bool TraceChunkSerializer::Write(H5File &h5, GridMesh<TraceChunk> &dataMesh) {
mNumChunks = dataMesh.GetNumBin();
ClockTimer timer;
mChunks = (struct FlowChunk *) malloc(sizeof(struct FlowChunk) * mNumChunks);
ArrangeDataForWriting(dataMesh, mChunks);
computeMicroSec = timer.GetMicroSec();
hsize_t dims1[1];
dims1[0] = mNumChunks;
hid_t fcDataSpace = H5Screate_simple(1, dims1, NULL);
hid_t charArrayType = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t charArrayType2 = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t fcType = H5Tcreate(H5T_COMPOUND, sizeof(struct FlowChunk));
H5Tinsert(fcType, "CompressionType", HOFFSET(struct FlowChunk, CompressionType), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipRow", HOFFSET(struct FlowChunk, ChipRow), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipCol", HOFFSET(struct FlowChunk, ChipCol), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipFrame", HOFFSET(struct FlowChunk, ChipFrame), H5T_NATIVE_B64);
H5Tinsert(fcType, "RowStart", HOFFSET(struct FlowChunk, RowStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "ColStart", HOFFSET(struct FlowChunk, ColStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStart", HOFFSET(struct FlowChunk, FrameStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStep", HOFFSET(struct FlowChunk, FrameStep), H5T_NATIVE_B64);
H5Tinsert(fcType, "Height", HOFFSET(struct FlowChunk, Height), H5T_NATIVE_B64);
H5Tinsert(fcType, "Width", HOFFSET(struct FlowChunk, Width), H5T_NATIVE_B64);
H5Tinsert(fcType, "Depth", HOFFSET(struct FlowChunk, Depth), H5T_NATIVE_B64);
H5Tinsert(fcType, "OrigFrames", HOFFSET(struct FlowChunk, OrigFrames), H5T_NATIVE_B64);
H5Tinsert(fcType, "StartDetailedTime", HOFFSET(struct FlowChunk, StartDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "StopDetailedTime", HOFFSET(struct FlowChunk, StopDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "LeftAvg", HOFFSET(struct FlowChunk, LeftAvg), H5T_NATIVE_INT);
H5Tinsert(fcType, "T0", HOFFSET(struct FlowChunk, T0), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "Sigma", HOFFSET(struct FlowChunk, Sigma), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "TMidNuc", HOFFSET(struct FlowChunk, TMidNuc), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "BaseFrameRate", HOFFSET(struct FlowChunk, BaseFrameRate), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "DeltaFrame", HOFFSET(struct FlowChunk, DeltaFrame), charArrayType2);
H5Tinsert(fcType, "Data", HOFFSET(struct FlowChunk, Data), charArrayType);
timer.StartTimer();
hid_t dataset = H5Dcreate2(h5.GetFileId(), "FlowChunk", fcType, fcDataSpace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
herr_t status = H5Dwrite(dataset, fcType, H5S_ALL, H5S_ALL, H5P_DEFAULT, mChunks);
status = H5Dvlen_reclaim(fcType, fcDataSpace, H5P_DEFAULT, mChunks);
// // delete [] mChunks;
free(mChunks);
mChunks = NULL;
ION_ASSERT(status == 0, "Couldn't write dataset");
H5Tclose(fcType);
H5Tclose(charArrayType);
H5Tclose(charArrayType2);
H5Sclose(fcDataSpace);
H5Dclose(dataset);
ioMicroSec += timer.GetMicroSec();
return status == 0;
}
bool TraceChunkSerializer::Read(H5File &h5, GridMesh<TraceChunk> &dataMesh) {
hid_t dataset = H5Dopen2(h5.GetFileId(), "FlowChunk", H5P_DEFAULT);
// hid_t datatype = H5Dget_type(dataset); /* datatype handle */
static pthread_once_t onceControl = PTHREAD_ONCE_INIT;
int err = pthread_once(&onceControl, InitSdatReadSem);
if (err != 0) { cout << "Error with pthread once." << endl; }
hid_t dataspace = H5Dget_space(dataset);
int rank = H5Sget_simple_extent_ndims(dataspace);
std::vector<hsize_t> dims;
dims.resize(rank);
int status = H5Sget_simple_extent_dims(dataspace, &dims[0], NULL);
if (mChunks != NULL) {
delete [] mChunks;
}
mChunks = new FlowChunk[dims[0]];
mNumChunks = dims[0];
hid_t fcDataSpace = H5Screate_simple(1, &dims[0], NULL);
hid_t charArrayType = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t charArrayType2 = H5Tvlen_create (H5T_NATIVE_CHAR);
hid_t fcType = H5Tcreate(H5T_COMPOUND, sizeof(struct FlowChunk));
H5Tinsert(fcType, "CompressionType", HOFFSET(struct FlowChunk, CompressionType), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipRow", HOFFSET(struct FlowChunk, ChipRow), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipCol", HOFFSET(struct FlowChunk, ChipCol), H5T_NATIVE_B64);
H5Tinsert(fcType, "ChipFrame", HOFFSET(struct FlowChunk, ChipFrame), H5T_NATIVE_B64);
H5Tinsert(fcType, "RowStart", HOFFSET(struct FlowChunk, RowStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "ColStart", HOFFSET(struct FlowChunk, ColStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStart", HOFFSET(struct FlowChunk, FrameStart), H5T_NATIVE_B64);
H5Tinsert(fcType, "FrameStep", HOFFSET(struct FlowChunk, FrameStep), H5T_NATIVE_B64);
H5Tinsert(fcType, "Height", HOFFSET(struct FlowChunk, Height), H5T_NATIVE_B64);
H5Tinsert(fcType, "Width", HOFFSET(struct FlowChunk, Width), H5T_NATIVE_B64);
H5Tinsert(fcType, "Depth", HOFFSET(struct FlowChunk, Depth), H5T_NATIVE_B64);
H5Tinsert(fcType, "OrigFrames", HOFFSET(struct FlowChunk, OrigFrames), H5T_NATIVE_B64);
H5Tinsert(fcType, "StartDetailedTime", HOFFSET(struct FlowChunk, StartDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "StopDetailedTime", HOFFSET(struct FlowChunk, StopDetailedTime), H5T_NATIVE_INT);
H5Tinsert(fcType, "LeftAvg", HOFFSET(struct FlowChunk, LeftAvg), H5T_NATIVE_INT);
H5Tinsert(fcType, "T0", HOFFSET(struct FlowChunk, T0), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "Sigma", HOFFSET(struct FlowChunk, Sigma), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "TMidNuc", HOFFSET(struct FlowChunk, TMidNuc), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "BaseFrameRate", HOFFSET(struct FlowChunk, BaseFrameRate), H5T_NATIVE_FLOAT);
H5Tinsert(fcType, "DeltaFrame", HOFFSET(struct FlowChunk, DeltaFrame), charArrayType2);
H5Tinsert(fcType, "Data", HOFFSET(struct FlowChunk, Data), charArrayType);
ClockTimer timer;
IonImageSem::Take();
status = H5Dread(dataset, fcType, H5S_ALL, H5S_ALL, H5P_DEFAULT, mChunks);
IonImageSem::Give();
ioMicroSec = timer.GetMicroSec();
ION_ASSERT(status == 0, "Couldn' read dataset");
timer.StartTimer();
dataMesh.Init(mChunks[0].ChipRow, mChunks[0].ChipCol, mChunks[0].Height, mChunks[0].Width);
ION_ASSERT(dataMesh.GetNumBin() == mNumChunks, "Didn't get number of chunks expected");
DecompressFromReading(mChunks, dataMesh);
computeMicroSec = timer.GetMicroSec();
timer.StartTimer();
status = H5Dvlen_reclaim(fcType, fcDataSpace, H5P_DEFAULT, mChunks);
delete [] mChunks;
mChunks = NULL;
H5Tclose(fcType);
H5Tclose(charArrayType);
H5Tclose(charArrayType2);
H5Sclose(fcDataSpace);
H5Dclose(dataset);
ioMicroSec += timer.GetMicroSec();
return status == 0;
}
