mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2026-01-31 11:14:56 +01:00
moved non public headers
This commit is contained in:
Erik Frojdh
952
slsReceiverSoftware/src/HDF5FileStatic.h
Executable file
952
slsReceiverSoftware/src/HDF5FileStatic.h
Executable file
@@ -0,0 +1,952 @@
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#ifdef HDF5C
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#pragma once
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/************************************************
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* @file HDF5FileStatic.h
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* @short creating, closing, writing and reading
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* from HDF5 files
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***********************************************/
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/**
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*@short creating, closing, writing and reading from HDF5 files
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*/
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#include "H5Cpp.h"
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#ifndef H5_NO_NAMESPACE
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using namespace H5;
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#endif
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#include "sls_detector_defs.h"
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#include "logger.h"
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#include <iostream>
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#include <string>
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#include <vector>
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#include <iomanip>
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#include <stdlib.h> //malloc
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#include <sstream>
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#include <cstring> //memset
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class HDF5FileStatic: public virtual slsDetectorDefs {
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public:
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/** Constructor */
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HDF5FileStatic(){};
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/** Destructor */
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virtual ~HDF5FileStatic(){};
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/**
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* Create File Name in format fpath/fnameprefix_fx_dy_z.raw,
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* where x is fnum, y is (dindex * numunits + unitindex) and z is findex
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* @param fpath file path
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* @param fnameprefix file name prefix
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* @param findex file index
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* @param subfindex sub file index
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* @param dindex readout index
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* @param numunits number of units per readout. eg. eiger has 2 udp units per readout
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* @param unitindex unit index
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* @returns complete file name created
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*/
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static std::string CreateFileName(std::string fpath, std::string fprefix,
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uint64_t findex, uint64_t subfindex,
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int dindex, int numunits = 1,
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int unitindex = 0) {
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std::ostringstream os;
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os << fpath << "/" << fprefix << "_d"
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<< (dindex * numunits + unitindex) << "_f" << subfindex << '_'
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<< findex << ".h5";
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return os.str();
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}
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/**
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* Create master file name
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* @param fpath file path
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* @param fnameprefix file name prefix
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* @param findex file index
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* @returns master file name
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*/
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static std::string CreateMasterFileName(std::string fpath, std::string fnameprefix, uint64_t findex)
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{
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std::ostringstream os;
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os << fpath << "/" << fnameprefix << "_master"
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<< "_" << findex << ".h5";
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return os.str();
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}
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/**
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* Create virtual file name
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* @param fpath file path
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* @param fnameprefix file name prefix
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* @param fnum current frame number
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* @param findex file index
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* @returns virtual file name
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*/
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static std::string CreateVirtualFileName(std::string fpath, std::string fnameprefix, uint64_t findex)
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{
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std::ostringstream osfn;
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osfn << fpath << "/" << fnameprefix;
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osfn << "_virtual";
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osfn << "_" << findex;
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osfn << ".h5";
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return osfn.str();
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}
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/**
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* Close File
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* @param ind index for debugging
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* @param fd file pointer
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* @param dp dataspace pointer
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* @param ds dataset pointer
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* @param ds_para pointer to array of parameter datasets
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*/
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static void CloseDataFile(int ind, H5File*& fd)
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{
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try {
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Exception::dontPrint(); //to handle errors
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if (fd) {
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delete fd;
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fd = 0;
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}
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} catch(const Exception& error) {
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FILE_LOG(logERROR) << "Could not close HDF5 handles of index " << ind;
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error.printErrorStack();
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}
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}
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/*
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* Close master file
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* @param fd master hdf5 file object
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*/
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static void CloseMasterDataFile(H5File*& fd)
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{
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try {
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Exception::dontPrint(); //to handle errors
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if (fd) {
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delete fd;
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fd = 0;
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}
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} catch(const Exception& error) {
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FILE_LOG(logERROR) << "Could not close master HDF5 handles";
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error.printErrorStack();
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}
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}
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/*
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* Close virtual file
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* (in C because H5Pset_virtual doesnt exist yet in C++)
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* @param fd virtual hdf5 file handle
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*/
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static void CloseVirtualDataFile(hid_t& fd)
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{
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if(fd) {
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if (H5Fclose(fd) < 0 ) {
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FILE_LOG(logERROR) << "Could not close virtual HDF5 handles";
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}
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fd = 0;
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}
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}
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/**
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* Write data to file
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* @param ind object index for debugging
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* @param buf buffer to write from
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* @param nDimx image number in file (imagenumber%maxframesinfile)
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* @param nDimy number of pixels in y direction
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* @param nDimz number of pixels in x direction
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* @param dspace dataspace pointer
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* @param dset dataset pointer
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* @param dtype datatype
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*/
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static void WriteDataFile(int ind, char* buf,
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uint64_t nDimx, uint32_t nDimy, uint32_t nDimz,
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DataSpace* dspace, DataSet* dset, DataType dtype)
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{
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hsize_t count[3] = {1, nDimy, nDimz};
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hsize_t start[3] = {nDimx, 0, 0};
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hsize_t dims2[2] = {nDimy, nDimz};
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try{
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Exception::dontPrint(); //to handle errors
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dspace->selectHyperslab( H5S_SELECT_SET, count, start);
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DataSpace memspace(2,dims2);
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dset->write(buf, dtype, memspace, *dspace);
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memspace.close();
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}
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catch(const Exception& error){
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FILE_LOG(logERROR) << "Could not write to file in object " << ind;
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error.printErrorStack();
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throw RuntimeError("Could not write to file in object " + std::to_string(ind));
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}
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}
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/**
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* Write Parameter Arrays as datasets (to virtual file)
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* @param ind self index
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* @param dspace_para parameter dataspace
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* @param fnum current frame number
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* @param dset_para vector or dataset pointers of parameters
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* @param rheader sls_receiver_header pointer
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* @param parameterDataTypes parameter datatypes
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*/
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static void WriteParameterDatasets(int ind, DataSpace* dspace_para, uint64_t fnum,
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std::vector <DataSet*> dset_para,sls_receiver_header* rheader,
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std::vector <DataType> parameterDataTypes)
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{
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sls_detector_header header = rheader->detHeader;
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hsize_t count[1] = {1};
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hsize_t start[1] = {fnum};
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int i = 0;
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try{
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Exception::dontPrint(); //to handle errors
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dspace_para->selectHyperslab( H5S_SELECT_SET, count, start);
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DataSpace memspace(H5S_SCALAR);
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dset_para[0]->write(&header.frameNumber, parameterDataTypes[0], memspace, *dspace_para);i=1;
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dset_para[1]->write(&header.expLength, parameterDataTypes[1], memspace, *dspace_para);i=2;
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dset_para[2]->write(&header.packetNumber, parameterDataTypes[2], memspace, *dspace_para);i=3;
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dset_para[3]->write(&header.bunchId, parameterDataTypes[3], memspace, *dspace_para);i=4;
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dset_para[4]->write(&header.timestamp, parameterDataTypes[4], memspace, *dspace_para);i=5;
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dset_para[5]->write(&header.modId, parameterDataTypes[5], memspace, *dspace_para);i=6;
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dset_para[6]->write(&header.row, parameterDataTypes[6], memspace, *dspace_para);i=7;
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dset_para[7]->write(&header.column, parameterDataTypes[7], memspace, *dspace_para);i=8;
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dset_para[8]->write(&header.reserved, parameterDataTypes[8], memspace, *dspace_para);i=9;
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dset_para[9]->write(&header.debug, parameterDataTypes[9], memspace, *dspace_para);i=10;
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dset_para[10]->write(&header.roundRNumber, parameterDataTypes[10], memspace, *dspace_para);i=11;
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dset_para[11]->write(&header.detType, parameterDataTypes[11], memspace, *dspace_para);i=12;
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dset_para[12]->write(&header.version, parameterDataTypes[12], memspace, *dspace_para);i=13;
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// contiguous bitset
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if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
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dset_para[13]->write((char*)&(rheader->packetsMask), parameterDataTypes[13], memspace, *dspace_para);
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}
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// not contiguous bitset
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else {
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// get contiguous representation of bit mask
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bitset_storage storage;
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memset(storage, 0 , sizeof(bitset_storage));
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sls_bitset bits = rheader->packetsMask;
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for (int i = 0; i < MAX_NUM_PACKETS; ++i)
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storage[i >> 3] |= (bits[i] << (i & 7));
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// write bitmask
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dset_para[13]->write((char*)storage, parameterDataTypes[13], memspace, *dspace_para);
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}i=14;
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}
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catch(const Exception& error){
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error.printErrorStack();
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throw RuntimeError("Could not write parameters (index:" + std::to_string(i) + ") to file in object " + std::to_string(ind));
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}
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}
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/**
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* Extend datasets in #images dimension (x dimension)
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* @param ind self index
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* @param dpace data space pointer address
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* @param dset data set pointer
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* @param dspace_para parameter dataspace address pointer
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* @param dset dataset parameter pointer
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* @param initialNumImages initial number of images
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*/
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static void ExtendDataset(int ind, DataSpace*& dspace, DataSet* dset,
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DataSpace*& dspace_para, std::vector <DataSet*> dset_para,
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uint64_t initialNumImages) {
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try{
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Exception::dontPrint(); //to handle errors
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hsize_t dims[3];
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dspace->getSimpleExtentDims(dims);
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dims[0] += initialNumImages;
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dset->extend(dims);
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delete dspace;
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dspace = 0;
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dspace = new DataSpace(dset->getSpace());
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hsize_t dims_para[1] = {dims[0]};
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for (unsigned int i = 0; i < dset_para.size(); ++i)
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dset_para[i]->extend(dims_para);
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delete dspace_para;
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dspace_para = 0;
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dspace_para = new DataSpace(dset_para[0]->getSpace());
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}
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catch(const Exception& error){
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error.printErrorStack();
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throw RuntimeError("Could not extend dataset in object " + std::to_string(ind));
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}
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}
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/**
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* Create master file
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* @param fname master file name
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* @param owenable overwrite enable
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* @param attr master file attributes
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*/
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static void CreateMasterDataFile(H5File*& fd, std::string fname, bool owenable,
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masterAttributes& attr)
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{
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try {
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Exception::dontPrint(); //to handle errors
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FileAccPropList flist;
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flist.setFcloseDegree(H5F_CLOSE_STRONG);
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fd = 0;
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if(!owenable)
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fd = new H5File( fname.c_str(), H5F_ACC_EXCL,
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FileCreatPropList::DEFAULT,
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flist );
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else
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fd = new H5File( fname.c_str(), H5F_ACC_TRUNC,
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FileCreatPropList::DEFAULT,
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flist );
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//variables
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DataSpace dataspace = DataSpace (H5S_SCALAR);
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Attribute attribute;
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DataSet dataset;
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int iValue=0;
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double dValue=0;
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StrType strdatatype(PredType::C_S1,256);
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//create attributes
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//version
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dValue = attr.version;
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attribute = fd->createAttribute("version",PredType::NATIVE_DOUBLE, dataspace);
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attribute.write(PredType::NATIVE_DOUBLE, &dValue);
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//Create a group in the file
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Group group1( fd->createGroup( "entry" ) );
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Group group2( group1.createGroup("data") );
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Group group3( group1.createGroup("instrument") );
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Group group4( group3.createGroup("beam") );
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Group group5( group3.createGroup("detector") );
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Group group6( group1.createGroup("sample") );
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//Dynamic Range
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dataset = group5.createDataSet ( "dynamic range", PredType::NATIVE_INT, dataspace );
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dataset.write ( &(attr.dynamicRange), PredType::NATIVE_INT);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, std::string("bits"));
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//Ten Giga
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iValue = attr.tenGiga;
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dataset = group5.createDataSet ( "ten giga enable", PredType::NATIVE_INT, dataspace );
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dataset.write ( &iValue, PredType::NATIVE_INT);
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//Image Size
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dataset = group5.createDataSet ( "image size", PredType::NATIVE_INT, dataspace );
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dataset.write ( &(attr.imageSize), PredType::NATIVE_INT);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, std::string("bytes"));
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//x
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dataset = group5.createDataSet ( "number of pixels in x axis", PredType::NATIVE_INT, dataspace );
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dataset.write ( &(attr.nPixelsX), PredType::NATIVE_INT);
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//y
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dataset = group5.createDataSet ( "number of pixels in y axis", PredType::NATIVE_INT, dataspace );
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dataset.write ( &(attr.nPixelsY), PredType::NATIVE_INT);
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//Maximum frames per file
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dataset = group5.createDataSet ( "maximum frames per file", PredType::NATIVE_INT, dataspace );
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dataset.write ( &(attr.maxFramesPerFile), PredType::NATIVE_INT);
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//Total Frames
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dataset = group5.createDataSet ( "total frames", PredType::STD_U64LE, dataspace );
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dataset.write ( &(attr.totalFrames), PredType::STD_U64LE);
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//Exptime
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dataset = group5.createDataSet ( "exposure time", PredType::STD_U64LE, dataspace );
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dataset.write ( &(attr.exptimeNs), PredType::STD_U64LE);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, std::string("ns"));
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//SubExptime
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dataset = group5.createDataSet ( "sub exposure time", PredType::STD_U64LE, dataspace );
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dataset.write ( &(attr.subExptimeNs), PredType::STD_U64LE);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, std::string("ns"));
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//SubPeriod
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dataset = group5.createDataSet ( "sub period", PredType::STD_U64LE, dataspace );
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dataset.write ( &(attr.subPeriodNs), PredType::STD_U64LE);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, std::string("ns"));
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||||
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//Period
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dataset = group5.createDataSet ( "acquisition period", PredType::STD_U64LE, dataspace );
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dataset.write ( &(attr.periodNs), PredType::STD_U64LE);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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||||
attribute.write(strdatatype, std::string("ns"));
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||||
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||||
//Gap Pixels Enable
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dataset = group5.createDataSet ( "gap pixels enable", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.gapPixelsEnable), PredType::NATIVE_INT);
|
||||
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||||
//Quad Enable
|
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dataset = group5.createDataSet ( "quad enable", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.quadEnable), PredType::NATIVE_INT);
|
||||
|
||||
//Gap Pixels Enable
|
||||
dataset = group5.createDataSet ( "gap pixels enable", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.gapPixelsEnable), PredType::NATIVE_INT);
|
||||
|
||||
//Quad Enable
|
||||
dataset = group5.createDataSet ( "quad enable", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.quadEnable), PredType::NATIVE_INT);
|
||||
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||||
//Analog Flag
|
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dataset = group5.createDataSet ( "analog flag", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.quadEnable), PredType::NATIVE_INT);
|
||||
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||||
//Digital Flag
|
||||
dataset = group5.createDataSet ( "digital flag", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.gapPixelsEnable), PredType::NATIVE_INT);
|
||||
|
||||
//ADC Mask
|
||||
dataset = group5.createDataSet ( "adc mask", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.quadEnable), PredType::NATIVE_INT);
|
||||
|
||||
//Dbit Offset
|
||||
dataset = group5.createDataSet ( "dbit offset", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.gapPixelsEnable), PredType::NATIVE_INT);
|
||||
|
||||
// Dbit List
|
||||
dataset = group5.createDataSet ( "dbit bitset list", PredType::STD_U64LE, dataspace );
|
||||
dataset.write ( &(attr.periodNs), PredType::STD_U64LE);
|
||||
|
||||
// Roi xmin
|
||||
dataset = group5.createDataSet ( "roi xmin", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.roiXmin), PredType::NATIVE_INT);
|
||||
|
||||
// Roi xmax
|
||||
dataset = group5.createDataSet ( "roi xmax", PredType::NATIVE_INT, dataspace );
|
||||
dataset.write ( &(attr.roiXmax), PredType::NATIVE_INT);
|
||||
|
||||
//Timestamp
|
||||
time_t t = time(0);
|
||||
dataset = group5.createDataSet ( "timestamp", strdatatype, dataspace );
|
||||
dataset.write ( std::string(ctime(&t)), strdatatype );
|
||||
|
||||
fd->close();
|
||||
|
||||
} catch(const Exception& error) {
|
||||
error.printErrorStack();
|
||||
if (fd) fd->close();
|
||||
throw RuntimeError("Could not create master HDF5 handles");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Create File
|
||||
* @param ind object index for debugging
|
||||
* @param owenable overwrite enable
|
||||
* @param fname complete file name
|
||||
* @param frindexenable frame index enable
|
||||
* @param fnum current image number
|
||||
* @param nDimx number of pixels in x dim (#frames)
|
||||
* @param nDimy number of pixels in y dim (height y dir)
|
||||
* @param nDimz number of pixels in z dim (width x dir)
|
||||
* @param dtype data type
|
||||
* @param fd file pointer
|
||||
* @param dspace dataspace pointer
|
||||
* @param dset dataset pointer
|
||||
* @param version version of software for hdf5 writing
|
||||
* @param maxchunkedimages maximum chunked images
|
||||
* @param dspace_para dataspace of parameters
|
||||
* @param dset_para vector of datasets of parameters
|
||||
* @param parameterNames parameter names
|
||||
* @param parameterDataTypes parameter datatypes
|
||||
*/
|
||||
static void CreateDataFile(int ind, bool owenable, std::string fname, bool frindexenable,
|
||||
uint64_t fnum, uint64_t nDimx, uint32_t nDimy, uint32_t nDimz,
|
||||
DataType dtype, H5File*& fd, DataSpace*& dspace, DataSet*& dset,
|
||||
double version, uint64_t maxchunkedimages,
|
||||
DataSpace*& dspace_para, std::vector<DataSet*>& dset_para,
|
||||
std::vector <const char*> parameterNames,
|
||||
std::vector <DataType> parameterDataTypes)
|
||||
{
|
||||
try {
|
||||
Exception::dontPrint(); //to handle errors
|
||||
|
||||
//file
|
||||
FileAccPropList fapl;
|
||||
fapl.setFcloseDegree(H5F_CLOSE_STRONG);
|
||||
fd = 0;
|
||||
if(!owenable)
|
||||
fd = new H5File( fname.c_str(), H5F_ACC_EXCL,
|
||||
FileCreatPropList::DEFAULT,
|
||||
fapl );
|
||||
else
|
||||
fd = new H5File( fname.c_str(), H5F_ACC_TRUNC,
|
||||
FileCreatPropList::DEFAULT,
|
||||
fapl );
|
||||
|
||||
//attributes - version
|
||||
double dValue=version;
|
||||
DataSpace dataspace_attr = DataSpace (H5S_SCALAR);
|
||||
Attribute attribute = fd->createAttribute("version",PredType::NATIVE_DOUBLE, dataspace_attr);
|
||||
attribute.write(PredType::NATIVE_DOUBLE, &dValue);
|
||||
|
||||
//dataspace
|
||||
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
|
||||
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
|
||||
dspace = 0;
|
||||
dspace = new DataSpace (3,srcdims,srcdimsmax);
|
||||
|
||||
|
||||
//dataset name
|
||||
std::ostringstream osfn;
|
||||
osfn << "/data";
|
||||
if (frindexenable) osfn << "_f" << std::setfill('0') << std::setw(12) << fnum;
|
||||
std::string dsetname = osfn.str();
|
||||
|
||||
//dataset
|
||||
//fill value
|
||||
DSetCreatPropList plist;
|
||||
int fill_value = -1;
|
||||
plist.setFillValue(dtype, &fill_value);
|
||||
// always create chunked dataset as unlimited is only supported with chunked layout
|
||||
hsize_t chunk_dims[3] ={maxchunkedimages, nDimy, nDimz};
|
||||
plist.setChunk(3, chunk_dims);
|
||||
dset = 0;
|
||||
dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace, plist));
|
||||
|
||||
//create parameter datasets
|
||||
hsize_t dims[1] = {nDimx};
|
||||
hsize_t dimsmax[1] = {H5S_UNLIMITED};
|
||||
dspace_para = 0;
|
||||
dspace_para = new DataSpace (1,dims,dimsmax);
|
||||
|
||||
// always create chunked dataset as unlimited is only supported with chunked layout
|
||||
DSetCreatPropList paralist;
|
||||
hsize_t chunkpara_dims[3] = {maxchunkedimages};
|
||||
paralist.setChunk(1, chunkpara_dims);
|
||||
|
||||
for (unsigned int i = 0; i < parameterNames.size(); ++i){
|
||||
DataSet* ds = new DataSet(fd->createDataSet(parameterNames[i],
|
||||
parameterDataTypes[i], *dspace_para, paralist));
|
||||
dset_para.push_back(ds);
|
||||
}
|
||||
}
|
||||
catch(const Exception& error){
|
||||
error.printErrorStack();
|
||||
if (fd) fd->close();
|
||||
throw RuntimeError("Could not create HDF5 handles in object " + ind);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Create virtual file
|
||||
* (in C because H5Pset_virtual doesnt exist yet in C++)
|
||||
* @param virtualFileName virtual file name
|
||||
* @param fd virtual file handle
|
||||
* @param masterFileName master file name
|
||||
* @param fpath file path
|
||||
* @param fnameprefix file name prefix
|
||||
* @param findex file index
|
||||
* @param frindexenable frame index enable
|
||||
* @param dindex readout index
|
||||
* @param numunits number of units per readout. eg. eiger has 2 udp units per readout
|
||||
* @param maxFramesPerFile maximum frames per file
|
||||
* @param numf number of frames caught
|
||||
* @param srcDataseName source dataset name
|
||||
* @param dataType datatype of data dataset
|
||||
* @param numDety number of readouts in Y dir
|
||||
* @param numDetz number of readouts in Z dir
|
||||
* @param nDimy number of objects in y dimension in source file (Number of pixels in y dir)
|
||||
* @param nDimz number of objects in z dimension in source file (Number of pixels in x dir)
|
||||
* @param version version of software for hdf5 writing
|
||||
* @param parameterNames parameter names
|
||||
* @param parameterDataTypes parameter datatypes
|
||||
*/
|
||||
static void CreateVirtualDataFile(
|
||||
std::string virtualFileName,
|
||||
hid_t& fd, std::string masterFileName,
|
||||
std::string fpath, std::string fnameprefix, uint64_t findex, bool frindexenable,
|
||||
int dindex, int numunits,
|
||||
uint32_t maxFramesPerFile, uint64_t numf,
|
||||
std::string srcDataseName, DataType dataType,
|
||||
int numDety, int numDetz, uint32_t nDimy, uint32_t nDimz,
|
||||
double version,
|
||||
std::vector <const char*> parameterNames,
|
||||
std::vector <DataType> parameterDataTypes)
|
||||
{
|
||||
try {
|
||||
//file
|
||||
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
||||
if (dfal < 0)
|
||||
throw RuntimeError("Could not create file access property for virtual file " + virtualFileName);
|
||||
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
|
||||
throw RuntimeError("Could not set strong file close degree for virtual file " + virtualFileName);
|
||||
fd = H5Fcreate( virtualFileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
|
||||
if (fd < 0)
|
||||
throw RuntimeError("Could not create virtual file " + virtualFileName);
|
||||
|
||||
//attributes - version
|
||||
hid_t dataspace_attr = H5Screate (H5S_SCALAR);
|
||||
if (dataspace_attr < 0)
|
||||
throw RuntimeError("Could not create dataspace for attribute in virtual file " + virtualFileName);
|
||||
hid_t attrid = H5Acreate2 (fd, "version", H5T_NATIVE_DOUBLE, dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
|
||||
if (attrid < 0)
|
||||
throw RuntimeError("Could not create attribute in virtual file " + virtualFileName);
|
||||
double attr_data = version;
|
||||
if (H5Awrite (attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
|
||||
throw RuntimeError("Could not write attribute in virtual file " + virtualFileName);
|
||||
if (H5Aclose (attrid) < 0)
|
||||
throw RuntimeError("Could not close attribute in virtual file " + virtualFileName);
|
||||
|
||||
|
||||
//virtual dataspace
|
||||
hsize_t vdsdims[3] = {numf, numDety * nDimy, numDetz * nDimz};
|
||||
hid_t vdsDataspace = H5Screate_simple(3, vdsdims ,NULL);
|
||||
if (vdsDataspace < 0)
|
||||
throw RuntimeError("Could not create virtual dataspace in virtual file " + virtualFileName);
|
||||
hsize_t vdsdims_para[2] = {numf, (unsigned int) numDety * numDetz};
|
||||
hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, NULL);
|
||||
if (vdsDataspace_para < 0)
|
||||
throw RuntimeError("Could not create virtual dataspace (parameters) in virtual file " + virtualFileName);
|
||||
|
||||
|
||||
//fill values
|
||||
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
|
||||
if (dcpl < 0)
|
||||
throw RuntimeError("Could not create file creation properties in virtual file " + virtualFileName);
|
||||
int fill_value = -1;
|
||||
if (H5Pset_fill_value (dcpl, GetDataTypeinC(dataType), &fill_value) < 0)
|
||||
throw RuntimeError("Could not create fill value in virtual file " + virtualFileName);
|
||||
hid_t dcpl_para[parameterNames.size()];
|
||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
||||
dcpl_para[i] = H5Pcreate (H5P_DATASET_CREATE);
|
||||
if (dcpl_para[i] < 0)
|
||||
throw RuntimeError("Could not create file creation properties (parameters) in virtual file " + virtualFileName);
|
||||
if (H5Pset_fill_value (dcpl_para[i], GetDataTypeinC(parameterDataTypes[i]), &fill_value) < 0)
|
||||
throw RuntimeError("Could not create fill value (parameters) in virtual file " + virtualFileName);
|
||||
}
|
||||
|
||||
//hyperslab
|
||||
int numMajorHyperslab = numf/maxFramesPerFile;
|
||||
if (numf%maxFramesPerFile) numMajorHyperslab++;
|
||||
uint64_t framesSaved = 0;
|
||||
for (int j = 0; j < numMajorHyperslab; j++) {
|
||||
|
||||
uint64_t nDimx = ((numf - framesSaved) > maxFramesPerFile)
|
||||
? maxFramesPerFile : (numf-framesSaved);
|
||||
hsize_t offset[3] = {framesSaved, 0, 0};
|
||||
hsize_t count[3] = {nDimx, nDimy, nDimz};
|
||||
hsize_t offset_para[2] = {framesSaved, 0};
|
||||
hsize_t count_para[2] = {nDimx, 1};
|
||||
|
||||
for (int i = 0; i < numDety * numDetz; ++i) {
|
||||
|
||||
//setect hyperslabs
|
||||
if (H5Sselect_hyperslab (vdsDataspace, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) {
|
||||
throw RuntimeError("Could not select hyperslab");
|
||||
}
|
||||
if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET,
|
||||
offset_para, NULL, count_para, NULL) < 0) {
|
||||
throw RuntimeError("Could not select hyperslab for parameters");
|
||||
}
|
||||
|
||||
//source file name
|
||||
std::string srcFileName = HDF5FileStatic::CreateFileName(fpath, fnameprefix, findex,
|
||||
j, dindex, numunits, i);
|
||||
|
||||
FILE_LOG(logERROR) << srcFileName;
|
||||
// find relative path
|
||||
std::string relative_srcFileName = srcFileName;
|
||||
{
|
||||
size_t i = srcFileName.rfind('/', srcFileName.length());
|
||||
if (i != std::string::npos)
|
||||
relative_srcFileName = (srcFileName.substr(i+1, srcFileName.length() - i));
|
||||
}
|
||||
|
||||
//source dataset name
|
||||
std::ostringstream osfn;
|
||||
osfn << "/data";
|
||||
if (frindexenable) osfn << "_f" << std::setfill('0') << std::setw(12) << j;
|
||||
std::string srcDatasetName = osfn.str();
|
||||
|
||||
//source dataspace
|
||||
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
|
||||
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
|
||||
hid_t srcDataspace = H5Screate_simple(3, srcdims, srcdimsmax);
|
||||
if (srcDataspace < 0)
|
||||
throw RuntimeError("Could not create source dataspace in virtual file " + virtualFileName);
|
||||
hsize_t srcdims_para[1] = {nDimx};
|
||||
hsize_t srcdimsmax_para[1] = {H5S_UNLIMITED};
|
||||
hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, srcdimsmax_para);
|
||||
if (srcDataspace_para < 0)
|
||||
throw RuntimeError("Could not create source dataspace (parameters) in virtual file " + virtualFileName);
|
||||
|
||||
//mapping
|
||||
if (H5Pset_virtual(dcpl, vdsDataspace, relative_srcFileName.c_str(),
|
||||
srcDatasetName.c_str(), srcDataspace) < 0) {
|
||||
throw RuntimeError("Could not set mapping for paramter 1");
|
||||
}
|
||||
|
||||
for (unsigned int k = 0; k < parameterNames.size(); ++k) {
|
||||
if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para, relative_srcFileName.c_str(),
|
||||
parameterNames[k], srcDataspace_para) < 0) {
|
||||
throw RuntimeError("Could not set mapping for paramter " + std::to_string(k));
|
||||
}
|
||||
}
|
||||
|
||||
//H5Sclose(srcDataspace);
|
||||
//H5Sclose(srcDataspace_para);
|
||||
offset[2] += nDimz;
|
||||
if (offset[2] >= (numDetz * nDimz)) {
|
||||
offset[2] = 0;
|
||||
offset[1] += nDimy;
|
||||
}
|
||||
offset_para[1]++;
|
||||
}
|
||||
framesSaved += nDimx;
|
||||
}
|
||||
|
||||
//dataset
|
||||
std::string virtualDatasetName = srcDataseName;
|
||||
hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(),
|
||||
GetDataTypeinC(dataType), vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
||||
if (vdsdataset < 0)
|
||||
throw RuntimeError("Could not create virutal dataset in virtual file " + virtualFileName);
|
||||
|
||||
|
||||
//virtual parameter dataset
|
||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
||||
hid_t vdsdataset_para = H5Dcreate2 (fd,
|
||||
parameterNames[i],
|
||||
GetDataTypeinC(parameterDataTypes[i]), vdsDataspace_para,
|
||||
H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
|
||||
if (vdsdataset_para < 0)
|
||||
throw RuntimeError("Could not create virutal dataset (parameters) in virtual file " + virtualFileName);
|
||||
}
|
||||
|
||||
//close
|
||||
H5Fclose(fd);
|
||||
fd = 0;
|
||||
|
||||
//link
|
||||
LinkVirtualInMaster(masterFileName, virtualFileName, virtualDatasetName, parameterNames);
|
||||
} catch (const RuntimeError &e) {
|
||||
if (fd > 0)
|
||||
H5Fclose(fd);
|
||||
fd = 0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Copy file to another file (mainly to view virutal files in hdfviewer)
|
||||
* @param dataType data type
|
||||
* @param owenable overwrite enable
|
||||
* @param oldFileName file name including path of file to copy
|
||||
* @param oldDatasetName dataset name to copy
|
||||
* @param newFileName file name including path of file to copy to
|
||||
* @param newDatasetName dataset name to copy to
|
||||
* @param rank rank
|
||||
* @param nDimx Number of objects in x dimension
|
||||
* @param nDimy Number of objects in y dimension
|
||||
* @param nDimz Number of objects in z dimension
|
||||
*/
|
||||
template <typename T>
|
||||
static void CopyVirtualFile(T datatype, bool owenable, std::string oldFileName, std::string oldDatasetName,
|
||||
std::string newFileName, std::string newDatasetName, int rank,
|
||||
uint64_t nDimx, uint32_t nDimy, uint32_t nDimz=0)
|
||||
{
|
||||
T *data_out;
|
||||
switch (rank) {
|
||||
case 2:
|
||||
data_out = (T*)malloc(sizeof(T)*(nDimx*nDimy));
|
||||
break;
|
||||
case 3:
|
||||
data_out = (T*)malloc(sizeof(T)*(nDimx*nDimy*nDimz));
|
||||
break;
|
||||
default:
|
||||
throw RuntimeError("Invalid rank. Options: 2 or 3");
|
||||
}
|
||||
if (datatype == PredType::STD_U16LE) {
|
||||
FILE_LOG(logINFO) << "datatype:16";
|
||||
} else if (datatype == PredType::STD_U32LE) {
|
||||
FILE_LOG(logINFO) << "datatype:32";
|
||||
} else if (datatype == PredType::STD_U64LE) {
|
||||
FILE_LOG(logINFO) << "datatype:64";
|
||||
} else if (datatype == PredType::STD_U8LE) {
|
||||
FILE_LOG(logINFO) << "datatype:8";
|
||||
} else {
|
||||
throw RuntimeError("Unknown datatype:" + std::to_string(datatype));
|
||||
}
|
||||
FILE_LOG(logINFO) << "owenable:" << (owenable?1:0) << std::endl
|
||||
<< "oldFileName:" << oldFileName << std::endl
|
||||
<< "oldDatasetName:" << oldDatasetName << std::endl
|
||||
<< "newFileName:" << newFileName << std::endl
|
||||
<< "newDatasetName:" << newDatasetName << std::endl
|
||||
<< "rank:" << rank << std::endl
|
||||
<< "nDimx:" << nDimx << std::endl
|
||||
<< "nDimy:" << nDimy << std::endl
|
||||
<< "nDimz:" << nDimz;
|
||||
|
||||
H5File* oldfd;
|
||||
H5File* newfd;
|
||||
try {
|
||||
Exception::dontPrint(); //to handle errors
|
||||
|
||||
//open old file
|
||||
oldfd = new H5File( oldFileName.c_str(), H5F_ACC_RDONLY);
|
||||
DataSet oldDataset = oldfd->openDataSet( oldDatasetName.c_str());
|
||||
//read dataset
|
||||
oldDataset.read( data_out, datatype);
|
||||
//new file
|
||||
FileAccPropList fapl;
|
||||
fapl.setFcloseDegree(H5F_CLOSE_STRONG);
|
||||
newfd = 0;
|
||||
if(!owenable)
|
||||
newfd = new H5File( newFileName.c_str(), H5F_ACC_EXCL,
|
||||
FileCreatPropList::DEFAULT,
|
||||
fapl );
|
||||
else
|
||||
newfd = new H5File( newFileName.c_str(), H5F_ACC_TRUNC,
|
||||
FileCreatPropList::DEFAULT,
|
||||
fapl );
|
||||
//dataspace and dataset
|
||||
DataSpace* newDataspace = 0;
|
||||
if (rank == 3) {
|
||||
hsize_t dims[3] = {nDimx, nDimy, nDimz};
|
||||
newDataspace = new DataSpace (3,dims);
|
||||
} else if (rank == 2) {
|
||||
hsize_t dims[2] = {nDimx, nDimy};
|
||||
newDataspace = new DataSpace (2,dims);
|
||||
}
|
||||
DataSet* newDataset = 0;
|
||||
newDataset = new DataSet( newfd->createDataSet(newDatasetName.c_str(), datatype, *newDataspace));
|
||||
//write and close
|
||||
newDataset->write(data_out,datatype);
|
||||
newfd->close();
|
||||
oldfd->close();
|
||||
} catch(const Exception& error){
|
||||
error.printErrorStack();
|
||||
free(data_out);
|
||||
oldfd->close();
|
||||
newfd->close();
|
||||
throw RuntimeError("Could not copy virtual files");
|
||||
}
|
||||
free(data_out);
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Link the Virtual File in the Master File
|
||||
* In C because H5Lcreate_external exists only in C
|
||||
* @param masterFileName master file name
|
||||
* @param virtualfname virtual file name
|
||||
* @param virtualDatasetname virtual dataset name
|
||||
* @param parameterNames parameter names
|
||||
*/
|
||||
static void LinkVirtualInMaster(std::string masterFileName, std::string virtualfname,
|
||||
std::string virtualDatasetname, std::vector <const char*> parameterNames) {
|
||||
char linkname[100];
|
||||
hid_t vfd = 0;
|
||||
|
||||
try {
|
||||
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
||||
if (dfal < 0)
|
||||
throw RuntimeError("Could not create file access property for link");
|
||||
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
|
||||
throw RuntimeError("Could not set strong file close degree for link");
|
||||
|
||||
//open master file
|
||||
hid_t mfd = H5Fopen( masterFileName.c_str(), H5F_ACC_RDWR, dfal);
|
||||
if (mfd < 0)
|
||||
throw RuntimeError("Could not open master file");
|
||||
|
||||
//open virtual file
|
||||
vfd = H5Fopen( virtualfname.c_str(), H5F_ACC_RDWR, dfal);
|
||||
if (vfd < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
throw RuntimeError("Could not open virtual file");
|
||||
}
|
||||
|
||||
// find relative path
|
||||
std::string relative_virtualfname = virtualfname;
|
||||
{
|
||||
size_t i = virtualfname.rfind('/', virtualfname.length());
|
||||
if (i != std::string::npos)
|
||||
relative_virtualfname = (virtualfname.substr(i+1, virtualfname.length() - i));
|
||||
}
|
||||
|
||||
//**data dataset**
|
||||
hid_t vdset = H5Dopen2( vfd, virtualDatasetname.c_str(), H5P_DEFAULT);
|
||||
if (vdset < 0) {
|
||||
H5Fclose(mfd);
|
||||
throw RuntimeError("Could not open virtual data dataset");
|
||||
}
|
||||
sprintf(linkname, "/entry/data/%s",virtualDatasetname.c_str());
|
||||
if(H5Lcreate_external( relative_virtualfname.c_str(), virtualDatasetname.c_str(),
|
||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
throw RuntimeError("Could not create link to data dataset");
|
||||
}
|
||||
H5Dclose(vdset);
|
||||
|
||||
//**paramter datasets**
|
||||
for (unsigned int i = 0; i < parameterNames.size(); ++i){
|
||||
hid_t vdset_para = H5Dopen2( vfd, (std::string (parameterNames[i])).c_str(), H5P_DEFAULT);
|
||||
if (vdset_para < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
throw RuntimeError("Could not open virtual parameter dataset to create link");
|
||||
}
|
||||
sprintf(linkname, "/entry/data/%s",(std::string (parameterNames[i])).c_str());
|
||||
|
||||
if(H5Lcreate_external( relative_virtualfname.c_str(), (std::string (parameterNames[i])).c_str(),
|
||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
throw RuntimeError("Could not create link to virtual parameter dataset");
|
||||
}
|
||||
}
|
||||
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
H5Fclose(vfd); vfd = 0;
|
||||
} catch () {
|
||||
if(vfd > 0)
|
||||
H5Fclose(vfd);
|
||||
vfd = 0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Get Data type in C
|
||||
* @param dtype datatype in C++
|
||||
* @returns datatype in C
|
||||
*/
|
||||
static hid_t GetDataTypeinC(DataType dtype) {
|
||||
if (dtype == PredType::STD_U8LE)
|
||||
return H5T_STD_U8LE;
|
||||
else if (dtype == PredType::STD_U16LE)
|
||||
return H5T_STD_U16LE;
|
||||
else if (dtype == PredType::STD_U32LE)
|
||||
return H5T_STD_U32LE;
|
||||
else if (dtype == PredType::STD_U64LE)
|
||||
return H5T_STD_U64LE;
|
||||
else {
|
||||
hid_t s = H5Tcopy(H5T_C_S1);
|
||||
H5Tset_size(s, MAX_NUM_PACKETS);
|
||||
return s;
|
||||
}
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
|
||||
|
||||
#endif
|
||||
Reference in New Issue
Block a user