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#include "fitsimageset.h"
#include <sstream>
#include <vector>
#include "../../structures/date.h"
#include "../../msio/fitsfile.h"
#include "../../structures/image2d.h"
#include "../../structures/timefrequencydata.h"
#include "../../structures/timefrequencymetadata.h"
#include "../../util/logger.h"
namespace rfiStrategy {
FitsImageSet::FitsImageSet(const std::string &file) :
ImageSet(),
_file(new FitsFile(file)),
_currentBaselineIndex(0),
_frequencyOffset(0.0),
_fitsType(UVFitsType)
{
_file->Open(FitsFile::ReadWriteMode);
}
FitsImageSet::FitsImageSet(const FitsImageSet& source) :
ImageSet(),
_file(source._file),
_baselines(source._baselines),
_bandCount(source._bandCount),
_antennaInfos(source._antennaInfos),
_bandInfos(source._bandInfos),
_bandIndexToNumber(source._bandIndexToNumber),
_currentBaselineIndex(source._currentBaselineIndex),
_currentBandIndex(source._currentBandIndex),
_frequencyOffset(source._frequencyOffset),
_baselineData(source._baselineData),
_fitsType(source._fitsType)
{
}
FitsImageSet::~FitsImageSet()
{
}
std::unique_ptr<ImageSet> FitsImageSet::Clone()
{
return std::unique_ptr<FitsImageSet>(new FitsImageSet(*this));
}
void FitsImageSet::Initialize()
{
if(_file->HasGroups())
_fitsType = UVFitsType;
else if(_file->GetHDUCount() > 1)
_fitsType = SDFitsType;
else
_fitsType = DynSpectrumType;
switch(_fitsType)
{
case UVFitsType: {
Logger::Debug << "This file has " << _file->GetGroupCount() << " groups with " << _file->GetParameterCount() << " parameters.\n";
_file->MoveToHDU(1);
if(_file->GetCurrentHDUType() != FitsFile::ImageHDUType)
throw FitsIOException("Primary table is not a grouped image");
long double *parameters = new long double[_file->GetParameterCount()];
int baselineIndex = _file->GetGroupParameterIndex("BASELINE");
size_t groupCount = _file->GetGroupCount();
std::set<std::pair<size_t,size_t> > baselineSet;
for(size_t g=0;g<groupCount;++g)
{
_file->ReadGroupParameters(g, parameters);
int a1 = (((int) parameters[baselineIndex]) & 255) - 1;
int a2 = (((int) parameters[baselineIndex] >> 8) & 255) - 1;
baselineSet.insert(std::pair<size_t,size_t>(a1,a2));
}
delete[] parameters;
Logger::Debug << "Baselines in file: " << baselineSet.size() << '\n';
for(std::set<std::pair<size_t,size_t> >::const_iterator i=baselineSet.begin();i!=baselineSet.end();++i)
_baselines.push_back(*i);
_bandCount = _file->GetCurrentImageSize(5);
} break;
case SDFitsType: {
_baselines.push_back(std::pair<size_t,size_t>(0, 0));
AntennaInfo antenna;
antenna.id = 0;
_antennaInfos.push_back(antenna);
// find number of bands
_file->MoveToHDU(2);
int ifColumn = 0;
bool hasIF = _file->HasTableColumn("IF", ifColumn);
if(!hasIF)
ifColumn = _file->GetTableColumnIndex("IFNUM");
int rowCount = _file->GetRowCount();
std::set<int> ifSet;
for(int i=1;i<=rowCount;++i)
{
double thisIndex;
_file->ReadTableCell(i, ifColumn, &thisIndex, 1);
ifSet.insert((int) round(thisIndex));
}
_bandCount = ifSet.size();
if(_bandCount == 0)
throw std::runtime_error("Could not find any IF's in this set");
_bandIndexToNumber.clear();
Logger::Debug << _bandCount << " IF's in set: [" << *ifSet.begin();
for(int i : ifSet)
{
_bandInfos.emplace(i, BandInfo());
if(_bandIndexToNumber.size()>0)
Logger::Debug << ", " << i;
_bandIndexToNumber.push_back(i);
}
Logger::Debug << "]\n";
} break;
case DynSpectrumType:
_baselines.push_back(std::pair<size_t,size_t>(0, 0));
AntennaInfo antenna;
antenna.id = 0;
antenna.name = "";
size_t height = _file->GetCurrentImageSize(2);
_antennaInfos.emplace_back(antenna);
_bandCount = 1;
_bandInfos.emplace(0, BandInfo());
_bandInfos[0].channels.resize(height);
double freq0 = _file->GetDoubleKeywordValue("CRVAL2");
double freqDelta = _file->GetDoubleKeywordValue("CDELT2");
_sourceName = _file->GetKeywordValue("SOURCE");
for(size_t i=0; i!=_bandInfos[0].channels.size(); ++i)
{
_bandInfos[0].channels[i].frequencyHz = freq0 + i*freqDelta;
_bandInfos[0].channels[i].frequencyIndex = i;
}
_file->MoveToHDU(1);
break;
}
}
BaselineData FitsImageSet::loadData(const ImageSetIndex &index)
{
size_t baselineIndex = index.Value() / _bandCount;
size_t bandIndex = index.Value() % _bandCount;
_frequencyOffset = 0.0;
_file->MoveToHDU(1);
TimeFrequencyMetaDataPtr metaData(new TimeFrequencyMetaData());
TimeFrequencyData data;
switch(_fitsType) {
case UVFitsType:
data = ReadPrimaryGroupTable(baselineIndex, bandIndex, 0, *metaData);
break;
case SDFitsType:
ReadPrimarySingleTable(data, *metaData);
break;
case DynSpectrumType:
ReadDynSpectrum(data, *metaData);
return BaselineData(data, metaData, index);
}
for(int hduIndex=2;hduIndex <= _file->GetHDUCount();hduIndex++)
{
_file->MoveToHDU(hduIndex);
switch(_file->GetCurrentHDUType())
{
case FitsFile::BinaryTableHDUType:
Logger::Debug << "Binary table found.\n";
ReadTable(data, *metaData, bandIndex);
break;
case FitsFile::ASCIITableHDUType:
Logger::Debug << "ASCII table found.\n";
ReadTable(data, *metaData, bandIndex);
break;
case FitsFile::ImageHDUType:
Logger::Debug << "Image found.\n";
break;
}
}
if(_fitsType == UVFitsType)
{
_currentBaselineIndex = baselineIndex;
_currentBandIndex = bandIndex;
int bandNumber = _bandIndexToNumber[bandIndex];
metaData->SetBand(_bandInfos[bandNumber]);
metaData->SetAntenna1(_antennaInfos[_baselines[_currentBaselineIndex].first]);
metaData->SetAntenna2(_antennaInfos[_baselines[_currentBaselineIndex].second]);
Logger::Debug << "Loaded metadata for: " << Date::AipsMJDToString(metaData->ObservationTimes()[0]) << ", band " << bandNumber << " (" << Frequency::ToString(_bandInfos[bandNumber].channels[0].frequencyHz) << " - " << Frequency::ToString(_bandInfos[bandNumber].channels.rbegin()->frequencyHz) << ")\n";
}
else {
metaData->SetAntenna1(_antennaInfos[0]);
metaData->SetAntenna2(_antennaInfos[0]);
}
return BaselineData(data, metaData, index);
}
TimeFrequencyData FitsImageSet::ReadPrimaryGroupTable(size_t baselineIndex, int band, int stokes, TimeFrequencyMetaData &metaData)
{
if(!_file->HasGroups() || _file->GetCurrentHDUType() != FitsFile::ImageHDUType)
throw FitsIOException("Primary table is not a grouped image");
std::vector<double> observationTimes;
std::vector<UVW> uvws;
std::vector<long double> parameters(_file->GetParameterCount());
int baseline = (_baselines[baselineIndex].first+1) + ((_baselines[baselineIndex].second+1)<<8);
int baselineColumn = _file->GetGroupParameterIndex("BASELINE");
size_t
complexCount = _file->GetCurrentImageSize(2),
stokesStep = complexCount,
stokesCount = _file->GetCurrentImageSize(3),
frequencyStep = stokesCount*complexCount,
frequencyCount = _file->GetCurrentImageSize(4),
bandStep = frequencyStep*frequencyCount;
std::vector<std::vector<long double> > valuesR(frequencyCount);
std::vector<std::vector<long double> > valuesI(frequencyCount);
std::vector<long double> data(_file->GetImageSize());
size_t groupCount = _file->GetGroupCount();
bool hasDate2 = _file->HasGroupParameter("DATE", 2);
int date2Index = 0, date1Index = _file->GetGroupParameterIndex("DATE");
if(hasDate2)
{
date2Index = _file->GetGroupParameterIndex("DATE", 2);
}
int uuIndex, vvIndex, wwIndex;
if(_file->HasGroupParameter("UU"))
{
uuIndex = _file->GetGroupParameterIndex("UU");
vvIndex = _file->GetGroupParameterIndex("VV");
wwIndex = _file->GetGroupParameterIndex("WW");
} else {
uuIndex = _file->GetGroupParameterIndex("UU---SIN");
vvIndex = _file->GetGroupParameterIndex("VV---SIN");
wwIndex = _file->GetGroupParameterIndex("WW---SIN");
}
size_t match = 0;
double frequencyFactor = 1.0;
if(_frequencyOffset != 0.0)
frequencyFactor = _frequencyOffset;
for(size_t g=0;g<groupCount;++g)
{
_file->ReadGroupParameters(g, ¶meters[0]);
if(parameters[baselineColumn] == baseline)
{
double date;
if(hasDate2)
date = parameters[date1Index] + parameters[date2Index];
else
date = parameters[date1Index];
UVW uvw;
uvw.u = parameters[uuIndex] * frequencyFactor;
uvw.v = parameters[vvIndex] * frequencyFactor;
uvw.w = parameters[wwIndex] * frequencyFactor;
_file->ReadGroupData(g, &data[0]);
for(size_t f=0;f<frequencyCount;++f)
{
size_t index = stokes*stokesStep + frequencyStep*f + bandStep*band;
long double r = data[index];
long double i = data[index + 1];
valuesR[f].push_back(r);
valuesI[f].push_back(i);
}
observationTimes.push_back(Date::JDToAipsMJD(date));
uvws.push_back(uvw);
++match;
}
}
Logger::Debug << match << " rows in table matched baseline.\n";
data.clear();
parameters.clear();
Logger::Debug << "Image is " << valuesR[0].size() << " x " << frequencyCount << '\n';
if(valuesR[0].size() == 0)
throw std::runtime_error("Baseline not found!");
Image2DPtr
real = Image2D::CreateUnsetImagePtr(valuesR[0].size(), frequencyCount),
imaginary = Image2D::CreateUnsetImagePtr(valuesR[0].size(), frequencyCount);
for(size_t i=0;i<valuesR[0].size();++i)
{
for(size_t f=0;f<frequencyCount;++f)
{
real->SetValue(i, f, valuesR[f][i]);
imaginary->SetValue(i, f, valuesI[f][i]);
}
}
metaData.SetUVW(uvws);
metaData.SetObservationTimes(observationTimes);
return TimeFrequencyData(aocommon::Polarization::StokesI, real, imaginary);
}
void FitsImageSet::ReadPrimarySingleTable(TimeFrequencyData &data, TimeFrequencyMetaData &metaData)
{
}
void FitsImageSet::ReadTable(TimeFrequencyData &data, TimeFrequencyMetaData &metaData, size_t bandIndex)
{
std::string extName = _file->GetKeywordValue("EXTNAME");
if(extName == "AIPS AN")
ReadAntennaTable(metaData);
else if(extName == "AIPS FQ")
ReadFrequencyTable(data, metaData);
else if(extName == "AIPS CL")
ReadCalibrationTable();
else if(extName == "SINGLE DISH")
ReadSingleDishTable(data, metaData, bandIndex);
}
void FitsImageSet::ReadAntennaTable(TimeFrequencyMetaData &metaData)
{
Logger::Debug << "Found antenna table\n";
_frequencyOffset = _file->GetDoubleKeywordValue("FREQ");
for(std::map<int, BandInfo>::iterator i=_bandInfos.begin();i!=_bandInfos.end();++i)
{
for(std::vector<ChannelInfo>::iterator j=i->second.channels.begin();j!=i->second.channels.end();++j) {
j->frequencyHz += _frequencyOffset;
}
}
std::vector<UVW> uvws(metaData.UVW());
for(std::vector<UVW>::iterator i=uvws.begin();i!=uvws.end();++i)
{
i->u = i->u * _frequencyOffset;
i->v = i->v * _frequencyOffset;
i->w = i->w * _frequencyOffset;
}
metaData.SetUVW(uvws);
_antennaInfos.clear();
for(int i=1;i<=_file->GetRowCount();++i)
{
AntennaInfo info;
char name[9];
long double pos[3];
_file->ReadTableCell(i, 1, name);
_file->ReadTableCell(i, 2, pos, 3);
info.name = name;
info.id = _antennaInfos.size();
info.position.x = pos[0];
info.position.y = pos[1];
info.position.z = pos[2];
_antennaInfos.push_back(info);
}
}
void FitsImageSet::ReadFrequencyTable(TimeFrequencyData &data, TimeFrequencyMetaData &metaData)
{
Logger::Debug << "Found frequency table\n";
const size_t numberIfs = _file->GetIntKeywordValue("NO_IF");
Logger::Debug << "Number of ifs: " << numberIfs << '\n';
_bandInfos.clear();
BandInfo bandInfo;
for(int i=1;i<=_file->GetRowCount();++i)
{
long double freqSel;
std::vector<long double> ifFreq(numberIfs), chWidth(numberIfs), totalBandwidth(numberIfs), sideband(numberIfs);
_file->ReadTableCell(i, 1, &freqSel, 1);
_file->ReadTableCell(i, 2, &ifFreq[0], numberIfs);
_file->ReadTableCell(i, 3, &chWidth[0], numberIfs);
_file->ReadTableCell(i, 4, &totalBandwidth[0], numberIfs);
_file->ReadTableCell(i, 5, &sideband[0], numberIfs);
for(size_t b=0;b<numberIfs;++b)
{
for(size_t channel=0;channel<data.ImageHeight();++channel)
{
ChannelInfo channelInfo;
channelInfo.channelWidthHz = chWidth[b];
channelInfo.effectiveBandWidthHz = chWidth[b];
channelInfo.frequencyHz = _frequencyOffset + ifFreq[b] + (chWidth[b] * channel);
channelInfo.frequencyIndex = channel;
channelInfo.resolutionHz = chWidth[b];
bandInfo.channels.push_back(channelInfo);
}
bandInfo.windowIndex = b;
_bandInfos.insert(std::pair<int, BandInfo>(b, bandInfo));
}
}
}
void FitsImageSet::ReadCalibrationTable()
{
Logger::Debug << "Found calibration table with " << _file->GetRowCount() << " rows.\n";
}
void FitsImageSet::ReadDynSpectrum(TimeFrequencyData& data, TimeFrequencyMetaData& metaData)
{
_file->MoveToHDU(1);
size_t width = _file->GetCurrentImageSize(1);
size_t height = _file->GetCurrentImageSize(2);
size_t npol = _file->GetCurrentImageSize(3);
Logger::Debug << "Reading fits file with dynspectrum, " << width << " x " << height << " x " << npol << "\n";
if(npol != 4)
throw std::runtime_error("Expected four polarizations in dynamic spectrum fits file");
size_t n = width * height * npol;
std::vector<num_t> buffer(n);
_file->ReadCurrentImageData(0, buffer.data(), n);
Image2DPtr imgs[4];
for(size_t i=0; i!=4; ++i)
imgs[i] = Image2D::CreateUnsetImagePtr(width, height);
Mask2DPtr flags = Mask2D::CreateSetMask<false>(width, height);
std::vector<num_t>::const_iterator bufferIter = buffer.begin();
for(size_t j=0; j!=npol; ++j)
{
for(size_t y=0; y!=height; ++y)
{
for(size_t x=0; x!=width; ++x)
{
imgs[j]->SetValue(x, y, *bufferIter);
if(!std::isfinite(*bufferIter))
flags->SetValue(x, y, true);
++bufferIter;
}
}
}
data = TimeFrequencyData::MakeFromPolarizationCombination(
TimeFrequencyData(TimeFrequencyData::RealPart, aocommon::Polarization::StokesI, imgs[0]),
TimeFrequencyData(TimeFrequencyData::RealPart, aocommon::Polarization::StokesQ, imgs[1]),
TimeFrequencyData(TimeFrequencyData::RealPart, aocommon::Polarization::StokesU, imgs[2]),
TimeFrequencyData(TimeFrequencyData::RealPart, aocommon::Polarization::StokesV, imgs[3])
);
data.SetGlobalMask(flags);
metaData.SetBand(_bandInfos[0]);
metaData.SetAntenna1(_antennaInfos[0]);
metaData.SetAntenna2(_antennaInfos[0]);
std::vector<double> times(width);
double timeDelta = _file->GetDoubleKeywordValue("CDELT1");
for(size_t i=0; i!=width; ++i)
times[i] = timeDelta * i;
metaData.SetObservationTimes(times);
}
void FitsImageSet::ReadSingleDishTable(TimeFrequencyData &data, TimeFrequencyMetaData &metaData, size_t ifIndex)
{
const int rowCount = _file->GetRowCount();
Logger::Debug << "Found single dish table with " << rowCount << " rows.\n";
const int
dateObsColumn = _file->GetTableColumnIndex("DATE-OBS"),
dataColumn = _file->GetTableColumnIndex("DATA"),
freqValColumn = _file->GetTableColumnIndex("CRVAL1"),
freqRefPixColumn = _file->GetTableColumnIndex("CRPIX1"),
freqDeltaColumn = _file->GetTableColumnIndex("CDELT1"),
freqResColumn = _file->GetTableColumnIndex("FREQRES"),
freqBandwidthColumn = _file->GetTableColumnIndex("BANDWID");
int timeColumn;
bool hasTime = _file->HasTableColumn("TIME", timeColumn); // optional
int flagColumn;
bool hasFlags = _file->HasTableColumn("FLAGGED", flagColumn); // optional
int ifColumn;
bool hasIF = _file->HasTableColumn("IF", ifColumn);
if(!hasIF)
ifColumn = _file->GetTableColumnIndex("IFNUM");
std::vector<long> axisDims = _file->GetColumnDimensions(dataColumn);
int freqCount = 0, polarizationCount = 0, raCount = 0, decCount = 0;
for(size_t i=0; i!=axisDims.size(); ++i) {
std::string name = _file->GetTableDimensionName(i);
if(name == "FREQ")
freqCount = axisDims[i];
else if(name == "STOKES")
polarizationCount = axisDims[i];
else if(name == "RA")
raCount = axisDims[i];
else if(name == "DEC")
decCount = axisDims[i];
}
const int totalSize = _file->GetTableColumnArraySize(dataColumn);
if(freqCount == 0)
{
freqCount = totalSize;
polarizationCount = 1;
raCount = 1;
decCount = 1;
}
const std::string telescopeName = _file->GetKeywordValue("TELESCOP");
_antennaInfos[0].name = telescopeName;
Logger::Debug << "Shape of data cells: " << freqCount << " channels x " << polarizationCount << " pols x " << raCount << " RAs x " << decCount << " decs" << "=" << totalSize << '\n';
std::vector<long double> cellData(totalSize);
std::unique_ptr<bool[]> flagData(new bool[totalSize]);
for(int i=0; i!=totalSize; ++i)
flagData[i] = false;
std::vector<Image2DPtr> images(polarizationCount);
std::vector<Mask2DPtr> masks(polarizationCount);
for(int i=0;i<polarizationCount;++i)
{
images[i] = Image2D::CreateZeroImagePtr(rowCount, freqCount);
masks[i] = Mask2D::CreateSetMaskPtr<true>(rowCount, freqCount);
}
std::vector<double> observationTimes(rowCount);
bool hasBand = false;
const int requestedIFNumber = _bandIndexToNumber[ifIndex];
size_t timeIndex = 0;
for(int row=1;row<=rowCount;++row)
{
long double time, date, ifNumber;
_file->ReadTableCell(row, ifColumn, &ifNumber, 1);
if(ifNumber == requestedIFNumber)
{
if(hasTime)
{
_file->ReadTableCell(row, timeColumn, &time, 1);
observationTimes[timeIndex] = time;
}
_file->ReadTableCell(row, dateObsColumn, &date, 1);
_file->ReadTableCell(row, dataColumn, &cellData[0], totalSize);
if(hasFlags)
_file->ReadTableCell(row, flagColumn, &flagData[0], totalSize);
if(!hasBand)
{
long double freqVal = 0.0, freqRefPix = 0.0, freqDelta = 0.0, freqRes = 0.0, freqBandwidth = 0.0;
_file->ReadTableCell(row, freqValColumn, &freqVal, 1);
_file->ReadTableCell(row, freqRefPixColumn, &freqRefPix, 1);
_file->ReadTableCell(row, freqDeltaColumn, &freqDelta, 1);
_file->ReadTableCell(row, freqResColumn, &freqRes, 1);
_file->ReadTableCell(row, freqBandwidthColumn, &freqBandwidth, 1);
if(freqBandwidth > 0.0)
{
Logger::Debug << "Frequency info: " <<freqVal << " Hz at index " << freqRefPix << ", delta " << freqDelta << "\n";
Logger::Debug << "Frequency res: " <<freqRes << " with bandwidth " << freqBandwidth << " Hz\n";
BandInfo bandInfo;
bandInfo.windowIndex = ifNumber;
for(int i=0;i<freqCount;++i)
{
ChannelInfo c;
c.frequencyIndex = i;
c.frequencyHz = ((double) i-freqRefPix)*freqDelta + freqVal;
bandInfo.channels.push_back(c);
}
_bandInfos[ifNumber] = bandInfo;
metaData.SetBand(bandInfo);
hasBand = true;
}
}
long double *dataPtr = &cellData[0];
bool *flagPtr = flagData.get();
for(int p=0;p<polarizationCount;++p)
{
for(int f=0;f<freqCount;++f)
{
images[p]->SetValue(timeIndex, f, *dataPtr);
masks[p]->SetValue(timeIndex, f, *flagPtr);
++dataPtr;
++flagPtr;
}
}
++timeIndex;
}
}
flagData.reset();
if(timeIndex == 0)
{
throw std::runtime_error("Couldn't find any rows in the fits image set for the requested IF");
}
for(int p=0;p<polarizationCount;++p)
{
images[p]->SetTrim(0, 0, timeIndex, images[p]->Height());
masks[p].reset(new Mask2D(masks[p]->Trim(0, 0, timeIndex, images[p]->Height())));
}
if(hasTime)
{
observationTimes.resize(timeIndex);
metaData.SetObservationTimes(observationTimes);
}
if(polarizationCount == 1)
{
data = TimeFrequencyData(TimeFrequencyData::AmplitudePart, aocommon::Polarization::StokesI, images[0]);
data.SetGlobalMask(masks[0]);
} else if(polarizationCount == 2)
{
data = TimeFrequencyData(TimeFrequencyData::AmplitudePart, aocommon::Polarization::XX, images[0], aocommon::Polarization::YY, images[1]);
data.SetIndividualPolarizationMasks(masks[0], masks[1]);
}
else {
std::ostringstream s;
s << "SDFits file has " << polarizationCount << " polarizations: don't know how to convert these";
throw std::runtime_error(s.str());
}
}
void FitsImageSet::AddWriteFlagsTask(const ImageSetIndex &index, std::vector<Mask2DCPtr> &flags)
{
switch(_fitsType)
{
case UVFitsType:
throw std::runtime_error("Not implemented for UV fits files");
case SDFitsType:
saveSingleDishFlags(flags, index.Value() % _bandCount);
break;
case DynSpectrumType:
saveDynSpectrumFlags(flags);
break;
}
}
void FitsImageSet::PerformWriteFlagsTask()
{
switch(_fitsType)
{
case UVFitsType:
throw std::runtime_error("Writing flags not implemented for UV fits files");
case SDFitsType:
case DynSpectrumType:
// Nothing to be done; Add..Task already wrote the flags.
break;
}
}
void FitsImageSet::saveSingleDishFlags(const std::vector<Mask2DCPtr>& flags, size_t ifIndex)
{
_file->Close();
_file->Open(FitsFile::ReadWriteMode);
_file->MoveToHDU(2);
Logger::Debug << "Writing single dish table for band " << ifIndex << " with " << _file->GetRowCount() << " rows.\n";
const int
dataColumn = _file->GetTableColumnIndex("DATA"),
flagColumn = _file->GetTableColumnIndex("FLAGGED");
int ifColumn = 0;
bool hasIF = _file->HasTableColumn("IF", ifColumn);
if(!hasIF)
ifColumn = _file->GetTableColumnIndex("IFNUM");
const int
freqCount = _file->GetColumnDimensionSize(dataColumn, 0),
polarizationCount = _file->GetColumnDimensionSize(dataColumn, 1);
const int totalSize = _file->GetTableColumnArraySize(dataColumn);
const int rowCount = _file->GetRowCount();
std::vector<double> cellData(totalSize);
std::unique_ptr<bool[]> flagData ( new bool[totalSize] );
std::vector<Mask2DCPtr> storedFlags = flags;
if(flags.size()==1)
{
while(storedFlags.size() < (unsigned) polarizationCount) storedFlags.push_back(flags[0]);
}
if(storedFlags.size() != (unsigned) polarizationCount)
{
std::stringstream s;
s << "saveSingleDishFlags() : mismatch in polarization count: the given vector contains " << flags.size() << " polarizations, the number of polarizations in the file is " << polarizationCount;
throw std::runtime_error(s.str());
}
for(std::vector<Mask2DCPtr>::const_iterator i=storedFlags.begin();i!=storedFlags.end();++i)
{
if((*i)->Height() != (unsigned) freqCount)
throw std::runtime_error("Frequency count in given mask does not match with the file");
}
size_t timeIndex = 0;
int specifiedIFNumber = _bandIndexToNumber[ifIndex];
for(int row=1;row<=rowCount;++row)
{
long double ifNumber;
_file->ReadTableCell(row, ifColumn, &ifNumber, 1);
if(ifNumber == specifiedIFNumber)
{
Logger::Debug << row << "\n";
_file->ReadTableCell(row, dataColumn, &cellData[0], totalSize);
double *dataPtr = &cellData[0];
bool *flagPtr = flagData.get();
for(int p=0;p<polarizationCount;++p)
{
for(int f=0;f<freqCount;++f)
{
if(storedFlags[p]->Value(timeIndex, f))
{
*flagPtr = true;
*dataPtr = 1e20;
} else {
*flagPtr = false;
}
++dataPtr;
++flagPtr;
}
}
_file->WriteTableCell(row, dataColumn, &cellData[0], totalSize);
_file->WriteTableCell(row, flagColumn, flagData.get(), totalSize);
++timeIndex;
}
}
}
void FitsImageSet::saveDynSpectrumFlags(const std::vector<Mask2DCPtr>& flags)
{
Logger::Debug << "Writing dynspectrum flags.\n";
_file->Close();
_file->Open(FitsFile::ReadWriteMode);
_file->MoveToHDU(1);
size_t width = _file->GetCurrentImageSize(1);
size_t height = _file->GetCurrentImageSize(2);
size_t npol = _file->GetCurrentImageSize(3);
size_t n = width * height * npol;
std::vector<num_t> buffer(n);
_file->ReadCurrentImageData(0, buffer.data(), buffer.size());
std::vector<num_t>::iterator bufferIter = buffer.begin();
for(size_t j=0; j!=npol; ++j)
{
for(size_t y=0; y!=height; ++y)
{
for(size_t x=0; x!=width; ++x)
{
if(flags[j]->Value(x, y))
*bufferIter = std::numeric_limits<num_t>::quiet_NaN();
++bufferIter;
}
}
}
_file->WriteImage(0, buffer.data(), buffer.size(), std::numeric_limits<num_t>::quiet_NaN());
}
std::string FitsImageSet::Description(const ImageSetIndex& index) const {
if(IsDynSpectrumType())
{
return SourceName();
}
else {
size_t baselineIndex = index.Value() / _bandCount;
size_t bandIndex = index.Value() % _bandCount;
int a1 = Baselines()[baselineIndex].first;
int a2 = Baselines()[baselineIndex].second;
AntennaInfo info1 = GetAntennaInfo(a1);
AntennaInfo info2 = GetAntennaInfo(a2);
std::stringstream s;
s << "Correlation " << info1.name << " x " << info2.name << ", band " << bandIndex;
return s.str();
}
}
std::vector<std::string> FitsImageSet::Files() const
{
return std::vector<std::string>{_file->Filename()};
}
std::string FitsImageSet::TelescopeName()
{
if(_fitsType == SDFitsType)
{
for(int hduIndex=2; hduIndex <= _file->GetHDUCount(); hduIndex++)
{
_file->MoveToHDU(hduIndex);
std::string extName = _file->GetKeywordValue("EXTNAME");
if(extName == "SINGLE DISH")
return _file->GetKeywordValue("TELESCOP");
}
return "";
}
else {
return "DynSpectrum";
}
}
}
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