std::pair<TimeFrequencyData,TimeFrequencyMetaDataPtr> RSPReader::ReadSingleBeamlet(unsigned long timestepStart, unsigned long timestepEnd, unsigned beamletCount, unsigned beamletIndex) { std::pair<TimeFrequencyData,TimeFrequencyMetaDataPtr> data = ReadAllBeamlets(timestepStart, timestepEnd, beamletCount); const unsigned width = timestepEnd - timestepStart; Image2DPtr realX = Image2D::CreateZeroImagePtr(width, 1); Image2DPtr imaginaryX = Image2D::CreateZeroImagePtr(width, 1); Image2DPtr realY = Image2D::CreateZeroImagePtr(width, 1); Image2DPtr imaginaryY = Image2D::CreateZeroImagePtr(width, 1); Mask2DPtr mask = Mask2D::CreateUnsetMaskPtr(width, 1); TimeFrequencyData allX = data.first.Make(Polarization::XX); TimeFrequencyData allY = data.first.Make(Polarization::YY); Image2DCPtr xr = allX.GetRealPart(); Image2DCPtr xi = allX.GetImaginaryPart(); Image2DCPtr yr = allY.GetRealPart(); Image2DCPtr yi = allY.GetImaginaryPart(); Mask2DCPtr maskWithBeamlets = data.first.GetSingleMask(); for(unsigned x=0;x<width;++x) { realX->SetValue(x, 0, xr->Value(x, beamletIndex)); imaginaryX->SetValue(x, 0, xi->Value(x, beamletIndex)); realY->SetValue(x, 0, yr->Value(x, beamletIndex)); imaginaryY->SetValue(x, 0, yi->Value(x, beamletIndex)); mask->SetValue(x, 0, maskWithBeamlets->Value(x, beamletIndex)); } data.first = TimeFrequencyData(Polarization::XX, realX, imaginaryX, Polarization::YY, realY, imaginaryY); data.first.SetGlobalMask(mask); BandInfo band = data.second->Band(); band.channels[0] = data.second->Band().channels[beamletIndex]; band.channels.resize(1); data.second->SetBand(band); return data; }
void HighPassFilter::elementWiseDivide(const Image2DPtr &leftHand, const Image2DCPtr &rightHand) { for(unsigned y=0;y<leftHand->Height();++y) { for(unsigned x=0;x<leftHand->Width();++x) { if(rightHand->Value(x, y) == 0.0) leftHand->SetValue(x, y, 0.0); else leftHand->SetValue(x, y, leftHand->Value(x, y) / rightHand->Value(x, y)); } } }
void TimeConvolutionAction::PerformFFTSincOperation(ArtifactSet &artifacts, Image2DPtr real, Image2DPtr imag) const { fftw_complex *fftIn = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * real->Width()), *fftOut = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * real->Width()); // FFTW plan routines are not thread safe, so lock. boost::mutex::scoped_lock lock(artifacts.IOMutex()); fftw_plan fftPlanForward = fftw_plan_dft_1d(real->Width(), fftIn, fftOut, FFTW_FORWARD, FFTW_MEASURE), fftPlanBackward = fftw_plan_dft_1d(real->Width(), fftIn, fftOut, FFTW_BACKWARD, FFTW_MEASURE); lock.unlock(); const size_t width = real->Width(); const BandInfo band = artifacts.MetaData()->Band(); for(unsigned y=0;y<real->Height();++y) { const numl_t sincScale = ActualSincScaleInSamples(artifacts, band.channels[y].frequencyHz); const numl_t limitFrequency = (numl_t) width / sincScale; if(y == real->Height()/2) { AOLogger::Debug << "Horizontal sinc scale: " << sincScale << " (filter scale: " << Angle::ToString(ActualSincScaleAsRaDecDist(artifacts, band.channels[y].frequencyHz)) << ")\n"; } if(sincScale > 1.0) { for(unsigned x=0;x<width;++x) { fftIn[x][0] = real->Value(x, y); fftIn[x][1] = imag->Value(x, y); } fftw_execute_dft(fftPlanForward, fftIn, fftOut); size_t filterIndexSize = (limitFrequency > 1.0) ? (size_t) ceil(limitFrequency/2.0) : 1; // Remove the high frequencies [filterIndexSize : n-filterIndexSize] for(size_t f=filterIndexSize;f<width - filterIndexSize;++f) { fftOut[f][0] = 0.0; fftOut[f][1] = 0.0; } fftw_execute_dft(fftPlanBackward, fftOut, fftIn); const double n = width; for(unsigned x=0;x<width;++x) { real->SetValue(x, y, fftIn[x][0] / n); imag->SetValue(x, y, fftIn[x][1] / n); } } } fftw_free(fftIn); fftw_free(fftOut); }
void HighPassFilter::setFlaggedValuesToZeroAndMakeWeights(const Image2DCPtr &inputImage, const Image2DPtr &outputImage, const Mask2DCPtr &inputMask, const Image2DPtr &weightsOutput) { const size_t width = inputImage->Width(); for(size_t y=0;y<inputImage->Height();++y) { for(size_t x=0;x<width;++x) { if(inputMask->Value(x, y) || !isfinite(inputImage->Value(x, y))) { outputImage->SetValue(x, y, 0.0); weightsOutput->SetValue(x, y, 0.0); } else { outputImage->SetValue(x, y, inputImage->Value(x, y)); weightsOutput->SetValue(x, y, 1.0); } } } }
void ImageTile::LineThreshold(bool evaluateBaseline, long double mean, long double variance, bool convolve) { Image2DPtr input = Image2D::CreateEmptyImagePtr(_scanCount, _channelCount); Mask2DPtr output = Mask2D::CreateSetMaskPtr<false>(_scanCount, _channelCount); if(evaluateBaseline) { for(unsigned channel = 0;channel<_channelCount;++channel) for(unsigned scan = 0;scan<_scanCount;++scan) input->SetValue(scan, channel, GetValueAt(channel, scan) - EvaluateBaselineFunction(scan, channel)); } else { for(unsigned channel = 0;channel<_channelCount;++channel) for(unsigned scan = 0;scan<_scanCount;++scan) input->SetValue(scan, channel, GetValueAt(channel, scan) - mean); } ThresholdMitigater::SumThreshold(input, output, 1, _trigger * variance); ThresholdMitigater::SumThreshold(input, output, 2, _trigger * variance * 1.6); ThresholdMitigater::SumThreshold(input, output, 3, _trigger * variance * 2.2); ThresholdMitigater::SumThreshold(input, output, 5, _trigger * variance * 3.0); ThresholdMitigater::SumThreshold(input, output, 10, _trigger * variance * 5.0); unsigned count = 0; for(unsigned channel = 0;channel<_channelCount;++channel) { for(unsigned scan = 0;scan<_scanCount;++scan) { if(output->Value(scan, channel)) { Window(scan, channel); count++; } } } while(count*2 > _channelCount*_scanCount) { size_t x = (size_t) (RNG::Uniform()*_scanCount); size_t y = (size_t) (RNG::Uniform()*_channelCount); if(_isWindowed[y][x]) { count--; _isWindowed[y][x]=false; } } if(convolve) ConvolveWindows(); }
num_t SpatialCompositionAction::eigenvalue(Image2DCPtr real, Image2DCPtr imaginary) const { try { Image2DPtr r = Image2D::CreateCopy(real), i = Image2D::CreateCopy(imaginary); for(size_t y=0;y<r->Height();++y) { for(size_t x=0;x<r->Width();++x) { if(!std::isfinite(r->Value(x,y))) r->SetValue(x, y, 0.0); if(!std::isfinite(i->Value(x,y))) i->SetValue(x, y, 0.0); } } if(r->ContainsOnlyZeros() && i->ContainsOnlyZeros()) return 0.0; return Eigenvalue::Compute(r, i); } catch(std::exception &e) { return std::numeric_limits<num_t>::quiet_NaN(); } }
Image2DPtr Compress::Read(std::ifstream &stream, Image2DPtr image, Mask2DCPtr mask) { num_t max = 0.0, min = 0.0; size_t width = 0, height = 0; char mode = 0; stream.read(reinterpret_cast<char*>(&max), sizeof(max)); stream.read(reinterpret_cast<char*>(&min), sizeof(min)); stream.read(reinterpret_cast<char*>(&width), sizeof(width)); stream.read(reinterpret_cast<char*>(&height), sizeof(height)); stream.read(&mode, sizeof(mode)); num_t normalizeFactor = (max - min) / (num_t) ((2<<22) + ((2<<22)-1)); for(unsigned y=0;y<height;++y) { for(unsigned x=0;x<width;++x) { if(!mask->Value(x, y)) { int32_t value; stream.read(reinterpret_cast<char*>(&value), 3); value >>= 8; image->SetValue(x, y, value / normalizeFactor + min); } } }
void BHFitsImageSet::loadImageData(TimeFrequencyData &data, const TimeFrequencyMetaDataPtr &metaData, const BHFitsImageSetIndex &index) { std::vector<num_t> buffer(_width * _height); _file->ReadCurrentImageData(0, &buffer[0], _width * _height); int rangeStart = _timeRanges[index._imageIndex].start, rangeEnd = _timeRanges[index._imageIndex].end; Image2DPtr image = Image2D::CreateZeroImagePtr(rangeEnd-rangeStart, _height); std::vector<num_t>::const_iterator bufferPtr = buffer.begin() + _height*rangeStart; for(int x=rangeStart; x!=rangeEnd; ++x) { for(int y=0; y!=_height; ++y) { image->SetValue(x-rangeStart, y, *bufferPtr); ++bufferPtr; } } data = TimeFrequencyData(TimeFrequencyData::AmplitudePart, SinglePolarisation, image); try { FitsFile flagFile(flagFilePath()); flagFile.Open(FitsFile::ReadOnlyMode); flagFile.ReadCurrentImageData(0, &buffer[0], _width * _height); bufferPtr = buffer.begin() + _height*rangeStart; Mask2DPtr mask = Mask2D::CreateUnsetMaskPtr(rangeEnd-rangeStart, _height); for(int x=rangeStart; x!=rangeEnd; ++x) { for(int y=0; y!=_height; ++y) { bool flag = false; if(*bufferPtr == 0.0) flag = false; else if(*bufferPtr == 1.0) flag = true; else std::runtime_error("Expecting a flag file with only ones and zeros, but this file contained other values."); mask->SetValue(x-rangeStart, y, flag); ++bufferPtr; } } data.SetGlobalMask(mask); } catch(std::exception &) { // Flag file could not be read; probably does not exist. Ignore this, flags will be initialized to false. } double frequencyDelta = _file->GetDoubleKeywordValue("CDELT1"), timeDelta = _file->GetDoubleKeywordValue("CDELT2"); BandInfo band; for(int ch=0; ch!=_height; ++ch) { ChannelInfo channel; channel.frequencyHz = ch * frequencyDelta * 1000000.0; band.channels.push_back(channel); } metaData->SetBand(band); const int rangeWidth = rangeEnd-rangeStart; std::vector<double> observationTimes(rangeWidth); for(int t=0; t!=rangeWidth; ++t) observationTimes[t] = (t + rangeStart) * timeDelta; metaData->SetObservationTimes(observationTimes); AntennaInfo antennaInfo; antennaInfo.id = 0; antennaInfo.name = RangeName(index._imageIndex); antennaInfo.diameter = 0.0; antennaInfo.mount = "Unknown"; antennaInfo.station = GetTelescopeName(); metaData->SetAntenna1(antennaInfo); metaData->SetAntenna2(antennaInfo); }
std::pair<TimeFrequencyData,TimeFrequencyMetaDataPtr> RSPReader::ReadAllBeamlets(unsigned long timestepStart, unsigned long timestepEnd, unsigned beamletCount) { const unsigned width = timestepEnd - timestepStart; Image2DPtr realX = Image2D::CreateZeroImagePtr(width, beamletCount); Image2DPtr imaginaryX = Image2D::CreateZeroImagePtr(width, beamletCount); Image2DPtr realY = Image2D::CreateZeroImagePtr(width, beamletCount); Image2DPtr imaginaryY = Image2D::CreateZeroImagePtr(width, beamletCount); Mask2DPtr mask = Mask2D::CreateSetMaskPtr<true>(width, beamletCount); std::ifstream file(_rawFile.c_str(), std::ios_base::binary | std::ios_base::in); size_t frame = 0; std::set<short> stations; TimeFrequencyMetaDataPtr metaData = TimeFrequencyMetaDataPtr(new TimeFrequencyMetaData()); BandInfo band; for(size_t i=0;i<beamletCount;++i) { ChannelInfo channel; channel.frequencyHz = i+1; channel.frequencyIndex = i; band.channels.push_back(channel); } metaData->SetBand(band); std::vector<double> observationTimes; // Read a header and determine the reading start position // Because timestepStart might fall within a block, the RCPApplicationHeader firstHeader; firstHeader.Read(file); const unsigned long bytesPerFrame = beamletCount * firstHeader.nofBlocks * RCPBeamletData::SIZE + RCPApplicationHeader::SIZE; const unsigned long startFrame = timestepStart / (unsigned long) firstHeader.nofBlocks; const unsigned long startByte = startFrame * bytesPerFrame; const unsigned long offsetFromStart = timestepStart - (startFrame * firstHeader.nofBlocks); //Logger::Debug << "Seeking to " << startByte << " (timestepStart=" << timestepStart << ", offsetFromStart=" << offsetFromStart << ", startFrame=" << startFrame << ",bytesPerFrame=" << bytesPerFrame << ")\n"; file.seekg(startByte, std::ios_base::beg); // Read the frames unsigned long x=0; while(x < width + offsetFromStart && file.good()) { RCPApplicationHeader header; header.Read(file); if(header.versionId != 2) { std::stringstream s; s << "Corrupted header found in frame " << frame << "!"; throw std::runtime_error(s.str()); } if(stations.count(header.stationId)==0) { stations.insert(header.stationId); AntennaInfo antenna; std::stringstream s; s << "LOFAR station with index " << header.stationId; antenna.name = s.str(); metaData->SetAntenna1(antenna); metaData->SetAntenna2(antenna); } for(size_t j=0;j<beamletCount;++j) { for(size_t i=0;i<header.nofBlocks;++i) { RCPBeamletData data; data.Read(file); if(i + x < width + offsetFromStart && i + x >= offsetFromStart) { const unsigned long pos = i + x - offsetFromStart; realX->SetValue(pos, j, data.xr); imaginaryX->SetValue(pos, j, data.xi); realY->SetValue(pos, j, data.yr); imaginaryY->SetValue(pos, j, data.yi); mask->SetValue(pos, j, false); } } } x += header.nofBlocks; ++frame; } //Logger::Debug << "Read " << frame << " frames.\n"; for(unsigned long i=0;i<width;++i) { const unsigned long pos = i + timestepStart; const double time = (double) pos * (double) STATION_INTEGRATION_STEPS / (double) _clockSpeed; observationTimes.push_back(time); } metaData->SetObservationTimes(observationTimes); std::pair<TimeFrequencyData,TimeFrequencyMetaDataPtr> data; data.first = TimeFrequencyData(Polarization::XX, realX, imaginaryX, Polarization::YY, realY, imaginaryY); data.first.SetGlobalMask(mask); data.second = metaData; return data; }