Example #1
0
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;
}
Example #2
0
void CompartmentReportHDF5::_createMappingAttributes( H5::DataSet& dataset )
{
//    const std::string type =
//                         boost::lexical_cast< std::string >( _spec.type( ));
    const std::string type = "1";   // COMPARTMENT_REPORT
    detail::addStringAttribute( dataset, mappingAttributes[0], type );
    dataset.createAttribute( mappingAttributes[1], H5::PredType::NATIVE_INT,
                             H5S_SCALAR );
    dataset.createAttribute( mappingAttributes[2], H5::PredType::NATIVE_INT,
                             H5S_SCALAR );
    dataset.createAttribute( mappingAttributes[3], H5::PredType::NATIVE_INT,
                             H5S_SCALAR );
    dataset.createAttribute( mappingAttributes[4], H5::PredType::NATIVE_INT,
                             H5S_SCALAR );
    dataset.createAttribute( mappingAttributes[5], H5::PredType::NATIVE_INT,
                             H5S_SCALAR );
}
Example #3
0
File: HDF5.hpp Project: rseal/HDF5R
      void WriteTAttrib(const std::string& name, const T& value, 
            const H5::DataType& dType, const H5::DataSpace& dSpace){
         //attributes are clunky in HDF5++ implementation - this is a workaround
         //template is required to pass the proper value type

         //create a new data set attribute
         H5::Attribute attrib = dSet_.createAttribute(name,dType,dSpace);

         //write the value to the attribute and close
         attrib.write(dType,&value);
         attrib.close();
      }
Example #4
0
void CompartmentReportHDF5::_createDataAttributes( H5::DataSet& dataset )
{
    const int rank = 0;
    const double startTime = getStartTime();
    const double endTime = getEndTime();
    const double timestep = getTimestep();

    H5::Attribute rankAttr = dataset.createAttribute( dataAttributes[0],
                                     H5::PredType::NATIVE_INT, H5S_SCALAR );
    H5::Attribute tstartAttr = dataset.createAttribute( dataAttributes[1],
                                  H5::PredType::NATIVE_DOUBLE, H5S_SCALAR );
    H5::Attribute tstopAttr = dataset.createAttribute( dataAttributes[2],
                                  H5::PredType::NATIVE_DOUBLE, H5S_SCALAR );
    H5::Attribute dtAttr = dataset.createAttribute( dataAttributes[3],
                                  H5::PredType::NATIVE_DOUBLE, H5S_SCALAR );

    rankAttr.write( H5::PredType::NATIVE_INT, &rank );
    tstartAttr.write( H5::PredType::NATIVE_DOUBLE, &startTime );
    tstopAttr.write( H5::PredType::NATIVE_DOUBLE, &endTime );
    dtAttr.write( H5::PredType::NATIVE_DOUBLE, &timestep );
    detail::addStringAttribute( dataset, dataAttributes[4], _dunit );
    detail::addStringAttribute( dataset, dataAttributes[5], _tunit );
}
Example #5
0
File: HDF5.hpp Project: rseal/HDF5R
   void WriteTStrAttrib(const std::string& name, const std::string& value){

      std::string str = value;
      str.resize( STRING_ATTRIB_SIZE );

      //define the data type as a string with the value's length
      H5::StrType strType(0, STRING_ATTRIB_SIZE );

      //open the data set and create a new attribute of type string
      H5::Attribute attrib = 
         dSet_.createAttribute(name, strType, H5::DataSpace(H5S_SCALAR));

      //write value to the attribute and close
      attrib.write(strType, str );
      attrib.close();
   }
Example #6
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 #7
0
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;
	
}
Example #8
0
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;
}
Example #9
0
void Bundle2::initFrameStream_() {
	H5::DataSpace scalar;

	// Creating datasets for each frame
	H5::Group bundleGroup = streamFile_->createGroup("/Bundle");
	H5::Group framesGroup = bundleGroup.createGroup("Frames");

	hsize_t count = frames_.size();
	H5::Attribute attr = framesGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
	attr.write(H5::PredType::NATIVE_HSIZE, &count);
	attr.close();

	// Defining frame dataset property
	hsize_t chunkDim[] = { 1, 2, 10 };
	H5::DSetCreatPropList propList;
	propList.setLayout(H5D_CHUNKED);
	propList.setChunk(3, chunkDim);
	propList.setDeflate(9);

	// Definig dataset dataspace
	hsize_t max_dim[] = { numCameras_, 2, H5S_UNLIMITED };
	hsize_t dim[] = { numCameras_, 2, 0 };
	H5::DataSpace ds(3, dim, max_dim);

	for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
		const std::string datasetName = boost::str(boost::format("Frame %1$04d") % (*it)->number());

		// Creating dataset
		H5::DataSet frameData = framesGroup.createDataSet(datasetName, H5::PredType::IEEE_F32LE, ds, propList);

		// Writing global number
		attr = frameData.createAttribute("globalNumber", H5::PredType::STD_U64LE, scalar);
		count = (*it)->globalNumber();
		attr.write(H5::PredType::NATIVE_HSIZE, &count);
		attr.close();

		// Clean up!
		frameData.close();
	}

	// Clean up!
	ds.close();
	propList.close();

	// Creating tracks dataset
	hsize_t chunkDim2[] = { 2, 10 };
	propList = H5::DSetCreatPropList();
	propList.setLayout(H5D_CHUNKED);
	propList.setChunk(2, chunkDim);
	propList.setDeflate(9);

	H5::VarLenType tracksDatasetType(&H5::PredType::STD_U64LE);

	hsize_t tracksDim[] = { 0, 2 };
	hsize_t tracksMaxDim[] = { H5S_UNLIMITED, 2 };
	H5::DataSpace tracksDataspace(2, tracksDim, tracksMaxDim);

	H5::DataSet tracksDataset = bundleGroup.createDataSet("Tracks", tracksDatasetType, tracksDataspace, propList);

	tracksDataset.close();
	tracksDataspace.close();
	tracksDatasetType.close();
	propList.close();

	framesGroup.close();
	bundleGroup.close();
	scalar.close();
}