Example #1
0
/*-------------------------------------------------------------------------
 * Function:    create_symbol_datatype
 *
 * Purpose:     Create's the HDF5 datatype used for elements in the SWMR
 *              testing datasets.
 *
 * Parameters:  N/A
 *
 * Return:      Success:    An HDF5 type ID
 *              Failure:    -1
 *
 *-------------------------------------------------------------------------
 */
hid_t
create_symbol_datatype(void)
{
    hid_t sym_type_id;          /* Datatype ID for symbol */
    hid_t opaq_type_id;         /* Datatype ID for opaque part of record */

    /* Create opaque datatype to represent other information for this record */
    if((opaq_type_id = H5Tcreate(H5T_OPAQUE, (size_t)DTYPE_SIZE)) < 0)
        return -1;

    /* Create compound datatype for symbol */
    if((sym_type_id = H5Tcreate(H5T_COMPOUND, sizeof(symbol_t))) < 0)
        return -1;

    /* Insert fields in symbol datatype */
    if(H5Tinsert(sym_type_id, "rec_id", HOFFSET(symbol_t, rec_id), H5T_NATIVE_UINT64) < 0)
        return -1;
    if(H5Tinsert(sym_type_id, "info", HOFFSET(symbol_t, info), opaq_type_id) < 0)
        return -1;

    /* Close opaque datatype */
    if(H5Tclose(opaq_type_id) < 0)
        return -1;

    return sym_type_id;
} /* end create_symbol_datatype() */
Example #2
0
/* Counterpart for complex256 */
hid_t create_ieee_complex256(const char *byteorder) {
  herr_t err = 0;
  hid_t float_id, complex_id;
  H5T_order_t h5order = H5Tget_order(H5T_NATIVE_LDOUBLE);

  complex_id = H5Tcreate(H5T_COMPOUND, sizeof(npy_complex256));
  float_id = H5Tcopy(H5T_NATIVE_LDOUBLE);
  if (float_id < 0)
  {
    H5Tclose(complex_id);
    return float_id;
  }

  if ((strcmp(byteorder, "little") == 0) && (h5order != H5T_ORDER_LE))
    err = H5Tset_order(float_id, H5T_ORDER_LE);
  else if ((strcmp(byteorder, "big") == 0) && (h5order != H5T_ORDER_BE))
    err = H5Tset_order(float_id, H5T_ORDER_BE);

  if (err < 0)
  {
    H5Tclose(complex_id);
    return err;
  }

  H5Tinsert(complex_id, "r", HOFFSET(npy_complex256, real), float_id);
  H5Tinsert(complex_id, "i", HOFFSET(npy_complex256, imag), float_id);
  H5Tclose(float_id);
  return complex_id;
}
Example #3
0
/*-------------------------------------------------------------------------
 * function to create a datatype representing the particle struct
 *-------------------------------------------------------------------------
 */
static hid_t
make_particle_type(void)
{
    hid_t type_id;
    hid_t string_type;
    size_t type_size = sizeof(particle_t);

    /* Create the memory data type. */
    if ((type_id = H5Tcreate (H5T_COMPOUND, type_size )) < 0 )
        return -1;

    /* Insert fields. */
    string_type = H5Tcopy( H5T_C_S1 );
    H5Tset_size( string_type, (size_t)16 );

    if ( H5Tinsert(type_id, "Name", HOFFSET(particle_t, name) , string_type ) < 0 )
        return -1;
    if ( H5Tinsert(type_id, "Lat", HOFFSET(particle_t, lati) , H5T_NATIVE_INT ) < 0 )
        return -1;
    if ( H5Tinsert(type_id, "Long", HOFFSET(particle_t, longi) , H5T_NATIVE_INT ) < 0 )
        return -1;
    if ( H5Tinsert(type_id, "Pressure", HOFFSET(particle_t, pressure) , H5T_NATIVE_FLOAT ) < 0 )
        return -1;
    if ( H5Tinsert(type_id, "Temperature", HOFFSET(particle_t, temperature) , H5T_NATIVE_DOUBLE ) < 0 )
        return -1;

    return type_id;
}
Example #4
0
    /** Creates a HDF5 type identifier for the [kmer,abundance] structure. This type will be used
     * for dumping Count instances in a HDF5 file (like SortingCount algorithm does).
     * \param[in] isCompound : tells whether the structure is compound (SHOULD BE OBSOLETE IN THE FUTURE)
     * \return the HDF5 identifier for the type. */
    static hid_t hdf5 (bool& isCompound)
    {
        hid_t abundanceType = H5T_NATIVE_UINT16;

        if (sizeof(Number)==1) {
            abundanceType = H5T_NATIVE_UINT8;
        }
        else if (sizeof(Number)==2) {
            abundanceType = H5T_NATIVE_UINT16;
        }
        else if (sizeof(Number)==4) {
            abundanceType = H5T_NATIVE_UINT32;
        }
        else if (sizeof(Number)==8) {
            abundanceType = H5T_NATIVE_UINT64;
        }
        else {
            throw "Bad type size for Abundance HDF5 serialization";
        }

        hid_t result = H5Tcreate (H5T_COMPOUND, sizeof(Abundance));
        H5Tinsert (result, "value",      HOFFSET(Abundance, value),     Type::hdf5(isCompound));
        H5Tinsert (result, "abundance",  HOFFSET(Abundance, abundance), abundanceType);

        isCompound = true;

        return result;
    }
Example #5
0
/*-------------------------------------------------------------------------
 * Function:    gent_compound
 *
 * Purpose:     Generate a compound dataset in LOC_ID
 *
 *-------------------------------------------------------------------------
 */
static void gent_compound(hid_t loc_id)
{
    typedef struct s_t
    {
        char str1[20];
        char str2[20];
    } s_t;
    hid_t   sid, did, tid_c, tid_s;
    hsize_t dims[1] = {2};
    s_t     buf[2]  = {{"str1", "str2"}, {"str3", "str4"}};

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

    /* create a compound type */
    tid_c = H5Tcreate(H5T_COMPOUND, sizeof(s_t));
    tid_s = H5Tcopy(H5T_C_S1);
    H5Tset_size(tid_s, 20);

    H5Tinsert(tid_c, "str1", HOFFSET(s_t,str1), tid_s);
    H5Tinsert(tid_c, "str2", HOFFSET(s_t,str2), tid_s);

    /* create dataset */
    did = H5Dcreate2(loc_id, DATASET_COMPOUND, tid_c, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

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

    /* close */
    H5Sclose(sid);
    H5Dclose(did);
    H5Tclose(tid_c);
    H5Tclose(tid_s);
}
Example #6
0
int main(int argc, char *argv[])
{
    hdf_sa_t arr[LEN];
    initArr(arr, LEN);

    // create data type corresponding to compound struct
    hid_t cid = H5Tcreate(H5T_COMPOUND, sizeof(hdf_sa_t));
    H5Tinsert(cid, "a", HOFFSET(hdf_sa_t, a), H5T_NATIVE_INT);
    H5Tinsert(cid, "b", HOFFSET(hdf_sa_t, b), H5T_NATIVE_FLOAT);
    H5Tinsert(cid, "c", HOFFSET(hdf_sa_t, c), H5T_NATIVE_DOUBLE);

    // write data to file
    hid_t fid = H5Fcreate("compound.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    // create data space
    hsize_t dim[1] = {LEN};
    hid_t space = H5Screate_simple(1, dim, NULL);
    hid_t dataset = H5Dcreate(fid, "compound", cid, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    // write data 
    H5Dwrite(dataset, cid, H5S_ALL, H5S_ALL, H5P_DEFAULT, arr);

    H5Sclose(space);
    H5Dclose(dataset);
    H5Fclose(fid);

    return 0;
}
Example #7
0
void pyne::Material::_load_comp_protocol1(H5::H5File * db, std::string datapath, int row)
{
  H5::DataSet data_set = (*db).openDataSet(datapath);

  hsize_t data_offset[1] = {row};
  if (row < 0)
  {
    // Handle negative row indecies
    H5::DataSpace data_space = data_set.getSpace();
    hsize_t data_dims[1];
    int data_rank = data_space.getSimpleExtentDims(data_dims);
    data_offset[0] += data_dims[0];
  };

  // Grab the nucpath
  std::string nucpath;
  H5::Attribute nuc_attr = data_set.openAttribute("nucpath");
  hsize_t nuc_attr_len = nuc_attr.getStorageSize() / sizeof(char);
  H5::StrType nuc_attr_type(0, nuc_attr_len);
  nuc_attr.read(nuc_attr_type, nucpath);

  // Grab the nuclides
  std::vector<int> nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(db, nucpath, H5::PredType::NATIVE_INT);
  int nuc_size = nuclides.size();
  hsize_t nuc_dims[1] = {nuc_size};

  // Get the data hyperslab
  H5::DataSpace data_hyperslab = data_set.getSpace();
  hsize_t data_count[1] = {1};
  data_hyperslab.selectHyperslab(H5S_SELECT_SET, data_count, data_offset);

  // Get memory space for writing
  H5::DataSpace mem_space (1, data_count);

  // Get material type
  size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*(nuc_size);
  H5::CompType data_desc(material_struct_size);
  H5::ArrayType comp_values_array_type (H5::PredType::NATIVE_DOUBLE, 1, nuc_dims);

  // make the data table type
  data_desc.insertMember("name", HOFFSET(pyne::material_struct, name), H5::StrType(0, 20));
  data_desc.insertMember("mass", HOFFSET(pyne::material_struct, mass), H5::PredType::NATIVE_DOUBLE);
  data_desc.insertMember("atoms_per_mol", HOFFSET(pyne::material_struct, atoms_per_mol), H5::PredType::NATIVE_DOUBLE);
  data_desc.insertMember("comp", HOFFSET(pyne::material_struct, comp), comp_values_array_type);

  // make the data array, have to over-allocate
  material_struct * mat_data = (material_struct *) malloc(material_struct_size);

  // Finally, get data and put in on this instance
  data_set.read(mat_data, data_desc, mem_space, data_hyperslab);

  name = std::string((*mat_data).name);
  mass = (*mat_data).mass;
  atoms_per_mol = (*mat_data).atoms_per_mol;
  for (int i = 0; i < nuc_size; i++)
    comp[nuclides[i]] = (double) (*mat_data).comp[i];

  free(mat_data);
};
Example #8
0
 inline static hid_t hdf5 (bool& compound)
 {
     hid_t result = H5Tcreate (H5T_COMPOUND, sizeof(Entry));
     H5Tinsert (result, "index",      HOFFSET(Entry, index),     H5T_NATIVE_UINT16);
     H5Tinsert (result, "abundance",  HOFFSET(Entry, abundance), H5T_NATIVE_UINT64);
     compound = true;
     return result;
 }
Example #9
0
void NSDFWriter::createEventMap()
{
    herr_t status;    
    hid_t eventMapContainer = require_group(filehandle_, MAPEVENTSRC);
    // Open the container for the event maps
    // Create the Datasets themselves (one for each field - each row
    // for one object).
    for (map< string, vector < string > >::iterator ii = classFieldToEventSrc_.begin();
         ii != classFieldToEventSrc_.end();
         ++ii){
        vector < string > pathTokens;
        tokenize(ii->first, "/", pathTokens);
        string className = pathTokens[0];
        string fieldName = pathTokens[1];
        hid_t classGroup = require_group(eventMapContainer, className);
        hid_t strtype = H5Tcopy(H5T_C_S1);
        status = H5Tset_size(strtype, H5T_VARIABLE);
        // create file space
        hid_t ftype = H5Tcreate(H5T_COMPOUND, sizeof(hvl_t) +sizeof(hobj_ref_t));
        status = H5Tinsert(ftype, "source", 0, strtype);
        status = H5Tinsert(ftype, "data", sizeof(hvl_t), H5T_STD_REF_OBJ);
        hsize_t dims[1] = {ii->second.size()};
        hid_t space = H5Screate_simple(1, dims, NULL);
        // The dataset for mapping is named after the field
        hid_t ds = H5Dcreate2(classGroup, fieldName.c_str(), ftype, space,
                              H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        status = H5Sclose(space);
        map_type * buf = (map_type*)calloc(ii->second.size(), sizeof(map_type));
        // Populate the buffer entries with source uid and data
        // reference
        for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
            buf->source = ii->second[jj].c_str();
            char * dsname = (char*)calloc(256, sizeof(char));
            ssize_t size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
            if (size > 255){
                free(dsname);
                dsname = (char*)calloc(size, sizeof(char));
                size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
            }
            status = H5Rcreate(&(buf->data), filehandle_, dsname, H5R_OBJECT, -1);
            free(dsname);
            assert(status >= 0);            
        }
        // create memory space
        hid_t memtype = H5Tcreate(H5T_COMPOUND, sizeof(map_type));
        status = H5Tinsert(memtype, "source",
                           HOFFSET(map_type, source), strtype);
        status = H5Tinsert(memtype, "data",
                           HOFFSET(map_type, data), H5T_STD_REF_OBJ);
        status = H5Dwrite(ds, memtype,  H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
        free(buf);
        status = H5Tclose(strtype);
        status = H5Tclose(ftype);
        status = H5Tclose(memtype);
        status = H5Dclose(ds);
    }
}
Example #10
0
inline
hid_t
get_hdf5_type< std::complex<double> >()
  {
  hid_t type = arma_H5Tcreate(H5T_COMPOUND, sizeof(hdf5_complex_t<double>));

  arma_H5Tinsert(type, "real", HOFFSET(hdf5_complex_t<double>, real), arma_H5T_NATIVE_DOUBLE);
  arma_H5Tinsert(type, "imag", HOFFSET(hdf5_complex_t<double>, imag), arma_H5T_NATIVE_DOUBLE);

  return type;
  }
inline
hid_t
get_hdf5_type< std::complex<float> >()
  {
  hid_t type = H5Tcreate(H5T_COMPOUND, sizeof(hdf5_complex_t<float>));
  
  H5Tinsert(type, "real", HOFFSET(hdf5_complex_t<float>, real), H5T_NATIVE_FLOAT);
  H5Tinsert(type, "imag", HOFFSET(hdf5_complex_t<float>, imag), H5T_NATIVE_FLOAT);
  
  return type;
  }
 static H5::CompType get_species_comp_type()
 {
     H5::CompType h5_species_comp_type(sizeof(h5_species_struct));
     h5_species_comp_type.insertMember(
         std::string("id"), HOFFSET(h5_species_struct, id),
         H5::PredType::STD_I32LE);
     h5_species_comp_type.insertMember(
         std::string("serial"), HOFFSET(h5_species_struct, serial),
         H5::StrType(H5::PredType::C_S1, 32));
     return h5_species_comp_type;
 }
 static H5::CompType get_particle_comp_type()
 {
     H5::CompType h5_particle_comp_type(sizeof(h5_particle_struct));
     h5_particle_comp_type.insertMember(
         std::string("lot"), HOFFSET(h5_particle_struct, lot),
         H5::PredType::NATIVE_INT);
     h5_particle_comp_type.insertMember(
         std::string("serial"), HOFFSET(h5_particle_struct, serial),
         H5::PredType::NATIVE_INT);
     h5_particle_comp_type.insertMember(
         std::string("sid"), HOFFSET(h5_particle_struct, sid),
         H5::PredType::STD_I32LE);
     h5_particle_comp_type.insertMember(
         std::string("posx"), HOFFSET(h5_particle_struct, posx),
         H5::PredType::NATIVE_DOUBLE);
     h5_particle_comp_type.insertMember(
         std::string("posy"), HOFFSET(h5_particle_struct, posy),
         H5::PredType::NATIVE_DOUBLE);
     h5_particle_comp_type.insertMember(
         std::string("posz"), HOFFSET(h5_particle_struct, posz),
         H5::PredType::NATIVE_DOUBLE);
     h5_particle_comp_type.insertMember(
         std::string("radius"), HOFFSET(h5_particle_struct, radius),
         H5::PredType::NATIVE_DOUBLE);
     h5_particle_comp_type.insertMember(
         std::string("D"), HOFFSET(h5_particle_struct, D),
         H5::PredType::NATIVE_DOUBLE);
     return h5_particle_comp_type;
 }
void write(hid_t& file, std::vector<Region>& regions)
{
  const size_t record_size = sizeof(Region);

  size_t record_offset[] = { HOFFSET(Region, bam_file_key),
                             HOFFSET(Region, chromosome),
                             HOFFSET(Region, region_name),
                             HOFFSET(Region, start),
                             HOFFSET(Region, stop),
                             HOFFSET(Region, strand),
                             HOFFSET(Region, count),
                             HOFFSET(Region, normalized_count) };

  size_t field_sizes[] = { sizeof(Region::bam_file_key),
                           sizeof(Region::chromosome),
                           sizeof(Region::region_name),
                           sizeof(Region::start),
                           sizeof(Region::stop),
                           sizeof(Region::strand),
                           sizeof(Region::count),
                           sizeof(Region::normalized_count) };

  herr_t status = H5TBappend_records(file, "region_counts", regions.size(), record_size, record_offset,
                                     field_sizes, regions.data());
  if (status != 0)
  {
    std::stringstream ss;
    ss << "Error appending record, status = " << status;
    throw std::runtime_error(ss.str());
  }
}
Example #15
0
hid_t linkDatatype()
{
	hid_t tLink;
	hid_t tPosition;
	hid_t tNumber;	
	
	tLink = H5Tcreate(H5T_COMPOUND, sizeof(link_t));
	tPosition = H5Tcopy(H5T_NATIVE_INT32);
	tNumber = H5Tcopy(H5T_NATIVE_INT32);
	H5Tinsert(tLink, "position", HOFFSET(link_t, position), tPosition);
	H5Tinsert(tLink, "number", HOFFSET(link_t, number), tNumber);
	H5Tclose(tPosition);
	H5Tclose(tNumber);
	return tLink;
}
Example #16
0
/* Counterpart for complex128 */
hid_t create_ieee_complex128(const char *byteorder) {
  hid_t float_id, complex_id;

  complex_id = H5Tcreate(H5T_COMPOUND, sizeof(npy_complex128));
  if (byteorder == NULL)
    float_id = H5Tcopy(H5T_NATIVE_DOUBLE);
  else if (strcmp(byteorder, "little") == 0)
    float_id = H5Tcopy(H5T_IEEE_F64LE);
  else
    float_id = H5Tcopy(H5T_IEEE_F64BE);
  H5Tinsert(complex_id, "r", HOFFSET(npy_complex128, real), float_id);
  H5Tinsert(complex_id, "i", HOFFSET(npy_complex128, imag), float_id);
  H5Tclose(float_id);
  return complex_id;
}
Example #17
0
int readDoubleComplexMatrix(int _iDatasetId, double *_pdblReal, double *_pdblImg)
{
    hid_t compoundId;
    herr_t status;
    int iDims = 0;
    int* piDims = NULL;
    int iComplex = 0;
    int iSize = 1;
    doublecomplex* pData = NULL;
    int i = 0;

    /*define compound dataset*/
    compoundId = H5Tcreate(H5T_COMPOUND, sizeof(doublecomplex));
    H5Tinsert(compoundId, "real", HOFFSET(doublecomplex, r), H5T_NATIVE_DOUBLE);
    H5Tinsert(compoundId, "imag", HOFFSET(doublecomplex, i), H5T_NATIVE_DOUBLE);

    //get dimension from dataset
    getDatasetInfo(_iDatasetId, &iComplex, &iDims, NULL);
    piDims = (int*)MALLOC(sizeof(int) * iDims);
    iSize = getDatasetInfo(_iDatasetId, &iComplex, &iDims, piDims);
    if (iSize < 0)
    {
        FREE(piDims);
        return -1;
    }

    FREE(piDims);
    //alloc temp array
    pData = (doublecomplex*)MALLOC(sizeof(doublecomplex) * iSize);
    //Read the data.
    status = H5Dread(_iDatasetId, compoundId, H5S_ALL, H5S_ALL, H5P_DEFAULT, pData);
    if (status < 0)
    {
        FREE(pData);
        return -1;
    }


    vGetPointerFromDoubleComplex(pData, iSize, _pdblReal, _pdblImg);
    FREE(pData);
    status = H5Dclose(_iDatasetId);
    if (status < 0)
    {
        return -1;
    }

    return 0;
}
Example #18
0
int main(){
  hid_t fprop;
  hid_t fid;
  hid_t vol_id = H5VL_memvol_init();
  char name[1024];

  // create some datatypes

  hid_t tid = H5Tcreate (H5T_COMPOUND, sizeof(complex_type));
  H5Tinsert(tid, "re", HOFFSET(complex_type,re), H5T_NATIVE_DOUBLE);
  H5Tinsert(tid, "im", HOFFSET(complex_type,im), H5T_NATIVE_DOUBLE);
  hid_t s10 = H5Tcopy(H5T_C_S1);
  H5Tset_size(s10, 10);
  H5Tinsert(tid, "name", HOFFSET(complex_type,name), s10);
  H5Tinsert(tid, "val", HOFFSET(complex_type,val), H5T_NATIVE_INT);

  // packed version of the datatype
  hid_t disk_tid = H5Tcopy (tid);
  H5Tpack(disk_tid);

  fprop = H5Pcreate(H5P_FILE_ACCESS);
  H5Pset_vol(fprop, vol_id, &fprop);

  fid = H5Fcreate("test", H5F_ACC_TRUNC, H5P_DEFAULT, fprop);
  H5VLget_plugin_name(fid, name, 1024);
  printf ("%s using VOL %s\n", __FILE__ , name);

  assert(H5Tcommit(fid, "t_complex", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT) >= 0);
  assert(H5Tcommit(fid, "t_complex_p", disk_tid,  H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT) >= 0);

  hid_t tid_stored1 = H5Topen(fid, "t_complex", H5P_DEFAULT);
  hid_t tid_stored2 = H5Topen(fid, "t_complex_p", H5P_DEFAULT);
  // hid_t tid_stored3 = H5Topen(fid, "NotExisting", H5P_DEFAULT);
  // assert(tid_stored3 < 0);

  assert(H5Tequal(tid_stored1, tid));
  assert(H5Tequal(tid_stored2, disk_tid));

  H5Fclose(fid);

  H5Tclose(tid);
  H5Tclose(disk_tid);

  H5VL_memvol_finalize();

  return 0;
}
Example #19
0
void pyne::_load_atomic_decay()
{
  // Loads the important parts of atomic_decay table into memory

  //Check to see if the file is in HDF5 format.
  if (!pyne::file_exists(pyne::NUC_DATA_PATH))
    throw pyne::FileNotFound(pyne::NUC_DATA_PATH);

  bool isH5 = H5::H5File::isHdf5(pyne::NUC_DATA_PATH);
  if (!isH5)
    throw h5wrap::FileNotHDF5(pyne::NUC_DATA_PATH);


  // Get the HDF5 compound type (table) description
  H5::CompType atom_dec_desc(sizeof(atomic_decay_struct));
  atom_dec_desc.insertMember("from_nuc_name", HOFFSET(atomic_decay_struct, from_nuc_name), H5::StrType(0, 6));
  atom_dec_desc.insertMember("from_nuc_zz",   HOFFSET(atomic_decay_struct, from_nuc_zz),   H5::PredType::NATIVE_INT);
  atom_dec_desc.insertMember("level", HOFFSET(atomic_decay_struct, level), H5::PredType::NATIVE_DOUBLE);
  atom_dec_desc.insertMember("to_nuc_name", HOFFSET(atomic_decay_struct, to_nuc_name), H5::StrType(0, 6));
  atom_dec_desc.insertMember("to_nuc_zz",   HOFFSET(atomic_decay_struct, to_nuc_zz),   H5::PredType::NATIVE_INT);
  atom_dec_desc.insertMember("half_life", HOFFSET(atomic_decay_struct, half_life), H5::PredType::NATIVE_DOUBLE);
  atom_dec_desc.insertMember("decay_const", HOFFSET(atomic_decay_struct, decay_const), H5::PredType::NATIVE_DOUBLE);
  atom_dec_desc.insertMember("branch_ratio", HOFFSET(atomic_decay_struct, branch_ratio), H5::PredType::NATIVE_DOUBLE);

  // Open the HDF5 file
  H5::H5File nuc_data_h5 (pyne::NUC_DATA_PATH.c_str(), H5F_ACC_RDONLY);

  // Open the data set
  H5::DataSet atom_dec_set = nuc_data_h5.openDataSet("/atomic_decay");
  H5::DataSpace atom_dec_space = atom_dec_set.getSpace();
  int atom_dec_length = atom_dec_space.getSimpleExtentNpoints();

  // Read in the data
  atomic_decay_struct * atom_dec_array = new atomic_decay_struct[atom_dec_length];
  atom_dec_set.read(atom_dec_array, atom_dec_desc);

  // close the nuc_data library, before doing anythng stupid
  nuc_data_h5.close();

  // Ok now that we have the array of stucts, put it in the maps
  // giving precednece to ground state values or those seen first.
  int from_nuc;
  double level;
  for(int n = 0; n < atom_dec_length; n++)
  {
    from_nuc = atom_dec_array[n].from_nuc_zz;
    level = atom_dec_array[n].level;

    if (0 == half_life_map.count(from_nuc) || 0.0 == level)
      half_life_map[from_nuc] = atom_dec_array[n].half_life;

    if (0 == decay_const_map.count(from_nuc) || 0.0 == level)
      decay_const_map[from_nuc] = atom_dec_array[n].decay_const;
  };
};
Example #20
0
/* Create a normal HL table just like the HL examples do */
static int create_hl_table(hid_t fid)
{
    /* Calculate the offsets of the particle struct members in memory */
    size_t part_offset[NFIELDS] = { HOFFSET( particle_t, name ),
                                    HOFFSET( particle_t, lati ),
                                    HOFFSET( particle_t, longi ),
                                    HOFFSET( particle_t, pressure ),
                                    HOFFSET( particle_t, temperature )
                                  };

    /* Define field information */
    const char *field_names[NFIELDS]  =
    { "Name","Latitude", "Longitude", "Pressure", "Temperature" };
    hid_t      field_type[NFIELDS];
    hid_t      string_type;
    hsize_t    chunk_size = 10;
    int        *fill_data = NULL;
    int        compress  = 0;
    herr_t     status;

    /* Initialize the field field_type */
    string_type = H5Tcopy( H5T_C_S1 );
    H5Tset_size( string_type, (size_t)16 );
    field_type[0] = string_type;
    field_type[1] = H5T_NATIVE_INT;
    field_type[2] = H5T_NATIVE_INT;
    field_type[3] = H5T_NATIVE_FLOAT;
    field_type[4] = H5T_NATIVE_DOUBLE;


    /*------------------------------------------------------------------------
    * H5TBmake_table
    *-------------------------------------------------------------------------
    */

    status=H5TBmake_table( "Table Title", fid, H5TB_TABLE_NAME, (hsize_t)NFIELDS,
                           (hsize_t)NRECORDS, sizeof(particle_t),
                           field_names, part_offset, field_type,
                           chunk_size, fill_data, compress, testPart  );

    if(status<0)
        return -1;
    else
        return 0;
}
Example #21
0
void pyne::_load_atomic_mass_map()
{
  // Loads the important parts of atomic_wight table into atomic_mass_map

  //Check to see if the file is in HDF5 format.
  if (!pyne::file_exists(pyne::NUC_DATA_PATH))
    throw pyne::FileNotFound(pyne::NUC_DATA_PATH);

  bool isH5 = H5::H5File::isHdf5(pyne::NUC_DATA_PATH);
  if (!isH5)
    throw h5wrap::FileNotHDF5(pyne::NUC_DATA_PATH);

  // Get the HDF5 compound type (table) description
  H5::CompType atomic_weight_desc(sizeof(atomic_weight_struct));
  atomic_weight_desc.insertMember("nuc_name", HOFFSET(atomic_weight_struct, nuc_name), H5::StrType(0, 6));
  atomic_weight_desc.insertMember("nuc_zz",   HOFFSET(atomic_weight_struct, nuc_zz),   H5::PredType::NATIVE_INT);
  atomic_weight_desc.insertMember("mass",     HOFFSET(atomic_weight_struct, mass),     H5::PredType::NATIVE_DOUBLE);
  atomic_weight_desc.insertMember("error",    HOFFSET(atomic_weight_struct, error),    H5::PredType::NATIVE_DOUBLE);
  atomic_weight_desc.insertMember("abund",    HOFFSET(atomic_weight_struct, abund),    H5::PredType::NATIVE_DOUBLE);

  // Open the HDF5 file
  H5::H5File nuc_data_h5 (pyne::NUC_DATA_PATH.c_str(), H5F_ACC_RDONLY);

  // Open the data set
  H5::DataSet atomic_weight_set = nuc_data_h5.openDataSet("/atomic_weight");
  H5::DataSpace atomic_weight_space = atomic_weight_set.getSpace();
  int atomic_weight_length = atomic_weight_space.getSimpleExtentNpoints();

  // Read in the data
  atomic_weight_struct * atomic_weight_array = new atomic_weight_struct[atomic_weight_length];
  atomic_weight_set.read(atomic_weight_array, atomic_weight_desc);

  // close the nuc_data library, before doing anythng stupid
  nuc_data_h5.close();

  // Ok now that we have the array of stucts, put it in the map
  for(int n = 0; n < atomic_weight_length; n++)
    atomic_mass_map[atomic_weight_array[n].nuc_zz] = atomic_weight_array[n].mass;
};
Example #22
0
/* Create a HDF5 compound datatype that represents complex numbers
   defined by numpy as complex64. */
hid_t create_ieee_complex64(const char *byteorder) {
  hid_t float_id, complex_id;

  complex_id = H5Tcreate(H5T_COMPOUND, sizeof(npy_complex64));
  if (byteorder == NULL)
    float_id = H5Tcopy(H5T_NATIVE_FLOAT);
  else if (strcmp(byteorder, "little") == 0)
    float_id = H5Tcopy(H5T_IEEE_F32LE);
  else
    float_id = H5Tcopy(H5T_IEEE_F32BE);

  if (float_id < 0)
  {
    H5Tclose(complex_id);
    return float_id;
  }

  H5Tinsert(complex_id, "r", HOFFSET(npy_complex64, real), float_id);
  H5Tinsert(complex_id, "i", HOFFSET(npy_complex64, imag), float_id);
  H5Tclose(float_id);
  return complex_id;
}
void write(hid_t& file,
           const std::vector<CountH5Record>& records)
{
  const size_t record_size = sizeof(CountH5Record);

  size_t record_offset[] = { HOFFSET(CountH5Record, bin_number),
                             HOFFSET(CountH5Record, cell_type),
                             HOFFSET(CountH5Record, chromosome),
                             HOFFSET(CountH5Record, count),
                             HOFFSET(CountH5Record, file_name) };

  size_t field_sizes[] = { sizeof(CountH5Record::bin_number),
                           sizeof(CountH5Record::cell_type),
                           sizeof(CountH5Record::chromosome),
                           sizeof(CountH5Record::count),
                           sizeof(CountH5Record::file_name) };

  herr_t status = H5TBappend_records(file, "bin_counts", records.size(), record_size,
                                     record_offset, field_sizes, records.data());
  if (status != 0)
  {
    std::cerr << "Error appending record, status = " << status << std::endl;
  }
}
Example #24
0
File: FileIO.cpp Project: xyuan/gkc
  // Constructor
  FileIO::FileIO(Parallel *_parallel, Setup *setup):     parallel(_parallel)
  {

    // Set Initial values
    inputFileName         = setup->get("DataOutput.InputFileName", "--- None ---");
    outputFileName        = setup->get("DataOutput.OutputFileName", "default.h5");
    info                  = setup->get("DataOutput.Info", "No information provided");
    resumeFile            = setup->get("DataOutput.Resume", 0);
    overwriteFile         = setup->get("DataOutput.Overwrite", 0) || (setup->flags & HELIOS_OVERWRITE);
   
     dataFileFlushTiming  = Timing(setup->get("DataOutput.Flush.Step", -1)       , setup->get("DataOutput.Flush.Time", 100.)); 
    

    ///////// Define Timeing Datatype
    timing_tid = H5Tcreate(H5T_COMPOUND, sizeof(Timing));
    H5Tinsert(timing_tid, "Timestep", HOFFSET(Timing, step), H5T_NATIVE_INT   );
    H5Tinsert(timing_tid, "Time"    , HOFFSET(Timing, time), H5T_NATIVE_DOUBLE);

    // don't changes r and i name otherwise it will break compatibiltiy with pyTables
    complex_tid = H5Tcreate(H5T_COMPOUND, sizeof (Complex));
    H5Tinsert(complex_tid, "r", HOFFSET(Complex,r), H5T_NATIVE_DOUBLE);
    H5Tinsert(complex_tid, "i", HOFFSET(Complex,i), H5T_NATIVE_DOUBLE);
    
    vector3D_tid = H5Tcreate(H5T_COMPOUND, sizeof (Vector3D));
    H5Tinsert(vector3D_tid, "x", HOFFSET(Vector3D,x), H5T_NATIVE_DOUBLE);
    H5Tinsert(vector3D_tid, "y", HOFFSET(Vector3D,y), H5T_NATIVE_DOUBLE);
    H5Tinsert(vector3D_tid, "z", HOFFSET(Vector3D,z), H5T_NATIVE_DOUBLE);
 
    hsize_t species_dim[] = { setup->get("Grid.Ns", 1)}; 
    species_tid = H5Tarray_create(H5T_NATIVE_DOUBLE, 1, species_dim);
    
    // used for species name
          // BUG : Somehow HDF-8 stores up to 8 chars fro 64 possible. Rest are truncated ! Why ?
    s256_tid = H5Tcopy(H5T_C_S1); H5Tset_size(s256_tid, 64); H5Tset_strpad(s256_tid, H5T_STR_NULLTERM);


    offset0[0] = 0;
    offset0[1] = 0;
    offset0[2] = 0;
    offset0[3] = 0;
    offset0[4] = 0;
    offset0[5] = 0;
    offset0[6] = 0;
    offset0[7] = 0;
    

    // Create/Load HDF5 file
    if(resumeFile == false || (inputFileName != outputFileName)) create(setup);

   }
Example #25
0
void pyne::_load_scattering_lengths()
{
  // Loads the important parts of atomic_wight table into atomic_mass_map

  //Check to see if the file is in HDF5 format.
  if (!pyne::file_exists(pyne::NUC_DATA_PATH))
    throw pyne::FileNotFound(pyne::NUC_DATA_PATH);

  bool isH5 = H5::H5File::isHdf5(pyne::NUC_DATA_PATH);
  if (!isH5)
    throw h5wrap::FileNotHDF5(pyne::NUC_DATA_PATH);


  // Get the HDF5 compound type (table) description
  H5::CompType scat_len_desc(sizeof(scattering_lengths_struct));
  scat_len_desc.insertMember("nuc_name", HOFFSET(scattering_lengths_struct, nuc_name), H5::StrType(0, 6));
  scat_len_desc.insertMember("nuc_zz",   HOFFSET(scattering_lengths_struct, nuc_zz),   H5::PredType::NATIVE_INT);
  scat_len_desc.insertMember("b_coherent", HOFFSET(scattering_lengths_struct, b_coherent), h5wrap::PYTABLES_COMPLEX128);
  scat_len_desc.insertMember("b_incoherent", HOFFSET(scattering_lengths_struct, b_incoherent), h5wrap::PYTABLES_COMPLEX128);
  scat_len_desc.insertMember("xs_coherent", HOFFSET(scattering_lengths_struct, xs_coherent), H5::PredType::NATIVE_DOUBLE);
  scat_len_desc.insertMember("xs_incoherent", HOFFSET(scattering_lengths_struct, xs_incoherent), H5::PredType::NATIVE_DOUBLE);
  scat_len_desc.insertMember("xs", HOFFSET(scattering_lengths_struct, xs), H5::PredType::NATIVE_DOUBLE);

  // Open the HDF5 file
  H5::H5File nuc_data_h5 (pyne::NUC_DATA_PATH.c_str(), H5F_ACC_RDONLY);

  // Open the data set
  H5::DataSet scat_len_set = nuc_data_h5.openDataSet("/neutron/scattering_lengths");
  H5::DataSpace scat_len_space = scat_len_set.getSpace();
  int scat_len_length = scat_len_space.getSimpleExtentNpoints();

  // Read in the data
  scattering_lengths_struct * scat_len_array = new scattering_lengths_struct[scat_len_length];
  scat_len_set.read(scat_len_array, scat_len_desc);

  // close the nuc_data library, before doing anythng stupid
  nuc_data_h5.close();

  // Ok now that we have the array of stucts, put it in the maps
  for(int n = 0; n < scat_len_length; n++)
  {
    b_coherent_map[scat_len_array[n].nuc_zz] = scat_len_array[n].b_coherent;
    b_incoherent_map[scat_len_array[n].nuc_zz] = scat_len_array[n].b_incoherent;
  };
};
Example #26
0
/*-------------------------------------------------------------------------
 * Function:	test_data_conv
 *
 * Purpose:	Test data conversion
 *
 * Return:	Success:	0
 *
 *		Failure:	1
 *
 * Programmer:  Raymond Lu	
 *              30 November 2012
 *
 *-------------------------------------------------------------------------
 */
static int
test_data_conv(hid_t file)
{
    typedef struct {
	int a, b, c[4], d, e;
    } src_type_t;
    typedef struct {
	int a,    c[4],    e;
    } dst_type_t;

    hid_t       dataspace = -1, dataset = -1;
    hid_t       mem_space = -1;
    hid_t       cparms = -1, dxpl = -1;
    hsize_t     dims[2]  = {NX, NY};        
    hsize_t     maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
    hsize_t     chunk_dims[2] ={CHUNK_NX, CHUNK_NY};
    herr_t      status;
    int         i, j, n;
    const hsize_t	four = 4;
    hid_t	st=-1, dt=-1;
    hid_t       array_dt;

    unsigned    filter_mask = 0;
    src_type_t  direct_buf[CHUNK_NX][CHUNK_NY];
    dst_type_t  check_chunk[CHUNK_NX][CHUNK_NY];
    hsize_t     offset[2] = {0, 0};
    size_t      buf_size = CHUNK_NX*CHUNK_NY*sizeof(src_type_t);

    hsize_t start[2];  /* Start of hyperslab */
    hsize_t stride[2]; /* Stride of hyperslab */
    hsize_t count[2];  /* Block count */
    hsize_t block[2];  /* Block sizes */

    TESTING("data conversion for H5DOwrite_chunk");

    /*
     * Create the data space with unlimited dimensions.
     */
    if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0)
        goto error;

    if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
        goto error;

    /*
     * Modify dataset creation properties, i.e. enable chunking
     */
    if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
        goto error;

    if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0)
        goto error;

    /* Build hdf5 datatypes */
    array_dt = H5Tarray_create2(H5T_NATIVE_INT, 1, &four);
    if((st = H5Tcreate(H5T_COMPOUND, sizeof(src_type_t))) < 0 ||
            H5Tinsert(st, "a", HOFFSET(src_type_t, a), H5T_NATIVE_INT) < 0 ||
            H5Tinsert(st, "b", HOFFSET(src_type_t, b), H5T_NATIVE_INT) < 0 ||
            H5Tinsert(st, "c", HOFFSET(src_type_t, c), array_dt) < 0 ||
            H5Tinsert(st, "d", HOFFSET(src_type_t, d), H5T_NATIVE_INT) < 0 ||
            H5Tinsert(st, "e", HOFFSET(src_type_t, e), H5T_NATIVE_INT) < 0)
        goto error;

    if(H5Tclose(array_dt) < 0)
        goto error;

    array_dt = H5Tarray_create2(H5T_NATIVE_INT, 1, &four);
    if((dt = H5Tcreate(H5T_COMPOUND, sizeof(dst_type_t))) < 0 ||
            H5Tinsert(dt, "a", HOFFSET(dst_type_t, a), H5T_NATIVE_INT) < 0 ||
            H5Tinsert(dt, "c", HOFFSET(dst_type_t, c), array_dt) < 0 ||
            H5Tinsert(dt, "e", HOFFSET(dst_type_t, e), H5T_NATIVE_INT) < 0)
        goto error;

    if(H5Tclose(array_dt) < 0)
        goto error;

    /*
     * Create a new dataset within the file using cparms
     * creation properties.
     */
    if((dataset = H5Dcreate2(file, DATASETNAME4, st, dataspace, H5P_DEFAULT,
			cparms, H5P_DEFAULT)) < 0)
        goto error;

    if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
        goto error;

    /* Initialize data for one chunk */
    for(i = n = 0; i < CHUNK_NX; i++) {
        for(j = 0; j < CHUNK_NY; j++) {
            (direct_buf[i][j]).a    = i*j+0;
            (direct_buf[i][j]).b    = i*j+1;
            (direct_buf[i][j]).c[0] = i*j+2;
            (direct_buf[i][j]).c[1] = i*j+3;
            (direct_buf[i][j]).c[2] = i*j+4;
            (direct_buf[i][j]).c[3] = i*j+5;
            (direct_buf[i][j]).d    = i*j+6;
            (direct_buf[i][j]).e    = i*j+7;
        }
    }

    /* write the chunk data to dataset, using the direct writing function. 
     * There should be no data conversion involved. */
    offset[0] = CHUNK_NX;
    offset[1] = CHUNK_NY;

    if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0)
        goto error;

    if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0) 
        goto error;

    if(H5Dclose(dataset) < 0)
        goto error;

    if((dataset = H5Dopen2(file, DATASETNAME4, H5P_DEFAULT)) < 0)
        goto error;

    /*
     * Select hyperslab for the chunk just written in the file
     */
    start[0]  = CHUNK_NX; start[1]  = CHUNK_NY;
    stride[0] = 1; stride[1] = 1;
    count[0]  = 1; count[1]  = 1;
    block[0]  = CHUNK_NX; block[1]  = CHUNK_NY;
    if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
        goto error;

    /* Read the chunk back. Data should be converted */
    if((status = H5Dread(dataset, dt, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
        goto error;

    /* Check that the values read are the same as the values written */
    for(i = 0; i < CHUNK_NX; i++) {
        for(j = 0; j < CHUNK_NY; j++) {
	    if ((direct_buf[i][j]).a    != (check_chunk[i][j]).a    ||
	        (direct_buf[i][j]).c[0] != (check_chunk[i][j]).c[0] ||
	        (direct_buf[i][j]).c[1] != (check_chunk[i][j]).c[1] ||
	        (direct_buf[i][j]).c[2] != (check_chunk[i][j]).c[2] ||
	        (direct_buf[i][j]).c[3] != (check_chunk[i][j]).c[3] ||
	        (direct_buf[i][j]).e    != (check_chunk[i][j]).e) {
                printf("    1. Read different values than written.");
                printf("    At index %d,%d\n", i, j);
	        printf("    src={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n",
                   (direct_buf[i][j]).a, (direct_buf[i][j]).b, (direct_buf[i][j]).c[0], (direct_buf[i][j]).c[1], 
                   (direct_buf[i][j]).c[2], (direct_buf[i][j]).c[3], (direct_buf[i][j]).d, (direct_buf[i][j]).e);
	        printf("    dst={a=%d, c=[%d,%d,%d,%d], e=%d\n",
                   (check_chunk[i][j]).a, (check_chunk[i][j]).c[0], (check_chunk[i][j]).c[1], (check_chunk[i][j]).c[2], 
                   (check_chunk[i][j]).c[3], (check_chunk[i][j]).e);

	    goto error;
            }
        }
    }

    /*
     * Close/release resources.
     */
    H5Dclose(dataset);
    H5Sclose(mem_space);
    H5Sclose(dataspace);
    H5Pclose(cparms);
    H5Pclose(dxpl);
    H5Tclose(st);
    H5Tclose(dt);


    PASSED();
    return 0;

error:
    H5E_BEGIN_TRY {
        H5Dclose(dataset);
        H5Sclose(mem_space);
        H5Sclose(dataspace);
        H5Pclose(cparms);
        H5Pclose(dxpl);
        H5Tclose(st);
        H5Tclose(dt);
    } H5E_END_TRY;

    return 1;
}
Example #27
0
void TChainWriteBuffer::write(const std::string& fname, const std::string& group, const std::string& chain, const std::string& meta) {
	H5::H5File* h5file = H5Utils::openFile(fname);
	H5::Group* h5group = H5Utils::openGroup(h5file, group);
	
	// Dataset properties: optimized for reading/writing entire buffer at once
	int rank = 3;
	hsize_t dim[3] = {length_, nSamples_+2, nDim_};
	H5::DataSpace dspace(rank, &(dim[0]));
	H5::DSetCreatPropList plist;
	plist.setDeflate(9);	// gzip compression level
	plist.setChunk(rank, &(dim[0]));
	float fillvalue = 0;
	plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
	
	H5::DataSet* dataset = NULL;
	try {
		dataset = new H5::DataSet(h5group->createDataSet(chain, H5::PredType::NATIVE_FLOAT, dspace, plist));
	} catch(H5::GroupIException &group_exception) {
		std::cerr << "Could not create dataset for chain." << std::endl;
		std::cerr << "Dataset '" << group << "/" << chain << "' most likely already exists." << std::endl;
		throw;
	}
	
	dataset->write(buf, H5::PredType::NATIVE_FLOAT);
	
	if(meta == "") {	// Store metadata as attributes
		bool *converged = new bool[length_];
		float *lnZ = new float[length_];
		for(unsigned int i=0; i<length_; i++) {
			converged[i] = metadata[i].converged;
			lnZ[i] = metadata[i].lnZ;
		}
		
		// Allow large attributes to be stored in dense storage, versus compact (which has 64 kB limit)
		//if(length_ > 5) {
		//	hid_t dID = dataset->getCreatePlist().getId();
		//	herr_t res = H5Pset_attr_phase_change(dID, 0, 0);
		//	std::cerr << res << std::endl;
		//	if(res < 0) {
		//		std::cerr << "Failed to specify dense storage." << std::endl;
		//	}
		//}
		
		H5::DataSpace convSpace(1, &(dim[0]));
		H5::Attribute convAtt = dataset->createAttribute("converged", H5::PredType::NATIVE_CHAR, convSpace);
		convAtt.write(H5::PredType::NATIVE_CHAR, reinterpret_cast<char*>(converged));
		
		H5::DataSpace lnZSpace(1, &(dim[0]));
		H5::Attribute lnZAtt = dataset->createAttribute("ln(Z)", H5::PredType::NATIVE_FLOAT, lnZSpace);
		lnZAtt.write(H5::PredType::NATIVE_FLOAT, lnZ);
		
		delete[] converged;
		delete[] lnZ;
	} else {	 	// Store metadata as separate dataset
		H5::CompType metaType(sizeof(TChainMetadata));
		metaType.insertMember("converged", HOFFSET(TChainMetadata, converged), H5::PredType::NATIVE_CHAR);
		metaType.insertMember("ln(Z)", HOFFSET(TChainMetadata, lnZ), H5::PredType::NATIVE_FLOAT);
		
		rank = 1;
		H5::DataSpace metaSpace(rank, &(dim[0]));
		H5::DSetCreatPropList metaProp;
		TChainMetadata emptyMetadata = {0, 0};
		metaProp.setFillValue(metaType, &emptyMetadata);
		metaProp.setDeflate(9);
		metaProp.setChunk(rank, &(dim[0]));
		
		H5::DataSet* metaDataset = new H5::DataSet(h5group->createDataSet(meta, metaType, metaSpace, metaProp));
		metaDataset->write(metadata.data(), metaType);
		
		delete metaDataset;
		metaDataset = NULL;
	}
	
	delete dataset;
	delete h5group;
	delete h5file;
	
	//std::cerr << "Cleaned up." << std::endl;
}
Example #28
0
bool TChain::save(std::string fname, std::string group_name, size_t index,
                  std::string dim_name, int compression, int subsample,
                  bool converged, float lnZ) const {
	if((compression<0) || (compression > 9)) {
		std::cerr << "! Invalid gzip compression level: " << compression << std::endl;
		return false;
	}
	
	H5::Exception::dontPrint();
	
	H5::H5File *file = H5Utils::openFile(fname);
	if(file == NULL) { return false; }
	
	/*
	try {
		file->unlink(group_name);
	} catch(...) {
		// pass
	}
	*/
	
	H5::Group *group = H5Utils::openGroup(file, group_name);
	if(group == NULL) {
		delete file;
		return false;
	}
	
	/*
	 *  Attributes
	 */
	
	// Datatype
	H5::CompType att_type(sizeof(TChainAttribute));
	hid_t tid = H5Tcopy(H5T_C_S1);
	H5Tset_size(tid, H5T_VARIABLE);
	att_type.insertMember("dim_name", HOFFSET(TChainAttribute, dim_name), tid);
	//att_type.insertMember("total_weight", HOFFSET(TChainAttribute, total_weight), H5::PredType::NATIVE_FLOAT);
	//att_type.insertMember("ndim", HOFFSET(TChainAttribute, ndim), H5::PredType::NATIVE_UINT64);
	//att_type.insertMember("length", HOFFSET(TChainAttribute, length), H5::PredType::NATIVE_UINT64);
	
	// Dataspace
	int att_rank = 1;
	hsize_t att_dim = 1;
	H5::DataSpace att_space(att_rank, &att_dim);
	
	// Dataset
	//H5::Attribute att = group->createAttribute("parameter names", att_type, att_space);
	
	TChainAttribute att_data;
	att_data.dim_name = new char[dim_name.size()+1];
	std::strcpy(att_data.dim_name, dim_name.c_str());
	//att_data.total_weight = total_weight;
	//att_data.ndim = N;
	//att_data.length = length;
	
	//att.write(att_type, &att_data);
	delete[] att_data.dim_name;
	
	//int att_rank = 1;
	//hsize_t att_dim = 1;
	
	H5::DataType conv_dtype = H5::PredType::NATIVE_UCHAR;
	H5::DataSpace conv_dspace(att_rank, &att_dim);
	//H5::Attribute conv_att = H5Utils::openAttribute(group, "converged", conv_dtype, conv_dspace);
	//conv_att.write(conv_dtype, &converged);
	
	H5::DataType lnZ_dtype = H5::PredType::NATIVE_FLOAT;
	H5::DataSpace lnZ_dspace(att_rank, &att_dim);
	//H5::Attribute lnZ_att = H5Utils::openAttribute(group, "ln Z", lnZ_dtype, lnZ_dspace);
	//lnZ_att.write(lnZ_dtype, &lnZ);
	
	// Creation property list to be used for all three datasets
	H5::DSetCreatPropList plist;
	//plist.setDeflate(compression);	// gzip compression level
	float fillvalue = 0;
	plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
	
	H5D_layout_t layout = H5D_COMPACT;
	plist.setLayout(layout);
	
	/*
	 *  Choose subsample of points in chain
	 */
	size_t *el_idx = NULL;
	size_t *subsample_idx = NULL;
	if(subsample > 0) {
		size_t tot_weight_tmp = (size_t)ceil(total_weight);
		el_idx = new size_t[tot_weight_tmp];
		size_t unrolled_idx = 0;
		size_t chain_idx = 0;
		std::vector<double>::const_iterator it, it_end;
		it_end = w.end();
		for(it = w.begin(); it != it_end; ++it, chain_idx++) {
			for(size_t n = unrolled_idx; n < unrolled_idx + (size_t)(*it); n++) {
				el_idx[n] = chain_idx;
			}
			unrolled_idx += (size_t)(*it);
		}
		
		assert(chain_idx == length);
		
		gsl_rng *r;
		seed_gsl_rng(&r);
		subsample_idx = new size_t[tot_weight_tmp];
		for(size_t i=0; i<subsample; i++) {
			subsample_idx[i] = el_idx[gsl_rng_uniform_int(r, tot_weight_tmp)];
		}
	}
	
	
	/*
	 *  Coordinates
	 */
	
	// Dataspace
	hsize_t dim;
	if(subsample > 0) {
		dim = subsample;
	} else {
		dim = length;
	}
	// Chunking (required for compression)
	int rank = 2;
	hsize_t coord_dim[2] = {dim, N};
	//if(dim < chunk) {
	//plist.setChunk(rank, &(coord_dim[0]));
	//} else {
	//	plist.setChunk(rank, &chunk);
	//}
	H5::DataSpace x_dspace(rank, &(coord_dim[0]));
	
	// Dataset
	//std::stringstream x_dset_path;
	//x_dset_path << group_name << "/chain/coords";
	std::stringstream coordname;
	coordname << "coords " << index;
	H5::DataSet* x_dataset = new H5::DataSet(group->createDataSet(coordname.str(), H5::PredType::NATIVE_FLOAT, x_dspace, plist));
	
	// Write
	float *buf = new float[N*dim];
	if(subsample > 0) {
		size_t tmp_idx;
		for(size_t i=0; i<subsample; i++) {
			tmp_idx = subsample_idx[i];
			for(size_t k=0; k<N; k++) {
				buf[N*i+k] = x[N*tmp_idx+k];
			}
		}
	} else {
		for(size_t i=0; i<dim; i++) { buf[i] = x[i]; }
	}
	x_dataset->write(buf, H5::PredType::NATIVE_FLOAT);
	
	
	/*
	 *  Weights
	 */
	
	// Dataspace
	if(subsample <= 0) {
		dim = w.size();
		
		rank = 1;
		H5::DataSpace w_dspace(rank, &dim);
		
		// Dataset
		//std::stringstream w_dset_path;
		//w_dset_path << group_name << "/chain/weights";
		H5::DataSet* w_dataset = new H5::DataSet(group->createDataSet("weights", H5::PredType::NATIVE_FLOAT, w_dspace, plist));
		
		// Write
		if(subsample > 0) {
			for(size_t i=0; i<subsample; i++) { buf[i] = 1.; }
		} else {
			assert(w.size() < x.size());
			for(size_t i=0; i<w.size(); i++) { buf[i] = w[i]; }
		}
		w_dataset->write(buf, H5::PredType::NATIVE_FLOAT);
		
		delete w_dataset;
	}
	
	/*
	 *  Probability densities
	 */
	
	// Dataspace
	rank = 1;
	H5::DataSpace L_dspace(rank, &dim);
	
	// Dataset
	//std::stringstream L_dset_path;
	//L_dset_path << group_name << "/chain/probs";
	std::stringstream lnpname;
	lnpname << "ln_p " << index;
	H5::DataSet* L_dataset = new H5::DataSet(group->createDataSet(lnpname.str(), H5::PredType::NATIVE_FLOAT, L_dspace, plist));
	
	// Write
	if(subsample > 0) {
		for(size_t i=0; i<subsample; i++) { buf[i] = L[subsample_idx[i]]; }
	} else {
		assert(L.size() < x.size());
		for(size_t i=0; i<L.size(); i++) { buf[i] = L[i]; }
	}
	L_dataset->write(buf, H5::PredType::NATIVE_FLOAT);
	
	
	if(subsample > 0) {
		delete[] el_idx;
		delete[] subsample_idx;
	}
	
	delete[] buf;
	
	delete x_dataset;
	delete L_dataset;
	
	delete group;
	delete file;
	
	return true;
}
Example #29
0
int main(int argc, char *argv[])
{
    (void)argc;
    (void)argv;

typedef struct rt {
    int channels;
    char date[DATELEN];
    char time[TIMELEN];
} rt;

//    H5Fis_hdf5("/dev/null");

/*
* Create a new file using H5ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
* Then close the file.
*/

    const int NRECORDS = 1;
    const int NFIELDS = 3;
    char fName[] = "tmp.h5";

    /* Calculate the size and the offsets of our struct members in memory */
    size_t rt_offset[NFIELDS] = {  HOFFSET( rt, channels ),
                                   HOFFSET( rt, date ),
                                   HOFFSET( rt, time )};

    rt p_data;
    p_data.channels = 1;
    strcpy( p_data.date, "1234-Dec-31");
    strcpy( p_data.time, "12:34:56");


    hid_t file_id = H5Fcreate(fName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);


    /* Define field information */
    const char *field_names[NFIELDS]  =  { "channels", "date", "time" };
    hid_t      field_type[NFIELDS];

    /* Initialize the field field_type */
    hid_t string_type1 = H5Tcopy( H5T_C_S1 );
    hid_t string_type2 = H5Tcopy( H5T_C_S1 );
    H5Tset_size( string_type1,  strlen(p_data.date));
    H5Tset_size( string_type2,  strlen(p_data.time));
    field_type[0] = H5T_NATIVE_INT;
    field_type[1] = string_type1;
    field_type[2] = string_type2;

    std::ostringstream desc;
    desc << "Description of " << fName;

    herr_t status = H5TBmake_table( desc.str().c_str(), file_id, "description", (hsize_t)NFIELDS, (hsize_t)NRECORDS, sizeof(rt),
                                    field_names, rt_offset, field_type, 10, NULL, 0, &p_data  );

    if (status < 0) {
        perror("Exception while writing description in stfio::exportHDF5File");
        H5Fclose(file_id);
        H5close();
        exit(-1);
    }

    H5Fclose(file_id);

    return(0);
}
Example #30
0
void HDF5Output::open(const std::string& filename) {
	file = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

	sid = H5Tcreate(H5T_COMPOUND, sizeof(OutputRow));
	H5Tinsert(sid, "D", HOFFSET(OutputRow, D), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "z", HOFFSET(OutputRow, z), H5T_NATIVE_DOUBLE);

	H5Tinsert(sid, "SN", HOFFSET(OutputRow, SN), H5T_NATIVE_UINT64);
	H5Tinsert(sid, "ID", HOFFSET(OutputRow, ID), H5T_NATIVE_INT32);
	H5Tinsert(sid, "E", HOFFSET(OutputRow, E), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "X", HOFFSET(OutputRow, X), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Y", HOFFSET(OutputRow, Y), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Z", HOFFSET(OutputRow, Z), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Px", HOFFSET(OutputRow, Px), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Py", HOFFSET(OutputRow, Py), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Pz", HOFFSET(OutputRow, Pz), H5T_NATIVE_DOUBLE);

	H5Tinsert(sid, "SN0", HOFFSET(OutputRow, SN0), H5T_NATIVE_UINT64);
	H5Tinsert(sid, "ID0", HOFFSET(OutputRow, ID0), H5T_NATIVE_INT32);
	H5Tinsert(sid, "E0", HOFFSET(OutputRow, E0), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "X0", HOFFSET(OutputRow, X0), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Y0", HOFFSET(OutputRow, Y0), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Z0", HOFFSET(OutputRow, Z0), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "P0x", HOFFSET(OutputRow, P0x), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "P0y", HOFFSET(OutputRow, P0y), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "P0z", HOFFSET(OutputRow, P0z), H5T_NATIVE_DOUBLE);

	H5Tinsert(sid, "SN1", HOFFSET(OutputRow, SN1), H5T_NATIVE_UINT64);
	H5Tinsert(sid, "ID1", HOFFSET(OutputRow, ID1), H5T_NATIVE_INT32);
	H5Tinsert(sid, "E1", HOFFSET(OutputRow, E1), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "X1", HOFFSET(OutputRow, X1), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Y1", HOFFSET(OutputRow, Y1), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "Z1", HOFFSET(OutputRow, Z1), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "P1x", HOFFSET(OutputRow, P1x), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "P1y", HOFFSET(OutputRow, P1y), H5T_NATIVE_DOUBLE);
	H5Tinsert(sid, "P1z", HOFFSET(OutputRow, P1z), H5T_NATIVE_DOUBLE);

	// chunked prop
	hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
	H5Pset_layout(plist, H5D_CHUNKED);
	hsize_t chunk_dims[RANK] = {BUFFER_SIZE};
	H5Pset_chunk(plist, RANK, chunk_dims);
	H5Pset_deflate(plist, 5);

	hsize_t dims[RANK] = {0};
	hsize_t max_dims[RANK] = {H5S_UNLIMITED};
	dataspace = H5Screate_simple(RANK, dims, max_dims);

	dset = H5Dcreate2(file, "CRPROPA3", sid, dataspace, H5P_DEFAULT, plist, H5P_DEFAULT);

	H5Pclose(plist);

	buffer.reserve(BUFFER_SIZE);
}