lsst::afw::fits Namespace Reference

Namespaces
namespace	_compression
namespace	_fitsContinued
namespace	_pickleFits
namespace	detail

Classes
struct	Bzero
	Scaling zero-point, set according to pixel type. More...
struct	Bzero< std::uint64_t >
struct	Bzero< T, typename std::enable_if< std::numeric_limits< T >::is_integer &&!std::numeric_limits< T >::is_signed >::type >
class	Fits
	A simple struct that combines the two arguments that must be passed to most cfitsio routines and contains thin and/or templated wrappers around common cfitsio routines. More...
class	FitsError
	An exception thrown when problems are found when reading or writing FITS files. More...
class	FitsTypeError
	An exception thrown when a FITS file has the wrong type. More...
class	HduMoveGuard
	RAII scoped guard for moving the HDU in a Fits object. More...
class	HeaderIterationFunctor
	Base class for polymorphic functors used to iterator over FITS key headers. More...
struct	ImageCompressionOptions
	Options for tile compression of image pixels. More...
struct	ImageScale
	Scale to apply to image. More...
class	ImageScalingOptions
	Options for scaling image pixels. More...
struct	ImageWriteOptions
	Options for writing an image to FITS. More...
class	MemFileManager
	Lifetime-management for memory that goes into FITS memory files. More...

Typedefs
using	dafPlistPtr = std::shared_ptr<daf::base::PropertyList>

Enumerations
enum class	HduType : int { IMAGE = 0 , ASCII_TABLE = 1 , BIN_TABLE = 2 , ANY = -1 }
	an enum representing the various types of FITS HDU that are available in cfitsio library More...

Functions
std::string	makeErrorMessage (std::string const &fileName="", int status=0, std::string const &msg="")
	Return an error message reflecting FITS I/O errors.
std::string	makeErrorMessage (std::string const &fileName, int status, boost::format const &msg)
std::string	makeErrorMessage (void *fptr, int status=0, std::string const &msg="")
	Return an error message reflecting FITS I/O errors.
std::string	makeErrorMessage (void *fptr, int status, boost::format const &msg)
std::string	makeLimitedFitsHeader (lsst::daf::base::PropertySet const &metadata, std::set< std::string > const &excludeNames={})
	Format a PropertySet into an FITS header string in a simplistic fashion.
template<typename T >
int	getBitPix ()
	Return the cfitsio integer BITPIX code for the given data type.
template<typename T , int N, int C>
ndarray::Array< T const, N, N > const	makeContiguousArray (ndarray::Array< T, N, C > const &array)
	Construct a contiguous ndarray.
std::shared_ptr< daf::base::PropertyList >	combineMetadata (daf::base::PropertyList const &first, daf::base::PropertyList const &second)
	Combine two sets of metadata in a FITS-appropriate fashion.
std::shared_ptr< daf::base::PropertyList >	readMetadata (std::string const &fileName, int hdu=DEFAULT_HDU, bool strip=false)
	Read FITS header.
std::shared_ptr< daf::base::PropertyList >	readMetadata (std::string const &fileName, std::string const &hduname, HduType type=HduType::ANY, int hduver=0, bool strip=false)
	Read FITS header.
std::shared_ptr< daf::base::PropertyList >	readMetadata (fits::MemFileManager &manager, int hdu=DEFAULT_HDU, bool strip=false)
	Read FITS header.
std::shared_ptr< daf::base::PropertyList >	readMetadata (fits::MemFileManager &manager, std::string const &hduname, HduType type=HduType::ANY, int hduver=0, bool strip=false)
	Read FITS header.
std::shared_ptr< daf::base::PropertyList >	readMetadata (fits::Fits &fitsfile, bool strip=false)
	Read FITS header.
void	setAllowImageCompression (bool allow)
bool	getAllowImageCompression ()
ImageCompressionOptions::CompressionAlgorithm	compressionAlgorithmFromString (std::string const &name)
	Interpret compression algorithm expressed in string.
std::string	compressionAlgorithmToString (ImageCompressionOptions::CompressionAlgorithm algorithm)
	Provide string version of compression algorithm.
ImageCompressionOptions::CompressionAlgorithm	compressionAlgorithmFromCfitsio (int cfitsio)
	Convert compression algorithm from cfitsio to ImageCompressionOptions::CompressionAlgorithm.
int	compressionAlgorithmToCfitsio (ImageCompressionOptions::CompressionAlgorithm algorithm)
	Convert ImageCompressionOptions::CompressionAlgorithm to cfitsio.
ImageScalingOptions::ScalingAlgorithm	scalingAlgorithmFromString (std::string const &name)
	Interpret scaling algorithm expressed in string.
std::string	scalingAlgorithmToString (ImageScalingOptions::ScalingAlgorithm algorithm)
	Provide string version of compression algorithm.
	PYBIND11_MODULE (_fits, mod)
template ImageScale	ImageScalingOptions::determine< std::uint8_t, 2 > (ndarray::Array< std::uint8_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::uint8_t > (ndarray::Array< std::uint8_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::uint8_t, 2, 2 >	ImageScale::fromFits< std::uint8_t > (ndarray::Array< std::uint8_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< std::uint16_t, 2 > (ndarray::Array< std::uint16_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::uint16_t > (ndarray::Array< std::uint16_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::uint16_t, 2, 2 >	ImageScale::fromFits< std::uint16_t > (ndarray::Array< std::uint16_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< std::int16_t, 2 > (ndarray::Array< std::int16_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::int16_t > (ndarray::Array< std::int16_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::int16_t, 2, 2 >	ImageScale::fromFits< std::int16_t > (ndarray::Array< std::int16_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< std::uint32_t, 2 > (ndarray::Array< std::uint32_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::uint32_t > (ndarray::Array< std::uint32_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::uint32_t, 2, 2 >	ImageScale::fromFits< std::uint32_t > (ndarray::Array< std::uint32_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< std::int32_t, 2 > (ndarray::Array< std::int32_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::int32_t > (ndarray::Array< std::int32_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::int32_t, 2, 2 >	ImageScale::fromFits< std::int32_t > (ndarray::Array< std::int32_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< std::uint64_t, 2 > (ndarray::Array< std::uint64_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::uint64_t > (ndarray::Array< std::uint64_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::uint64_t, 2, 2 >	ImageScale::fromFits< std::uint64_t > (ndarray::Array< std::uint64_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< std::int64_t, 2 > (ndarray::Array< std::int64_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< std::int64_t > (ndarray::Array< std::int64_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< std::int64_t, 2, 2 >	ImageScale::fromFits< std::int64_t > (ndarray::Array< std::int64_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< boost::float32_t, 2 > (ndarray::Array< boost::float32_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< boost::float32_t > (ndarray::Array< boost::float32_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< boost::float32_t, 2, 2 >	ImageScale::fromFits< boost::float32_t > (ndarray::Array< boost::float32_t, 2, 2 > const &) const
template ImageScale	ImageScalingOptions::determine< boost::float64_t, 2 > (ndarray::Array< boost::float64_t const, 2, 2 > const &image, ndarray::Array< bool, 2, 2 > const &mask) const
template std::shared_ptr< detail::PixelArrayBase >	ImageScale::toFits< boost::float64_t > (ndarray::Array< boost::float64_t const, 2, 2 > const &, bool, bool, ndarray::Array< long, 1 > const &, int) const
template ndarray::Array< boost::float64_t, 2, 2 >	ImageScale::fromFits< boost::float64_t > (ndarray::Array< boost::float64_t, 2, 2 > const &) const

Variables
const int	DEFAULT_HDU = INT_MIN
	Specify that the default HDU should be read.

Typedef Documentation

dafPlistPtr

using lsst::afw::fits::dafPlistPtr = std::shared_ptr<daf::base::PropertyList>

Definition at line 1677 of file fits.cc.

Enumeration Type Documentation

HduType

enum class lsst::afw::fits::HduType : int

strong

an enum representing the various types of FITS HDU that are available in cfitsio library

This is an int because the value it maps to in cfitsio is also an int.

Enumerator
IMAGE
ASCII_TABLE
BIN_TABLE
ANY

Definition at line 290 of file fits.h.

: int { IMAGE = 0, ASCII_TABLE = 1, BIN_TABLE = 2, ANY = -1 };

Function Documentation

combineMetadata()

std::shared_ptr< daf::base::PropertyList > lsst::afw::fits::combineMetadata	(	daf::base::PropertyList const &	first,
		daf::base::PropertyList const &	second )

Combine two sets of metadata in a FITS-appropriate fashion.

"COMMENT" and "HISTORY" entries:

• If of type std::string then the values in second are appended to values in first
• If not of type std::string then they are silently ignored

All other entries:

• Values in second override values in first (regardless of type)
• Only scalars are copied; if a vector is found, only the last value is copied

Parameters

[in]	first	The first set of metadata to combine
[in]	second	The second set of metadata to combine

Returns

The combined metadata. Item names have the following order:

• names in first, omitting all names except "COMMENT" and "HISTORY" that appear in second
• names in second, omitting "COMMENT" and "HISTORY" if valid versions appear in first

Definition at line 1648 of file fits.cc.

                                            {
    auto combined = std::make_shared<daf::base::PropertyList>();
    bool const asScalar = true;
    for (auto const &name : first.getOrderedNames()) {
        auto const iscv = isCommentIsValid(first, name);
        if (iscv.isComment) {
            if (iscv.isValid) {
                combined->add<std::string>(name, first.getArray<std::string>(name));
            }
        } else {
            combined->copy(name, first, name, asScalar);
        }
    }
    for (auto const &name : second.getOrderedNames()) {
        auto const iscv = isCommentIsValid(second, name);
        if (iscv.isComment) {
            if (iscv.isValid) {
                combined->add<std::string>(name, second.getArray<std::string>(name));
            }
        } else {
            // `copy` will replace an item, even if has a different type, so no need to call `remove`
            combined->copy(name, second, name, asScalar);
        }
    }
    return combined;
}

compressionAlgorithmFromCfitsio()

ImageCompressionOptions::CompressionAlgorithm lsst::afw::fits::compressionAlgorithmFromCfitsio

(

int

cfitsio

)

Convert compression algorithm from cfitsio to ImageCompressionOptions::CompressionAlgorithm.

Definition at line 49 of file fitsCompression.cc.

                                                                                         {
    switch (cfitsio) {
        case 0:
            return ImageCompressionOptions::NONE;
        case RICE_1:
            return ImageCompressionOptions::RICE;
        case GZIP_1:
            return ImageCompressionOptions::GZIP;
        case GZIP_2:
            return ImageCompressionOptions::GZIP_SHUFFLE;
        case PLIO_1:
            return ImageCompressionOptions::PLIO;
        case HCOMPRESS_1:
            throw LSST_EXCEPT(pex::exceptions::InvalidParameterError,
                              "Unsupported compression algorithm: HCOMPRESS_1");
        default:
            std::ostringstream os;
            os << "Unrecognized cfitsio compression: " << cfitsio;
            throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, os.str());
    }
}

compressionAlgorithmFromString()

ImageCompressionOptions::CompressionAlgorithm lsst::afw::fits::compressionAlgorithmFromString

(

std::string const &

name

)

Interpret compression algorithm expressed in string.

Definition at line 19 of file fitsCompression.cc.

                                                                                                  {
    if (name == "NONE") return ImageCompressionOptions::NONE;
    if (name == "GZIP") return ImageCompressionOptions::GZIP;
    if (name == "GZIP_SHUFFLE") return ImageCompressionOptions::GZIP_SHUFFLE;
    if (name == "RICE") return ImageCompressionOptions::RICE;
    if (name == "HCOMPRESS")
        throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, "HCOMPRESS is unsupported");
    if (name == "PLIO") return ImageCompressionOptions::PLIO;
    throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, "Unrecognised compression algorithm: " + name);
}

compressionAlgorithmToCfitsio()

int lsst::afw::fits::compressionAlgorithmToCfitsio

(

ImageCompressionOptions::CompressionAlgorithm

algorithm

)

Convert ImageCompressionOptions::CompressionAlgorithm to cfitsio.

Definition at line 71 of file fitsCompression.cc.

                                                                                         {
    switch (algorithm) {
        case ImageCompressionOptions::NONE:
            return 0;
        case ImageCompressionOptions::GZIP:
            return GZIP_1;
        case ImageCompressionOptions::GZIP_SHUFFLE:
            return GZIP_2;
        case ImageCompressionOptions::RICE:
            return RICE_1;
        case ImageCompressionOptions::PLIO:
            return PLIO_1;
        default:
            std::ostringstream os;
            os << "Unrecognized compression algorithm: " << algorithm;
            throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, os.str());
    }
}

compressionAlgorithmToString()

std::string lsst::afw::fits::compressionAlgorithmToString

(

ImageCompressionOptions::CompressionAlgorithm

algorithm

)

Provide string version of compression algorithm.

Definition at line 30 of file fitsCompression.cc.

                                                                                              {
    switch (algorithm) {
        case ImageCompressionOptions::NONE:
            return "NONE";
        case ImageCompressionOptions::GZIP:
            return "GZIP";
        case ImageCompressionOptions::GZIP_SHUFFLE:
            return "GZIP_SHUFFLE";
        case ImageCompressionOptions::RICE:
            return "RICE";
        case ImageCompressionOptions::PLIO:
            return "PLIO";
        default:
            std::ostringstream os;
            os << "Unrecognized compression algorithm: " << algorithm;
            throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, os.str());
    }
}

getAllowImageCompression()

bool lsst::afw::fits::getAllowImageCompression

(

)

Definition at line 1568 of file fits.cc.

{ return allowImageCompression; }

getBitPix()

template<typename T >

int lsst::afw::fits::getBitPix

(

)

Return the cfitsio integer BITPIX code for the given data type.

Definition at line 501 of file fits.cc.

                {
    return FitsBitPix<T>::CONSTANT;
}

ImageScale::fromFits< boost::float32_t >()

template ndarray::Array< boost::float32_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< boost::float32_t >

(

ndarray::Array< boost::float32_t, 2, 2 > const &

)

const

ImageScale::fromFits< boost::float64_t >()

template ndarray::Array< boost::float64_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< boost::float64_t >

(

ndarray::Array< boost::float64_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::int16_t >()

template ndarray::Array< std::int16_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::int16_t >

(

ndarray::Array< std::int16_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::int32_t >()

template ndarray::Array< std::int32_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::int32_t >

(

ndarray::Array< std::int32_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::int64_t >()

template ndarray::Array< std::int64_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::int64_t >

(

ndarray::Array< std::int64_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::uint16_t >()

template ndarray::Array< std::uint16_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::uint16_t >

(

ndarray::Array< std::uint16_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::uint32_t >()

template ndarray::Array< std::uint32_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::uint32_t >

(

ndarray::Array< std::uint32_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::uint64_t >()

template ndarray::Array< std::uint64_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::uint64_t >

(

ndarray::Array< std::uint64_t, 2, 2 > const &

)

const

ImageScale::fromFits< std::uint8_t >()

template ndarray::Array< std::uint8_t, 2, 2 > lsst::afw::fits::ImageScale::fromFits< std::uint8_t >

(

ndarray::Array< std::uint8_t, 2, 2 > const &

)

const

ImageScale::toFits< boost::float32_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< boost::float32_t >	(	ndarray::Array< boost::float32_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< boost::float64_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< boost::float64_t >	(	ndarray::Array< boost::float64_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::int16_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::int16_t >	(	ndarray::Array< std::int16_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::int32_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::int32_t >	(	ndarray::Array< std::int32_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::int64_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::int64_t >	(	ndarray::Array< std::int64_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::uint16_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::uint16_t >	(	ndarray::Array< std::uint16_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::uint32_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::uint32_t >	(	ndarray::Array< std::uint32_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::uint64_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::uint64_t >	(	ndarray::Array< std::uint64_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScale::toFits< std::uint8_t >()

template std::shared_ptr< detail::PixelArrayBase > lsst::afw::fits::ImageScale::toFits< std::uint8_t >	(	ndarray::Array< std::uint8_t const, 2, 2 > const &	,
		bool	,
		bool	,
		ndarray::Array< long, 1 > const &	,
		int	) const

ImageScalingOptions::determine< boost::float32_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< boost::float32_t, 2 >	(	ndarray::Array< boost::float32_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< boost::float64_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< boost::float64_t, 2 >	(	ndarray::Array< boost::float64_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::int16_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::int16_t, 2 >	(	ndarray::Array< std::int16_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::int32_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::int32_t, 2 >	(	ndarray::Array< std::int32_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::int64_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::int64_t, 2 >	(	ndarray::Array< std::int64_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::uint16_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::uint16_t, 2 >	(	ndarray::Array< std::uint16_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::uint32_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::uint32_t, 2 >	(	ndarray::Array< std::uint32_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::uint64_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::uint64_t, 2 >	(	ndarray::Array< std::uint64_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

ImageScalingOptions::determine< std::uint8_t, 2 >()

template ImageScale lsst::afw::fits::ImageScalingOptions::determine< std::uint8_t, 2 >	(	ndarray::Array< std::uint8_t const, 2, 2 > const &	image,
		ndarray::Array< bool, 2, 2 > const &	mask ) const

makeContiguousArray()

template<typename T , int N, int C>

ndarray::Array< T const, N, N > const lsst::afw::fits::makeContiguousArray

(

ndarray::Array< T, N, C > const &

array

)

Construct a contiguous ndarray.

A deep copy is only performed if the array is not already contiguous.

Definition at line 212 of file fits.h.

                                                                                          {
    ndarray::Array<T const, N, N> contiguous = ndarray::dynamic_dimension_cast<N>(array);
    if (contiguous.empty()) contiguous = ndarray::copy(array);
    return contiguous;
}

makeErrorMessage() [1/4]

std::string lsst::afw::fits::makeErrorMessage ( std::string const & fileName, int status, boost::format const & msg )

inline

Definition at line 65 of file fits.h.

                                                                                                 {
    return makeErrorMessage(fileName, status, msg.str());
}

makeErrorMessage() [2/4]

std::string lsst::afw::fits::makeErrorMessage	(	std::string const &	fileName = "",
		int	status = 0,
		std::string const &	msg = "" )

Return an error message reflecting FITS I/O errors.

Parameters

[in]	fileName	FITS filename to be included in the error message.
[in]	status	The last status value returned by the cfitsio library; if nonzero, the error message will include a description from cfitsio.
[in]	msg	An additional custom message to include.

Definition at line 431 of file fits.cc.

                                                                                        {
    std::ostringstream os;
    os << "cfitsio error";
    if (fileName != "") {
        os << " (" << fileName << ")";
    }
    if (status != 0) {
        char fitsErrMsg[FLEN_ERRMSG];
        fits_get_errstatus(status, fitsErrMsg);
        os << ": " << fitsErrMsg << " (" << status << ")";
    }
    if (msg != "") {
        os << " : " << msg;
    }
    os << "\ncfitsio error stack:\n";
    char cfitsioMsg[FLEN_ERRMSG];
    // fits_read_errmsg can return a junk string with non printable characters
    // creating problem with python exception bindings
    while (fits_read_errmsg(cfitsioMsg) != 0) {
        cfitsioMsg[FLEN_ERRMSG-1] = char(0); // ensure termination
        std::size_t len=strlen(cfitsioMsg);
        for(std::size_t i = 0; i < len; i++)
            if( !isprint(cfitsioMsg[i]) ) cfitsioMsg[i] = '.';
        os << "  " << cfitsioMsg << "\n";
    }
    return os.str();
}

makeErrorMessage() [3/4]

std::string lsst::afw::fits::makeErrorMessage ( void * fptr, int status, boost::format const & msg )

inline

Definition at line 79 of file fits.h.

                                                                                  {
    return makeErrorMessage(fptr, status, msg.str());
}

makeErrorMessage() [4/4]

std::string lsst::afw::fits::makeErrorMessage	(	void *	fptr,
		int	status = 0,
		std::string const &	msg = "" )

Return an error message reflecting FITS I/O errors.

Parameters

[in]	fptr	A cfitsio fitsfile pointer to be inspected for a filename. Passed as void* to avoid including fitsio.h in the header file.
[in]	status	The last status value returned by the cfitsio library; if nonzero, the error message will include a description from cfitsio.
[in]	msg	An additional custom message to include.

Definition at line 459 of file fits.cc.

                                                                         {
    std::string fileName = "";
    fitsfile *fd = reinterpret_cast<fitsfile *>(fptr);
    if (fd != nullptr && fd->Fptr != nullptr && fd->Fptr->filename != nullptr) {
        fileName = fd->Fptr->filename;
    }
    return makeErrorMessage(fileName, status, msg);
}

makeLimitedFitsHeader()

std::string lsst::afw::fits::makeLimitedFitsHeader	(	lsst::daf::base::PropertySet const &	metadata,
		std::set< std::string > const &	excludeNames = {} )

Format a PropertySet into an FITS header string in a simplistic fashion.

This function is designed to format data for creating a WCS. As such, it is quite limited:

• It skips entries whose name is longer than 8 characters, since none are used for FITS-WCS
• It skips string entries if the fully formatted string is longer than 80 characters
• It skips entries with types it cannot handle (e.g. long, long long)
• For entries that have array data, it only writes the final value, since that is the value that should be used by code that reads FITS headers.
• It makes no attempt to insure that required entries, such as SIMPLE, are present.

Parameters

[in]	metadata	Metadata to format; if this is a PropertyList then the order of items is preserved
[in]	excludeNames	Names of entries to exclude from the returned header string

Returns

a FITS header string (exactly 80 characters per entry, no line terminators)

Definition at line 468 of file fits.cc.

                                                                         {
    daf::base::PropertyList const *pl = dynamic_cast<daf::base::PropertyList const *>(&metadata);
    std::vector<std::string> allParamNames;
    if (pl) {
        allParamNames = pl->getOrderedNames();
    } else {
        allParamNames = metadata.paramNames(false);
    }
    std::vector<std::string> desiredParamNames;
    for (auto const &name : allParamNames) {
        if (excludeNames.count(name) == 0) {
            desiredParamNames.push_back(name);
        }
    }
    return makeLimitedFitsHeaderImpl(desiredParamNames, metadata);
}

PYBIND11_MODULE()

lsst::afw::fits::PYBIND11_MODULE	(	_fits	,
		mod	)

Definition at line 284 of file _fits.cc.

                            {
    lsst::utils::python::WrapperCollection wrappers(mod, "lsst.afw.fits");
    wrappers.addInheritanceDependency("lsst.pex.exceptions");
    wrappers.addSignatureDependency("lsst.daf.base");
    // FIXME: after afw.image pybind wrappers are converted
    //wrappers.addSignatureDependency("lsst.afw.image");
    auto cls = wrappers.wrapException<FitsError, lsst::pex::exceptions::IoError>("FitsError", "IoError");
    cls.def(py::init<std::string const &>());
    declareImageCompression(wrappers);
    declareImageScalingOptions(wrappers);
    declareImageScale(wrappers);
    declareImageWriteOptions(wrappers);
    declareFits(wrappers);
    declareFitsModule(wrappers);
    wrappers.finish();
}

readMetadata() [1/5]

std::shared_ptr< daf::base::PropertyList > lsst::afw::fits::readMetadata	(	fits::Fits &	fitsfile,
		bool	strip = false )

Read FITS header.

Includes support for the INHERIT convention: if 'INHERIT = T' is in the header, the PHU will be read as well, and nominated HDU will override any duplicated values.

Parameters

fitsfile	the file and HDU to be read
strip	if true, common FITS keys that usually have non-metadata intepretations (e.g. NAXIS, BITPIX) will be ignored.

Definition at line 1707 of file fits.cc.

                                                                                {
    auto metadata = std::make_shared<lsst::daf::base::PropertyList>();
    fitsfile.readMetadata(*metadata, strip);
    // if INHERIT=T, we want to also include header entries from the primary HDU
    int oldHdu = fitsfile.getHdu();
    if (oldHdu != 0 && metadata->exists("INHERIT")) {
        bool inherit = false;
        if (metadata->typeOf("INHERIT") == typeid(std::nullptr_t)) {
            // Assume false if INHERIT exists but is undefined.
            inherit = false;
        } else if (metadata->typeOf("INHERIT") == typeid(std::string)) {
            inherit = (metadata->get<std::string>("INHERIT") == "T");
        } else {
            inherit = metadata->get<bool>("INHERIT");
        }
        if (strip) metadata->remove("INHERIT");
        if (inherit) {
            HduMoveGuard guard(fitsfile, 0);
            // Combine the metadata from the primary HDU with the metadata from the specified HDU,
            // with non-comment values from the specified HDU superseding those in the primary HDU
            // and comments from the specified HDU appended to comments from the primary HDU
            auto primaryHduMetadata = std::make_shared<daf::base::PropertyList>();
            fitsfile.readMetadata(*primaryHduMetadata, strip);
            metadata = combineMetadata(*primaryHduMetadata, *metadata);
        } else {
            // Purge invalid values
            auto const emptyMetadata = std::make_shared<lsst::daf::base::PropertyList>();
            metadata = combineMetadata(*metadata, *emptyMetadata);
        }
    }
    return metadata;
}

readMetadata() [2/5]

dafPlistPtr lsst::afw::fits::readMetadata	(	fits::MemFileManager &	manager,
		int	hdu = DEFAULT_HDU,
		bool	strip = false )

Read FITS header.

Includes support for the INHERIT convention: if 'INHERIT = T' is in the header, the PHU will be read as well, and nominated HDU will override any duplicated values.

Parameters

manager	the in-memory file whose header will be read
hdu	the HDU to read (0-indexed; 0 is the Primary HDU).
strip	if true, common FITS keys that usually have non-metadata intepretations (e.g. NAXIS, BITPIX) will be ignored.

Definition at line 1698 of file fits.cc.

                                                                           {
    return detail::_readMetadata(manager, strip, hdu);
}

readMetadata() [3/5]

dafPlistPtr lsst::afw::fits::readMetadata	(	fits::MemFileManager &	manager,
		std::string const &	hduname,
		HduType	type = HduType::ANY,
		int	hduver = 0,
		bool	strip = false )

Read FITS header.

Includes support for the INHERIT convention: if 'INHERIT = T' is in the header, the PHU will be read as well, and nominated HDU will override any duplicated values.

Parameters

manager	the in-memory file whose header will be read
hduname	the name of the HDU to read
type	type of FITS header to match. Defaults to ANY_HDU
hduver	version of HDU header to match, defaults to 0 (version ignored)
strip	if true, common FITS keys that usually have non-metadata intepretations (e.g. NAXIS, BITPIX) will be ignored.

Definition at line 1702 of file fits.cc.

                                     {
    return detail::_readMetadata(manager, strip, hduname, type, hduver);
}

readMetadata() [4/5]

dafPlistPtr lsst::afw::fits::readMetadata	(	std::string const &	fileName,
		int	hdu = DEFAULT_HDU,
		bool	strip = false )

Read FITS header.

Includes support for the INHERIT convention: if 'INHERIT = T' is in the header, the PHU will be read as well, and nominated HDU will override any duplicated values.

Parameters

fileName	the file whose header will be read
hdu	the HDU to read (0-indexed; 0 is the Primary HDU).
strip	if true, common FITS keys that usually have non-metadata intepretations (e.g. NAXIS, BITPIX) will be ignored.

Definition at line 1689 of file fits.cc.

                                                                         {
    return detail::_readMetadata(fileName, strip, hdu);
}

readMetadata() [5/5]

dafPlistPtr lsst::afw::fits::readMetadata	(	std::string const &	fileName,
		std::string const &	hduname,
		HduType	type = HduType::ANY,
		int	hduver = 0,
		bool	strip = false )

Read FITS header.

Includes support for the INHERIT convention: if 'INHERIT = T' is in the header, the PHU will be read as well, and nominated HDU will override any duplicated values.

Parameters

fileName	the file whose header will be read
hduname	the name of the HDU to read
type	type of FITS header to match. Defaults to ANY_HDU
hduver	version of HDU header to match, defaults to 0 (version ignored)
strip	if true, common FITS keys that usually have non-metadata intepretations (e.g. NAXIS, BITPIX) will be ignored.

Definition at line 1693 of file fits.cc.

                                     {
    return detail::_readMetadata(fileName, strip, hduname, type, hduver);
}

scalingAlgorithmFromString()

ImageScalingOptions::ScalingAlgorithm lsst::afw::fits::scalingAlgorithmFromString

(

std::string const &

name

)

Interpret scaling algorithm expressed in string.

Definition at line 98 of file fitsCompression.cc.

                                                                                      {
    if (name == "NONE") return ImageScalingOptions::NONE;
    if (name == "RANGE") return ImageScalingOptions::RANGE;
    if (name == "STDEV_POSITIVE") return ImageScalingOptions::STDEV_POSITIVE;
    if (name == "STDEV_NEGATIVE") return ImageScalingOptions::STDEV_NEGATIVE;
    if (name == "STDEV_BOTH") return ImageScalingOptions::STDEV_BOTH;
    if (name == "MANUAL") return ImageScalingOptions::MANUAL;
    throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, "Unrecognized scaling algorithm: " + name);
}

scalingAlgorithmToString()

std::string lsst::afw::fits::scalingAlgorithmToString

(

ImageScalingOptions::ScalingAlgorithm

algorithm

)

Provide string version of compression algorithm.

Definition at line 108 of file fitsCompression.cc.

                                                                                  {
    switch (algorithm) {
        case ImageScalingOptions::NONE:
            return "NONE";
        case ImageScalingOptions::RANGE:
            return "RANGE";
        case ImageScalingOptions::STDEV_POSITIVE:
            return "STDEV_POSITIVE";
        case ImageScalingOptions::STDEV_NEGATIVE:
            return "STDEV_NEGATIVE";
        case ImageScalingOptions::STDEV_BOTH:
            return "STDEV_BOTH";
        case ImageScalingOptions::MANUAL:
            return "MANUAL";
        default:
            std::ostringstream os;
            os << "Unrecognized scaling algorithm: " << algorithm;
            throw LSST_EXCEPT(pex::exceptions::InvalidParameterError, os.str());
    }
}

setAllowImageCompression()

void lsst::afw::fits::setAllowImageCompression

(

bool

allow

)

Definition at line 1566 of file fits.cc.

{ allowImageCompression = allow; }

Variable Documentation

DEFAULT_HDU

const int lsst::afw::fits::DEFAULT_HDU = INT_MIN

Specify that the default HDU should be read.

This special HDU number indicates that the first extension should be used if the primary HDU is empty (i.e., has NAXIS=0) and the Primary HDU is the current.

Definition at line 18 of file fitsDefaults.h.