Example #1
0
/**
 * Write a hyperslab into the dataset.
 * 
 * @param [in] HDF5_Dataset_id - Dataset id
 * @param [in] Position - Position in the dataset
 * @param [in] Size - Size of the hyperslab
 * @param [in] Data
 * @throw ios::failure
 * 
 */
void THDF5_File::WriteHyperSlab(const hid_t HDF5_Dataset_id, const TDimensionSizes & Position , const TDimensionSizes & Size, const float * Data){
    
    
    
     // Select hyperslab
    const int MatrixRank = 3;    
    hsize_t ElementCount[MatrixRank] = {Size.Z, Size.Y, Size.X};    
    hsize_t Offset[MatrixRank] = {Position.Z,Position.Y,Position.X};
    
    herr_t status;
    hid_t  HDF5_Filespace,HDF5_Memspace;
    
    // Select hyperslab in the file.     
    HDF5_Filespace = H5Dget_space(HDF5_Dataset_id);  
    
    
    status = H5Sselect_hyperslab(HDF5_Filespace, H5S_SELECT_SET, Offset, 0, ElementCount, NULL);
    if (status < 0) {
        char ErrorMessage[256];
        sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotWriteTo,"");        
        throw ios::failure(ErrorMessage);
     } 
    
    
    // assign memspace
    HDF5_Memspace = H5Screate_simple(MatrixRank, ElementCount, NULL);

    
     status = H5Dwrite(HDF5_Dataset_id, H5T_NATIVE_FLOAT, HDF5_Memspace, HDF5_Filespace,  H5P_DEFAULT, Data);
     if (status < 0) {
        char ErrorMessage[256];
        sprintf(ErrorMessage,HDF5_ERR_FMT_CouldNotWriteTo,"");
        
        throw ios::failure(ErrorMessage);
     } 
    
    H5Sclose(HDF5_Memspace);
    H5Sclose(HDF5_Filespace);  
    
    
    
}// end of WriteHyperSlab
Example #2
0
bool save_quad_bc(hid_t parent_group_id, JudyArray<Boundary *> &bcs) {
	herr_t status;

	// create main group
	hid_t group_id = H5Gcreate(parent_group_id, "quad", 0);

	// count
	hid_t dataspace_id = H5Screate(H5S_SCALAR);
	hid_t attr_count = H5Acreate(group_id, "count", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
	uint count = bcs.count();
	status = H5Awrite(attr_count, H5T_NATIVE_UINT32, &count);
	H5Aclose(attr_count);

    ///
	hsize_t dims = Quad::NUM_VERTICES;
	hid_t elem_dataspace_id = H5Screate_simple(1, &dims, NULL);

	hid_t merker_dataspace_id = H5Screate(H5S_SCALAR);

    // dump vertices
    for (int i = 0; i < count; i++) {
    	char name[256];
    	sprintf(name, "%d", i);

		// the dataset
		hid_t dataset_id = H5Dcreate(group_id, name, H5T_NATIVE_UINT32, elem_dataspace_id, H5P_DEFAULT);
		status = H5Dwrite(dataset_id, H5T_NATIVE_UINT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, bcs[i]->get_vertices());

		// marker
		hid_t attr_marker = H5Acreate(dataset_id, "marker", H5T_NATIVE_UINT32, dataspace_id, H5P_DEFAULT);
		uint marker = bcs[i]->get_marker();
		status = H5Awrite(attr_marker, H5T_NATIVE_UINT32, &marker);
		H5Aclose(attr_marker);

		status = H5Dclose(dataset_id);
    }

    H5Sclose(elem_dataspace_id);
    H5Sclose(dataspace_id);

	status = H5Gclose(group_id);		// close the group
}
Example #3
0
void seissol::checkpoint::h5::Fault::write(int timestepFault)
{
	EPIK_TRACER("CheckPointFault_write");
	SCOREP_USER_REGION("CheckPointFault_write", SCOREP_USER_REGION_TYPE_FUNCTION);

	if (numSides() == 0)
		return;

	logInfo(rank()) << "Writing fault check point.";

	// Create array with all pointers
	EPIK_USER_REG(r_write_fault, "checkpoint_write_fault");
	SCOREP_USER_REGION_DEFINE(r_write_fault);
	EPIK_USER_START(r_write_fault);
	SCOREP_USER_REGION_BEGIN(r_write_fault, "checkpoint_write_fault", SCOREP_USER_REGION_TYPE_COMMON);

	// Attributes
	checkH5Err(H5Awrite(m_h5timestepFault[odd()], H5T_NATIVE_INT, &timestepFault));

	// Set memory and file space
	hsize_t fStart[2] = {fileOffset(), 0};
	hsize_t count[2] = {numSides(), numBndGP()};
	hid_t h5memSpace = H5Screate_simple(2, count, 0L);
	checkH5Err(h5memSpace);
	checkH5Err(H5Sselect_all(h5memSpace));
	checkH5Err(H5Sselect_hyperslab(m_h5fSpaceData, H5S_SELECT_SET, fStart, 0L, count, 0L));

	for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
		checkH5Err(H5Dwrite(m_h5data[odd()][i], H5T_NATIVE_DOUBLE, h5memSpace, m_h5fSpaceData,
				h5XferList(), data(i)));
	}

	checkH5Err(H5Sclose(h5memSpace));

	EPIK_USER_END(r_write_fault);
	SCOREP_USER_REGION_END(r_write_fault);

	// Finalize the checkpoint
	finalizeCheckpoint();

	logInfo(rank()) << "Writing fault check point. Done.";
}
Example #4
0
herr_t H5TBOwrite_elements( hid_t dataset_id,
                            hid_t mem_type_id,
                            hsize_t nrecords,
                            const void *coords,
                            const void *data )
{

 hsize_t  count[1];
 hid_t    space_id;
 hid_t    mem_space_id;

 /* Get the dataspace handle */
 if ( (space_id = H5Dget_space( dataset_id )) < 0 )
  goto out;

 /* Define a selection of points in the dataset */

 if ( H5Sselect_elements(space_id, H5S_SELECT_SET, (size_t)nrecords, (const hsize_t *)coords) < 0 )
  goto out;

 /* Create a memory dataspace handle */
 count[0] = nrecords;
 if ( (mem_space_id = H5Screate_simple( 1, count, NULL )) < 0 )
  goto out;

 if ( H5Dwrite( dataset_id, mem_type_id, mem_space_id, space_id, H5P_DEFAULT, data ) < 0 )
  goto out;

 /* Terminate access to the memory dataspace */
 if ( H5Sclose( mem_space_id ) < 0 )
  goto out;

 /* Terminate access to the dataspace */
 if ( H5Sclose( space_id ) < 0 )
  goto out;

return 0;

out:
 return -1;

}
Example #5
0
/* ------- begin --------------------------   writeMPI_p.c ----- */
void writeMPI_p(int task) {
/* Writes output on indata file, MPI group, one task at once */
  const char routineName[] = "writeMPI_p";
  hsize_t  offset[] = {0, 0, 0, 0};
  hsize_t  count[] = {1, 1, 1, 1};
  hsize_t  dims[4];
  hid_t    file_dspace, mem_dspace;

  dims[0] = 1;
  if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0) HERR(routineName);
  offset[0] = mpi.ix;
  offset[1] = mpi.iy;
  if (( file_dspace = H5Dget_space(io.in_mpi_tm) ) < 0) HERR(routineName);
  if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
                            NULL, count, NULL) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_tm, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.rank) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_tn, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &task) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_it, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.niter[0]) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_conv, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.convergence[0]) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_zc, H5T_NATIVE_INT, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.zcut_hist[0]) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_dm, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
                   H5P_DEFAULT, &mpi.dpopsmax[0]) ) < 0) HERR(routineName);
  if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
  if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);

  dims[0] = mpi.niter[0];
  if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0) HERR(routineName);
  offset[0] = mpi.ix;
  offset[1] = mpi.iy;
  count[2] = mpi.niter[0];
  if (( file_dspace = H5Dget_space(io.in_mpi_dmh) ) < 0) HERR(routineName);
  if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
                            NULL, count, NULL) ) < 0) HERR(routineName);
  if (( H5Dwrite(io.in_mpi_dmh, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
                 H5P_DEFAULT, mpi.dpopsmax_hist[0]) ) < 0) HERR(routineName);
  if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
  if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
  return;
}
void hdf5_dataset::write(hdf5_datatype const& type, void const* buffer)
{
    herr_t status =
            H5Dwrite(
                get_id(),
                type.get_id(),
                H5S_ALL,
                H5S_ALL,
                H5P_DEFAULT,
                buffer
            );

    if(status < 0) {
        boost::serialization::throw_exception(
            hdf5_archive_exception(
                hdf5_archive_exception::hdf5_archive_dataset_write_error
            )
        );
    }
}
Example #7
0
static int Write_hdf5(void *buf, size_t nbytes)
{
    hid_t dsid;
    herr_t n1, n2;
    char dsname[256];
    static int n = 0;
    if (dspc == -1)
    {
        hsize_t dims = nbytes;
        dspc = H5Screate_simple(1, &dims, &dims);
    }

    sprintf(dsname, "data_%07d", n++);
    dsid = H5Dcreate(fid, dsname, H5T_NATIVE_UCHAR, dspc, H5P_DEFAULT);
    if (dsid < 0) return 0;
    n1 = H5Dwrite(dsid, H5T_NATIVE_UCHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
    n2 = H5Dclose(dsid);
    if (n1 < 0 || n2 < 0) return 0;
    return nbytes;
}
Example #8
0
int create_new_dataset(H5block *d){
    hid_t file_id, dataset_id, dataspace_id, status, dcpl, datatype;
    file_id = H5Fopen(d->name, H5F_ACC_RDWR, H5P_DEFAULT);
    hsize_t dims[2];
    dims[0] = d->x_index_dim;
    dims[1] = d->y_index_dim;
    dataspace_id = H5Screate_simple(2, dims, NULL);
    datatype = H5Tcopy(H5T_NATIVE_FLOAT);
     status = H5Tset_order(datatype, H5T_ORDER_LE);
    char buffer[50];
    sprintf(buffer, "/dset%ld", d->ticks);

    dataset_id = H5Dcreate(file_id, buffer, datatype, dataspace_id, H5P_DEFAULT);
    status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                        d->field);
    status = H5Dclose(dataset_id);
    status = H5Tclose(datatype);
    status = H5Sclose(dataspace_id);
    status = H5Fclose(file_id);
}
Example #9
0
void testCreateStringDataset()
{
    const char * data[STR_DSET_LEN] = {"You have to", "live", "life", "to the limit"};
    hid_t file, memtype, dset;
    hsize_t size = STR_DSET_LEN;
    herr_t status;
    HDF5WriterBase writer;
    string h5Filename = moose::random_string( 10 );
    file = H5Fcreate(h5Filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
    dset = writer.createStringDataset(file, STR_DSET_NAME, size, size);
    assert(dset >= 0);
    memtype = H5Tcopy(H5T_C_S1);
    status = H5Tset_size(memtype, H5T_VARIABLE);
    assert(status >= 0);
    status = H5Dwrite(dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
    assert(status >= 0);
    status = H5Dclose(dset);
    H5Tclose(memtype);
    H5Fclose(file);
}
Example #10
0
herr_t ASDF_write_quakeml(hid_t loc_id, const char *quakeml_string) {
  hsize_t dims[1] = {strlen(quakeml_string)};
  hsize_t maxdims[1] = {H5S_UNLIMITED};

  hid_t space_id, dcpl_id, array_id;

  CHK_H5(space_id = H5Screate_simple(1, dims, maxdims));
  CHK_H5(dcpl_id = H5Pcreate(H5P_DATASET_CREATE));
  CHK_H5(H5Pset_chunk(dcpl_id, 1, dims));

  CHK_H5(array_id = H5Dcreate(loc_id, "/QuakeML", H5T_STD_I8LE, space_id,
        H5P_DEFAULT, dcpl_id, H5P_DEFAULT));
  CHK_H5(H5Dwrite(array_id, H5T_STD_I8LE, H5S_ALL, H5S_ALL,
        H5P_DEFAULT, quakeml_string));

  CHK_H5(H5Dclose(array_id));
  CHK_H5(H5Sclose(space_id));

  return 0; // Success
}
Example #11
0
herr_t writeDouble2d(hid_t file_id,const char *dsName, void * matrix, int DIM_X, int DIM_Y) {
    hid_t  dataset_id,dataspace_id;
    hsize_t     dims[] = {DIM_Y,DIM_X}; /*DIM_Y corresponds to number of rows, DIM_X to columns*/
    herr_t status;
    /* Create the data space for the dataset. */

    dataspace_id = H5Screate_simple(2, dims, NULL);
    /* Create the dataset. */

    dataset_id = H5Dcreate(file_id, dsName,  H5T_IEEE_F64LE, dataspace_id, 
                          H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    status = H5Sclose(dataspace_id);
    /*Write the dataset*/
    status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, 
                     matrix);
    /* End access to the dataset and release resources used by it. */
    status = H5Dclose(dataset_id);
    return status;    
}
asynStatus NDFileHDF5AttributeDataset::writeAttributeDataset(hdf5::When_t whenToSave, hsize_t *offsets, NDAttribute *ndAttr, int flush, int indexed)
{
  asynStatus status = asynSuccess;
  char * stackbuf[MAX_ATTRIBUTE_STRING_SIZE];
  void* pDatavalue = stackbuf;
  int ret;
  //check if the attribute is meant to be saved at this time
  if (whenToSave_ == whenToSave) {
    // Extend the dataset as required to store the data
    if (indexed == -1){
      extendDataSet(offsets);
    } else {
      extendIndexDataSet(offsets[indexed]);
    }
    // find the data based on datatype
    ret = ndAttr->getValue(ndAttr->getDataType(), pDatavalue, MAX_ATTRIBUTE_STRING_SIZE);
    if (ret == ND_ERROR) {
      memset(pDatavalue, 0, MAX_ATTRIBUTE_STRING_SIZE);
    }
    // Work with HDF5 library to select a suitable hyperslab (one element) and write the new data to it
    H5Dset_extent(dataset_, dims_);
    filespace_ = H5Dget_space(dataset_);

    // Select the hyperslab
    H5Sselect_hyperslab(filespace_, H5S_SELECT_SET, offset_, NULL, elementSize_, NULL);

    // Write the data to the hyperslab.
    H5Dwrite(dataset_, datatype_, memspace_, filespace_, H5P_DEFAULT, pDatavalue);


    // Check if we are being asked to flush
    if (flush == 1){
      status = this->flushDataset();
    }

    H5Sclose(filespace_);
    nextRecord_++;
  }

  return status;
}
Example #13
0
void saveParticleComp_Int(int *data,char *fileName,char *dataName,int totalCnt,int cnt,int offSet)
{
  int i,j,k;
  int myrank, nTasks;
  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
  MPI_Comm_size(MPI_COMM_WORLD, &nTasks);

  hid_t file_id,dset_id,plist_id,tic_id;
  herr_t status;
  hid_t total_file_space,subfilespace,filespace,memspace,ticspace;
  hsize_t dimsf[1],count[1],offset[1];

  plist_id=H5Pcreate(H5P_FILE_ACCESS);
  H5Pset_fapl_mpio(plist_id,MPI_COMM_WORLD,MPI_INFO_NULL);
//    H5Pset_fclose_degree(plist_id,H5F_CLOSE_SEMI);
//    MPI_Barrier(MPI_COMM_WORLD);

  file_id=H5Fopen(fileName,H5F_ACC_RDWR,plist_id);
  H5Pclose(plist_id);

  dimsf[0]=totalCnt;
  filespace=H5Screate_simple(1,dimsf,NULL);

  count[0]=cnt;
  offset[0]=offSet;
  memspace=H5Screate_simple(1,count,NULL);

  dset_id=H5Dcreate2(file_id,dataName,H5T_NATIVE_INT,filespace,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
  subfilespace=H5Dget_space(dset_id);
  H5Sselect_hyperslab(subfilespace,H5S_SELECT_SET,offset,NULL,count,NULL);
  plist_id=H5Pcreate(H5P_DATASET_XFER);
  H5Pset_dxpl_mpio(plist_id,H5FD_MPIO_INDEPENDENT);
  status = H5Dwrite(dset_id, H5T_NATIVE_INT,memspace,subfilespace,plist_id,data);
  H5Pclose(plist_id);
  H5Sclose(subfilespace);
  H5Dclose(dset_id);

  H5Sclose(memspace);
  H5Sclose(filespace);
  H5Fclose(file_id);
}
Example #14
0
void F77_FUNC_(pwhdf_open_file,PWHDF_OPEN_FILE)(const char* fname, const int* length)
{
  char * hfname = ( char * ) malloc( (*length) + 1 ) ;
  memcpy( hfname , fname , *length ) ;
  hfname[*length] = '\0' ; 

  if(h_file>=0) H5Fclose(h_file);

  h_file = H5Fcreate(hfname,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT);

  /* impelements version 1.00 hdf5 format */
  int version[]={1,10};
  hsize_t dim=2;
  hid_t dataspace= H5Screate_simple(1, &dim, NULL);
  hid_t dataset= H5Dcreate(h_file, "version", H5T_NATIVE_INT, dataspace, H5P_DEFAULT);
  hid_t ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,version);
  H5Sclose(dataspace);
  H5Dclose(dataset);

  free(hfname);
}
Example #15
0
void dumpToH5(int Ni, int Nj, int Nk, int is, int js, int ks, int ie, int je, int ke, float ***f, char *format, ...) {
	char filename[1024];
	va_list ap;
	va_start(ap, format);
	vsprintf(filename, format, ap);
	hid_t file, dataset, filespace, memspace;

	hsize_t dimsm[3] = { Ni, Nj, Nk };
	hsize_t start[3] = { is, js, ks };
	hsize_t count[3] = { 1-is+ie, 1-js+je, 1-ks+ke };
	memspace = H5Screate_simple(3, dimsm, 0);
	filespace = H5Screate_simple(3, count, 0);
	file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
	dataset = H5Dcreate(file, "Data", H5T_NATIVE_FLOAT, filespace, H5P_DEFAULT);
	H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, 0, count, 0);
	H5Dwrite(dataset, H5T_NATIVE_FLOAT, memspace, filespace, H5P_DEFAULT, f[0][0]);
	H5Dclose(dataset);
	H5Sclose(filespace);
	H5Sclose(memspace);
	H5Fclose(file);
}
Example #16
0
//-*****************************************************************************
void
WriteReferences( hid_t iParent,
                 const std::string& iRefName,
                 size_t iNumRefs,
                 const void *iRefs )
{
    hsize_t dims[1];
    dims[0] = iNumRefs;

    hid_t dspaceId = H5Screate_simple( 1, dims, NULL );
    DspaceCloser dspaceCloser( dspaceId );

    hid_t dsetId = H5Dcreate2( iParent, iRefName.c_str(), H5T_STD_REF_OBJ,
                               dspaceId, H5P_DEFAULT, H5P_DEFAULT,H5P_DEFAULT);
    DsetCloser dsetCloser( dsetId );

    herr_t status = H5Dwrite( dsetId, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL,
                       H5P_DEFAULT, iRefs);

    ABCA_ASSERT( status >= 0, "Couldn't write reference: " << iRefName );
}
Example #17
0
herr_t Compartment::saveHdf5(hid_t group) const
{
	hid_t dataspace, dataset;
	herr_t status;

	hsize_t dims[1];
	dims[0]=4;

	dataspace = H5Screate_simple(1, dims, NULL);
	// dataset = H5Dcreate(group, id().c_str(), H5T_NATIVE_INT, dataspace,
        //                 H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
	dataset = H5Dcreate2(group, id().c_str(), H5T_NATIVE_INT, dataspace,
                        H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    
	int boundaries[4] = { x0_, y0_, x1_, y1_ };
    status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &(boundaries));
	status = H5Dclose(dataset);
	status = H5Sclose(dataspace);

	return status;
}
Example #18
0
int
write_data_to_hdf5_file (int nx, int ny, double **data, hid_t file)
{

  hid_t dataset;		/* file and dataset handles */
  hid_t datatype, dataspace;	/* handles */
  hsize_t dimsf[2];		/* dataset dimensions */
  herr_t status;


  dimsf[0] = nx;
  dimsf[1] = ny;
  dataspace = H5Screate_simple (RANK, dimsf, NULL);
  /*
   * Define datatype for the data in the file.
   * We will store little endian DOUBLE numbers.
   */
  datatype = H5Tcopy (H5T_NATIVE_DOUBLE);
  status = H5Tset_order (datatype, H5T_ORDER_LE);
  /*
   * Create a new dataset within the file using defined dataspace and
   * datatype and default dataset creation properties.
   */
  dataset = H5Dcreate (file, "Temperature", datatype, dataspace, H5P_DEFAULT);

  /*
   * Write the data to the dataset using default transfer properties.
   */
  status = H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
		     H5P_DEFAULT, data);

  /*
   * Close/release resources.
   */
  H5Sclose (dataspace);
  H5Tclose (datatype);
  H5Dclose (dataset);

  return 0;
}
Example #19
0
/*-------------------------------------------------------------------------
 * Function:	create_dataset
 *
 * Purpose:	Creates a square dataset with square chunks, registers a
 *		stupid compress/uncompress pair for counting I/O, and
 *		initializes the dataset.  The chunk size is in bytes, the
 *		dataset size is in terms of chunks.
 *
 * Return:	void
 *
 * Programmer:	Robb Matzke
 *              Thursday, May 14, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static void
create_dataset (void)
{
    hid_t	file, space, dcpl, dset;
    hsize_t	size[2];
    signed char	*buf;

    /* The file */
    file = H5Fcreate (FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_g);

    /* The data space */
    size[0] = size[1] = DS_SIZE * CH_SIZE;
    space = H5Screate_simple (2, size, size);

    /* The storage layout and compression */
    dcpl = H5Pcreate (H5P_DATASET_CREATE);
    size[0] = size[1] = CH_SIZE;
    H5Pset_chunk (dcpl, 2, size);
#ifdef H5_WANT_H5_V1_4_COMPAT
    H5Zregister (FILTER_COUNTER, "counter", counter);
#else /* H5_WANT_H5_V1_4_COMPAT */
    H5Zregister (H5Z_COUNTER);
#endif /* H5_WANT_H5_V1_4_COMPAT */
    H5Pset_filter (dcpl, FILTER_COUNTER, 0, 0, NULL);

    /* The dataset */
    dset = H5Dcreate (file, "dset", H5T_NATIVE_SCHAR, space, dcpl);
    assert (dset>=0);

    /* The data */
    buf = calloc (1, SQUARE (DS_SIZE*CH_SIZE));
    H5Dwrite (dset, H5T_NATIVE_SCHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
    free (buf);

    /* Close */
    H5Dclose (dset);
    H5Sclose (space);
    H5Pclose (dcpl);
    H5Fclose (file);
}
Example #20
0
/**
   create the DS for uniform data.
 */
void NSDFWriter::createUniformMap()
{
    // Create the container for all the DS
    // TODO: make a common function like `mkdir -p` to avoid repeating this
    htri_t exists;
    herr_t status;
    hid_t uniformMapContainer = require_group(filehandle_, MAPUNIFORMSRC);
    // Create the DS themselves
    for (map< string, vector < unsigned int > >::iterator ii = classFieldToSrcIndex_.begin();
         ii != classFieldToSrcIndex_.end(); ++ii){
        vector < string > pathTokens;
        tokenize(ii->first, "/", pathTokens);
        string className = pathTokens[0];
        string fieldName = pathTokens[1];
        hid_t container = require_group(uniformMapContainer, className);
        char ** sources = (char **)calloc(ii->second.size(), sizeof(char*));
        for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
            sources[jj] = (char*)calloc(src_[ii->second[jj]].path().length()+1, sizeof(char));
            strcpy(sources[jj],src_[ii->second[jj]].path().c_str());
        }
        hid_t ds = createStringDataset(container, fieldName, (hsize_t)ii->second.size(), (hsize_t)ii->second.size());
        hid_t memtype = H5Tcopy(H5T_C_S1);
        status = H5Tset_size(memtype, H5T_VARIABLE);
        assert(status >= 0);
        status = H5Dwrite(ds, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, sources);
#ifndef NDEBUG        
        cout << "Write dataset: status=" << status << endl;
#endif
        assert(status >= 0);
        for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
            free(sources[jj]);
        }
        free(sources);
        status = H5DSset_scale(ds, "source");
        status = H5DSattach_scale(classFieldToUniform_[ii->first], ds, 0);
        status = H5DSset_label(classFieldToUniform_[ii->first], 0, "source");
        status = H5Dclose(ds);
        status = H5Tclose(memtype);                          
    } 
}
Example #21
0
File: hdf5.c Project: leobago/fti
int FTI_WriteElements(hid_t dataspace, hid_t dataType, hid_t dataset, hsize_t *count, hsize_t *offset, hsize_t ranks, void *ptr)
{
    char str[FTI_BUFS];
    hid_t status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL,count, NULL);
    hsize_t *dims_in= (hsize_t*) malloc (sizeof(hsize_t)*ranks);
    memcpy(dims_in,count,ranks*sizeof(hsize_t));
    hid_t memspace = H5Screate_simple(ranks,dims_in, NULL); 
    hsize_t *offset_in = (hsize_t*) calloc (ranks,sizeof(ranks));
    status = H5Sselect_hyperslab( memspace, H5S_SELECT_SET, offset_in, NULL, count, NULL);
    status = H5Dwrite(dataset, dataType, memspace, dataspace, H5P_DEFAULT, ptr);  
    if (status < 0) {
        free(offset);
        free(count);
        sprintf(str, "Dataset could not be written");
        FTI_Print(str, FTI_EROR);
        return FTI_NSCS;
    }
    free(offset_in);
    free(dims_in);
    return FTI_SCES;

}
Example #22
0
/**
* \brief Writes an entire set of region definitions to the file overwriting
*        any existing regions data.
* \param[in] file_id The HDF file reference id
* \param[in] n       Number of regions to write
* \param[in] points  The regions data in a contiguous array
* \returns Status code
* \retval 1 Failure
* \retval 0 Success
*/
int ch5m_regn_set_all(hid_t file_id, int n, int *regions) {
  hid_t group_id = ch5_gnrc_open_or_create_group(file_id,
    CH5_REGN_GROUP_NAME);
  if (group_id < 0) return 1;
  
  hid_t dset_id = ch5_gnrc_open_or_create_chunked_dset(group_id,
    CH5_REGN_DSET_NAME, H5T_STD_U32LE, 2,
    (hsize_t[2]){ n, 2 },
    (hsize_t[2]){ H5S_UNLIMITED, 2 },
    (hsize_t[2]){ CH5_REGN_CHUNK_SIZE, 2 }, 1);
  if (dset_id < 0) {
    H5Gclose(group_id);
    return 1;
  }
  
  herr_t status = H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
    H5P_DEFAULT, regions);
  
  H5Dclose(dset_id);
  
  return (status < 0);
}
Example #23
0
/**
* \brief Writes an entire set of points to the file overwriting any existing
*        points data.
* \param[in] file_id The HDF file reference id
* \param[in] n       Number of points to write
* \param[in] points  The points data in a contiguous array
* \returns Status code
* \retval 1 Failure
* \retval 0 Success
*/
int ch5m_pnts_set_all(hid_t file_id, int n, float *points) {
  hid_t group_id = ch5_gnrc_open_or_create_group(file_id,
    CH5_POINTS_GROUP_NAME);
  if (group_id < 0) return 1;
  
  hid_t dset_id = ch5_gnrc_open_or_create_chunked_dset(group_id,
    CH5_POINTS_DSET_NAME, H5T_IEEE_F32LE, 2,
    (hsize_t[2]){ n, 3 },
    (hsize_t[2]){ H5S_UNLIMITED, 3 },
    (hsize_t[2]){ CH5_POINTS_CHUNK_SIZE, 3 }, 1);
  if (dset_id < 0) {
    H5Gclose(group_id);
    return 1;
  }
  
  herr_t status = H5Dwrite(dset_id, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
    H5P_DEFAULT, points);
  
  H5Dclose(dset_id);
  
  return (status < 0);
}
Example #24
0
File: cxi.c Project: cxidb/libcxi
int cxi_write_dataset_slice(CXI_Dataset * dataset,unsigned int slice, void * data, hid_t datatype){
  if(!dataset){
    return -1;
  }
  if(!data){
    return -1;
  }
  if(slice >= dataset->dimensions[0]){
    return -1;
  }
  if(dataset->handle < 0){
    return -1;
  }

  hid_t s = H5Dget_space(dataset->handle);
  if(s < 0){
    return -1;
  }
  hsize_t *start;
  start = malloc(sizeof(hsize_t)*dataset->dimension_count);
  hsize_t *count;
  count = malloc(sizeof(hsize_t)*dataset->dimension_count);
  for(int i =0;i<dataset->dimension_count;i++){
    start[i] = 0;
    count[i] = dataset->dimensions[i];
  }

  start[0] = slice;
  count[0] = 1;
  hid_t memspace = H5Screate_simple (dataset->dimension_count, count, NULL);
  
  H5Sselect_hyperslab(s, H5S_SELECT_SET, start, NULL, count, NULL);
  H5Dwrite(dataset->handle,datatype,memspace,s,H5P_DEFAULT,data);      
  H5Sclose(s);
  free(start);
  free(count);

  return 0;
}
Example #25
0
herr_t H5ARRAYwrite_records( hid_t dataset_id,
			     hid_t type_id,
			     const int rank,
			     hsize_t *start,
			     hsize_t *step,
			     hsize_t *count,
			     const void *data )
{

 hid_t    space_id;
 hid_t    mem_space_id;

 /* Create a simple memory data space */
 if ( (mem_space_id = H5Screate_simple( rank, count, NULL )) < 0 )
   return -3;

 /* Get the file data space */
 if ( (space_id = H5Dget_space( dataset_id )) < 0 )
  return -4;

 /* Define a hyperslab in the dataset */
 if ( rank != 0 && H5Sselect_hyperslab( space_id, H5S_SELECT_SET, start,
					step, count, NULL) < 0 )
  return -5;

 if ( H5Dwrite( dataset_id, type_id, mem_space_id, space_id, H5P_DEFAULT, data ) < 0 )
   return -6;

 /* Terminate access to the dataspace */
 if ( H5Sclose( mem_space_id ) < 0 )
   return -7;

 if ( H5Sclose( space_id ) < 0 )
   return -8;

 /* Everything went smoothly */
 return 0;
}
Example #26
0
int luaC_h5_write_string(lua_State *L)
{
  const char *dsetnm = luaL_checkstring(L, 1);
  const char *string = luaL_checkstring(L, 2);

  if (PresentFile < 0) {
    luaL_error(L, "no open file");
  }

  hsize_t size = strlen(string);
  hid_t fspc = H5Screate(H5S_SCALAR);
  hid_t strn = H5Tcopy(H5T_C_S1);
  H5Tset_size(strn, size);

  hid_t dset = H5Dcreate(PresentFile, dsetnm, strn, fspc,
                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  H5Dwrite(dset, strn, fspc, fspc, H5P_DEFAULT, string);
  H5Dclose(dset);
  H5Tclose(strn);
  H5Sclose(fspc);

  return 0;
}
Example #27
0
herr_t ASDF_write_provenance_data(hid_t loc_id, const char *provenance_string) {
  hsize_t dims[1] = {strlen(provenance_string)};
  hsize_t maxdims[1] = {H5S_UNLIMITED};

  hid_t array_id, group_id, space_id, dcpl_id;

  CHK_H5(space_id = H5Screate_simple(1, dims, maxdims));
  CHK_H5(dcpl_id = H5Pcreate(H5P_DATASET_CREATE));
  CHK_H5(H5Pset_chunk(dcpl_id, 1, dims));

  CHK_H5(group_id = H5Gcreate(loc_id, "Provenance",
        H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
  CHK_H5(array_id = H5Dcreate(group_id, "373da5fe_d424_4f44_9bca_4334d77ed10b", H5T_STD_I8LE, space_id,
	H5P_DEFAULT, dcpl_id, H5P_DEFAULT));
  CHK_H5(H5Dwrite(array_id, H5T_STD_I8LE, H5S_ALL, H5S_ALL,
	H5P_DEFAULT, provenance_string));

  CHK_H5(H5Dclose(array_id));
  CHK_H5(H5Gclose(group_id));
  CHK_H5(H5Sclose(space_id));

  return 0; // Success
}
Example #28
0
/* open twist# */
void F77_FUNC_(pwhdf_open_twist,PWHDF_OPEN_TWIST)(const int* ik, const double *xk,
    const int* nband, const int* nspin)
{
  char twistname[16];
  sprintf(twistname,"twist%i",(*ik)-1);
  if(h_twist>=0) H5Gclose(h_twist);
  h_twist = H5Gcreate(h_main,twistname,0);

  /* write twist_angle */
  hsize_t dim=3;
  hid_t dataspace= H5Screate_simple(1, &dim, NULL);
  hid_t dataset= H5Dcreate(h_twist, "twist_angle", H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT);
  hid_t ret = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,xk);
  H5Sclose(dataspace);
  H5Dclose(dataset);

  if((xk[0]*xk[0]+xk[1]*xk[1]+xk[2]*xk[2]) < 1e-12)
    is_gamma=1;
  else
    is_gamma=0;
  
  /* create band#/spin# groups so that H5Gopen can be used */
  for(int ib=0; ib<*nband; ib++) 
  {
    char bandname[16];
    sprintf(bandname,"band%i",ib);
    hid_t h_band = H5Gcreate(h_twist,bandname,0);
    for(int ispin=0; ispin<*nspin; ispin++)
    {
      char spinname[16];
      sprintf(spinname,"spin%i",ispin);
      hid_t h_spin = H5Gcreate(h_band,spinname,0);
      H5Gclose(h_spin);
    }
    H5Gclose(h_band);
  }
}
Example #29
0
void BigArray<T>::setMatrix(unsigned long startingRow, unsigned long startingCol, const T* M, const unsigned long M_rows, const unsigned long M_cols)
{
    if(startingRow >= this->numrows || startingCol >= this->numcols)
        throw gException(Exception_Index_Out_of_Bound);

    if(startingRow+M_rows > this->numrows || startingCol+M_cols > this->numcols)
        throw gException(Exception_Index_Out_of_Bound);

    std::string errorString("Error writing matrix data");

    hsize_t dims[2] = {M_cols, M_rows};
    hid_t memspace = H5Screate_simple(2, dims, NULL);
    CHECK_HDF5_ERR(memspace, errorString)

    hsize_t	count[2] = {1, 1};
    hsize_t	stride[2] = {1, 1};
    hsize_t	block[2] = {dims[0], dims[1]};
    hsize_t	offset[2] = {startingCol, startingRow};


    // Select hyperslab in the file.
    hid_t filespace = H5Dget_space(dset_id);
    CHECK_HDF5_ERR(filespace, errorString)

    herr_t status;
    status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, stride, count, block);
    CHECK_HDF5_ERR(status, errorString)

    status = H5Dwrite(dset_id, getHdfType<T>(), memspace, filespace, plist_id, M);
    CHECK_HDF5_ERR(status, errorString)

    H5Sclose(memspace);
    CHECK_HDF5_ERR(status, errorString)

    H5Sclose(filespace);
    CHECK_HDF5_ERR(status, errorString)
}
Example #30
0
/*-------------------------------------------------------------------------
 * Function:    gent_named_vl
 *
 * Purpose:     Generate a variable lenght named datatype for a dataset in
                LOC_ID
 *
 *-------------------------------------------------------------------------
 */
static void gent_named_vl(hid_t loc_id)
{
    hid_t   sid, did, tid;
    hsize_t dims[1] = {2};
    hvl_t   buf[2];

    /* allocate and initialize VL dataset to write */
    buf[0].len = 1;
    buf[0].p = HDmalloc( 1 * sizeof(int));
    ((int *)buf[0].p)[0]=1;
    buf[1].len = 2;
    buf[1].p = HDmalloc( 2 * sizeof(int));
    ((int *)buf[1].p)[0]=2;
    ((int *)buf[1].p)[1]=3;

    /* create dataspace */
    sid = H5Screate_simple(1, dims, NULL);

    /* create datatype */
    tid = H5Tvlen_create(H5T_NATIVE_INT);

    /* create named datatype */
    H5Tcommit2(loc_id, "vl", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    /* create dataset */
    did = H5Dcreate2(loc_id, DATASET_NAMED_VL, tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    /* write */
    H5Dwrite(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);

    /* close */
    H5Dvlen_reclaim(tid,sid,H5P_DEFAULT,buf);
    H5Sclose(sid);
    H5Dclose(did);
    H5Tclose(tid);
}