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slsDetectorPackage/slsReceiverSoftware/include/HDF5FileStatic.h

993 lines
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C++
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#ifdef HDF5C
#pragma once
/************************************************
* @file HDF5FileStatic.h
* @short creating, closing, writing and reading
* from HDF5 files
***********************************************/
/**
*@short creating, closing, writing and reading from HDF5 files
*/
#include "H5Cpp.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif
#include "sls_receiver_defs.h"
#include "logger.h"
#include <iostream>
#include <string>
#include <vector>
#include <iomanip>
#include <stdlib.h> //malloc
#include <sstream>
#include <cstring> //memset
class HDF5FileStatic: public virtual slsReceiverDefs {
public:
/** Constructor */
HDF5FileStatic(){};
/** Destructor */
virtual ~HDF5FileStatic(){};
/**
* Create File Name in format fpath/fnameprefix_fx_dy_z.raw,
* where x is fnum, y is (dindex * numunits + unitindex) and z is findex
* @param fpath file path
* @param fnameprefix file name prefix (includes scan and position variables)
* @param findex file index
* @param frindexenable frame index enable
* @param fnum frame number index
* @param dindex readout index
* @param numunits number of units per readout. eg. eiger has 2 udp units per readout
* @param unitindex unit index
* @returns complete file name created
*/
static string CreateFileName(char* fpath, char* fnameprefix, uint64_t findex, bool frindexenable,
uint64_t fnum = 0, int dindex = -1, int numunits = 1, int unitindex = 0)
{
ostringstream osfn;
osfn << fpath << "/" << fnameprefix;
if (dindex >= 0) osfn << "_d" << (dindex * numunits + unitindex);
if (frindexenable) osfn << "_f" << setfill('0') << setw(12) << fnum;
osfn << "_" << findex;
osfn << ".h5";
return osfn.str();
}
/**
* Create master file name
* @param fpath file path
* @param fnameprefix file name prefix (includes scan and position variables)
* @param findex file index
* @returns master file name
*/
static string CreateMasterFileName(char* fpath, char* fnameprefix, uint64_t findex)
{
ostringstream osfn;
osfn << fpath << "/" << fnameprefix;
osfn << "_master";
osfn << "_" << findex;
osfn << ".h5";
return osfn.str();
}
/**
* Create virtual file name
* @param fpath file path
* @param fnameprefix file name prefix (includes scan and position variables)
* @param fnum current frame number
* @param findex file index
* @returns virtual file name
*/
static string CreateVirtualFileName(char* fpath, char* fnameprefix, uint64_t findex)
{
ostringstream osfn;
osfn << fpath << "/" << fnameprefix;
osfn << "_virtual";
osfn << "_" << findex;
osfn << ".h5";
return osfn.str();
}
/**
* Close File
* @param ind index for debugging
* @param fd file pointer
* @param dp dataspace pointer
* @param ds dataset pointer
* @param ds_para pointer to array of parameter datasets
*/
static void CloseDataFile(int ind, H5File*& fd)
{
try {
Exception::dontPrint(); //to handle errors
if (fd) {
delete fd;
fd = 0;
}
} catch(Exception error) {
cprintf(RED,"Error in closing HDF5 handles of index %d\n", ind);
error.printErrorStack();
}
}
/*
* Close master file
* @param fd master hdf5 file object
*/
static void CloseMasterDataFile(H5File*& fd)
{
try {
Exception::dontPrint(); //to handle errors
if (fd) {
delete fd;
fd = 0;
}
} catch(Exception error) {
cprintf(RED,"Error in closing master HDF5 handles\n");
error.printErrorStack();
}
}
/*
* Close virtual file
* (in C because H5Pset_virtual doesnt exist yet in C++)
* @param fd virtual hdf5 file handle
*/
static void CloseVirtualDataFile(hid_t& fd)
{
if(fd) {
if (H5Fclose(fd) < 0 )
cprintf(RED,"Error in closing virtual HDF5 handles\n");
fd = 0;
}
}
/**
* Write data to file
* @param ind object index for debugging
* @param buf buffer to write from
* @param nDimx image number in file (imagenumber%maxframesinfile)
* @param nDimy number of pixels in y direction
* @param nDimz number of pixels in x direction
* @param dspace dataspace pointer
* @param dset dataset pointer
* @param dtype datatype
* @returns 0 for success and 1 for fail
*/
static int WriteDataFile(int ind, char* buf,
uint64_t nDimx, uint32_t nDimy, uint32_t nDimz,
DataSpace* dspace, DataSet* dset, DataType dtype)
{
hsize_t count[3] = {1, nDimy, nDimz};
hsize_t start[3] = {nDimx, 0, 0};
hsize_t dims2[2] = {nDimy, nDimz};
try{
Exception::dontPrint(); //to handle errors
dspace->selectHyperslab( H5S_SELECT_SET, count, start);
DataSpace memspace(2,dims2);
dset->write(buf, dtype, memspace, *dspace);
memspace.close();
}
catch(Exception error){
cprintf(RED,"Error in writing to file in object %d\n",ind);
error.printErrorStack();
return 1;
}
return 0;
}
/**
* Write Parameter Arrays as datasets (to virtual file)
* @param ind self index
* @param dspace_para parameter dataspace
* @param fnum current frame number
* @param dset_para vector or dataset pointers of parameters
* @param rheader sls_receiver_header pointer
* @param parameterDataTypes parameter datatypes
*/
static int WriteParameterDatasets(int ind, DataSpace* dspace_para, uint64_t fnum,
vector <DataSet*> dset_para,sls_receiver_header* rheader,
vector <DataType> parameterDataTypes)
{
sls_detector_header header = rheader->detHeader;
hsize_t count[1] = {1};
hsize_t start[1] = {fnum};
int i = 0;
try{
Exception::dontPrint(); //to handle errors
dspace_para->selectHyperslab( H5S_SELECT_SET, count, start);
DataSpace memspace(H5S_SCALAR);
dset_para[0]->write(&header.frameNumber, parameterDataTypes[0], memspace, *dspace_para);i=1;
dset_para[1]->write(&header.expLength, parameterDataTypes[1], memspace, *dspace_para);i=2;
dset_para[2]->write(&header.packetNumber, parameterDataTypes[2], memspace, *dspace_para);i=3;
dset_para[3]->write(&header.bunchId, parameterDataTypes[3], memspace, *dspace_para);i=4;
dset_para[4]->write(&header.timestamp, parameterDataTypes[4], memspace, *dspace_para);i=5;
dset_para[5]->write(&header.modId, parameterDataTypes[5], memspace, *dspace_para);i=6;
dset_para[6]->write(&header.xCoord, parameterDataTypes[6], memspace, *dspace_para);i=7;
dset_para[7]->write(&header.yCoord, parameterDataTypes[7], memspace, *dspace_para);i=8;
dset_para[8]->write(&header.zCoord, parameterDataTypes[8], memspace, *dspace_para);i=9;
dset_para[9]->write(&header.debug, parameterDataTypes[9], memspace, *dspace_para);i=10;
dset_para[10]->write(&header.roundRNumber, parameterDataTypes[10], memspace, *dspace_para);i=11;
dset_para[11]->write(&header.detType, parameterDataTypes[11], memspace, *dspace_para);i=12;
dset_para[12]->write(&header.version, parameterDataTypes[12], memspace, *dspace_para);i=13;
// contiguous bitset
if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
dset_para[13]->write((char*)&(rheader->packetsMask), parameterDataTypes[13], memspace, *dspace_para);
}
// not contiguous bitset
else {
// get contiguous representation of bit mask
bitset_storage storage;
memset(storage, 0 , sizeof(bitset_storage));
sls_bitset bits = rheader->packetsMask;
for (int i = 0; i < MAX_NUM_PACKETS; ++i)
storage[i >> 3] |= (bits[i] << (i & 7));
// write bitmask
dset_para[13]->write((char*)storage, parameterDataTypes[13], memspace, *dspace_para);
}i=14;
}
catch(Exception error){
cprintf(RED,"Error in writing parameters (index:%d) to file in object %d\n", i, ind);
error.printErrorStack();
return 1;
}
return 0;
}
/**
* Extend datasets in #images dimension (x dimension)
* @param ind self index
* @param dpace data space pointer address
* @param dset data set pointer
* @param dspace_para parameter dataspace address pointer
* @param dset dataset parameter pointer
* @param initialNumImages initial number of images
* @returns 0 for success and 1 for fail
*/
static int ExtendDataset(int ind, DataSpace*& dspace, DataSet* dset,
DataSpace*& dspace_para, vector <DataSet*> dset_para,
uint64_t initialNumImages) {
try{
Exception::dontPrint(); //to handle errors
hsize_t dims[3];
dspace->getSimpleExtentDims(dims);
dims[0] += initialNumImages;
dset->extend(dims);
delete dspace;
dspace = 0;
dspace = new DataSpace(dset->getSpace());
hsize_t dims_para[1] = {dims[0]};
for (unsigned int i = 0; i < dset_para.size(); ++i)
dset_para[i]->extend(dims_para);
delete dspace_para;
dspace_para = 0;
dspace_para = new DataSpace(dset_para[0]->getSpace());
}
catch(Exception error){
cprintf(RED,"Error in extending dataset in object %d\n",ind);
error.printError();
return 1;
}
return 0;
}
/**
* Create master file
* @param fname master file name
* @param owenable overwrite enable
* @param dr dynamic range
* @param tenE ten giga enable
* @param size image size
* @param nx number of pixels in x direction
* @param ny number of pixels in y direction
* @param nf number of images
* @param maxf maximum frames per file
* @param acquisitionTime acquisition time
* @param subexposuretime sub exposure time
* @param subperiod sub period
* @param acquisitionPeriod acquisition period
* @param version version of software for hdf5 writing
* @returns 0 for success and 1 for fail
*/
static int CreateMasterDataFile(H5File*& fd, string fname, bool owenable,
uint32_t dr, bool tenE, uint32_t size,
uint32_t nPixelsx, uint32_t nPixelsy, uint64_t nf,
uint32_t maxf,
uint64_t acquisitionTime, uint64_t subexposuretime,
uint64_t subperiod, uint64_t acquisitionPeriod, double version)
{
try {
Exception::dontPrint(); //to handle errors
FileAccPropList flist;
flist.setFcloseDegree(H5F_CLOSE_STRONG);
fd = 0;
if(!owenable)
fd = new H5File( fname.c_str(), H5F_ACC_EXCL,
FileCreatPropList::DEFAULT,
flist );
else
fd = new H5File( fname.c_str(), H5F_ACC_TRUNC,
FileCreatPropList::DEFAULT,
flist );
//variables
DataSpace dataspace = DataSpace (H5S_SCALAR);
Attribute attribute;
DataSet dataset;
int iValue=0;
double dValue=0;
StrType strdatatype(PredType::C_S1,256);
//create attributes
//version
dValue=version;
attribute = fd->createAttribute("version",PredType::NATIVE_DOUBLE, dataspace);
attribute.write(PredType::NATIVE_DOUBLE, &dValue);
//Create a group in the file
Group group1( fd->createGroup( "entry" ) );
Group group2( group1.createGroup("data") );
Group group3( group1.createGroup("instrument") );
Group group4( group3.createGroup("beam") );
Group group5( group3.createGroup("detector") );
Group group6( group1.createGroup("sample") );
//Dynamic Range
dataset = group5.createDataSet ( "dynamic range", PredType::NATIVE_INT, dataspace );
dataset.write ( &dr, PredType::NATIVE_INT);
attribute = dataset.createAttribute("unit",strdatatype, dataspace);
attribute.write(strdatatype, string("bits"));
//Ten Giga
iValue = tenE;
dataset = group5.createDataSet ( "ten giga enable", PredType::NATIVE_INT, dataspace );
dataset.write ( &iValue, PredType::NATIVE_INT);
//Image Size
dataset = group5.createDataSet ( "image size", PredType::NATIVE_INT, dataspace );
dataset.write ( &size, PredType::NATIVE_INT);
attribute = dataset.createAttribute("unit",strdatatype, dataspace);
attribute.write(strdatatype, string("bytes"));
//x
dataset = group5.createDataSet ( "number of pixels in x axis", PredType::NATIVE_INT, dataspace );
dataset.write ( &nPixelsx, PredType::NATIVE_INT);
//y
dataset = group5.createDataSet ( "number of pixels in y axis", PredType::NATIVE_INT, dataspace );
dataset.write ( &nPixelsy, PredType::NATIVE_INT);
//Maximum frames per file
dataset = group5.createDataSet ( "maximum frames per file", PredType::NATIVE_INT, dataspace );
dataset.write ( &maxf, PredType::NATIVE_INT);
//Total Frames
dataset = group5.createDataSet ( "total frames", PredType::STD_U64LE, dataspace );
dataset.write ( &nf, PredType::STD_U64LE);
//Exptime
dataset = group5.createDataSet ( "exposure time", PredType::STD_U64LE, dataspace );
dataset.write ( &acquisitionTime, PredType::STD_U64LE);
attribute = dataset.createAttribute("unit",strdatatype, dataspace);
attribute.write(strdatatype, string("ns"));
//SubExptime
dataset = group5.createDataSet ( "sub exposure time", PredType::STD_U64LE, dataspace );
dataset.write ( &subexposuretime, PredType::STD_U64LE);
attribute = dataset.createAttribute("unit",strdatatype, dataspace);
attribute.write(strdatatype, string("ns"));
//SubPeriod
dataset = group5.createDataSet ( "sub period", PredType::STD_U64LE, dataspace );
dataset.write ( &subperiod, PredType::STD_U64LE);
attribute = dataset.createAttribute("unit",strdatatype, dataspace);
attribute.write(strdatatype, string("ns"));
//Period
dataset = group5.createDataSet ( "acquisition period", PredType::STD_U64LE, dataspace );
dataset.write ( &acquisitionPeriod, PredType::STD_U64LE);
attribute = dataset.createAttribute("unit",strdatatype, dataspace);
attribute.write(strdatatype, string("ns"));
//Timestamp
time_t t = time(0);
dataset = group5.createDataSet ( "timestamp", strdatatype, dataspace );
dataset.write ( string(ctime(&t)), strdatatype );
fd->close();
} catch(Exception error) {
cprintf(RED,"Error in creating master HDF5 handles\n");
error.printErrorStack();
if (fd) fd->close();
return 1;
}
return 0;
}
/**
* 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
* @returns 0 for success and 1 for fail
*/
static int CreateDataFile(int ind, bool owenable, 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, vector<DataSet*>& dset_para,
vector <const char*> parameterNames,
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
ostringstream osfn;
osfn << "/data";
if (frindexenable) osfn << "_f" << setfill('0') << setw(12) << fnum;
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){
cprintf(RED,"Error in creating HDF5 handles in object %d\n",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(
string virtualFileName,
hid_t& fd, string masterFileName,
char* fpath, char* fnameprefix, uint64_t findex, bool frindexenable,
int dindex, int numunits,
uint32_t maxFramesPerFile, uint64_t numf,
string srcDataseName, DataType dataType,
int numDety, int numDetz, uint32_t nDimy, uint32_t nDimz,
double version,
vector <const char*> parameterNames,
vector <DataType> parameterDataTypes)
{
//file
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
if (dfal < 0)
return CloseFileOnError(fd,
string("Error in creating file access property for virtual file ")
+ virtualFileName + string("\n"));
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
return CloseFileOnError(fd,
string("Error in setting strong file close degree for virtual file ")
+ virtualFileName + string("\n"));
fd = H5Fcreate( virtualFileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
if (fd < 0)
return CloseFileOnError(fd,
string("Error in creating virtual file ") + virtualFileName + string("\n"));
//attributes - version
hid_t dataspace_attr = H5Screate (H5S_SCALAR);
if (dataspace_attr < 0)
return CloseFileOnError(fd,
string("Error in creating dataspace for attribute in virtual file ")
+ virtualFileName + string("\n"));
hid_t attrid = H5Acreate2 (fd, "version", H5T_NATIVE_DOUBLE, dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
if (attrid < 0)
return CloseFileOnError(fd,
string("Error in creating attribute in virtual file ")
+ virtualFileName + string("\n"));
double attr_data = version;
if (H5Awrite (attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
return CloseFileOnError(fd,
string("Error in writing attribute in virtual file ")
+ virtualFileName + string("\n"));
if (H5Aclose (attrid) < 0)
return CloseFileOnError(fd,
string("Error in closing attribute in virtual file ")
+ virtualFileName + 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,
string("Error in creating virtual dataspace in virtual file ")
+ virtualFileName + 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,
string("Error in creating virtual dataspace (parameters) in virtual file ")
+ virtualFileName + string("\n"));
//fill values
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
if (dcpl < 0)
return CloseFileOnError(fd,
string("Error in creating file creation properties in virtual file ")
+ virtualFileName + string("\n"));
int fill_value = -1;
if (H5Pset_fill_value (dcpl, GetDataTypeinC(dataType), &fill_value) < 0)
return CloseFileOnError(fd,
string("Error in creating fill value in virtual file ")
+ virtualFileName + 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,
string("Error in creating file creation properties (parameters) in virtual file ")
+ virtualFileName + string("\n"));
if (H5Pset_fill_value (dcpl_para[i], GetDataTypeinC(parameterDataTypes[i]), &fill_value) < 0)
return CloseFileOnError(fd,
string("Error in creating fill value (parameters) in virtual file ")
+ virtualFileName + 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) {
cprintf(RED,"could not select hyperslab\n");
error = true;
break;
}
if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET,
offset_para, NULL, count_para, NULL) < 0) {
cprintf(RED,"could not select hyperslab for parameters\n");
error = true;
break;
}
//source file name
string srcFileName = HDF5FileStatic::CreateFileName(fpath, fnameprefix, findex,
frindexenable, framesSaved, dindex, numunits, i);
// find relative path
string relative_srcFileName = srcFileName;
{
size_t i = srcFileName.rfind('/', srcFileName.length());
if (i != string::npos)
relative_srcFileName = (srcFileName.substr(i+1, srcFileName.length() - i));
}
//source dataset name
ostringstream osfn;
osfn << "/data";
if (frindexenable) osfn << "_f" << setfill('0') << setw(12) << framesSaved;
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,
string("Error in creating source dataspace in virtual file ")
+ virtualFileName + 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,
string("Error in creating source dataspace (parameters) in virtual file ")
+ virtualFileName + string("\n"));
//mapping
if (H5Pset_virtual(dcpl, vdsDataspace, relative_srcFileName.c_str(),
srcDatasetName.c_str(), srcDataspace) < 0) {
cprintf(RED,"could not set mapping for paramter 1\n");
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) {
cprintf(RED,"could not set mapping for paramter %d\n", 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,
string("Error in mapping files in virtual file ")
+ virtualFileName + string("\n"));
//dataset
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,
string("Error in creating virutal dataset in virtual file ")
+ virtualFileName + 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,
string("Error in creating virutal dataset (parameters) in virtual file ")
+ virtualFileName + 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, string oldFileName, string oldDatasetName,
string newFileName, 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:
cprintf(RED,"invalid rank. Options: 2 or 3\n");
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";
return 1;
}
FILE_LOG(logINFO) << "owenable:" << (owenable?1:0) << endl
<< "oldFileName:" << oldFileName << endl
<< "oldDatasetName:" << oldDatasetName << endl
<< "newFileName:" << newFileName << endl
<< "newDatasetName:" << newDatasetName << endl
<< "rank:" << rank << endl
<< "nDimx:" << nDimx << endl
<< "nDimy:" << nDimy << 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){
cprintf(RED,"Error in copying virtual files\n");
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(string masterFileName, string virtualfname,
string virtualDatasetname, vector <const char*> parameterNames) {
char linkname[100];
hid_t vfd = 0;
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
if (dfal < 0)
return CloseFileOnError( vfd, string("Error in creating file access property for link\n"));
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
return CloseFileOnError( vfd, string("Error in setting 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, string("Error in opening 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, string("Error in opening virtual file\n"));
}
// find relative path
string relative_virtualfname = virtualfname;
{
size_t i = virtualfname.rfind('/', virtualfname.length());
if (i != 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, string("Error in opening 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, string("Error in creating link to data dataset\n"));
}
H5Dclose(vdset);
//**paramter datasets**
for (unsigned int i = 0; i < parameterNames.size(); ++i){
hid_t vdset_para = H5Dopen2( vfd, (string (parameterNames[i])).c_str(), H5P_DEFAULT);
if (vdset_para < 0) {
H5Fclose(mfd); mfd = 0;
return CloseFileOnError( vfd, string("Error in opening virtual parameter dataset to create link\n"));
}
sprintf(linkname, "/entry/data/%s",(string (parameterNames[i])).c_str());
if(H5Lcreate_external( relative_virtualfname.c_str(), (string (parameterNames[i])).c_str(),
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
H5Fclose(mfd); mfd = 0;
return CloseFileOnError( vfd, string("Error in creating 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 string msg) {
cprintf(RED, "%s", msg.c_str());
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
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