->imax_id >= 0) {
H5Dclose(volume->imax_id);
}
sprintf(path, "%d/image-max", depth);
volume->imax_id = H5Dopen1(grp_id, path);
if (volume->imin_id >= 0) {
H5Dclose(volume->imin_id);
}
sprintf(path, "%d/image-min", depth);
volume->imin_id = H5Dopen1(grp_id, path);
}
return (MI_NOERROR);
}
/** Return the byte size of the voxel datatytpe
*/
int miget_data_type_size ( mihandle_t volume, misize_t *voxel_size )
{
hid_t grp_id;
hid_t dset_id;
hid_t type_id;
hid_t file_id = volume->hdf_id;
grp_id = midescend_path ( file_id, MI_FULLIMAGE_PATH );
if ( grp_id < 0 ) {
return ( MI_ERROR );
}
dset_id = H5Dopen1 ( grp_id, "image" );
if ( dset_id < 0 ) {
return ( MI_ERROR );
}
type_id = H5Dget_type ( dset_id );
if ( type_id < 0 ) {
return ( MI_ERROR );
}
*voxel_size = H5Tget_size ( type_id );
H5Tclose ( type_id );
H5Dclose ( dset_id );
H5Gclose ( grp_id );
return ( MI_NOERROR );
}
void readSimple( char * file , char * group , char * dset , void * data , hid_t type ){
hid_t h5fil = H5Fopen( file , H5F_ACC_RDWR , H5P_DEFAULT );
hid_t h5grp = H5Gopen1( h5fil , group );
hid_t h5dst = H5Dopen1( h5grp , dset );
H5Dread( h5dst , type , H5S_ALL , H5S_ALL , H5P_DEFAULT , data );
H5Dclose( h5dst );
H5Gclose( h5grp );
H5Fclose( h5fil );
}
bool hdfutil::HasDataSet (const H5::H5File & h5file, const std::string & name) {
hid_t loc_id = h5file.getLocId();
#if H5_VERS_MINOR >= 8
hid_t dataset_id = H5Dopen1( loc_id, name.c_str());
#else
hid_t dataset_id = H5Dopen( loc_id, name.c_str());
#endif
if(dataset_id < 0)
return false;
H5Dclose(dataset_id);
return true;
}
void getH5dims( char * file , char * group , char * dset , hsize_t * dims ){
hid_t h5fil = H5Fopen( file , H5F_ACC_RDWR , H5P_DEFAULT );
hid_t h5grp = H5Gopen1( h5fil , group );
hid_t h5dst = H5Dopen1( h5grp , dset );
hid_t h5spc = H5Dget_space( h5dst );
H5Sget_simple_extent_dims( h5spc , dims , NULL);
H5Sclose( h5spc );
H5Dclose( h5dst );
H5Gclose( h5grp );
H5Fclose( h5fil );
}
int AMRreader::
GetInterfaceVariable( int vid, void* dat )
{
std::string vname;
hid_t mtype;
switch(vid) {
case(i_coor): vname = intf_coor_name; mtype=H5T_NATIVE_FLOAT; break;
case(i_velo): vname = intf_velo_name; mtype=H5T_NATIVE_FLOAT; break;
case(i_pres): vname = intf_pres_name; mtype=H5T_NATIVE_FLOAT; break;
case(i_segt): vname = intf_segt_name; mtype=H5T_NATIVE_INT; break;
default:
debug1 << "Unknown variable id " << vid << " .\n";
return -1;
}
hid_t file_id = H5Fopen( filename_.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
if( file_id<0 ) {
debug1 << "Failed to open AMR file: " << filename_ << " when read in mesh.\n";
return -2;
}
hid_t gid = H5Gopen1( file_id, intf_grp_name );
if( gid<0 ) {
debug1 << "Failed to open interface group in " << filename_ << " when read in mesh.\n";
return -3;
}
hid_t dtid = H5Dopen1( gid, vname.c_str() );
if( dtid<0 ) {
debug1 << "Failed to open interface variable " << vname << " in " << filename_ << ".\n";
return -4;
}
herr_t herr = H5Dread( dtid, mtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, dat );
H5Dclose(dtid);
if( herr<0 ) {
debug1 << "Failed to read interface variable " << vname << " in " << filename_ << ".\n";
return -5;
}
H5Gclose( gid );
H5Fclose( file_id );
return 0;
}
void UPCdata::readHDF5file(char* filename){
#if HDF5_AVAILABLE==1
int matrix[5][5];
hid_t file, dataset; // File and dataset identifiers
herr_t status;
file = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset = H5Dopen1(file,"dataset1");
status = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, matrix);
for (int i=0; i < 5; i++) {
for(int j=0; j < 5; j++)
printf("%3d \n", matrix[i][j]);
printf("\n");
}
#endif
}
int AMRreader::
readAMRdata()
{
// if( datbuf_!=NULL ) return 0;
hid_t file_id = H5Fopen( filename_.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
if( file_id<0 ) {
debug1 << "Failed to open AMR file: " << filename_ << " when read in mesh.\n";
return -1;
}
hid_t gid = H5Gopen1( file_id, amr_grpname );
if( gid<0 ) {
debug1 << "Failed to open AMR group in " << filename_ << " when read in mesh.\n";
return -2;
}
datbuf_ = new float[ 5*blksz_*nblks_];
if( datbuf_==NULL ) {
debug1 << "Failed to allocate datbuf_ for " << filename_ << ".\n";
return -3;
}
hid_t datid = H5Dopen1( gid, amr_datname );
if( datid<0 ) {
debug1 << "Failed to open block data in " << filename_ << ".\n";
return -4;
}
herr_t herr = H5Dread( datid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, datbuf_ );
H5Dclose(datid);
if( herr<0 ) {
debug1 << "Failed to read block data in " << filename_ << ".\n";
return -5;
}
H5Gclose( gid );
H5Fclose( file_id );
return 0;
}
void readPatch( char * file , char * group , char * dset , void * data , hid_t type , int dim , int * start , int * loc_size , int * glo_size){
hid_t h5fil = H5Fopen( file , H5F_ACC_RDWR , H5P_DEFAULT );
hid_t h5grp = H5Gopen1( h5fil , group );
hid_t h5dst = H5Dopen1( h5grp , dset );
hsize_t mdims[dim];
hsize_t fdims[dim];
hsize_t fstart[dim];
hsize_t fstride[dim];
hsize_t fcount[dim];
hsize_t fblock[dim];
int d;
for( d=0 ; d<dim ; ++d ){
mdims[d] = loc_size[d];
fdims[d] = glo_size[d];
fstart[d] = start[d];
fstride[d] = 1;
fcount[d] = loc_size[d];
fblock[d] = 1;
}
hid_t mspace = H5Screate_simple(dim,mdims,NULL);
hid_t fspace = H5Screate_simple(dim,fdims,NULL);
H5Sselect_hyperslab( fspace , H5S_SELECT_SET , fstart , fstride , fcount , fblock );
H5Dread( h5dst , type , mspace , fspace , H5P_DEFAULT , data );
H5Sclose( mspace );
H5Sclose( fspace );
H5Dclose( h5dst );
H5Gclose( h5grp );
H5Fclose( h5fil );
}
int
main()
{
printf("\n*** Checking HDF5 dimscales some more.\n");
printf("*** Creating a file with one var with one dimension scale...");
{
hid_t fileid, spaceid, datasetid, dimscaleid, cparmsid;
hsize_t dims[NDIMS] = {DIM1_LEN}, maxdims[NDIMS] = {H5S_UNLIMITED};
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the space that will be used both for the dimscale and
* the 1D dataset that will attach it. */
if ((spaceid = H5Screate_simple(NDIMS, dims, maxdims)) < 0) ERR;
/* Modify dataset creation properties, i.e. enable chunking. */
dims[0] = 1;
if ((cparmsid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(cparmsid, NDIMS, dims) < 0) ERR;
/* Create our dimension scale, as an unlimited dataset. */
if ((dimscaleid = H5Dcreate(fileid, DIMSCALE_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(dimscaleid, NAME_ATTRIBUTE) < 0) ERR;
/* Create a variable which uses it. */
if ((datasetid = H5Dcreate(fileid, VAR1_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(datasetid, dimscaleid, 0) < 0) ERR;
if (H5DSset_label(datasetid, 0, DIMSCALE_LABEL) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(dimscaleid) < 0 ||
H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, one dimscale file can be read...");
{
hid_t fileid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
char dimscale_name[NC_MAX_NAME+1];
htri_t is_scale;
char label[NC_MAX_NAME+1];
int num_scales;
hsize_t dims[1], maxdims[1];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj, vars_dimscale_obj;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n",
obj_class, obj_name);*/
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* This should be an unlimited dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if (maxdims[0] != H5S_UNLIMITED) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale && strcmp(obj_name, DIMSCALE_NAME)) ERR;
if (is_scale)
{
/* A dimscale comes with a NAME attribute, in
* addition to its real name. */
if (H5DSget_scale_name(datasetid, dimscale_name, NC_MAX_NAME) < 0) ERR;
if (strcmp(dimscale_name, NAME_ATTRIBUTE)) ERR;
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj.fileno[0] = statbuf.fileno[0];
dimscale_obj.objno[0] = statbuf.objno[0];
dimscale_obj.fileno[1] = statbuf.fileno[1];
dimscale_obj.objno[1] = statbuf.objno[1];
/*printf("statbuf.fileno = %d statbuf.objno = %d\n",
statbuf.fileno, statbuf.objno);*/
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
if (H5DSiterate_scales(datasetid, 0, NULL, alien_visitor,
&vars_dimscale_obj) < 0) ERR;
/*printf("vars_dimscale_obj.fileno = %d vars_dimscale_obj.objno = %d\n",
vars_dimscale_obj.fileno, vars_dimscale_obj.objno);*/
if (vars_dimscale_obj.fileno[0] != dimscale_obj.fileno[0] ||
vars_dimscale_obj.objno[0] != dimscale_obj.objno[0] ||
vars_dimscale_obj.fileno[1] != dimscale_obj.fileno[1] ||
vars_dimscale_obj.objno[1] != dimscale_obj.objno[1]) ERR;
/* There's also a label for dimension 0. */
if (H5DSget_label(datasetid, 0, label, NC_MAX_NAME) < 0) ERR;
/*printf("found non-scale dataset %s, label %s\n", obj_name, label);*/
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with one var with two dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define DIMS_2 2
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME "pres"
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS_2];
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, two dimscales file can be read...");
{
#define NDIMS2 2
hid_t fileid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t dims[NDIMS2], maxdims[NDIMS2];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[2], vars_dimscale_obj[2];
int dimscale_cnt = 0;
int d, ndims;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
if (ndims > NDIMS2) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with one var with two unlimited dimension scales...");
{
#define U1_LEN 3
#define U2_LEN 2
#define DIMS2 2
#define U1_NAME "u1"
#define U2_NAME "u2"
#define VNAME "v1"
hid_t fapl_id, fcpl_id, grpid, plistid, plistid2;
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS2], maxdims[DIMS2], chunksize[DIMS2] = {10, 10};
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[2], vars_dimscale_obj[2];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
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;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = 0;
maxdims[0] = H5S_UNLIMITED;
if ((lat_spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
if ((lon_spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = 0;
dims[1] = 0;
maxdims[0] = H5S_UNLIMITED;
maxdims[1] = H5S_UNLIMITED;
if ((pres_spaceid = H5Screate_simple(DIMS2, dims, maxdims)) < 0) ERR;
/* Set up the dataset creation property list for the two dimensions. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid, 1, chunksize) < 0) ERR;
if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate(grpid, U1_NAME, H5T_NATIVE_INT,
lat_spaceid, plistid)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate(grpid, U2_NAME, H5T_NATIVE_INT,
lon_spaceid, plistid)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Set up the dataset creation property list for the variable. */
if ((plistid2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid2, DIMS2, chunksize) < 0) ERR;
if (H5Pset_attr_creation_order(plistid2, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate(grpid, VNAME, H5T_NATIVE_DOUBLE, pres_spaceid,
plistid2)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Close down the show. */
if (H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Pclose(plistid) < 0 ||
H5Pclose(plistid2) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
/*Get the type (i.e. group, dataset, etc.), and the name of
the object. */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(grpid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Check the dimension lengths. */
{
hid_t spaceid1;
hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2];
int dataset_ndims;
/* Check U1. */
if ((datasetid = H5Dopen1(grpid, U1_NAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 1 || h5dimlen[0] != 0 || h5dimlenmax[0] != H5S_UNLIMITED) ERR;
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
/* Check U2. */
if ((datasetid = H5Dopen1(grpid, U2_NAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 1 || h5dimlen[0] != 0 || h5dimlenmax[0] != H5S_UNLIMITED) ERR;
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
/* Check V1. */
if ((datasetid = H5Dopen1(grpid, VNAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 0 || h5dimlen[1] != 0 ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* All done. */
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
}
/* Write two hyperslabs. */
{
#define NUM_VALS 3
hid_t file_spaceid, mem_spaceid;
hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2], xtend_size[DIMS2] = {1, NUM_VALS};
hsize_t start[DIMS2] = {0, 0};
hsize_t count[DIMS2] = {1, NUM_VALS};
double value[NUM_VALS];
int dataset_ndims;
int i;
/* Set up phony data. */
for (i = 0; i < NUM_VALS; i++)
value[i] = (float)i;
/* Open the dataset, check its dimlens. */
if ((datasetid = H5Dopen1(grpid, VNAME)) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 0 || h5dimlen[1] != 0 ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Extend the size of the dataset. */
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
/* Check the size. */
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 1 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Set up the file and memory spaces. */
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0) ERR;
if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
/* Write a slice of data. */
if (H5Dwrite(datasetid, H5T_NATIVE_DOUBLE, mem_spaceid, file_spaceid,
H5P_DEFAULT, value) < 0)
/* Check the size. */
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 1 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Extend the size of the dataset for the second slice. */
xtend_size[0]++;
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
/* Set up the file and memory spaces for a second slice. */
start[0]++;
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0) ERR;
if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
/* Write a second slice of data. */
if (H5Dwrite(datasetid, H5T_NATIVE_DOUBLE, mem_spaceid, file_spaceid,
H5P_DEFAULT, value) < 0)
/* Check the size again. */
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 2 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* All done. */
if (H5Dclose(datasetid) ||
H5Sclose(mem_spaceid) ||
H5Sclose(file_spaceid)) ERR;
}
/* Close up the shop. */
if (H5Sclose(spaceid)) ERR;
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking dimension scales with attached dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define TIME_LEN 5
#define LEN_LEN 10
#define DIMS_3 3
#define NUM_DIMSCALES1 4
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME1 "z_pres"
#define TIME_NAME "time"
#define LEN_NAME "u_len"
hid_t fileid, lat_spaceid, lon_spaceid, time_spaceid, pres_spaceid, len_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid, time_dimscaleid, len_dimscaleid;
hid_t fapl_id, fcpl_id;
hsize_t dims[DIMS_3];
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t maxdims[DIMS_3];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[NUM_DIMSCALES1], vars_dimscale_obj[NUM_DIMSCALES1];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
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;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = TIME_LEN;
if ((time_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LEN_LEN;
if ((len_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
dims[2] = TIME_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_3, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
if ((time_dimscaleid = H5Dcreate1(fileid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(time_dimscaleid, NULL) < 0) ERR;
if ((len_dimscaleid = H5Dcreate1(fileid, LEN_NAME, H5T_NATIVE_INT,
len_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(len_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these three dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME1, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, time_dimscaleid, 2) < 0) ERR;
/* Attach a dimscale to a dimscale. Unfortunately, HDF5 does not
* allow this. Woe is me. */
/*if (H5DSattach_scale(time_dimscaleid, len_dimscaleid, 0) < 0) ERR;*/
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(time_dimscaleid) < 0 ||
H5Dclose(len_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(time_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Sclose(len_spaceid) < 0 ||
H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking cration ordering of datasets which are also dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define TIME_LEN 5
#define LEN_LEN 10
#define DIMS_3 3
#define NUM_DIMSCALES2 4
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME1 "z_pres"
#define TIME_NAME "time"
#define LEN_NAME "u_len"
hid_t fileid, lat_spaceid, lon_spaceid, time_spaceid, pres_spaceid, len_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid, time_dimscaleid, len_dimscaleid;
hid_t fapl_id, fcpl_id;
hsize_t dims[DIMS_3];
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t maxdims[DIMS_3];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[NUM_DIMSCALES2], vars_dimscale_obj[NUM_DIMSCALES2];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
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;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = TIME_LEN;
if ((time_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LEN_LEN;
if ((len_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
dims[2] = TIME_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_3, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
if ((time_dimscaleid = H5Dcreate1(fileid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(time_dimscaleid, NULL) < 0) ERR;
if ((len_dimscaleid = H5Dcreate1(fileid, LEN_NAME, H5T_NATIVE_INT,
len_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(len_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these three dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME1, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, time_dimscaleid, 2) < 0) ERR;
/* Attach a dimscale to a dimscale. Unfortunately, HDF5 does not
* allow this. Woe is me. */
/*if (H5DSattach_scale(time_dimscaleid, len_dimscaleid, 0) < 0) ERR;*/
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(time_dimscaleid) < 0 ||
H5Dclose(len_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(time_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Sclose(len_spaceid) < 0 ||
H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
/** Read/write a hyperslab of data, performing dimension remapping
* and data rescaling as needed.
*/
static int mirw_hyperslab_icv(int opcode,
mihandle_t volume,
mitype_t buffer_data_type,
const misize_t start[],
const misize_t count[],
void *buffer)
{
hid_t dset_id = -1;
hid_t mspc_id = -1;
hid_t fspc_id = -1;
hid_t buffer_type_id = -1;
int result = MI_ERROR;
hsize_t hdf_start[MI2_MAX_VAR_DIMS];
hsize_t hdf_count[MI2_MAX_VAR_DIMS];
int dir[MI2_MAX_VAR_DIMS]; /* Direction vector in file order */
hsize_t ndims;
int slice_ndims;
int n_different = 0;
double volume_valid_min, volume_valid_max;
misize_t buffer_size;
void *temp_buffer=NULL;
size_t icount[MI2_MAX_VAR_DIMS];
int idir[MI2_MAX_VAR_DIMS];
int imap[MI2_MAX_VAR_DIMS];
double *image_slice_max_buffer=NULL;
double *image_slice_min_buffer=NULL;
int scaling_needed=0;
char path[MI2_MAX_PATH];
hsize_t image_slice_start[MI2_MAX_VAR_DIMS];
hsize_t image_slice_count[MI2_MAX_VAR_DIMS];
hsize_t image_slice_length=0;
hsize_t total_number_of_slices=0;
hsize_t i;
int j;
/* Disallow write operations to anything but the highest resolution.
*/
if (opcode == MIRW_OP_WRITE && volume->selected_resolution != 0) {
return MI_LOG_ERROR(MI2_MSG_GENERIC,"Trying to write to a volume thumbnail");
}
sprintf(path, MI_ROOT_PATH "/image/%d/image", volume->selected_resolution);
/*printf("Using:%s\n",path);*/
/* Open the dataset with the specified path
*/
MI_CHECK_HDF_CALL(dset_id = H5Dopen1(volume->hdf_id, path),"H5Dopen1");
if (dset_id < 0) {
return (MI_ERROR);
}
MI_CHECK_HDF_CALL(fspc_id = H5Dget_space(dset_id),"H5Dget_space");
if (fspc_id < 0) {
goto cleanup;
}
buffer_type_id = mitype_to_hdftype(buffer_data_type, TRUE);
if(buffer_type_id<0)
{
goto cleanup;
}
ndims = volume->number_of_dims;
if (ndims == 0) {
/* A scalar volume is possible but extremely unlikely, not to
* mention useless!
*/
mspc_id = H5Screate(H5S_SCALAR);
hdf_count[0]=1;
} else {
n_different = mitranslate_hyperslab_origin(volume, start, count, hdf_start, hdf_count, dir);
mspc_id = H5Screate_simple(ndims, hdf_count, NULL);
if (mspc_id < 0) {
fprintf(stderr,"H5Screate_simple: Fail %s:%d\n",__FILE__,__LINE__);
goto cleanup;
}
}
miget_hyperslab_size_hdf(buffer_type_id, ndims, hdf_count, &buffer_size);
MI_CHECK_HDF_CALL(result = H5Sselect_hyperslab(fspc_id, H5S_SELECT_SET, hdf_start, NULL,
hdf_count, NULL),"H5Sselect_hyperslab");
if (result < 0) {
goto cleanup;
}
if((result=miget_volume_valid_range( volume, &volume_valid_max, &volume_valid_min))<0)
{
goto cleanup;
}
#ifdef _DEBUG
printf("mirw_hyperslab_icv:Volume:%lx valid_max:%f valid_min:%f scaling:%d n_different:%d\n",(long int)(volume),volume_valid_max,volume_valid_min,volume->has_slice_scaling,n_different);
#endif
if(volume->has_slice_scaling)
{
hid_t image_max_fspc_id;
hid_t image_min_fspc_id;
hid_t scaling_mspc_id;
total_number_of_slices=1;
image_slice_length=1;
scaling_needed=1;
image_max_fspc_id=H5Dget_space(volume->imax_id);
image_min_fspc_id=H5Dget_space(volume->imin_id);
if ( image_max_fspc_id < 0 ) {
/*Report error that image-max is not found!*/
return ( MI_ERROR );
}
slice_ndims = H5Sget_simple_extent_ndims ( image_max_fspc_id );
if(slice_ndims<0)
{
/*TODO: report read error somehow*/
fprintf(stderr,"H5Sget_simple_extent_ndims: Fail %s:%d\n",__FILE__,__LINE__);
goto cleanup;
}
if ( (hsize_t)slice_ndims > ndims ) { /*Can this really happen?*/
slice_ndims = ndims;
}
for ( j = 0; j < slice_ndims; j++ ) {
image_slice_count[j] = hdf_count[j];
image_slice_start[j] = hdf_start[j];
if(hdf_count[j]>1) /*avoid zero sized dimensions?*/
total_number_of_slices*=hdf_count[j];
}
for (i = slice_ndims; i < ndims; i++ ) {
if(hdf_count[i]>1) /*avoid zero sized dimensions?*/
image_slice_length*=hdf_count[i];
image_slice_count[i] = 0;
image_slice_start[i] = 0;
}
image_slice_max_buffer=malloc(total_number_of_slices*sizeof(double));
if(!image_slice_max_buffer)
{
result=MI_ERROR;
MI_LOG_ERROR(MI2_MSG_OUTOFMEM,total_number_of_slices*sizeof(double));
goto cleanup;
}
image_slice_min_buffer=malloc(total_number_of_slices*sizeof(double));
if(!image_slice_min_buffer)
{
result=MI_ERROR;
MI_LOG_ERROR(MI2_MSG_OUTOFMEM,total_number_of_slices*sizeof(double));
goto cleanup;
}
scaling_mspc_id = H5Screate_simple(slice_ndims, image_slice_count, NULL);
if( (result=H5Sselect_hyperslab(image_max_fspc_id, H5S_SELECT_SET, image_slice_start, NULL, image_slice_count, NULL))>=0 )
{
if((result=H5Dread(volume->imax_id, H5T_NATIVE_DOUBLE, scaling_mspc_id, image_max_fspc_id, H5P_DEFAULT,image_slice_max_buffer))<0)
{
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Dread");
goto cleanup;
}
} else {
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Sselect_hyperslab");
goto cleanup;
}
if((result=H5Sselect_hyperslab(image_min_fspc_id, H5S_SELECT_SET, image_slice_start, NULL, image_slice_count, NULL))>=0 )
{
if((result=H5Dread(volume->imin_id, H5T_NATIVE_DOUBLE, scaling_mspc_id, image_min_fspc_id, H5P_DEFAULT,image_slice_min_buffer))<0)
{
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Dread");
goto cleanup;
}
} else {
/*TODO: report read error somehow*/
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Sselect_hyperslab");
goto cleanup;
}
H5Sclose(scaling_mspc_id);
H5Sclose(image_max_fspc_id);
} else {
slice_ndims=0;
total_number_of_slices=1;
image_slice_max_buffer=malloc(sizeof(double));
image_slice_min_buffer=malloc(sizeof(double));
miget_volume_range(volume,image_slice_max_buffer,image_slice_min_buffer);
image_slice_length=1;
/*it produces unity scaling*/
scaling_needed=(*image_slice_max_buffer!=volume_valid_max) || (*image_slice_min_buffer!=volume_valid_min);
for (i = 0; i < ndims; i++) {
image_slice_length *= hdf_count[i];
}
#ifdef _DEBUG
printf("mirw_hyperslab_icv:Real max:%f min:%f\n",*image_slice_max_buffer,*image_slice_min_buffer);
#endif
}
//A hack to disable interslice scaling when it is not needed according to MINC1 specs
if( volume->volume_type==MI_TYPE_FLOAT || volume->volume_type==MI_TYPE_DOUBLE ||
volume->volume_type==MI_TYPE_FCOMPLEX || volume->volume_type==MI_TYPE_DCOMPLEX )
{
scaling_needed=0;
}
#ifdef _DEBUG
printf("mirw_hyperslab_icv:Slice_ndim:%d total_number_of_slices:%d image_slice_length:%d scaling_needed:%d\n",slice_ndims,total_number_of_slices,image_slice_length,scaling_needed);
#endif
if (opcode == MIRW_OP_READ)
{
MI_CHECK_HDF_CALL(result = H5Dread(dset_id, buffer_type_id, mspc_id, fspc_id, H5P_DEFAULT, buffer),"H5Dread");
if(result<0)
{
goto cleanup;
}
if(scaling_needed)
{
switch(buffer_data_type)
{
case MI_TYPE_FLOAT:
#ifdef _DEBUG
printf("Descaling float\n");
#endif
APPLY_DESCALING(float,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_DOUBLE:
#ifdef _DEBUG
printf("Descaling double\n");
#endif
APPLY_DESCALING(double,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_INT:
#ifdef _DEBUG
printf("Descaling int\n");
#endif
APPLY_DESCALING(int,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_UINT:
#ifdef _DEBUG
printf("Descaling uint\n");
#endif
APPLY_DESCALING(unsigned int,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_SHORT:
#ifdef _DEBUG
printf("Descaling short\n");
#endif
APPLY_DESCALING(short,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_USHORT:
#ifdef _DEBUG
printf("Descaling ushort\n");
#endif
APPLY_DESCALING(unsigned short,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_BYTE:
#ifdef _DEBUG
printf("Descaling byte\n");
#endif
APPLY_DESCALING(char,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_UBYTE:
#ifdef _DEBUG
printf("Descaling ubyte\n");
#endif
APPLY_DESCALING(unsigned char,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
default:
/*TODO: report unsupported conversion*/
result=MI_ERROR;
goto cleanup;
}
} else {
#ifdef _DEBUG
printf("Descaling not needed!\n");
#endif
}
if (n_different != 0 ) {
for (i = 0; i < ndims; i++) {
icount[i] = count[i];
}
restructure_array(ndims, buffer, icount, H5Tget_size(buffer_type_id),volume->dim_indices, dir);
/*TODO: check if we managed to restructure the array*/
result=0;
}
} else { /*opcode != MIRW_OP_READ*/
volume->is_dirty = TRUE; /* Mark as modified. */
if (n_different != 0 ) {
/* Invert before calling */
for (i = 0; i < ndims; i++) {
icount[volume->dim_indices[i]] = count[i];
idir[volume->dim_indices[i]] = dir[i];
/* this one was correct the original way*/
imap[volume->dim_indices[i]] = i;
}
}
if(scaling_needed || n_different != 0)
{
/*create temporary copy, to be destroyed*/
temp_buffer=malloc(buffer_size);
if(!temp_buffer)
{
MI_LOG_ERROR(MI2_MSG_OUTOFMEM,buffer_size);
result=MI_ERROR; /*TODO: error code?*/
goto cleanup;
}
memcpy(temp_buffer,buffer,buffer_size);
if (n_different != 0 )
restructure_array(ndims, temp_buffer, icount, H5Tget_size(buffer_type_id), imap, idir);
if(scaling_needed)
{
switch(buffer_data_type)
{
case MI_TYPE_FLOAT:
#ifdef _DEBUG
printf("scaling float\n");
#endif
APPLY_SCALING(float,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_DOUBLE:
#ifdef _DEBUG
printf("scaling double\n");
#endif
APPLY_SCALING(double,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_INT:
#ifdef _DEBUG
printf("scaling int\n");
#endif
APPLY_SCALING(int,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_UINT:
#ifdef _DEBUG
printf("scaling unsigned int\n");
#endif
APPLY_SCALING(unsigned int,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_SHORT:
#ifdef _DEBUG
printf("scaling short\n");
#endif
APPLY_SCALING(short,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_USHORT:
#ifdef _DEBUG
printf("scaling unsigned short\n");
#endif
APPLY_SCALING(unsigned short,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_BYTE:
#ifdef _DEBUG
printf("scaling char\n");
#endif
APPLY_SCALING(char,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
case MI_TYPE_UBYTE:
#ifdef _DEBUG
printf("scaling unsigned char\n");
#endif
APPLY_SCALING(unsigned char,temp_buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max);
break;
default:
/*TODO: report unsupported conversion*/
result=MI_ERROR;
goto cleanup;
}
}
MI_CHECK_HDF_CALL(result = H5Dwrite(dset_id, buffer_type_id, mspc_id, fspc_id, H5P_DEFAULT, temp_buffer),"H5Dwrite");
} else {
MI_CHECK_HDF_CALL(result = H5Dwrite(dset_id, buffer_type_id, mspc_id, fspc_id, H5P_DEFAULT, buffer),"H5Dwrite");
}
if(result<0)
{
goto cleanup;
}
}
cleanup:
if (buffer_type_id >= 0) {
H5Tclose(buffer_type_id);
}
if (mspc_id >= 0) {
H5Sclose(mspc_id);
}
if (fspc_id >= 0) {
H5Sclose(fspc_id);
}
if ( dset_id >=0 ) {
H5Dclose(dset_id);
}
if(temp_buffer!=NULL)
{
free(temp_buffer);
}
if(image_slice_min_buffer!=NULL)
{
free(image_slice_min_buffer);
}
if(image_slice_max_buffer!=NULL)
{
free(image_slice_max_buffer);
}
return (result);
}
/** Read/write a hyperslab of data, performing dimension remapping
* and data rescaling as needed. Data in the range (min-max) will map to the appropriate full range of buffer_data_type
*/
static int mirw_hyperslab_normalized(int opcode,
mihandle_t volume,
mitype_t buffer_data_type,
const misize_t start[],
const misize_t count[],
double data_min,
double data_max,
void *buffer)
{
hid_t dset_id = -1;
hid_t mspc_id = -1;
hid_t fspc_id = -1;
hid_t volume_type_id = -1;
hid_t buffer_type_id = -1;
int result = MI_ERROR;
hsize_t hdf_start[MI2_MAX_VAR_DIMS];
hsize_t hdf_count[MI2_MAX_VAR_DIMS];
int dir[MI2_MAX_VAR_DIMS]; /* Direction vector in file order */
hsize_t ndims;
int slice_ndims;
int n_different = 0;
double volume_valid_min, volume_valid_max;
misize_t buffer_size;
misize_t input_buffer_size;
double *temp_buffer=NULL;
size_t icount[MI2_MAX_VAR_DIMS];
int idir[MI2_MAX_VAR_DIMS];
int imap[MI2_MAX_VAR_DIMS];
double *image_slice_max_buffer=NULL;
double *image_slice_min_buffer=NULL;
char path[MI2_MAX_PATH];
hsize_t image_slice_start[MI2_MAX_VAR_DIMS];
hsize_t image_slice_count[MI2_MAX_VAR_DIMS];
hsize_t image_slice_length=0;
hsize_t total_number_of_slices=0;
hsize_t i;
int j;
/* Disallow write operations to anything but the highest resolution.
*/
if (opcode == MIRW_OP_WRITE && volume->selected_resolution != 0) {
/*TODO: report error that we are not dealing with the rihgt image here*/
return (MI_ERROR);
}
sprintf(path, MI_ROOT_PATH "/image/%d/image", volume->selected_resolution);
/* Open the dataset with the specified path
*/
MI_CHECK_HDF_CALL(dset_id = H5Dopen1(volume->hdf_id, path),"H5Dopen1");
if (dset_id < 0) {
return (MI_ERROR);
}
MI_CHECK_HDF_CALL(fspc_id = H5Dget_space(dset_id),"H5Dget_space");
if (fspc_id < 0) {
/*TODO: report can't get dataset*/
goto cleanup;
}
buffer_type_id = mitype_to_hdftype(buffer_data_type,TRUE);
if(buffer_type_id<0)
{
goto cleanup;
}
MI_CHECK_HDF_CALL(volume_type_id = H5Tcopy ( H5T_NATIVE_DOUBLE ),"H5Tcopy");
if(volume_type_id<0)
{
fprintf(stderr,"H5Tcopy: Fail %s:%d\n",__FILE__,__LINE__);
goto cleanup;
}
ndims = volume->number_of_dims;
if (ndims == 0) {
/* A scalar volume is possible but extremely unlikely, not to
* mention useless!
*/
mspc_id = H5Screate(H5S_SCALAR);
} else {
n_different = mitranslate_hyperslab_origin(volume,start,count, hdf_start,hdf_count,dir);
MI_CHECK_HDF_CALL(mspc_id = H5Screate_simple(ndims, hdf_count, NULL),"H5Screate_simple");
if (mspc_id < 0) {
goto cleanup;
}
}
miget_hyperslab_size_hdf(volume_type_id,ndims,hdf_count,&buffer_size);
miget_hyperslab_size_hdf(buffer_type_id,ndims,hdf_count,&input_buffer_size);
MI_CHECK_HDF_CALL(result = H5Sselect_hyperslab(fspc_id, H5S_SELECT_SET, hdf_start, NULL,
hdf_count, NULL),"H5Sselect_hyperslab");
if (result < 0) {
goto cleanup;
}
miget_volume_valid_range( volume, &volume_valid_max, &volume_valid_min);
#ifdef _DEBUG
printf("mirw_hyperslab_normalized:Volume:%x valid_max:%f valid_min:%f scaling:%d\n",volume,volume_valid_max,volume_valid_min,volume->has_slice_scaling);
#endif
if(volume->has_slice_scaling &&
!(volume->volume_type==MI_TYPE_FLOAT || volume->volume_type==MI_TYPE_DOUBLE ||
volume->volume_type==MI_TYPE_FCOMPLEX || volume->volume_type==MI_TYPE_DCOMPLEX) )
{
hid_t image_max_fspc_id;
hid_t image_min_fspc_id;
hid_t scaling_mspc_id;
total_number_of_slices=1;
image_slice_length=1;
MI_CHECK_HDF_CALL(image_max_fspc_id=H5Dget_space(volume->imax_id),"H5Dget_space");
MI_CHECK_HDF_CALL(image_min_fspc_id=H5Dget_space(volume->imin_id),"H5Dget_space");
if ( image_max_fspc_id < 0 || image_min_fspc_id<0 ) {
result=MI_ERROR;
goto cleanup;
}
MI_CHECK_HDF_CALL(slice_ndims = H5Sget_simple_extent_ndims ( image_max_fspc_id ),"H5Sget_simple_extent_ndims");
if(slice_ndims<0)
{
goto cleanup;
}
if ( (hsize_t)slice_ndims > ndims ) { /*Can this really happen?*/
slice_ndims = ndims;
}
for ( j = 0; j < slice_ndims; j++ ) {
image_slice_count[j] = hdf_count[j];
image_slice_start[j] = hdf_start[j];
if(hdf_count[j]>1) /*avoid zero sized dimensions?*/
total_number_of_slices*=hdf_count[j];
}
for (i = slice_ndims; i < ndims; i++ ) {
if(hdf_count[i]>1) /*avoid zero sized dimensions?*/
image_slice_length*=hdf_count[i];
image_slice_count[i] = 0;
image_slice_start[i] = 0;
}
image_slice_max_buffer=malloc(total_number_of_slices*sizeof(double));
image_slice_min_buffer=malloc(total_number_of_slices*sizeof(double));
/*TODO check for allocation failure ?*/
MI_CHECK_HDF_CALL(scaling_mspc_id = H5Screate_simple(slice_ndims, image_slice_count, NULL),"H5Screate_simple");
if( (result=H5Sselect_hyperslab(image_max_fspc_id, H5S_SELECT_SET, image_slice_start, NULL, image_slice_count, NULL))>=0 )
{
if( ( result=H5Dread(volume->imax_id, H5T_NATIVE_DOUBLE, scaling_mspc_id, image_max_fspc_id, H5P_DEFAULT,image_slice_max_buffer))<0)
{
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Dread");
goto cleanup;
}
} else {
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Sselect_hyperslab");
goto cleanup;
}
if( (result=H5Sselect_hyperslab(image_min_fspc_id, H5S_SELECT_SET, image_slice_start, NULL, image_slice_count, NULL))>=0 )
{
if( (result=H5Dread(volume->imin_id, H5T_NATIVE_DOUBLE, scaling_mspc_id, image_min_fspc_id, H5P_DEFAULT,image_slice_min_buffer))<0)
{
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Dread");
goto cleanup;
}
} else {
MI_LOG_ERROR(MI2_MSG_HDF5,"H5Sselect_hyperslab");
goto cleanup;
}
H5Sclose(scaling_mspc_id);
H5Sclose(image_max_fspc_id);
} else {
slice_ndims=0;
total_number_of_slices=1;
image_slice_max_buffer=malloc(sizeof(double));
image_slice_min_buffer=malloc(sizeof(double));
miget_volume_range( volume,image_slice_max_buffer,image_slice_min_buffer );
image_slice_length=1;
for (i = 0; i < ndims; i++) {
image_slice_length *= hdf_count[i];
}
#ifdef _DEBUG
printf("mirw_hyperslab_normalized:Real max:%f min:%f\n",*image_slice_max_buffer,*image_slice_min_buffer);
#endif
}
#ifdef _DEBUG
printf("mirw_hyperslab_normalized:Slice_ndim:%d total_number_of_slices:%d image_slice_length:%d\n",slice_ndims,total_number_of_slices,image_slice_length);
printf("mirw_hyperslab_normalized:data min:%f data max:%f buffer_data_type:%d\n",data_min,data_max,buffer_data_type);
#endif
/*Allocate temporary Buffer*/
temp_buffer=(double*)malloc(buffer_size);
if(!temp_buffer)
{
MI_LOG_ERROR(MI2_MSG_OUTOFMEM,buffer_size);
result=MI_ERROR;
goto cleanup;
}
if (opcode == MIRW_OP_READ)
{
MI_CHECK_HDF_CALL(result = H5Dread(dset_id, volume_type_id, mspc_id, fspc_id, H5P_DEFAULT, temp_buffer),"H5Dread");
if(result<0)
{
goto cleanup;
}
/*WARNING: floating point types will be normalized between 0.0 and 1.0*/
switch(buffer_data_type)
{
case MI_TYPE_FLOAT:
APPLY_DESCALING_NORM(float,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,0.0f,1.0f);
break;
case MI_TYPE_DOUBLE:
APPLY_DESCALING_NORM(double,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,0.0,1.0);
break;
case MI_TYPE_INT:
APPLY_DESCALING_NORM(int,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,INT_MIN,INT_MAX);
break;
case MI_TYPE_UINT:
APPLY_DESCALING_NORM(unsigned int,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,0,UINT_MAX);
break;
case MI_TYPE_SHORT:
APPLY_DESCALING_NORM(short,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,SHRT_MIN,SHRT_MAX);
break;
case MI_TYPE_USHORT:
APPLY_DESCALING_NORM(unsigned short,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,0,USHRT_MAX);
break;
case MI_TYPE_BYTE:
APPLY_DESCALING_NORM(char,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,SCHAR_MIN,SCHAR_MAX);
break;
case MI_TYPE_UBYTE:
APPLY_DESCALING_NORM(unsigned char,temp_buffer,buffer,image_slice_length,total_number_of_slices,image_slice_min_buffer,image_slice_max_buffer,volume_valid_min,volume_valid_max,data_min,data_max,0,UCHAR_MAX);
break;
default:
/*TODO: report unsupported conversion*/
result=MI_ERROR;
goto cleanup;
}
if (n_different != 0 ) {
for (i = 0; i < ndims; i++) {
icount[i] = count[i];
}
restructure_array(ndims, buffer, icount, H5Tget_size(buffer_type_id),volume->dim_indices, dir);
/*TODO: check if we managed to restructure the array*/
result=0;
}
} else { /*opcode != MIRW_OP_READ*/
void UPCdata::readHDFfile(char* filename, int count){ // count: 11040 for segmentation and 14640 for classification
#if HDF5_AVAILABLE==2
// based on http://www.hdfgroup.org/HDF5/doc/cpplus_RM/readdata_8cpp-example.html
// maybe first deleting all data? does it do that automatically or is there some possible memory leak?
// I need to know first the data set sizes... so I create one dummy sample... this is only a hack
samples.resize(0);
/*
Sample dummy;
dummy.data.resize(1020,0);
dummy.concentrations[0]=1;dummy.concentrations[1]=1;dummy.concentrations[2]=1;
dummy.samplenr=1;
dummy.set=Sample::Training;
dummy.compoundnr=1;
*/
const int NFIELDS = 5;
hsize_t chunk_size = 10; // ??
typedef struct _samplestruct{
int concentrations[3];
int samplenr;
int set;
int compoundnr;
float data[1020]; // having difficulties here; dynamic allocation?
}samplestruct;
samplestruct *sampledata;
void *sampleptr = malloc(NRECORDS*sizeof(samplestruct));
sampledata = (samplestruct*)sampleptr;
if (sampleptr == NULL) {
// Memory could not be allocated, the program should handle the error here as appropriate.
cout << "memory could not be allocated!";
return;
}
// ...
// free(samplestruct);
/* size_t dst_size = sizeof(Sample);
size_t dst_offset[NFIELDS] = {
HOFFSET(Sample, concentrations),
HOFFSET(Sample, samplenr),
HOFFSET(Sample, set),
HOFFSET(Sample, compoundnr),
HOFFSET(Sample, data)
};
size_t dst_sizes[NFIELDS] = { sizeof( samples[0].data),
sizeof(samples[0].concentrations),
sizeof(samples[0].samplenr),
sizeof(samples[0].set),
sizeof(samples[0].compoundnr)};
*/
size_t dst_size = sizeof(samplestruct);
size_t dst_offset[NFIELDS] = {HOFFSET(samplestruct, concentrations),
HOFFSET(samplestruct, samplenr),
HOFFSET(samplestruct, set),
HOFFSET(samplestruct, compoundnr),
HOFFSET(samplestruct, data),
};
size_t dst_sizes[NFIELDS] = { sizeof( sampledata[0].data),
sizeof(sampledata[0].concentrations),
sizeof(sampledata[0].samplenr),
sizeof(sampledata[0].set),
sizeof(sampledata[0].compoundnr)
};
hid_t file_id;
int *fill_data = NULL;
int compress = 1;
herr_t status;
//const hsize_t datadim[] = {samples[0].data.size()};
const hsize_t datadim[] = {1020*sizeof(float)};
const hsize_t concdim[] = {3};
hid_t floatarray = H5Tarray_create(H5T_NATIVE_FLOAT, 1, datadim);
hid_t concarray = H5Tarray_create(H5T_NATIVE_FLOAT, 1, concdim);
// Initialize field_type
hid_t field_type[NFIELDS];
field_type[0] = floatarray;
field_type[1] = concarray;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_INT;
field_type[4] = H5T_NATIVE_INT;
// opening file
file_id=H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if ( file_id < 0 ){
std::cout << "UPCdata::readHDFfile(): Error opening " << filename <<": " << file_id << std::endl;
return;
}
//const int NRECORDS=samples.size(); // how to get the data set size?
// is this the way?
hid_t dataset_id=H5Dopen1(file_id, "Dataset");
hsize_t size = H5Dget_storage_size(dataset_id);
//vector<Sample> buf(NRECORDS+1);
//vector<Sample> buf(static_cast<int>(size+1), 0x00);
status=H5TBread_table(file_id, "Dataset", dst_size, dst_offset, dst_sizes, sampledata);
cout << "converting data format" << endl;
for(int i=0;i<NRECORDS;i++){
Sample dummysample;
dummysample.concentrations[0]=sampledata[i].concentrations[0];
dummysample.concentrations[1]=sampledata[i].concentrations[1];
dummysample.concentrations[2]=sampledata[i].concentrations[2];
dummysample.samplenr=sampledata[i].samplenr;
dummysample.set=(Sample::SetType)sampledata[i].set;
dummysample.compoundnr=sampledata[i].compoundnr;
dummysample.data.resize(1020);
for(int j=0;j<1020;j++)
dummysample.data[j]=sampledata[i].data[j];
samples.push_back(dummysample);
}
// close type(s)??
// close the file /
H5Fclose( file_id );
#endif
}
/** Read/write a hyperslab of data. This is the simplified function
* which performs no value conversion. It is much more efficient than
* mirw_hyperslab_icv()
*/
static int mirw_hyperslab_raw(int opcode,
mihandle_t volume,
mitype_t midatatype,
const misize_t start[],
const misize_t count[],
void *buffer)
{
hid_t dset_id = -1;
hid_t mspc_id = -1;
hid_t fspc_id = -1;
hid_t type_id = -1;
int result = MI_ERROR;
hsize_t hdf_start[MI2_MAX_VAR_DIMS];
hsize_t hdf_count[MI2_MAX_VAR_DIMS];
int dir[MI2_MAX_VAR_DIMS]; /* Direction vector in file order */
int ndims;
int n_different = 0;
misize_t buffer_size;
void *temp_buffer=NULL;
char path[MI2_MAX_PATH];
size_t icount[MI2_MAX_VAR_DIMS];
/* Disallow write operations to anything but the highest resolution.
*/
if (opcode == MIRW_OP_WRITE && volume->selected_resolution != 0) {
return MI_LOG_ERROR(MI2_MSG_GENERIC,"Trying to write to a volume thumbnail");
}
sprintf(path, MI_ROOT_PATH "/image/%d/image", volume->selected_resolution);
/*printf("Using:%s\n",path);*/
/* Open the dataset with the specified path
*/
MI_CHECK_HDF_CALL(dset_id = H5Dopen1(volume->hdf_id, path),"H5Dopen1");
if (dset_id < 0) {
return (MI_ERROR);
}
MI_CHECK_HDF_CALL(fspc_id = H5Dget_space(dset_id),"H5Dget_space");
if (fspc_id < 0) {
/*TODO: report can't get dataset*/
goto cleanup;
}
MI_CHECK_HDF_CALL(fspc_id = H5Dget_space(dset_id),"H5Dget_space");
if (fspc_id < 0) {
goto cleanup;
}
if (midatatype == MI_TYPE_UNKNOWN) {
type_id = H5Tcopy(volume->mtype_id);
} else {
type_id = mitype_to_hdftype(midatatype, TRUE);
}
ndims = volume->number_of_dims;
if (ndims == 0) {
/* A scalar volume is possible but extremely unlikely, not to
* mention useless!
*/
mspc_id = H5Screate(H5S_SCALAR);
} else {
n_different = mitranslate_hyperslab_origin(volume, start, count, hdf_start, hdf_count, dir);
MI_CHECK_HDF_CALL(mspc_id = H5Screate_simple(ndims, hdf_count, NULL),"H5Screate_simple");
if (mspc_id < 0) {
goto cleanup;
}
}
MI_CHECK_HDF_CALL(result = H5Sselect_hyperslab(fspc_id, H5S_SELECT_SET, hdf_start, NULL,
hdf_count, NULL),"H5Sselect_hyperslab");
if (result < 0) {
goto cleanup;
}
miget_hyperslab_size_hdf(type_id,ndims,hdf_count,&buffer_size);
if (opcode == MIRW_OP_READ) {
MI_CHECK_HDF_CALL(result = H5Dread(dset_id, type_id, mspc_id, fspc_id, H5P_DEFAULT,buffer),"H5Dread");
/* Restructure the array after reading the data in file orientation.
*/
if (n_different != 0) {
int i;
for (i = 0; i < ndims; i++) {
icount[i] = count[i];
}
restructure_array(ndims, buffer, icount, H5Tget_size(type_id),
volume->dim_indices, dir);
}
} else {
volume->is_dirty = TRUE; /* Mark as modified. */
/* Restructure array before writing to file.
* TODO: use temporary buffer for that!
*/
if (n_different != 0) {
int idir[MI2_MAX_VAR_DIMS];
int imap[MI2_MAX_VAR_DIMS];
int i;
/* Invert before calling */
for (i = 0; i < ndims; i++) {
icount[volume->dim_indices[i]] = count[i];
idir[volume->dim_indices[i]] = dir[i];
// this one was correct the original way
imap[volume->dim_indices[i]] = i;
}
/*Use temporary array to preserve input data*/
temp_buffer=malloc(buffer_size);
if(temp_buffer==NULL)
{
/*TODO: report memory error*/
result=MI_ERROR;
goto cleanup;
}
memcpy(temp_buffer,buffer,buffer_size);
restructure_array(ndims, temp_buffer, icount, H5Tget_size(type_id),
imap, idir);
MI_CHECK_HDF_CALL(result = H5Dwrite(dset_id, type_id, mspc_id, fspc_id, H5P_DEFAULT,
temp_buffer),"H5Dwrite");
} else {
MI_CHECK_HDF_CALL(result = H5Dwrite(dset_id, type_id, mspc_id, fspc_id, H5P_DEFAULT,
buffer),"H5Dwrite");
}
}
cleanup:
if (type_id >= 0) {
H5Tclose(type_id);
}
if (mspc_id >= 0) {
H5Sclose(mspc_id);
}
if (fspc_id >= 0) {
H5Sclose(fspc_id);
}
if ( dset_id >=0 ) {
H5Dclose(dset_id);
}
if ( temp_buffer!= NULL) {
free( temp_buffer );
}
return (result);
}
//*****************************************************************************
// CONSTRUCTOR: ossimHdfGridModel(filename)
//
// Constructs model from geometry file
//
//*****************************************************************************
ossimHdfGridModel::ossimHdfGridModel(const ossimFilename& file,
const ossimDrect& imageRect,
ossimString latGridIndexOrName,
ossimString lonGridIndexOrName,
const ossimIpt& gridSpacing)
: ossimCoarseGridModel(),
m_isHdf4(true)
{
theLatGrid.setDomainType(ossimDblGrid::SAWTOOTH_90);
theLonGrid.setDomainType(ossimDblGrid::WRAP_180);
if (latGridIndexOrName.contains("/Latitude") == false &&
lonGridIndexOrName.contains("/Longitude") == false)//hdf4
{
ossim_int32 latGridIndex = ossimString::toInt(latGridIndexOrName);
ossim_int32 lonGridIndex = ossimString::toInt(lonGridIndexOrName);
int32 sd_id = SDstart(file.c_str(), DFACC_READ);
if (sd_id > 0)
{
int32 sds_id = SDselect(sd_id, latGridIndex);
if (sds_id > 0)
{
setGridNodes(theLatGrid, sds_id, gridSpacing);
}
SDendaccess (sds_id);
sds_id = SDselect(sd_id, lonGridIndex);
if (sds_id > 0)
{
setGridNodes(theLonGrid, sds_id, gridSpacing);
}
SDendaccess (sds_id);
}
SDend(sd_id);
}
else //hdf5
{
m_isHdf4 = false;
ossim_int32 file_id = H5Fopen(file.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
// Depreciated, need to fix... (drb)
// ossim_int32 dataset_id = H5Dopen(file_id, latGridIndexOrName);
ossim_int32 dataset_id = H5Dopen1(file_id, latGridIndexOrName);
if (dataset_id >= 0)
{
setGridNodes(theLatGrid, dataset_id, gridSpacing);
}
H5Dclose(dataset_id);
// Depreciated, need to fix... (drb)
// dataset_id = H5Dopen(file_id, lonGridIndexOrName);
dataset_id = H5Dopen1(file_id, lonGridIndexOrName);
if (dataset_id > 0)
{
setGridNodes(theLatGrid, dataset_id, gridSpacing);
}
H5Dclose(dataset_id);
H5Fclose(file_id);
}
// Filter this HDF data as it is often very noisy:
double filter_kernel[81];
double weight = 1.0/81.0;
for (int i=0; i<81; i++)
filter_kernel[i] = weight;
theLatGrid.filter(9,9, filter_kernel);
theLonGrid.filter(9,9, filter_kernel);
theLatGrid.enableExtrapolation();
theLonGrid.enableExtrapolation();
theHeightEnabledFlag = false;
initializeModelParams(imageRect);
//debugDump(); //###
}
void readSpectrumEnergyScale(cGlobal *global, char *filename) {
char groupname[1024];
char fieldname[1024];
hid_t file_id;
hid_t datagroup_id;
hid_t dataset_id;
hid_t dataspace_id;
hid_t datatype_id;
H5T_class_t dataclass;
size_t size;
int ndims;
sprintf(groupname, "energySpectrum");
sprintf(fieldname, "runIntegratedEnergyScale");
// Check if an energy scale calibration file has been specified
if ( strcmp(filename,"") == 0 ){
printf("spectrum energy scale calibration file path was not specified\n");
printf("spectra will be output with default (0) energy scale\n");
return;
}
// Check whether file exists!
FILE* fp = fopen(filename, "r");
if (fp) // file exists
fclose(fp);
else { // file doesn't exist
printf("specified energy scale calibration file does not exist: %s\n",filename);
printf("spectra will be output with default (0) energy scale\n");
return;
}
printf("Reading energy spectrum scale calibration file:\n");
printf("\t%s\n",filename);
// Open the file
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if(file_id < 0){
printf("ERROR: Could not open file %s\n",filename);
printf("spectra will be output with default (0) energy scale\n");
return;
}
// Open the dataset
datagroup_id = H5Gopen1(file_id, groupname);
dataset_id = H5Dopen1(datagroup_id, fieldname);
dataspace_id = H5Dget_space(dataset_id);
// Test if correct dimensions / size
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if(ndims != 1) {
printf("the specified file does not have the correct dimensions for energy scale calibration, ndims=%i\n",ndims);
printf("spectra will be output with default (0) energy scale\n");
return;
}
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dataspace_id,dims,NULL);
if (dims[0]!=1 || dims[1]!=(hsize_t)global->espectrumLength) {
printf("the specified file does not have the correct dimensions for energy scale calibration\n");
printf("spectra will be output with default (0) energy scale\n");
return;
}
datatype_id = H5Dget_type(dataset_id);
dataclass = H5Tget_class(datatype_id);
size = H5Tget_size(datatype_id);
double* energyscale = (double *) calloc(global->espectrumLength, sizeof(double));
H5Dread(dataset_id, datatype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, energyscale);
for(int i=0; i<global->espectrumLength; i++) {
global->espectrumScale[i] = energyscale[i];
}
free(energyscale);
// Close and cleanup
H5Dclose(dataset_id);
H5Gclose(datagroup_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
printf("energy spectrum scale calibration file read successful:\n");
return;
}
int AMRreader::
readAMRadditionData()
{
hid_t file_id = H5Fopen( filename_.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
if( file_id<0 ) {
debug1 << "Failed to open AMR file: " << filename_ << " when read in mesh.\n";
return -1;
}
hid_t gid = H5Gopen1( file_id, amr_grpname );
if( gid<0 ) {
debug1 << "Failed to open AMR group in " << filename_ << " when read in mesh.\n";
return -2;
}
prebuf_ = new float[ blksz_*nblks_ ];
sndbuf_ = new float[ blksz_*nblks_ ];
tmpbuf_ = new float[ blksz_*nblks_ ];
if( prebuf_==NULL || sndbuf_==NULL || tmpbuf_==NULL ) {
debug1 << "Failed to allocate additional datbuf for " << filename_ << ".\n";
return -3;
}
hid_t datid = H5Dopen1( gid, amr_prename );
if( datid<0 ) {
debug1 << "Failed to open " << amr_prename << " data in " << filename_ << ".\n";
return -4;
}
herr_t herr = H5Dread( datid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, prebuf_ );
H5Dclose(datid);
if( herr<0 ) {
debug1 << "Failed to read " << amr_prename << " in " << filename_ << ".\n";
return -5;
}
datid = H5Dopen1( gid, amr_sndname );
if( datid<0 ) {
debug1 << "Failed to open " << amr_sndname << " data in " << filename_ << ".\n";
return -4;
}
herr = H5Dread( datid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, sndbuf_ );
H5Dclose(datid);
if( herr<0 ) {
debug1 << "Failed to read " << amr_sndname << " in " << filename_ << ".\n";
return -5;
}
datid = H5Dopen1( gid, amr_tmpname );
if( datid<0 ) {
debug1 << "Failed to open " << amr_tmpname << " data in " << filename_ << ".\n";
return -4;
}
herr = H5Dread( datid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, tmpbuf_ );
H5Dclose(datid);
if( herr<0 ) {
debug1 << "Failed to read " << amr_tmpname << " in " << filename_ << ".\n";
return -5;
}
H5Gclose( gid );
H5Fclose( file_id );
return 0;
}
void cData2d::readHDF5(char* filename, char* fieldname){
// Open the file
hid_t file_id;
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if(file_id < 0){
printf("ERROR: Could not open file %s\n",filename);
return;
}
// Open the dataset
hid_t dataset_id;
hid_t dataspace_id;
dataset_id = H5Dopen1(file_id, fieldname);
dataspace_id = H5Dget_space(dataset_id);
// Test if 2D data
int ndims;
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if(ndims != 2) {
printf("2dData::readHDF5: Not 2D data set, ndims=%i\n",ndims);
exit(0);
}
// Get dimensions of data set (nx, ny, nn)
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dataspace_id,dims,NULL);
ny = dims[0];
nx = dims[1];
nn = 1;
for(int i = 0;i<ndims;i++)
nn *= dims[i];
// Create space for the new data
free(data); data = NULL;
data = (tData2d *) calloc(nn, sizeof(tData2d));
// Read in data after setting up a temporary buffer of the appropriate variable type
// Somehow this works best when split out accordint to different data types
// Fix into general form later
hid_t datatype_id;
H5T_class_t dataclass;
size_t size;
datatype_id = H5Dget_type(dataset_id);
dataclass = H5Tget_class(datatype_id);
size = H5Tget_size(datatype_id);
if(dataclass == H5T_FLOAT){
if (size == sizeof(float)) {
float* buffer = (float *) calloc(nn, sizeof(float));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(double)) {
double* buffer = (double *) calloc(nn, sizeof(double));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown floating point type, size=%i\n",(int) size);
return;
}
}
else if(dataclass == H5T_INTEGER){
if (size == sizeof(char)) {
char* buffer = (char*) calloc(nn, sizeof(char));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(short)) {
short* buffer = (short*) calloc(nn, sizeof(short));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(int)) {
int* buffer = (int *) calloc(nn, sizeof(int));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(long)) {
long* buffer = (long *) calloc(nn, sizeof(long));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown integer type, size=%lu\n",size);
exit(1);
}
}
else {
printf("2dData::readHDF5: unknown HDF5 data type\n");
return;
}
// Close and cleanup
H5Dclose(dataset_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
}
int
main()
{
printf("\n*** Checking HDF5 group functions.\n");
printf("*** Checking out root group...");
{
hid_t fileid, grpid, access_plistid;
/* Open the root group of a new file. */
if ((access_plistid = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(access_plistid, H5F_CLOSE_SEMI)) ERR;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
access_plistid)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen file and root group. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR,
access_plistid)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
}
SUMMARIZE_ERR;
printf("*** Checking out H5Gmove...");
{
hid_t fileid, grpid;
hid_t datasetid, spaceid;
/* Create file with one dataset. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
if ((spaceid = H5Screate(H5S_SCALAR)) < 0) ERR;
if ((datasetid = H5Dcreate(grpid, DATASET_NAME, H5T_NATIVE_INT,
spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen file and check, then rename dataset. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
if ((datasetid = H5Dopen1(grpid, DATASET_NAME)) < 0) ERR;
if (H5Dclose(datasetid) < 0) ERR;
if (H5Gmove(grpid, DATASET_NAME, NEW_NAME) < 0) ERR;
if ((datasetid = H5Dopen1(grpid, NEW_NAME)) < 0) ERR;
if (H5Dclose(datasetid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
}
SUMMARIZE_ERR;
printf("*** Checking out sub-groups...");
{
hid_t fileid, grpid, subgrpid;
/* Create file with some nested groups. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, GRP_NAME, 0)) < 0) ERR;
if ((subgrpid = H5Gcreate(grpid, SUB_GRP_NAME, 0)) < 0) ERR;
if (H5Gclose(subgrpid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen file and discover groups. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, GRP_NAME)) < 0) ERR;
if ((subgrpid = H5Gopen(grpid, SUB_GRP_NAME)) < 0) ERR;
if (H5Gclose(subgrpid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking out UTF8 named sub-group...");
{
hid_t fileid, grpid, subgrpid;
/* Create file with nested group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, (char *)norm_utf8, 0)) < 0) ERR;
if ((subgrpid = H5Gcreate(grpid, SUB_GRP_NAME, 0)) < 0) ERR;
if (H5Gclose(subgrpid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen file and discover groups. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, (char *)norm_utf8)) < 0) ERR;
if ((subgrpid = H5Gopen(grpid, SUB_GRP_NAME)) < 0) ERR;
if (H5Gclose(subgrpid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking out UTF8 named sub-group with group creation ordering...");
{
hid_t fileid, grpid, subgrpid;
hid_t fapl_id, fcpl_id, gcpl_id;
/* Create file with nested group. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 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 ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if ((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((grpid = H5Gcreate_anon(fileid, gcpl_id, H5P_DEFAULT)) < 0) ERR;
if ((H5Olink(grpid, fileid, (char *)norm_utf8, H5P_DEFAULT, H5P_DEFAULT)) < 0) ERR;
if ((subgrpid = H5Gcreate(grpid, SUB_GRP_NAME, 0)) < 0) ERR;
if (H5Gclose(subgrpid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen file and discover groups. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, (char *)norm_utf8)) < 0) ERR;
if ((subgrpid = H5Gopen(grpid, SUB_GRP_NAME)) < 0) ERR;
if (H5Gclose(subgrpid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
bool ReadHDF5file(char* filename, char* fieldname, dtype** outArray, int* dims)
{
#ifdef _HDF5_H
// Open the file
hid_t file_id;
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
//? file_id = H5Fopen(filename,H5F_ACC_RDONLY,faplist_id);
if(file_id < 0){
printf("ERROR: Could not open file %s\n",filename);
return false;
}
// Open the dataset
hid_t dataset_id;
hid_t dataspace_id;
dataset_id = H5Dopen1(file_id, fieldname);
if(dataset_id < 0){
printf("ERROR: Could not open the data field %s\n",fieldname);
return false;
}
dataspace_id = H5Dget_space(dataset_id);
// Test if 2D data
int ndims;
ndims = H5Sget_simple_extent_ndims(dataspace_id);
// Get dimensions of data set (nx, ny, nn)
hsize_t* dimsl = new hsize_t[ndims];
H5Sget_simple_extent_dims(dataspace_id,dimsl,NULL);
for(int i = 0;(i<ndims&&i<3);i++)
dims[i] = dimsl[ndims-1-i]; //!!!!!!!! NOT SURE
size_t nn = 1;
for(int i = 0;i<ndims;i++)
nn *= dimsl[i];
// Create space for the new data
dtype* data = *outArray;
if (data!=NULL) delete data;//free(data);
*outArray = new dtype[nn];
data = *outArray;
hid_t datatype_id;
H5T_class_t dataclass;
size_t size;
datatype_id = H5Dget_type(dataset_id);
dataclass = H5Tget_class(datatype_id);
size = H5Tget_size(datatype_id);
int rrr = sizeof(int);
if(dataclass == H5T_FLOAT){
if (size == sizeof(float)) {
float* buffer = (float *) calloc(nn, sizeof(float));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(double)) {
double* buffer = (double *) calloc(nn, sizeof(double));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown floating point type, size=%i\n",(int) size);
return false;
}
}
else if(dataclass == H5T_INTEGER){
if (size == sizeof(short)) {
short* buffer = (short*) calloc(nn, sizeof(short));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(int)) {
int* buffer = (int *) calloc(nn, sizeof(int));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(long)) {
long* buffer = (long *) calloc(nn, sizeof(long));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown integer type, size=%i\n",(int) size);
return false;
}
}
else {
printf("2dData::readHDF5: unknown HDF5 data type\n");
return false;
}
// Close and cleanup
H5Dclose(dataset_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
return true;
#endif
return false;
}
void restart(int restart_flag)
{
extern int qpts, dimR, dimQ, Nx, Nz;
extern mcomplex ****U, ****C;
extern mcomplex ****IU, ****IC;
int x, y, z, i;
hid_t file_id1, dataset_u, dataset_v, dataset_w; /* file identifier */
hid_t dataset_iu, dataset_iv, dataset_iw;
hid_t complex_id;
herr_t ret;
char filename[50];
/* define compound datatype for the complex number */
typedef struct {
double re; /*real part */
double im; /*imaginary part */
} complex_t;
complex_id = H5Tcreate(H5T_COMPOUND, sizeof(complex_t));
H5Tinsert(complex_id, "real", HOFFSET(complex_t, re),
H5T_NATIVE_DOUBLE);
H5Tinsert(complex_id, "imaginary", HOFFSET(complex_t, im),
H5T_NATIVE_DOUBLE);
/* define some temporal matrix to store the data to the hdf file */
complex_t Matrix1[qpts][Nz][Nx / 2];
complex_t Matrix2[qpts][Nz][Nx / 2];
complex_t Matrix3[qpts][Nz][Nx / 2];
complex_t IMatrix1[qpts][Nz][Nx / 2];
complex_t IMatrix2[qpts][Nz][Nx / 2];
complex_t IMatrix3[qpts][Nz][Nx / 2]; // find the restart file
sprintf(filename, "data_t=%d.h5", restart_flag);
// open the file and dataset
file_id1 = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset_u = H5Dopen1(file_id1, "/data_u");
dataset_v = H5Dopen1(file_id1, "/data_v");
dataset_w = H5Dopen1(file_id1, "/data_w");
dataset_iu = H5Dopen1(file_id1, "/data_iu");
dataset_iv = H5Dopen1(file_id1, "/data_iv");
dataset_iw = H5Dopen1(file_id1, "/data_iw");
ret =
H5Dread(dataset_u, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
Matrix1);
ret =
H5Dread(dataset_v, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
Matrix2);
ret =
H5Dread(dataset_w, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
Matrix3);
ret =
H5Dread(dataset_iu, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
IMatrix1);
ret =
H5Dread(dataset_iv, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
IMatrix2);
ret =
H5Dread(dataset_iw, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
IMatrix3);
ret = H5Dclose(dataset_u);
ret = H5Dclose(dataset_v);
ret = H5Dclose(dataset_w);
ret = H5Dclose(dataset_iu);
ret = H5Dclose(dataset_iv);
ret = H5Dclose(dataset_iw);
ret = H5Fclose(file_id1);
for (y = 0; y < qpts; y++) {
for (z = 0; z < Nz; ++z) {
for (x = 0; x < Nx / 2; ++x) {
Re(U[z][XEL][y][x]) = Matrix1[y][z][x].re;
Im(U[z][XEL][y][x]) = Matrix1[y][z][x].im;
Re(U[z][YEL][y][x]) = Matrix2[y][z][x].re;
Im(U[z][YEL][y][x]) = Matrix2[y][z][x].im;
Re(U[z][ZEL][y][x]) = Matrix3[y][z][x].re;
Im(U[z][ZEL][y][x]) = Matrix3[y][z][x].im;
Re(IU[z][XEL][y][x]) = IMatrix1[y][z][x].re;
Im(IU[z][XEL][y][x]) = IMatrix1[y][z][x].im;
Re(IU[z][YEL][y][x]) = IMatrix2[y][z][x].re;
Im(IU[z][YEL][y][x]) = IMatrix2[y][z][x].im;
Re(IU[z][ZEL][y][x]) = IMatrix3[y][z][x].re;
Im(IU[z][ZEL][y][x]) = IMatrix3[y][z][x].im;
}
}
}
/* compute inital coefficients in expansion given the value of ux hat, uy hat, uz hat. */
initAlphaBeta();
/* compute the boundary condition for previous stage or time step, result is stored in Uxb and Uzb */
if (increBoundary() != NO_ERR) {
printf("increBoundary failure\n");
}
/* compute initial coefficients for incremental state solver */
incre_initAlphaBeta();
printf(" restart computed coefficients!\n");
for (i = 0; i < dimQ; ++i) {
for (z = 0; z < Nz; ++z) {
for (x = 0; x < Nx / 2; ++x) {
printf(" IC[%d][ALPHA][%d][%d]=%f+%fi\n", z, i, x,
Re(IC[z][ALPHA][i][x]), Im(IC[z][ALPHA][i][x]));
}
}
}
for (i = 0; i < dimR; ++i) {
for (z = 0; z < Nz; ++z) {
for (x = 0; x < Nx / 2; ++x) {
printf(" IC[%d][BETA][%d][%d]=%f+%fi\n", z, i, x,
Re(IC[z][BETA][i][x]), Im(IC[z][BETA][i][x]));
}
}
}
printf(" finish restart computing coefficients!\n\n");
}
// expose restart2 to python
void read_solution(char * filename, mcomplex * C_ptr)
{
extern int qpts, dimR, dimQ, Nx, Nz;
extern mcomplex ****U, ****C;
extern mcomplex ****IU, ****IC;
int x, y, z;
hid_t file_id1, dataset_a, dataset_b; /* file identifier */
hid_t dataset_ia, dataset_ib;
hid_t complex_id;
/* define compound datatype for the complex number */
typedef struct {
double re; /*real part */
double im; /*imaginary part */
} complex_t;
complex_id = H5Tcreate(H5T_COMPOUND, sizeof(complex_t));
H5Tinsert(complex_id, "real", HOFFSET(complex_t, re),
H5T_NATIVE_DOUBLE);
H5Tinsert(complex_id, "imaginary", HOFFSET(complex_t, im),
H5T_NATIVE_DOUBLE);
/* define some temporal matrix to store the data to the hdf file */
complex_t Matrix1[dimR][Nz][Nx / 2];
complex_t Matrix2[dimR][Nz][Nx / 2];
complex_t IMatrix1[dimR][Nz][Nx / 2];
complex_t IMatrix2[dimR][Nz][Nx / 2];
// open the file and dataset
file_id1 = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset_a = H5Dopen1(file_id1, "/data_alpha");
dataset_b = H5Dopen1(file_id1, "/data_beta");
dataset_ia = H5Dopen1(file_id1, "/data_ialpha");
dataset_ib = H5Dopen1(file_id1, "/data_ibeta");
assert(EXIT_SUCCESS ==
H5Dread(dataset_a, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
Matrix1));
assert(EXIT_SUCCESS ==
H5Dread(dataset_b, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
Matrix2));
assert(EXIT_SUCCESS ==
H5Dread(dataset_ia, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
IMatrix1));
assert(EXIT_SUCCESS ==
H5Dread(dataset_ib, complex_id, H5S_ALL, H5S_ALL, H5P_DEFAULT,
IMatrix2));
assert(EXIT_SUCCESS == H5Dclose(dataset_a));
assert(EXIT_SUCCESS == H5Dclose(dataset_b));
assert(EXIT_SUCCESS == H5Dclose(dataset_ia));
assert(EXIT_SUCCESS == H5Dclose(dataset_ib));
assert(EXIT_SUCCESS == H5Fclose(file_id1));
for (y = 0; y < dimR; y++) {
for (z = 0; z < Nz; ++z) {
for (x = 0; x < Nx / 2; ++x) {
Re(C[z][ALPHA][y][x]) = Matrix1[y][z][x].re;
Im(C[z][ALPHA][y][x]) = Matrix1[y][z][x].im;
Re(C[z][BETA][y][x]) = Matrix2[y][z][x].re;
Im(C[z][BETA][y][x]) = Matrix2[y][z][x].im;
Re(IC[z][ALPHA][y][x]) = IMatrix1[y][z][x].re;
Im(IC[z][ALPHA][y][x]) = IMatrix1[y][z][x].im;
Re(IC[z][BETA][y][x]) = IMatrix2[y][z][x].re;
Im(IC[z][BETA][y][x]) = IMatrix2[y][z][x].im;
}
}
}
/* compute ux hat, uy hat, uz hat given alpha, beta,. */
initAlphaBeta2();
/* compute the boundary condition for previous stage or time step,
result is stored in Uxb and Uzb */
if (increBoundary() != NO_ERR) {
printf("increBoundary failure\n");
}
/* compute iux, iuy, iuz given i-alpha, i-beta */
incre_initAlphaBeta2();
memset(U[Nz / 2][0][0], 0, 5 * qpts * (Nx / 2) * sizeof(mcomplex));
memset(IU[Nz / 2][0][0], 0, 5 * qpts * (Nx / 2) * sizeof(mcomplex));
memmove(C_ptr, C[0][0][0], Nz * 2 * dimR * (Nx / 2) * sizeof(mcomplex));
}
