/**
* Appends along the last dimensions.
*/
static hid_t make_dataset(ndio_hdf5_t self,nd_type_id_t type_id,unsigned ndim,size_t *shape, hid_t* filespace)
{ hsize_t *sh=0,*ori=0,*ext=0;
TRY(self->isw);
STACK_ALLOC(hsize_t,sh ,ndim);
STACK_ALLOC(hsize_t,ori,ndim);
STACK_ALLOC(hsize_t,ext,ndim);
if(self->dataset>=0) // data set already exists...needs extending, append on slowest dim
{ HTRY(H5Sget_simple_extent_dims(space(self),sh,NULL));
ZERO(hsize_t,ori,ndim);
ori[0]=sh[0];
sh[0]+=shape[ndim-1];
reverse_hsz_sz(ndim,ext,shape);
HTRY(H5Dextend(self->dataset,sh));
HTRY(*filespace=H5Dget_space(self->dataset));
HTRY(H5Sselect_hyperslab(*filespace,H5S_SELECT_SET,ori,NULL,ext,NULL));
} else
{ HTRY(self->dataset=H5Dcreate(
self->file,name(self),
nd_to_hdf5_type(type_id),
make_space(self,ndim,shape),
H5P_DEFAULT,/*(rare) link creation props*/
dataset_creation_properties(
/*set_deflate*/(
set_chunk(self,ndim,shape))),
H5P_DEFAULT /*(rare) dataset access props*/
));
reverse_hsz_sz(ndim,sh,shape);
*filespace=H5S_ALL;
}
HTRY(H5Dset_extent(self->dataset,sh));
return self->dataset;
Error:
return -1;
}
void extend1dDoubleExt(hdf5_ext_info *hi, void *array, hsize_t len) {
if(!hi || !array || len <=0)
return;
if(hi->cur_dim == 0) {
hi->cur_dim = len;
/* Create the data space with unlimited dimensions. */
hsize_t maxdim = H5S_UNLIMITED;
hi->dataspace = H5Screate_simple (1, &(hi->cur_dim),&maxdim);
/* Modify dataset creation properties, i.e. enable chunking */
hid_t prop = H5Pcreate (H5P_DATASET_CREATE);
hi->status = H5Pset_chunk (prop, 1, &(hi->chunk_len));
/* Create a new dataset within the file using chunk
creation properties. */
hi->dataset = H5Dcreate (hi->file_id, hi->dsetName, H5T_NATIVE_DOUBLE, hi->dataspace,
H5P_DEFAULT, prop, H5P_DEFAULT);
/* Write data to dataset */
hi->status = H5Dwrite (hi->dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, array);
hi->status = H5Pclose (prop);
hi->status = H5Sclose (hi->dataspace);
}
else {
/* Extend the dataset */
hi->cur_offset = hi->cur_dim ;
hi->cur_dim += len;
hi->status = H5Dextend (hi->dataset, &(hi->cur_dim));
/* Select a hyperslab in extened portion of dataset */
hi->filespace = H5Dget_space (hi->dataset);
hi->status = H5Sselect_hyperslab (hi->filespace, H5S_SELECT_SET, &(hi->cur_offset), NULL,
&len, NULL);
/* Define memory space */
hi->memspace = H5Screate_simple (1, &len, NULL);
/* Write the data to the extended portion of dataset */
hi->status = H5Dwrite (hi->dataset, H5T_NATIVE_DOUBLE, hi->memspace, hi->filespace,
H5P_DEFAULT, array);
hi->status = H5Sclose (hi->memspace);
hi->status = H5Sclose (hi->filespace);
}
}
int
main()
{
printf("\n*** Checking HDF5 integer dataset with extension.\n");
printf("*** checking 1D int dataset with extend...");
{
/* Misspelling is deliberite. Please dont correct. */
#define INTERGERS "Intergers"
#define NUM_STR 1
#define NDIMS 1
hid_t fileid, grpid, spaceid;
hid_t datasetid, plistid;
hsize_t dims[NDIMS] = {NUM_STR}, max_dims[NDIMS] = {H5S_UNLIMITED};
hsize_t chunk_dims[NDIMS] = {1};
hsize_t xtend_size[NDIMS] = {2};
int data[NUM_STR] = {42};
int empty = -42;
/* Create the file, open root group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create a space for the dataset. */
if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
/* Create the dataset. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid, 1, chunk_dims) < 0) ERR;
if (H5Pset_fill_value(plistid, H5T_NATIVE_INT32, &empty) < 0) ERR;
if ((datasetid = H5Dcreate1(grpid, INTERGERS, H5T_NATIVE_INT32,
spaceid, plistid)) < 0) ERR;
/* Now extend the dataset. */
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if (H5Dwrite(datasetid, H5T_NATIVE_INT, spaceid, spaceid,
H5P_DEFAULT, &data) < 0) ERR;
/* Close up. */
if (H5Dclose(datasetid) < 0) ERR;
if (H5Pclose(plistid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
int H5mdfile::H5_Dextend(int argc, char **argv, Tcl_Interp *interp)
{
/* Extend dataset to higher dimensions */
for(int i=0;i<dataset_rank;i++)
{
if(atoi(argv[3+i])>(int)dims[i])
{
dims[i]=atoi(argv[3+i])-dimstotal[i];
}
dimstotal[i] = atoi(argv[3+i]);
}
status = H5Dextend(dataset_id, dimstotal);
return TCL_OK;
}
herr_t H5ARRAYappend_records( hid_t dataset_id,
hid_t type_id,
const int rank,
hsize_t *dims_orig,
hsize_t *dims_new,
int extdim,
const void *data )
{
hid_t space_id;
hid_t mem_space_id;
hsize_t *dims = NULL; /* Shut up the compiler */
hsize_t *start = NULL; /* Shut up the compiler */
int i;
/* Compute the arrays for new dimensions and coordinates and extents */
dims = malloc(rank*sizeof(hsize_t));
start = malloc(rank*sizeof(hsize_t));
for(i=0;i<rank;i++) {
dims[i] = dims_orig[i];
start[i] = 0;
}
dims[extdim] += dims_new[extdim];
start[extdim] = (hsize_t )dims_orig[extdim];
/* Extend the dataset */
if ( H5Dextend ( dataset_id, dims ) < 0 )
goto out;
/* Create a simple memory data space */
if ( (mem_space_id = H5Screate_simple( rank, dims_new, NULL )) < 0 )
return -1;
/* Get the file data space */
if ( (space_id = H5Dget_space( dataset_id )) < 0 )
return -1;
/* Define a hyperslab in the dataset */
if ( H5Sselect_hyperslab( space_id, H5S_SELECT_SET, start, NULL, dims_new, NULL) < 0 )
goto out;
if ( H5Dwrite( dataset_id, type_id, mem_space_id, space_id, H5P_DEFAULT, data ) < 0 )
goto out;
/* Update the original dimensions of the array after a successful append */
dims_orig[extdim] += dims_new[extdim];
/* Terminate access to the dataspace */
if ( H5Sclose( mem_space_id ) < 0 )
goto out;
if ( H5Sclose( space_id ) < 0 )
goto out;
/* Release resources */
free(start);
free(dims);
return 0;
out:
if (start) free(start);
if (dims) free(dims);
return -1;
}
//////////////////////////////////////////////////////////////////////////////////////////
//HaloTrees Append Datasets Group//
//////////////////////////////////////////////////////////////////////////////////////////
void HaloTreesGroupDataAppend(hid_t file_out_hdf5, MergerTree **halo, int tree_levels, int nb_nodes)
{
int i, j, count;
int rank, nb_elements;
int *nodeIndex, *nodeHost, *nodeDescendent;
hid_t dataset, dataspace, cparams, filespace;
hsize_t newdims[1], finaldims[1], newdims2[2], finaldims2[2], offset[1], offset2[2];
newdims[0] = nb_nodes;
newdims2[0] = nb_nodes; newdims2[1] = 3;
double *time, *expansionFactor, *redshift;
double *nodeMass;
double nodePosition[nb_nodes][3], nodeVelocity[nb_nodes][3]; //for some reason dynamic memory allocation don't work with hdf5 2D datasets
nodeIndex = (int *)malloc(nb_nodes*sizeof(int));
nodeDescendent = (int *)malloc(nb_nodes*sizeof(int));
nodeMass = (double *)malloc(nb_nodes*sizeof(double));
expansionFactor = (double *)malloc(nb_nodes*sizeof(double));
redshift = (double *)malloc(nb_nodes*sizeof(double));
time = (double *)malloc(nb_nodes*sizeof(double));
for(i = 0, count = 0; i < tree_levels; i++)
for(j = 0; j < halo[i][0].snapshot.nb_halos; j++)
{
nodeIndex[count] = halo[i][j].idAlias;
nodeMass[count] = halo[i][j].mvir;
nodeDescendent[count] = halo[i][j].son_idAlias;
expansionFactor[count] = halo[i][j].sfactor;
time[count] = halo[i][j].age;
redshift[count] = 1.0/halo[i][j].sfactor - 1.0;
nodePosition[count][0] = halo[i][j].position[0];
nodePosition[count][1] = halo[i][j].position[1];
nodePosition[count][2] = halo[i][j].position[2];
count++;
}
/* hostIndex Dataset */
dataset = H5Dopen (file_out_hdf5, "/haloTrees/hostIndex", H5P_DEFAULT);
filespace = H5Dget_space (dataset);
rank = H5Sget_simple_extent_ndims (filespace);
nb_elements = H5Sget_simple_extent_npoints( filespace );
finaldims[0] = nb_elements+10;// + nb_nodes-1000;
finaldims2[0] = nb_elements + nb_nodes; finaldims2[1] = 3;
offset[0] = nb_elements;
offset2[0] = nb_elements; offset2[1] = 0;
printf("finaldims:%d\n",(int)finaldims[0]);
H5Dextend(dataset, finaldims);
filespace = H5Dget_space( dataset );
H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL);
dataspace = H5Screate_simple (1, newdims, NULL);
//H5Dwrite (dataset, H5T_NATIVE_INT, dataspace, filespace, H5P_DEFAULT, nodeIndex);
H5Sclose(dataspace);
H5Sclose(filespace);
H5Dclose(dataset);
/* nodeIndex Dataset */
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/nodeIndex", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL); */
/* dataspace = H5Screate_simple (1, newdims, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_INT, dataspace, filespace, H5P_DEFAULT, nodeIndex); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* descendentIndex Dataset*/
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/descendentIndex", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL); */
/* dataspace = H5Screate_simple (1, newdims, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_INT, dataspace, filespace, H5P_DEFAULT, nodeDescendent); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* nodeMass Dataset*/
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/nodeMass", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL); */
/* dataspace = H5Screate_simple (1, newdims, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, nodeMass); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* /\* exapansionFactor Dataset*\/ */
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/exapansionFactor", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL); */
/* dataspace = H5Screate_simple (1, newdims, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, expansionFactor); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* /\* redshift Dataset *\/ */
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/redshift", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL); */
/* dataspace = H5Screate_simple (1, newdims, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, redshift); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* /\* time Dataset *\/ */
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/time", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, newdims, NULL); */
/* dataspace = H5Screate_simple (1, newdims, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, time); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* /\* position Dataset *\/ */
/* dataset = H5Dopen (file_out_hdf5, "/haloTrees/position", H5P_DEFAULT); */
/* H5Dextend(dataset, finaldims2); */
/* filespace = H5Dget_space( dataset ); */
/* H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset2, NULL, newdims2, NULL); */
/* dataspace = H5Screate_simple (2, newdims2, NULL); */
/* H5Dwrite (dataset, H5T_NATIVE_DOUBLE, dataspace, filespace, H5P_DEFAULT, nodePosition); */
/* H5Sclose(dataspace); */
/* H5Dclose(filespace); */
/* H5Dclose(dataset); */
/* velocity Dataset */ //not used by Galacticus yet!
/* dataspace = H5Screate_simple(2, dims2, maxdims2); */
/* cparams = H5Pcreate (H5P_DATASET_CREATE); */
/* H5Pset_chunk ( cparams, 2, chunk_dims2); */
/* dataset = H5Dcreate(file_out_hdf5, "/haloTrees/velocity", H5T_IEEE_F64LE, dataspace, H5P_DEFAULT, cparams, H5P_DEFAULT); */
/* H5Dwrite( dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nodeVelocity); */
/* H5Pclose(cparams); */
/* H5Sclose(dataspace); */
/* H5Dclose(dataset); */
}
/*
* This program performs three different types of parallel access. It writes on
* the entire dataset, it extends the dataset to nchunks*CHUNKSIZE, and it only
* opens the dataset. At the end, it verifies the size of the dataset to be
* consistent with argument 'nchunks'.
*/
void
parallel_access_dataset(const char *filename, int nchunks, access_type action, hid_t *file_id, hid_t *dataset)
{
/* HDF5 gubbins */
hid_t memspace, dataspace; /* HDF5 file identifier */
hid_t access_plist; /* HDF5 ID for file access property list */
herr_t hrc; /* HDF5 return code */
hsize_t size[1];
hsize_t dim_size;
hsize_t chunk_dims[1] ={CHUNKSIZE};
hsize_t count[1];
hsize_t stride[1];
hsize_t block[1];
hsize_t offset[1]; /* Selection offset within dataspace */
/* Variables used in reading data back */
char buffer[CHUNKSIZE];
int i;
/* MPI Gubbins */
MPI_Offset filesize, /* actual file size */
est_filesize; /* estimated file size */
int mpierr;
/* Initialize MPI */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* Set up MPIO file access property lists */
access_plist = H5Pcreate(H5P_FILE_ACCESS);
VRFY((access_plist >= 0), "");
hrc = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL);
VRFY((hrc >= 0), "");
/* Open the file */
if (*file_id<0){
*file_id = H5Fopen(filename, H5F_ACC_RDWR, access_plist);
VRFY((*file_id >= 0), "");
}
/* Open dataset*/
if (*dataset<0){
*dataset = H5Dopen(*file_id, DATASETNAME);
VRFY((*dataset >= 0), "");
}
memspace = H5Screate_simple(1, chunk_dims, NULL);
VRFY((memspace >= 0), "");
dataspace = H5Dget_space(*dataset);
VRFY((dataspace >= 0), "");
size[0] = nchunks*CHUNKSIZE;
switch (action) {
/* all chunks are written by all the processes in an interleaved way*/
case write_all:
memset(buffer, mpi_rank+1, CHUNKSIZE);
count[0] = 1;
stride[0] = 1;
block[0] = chunk_dims[0];
for (i=0; i<(nchunks+mpi_size-1)/mpi_size; i++){
if (i*mpi_size+mpi_rank < nchunks){
offset[0] = (i*mpi_size+mpi_rank)*chunk_dims[0];
hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block);
VRFY((hrc >= 0), "");
/* Write the buffer out */
hrc = H5Dwrite(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer);
VRFY((hrc >= 0), "H5Dwrite");
}
}
break;
/* only extends the dataset */
case extend_only:
/* Extend dataset*/
hrc = H5Dextend(*dataset, size);
VRFY((hrc >= 0), "");
break;
/* only opens the dataset */
case open_only:
break;
}
/* Close up */
hrc = H5Dclose(*dataset);
VRFY((hrc >= 0), "");
*dataset = -1;
hrc = H5Sclose (dataspace);
VRFY((hrc >= 0), "");
hrc = H5Sclose (memspace);
VRFY((hrc >= 0), "");
hrc = H5Fclose(*file_id);
VRFY((hrc >= 0), "");
*file_id = -1;
/* verify file size */
filesize = get_filesize(filename);
est_filesize = nchunks*CHUNKSIZE*sizeof(unsigned char);
VRFY((filesize >= est_filesize), "file size check");
/* Can close some plists */
hrc = H5Pclose(access_plist);
VRFY((hrc >= 0), "");
/* Make sure all processes are done before exiting this routine. Otherwise,
* other tests may start and change the test data file before some processes
* of this test are still accessing the file.
*/
MPI_Barrier(MPI_COMM_WORLD);
}
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;
}
