h5d::dataset::ptr_type
create_dataset(std::string const & name,
std::vector<MemType> const & data,
int compression=0) {
if (H5Lexists(_self, name.c_str(), H5P_DEFAULT) > 0)
throw Exception("Object already exists with that name");
h5t::wrapper<StorageType> t;
h5t::datatype type(t);
h5s::dataspace dspace(std::vector<hsize_t>(1,data.size()), std::vector<hsize_t>(1,H5S_UNLIMITED));
h5d::dataset::ptr_type ds = boost::make_shared<h5d::dataset>(_self, name.c_str(), dspace,
type, compression);
ds->write(data);
return ds;
}
void TImgWriteBuffer::write(const std::string& fname, const std::string& group, const std::string& img) {
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_, rect_.N_bins[0], rect_.N_bins[1]};
hsize_t chunk_dim[3] = {length_, rect_.N_bins[0], rect_.N_bins[1]};
if(length_ > 1000) {
float div = ceil((float)length_ / 1000.);
chunk_dim[0] = (int)ceil(length_ / div);
std::cerr << "! Changing chunk length to " << chunk_dim[0] << " stars." << std::endl;
}
H5::DataSpace dspace(rank, &(dim[0]));
H5::DSetCreatPropList plist;
plist.setDeflate(9); // gzip compression level
plist.setChunk(rank, &(chunk_dim[0]));
float fillvalue = 0;
plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
H5::DataSet* dataset = new H5::DataSet(h5group->createDataSet(img, H5::PredType::NATIVE_FLOAT, dspace, plist));
dataset->write(buf, H5::PredType::NATIVE_FLOAT);
/*
* Attributes
*/
hsize_t att_dim = 2;
H5::DataSpace att_dspace(1, &att_dim);
H5::PredType att_dtype = H5::PredType::NATIVE_UINT32;
H5::Attribute att_N = dataset->createAttribute("nPix", att_dtype, att_dspace);
att_N.write(att_dtype, &(rect_.N_bins));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_min = dataset->createAttribute("min", att_dtype, att_dspace);
att_min.write(att_dtype, &(rect_.min));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_max = dataset->createAttribute("max", att_dtype, att_dspace);
att_max.write(att_dtype, &(rect_.max));
delete dataset;
delete h5group;
delete h5file;
}
/* only for Eigen3 matrix/vector */
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const RealVectorType& V)
{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dspace);
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
}
static void save_molecular_type(const MolecularTypeBase* mtb,
std::vector<std::pair<ParticleID, Voxel> > voxels, H5::Group* group)
{
const Species species(mtb->species());
boost::scoped_ptr<H5::Group> mtgroup(
new H5::Group(group->createGroup(species.serial().c_str())));
h5_species_struct property;
property.radius = mtb->radius();
property.D = mtb->D();
const MolecularTypeBase* loc(mtb->location());
if (loc->is_vacant())
std::strcpy(property.location, "");
else
std::strcpy(property.location, loc->species().serial().c_str());
property.is_structure = mtb->is_structure() ? 1 : 0;
property.dimension = mtb->get_dimension();
H5::CompType property_comp_type(get_property_comp());
mtgroup->createAttribute("property", property_comp_type,
H5::DataSpace(H5S_SCALAR)).write(property_comp_type, &property);
// Save voxels
const Integer num_voxels(voxels.size());
std::size_t vidx(0);
boost::scoped_array<h5_voxel_struct> h5_voxel_array(new h5_voxel_struct[num_voxels]);
for (std::vector<std::pair<ParticleID, Voxel> >::const_iterator itr(voxels.begin());
itr != voxels.end(); ++itr)
{
h5_voxel_array[vidx].lot = (*itr).first.lot();
h5_voxel_array[vidx].serial = (*itr).first.serial();
h5_voxel_array[vidx].coordinate = (*itr).second.coordinate();
++vidx;
}
H5::CompType voxel_comp_type(get_voxel_comp());
hsize_t dims[] = {num_voxels};
H5::DataSpace dspace(/* RANK= */1, dims);
boost::scoped_ptr<H5::DataSet> dset(new H5::DataSet(
mtgroup->createDataSet("voxels", voxel_comp_type, dspace)));
dset->write(h5_voxel_array.get(), dset->getDataType());
}
void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<size_t>& V)
{
try{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(),H5::PredType::NATIVE_ULONG, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_ULONG, dspace);
DataSet.write(V.data(), H5::PredType::NATIVE_ULONG);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveUlongStdVector ");
}
}
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const ComplexVectorType& V)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(), ComplexDataType, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(), ComplexDataType,
dspace);
DataSet.write(V.data(), ComplexDataType);
}
FG.close();
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexVector at ");
}
}
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;
}
bool save_mat_image(cv::Mat& img, TRect& rect, std::string fname, std::string group_name,
std::string dset_name, std::string dim1, std::string dim2, int compression) {
assert((img.dims == 2) && (img.rows == rect.N_bins[0]) && (img.cols == rect.N_bins[1]));
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; }
H5::Group *group = H5Utils::openGroup(file, group_name);
if(group == NULL) {
delete file;
return false;
}
/*
* Image Data
*/
// Creation property list
H5::DSetCreatPropList plist;
int rank = 2;
hsize_t dim[2] = {rect.N_bins[0], rect.N_bins[1]};
plist.setDeflate(compression); // gzip compression level
float fillvalue = 0;
plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
plist.setChunk(rank, &(dim[0]));
H5::DataSpace dspace(rank, &(dim[0]));
H5::DataSet* dataset;
try {
dataset = new H5::DataSet(group->createDataSet(dset_name, H5::PredType::NATIVE_FLOAT, dspace, plist));
} catch(H5::FileIException create_dset_err) {
std::cerr << "Unable to create dataset '" << dset_name << "'." << std::endl;
delete group;
delete file;
return false;
}
float *buf = new float[rect.N_bins[0]*rect.N_bins[1]];
for(size_t j=0; j<rect.N_bins[0]; j++) {
for(size_t k=0; k<rect.N_bins[1]; k++) {
buf[rect.N_bins[1]*j + k] = img.at<double>(j,k);
/*float tmp = img.at<double>(j,k);
if(tmp > 0.) {
std::cerr << j << ", " << k << " --> " << j + rect.N_bins[0]*k << " --> " << tmp << std::endl;
}*/
}
}
dataset->write(buf, H5::PredType::NATIVE_FLOAT);
/*
* Attributes
*/
hsize_t att_dim = 2;
H5::DataSpace att_dspace(1, &att_dim);
H5::PredType att_dtype = H5::PredType::NATIVE_UINT32;
H5::Attribute att_N = dataset->createAttribute("N_pix", att_dtype, att_dspace);
att_N.write(att_dtype, &(rect.N_bins));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_min = dataset->createAttribute("min", att_dtype, att_dspace);
att_min.write(att_dtype, &(rect.min));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_max = dataset->createAttribute("max", att_dtype, att_dspace);
att_max.write(att_dtype, &(rect.max));
att_dim = 1;
H5::StrType vls_type(0, H5T_VARIABLE);
H5::DataSpace att_space_str(H5S_SCALAR);
H5::Attribute att_name_1 = dataset->createAttribute("dim_name_1", vls_type, att_space_str);
att_name_1.write(vls_type, dim1);
H5::Attribute att_name_2 = dataset->createAttribute("dim_name_2", vls_type, att_space_str);
att_name_2.write(vls_type, dim2);
file->close();
delete[] buf;
delete dataset;
delete group;
delete file;
return true;
}
bool TStellarData::save(const std::string& fname, const std::string& group, const std::string &dset, int compression) {
if((compression < 0) || (compression > 9)) {
std::cerr << "! Invalid gzip compression level: " << compression << std::endl;
return false;
}
hsize_t nstars = star.size();
if(nstars == 0) {
std::cerr << "! No stars to write." << std::endl;
return false;
}
H5::Exception::dontPrint();
H5::H5File *file = H5Utils::openFile(fname);
if(file == NULL) { return false; }
H5::Group *gp = H5Utils::openGroup(file, group);
if(gp == NULL) {
delete file;
return false;
}
/*
* Photometry
*/
// Datatype
hsize_t nbands = NBANDS;
H5::ArrayType f4arr(H5::PredType::NATIVE_FLOAT, 1, &nbands);
H5::ArrayType u4arr(H5::PredType::NATIVE_FLOAT, 1, &nbands);
H5::CompType dtype(sizeof(TFileData));
dtype.insertMember("obj_id", HOFFSET(TFileData, obj_id), H5::PredType::NATIVE_UINT64);
dtype.insertMember("l", HOFFSET(TFileData, l), H5::PredType::NATIVE_DOUBLE);
dtype.insertMember("b", HOFFSET(TFileData, b), H5::PredType::NATIVE_DOUBLE);
dtype.insertMember("mag", HOFFSET(TFileData, mag), f4arr);
dtype.insertMember("err", HOFFSET(TFileData, err), f4arr);
dtype.insertMember("maglimit", HOFFSET(TFileData, maglimit), f4arr);
dtype.insertMember("nDet", HOFFSET(TFileData, N_det), u4arr);
dtype.insertMember("EBV", HOFFSET(TFileData, EBV), H5::PredType::NATIVE_FLOAT);
// Dataspace
hsize_t dim = nstars;
H5::DataSpace dspace(1, &dim);
// Property List
H5::DSetCreatPropList plist;
plist.setChunk(1, &nstars);
plist.setDeflate(compression);
// Dataset
H5::DataSet dataset = gp->createDataSet(dset, dtype, dspace, plist);
// Write dataset
TFileData* data = new TFileData[nstars];
for(size_t i=0; i<nstars; i++) {
data[i].obj_id = star[i].obj_id;
data[i].l = star[i].l;
data[i].b = star[i].b;
for(size_t k=0; k<NBANDS; k++) {
data[i].mag[k] = star[i].m[k];
data[i].err[k] = star[i].err[k];
data[i].maglimit[k] = star[i].maglimit[k];
}
data[i].EBV = star[i].EBV;
}
dataset.write(data, dtype);
/*
* Attributes
*/
dim = 1;
H5::DataSpace att_dspace(1, &dim);
H5::PredType att_dtype = H5::PredType::NATIVE_UINT64;
H5::Attribute att_healpix_index = dataset.createAttribute("healpix_index", att_dtype, att_dspace);
att_healpix_index.write(att_dtype, &healpix_index);
att_dtype = H5::PredType::NATIVE_UINT32;
H5::Attribute att_nside = dataset.createAttribute("nside", att_dtype, att_dspace);
att_nside.write(att_dtype, &nside);
att_dtype = H5::PredType::NATIVE_UCHAR;
H5::Attribute att_nested = dataset.createAttribute("nested", att_dtype, att_dspace);
att_nested.write(att_dtype, &nested);
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_l = dataset.createAttribute("l", att_dtype, att_dspace);
att_l.write(att_dtype, &l);
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_b = dataset.createAttribute("b", att_dtype, att_dspace);
att_b.write(att_dtype, &b);
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_EBV = dataset.createAttribute("EBV", att_dtype, att_dspace);
att_EBV.write(att_dtype, &EBV);
file->close();
delete[] data;
delete gp;
delete file;
return true;
}
