lsst::ip::isr Namespace Reference

Namespaces
	assembleCcdTask
	fringe
	isr
	isrTask
	version

Classes
class	LookupTableMultiplicative
class	LookupTableReplace
class	CountMaskedPixels

Enumerations
enum	StageId {   ISR_LINid = 0x1, ISR_OSCANid = 0x2, ISR_TRIMid = 0x4, ISR_BIASid = 0x8,   ISR_DFLATid = 0x10, ISR_ILLUMid = 0x20, ISR_BADPid = 0x40, ISR_SATid = 0x80,   ISR_FRINid = 0x100, ISR_DARKid = 0x200, ISR_PUPILid = 0x400, ISR_CRREJid = 0x800,   ISR_BACKSUBid = 0x1000 }

Functions
template<typename PixelT >
size_t	maskNans (afw::image::MaskedImage< PixelT > const &mi, afw::image::MaskPixel maskVal, afw::image::MaskPixel allow=0)
template<typename ImagePixelT , typename FunctionT >
void	fitOverscanImage (boost::shared_ptr< lsst::afw::math::Function1< FunctionT > > &overscanFunction, lsst::afw::image::MaskedImage< ImagePixelT > const &overscan, double ssize=1., int sigma=1)
template<typename ImagePixelT , typename FunctionT >
void	fitOverscanImage (boost::shared_ptr< afw::math::Function1< FunctionT > > &overscanFunction, afw::image::MaskedImage< ImagePixelT > const &overscan, double ssize, int sigma)
std::string	between (std::string &s, char ldelim, char rdelim)
template void	fitOverscanImage (boost::shared_ptr< afw::math::Function1< double > > &overscanFunction, afw::image::MaskedImage< float > const &overscan, double ssize, int sigma)
template void	fitOverscanImage (boost::shared_ptr< afw::math::Function1< double > > &overscanFunction, afw::image::MaskedImage< double > const &overscan, double ssize, int sigma)
template size_t	maskNans< float > (afw::image::MaskedImage< float > const &, afw::image::MaskPixel, afw::image::MaskPixel)
template size_t	maskNans< double > (afw::image::MaskedImage< double > const &, afw::image::MaskPixel, afw::image::MaskPixel)

Variables
std::string const &	ISR_LIN = "ISR_LIN"
	Linearization. More...
std::string const &	ISR_OSCAN = "ISR_OSCAN"
	Overscan. More...
std::string const &	ISR_TRIM = "ISR_TRIM"
	Trim. More...
std::string const &	ISR_BIAS = "ISR_BIAS"
	Bias. More...
std::string const &	ISR_DFLAT = "ISR_DFLAT"
	Dome flat. More...
std::string const &	ISR_ILLUM = "ISR_ILLUM"
	Illumination correction. More...
std::string const &	ISR_BADP = "ISR_BADP"
	Bad pixel mask. More...
std::string const &	ISR_SAT = "ISR_SAT"
	Saturated pixels. More...
std::string const &	ISR_FRING = "ISR_FRING"
	Fringe correction. More...
std::string const &	ISR_DARK = "ISR_DARK"
	Dark correction. More...
std::string const &	ISR_PUPIL = "ISR_PUPIL"
	Pupil correction. More...
std::string const &	ISR_CRREJ = "ISR_CRREJ"
	Cosmic ray rejection. More...
std::string const &	ISR_BACKSUB = "ISR_BACKSUB"
	Background subtraction. More...

Enumeration Type Documentation

enum lsst::ip::isr::StageId

Enumerator
ISR_LINid	Linearization.
ISR_OSCANid	Overscan.
ISR_TRIMid	Trim.
ISR_BIASid	Bias.
ISR_DFLATid	Dome flat.
ISR_ILLUMid	Illumination correction.
ISR_BADPid	Bad pixel mask.
ISR_SATid	Saturated pixels.
ISR_FRINid	Fringe correction.
ISR_DARKid	Dark correction.
ISR_PUPILid	Pupil correction.
ISR_CRREJid	Cosmic ray rejection.
ISR_BACKSUBid	Cosmic ray rejection.

Definition at line 85 of file isr.h.

                 {
        ISR_LINid   = 0x1,   
        ISR_OSCANid = 0x2,   
        ISR_TRIMid  = 0x4,   
        ISR_BIASid  = 0x8,   
        ISR_DFLATid = 0x10,  
        ISR_ILLUMid = 0x20,  
        ISR_BADPid  = 0x40,  
        ISR_SATid   = 0x80,  
        ISR_FRINid  = 0x100, 
        ISR_DARKid  = 0x200, 
        ISR_PUPILid = 0x400, 
        ISR_CRREJid = 0x800, 
        ISR_BACKSUBid = 0x1000, 
    };

Function Documentation

std::string lsst::ip::isr::between	(	std::string &	s,
		char	ldelim,
		char	rdelim
	)

Definition at line 126 of file Isr.cc.

                                                          {
    std::string::iterator b(s.begin());
    std::string::iterator e(s.end());
    std::string::iterator lp;
    std::string::iterator rp;
    
    std::string result;
    
    if((lp = std::find(b, e, ldelim)) != e)
        if((rp = std::find(++lp, e, rdelim)) != e)
            result = std::string(lp, rp);
    
    return result;
}

template<typename ImagePixelT , typename FunctionT >

void lsst::ip::isr::fitOverscanImage	(	boost::shared_ptr< afw::math::Function1< FunctionT > > &	overscanFunction,
		afw::image::MaskedImage< ImagePixelT > const &	overscan,
		double	ssize,
		int	sigma
	)

afw::geom::Box2I bbox = afw::geom::Box2I( afw::geom::Point2I(0, y), afw::geom::Point2I(0, width) ); The above was how this was defined before ticket #1556. As I understand it the following is the new way to do this

Definition at line 79 of file Isr.cc.

  {
    typedef afw::image::MaskedImage<ImagePixelT> MaskedImage;


    const int height = overscan.getHeight();
    const int width  = overscan.getWidth();
    std::vector<double> values(height);
    std::vector<double> errors(height);
    std::vector<double> positions(height);

    std::vector<double> parameters(overscanFunction->getNParameters(), 0.);
    std::vector<double> stepsize(overscanFunction->getNParameters(), ssize);
    
    for (int y = 0; y < height; ++y) {
        afw::geom::Box2I bbox = afw::geom::Box2I(afw::geom::Point2I(0,y), afw::geom::Point2I(width,y));
        MaskedImage mi         = MaskedImage(overscan, bbox);
        afw::math::Statistics stats = afw::math::makeStatistics(*(mi.getImage()), afw::math::MEAN | afw::math::STDEV);

        values[y]    = stats.getValue(afw::math::MEAN);
        errors[y]    = stats.getValue(afw::math::STDEV);
        positions[y] = y;
     
    }
    afw::math::FitResults fitResults = afw::math::minimize(
        *overscanFunction,
        parameters,
        stepsize,
        values,
        errors,
        positions,
        sigma
        );
    
    overscanFunction->setParameters(fitResults.parameterList);
}

template void lsst::ip::isr::fitOverscanImage	(	boost::shared_ptr< afw::math::Function1< double > > &	overscanFunction,
		afw::image::MaskedImage< float > const &	overscan,
		double	ssize,
		int	sigma
	)

template void lsst::ip::isr::fitOverscanImage	(	boost::shared_ptr< afw::math::Function1< double > > &	overscanFunction,
		afw::image::MaskedImage< double > const &	overscan,
		double	ssize,
		int	sigma
	)

template<typename ImagePixelT , typename FunctionT >

void lsst::ip::isr::fitOverscanImage	(	boost::shared_ptr< lsst::afw::math::Function1< FunctionT > > &	overscanFunction,
		lsst::afw::image::MaskedImage< ImagePixelT > const &	overscan,
		double	ssize = 1.,
		int	sigma = 1
	)

template<typename PixelT >

size_t lsst::ip::isr::maskNans	(	afw::image::MaskedImage< PixelT > const &	mi,
		afw::image::MaskPixel	maskVal,
		afw::image::MaskPixel	allow = 0
	)

Mask NANs in an image

NANs in the image or variance that are not already masked by the 'allow' value are masked with the 'maskVal'.

Returns

Number of pixels masked

Parameters

mi	Input image
maskVal	Bit mask value to give a NaN
allow	Allow NANs with this bit mask (0 to disallow all NANs)

Definition at line 61 of file Isr.cc.

{
    typedef typename afw::image::MaskedImage<PixelT>::x_iterator x_iterator;
    size_t nPix = 0;
    for (int y = 0; y != mi.getHeight(); ++y) {
        for (x_iterator ptr = mi.row_begin(y), end = mi.row_end(y); ptr != end; ++ptr) {
            if (!(ptr.mask() & allow) && (!utils::lsst_isfinite(ptr.image()) ||
                                          !utils::lsst_isfinite(ptr.variance()))) {
                nPix += 1;
                ptr.mask() |= maskVal;
            }
        }
    }
    return nPix;
}

template size_t lsst::ip::isr::maskNans< double >	(	afw::image::MaskedImage< double > const &	,
		afw::image::MaskPixel	,
		afw::image::MaskPixel
	)

template size_t lsst::ip::isr::maskNans< float >	(	afw::image::MaskedImage< float > const &	,
		afw::image::MaskPixel	,
		afw::image::MaskPixel
	)

Variable Documentation

std::string const& lsst::ip::isr::ISR_BACKSUB = "ISR_BACKSUB"

Background subtraction.

Definition at line 83 of file isr.h.

std::string const& lsst::ip::isr::ISR_BADP = "ISR_BADP"

Bad pixel mask.

Definition at line 77 of file isr.h.

std::string const& lsst::ip::isr::ISR_BIAS = "ISR_BIAS"

Bias.

Definition at line 74 of file isr.h.

std::string const& lsst::ip::isr::ISR_CRREJ = "ISR_CRREJ"

Cosmic ray rejection.

Definition at line 82 of file isr.h.

std::string const& lsst::ip::isr::ISR_DARK = "ISR_DARK"

Dark correction.

Definition at line 80 of file isr.h.

std::string const& lsst::ip::isr::ISR_DFLAT = "ISR_DFLAT"

Dome flat.

Definition at line 75 of file isr.h.

std::string const& lsst::ip::isr::ISR_FRING = "ISR_FRING"

Fringe correction.

Definition at line 79 of file isr.h.

std::string const& lsst::ip::isr::ISR_ILLUM = "ISR_ILLUM"

Illumination correction.

Definition at line 76 of file isr.h.

std::string const& lsst::ip::isr::ISR_LIN = "ISR_LIN"

Linearization.

Signature strings associated with each stage of the ISR

Note

Added to Exposure metadata after stage processing

As implementation detail, no more than 8 characters for fits compliance?

Definition at line 71 of file isr.h.

std::string const& lsst::ip::isr::ISR_OSCAN = "ISR_OSCAN"

Overscan.

Definition at line 72 of file isr.h.

std::string const& lsst::ip::isr::ISR_PUPIL = "ISR_PUPIL"

Pupil correction.

Definition at line 81 of file isr.h.

std::string const& lsst::ip::isr::ISR_SAT = "ISR_SAT"

Saturated pixels.

Definition at line 78 of file isr.h.

std::string const& lsst::ip::isr::ISR_TRIM = "ISR_TRIM"

Trim.

Definition at line 73 of file isr.h.