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 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 #3
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 #4
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;
	
}