lsst::afw::image::MaskFitsReader Class Reference

A FITS reader class for Masks. More...

#include <MaskFitsReader.h>

Inheritance diagram for lsst::afw::image::MaskFitsReader:

Public Member Functions
template<typename PixelT >
Mask< PixelT >	read (lsst::geom::Box2I const &bbox=lsst::geom::Box2I(), ImageOrigin origin=PARENT, bool conformMasks=false, bool allowUnsafe=false)
	Read the Mask. More...
	ImageBaseFitsReader (std::string const &fileName, int hdu=fits::DEFAULT_HDU)
	Construct a FITS reader object. More...
	ImageBaseFitsReader (fits::MemFileManager &manager, int hdu=fits::DEFAULT_HDU)
	Construct a FITS reader object. More...
	ImageBaseFitsReader (fits::Fits *fitsFile)
	Construct a FITS reader object. More...
	ImageBaseFitsReader (ImageBaseFitsReader const &)=delete
	ImageBaseFitsReader (ImageBaseFitsReader &&)=delete
std::string	readDType () const
	Read a string describing the pixel type of the on-disk image. More...
lsst::geom::Box2I	readBBox (ImageOrigin origin=PARENT)
	Read the bounding box of the on-disk image. More...
lsst::geom::Point2I	readXY0 (lsst::geom::Box2I const &bbox=lsst::geom::Box2I(), ImageOrigin origin=PARENT)
	Read the image origin from the on-disk image or a subimage thereof. More...
std::shared_ptr< daf::base::PropertyList >	readMetadata ()
	Read the image's FITS header. More...
template<typename T >
ndarray::Array< T, 2, 2 >	readArray (lsst::geom::Box2I const &bbox, ImageOrigin origin=PARENT, bool allowUnsafe=false)
	Read the image's data array. More...
int	getHdu () const noexcept
	Return the HDU this reader targets. More...
std::string	getFileName () const
	Return the name of the file this reader targets. More...

Detailed Description

A FITS reader class for Masks.

Exception Safety

All MaskFitsReader methods provide strong exception safety, but exceptions thrown by the internal fits::Fits object itself may change its status variable or HDU pointer; MaskFitsReader guards against this by resetting those before any use of the Fits object.

Definition at line 39 of file MaskFitsReader.h.

Member Function Documentation

getFileName()

std::string lsst::afw::image::ImageBaseFitsReader::getFileName ( ) const

inlineinherited

Return the name of the file this reader targets.

Definition at line 141 of file ImageBaseFitsReader.h.

{ return _fitsFile->getFileName(); }

getHdu()

int lsst::afw::image::ImageBaseFitsReader::getHdu ( ) const

inlinenoexceptinherited

Return the HDU this reader targets.

Definition at line 136 of file ImageBaseFitsReader.h.

{ return _hdu; }

ImageBaseFitsReader() [1/5]

lsst::afw::image::ImageBaseFitsReader::ImageBaseFitsReader

explicit

Construct a FITS reader object.

Parameters

fitsFile

Pointer to a CFITSIO file object. Lifetime will not be managed by the Reader object.

Definition at line 74 of file ImageBaseFitsReader.cc.

                                                            :
    _ownsFitsFile(false),
    _hdu(0),
    _fitsFile(fitsFile)
{
    if (_fitsFile) {
        if (_fitsFile->getHdu() == 0 && _fitsFile->getImageDim() == 0) {
            _fitsFile->setHdu(fits::DEFAULT_HDU);
        }
        _fitsFile->checkCompressedImagePhu();
        _hdu = _fitsFile->getHdu();
    }
}

ImageBaseFitsReader() [2/5]

lsst::afw::image::ImageBaseFitsReader::ImageBaseFitsReader

explicit

Construct a FITS reader object.

Parameters

manager	Memory block containing a FITS file.
hdu	HDU index, where 0 is the primary HDU and DEFAULT_HDU is the first non-empty HDU.

Definition at line 66 of file ImageBaseFitsReader.cc.

                                                                             :
    _ownsFitsFile(true),
    _hdu(0),
    _fitsFile(new fits::Fits(manager, "r", fits::Fits::AUTO_CLOSE | fits::Fits::AUTO_CHECK))
{
    _fitsFile->setHdu(hdu);
    _fitsFile->checkCompressedImagePhu();
    _hdu = _fitsFile->getHdu();
}

ImageBaseFitsReader() [3/5]

lsst::afw::image::ImageBaseFitsReader::ImageBaseFitsReader

delete

ImageBaseFitsReader() [4/5]

lsst::afw::image::ImageBaseFitsReader::ImageBaseFitsReader

delete

ImageBaseFitsReader() [5/5]

lsst::afw::image::ImageBaseFitsReader::ImageBaseFitsReader

explicit

Construct a FITS reader object.

Parameters

fileName	Name of a file to open.
hdu	HDU index, where 0 is the primary HDU and DEFAULT_HDU is the first non-empty HDU.

Definition at line 57 of file ImageBaseFitsReader.cc.

                                                                           :
    _ownsFitsFile(true),
    _hdu(0),
    _fitsFile(new fits::Fits(fileName, "r", fits::Fits::AUTO_CLOSE | fits::Fits::AUTO_CHECK))
{
    _fitsFile->setHdu(hdu);
    _fitsFile->checkCompressedImagePhu();
    _hdu = _fitsFile->getHdu();
}

read()

template<typename PixelT >

template Mask< MaskPixel > lsst::afw::image::MaskFitsReader::read	(	lsst::geom::Box2I const &	bbox = lsst::geom::Box2I(),
		ImageOrigin	origin = PARENT,
		bool	conformMasks = false,
		bool	allowUnsafe = false
	)

Read the Mask.

Parameters

bbox	A bounding box used to defined a subimage, or an empty box (default) to read the whole image.
origin	Coordinate system convention for the given box.
conformMasks	If True, conform the global mask dict to match this file.
allowUnsafe	Permit reading into the requested pixel type even when on-disk values may overflow or truncate.

In Python, this templated method is wrapped with an additional dtype argument to provide the type to read. This defaults to the type of the on-disk image.

Definition at line 28 of file MaskFitsReader.cc.

                                                    {
    Mask<PixelT> result(readArray<PixelT>(bbox, origin, allowUnsafe), false, readXY0(bbox, origin));
    auto metadata = readMetadata();
    // look for mask planes in the file
    detail::MaskPlaneDict fileMaskDict = Mask<PixelT>::parseMaskPlaneMetadata(metadata);
    std::shared_ptr<detail::MaskDict> fileMD = detail::MaskDict::copyOrGetDefault(fileMaskDict);
    if (*fileMD == *detail::MaskDict::getDefault()) {  // file is already consistent with Mask
        return result;
    }
    if (conformMasks) {  // adopt the definitions in the file
        detail::MaskDict::setDefault(fileMD);
        result._maskDict = fileMD;
    }
    result.conformMaskPlanes(fileMaskDict);  // convert planes defined by fileMaskDict to the order
                                             // defined by Mask::_maskPlaneDict
    return result;
}

readArray()

template<typename T >

template ndarray::Array< std::uint64_t, 2, 2 > lsst::afw::image::ImageBaseFitsReader::readArray ( lsst::geom::Box2I const &  bbox, ImageOrigin  origin = PARENT, bool  allowUnsafe = false  )

inherited

Read the image's data array.

Parameters

bbox	A bounding box used to defined a subimage, or an empty box (default) to read the whole image.
origin	Coordinate system convention for the given box.
allowUnsafe	Permit reading into the requested pixel type even when on-disk values may overflow or truncate.

Definition at line 171 of file ImageBaseFitsReader.cc.

                                                                         {
    checkFitsFile(_fitsFile);
    auto fullBBox = readBBox(origin);
    auto subBBox = bbox;
    if (subBBox.isEmpty()) {
        subBBox = fullBBox;
    } else if (!fullBBox.contains(subBBox)) {
        throw LSST_EXCEPT(
            pex::exceptions::LengthError,
            str(boost::format("Subimage box (%d,%d) %dx%d doesn't fit in image (%d,%d) %dx%d in HDU %d") %
                subBBox.getMinX() % subBBox.getMinY() % subBBox.getWidth() % subBBox.getHeight() %
                fullBBox.getMinX() % fullBBox.getMinY() % fullBBox.getWidth() % fullBBox.getHeight() % _hdu)
        );
    }
    fits::HduMoveGuard guard(*_fitsFile, _hdu);
    if (!allowUnsafe & !_fitsFile->checkImageType<T>()) {
        throw LSST_FITS_EXCEPT(
            fits::FitsTypeError, *_fitsFile,
            str(boost::format("Incompatible type for FITS image: on disk is %s (HDU %d), in-memory is %s. "
                              "Read with allowUnsafe=True to permit conversions that may overflow.") %
                _fitsFile->getImageDType() % _hdu % makeDTypeString<T>())
        );
    }
    ndarray::Array<T, 2, 2> result = ndarray::allocate(subBBox.getHeight(), subBBox.getWidth());
    ndarray::Vector<int, 2> offset = ndarray::makeVector(subBBox.getMinY() - fullBBox.getMinY(),
                                                         subBBox.getMinX() - fullBBox.getMinX());
    _fitsFile->readImage(result, offset);
    return result;
}

readBBox()

lsst::geom::Box2I lsst::afw::image::ImageBaseFitsReader::readBBox ( ImageOrigin  origin = PARENT )

inherited

Read the bounding box of the on-disk image.

Parameters

origin

Coordinate system convention for the returned box. If LOCAL, the returned box will always have a minimum of (0, 0).

Definition at line 86 of file ImageBaseFitsReader.cc.

                                                              {
    readMetadata();  // guarantees _bbox is initialized
    if (origin == LOCAL) {
        return lsst::geom::Box2I(lsst::geom::Point2I(), _bbox.getDimensions());
    }
    return _bbox;
}

readDType()

std::string lsst::afw::image::ImageBaseFitsReader::readDType ( ) const

inherited

Read a string describing the pixel type of the on-disk image.

Returns

A string of the form [u](int|float)<bits> (e.g. "uint16", "float64").

Definition at line 80 of file ImageBaseFitsReader.cc.

                                               {
    checkFitsFile(_fitsFile);
    fits::HduMoveGuard guard(*_fitsFile, _hdu);
    return _fitsFile->getImageDType();
}

readMetadata()

std::shared_ptr< daf::base::PropertyList > lsst::afw::image::ImageBaseFitsReader::readMetadata ( )

inherited

Read the image's FITS header.

Definition at line 105 of file ImageBaseFitsReader.cc.

                                                                     {
    checkFitsFile(_fitsFile);
    if (_metadata == nullptr) {
        fits::HduMoveGuard guard(*_fitsFile, _hdu);
        auto metadata = fits::readMetadata(*_fitsFile, /*strip=*/true);
        // One-use lambda avoids declare-then-initialize; see C++ Core Guidelines, ES28.
        auto computeShape = [this](){
            int nAxis = _fitsFile->getImageDim();
            if (nAxis == 2) {
                return _fitsFile->getImageShape<2>();
            }
            if (nAxis == 3) {
                ndarray::Vector<ndarray::Size, 3> shape3 = _fitsFile->getImageShape<3>();
                if (shape3[0] != 1) {
                    throw LSST_EXCEPT(
                        fits::FitsError,
                        str(boost::format("Error reading %s: HDU %d has 3rd dimension %d != 1") %
                            getFileName() % _hdu % shape3[0]));
                }
                return shape3.last<2>();
            }
            throw LSST_EXCEPT(
                fits::FitsError,
                str(boost::format("Error reading %s: HDU %d has %d dimensions") %
                    getFileName() % _hdu % nAxis)
            );
        };
        // Construct _bbox and check dimensions at the same time both to make
        // one less valid state for this class to be in and to make sure
        // the appropriate metadata is stripped before we ever return it.
        ndarray::Vector<ndarray::Size, 2> shape = computeShape();
        auto xy0 = afw::geom::getImageXY0FromMetadata(*metadata, detail::wcsNameForXY0, /*strip=*/true);
        _bbox = lsst::geom::Box2I(xy0, lsst::geom::Extent2I(shape[1], shape[0]));
        _metadata = std::move(metadata);
    }
    return _metadata;
}

readXY0()

lsst::geom::Point2I lsst::afw::image::ImageBaseFitsReader::readXY0 ( lsst::geom::Box2I const &  bbox = lsst::geom::Box2I(), ImageOrigin  origin = PARENT  )

inherited

Read the image origin from the on-disk image or a subimage thereof.

Parameters

bbox	A bounding box used to defined a subimage, or an empty box (default) to use the whole image.
origin	Coordinate system convention for the given box. Ignored if bbox is empty.

Definition at line 94 of file ImageBaseFitsReader.cc.

                                                                                           {
    if (bbox.isEmpty()) {
        return readBBox().getMin();
    } else if (origin == PARENT) {
        return bbox.getMin();
    } else {
        auto full = readBBox();
        return full.getMin() + lsst::geom::Extent2I(bbox.getMin());
    }
}

---

The documentation for this class was generated from the following files:

• /j/snowflake/release/lsstsw/stack/lsst-scipipe-0.7.0/Linux64/afw/22.0.1-42-gca6935d93+ba5e5ca3eb/include/lsst/afw/image/MaskFitsReader.h
• /j/snowflake/release/lsstsw/stack/lsst-scipipe-0.7.0/Linux64/afw/22.0.1-42-gca6935d93+ba5e5ca3eb/src/image/MaskFitsReader.cc