lsst::ip::isr Namespace Reference

Namespaces
	ampOffset
	assembleCcdTask
	brighterFatterKernel
	calibType
	crosstalk
	defects
	fringe
	isrFunctions
	isrMock
	isrQa
	isrTask
	linearize
	masking
	overscan
	photodiode
	ptcDataset
	straylight
	version
	vignette

Classes
class	CountMaskedPixels

Functions
template<typename PixelT >
int	applyLookupTable (afw::image::Image< PixelT > &image, ndarray::Array< PixelT, 1, 1 > const &table, PixelT indOffset)
	Add the values in a lookup table to an image, e.g. More...
template<typename PixelT >
size_t	maskNans (afw::image::MaskedImage< PixelT > const &mi, afw::image::MaskPixel maskVal, afw::image::MaskPixel allow=0)
	Mask NANs in an image. More...
template<typename ImagePixelT , typename FunctionT >
void	fitOverscanImage (std::shared_ptr< lsst::afw::math::Function1< FunctionT > > &overscanFunction, lsst::afw::image::MaskedImage< ImagePixelT > const &overscan, double ssize=1., int sigma=1)
	PYBIND11_MODULE (applyLookupTable, mod)
	PYBIND11_MODULE (isr, mod)
template int	applyLookupTable< float > (afw::image::Image< float > &, ndarray::Array< float, 1, 1 > const &, float)
template int	applyLookupTable< double > (afw::image::Image< double > &, ndarray::Array< double, 1, 1 > const &, double)
std::string	between (std::string &s, char ldelim, char rdelim)
template void	fitOverscanImage (std::shared_ptr< afw::math::Function1< double > > &overscanFunction, afw::image::MaskedImage< float > const &overscan, double ssize, int sigma)
template void	fitOverscanImage (std::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)

Function Documentation

applyLookupTable()

template<typename PixelT >

int lsst::ip::isr::applyLookupTable	(	afw::image::Image< PixelT > &	image,
		ndarray::Array< PixelT, 1, 1 > const &	table,
		PixelT	indOffset
	)

Add the values in a lookup table to an image, e.g.

for non-linearity correction

The algorithm is as follows: numOutOfRange = 0 For each i,j of the image: lookupInd = int(indOffset + image[i,j]) if lookupInd not in range [0, table.size() - 1]: set lookupInd to nearest edge and increment numOutOfRange image[i,j] += table[lookupInd] return numOutOfRange

Parameters

[in,out]	image	image to which to add the values; modified in place
[in]	table	lookup table
[in]	indOffset	scalar added to image value before truncating to lookup column

Returns

the number of pixels whose values were out of range

Definition at line 35 of file applyLookupTable.cc.

  {
    if (table.size() == 0u) {
        throw LSST_EXCEPT(
            pex::exceptions::LengthError,
            "Lookup table has zero size."
        );
    }
    int numOutOfRange = 0;
    int const maxLookupCol = table.size() - 1;
    for (int col = 0, imHeight = image.getHeight(); col < imHeight; ++col) {
        for (auto imPtr = image.row_begin(col), end = image.row_end(col); imPtr != end; ++imPtr) {
            int lookupCol = indOffset + *imPtr;
            if (lookupCol < 0) {
                lookupCol = 0;
                ++numOutOfRange;
            } else if (lookupCol > maxLookupCol) {
                lookupCol = maxLookupCol;
                ++numOutOfRange;
            }
            *imPtr += table[lookupCol];
        }
    }
    return numOutOfRange;
}

applyLookupTable< double >()

template int lsst::ip::isr::applyLookupTable< double >	(	afw::image::Image< double > &	,
		ndarray::Array< double, 1, 1 > const &	,
		double
	)

applyLookupTable< float >()

template int lsst::ip::isr::applyLookupTable< float >	(	afw::image::Image< float > &	,
		ndarray::Array< float, 1, 1 > const &	,
		float
	)

between()

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

Definition at line 100 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;
}

fitOverscanImage() [1/3]

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

fitOverscanImage() [2/3]

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

fitOverscanImage() [3/3]

template<typename ImagePixelT , typename FunctionT >

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

geom::Box2I bbox = geom::Box2I( geom::Point2I(0, y), 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

geom::Box2I bbox = geom::Box2I( geom::Point2I(0, y), 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 53 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) {
        geom::Box2I bbox = geom::Box2I(geom::Point2I(0,y), 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);
}

maskNans()

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	Retain NANs with this bit mask (0 to mask all NANs)

Definition at line 35 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) && (!std::isfinite(ptr.image()) ||
                                          !std::isfinite(ptr.variance()))) {
                nPix += 1;
                ptr.mask() |= maskVal;
            }
        }
    }
    return nPix;
}

maskNans< double >()

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

maskNans< float >()

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

PYBIND11_MODULE() [1/2]

lsst::ip::isr::PYBIND11_MODULE	(	applyLookupTable	,
		mod
	)

Definition at line 45 of file applyLookupTable.cc.

                                       {
    declareApplyLookupTable<float>(mod);
    declareApplyLookupTable<double>(mod);
}

PYBIND11_MODULE() [2/2]

lsst::ip::isr::PYBIND11_MODULE	(	isr	,
		mod
	)

Definition at line 68 of file isr.cc.

                          {
    declareAll<float>(mod, "F");
    declareAll<double>(mod, "D");
}