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#include "indirectbaselinereader.h"
#include <casacore/ms/MeasurementSets/MeasurementSet.h>
#include <fstream>
#include <set>
#include <stdexcept>
#include <vector>
#include <fcntl.h>
#include <boost/filesystem.hpp>
#include "../structures/arraycolumniterator.h"
#include "../structures/scalarcolumniterator.h"
#include "../structures/timefrequencydata.h"
#include "../structures/system.h"
#include "../util/logger.h"
#include "../util/stopwatch.h"
#include "reorderedfilebuffer.h"
IndirectBaselineReader::IndirectBaselineReader(const std::string &msFile) : BaselineReader(msFile), _directReader(msFile),
_seqIndexTable(0),
_msIsReordered(false), _removeReorderedFiles(false), _reorderedDataFilesHaveChanged(false), _reorderedFlagFilesHaveChanged(false), _readUVW(false)
{
}
IndirectBaselineReader::~IndirectBaselineReader()
{
if(_reorderedDataFilesHaveChanged)
updateOriginalMSData();
if(_reorderedFlagFilesHaveChanged)
updateOriginalMSFlags();
removeTemporaryFiles();
delete _seqIndexTable;
_filePositions.clear();
}
void IndirectBaselineReader::PerformReadRequests()
{
initializeMeta();
if(!_msIsReordered) reorderedMS();
_results.clear();
Logger::Debug << "Performing " << _readRequests.size() << " read requests...\n";
for(size_t i=0;i<_readRequests.size();++i)
{
const ReadRequest request = _readRequests[i];
_results.push_back(Result());
const size_t width = ObservationTimes(request.sequenceId).size();
for(size_t p=0;p<Polarizations().size();++p)
{
if(ReadData()) {
_results[i]._realImages.push_back(Image2D::CreateZeroImagePtr(width, Set().FrequencyCount(request.spectralWindow)));
_results[i]._imaginaryImages.push_back(Image2D::CreateZeroImagePtr(width, Set().FrequencyCount(request.spectralWindow)));
}
if(ReadFlags()) {
// The flags should be initialized to true, as a baseline might
// miss some time scans that other baselines do have, and these
// should be flagged.
_results[i]._flags.push_back(Mask2D::CreateSetMaskPtr<true>(width, Set().FrequencyCount(request.spectralWindow)));
}
}
if(_readUVW)
_results[i]._uvw = _directReader.ReadUVW(request.antenna1, request.antenna2, request.spectralWindow, request.sequenceId);
else {
_results[i]._uvw.clear();
for(unsigned j=0;j<width;++j)
_results[i]._uvw.push_back(UVW(0.0, 0.0, 0.0));
}
std::ifstream dataFile(DataFilename(), std::ifstream::binary);
std::ifstream flagFile(FlagFilename(), std::ifstream::binary);
size_t index = _seqIndexTable->Value(request.antenna1, request.antenna2, request.spectralWindow, request.sequenceId);
size_t filePos = _filePositions[index];
dataFile.seekg(filePos * (sizeof(float)*2), std::ios_base::beg);
flagFile.seekg(filePos * sizeof(bool), std::ios_base::beg);
const size_t bufferSize = Set().FrequencyCount(request.spectralWindow) * Polarizations().size();
for(size_t x=0;x<width;++x)
{
std::vector<float> dataBuffer(bufferSize*2);
std::vector<char> flagBuffer(bufferSize);
dataFile.read((char *) &dataBuffer[0], bufferSize * sizeof(float) * 2);
size_t dataBufferPtr = 0;
flagFile.read((char *) &flagBuffer[0], bufferSize * sizeof(bool));
size_t flagBufferPtr = 0;
for(size_t f=0;f<Set().FrequencyCount(request.spectralWindow);++f) {
for(size_t p=0;p<Polarizations().size();++p)
{
_results[i]._realImages[p]->SetValue(x, f, dataBuffer[dataBufferPtr]);
++dataBufferPtr;
_results[i]._imaginaryImages[p]->SetValue(x, f, dataBuffer[dataBufferPtr]);
++dataBufferPtr;
_results[i]._flags[p]->SetValue(x, f, flagBuffer[flagBufferPtr]);
++flagBufferPtr;
}
}
}
}
Logger::Debug << "Done reading.\n";
_readRequests.clear();
}
void IndirectBaselineReader::PerformFlagWriteRequests()
{
for(size_t i=0;i!=_writeRequests.size();++i)
{
const FlagWriteRequest request = _writeRequests[i];
performFlagWriteTask(request.flags, request.antenna1, request.antenna2, request.spectralWindow, request.sequenceId);
}
_writeRequests.clear();
}
void IndirectBaselineReader::reorderedMS()
{
boost::filesystem::path path(MetaFilename());
bool reorderRequired = true;
if(boost::filesystem::exists(path))
{
std::ifstream str(path.string().c_str());
std::string name;
std::getline(str, name);
if(boost::filesystem::equivalent(boost::filesystem::path(name), Set().Path()))
{
Logger::Debug << "Measurement set has already been reordered; using old temporary files.\n";
reorderRequired = false;
_msIsReordered = true;
_removeReorderedFiles = false;
_reorderedDataFilesHaveChanged = false;
_reorderedFlagFilesHaveChanged = false;
}
}
if(reorderRequired)
{
reorderFull();
std::ofstream str(path.string().c_str());
str << Set().Path() << '\n';
} else {
size_t fileSize;
makeLookupTables(fileSize);
}
}
void IndirectBaselineReader::makeLookupTables(size_t &fileSize)
{
std::vector<MeasurementSet::Sequence> sequences = Set().GetSequences();
const size_t
antennaCount = Set().AntennaCount(),
polarizationCount = Polarizations().size(),
bandCount = Set().BandCount(),
sequencesPerBaselineCount = Set().SequenceCount();
_seqIndexTable = new SeqIndexLookupTable(antennaCount, bandCount, sequencesPerBaselineCount);
fileSize = 0;
for(size_t i=0;i<sequences.size();++i)
{
// Initialize look-up table to get index into Sequence-array quickly
const MeasurementSet::Sequence &s = sequences[i];
_seqIndexTable->Value(s.antenna1, s.antenna2, s.spw, s.sequenceId) = i;
// Initialize look-up table to go from sequence array to file position. Is in samples, so
// multiple times sizeof(bool) or ..(float)) for exact position.
_filePositions.push_back(fileSize);
fileSize += ObservationTimes(s.sequenceId).size() * Set().FrequencyCount(s.spw) * polarizationCount;
}
}
void IndirectBaselineReader::preAllocate(const char *filename, size_t fileSize)
{
Logger::Debug << "Pre-allocating " << (fileSize/(1024*1024)) << " MB...\n";
int fd = open(filename, O_WRONLY | O_TRUNC | O_CREAT, S_IWUSR | S_IRUSR);
if(fd < 0)
{
std::ostringstream s;
s << "Error while opening file '" << filename << "', check access rights and free space";
throw std::runtime_error(s.str());
}
#if defined(HAVE_POSIX_FALLOCATE)
int allocResult = posix_fallocate(fd, 0, fileSize);
close(fd);
if(allocResult != 0)
{
Logger::Warn <<
"Could not allocate temporary file '" << filename << "': posix_fallocate returned " << allocResult << ".\n"
"Tried to allocate " << (fileSize/(1024*1024)) << " MB.\n"
"Disk could be full or filesystem could not support fallocate.\n";
}
#else
close(fd);
Logger::Warn << "Compiled without posix_fallocate() support: skipping pre-allocation.\n";
#endif
}
void IndirectBaselineReader::reorderFull()
{
Stopwatch watch(true);
casacore::Table &table = *Table();
casacore::ROScalarColumn<double> timeColumn(*Table(), "TIME");
casacore::ROArrayColumn<bool> flagColumn(table, "FLAG");
casacore::ROScalarColumn<int> fieldIdColumn(table, "FIELD_ID");
casacore::ROScalarColumn<int> dataDescIdColumn(table, "DATA_DESC_ID");
casacore::ROScalarColumn<int> antenna1Column(table, "ANTENNA1");
casacore::ROScalarColumn<int> antenna2Column(table, "ANTENNA2");
size_t rowCount = table.nrow();
if(rowCount == 0)
throw std::runtime_error("Measurement set is empty (zero rows)");
std::unique_ptr<casacore::ROArrayColumn<casacore::Complex>> dataColumn( new casacore::ROArrayColumn<casacore::Complex>(table, DataColumnName()) );
std::vector<size_t> dataIdToSpw;
Set().GetDataDescToBandVector(dataIdToSpw);
size_t fileSize;
makeLookupTables(fileSize);
Logger::Debug << "Opening temporary files.\n";
ReorderInfo reorderInfo;
preAllocate(DataFilename(), fileSize*sizeof(float)*2);
reorderInfo.dataFile.reset(new std::ofstream(DataFilename(), std::ofstream::binary | std::ios_base::in | std::ios_base::out));
if(reorderInfo.dataFile->fail())
throw std::runtime_error("Error: failed to open temporary data files for writing! Check access rights and free disk space.");
preAllocate(FlagFilename(), fileSize*sizeof(bool));
reorderInfo.flagFile.reset(new std::ofstream(FlagFilename(), std::ofstream::binary | std::ios_base::in | std::ios_base::out));
if(reorderInfo.flagFile->fail())
throw std::runtime_error("Error: failed to open temporary data files for writing! Check access rights and free disk space.");
Logger::Debug << "Reordering data set...\n";
size_t bufferMem = std::min<size_t>(System::TotalMemory()/10, 1024l*1024l*1024l);
ReorderedFileBuffer dataFile(reorderInfo.dataFile.get(), bufferMem);
ReorderedFileBuffer flagFile(reorderInfo.flagFile.get(), bufferMem/8);
size_t prevFieldId = size_t(-1), sequenceId = size_t(-1);
std::vector<std::size_t> writeFilePositions = _filePositions;
std::vector<std::size_t> timePositions(_filePositions.size(), size_t(-1));
double prevTime = -1.0;
size_t timeIndex = size_t(-1);
unsigned progress = 0;
for(size_t rowIndex = 0; rowIndex!=rowCount; ++rowIndex)
{
if(rowIndex*1000/rowCount != progress)
{
progress = rowIndex*1000/rowCount;
if(progress%10 == 0)
Logger::Debug << "\nReorder progress: ";
Logger::Debug << progress/10.0 << "% ";
Logger::Debug.Flush();
}
size_t fieldId = fieldIdColumn(rowIndex);
if(fieldId != prevFieldId)
{
prevFieldId = fieldId;
sequenceId++;
prevTime = -1.0;
}
double time = timeColumn(rowIndex);
if(time != prevTime)
{
timeIndex = ObservationTimes(sequenceId).find(time)->second;
prevTime = time;
}
size_t polarizationCount = Polarizations().size();
size_t antenna1 = antenna1Column(rowIndex);
size_t antenna2 = antenna2Column(rowIndex);
size_t spw = dataIdToSpw[dataDescIdColumn(rowIndex)];
size_t channelCount = Set().FrequencyCount(spw);
size_t arrayIndex = _seqIndexTable->Value(antenna1, antenna2, spw, sequenceId);
size_t &filePos = writeFilePositions[arrayIndex];
size_t &timePos = timePositions[arrayIndex];
size_t sampleCount = channelCount * polarizationCount;
casacore::Array<casacore::Complex> data = (*dataColumn)(rowIndex);
casacore::Array<bool> flag = flagColumn(rowIndex);
dataFile.seekp(filePos * (sizeof(float)*2));
flagFile.seekp(filePos * sizeof(bool));
// If this baseline missed some time steps, pad the files
// (we can't just skip over, because the flags should be set to true)
++timePos;
while(timePos < timeIndex)
{
const std::vector<float> nullData(sampleCount*2, 0.0);
const std::vector<char> nullFlags(sampleCount, (char) true);
dataFile.write(reinterpret_cast<const char*>(&*nullData.begin()), sampleCount * 2 * sizeof(float));
flagFile.write(reinterpret_cast<const char*>(&*nullFlags.begin()), sampleCount * sizeof(bool));
++timePos;
filePos += sampleCount;
}
dataFile.write(reinterpret_cast<const char*>(&*data.cbegin()), sampleCount * 2 * sizeof(float));
flagFile.write(reinterpret_cast<const char*>(&*flag.cbegin()), sampleCount * sizeof(bool));
filePos += sampleCount;
}
uint64_t dataSetSize = (uint64_t) fileSize * (uint64_t) (sizeof(float)*2 + sizeof(bool));
Logger::Debug << "Done reordering data set of " << dataSetSize/(1024*1024) << " MB in " << watch.Seconds() << " s (" << (long double) dataSetSize/(1024.0L*1024.0L*watch.Seconds()) << " MB/s)\n";
_msIsReordered = true;
_removeReorderedFiles = true;
_reorderedDataFilesHaveChanged = false;
_reorderedFlagFilesHaveChanged = false;
}
void IndirectBaselineReader::removeTemporaryFiles()
{
if(_msIsReordered && _removeReorderedFiles)
{
boost::filesystem::remove(MetaFilename());
boost::filesystem::remove(DataFilename());
boost::filesystem::remove(FlagFilename());
Logger::Debug << "Temporary files removed.\n";
}
_msIsReordered = false;
_removeReorderedFiles = false;
_reorderedDataFilesHaveChanged = false;
_reorderedFlagFilesHaveChanged = false;
}
void IndirectBaselineReader::PerformDataWriteTask(std::vector<Image2DCPtr> _realImages, std::vector<Image2DCPtr> _imaginaryImages, int antenna1, int antenna2, int spectralWindow, unsigned sequenceId)
{
initializeMeta();
Logger::Debug << "Performing data write task with indirect baseline reader...\n";
const size_t polarizationCount = Polarizations().size();
if(_realImages.size() != polarizationCount || _imaginaryImages.size() != polarizationCount)
throw std::runtime_error("PerformDataWriteTask: input format did not match number of polarizations in measurement set");
for(size_t i=1;i<_realImages.size();++i)
{
if(_realImages[0]->Width() != _realImages[i]->Width() || _realImages[0]->Height() != _realImages[i]->Height() || _realImages[0]->Width() != _imaginaryImages[i]->Width() || _realImages[0]->Height() != _imaginaryImages[i]->Height())
throw std::runtime_error("PerformDataWriteTask: width and/or height of input images did not match");
}
if(!_msIsReordered) reorderedMS();
const size_t width = _realImages[0]->Width();
const size_t bufferSize = Set().FrequencyCount(spectralWindow) * Polarizations().size();
std::ofstream dataFile(DataFilename(), std::ofstream::binary | std::ios_base::in | std::ios_base::out);
size_t index = _seqIndexTable->Value(antenna1, antenna2, spectralWindow, sequenceId);
size_t filePos = _filePositions[index];
dataFile.seekp(filePos*(sizeof(float)*2), std::ios_base::beg);
std::vector<float> dataBuffer(bufferSize*2);
for(size_t x=0;x<width;++x)
{
size_t dataBufferPtr = 0;
for(size_t f=0;f<Set().FrequencyCount(spectralWindow);++f) {
for(size_t p=0; p<Polarizations().size(); ++p)
{
dataBuffer[dataBufferPtr] = _realImages[p]->Value(x, f);
++dataBufferPtr;
dataBuffer[dataBufferPtr] = _imaginaryImages[p]->Value(x, f);
++dataBufferPtr;
}
}
dataFile.write(reinterpret_cast<char*>(&dataBuffer[0]), bufferSize * sizeof(float) * 2);
if(dataFile.bad())
throw std::runtime_error("Error: failed to update temporary data files! Check access rights and free disk space.");
}
_reorderedDataFilesHaveChanged = true;
Logger::Debug << "Done writing.\n";
}
void IndirectBaselineReader::performFlagWriteTask(std::vector<Mask2DCPtr> flags, unsigned antenna1, unsigned antenna2, unsigned spw, unsigned sequenceId)
{
initializeMeta();
const unsigned polarizationCount = Polarizations().size();
if(flags.size() != polarizationCount)
throw std::runtime_error("PerformDataWriteTask: input format did not match number of polarizations in measurement set");
for(size_t i=1;i<flags.size();++i)
{
if(flags[0]->Width() != flags[i]->Width() || flags[0]->Height() != flags[i]->Height())
throw std::runtime_error("PerformDataWriteTask: width and/or height of input images did not match");
}
if(!_msIsReordered) reorderedMS();
const size_t width = flags[0]->Width();
const size_t bufferSize = Set().FrequencyCount(spw) * Polarizations().size();
std::ofstream flagFile(FlagFilename(), std::ofstream::binary | std::ios_base::in | std::ios_base::out);
size_t index = _seqIndexTable->Value(antenna1, antenna2, spw, sequenceId);
size_t filePos = _filePositions[index];
flagFile.seekp(filePos*(sizeof(bool)), std::ios_base::beg);
std::unique_ptr<bool[]> flagBuffer( new bool[bufferSize] );
for(size_t x=0;x<width;++x)
{
size_t flagBufferPtr = 0;
for(size_t f=0;f<Set().FrequencyCount(spw);++f) {
for(size_t p=0; p<polarizationCount; ++p)
{
flagBuffer[flagBufferPtr] = flags[p]->Value(x, f);
++flagBufferPtr;
}
}
flagFile.write(reinterpret_cast<char*>(flagBuffer.get()), bufferSize * sizeof(bool));
if(flagFile.bad())
throw std::runtime_error("Error: failed to update temporary flag files! Check access rights and free disk space.");
}
_reorderedFlagFilesHaveChanged = true;
}
template<bool UpdateData, bool UpdateFlags>
void IndirectBaselineReader::updateOriginalMS()
{
casacore::Table &table = *Table();
casacore::ROScalarColumn<double> timeColumn(*Table(), "TIME");
casacore::ROScalarColumn<int> antenna1Column(table, "ANTENNA1");
casacore::ROScalarColumn<int> antenna2Column(table, "ANTENNA2");
casacore::ROScalarColumn<int> fieldIdColumn(table, "FIELD_ID");
casacore::ROScalarColumn<int> dataDescIdColumn(table, "DATA_DESC_ID");
casacore::ArrayColumn<bool> flagColumn(table, "FLAG");
std::unique_ptr<casacore::ArrayColumn<casacore::Complex>> dataColumn ( new casacore::ArrayColumn<casacore::Complex>(table, DataColumnName()) );
int rowCount = table.nrow();
std::vector<MeasurementSet::Sequence> sequences = Set().GetSequences();
std::vector<size_t> dataIdToSpw;
Set().GetDataDescToBandVector(dataIdToSpw);
size_t polarizationCount = Polarizations().size();
Logger::Debug << "Opening updated files\n";
UpdateInfo updateInfo;
if(UpdateData)
{
updateInfo.dataFile.reset(new std::ifstream(DataFilename(), std::ifstream::binary));
if(updateInfo.dataFile->fail())
throw std::runtime_error("Failed to open temporary data file");
}
if(UpdateFlags)
{
updateInfo.flagFile.reset(new std::ifstream(FlagFilename(), std::ifstream::binary));
if(updateInfo.flagFile->fail())
throw std::runtime_error("Failed to open temporary flag file");
}
size_t prevFieldId = size_t(-1), sequenceId = size_t(-1);
std::vector<size_t> updatedFilePos = _filePositions;
std::vector<size_t> timePositions(updatedFilePos.size(), size_t(-1));
double prevTime = -1.0;
size_t timeIndex = size_t(-1);
for(int rowIndex = 0; rowIndex!=rowCount; ++rowIndex)
{
size_t fieldId = fieldIdColumn(rowIndex);
if(fieldId != prevFieldId)
{
prevFieldId = fieldId;
sequenceId++;
}
double time = timeColumn(rowIndex);
if(time != prevTime)
{
timeIndex = ObservationTimes(sequenceId).find(time)->second;
prevTime = time;
}
size_t antenna1 = antenna1Column(rowIndex);
size_t antenna2 = antenna2Column(rowIndex);
size_t spw = dataIdToSpw[dataDescIdColumn(rowIndex)];
size_t channelCount = Set().FrequencyCount(spw);
size_t arrayIndex = _seqIndexTable->Value(antenna1, antenna2, spw, sequenceId);
size_t sampleCount = channelCount * polarizationCount;
size_t &filePos = updatedFilePos[arrayIndex];
size_t &timePos = timePositions[arrayIndex];
casacore::IPosition shape(2, polarizationCount, channelCount);
// Skip over samples in the temporary files that are missing in the measurement set
++timePos;
while(timePos < timeIndex)
{
filePos += sampleCount;
++timePos;
}
if(UpdateData)
{
casacore::Array<casacore::Complex> data(shape);
std::ifstream &dataFile = *updateInfo.dataFile;
dataFile.seekg(filePos*(sizeof(float)*2), std::ios_base::beg);
dataFile.read(reinterpret_cast<char*>(&*data.cbegin()), sampleCount * 2 * sizeof(float));
if(dataFile.fail())
throw std::runtime_error("Error: failed to read temporary data files!");
dataColumn->basePut(rowIndex, data);
}
if(UpdateFlags)
{
casacore::Array<bool> flagArray(shape);
std::ifstream &flagFile = *updateInfo.flagFile;
flagFile.seekg(filePos*sizeof(bool), std::ios_base::beg);
flagFile.read(reinterpret_cast<char*>(&*flagArray.cbegin()), sampleCount * sizeof(bool));
if(flagFile.fail())
throw std::runtime_error("Error: failed to read temporary flag files!");
flagColumn.basePut(rowIndex, flagArray);
}
filePos += sampleCount;
}
Logger::Debug << "Freeing the data\n";
// Close the files
updateInfo.dataFile.reset();
updateInfo.flagFile.reset();
if(UpdateData)
Logger::Debug << "Done updating measurement set data\n";
if(UpdateFlags)
Logger::Debug << "Done updating measurement set flags\n";
}
void IndirectBaselineReader::updateOriginalMSData()
{
Logger::Debug << "Data was changed, need to update the original MS...\n";
updateOriginalMS<true, false>();
_reorderedDataFilesHaveChanged = false;
}
void IndirectBaselineReader::updateOriginalMSFlags()
{
Stopwatch watch(true);
Logger::Debug << "Flags were changed, need to update the original MS...\n";
updateOriginalMS<false, true>();
_reorderedFlagFilesHaveChanged = false;
Logger::Debug << "Storing flags toke: " << watch.ToString() << '\n';
}
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