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Merge pull request #300 from slsdetectorgroup/framescaught

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Framescaught
This commit is contained in:
Dhanya Thattil 2021-09-17 12:05:25 +02:00 committed by GitHub
commit cff758d2f2
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9 changed files with 153 additions and 21 deletions
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14
slsReceiverSoftware/src/BinaryMasterFile.cpp
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@ -42,3 +42,17 @@ void BinaryMasterFile::CreateMasterFile(const std::string filePath,
attr->WriteMasterBinaryAttributes(fd_);
CloseFile();
}
void BinaryMasterFile::UpdateMasterFile(MasterAttributes *attr,
bool silentMode) {
if (nullptr == (fd_ = fopen((const char *)fileName_.c_str(), "a"))) {
fd_ = nullptr;
throw sls::RuntimeError("Could not append binary master file " +
fileName_);
}
attr->WriteFinalBinaryAttributes(fd_);
CloseFile();
if (!silentMode) {
LOG(logINFO) << "Updated Master File";
}
}

1
slsReceiverSoftware/src/BinaryMasterFile.h
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@ -15,6 +15,7 @@ class BinaryMasterFile : private virtual slsDetectorDefs, public File {
const uint64_t fileIndex, const bool overWriteEnable,
const bool silentMode,
MasterAttributes *attr) override;
void UpdateMasterFile(MasterAttributes *attr, bool silentMode) override;
private:
FILE *fd_{nullptr};

44
slsReceiverSoftware/src/DataProcessor.cpp
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@ -17,6 +17,7 @@
#include "HDF5VirtualFile.h"
#endif
#include "DataStreamer.h"
#include "sls/container_utils.h"
#include "sls/sls_detector_exceptions.h"
#include <cerrno>
@ -56,6 +57,10 @@ bool DataProcessor::GetStartedFlag() { return startedFlag_; }
uint64_t DataProcessor::GetNumFramesCaught() { return numFramesCaught_; }
uint64_t DataProcessor::GetNumCompleteFramesCaught() {
return numCompleteFramesCaught_;
}
uint64_t DataProcessor::GetCurrentFrameIndex() { return currentFrameIndex_; }
uint64_t DataProcessor::GetProcessedIndex() {
@ -68,6 +73,7 @@ void DataProcessor::ResetParametersforNewAcquisition() {
StopRunning();
startedFlag_ = false;
numFramesCaught_ = 0;
numCompleteFramesCaught_ = 0;
firstIndex_ = 0;
currentFrameIndex_ = 0;
firstStreamerFrame_ = true;
@ -248,6 +254,41 @@ void DataProcessor::LinkDataInMasterFile(const bool silentMode) {
}
#endif
void DataProcessor::UpdateMasterFile(bool silentMode) {
if (masterFile_) {
// final attributes
std::unique_ptr<MasterAttributes> masterAttributes;
switch (detectorType_) {
case GOTTHARD:
masterAttributes = sls::make_unique<GotthardMasterAttributes>();
break;
case JUNGFRAU:
masterAttributes = sls::make_unique<JungfrauMasterAttributes>();
break;
case EIGER:
masterAttributes = sls::make_unique<EigerMasterAttributes>();
break;
case MYTHEN3:
masterAttributes = sls::make_unique<Mythen3MasterAttributes>();
break;
case GOTTHARD2:
masterAttributes = sls::make_unique<Gotthard2MasterAttributes>();
break;
case MOENCH:
masterAttributes = sls::make_unique<MoenchMasterAttributes>();
break;
case CHIPTESTBOARD:
masterAttributes = sls::make_unique<CtbMasterAttributes>();
break;
default:
throw sls::RuntimeError(
"Unknown detector type to set up master file attributes");
}
masterAttributes->framesInFile = numFramesCaught_;
masterFile_->UpdateMasterFile(masterAttributes.get(), silentMode);
}
}
void DataProcessor::ThreadExecution() {
char *buffer = nullptr;
fifo_->PopAddress(buffer);
@ -306,9 +347,10 @@ uint64_t DataProcessor::ProcessAnImage(char *buf) {
sls_detector_header header = rheader->detHeader;
uint64_t fnum = header.frameNumber;
currentFrameIndex_ = fnum;
numFramesCaught_++;
uint32_t nump = header.packetNumber;
if (nump == generalData_->packetsPerFrame) {
numFramesCaught_++;
numCompleteFramesCaught_++;
}
LOG(logDEBUG1) << "DataProcessing " << index << ": fnum:" << fnum;

7
slsReceiverSoftware/src/DataProcessor.h
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@ -37,6 +37,7 @@ class DataProcessor : private virtual slsDetectorDefs, public ThreadObject {
bool GetStartedFlag();
uint64_t GetNumFramesCaught();
uint64_t GetNumCompleteFramesCaught();
/** (-1 if no frames have been caught */
uint64_t GetCurrentFrameIndex();
/** (-1 if no frames have been caught) */
@ -76,6 +77,7 @@ class DataProcessor : private virtual slsDetectorDefs, public ThreadObject {
const int numModY);
void LinkDataInMasterFile(const bool silentMode);
#endif
void UpdateMasterFile(bool silentMode);
/**
* Call back for raw data
* args to raw data ready callback are
@ -174,9 +176,12 @@ class DataProcessor : private virtual slsDetectorDefs, public ThreadObject {
std::atomic<uint64_t> firstIndex_{0};
// for statistics
/** Number of complete frames caught */
/** Number of frames caught */
uint64_t numFramesCaught_{0};
/** Number of complete frames caught */
uint64_t numCompleteFramesCaught_{0};
/** Frame Number of latest processed frame number */
std::atomic<uint64_t> currentFrameIndex_{0};

5
slsReceiverSoftware/src/File.h
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@ -118,6 +118,11 @@ class File : private virtual slsDetectorDefs {
"should be overloaded by a derived class";
};
virtual void UpdateMasterFile(MasterAttributes *attr, bool silentMode) {
LOG(logERROR) << "This is a generic function UpdateMasterFile that "
"should be overloaded by a derived class";
};
protected:
slsDetectorDefs::fileFormat format_;
};

28
slsReceiverSoftware/src/HDF5MasterFile.cpp
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@ -117,6 +117,9 @@ void HDF5MasterFile::CreateMasterFile(const std::string filePath,
Group group5(group3.createGroup("detector"));
Group group6(group1.createGroup("sample"));
// TODO find a way to get complete group link
attrGroupName_ = "/entry/instrument/detector";
attr->WriteMasterHDF5Attributes(fd_, &group5);
fd_->close();
@ -129,4 +132,29 @@ void HDF5MasterFile::CreateMasterFile(const std::string filePath,
if (!silentMode) {
LOG(logINFO) << "Master File: " << fileName_;
}
}
void HDF5MasterFile::UpdateMasterFile(MasterAttributes *attr, bool silentMode) {
std::lock_guard<std::mutex> lock(*hdf5Lib_);
try {
Exception::dontPrint(); // to handle errors
FileAccPropList flist;
flist.setFcloseDegree(H5F_CLOSE_STRONG);
fd_ = new H5File(fileName_.c_str(), H5F_ACC_RDWR,
FileCreatPropList::DEFAULT, flist);
Group group = fd_->openGroup(attrGroupName_.c_str());
attr->WriteFinalHDF5Attributes(fd_, &group);
fd_->close();
} catch (const Exception &error) {
error.printErrorStack();
CloseFile();
throw sls::RuntimeError(
"Could not create/overwrite master HDF5 handles");
}
if (!silentMode) {
LOG(logINFO) << "Updated Master File";
}
}

2
slsReceiverSoftware/src/HDF5MasterFile.h
View File

@ -19,9 +19,11 @@ class HDF5MasterFile : private virtual slsDetectorDefs, public File {
const uint64_t fileIndex, const bool overWriteEnable,
const bool silentMode,
MasterAttributes *attr) override;
void UpdateMasterFile(MasterAttributes *attr, bool silentMode) override;
private:
std::mutex *hdf5Lib_;
H5File *fd_{nullptr};
std::string fileName_;
std::string attrGroupName_;
};

11
slsReceiverSoftware/src/Implementation.cpp
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@ -429,7 +429,7 @@ uint64_t Implementation::getFramesCaught() const {
for (const auto &it : dataProcessor) {
flagsum += it->GetStartedFlag();
min = std::min(min, it->GetNumFramesCaught());
min = std::min(min, it->GetNumCompleteFramesCaught());
}
// no data processed
if (flagsum != dataProcessor.size())
@ -571,6 +571,13 @@ void Implementation::stopReceiver() {
}
}
#endif
if (fileWriteEnable && masterFileWriteEnable && modulePos == 0) {
try {
dataProcessor[0]->UpdateMasterFile(silentMode);
} catch (...) {
; // ignore it and just print it
}
}
// wait for the processes (dataStreamer) to be done
running = true;
@ -589,7 +596,7 @@ void Implementation::stopReceiver() {
std::vector<uint64_t> mp = getNumMissingPackets();
uint64_t tot = 0;
for (int i = 0; i < numThreads; i++) {
int nf = dataProcessor[i]->GetNumFramesCaught();
int nf = dataProcessor[i]->GetNumCompleteFramesCaught();
tot += nf;
std::string mpMessage = std::to_string((int64_t)mp[i]);
if ((int64_t)mp[i] < 0) {

62
slsReceiverSoftware/src/MasterAttributes.h
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@ -16,6 +16,7 @@ using namespace H5;
using ns = std::chrono::nanoseconds;
struct MasterAttributes {
// (before acquisition)
slsDetectorDefs::detectorType detType{slsDetectorDefs::GENERIC};
slsDetectorDefs::timingMode timingMode{slsDetectorDefs::AUTO_TIMING};
uint32_t imageSize{0};
@ -57,6 +58,9 @@ struct MasterAttributes {
uint32_t gates;
std::map<std::string, std::string> additionalJsonHeader;
// Final Attributes (after acquisition)
uint64_t framesInFile{0};
MasterAttributes(){};
virtual ~MasterAttributes(){};
@ -87,30 +91,42 @@ struct MasterAttributes {
};
void WriteBinaryAttributes(FILE *fd, std::string message) {
if (fwrite((void *)message.c_str(), 1, message.length(), fd) !=
message.length()) {
throw sls::RuntimeError(
"Master binary file incorrect number of bytes written to file");
}
};
void WriteFinalBinaryAttributes(FILE *fd) {
// adding few common parameters to the end
std::ostringstream oss;
if (!additionalJsonHeader.empty()) {
std::ostringstream oss;
oss << "Additional Json Header : "
<< sls::ToString(additionalJsonHeader) << '\n';
message += oss.str();
}
oss << "Frames in File : " << framesInFile << '\n';
// adding sls_receiver header format
message += std::string("\n#Frame Header\n"
"Frame Number : 8 bytes\n"
"SubFrame Number/ExpLength : 4 bytes\n"
"Packet Number : 4 bytes\n"
"Bunch ID : 8 bytes\n"
"Timestamp : 8 bytes\n"
"Module Id : 2 bytes\n"
"Row : 2 bytes\n"
"Column : 2 bytes\n"
"Reserved : 2 bytes\n"
"Debug : 4 bytes\n"
"Round Robin Number : 2 bytes\n"
"Detector Type : 1 byte\n"
"Header Version : 1 byte\n"
"Packets Caught Mask : 64 bytes\n");
oss << '\n'
<< "#Frame Header" << '\n'
<< "Frame Number : 8 bytes" << '\n'
<< "SubFrame Number/ExpLength : 4 bytes" << '\n'
<< "Packet Number : 4 bytes" << '\n'
<< "Bunch ID : 8 bytes" << '\n'
<< "Timestamp : 8 bytes" << '\n'
<< "Module Id : 2 bytes" << '\n'
<< "Row : 2 bytes" << '\n'
<< "Column : 2 bytes" << '\n'
<< "Reserved : 2 bytes" << '\n'
<< "Debug : 4 bytes" << '\n'
<< "Round Robin Number : 2 bytes" << '\n'
<< "Detector Type : 1 byte" << '\n'
<< "Header Version : 1 byte" << '\n'
<< "Packets Caught Mask : 64 bytes" << '\n';
std::string message = oss.str();
// writing to file
if (fwrite((void *)message.c_str(), 1, message.length(), fd) !=
@ -233,6 +249,18 @@ struct MasterAttributes {
"Total Frames", PredType::STD_U64LE, dataspace);
dataset.write(&totalFrames, PredType::STD_U64LE);
}
};
void WriteFinalHDF5Attributes(H5File *fd, Group *group) {
char c[1024];
memset(c, 0, sizeof(c));
// Total Frames in file
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet(
"Frames in File", PredType::STD_U64LE, dataspace);
dataset.write(&framesInFile, PredType::STD_U64LE);
}
// additional json header
if (!additionalJsonHeader.empty()) {
std::string json = sls::ToString(additionalJsonHeader);