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https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-12-15 09:01:21 +01:00
master hdf5 does not work, but so far good
This commit is contained in:
Dhanya Maliakal
@@ -4,19 +4,36 @@
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* creates/closes the file and writes data to it
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***********************************************/
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//#define HDF5C /*********************?????????????????* Need to remove this in the header file to o*************************************?????????????????????***/
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//#ifdef HDF5C
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#include "HDF5File.h"
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#include "receiver_defs.h"
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#include <iostream>
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#include <iomanip>
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using namespace std;
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pthread_mutex_t HDF5File::Mutex = PTHREAD_MUTEX_INITIALIZER;
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H5File* HDF5File::masterfd = 0;
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H5File* HDF5File::virtualfd = 0;
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HDF5File::HDF5File(int ind, char* fname, char* fpath, uint64_t* findex,
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bool* frindexenable, bool* owenable, int* dindex, int* nunits):
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File(ind, fname, fpath, findex, frindexenable, owenable, dindex, nunits)
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bool* frindexenable, bool* owenable, int* dindex, int* nunits, uint64_t* nf, uint32_t* dr,
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int nx, int ny):
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File(ind, fname, fpath, findex, frindexenable, owenable, dindex, nunits, nf, dr),
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filefd(0),
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dataspace(0),
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dataset(0),
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datatype(PredType::STD_U16LE),
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nPixelsX(nx),
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nPixelsY(ny)
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{
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printf("%d HDF5File constructor\n",index);
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#ifdef VERBOSE
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PrintMembers();
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#endif
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}
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@@ -26,25 +43,88 @@ HDF5File::~HDF5File() {
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void HDF5File::PrintMembers() {
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File::PrintMembers();
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printf("\nHDF5 Print Members \n");
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UpdateDataType();
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if (datatype == PredType::STD_U8LE) {
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printf("Data Type: 4 or 8\n");
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} else if (datatype == PredType::STD_U16LE) {
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printf("Data Type: 16\n");
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} else if (datatype == PredType::STD_U32LE) {
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printf("Data Type: 32\n");
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} else {
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cprintf(BG_RED,"unknown data type\n");
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}
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}
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void HDF5File::SetNumberofPixels(uint32_t nx, uint32_t ny) {
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nPixelsX = nx;
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nPixelsY = ny;
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}
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slsReceiverDefs::fileFormat HDF5File::GetType() {
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slsReceiverDefs::fileFormat HDF5File::GetFileType() {
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return HDF5;
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}
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void HDF5File::UpdateDataType() {
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switch(*dynamicRange){
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case 4: datatype = PredType::STD_U8LE; break;
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case 8: datatype = PredType::STD_U8LE; break;
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case 16: datatype = PredType::STD_U16LE; break;
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case 32: datatype = PredType::STD_U32LE; break;
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default: cprintf(BG_RED,"unknown dynamic range\n");
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datatype = PredType::STD_U16LE; break;
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}
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}
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int HDF5File::CreateFile(uint64_t fnum) {
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currentFileName = CreateFileName(filePath, fileNamePrefix, *fileIndex,
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*frameIndexEnable, fnum, *detIndex, *numUnitsPerDetector, index);
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//create file
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UpdateDataType();
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if (CreateDataFile(index, *overWriteEnable, *numImages, currentFileName, fnum,
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((*dynamicRange==4) ? (nPixelsX/2) : nPixelsX), nPixelsY,
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datatype, filefd, dataspace, dataset) == FAIL)
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return FAIL;
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printf("%d HDF5 File: %s\n", index, currentFileName.c_str());
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return OK;
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}
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void HDF5File::CloseFile() {
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void HDF5File::CloseCurrentFile() {
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CloseDataFile(filefd, dataspace, dataset);
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}
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void HDF5File::CloseAllFiles() {
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CloseDataFile(filefd, dataspace, dataset);
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if (master)
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CloseCommonDataFiles();
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}
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int HDF5File::WriteToFile(char* buffer, int buffersize, uint64_t fnum) {
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if (WriteDataFile(index, buffer, *numImages,
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((*dynamicRange==4) ? (nPixelsX/2) : nPixelsX), nPixelsY, fnum,
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dataspace, dataset, datatype) == OK)
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return OK;
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cprintf(RED,"%d Error: Write to file failed\n", index);
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return FAIL;
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}
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int HDF5File::CreateCommonFiles(bool en, uint32_t size,
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uint32_t nx, uint32_t ny, uint64_t at, uint64_t ap) {
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if (master) {
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string masterFileName="", virtualFileName="";
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CreateCommonFileNames(masterFileName, virtualFileName, filePath, fileNamePrefix, *fileIndex);
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printf("Master HDF5 File: %s\nVirtual HDF5 File: %s\n", masterFileName.c_str(), virtualFileName.c_str());
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//create common files
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return CreateCommonDataFiles(masterFileName, virtualFileName, *overWriteEnable,
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en, size, nx, ny, at, ap);
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}
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return OK;
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}
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/*** static function ***/
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string HDF5File::CreateFileName(char* fpath, char* fnameprefix, uint64_t findex,
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bool frindexenable, uint64_t fnum, int dindex, int numunits, int unitindex) {
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ostringstream osfn;
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@@ -56,10 +136,208 @@ string HDF5File::CreateFileName(char* fpath, char* fnameprefix, uint64_t findex,
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return osfn.str();
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}
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int HDF5File::CreateDataFile(bool owenable, char* fname) {
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/*** static function ***/
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int HDF5File::CreateDataFile(int ind, bool owenable, uint64_t numf, string fname, uint64_t fnum, int nx, int ny,
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DataType dtype, H5File*& fd, DataSpace*& dspace, DataSet*& dset) {
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pthread_mutex_lock(&Mutex);
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try {
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Exception::dontPrint(); //to handle errors
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//file
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FileAccPropList flist;
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flist.setFcloseDegree(H5F_CLOSE_STRONG);
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if(!owenable)
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fd = new H5File( fname.c_str(), H5F_ACC_EXCL, NULL,flist );
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else
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fd = new H5File( fname.c_str(), H5F_ACC_TRUNC, NULL, flist );
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//attributes - version
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double dValue=HDF5_WRITER_VERSION;
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DataSpace dataspace_attr = DataSpace (H5S_SCALAR);
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Attribute attribute = fd->createAttribute("version",PredType::NATIVE_DOUBLE, dataspace_attr);
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attribute.write(PredType::NATIVE_DOUBLE, &dValue);
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//dataspace
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char dsetname[100];
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hsize_t srcdims[3] = {numf,ny,nx};
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dspace = new DataSpace (3,srcdims);
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sprintf(dsetname, "/data_%012lld", (long long int)fnum);
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//dataset
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//create chunked dataset if greater than max_chunked_images
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if(numf > MAX_CHUNKED_IMAGES){
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DSetCreatPropList plist;
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hsize_t chunk_dims[3] ={MAX_CHUNKED_IMAGES, ny, nx};
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plist.setChunk(3, chunk_dims);
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dset = new DataSet (fd->createDataSet(dsetname, dtype, *dspace, plist));
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}else
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dset = new DataSet (fd->createDataSet(dsetname, dtype, *dspace));
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}
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catch(Exception error){
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cprintf(RED,"Error in creating HDF5 handles in object %d\n",ind);
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error.printError();
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fd->close();
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pthread_mutex_unlock(&Mutex);
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return FAIL;
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}
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pthread_mutex_unlock(&Mutex);
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return OK;
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}
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void HDF5File::CloseDataFile() {
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/*** static function ***/
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void HDF5File::CloseDataFile(H5File*& fd, DataSpace*& dp, DataSet*& ds) {
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pthread_mutex_lock(&Mutex);
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try {
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Exception::dontPrint(); //to handle errors
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if(dp) {delete dp; dp = 0;}
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if(ds) {delete ds; ds = 0;}
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if(fd) {delete fd; fd = 0;}
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} catch(Exception error) {
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cprintf(RED,"Error in closing HDF5 handles\n");
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error.printError();
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}
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pthread_mutex_unlock(&Mutex);
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}
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/*** static function ***/
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int HDF5File::WriteDataFile(int ind, char* buf, uint64_t numImages, int nx, int ny, uint64_t fnum,
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DataSpace* dspace, DataSet* dset, DataType dtype) {
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pthread_mutex_lock(&Mutex);
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hsize_t count[3] = {1, ny,nx};
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hsize_t start[3] = {fnum%numImages, 0 , 0};
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hsize_t dims2[2]={ny,nx};
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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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cprintf(RED,"Error in writing to file in object %d\n",ind);
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error.printError();
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pthread_mutex_unlock(&Mutex);
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return FAIL;
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}
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pthread_mutex_unlock(&Mutex);
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return OK;
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}
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void HDF5File::CreateCommonFileNames(string& m, string& v, char* fpath, char* fnameprefix, uint64_t findex) {
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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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m = osfn.str();
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v.assign(m);
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v.replace(v.find("_master", 0), 7, "_virtual");
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}
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void HDF5File::CloseCommonDataFiles() {
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pthread_mutex_lock(&Mutex);
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try {
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Exception::dontPrint(); //to handle errors
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if(masterfd) {delete masterfd; masterfd = 0;}
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if(virtualfd) {delete virtualfd; virtualfd = 0;}
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} catch(Exception error) {
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cprintf(RED,"Error in closing common HDF5 handles\n");
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error.printError();
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}
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pthread_mutex_unlock(&Mutex);
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}
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int HDF5File::CreateCommonDataFiles(string m, string v, bool owenable,
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bool tengigaEnable, uint32_t imageSize, uint32_t nPixelsX, uint32_t nPixelsY,
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uint64_t acquisitionTime, uint64_t acquisitionPeriod) {
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pthread_mutex_lock(&Mutex);
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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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if(!owenable)
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masterfd = new H5File( m.c_str(), H5F_ACC_EXCL, NULL, flist );
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else
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masterfd = new H5File( m.c_str(), H5F_ACC_TRUNC, NULL, 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=HDF5_WRITER_VERSION;
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attribute = masterfd->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( masterfd->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 ( dynamicRange, PredType::NATIVE_INT);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, string("bits"));
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//Ten Giga
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iValue = tengigaEnable;
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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 ( &imageSize, PredType::NATIVE_INT);
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attribute = dataset.createAttribute("unit",strdatatype, dataspace);
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attribute.write(strdatatype, 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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//Total Frames
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dataset = group5.createDataSet ( "total frames", PredType::STD_U64LE, dataspace );
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dataset.write ( &numImages, 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, 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, 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 ( string(ctime(&t)), strdatatype );
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masterfd->close();
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} catch(Exception error) {
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cprintf(RED,"Error in creating common HDF5 handles\n");
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error.printError();
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pthread_mutex_unlock(&Mutex);
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return FAIL;
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}
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pthread_mutex_unlock(&Mutex);
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return OK;
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}
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//#endif
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