mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-04-22 14:38:14 +02:00
994 lines
33 KiB
C++
Executable File
994 lines
33 KiB
C++
Executable File
#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 (includes scan and position variables)
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* @param findex file index
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* @param frindexenable frame index enable
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* @param fnum frame number 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(char* fpath, char* fnameprefix, uint64_t findex, bool frindexenable,
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uint64_t fnum = 0, int dindex = -1, int numunits = 1, int unitindex = 0)
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{
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std::ostringstream osfn;
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osfn << fpath << "/" << fnameprefix;
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if (dindex >= 0) osfn << "_d" << (dindex * numunits + unitindex);
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if (frindexenable) osfn << "_f" << std::setfill('0') << std::setw(12) << fnum;
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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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* Create master file name
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* @param fpath file path
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* @param fnameprefix file name prefix (includes scan and position variables)
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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(char* fpath, char* 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 << "_master";
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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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* Create virtual file name
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* @param fpath file path
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* @param fnameprefix file name prefix (includes scan and position variables)
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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(char* fpath, char* 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(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(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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* @returns 0 for success and 1 for fail
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*/
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static int 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(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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return 1;
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}
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return 0;
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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 int 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(Exception error){
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FILE_LOG(logERROR) << "Could not write parameters (index:" << i << ") to file in object " << ind;
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error.printErrorStack();
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return 1;
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}
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return 0;
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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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* @returns 0 for success and 1 for fail
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*/
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static int 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(Exception error){
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FILE_LOG(logERROR) << "Could not extend dataset in object " << ind;
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error.printErrorStack();
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return 1;
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}
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return 0;
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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 dr dynamic range
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* @param tenE ten giga enable
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* @param size image size
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* @param nx number of pixels in x direction
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* @param ny number of pixels in y direction
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* @param nf number of images
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* @param maxf maximum frames per file
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* @param acquisitionTime acquisition time
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* @param subexposuretime sub exposure time
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* @param subperiod sub period
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* @param acquisitionPeriod acquisition period
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* @param version version of software for hdf5 writing
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* @returns 0 for success and 1 for fail
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*/
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static int CreateMasterDataFile(H5File*& fd, std::string fname, bool owenable,
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uint32_t dr, bool tenE, uint32_t size,
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uint32_t nPixelsx, uint32_t nPixelsy, uint64_t nf,
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uint32_t maxf,
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uint64_t acquisitionTime, uint64_t subexposuretime,
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uint64_t subperiod, uint64_t acquisitionPeriod, double version)
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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=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 ( &dr, 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 = tenE;
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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 ( &size, 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 ( &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 ( &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 ( &maxf, 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 ( &nf, 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 ( &acquisitionTime, 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 ( &subexposuretime, 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 ( &subperiod, 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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//Period
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dataset = group5.createDataSet ( "acquisition period", PredType::STD_U64LE, dataspace );
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dataset.write ( &acquisitionPeriod, 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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//Timestamp
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time_t t = time(0);
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dataset = group5.createDataSet ( "timestamp", strdatatype, dataspace );
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dataset.write ( std::string(ctime(&t)), strdatatype );
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fd->close();
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} catch(Exception error) {
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FILE_LOG(logERROR) << "Could not create master HDF5 handles";
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error.printErrorStack();
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if (fd) fd->close();
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return 1;
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}
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return 0;
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}
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/**
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* Create File
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* @param ind object index for debugging
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* @param owenable overwrite enable
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* @param fname complete file name
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* @param frindexenable frame index enable
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* @param fnum current image number
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* @param nDimx number of pixels in x dim (#frames)
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* @param nDimy number of pixels in y dim (height y dir)
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* @param nDimz number of pixels in z dim (width x dir)
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* @param dtype data type
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* @param fd file pointer
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* @param dspace dataspace pointer
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* @param dset dataset pointer
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* @param version version of software for hdf5 writing
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* @param maxchunkedimages maximum chunked images
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* @param dspace_para dataspace of parameters
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* @param dset_para vector of datasets of parameters
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* @param parameterNames parameter names
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* @param parameterDataTypes parameter datatypes
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* @returns 0 for success and 1 for fail
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*/
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static int CreateDataFile(int ind, bool owenable, std::string fname, bool frindexenable,
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uint64_t fnum, uint64_t nDimx, uint32_t nDimy, uint32_t nDimz,
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DataType dtype, H5File*& fd, DataSpace*& dspace, DataSet*& dset,
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double version, uint64_t maxchunkedimages,
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DataSpace*& dspace_para, std::vector<DataSet*>& dset_para,
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std::vector <const char*> parameterNames,
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std::vector <DataType> parameterDataTypes)
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{
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try {
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Exception::dontPrint(); //to handle errors
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//file
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FileAccPropList fapl;
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fapl.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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fapl );
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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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fapl );
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//attributes - version
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double dValue=version;
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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(Exception error){
|
|
FILE_LOG(logERROR) << "Could not create HDF5 handles in object " << ind;
|
|
error.printErrorStack();
|
|
if (fd) fd->close();
|
|
return 1;
|
|
}
|
|
return 0;
|
|
}
|
|
|
|
|
|
/**
|
|
* 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 (includes scan and position variables)
|
|
* @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
|
|
* @returns 0 for success and 1 for fail
|
|
*/
|
|
static int CreateVirtualDataFile(
|
|
std::string virtualFileName,
|
|
hid_t& fd, std::string masterFileName,
|
|
char* fpath, char* 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)
|
|
{
|
|
//file
|
|
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
|
if (dfal < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create file access property for virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not set strong file close degree for virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
fd = H5Fcreate( virtualFileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
|
|
if (fd < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create virtual file ") + virtualFileName + std::string("\n"));
|
|
|
|
//attributes - version
|
|
hid_t dataspace_attr = H5Screate (H5S_SCALAR);
|
|
if (dataspace_attr < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create dataspace for attribute in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
hid_t attrid = H5Acreate2 (fd, "version", H5T_NATIVE_DOUBLE, dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
|
|
if (attrid < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create attribute in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
double attr_data = version;
|
|
if (H5Awrite (attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not write attribute in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
if (H5Aclose (attrid) < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not close attribute in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
|
|
|
|
//virtual dataspace
|
|
hsize_t vdsdims[3] = {numf, numDety * nDimy, numDetz * nDimz};
|
|
hid_t vdsDataspace = H5Screate_simple(3, vdsdims ,NULL);
|
|
if (vdsDataspace < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create virtual dataspace in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
hsize_t vdsdims_para[2] = {numf, (unsigned int) numDety * numDetz};
|
|
hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, NULL);
|
|
if (vdsDataspace_para < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create virtual dataspace (parameters) in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
|
|
|
|
//fill values
|
|
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
|
|
if (dcpl < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create file creation properties in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
int fill_value = -1;
|
|
if (H5Pset_fill_value (dcpl, GetDataTypeinC(dataType), &fill_value) < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create fill value in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
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)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create file creation properties (parameters) in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
if (H5Pset_fill_value (dcpl_para[i], GetDataTypeinC(parameterDataTypes[i]), &fill_value) < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create fill value (parameters) in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
}
|
|
|
|
//hyperslab
|
|
int numMajorHyperslab = numf/maxFramesPerFile;
|
|
if (numf%maxFramesPerFile) numMajorHyperslab++;
|
|
bool error = false;
|
|
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) {
|
|
FILE_LOG(logERROR) << "Could not select hyperslab";
|
|
error = true;
|
|
break;
|
|
}
|
|
if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET,
|
|
offset_para, NULL, count_para, NULL) < 0) {
|
|
FILE_LOG(logERROR) << "Could not select hyperslab for parameters";
|
|
error = true;
|
|
break;
|
|
}
|
|
|
|
//source file name
|
|
std::string srcFileName = HDF5FileStatic::CreateFileName(fpath, fnameprefix, findex,
|
|
frindexenable, framesSaved, dindex, numunits, i);
|
|
|
|
// 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) << framesSaved;
|
|
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)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create source dataspace in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
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)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create source dataspace (parameters) in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
|
|
//mapping
|
|
if (H5Pset_virtual(dcpl, vdsDataspace, relative_srcFileName.c_str(),
|
|
srcDatasetName.c_str(), srcDataspace) < 0) {
|
|
FILE_LOG(logERROR) << "Could not set mapping for paramter 1";
|
|
error = true;
|
|
break;
|
|
}
|
|
|
|
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) {
|
|
FILE_LOG(logERROR) << "Could not set mapping for paramter " << k;
|
|
error = true;
|
|
break;
|
|
}
|
|
}
|
|
|
|
//H5Sclose(srcDataspace);
|
|
//H5Sclose(srcDataspace_para);
|
|
offset[2] += nDimz;
|
|
if (offset[2] >= (numDetz * nDimz)) {
|
|
offset[2] = 0;
|
|
offset[1] += nDimy;
|
|
}
|
|
offset_para[1]++;
|
|
}
|
|
framesSaved += nDimx;
|
|
}
|
|
if (error)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not map files in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
|
|
//dataset
|
|
std::string virtualDatasetName = srcDataseName;
|
|
hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(),
|
|
GetDataTypeinC(dataType), vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
if (vdsdataset < 0)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create virutal dataset in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
|
|
|
|
//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)
|
|
return CloseFileOnError(fd,
|
|
std::string("Could not create virutal dataset (parameters) in virtual file ")
|
|
+ virtualFileName + std::string("\n"));
|
|
}
|
|
|
|
//close
|
|
H5Fclose(fd); fd = 0;
|
|
|
|
//link
|
|
return LinkVirtualInMaster(masterFileName, virtualFileName, virtualDatasetName, parameterNames);
|
|
}
|
|
|
|
|
|
|
|
/**
|
|
* 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
|
|
* @returns 0 for success and 1 for fail
|
|
*/
|
|
template <typename T>
|
|
static int 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:
|
|
FILE_LOG(logERROR) << "Invalid rank. Options: 2 or 3";
|
|
return 0;
|
|
}
|
|
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 {
|
|
FILE_LOG(logERROR) << "Unknown datatype: " << datatype;
|
|
return 1;
|
|
}
|
|
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(Exception error){
|
|
FILE_LOG(logERROR) << "Could not copy virtual files";
|
|
error.printErrorStack();
|
|
free(data_out);
|
|
oldfd->close();
|
|
newfd->close();
|
|
return 1;
|
|
}
|
|
free(data_out);
|
|
return 0;
|
|
}
|
|
|
|
|
|
|
|
/**
|
|
* 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
|
|
* @returns 0 for success and 1 for fail
|
|
*/
|
|
static int LinkVirtualInMaster(std::string masterFileName, std::string virtualfname,
|
|
std::string virtualDatasetname, std::vector <const char*> parameterNames) {
|
|
char linkname[100];
|
|
hid_t vfd = 0;
|
|
|
|
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
|
if (dfal < 0)
|
|
return CloseFileOnError( vfd, std::string("Could not create file access property for link\n"));
|
|
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
|
|
return CloseFileOnError( vfd, std::string("Could not set strong file close degree for link\n"));
|
|
|
|
//open master file
|
|
hid_t mfd = H5Fopen( masterFileName.c_str(), H5F_ACC_RDWR, dfal);
|
|
if (mfd < 0)
|
|
return CloseFileOnError( vfd, std::string("Could not open master file\n"));
|
|
|
|
//open virtual file
|
|
vfd = H5Fopen( virtualfname.c_str(), H5F_ACC_RDWR, dfal);
|
|
if (vfd < 0) {
|
|
H5Fclose(mfd); mfd = 0;
|
|
return CloseFileOnError( vfd, std::string("Could not open virtual file\n"));
|
|
}
|
|
|
|
// 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);
|
|
return CloseFileOnError( vfd, std::string("Could not open virtual data dataset\n"));
|
|
}
|
|
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;
|
|
return CloseFileOnError( vfd, std::string("Could not create link to data dataset\n"));
|
|
}
|
|
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;
|
|
return CloseFileOnError( vfd, std::string("Could not open virtual parameter dataset to create link\n"));
|
|
}
|
|
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;
|
|
return CloseFileOnError( vfd, std::string("Could not create link to virtual parameter dataset\n"));
|
|
}
|
|
}
|
|
|
|
H5Fclose(mfd); mfd = 0;
|
|
H5Fclose(vfd); vfd = 0;
|
|
return 0;
|
|
}
|
|
|
|
|
|
|
|
/**
|
|
* Print Error msg and Close File and called on error
|
|
* @returns 1 for fail
|
|
*/
|
|
static int CloseFileOnError(hid_t& fd, const std::string msg) {
|
|
FILE_LOG(logERROR) << msg;
|
|
if(fd > 0)
|
|
H5Fclose(fd);
|
|
fd = 0;
|
|
return 1;
|
|
}
|
|
|
|
|
|
/**
|
|
* 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
|