ImageFITSConverter.h

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//# ImageFITSConverter.h: Interconvert between Casacore Images and FITS files
//# Copyright (C) 1996,1999,2001,2002
//# Associated Universities, Inc. Washington DC, USA.
//#
//# This library is free software; you can redistribute it and/or modify it
//# under the terms of the GNU Library General Public License as published by
//# the Free Software Foundation; either version 2 of the License, or (at your
//# option) any later version.
//#
//# This library is distributed in the hope that it will be useful, but WITHOUT
//# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
//# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Library General Public
//# License for more details.
//#
//# You should have received a copy of the GNU Library General Public License
//# along with this library; if not, write to the Free Software Foundation,
//# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
//#
//# Correspondence concerning AIPS++ should be addressed as follows:
//#        Internet email: casa-feedback@nrao.edu.
//#        Postal address: AIPS++ Project Office
//#                        National Radio Astronomy Observatory
//#                        520 Edgemont Road
//#                        Charlottesville, VA 22903-2475 USA
 
 
#ifndef IMAGES_IMAGEFITSCONVERTER_H
#define IMAGES_IMAGEFITSCONVERTER_H
 
#include <casacore/casa/aips.h>
#include <casacore/fits/FITS/fits.h>
#include <casacore/casa/Arrays/ArrayFwd.h>
#include <casacore/casa/Arrays/IPosition.h>
#include <casacore/casa/BasicSL/String.h>
#include <casacore/casa/Utilities/DataType.h>
#include <memory>
 
 
#ifndef WCSLIB_GETWCSTAB
#define WCSLIB_GETWCSTAB
#endif
 
namespace casacore { //# NAMESPACE CASACORE - BEGIN
 
  template<class T> class PagedImage;
  template<class T> class ImageInterface;
  class FitsOutput;
  class File;
  class ImageInfo;
  class CoordinateSystem;
  class RecordInterface;
  class TableRecord;
  class LogIO;
  class Unit;
  class LoggerHolder;
  class ConstFitsKeywordList;
  class FitsInput;
 
  // <summary>
  // Struct holding information derived from the image and its header
  // </summary>
  // <synopsis>
  // This is a helper struct to pass information from ImageHeaderToFITS
  // to ImageToFITSOut.
  // </synopsis>
  struct ImageFITSHeaderInfo {
    Bool applyMask;
    Bool needNonOptimalCursor;
    Bool hasBlanks;
    Double bzero;
    Double bscale;
    Short minshort;
    Short maxshort;
    double minPix;
    double maxPix;
    IPosition newShape;
    IPosition cursorOrder;
    FitsKeywordList kw;
    std::shared_ptr<Array<Bool>> pMask;
  };
 
 
  // <summary>
  // Interconvert between Casacore Images and FITS files.
  // </summary>
 
  // <use visibility=export>
 
  // <reviewed reviewer="" date="yyyy/mm/dd" tests="" demos="">
  // </reviewed>
 
  // <prerequisite>
  // <li> <linkto class="PagedImage">PagedImage</linkto>
  // <li> <linkto class="PrimaryArray">PrimaryArray</linkto> (and FITS concepts in
  //      general).
  // </prerequisite>
  //
  // <synopsis>
  // This class is a helper class that is used to interconvert between Casacore
  // images and FITS files. This adds no functionality over the general abilities
  // available in the underlying FITS classes, however it is a useful higher-level
  // packaging.
  //
  // There are two fundamental member functions in this class.
  // <src>FITSToImage</src> which turns a FITS file into a Casacore image, and
  // <src>ImageToFITS</src> which does the opposite.
  //
  // We can read images from any HDU inside the FITS file (although this isn't
  // well tested). Images with a quality axis (i.e. contain data and error values)
  // are stored in the primary HDU (data) and an extension HDU (error). Other
  // images are always written to the primary HDU.
  //
  // Pixels in the FITS file which are blanked are masked out (the mask
  // is set to False) in the output image.   On conversion to FITS,
  // masked values are blanked.    The mask which is read is the current
  // default mask.
  // </synopsis>
  //
  // <example>
  // A FITS to image conversion may be accomplished as follows:
  // <srcBlock>
  //    PagedImage<Float> *image = 0;
  //    String fitsName = "exists.fits";
  //    String imageName = "new.image";
  //    String error;
  //    Bool ok = ImageFITSConverter::FITSToImage(image, error, imageName, fitsName);
  //    if (!image) ... error ...
  // </srcBlock>
  // A couple of things to note:
  // <ul>
  //    <li> If <src>ok</src> is False, the conversion failed and <src>error</src>
  //         will be set.
  //    <li> The pointer "image" is set if the conversion succeeds. If it is
  //         zero the conversion failed and <src>error</src> will contain an
  //         error message.
  //    <li> The caller is responsible for deleting the pointer <src>image</src>
  //         when the conversion is successful.
  // </ul>
  // Similarly, an image to FITS conversion may be accomplished as follows:
  // <srcBlock>
  //    String imageName = argv[1];
  //    PagedImage<Float> image = ...; // An existing image from somewhere
  //    String fitsName = "new.fits";
  //    String error;
  //    Bool ok = ImageFITSConverter::ImageToFITS(error, image, fitsName);
  // </srcBlock>
  // A couple of similar remarks can be made about this example:
  // <ul>
  //    <li> If <src>ok</src> is False, the conversion failed and <src>error</src>
  //         will be set.
  // </ul>
  // </example>
  //
  // <motivation>
  // FITS files are the fundamental transport format for images in Astronomy.
  // </motivation>
  //
  // <todo asof="1999/02/15">
  //   <li> It might be useful to have functions that convert between FITS
  //        and general lattices.
  //   <li> Add support for PagedImage<Complex>
  //   <li> Convert multiple images at once?
  //   <li> Allow writing FITS files to an image extension in an existing
  //        FITS file.
  // </todo>
 
  class ImageFITSConverter
  {
  public:
    const static String CASAMBM;
 
    // Convert a FITS file to a Casacore image.
    // <ul>
    //   <li> <src>newImage</src> will be zero if the conversion fail. If the 
    //        conversion succeeds, the caller is responsible for deleting this
    //        pointer.
    //   <li> <src>error</src> will be set if the conversion fails.
    //   <li> If <src>imageName</src> is empty, a TempImage will be created,
    //        otherwise a PagedImage on disk.
    //   <li> <src>fitsName</src> must already exist (and have an image at the
    //        indicated HDU).
    //   <li> <src>whichRep</src> Zero-relative coordinate representation
    //        (Starting with wcs FITS multiple coordinate representations
    //         can be stored in a FITS file)
    //   <li> <src>whichHDU</src> Zero-relative hdu. The default is correct for
    //        a primary array, set it for an image extension. A value of -1
    //        makes the code look for the first readable HDU.
    //   <li> <src>memoryInMB</src>. Setting this to zero will result in
    //        row-by-row copying, otherwise it will attempt to with as large
    //        a chunk-size as possible, while fitting in the desired memory.
    //   <li> <src>allowOverwrite</src> If True, allow imageName to be 
    //        overwritten if it already exists.
    //   <li> <src>zeroBlanks</src> If True, allow any blanked pixels are set
    //         to zero rather than NaN
    // </ul>
    static Bool FITSToImage(ImageInterface<Float>*& newImage,
                String &error,
                const String &imageName,
                const String &fitsName, 
                uInt whichRep = 0,
                Int whichHDU = 0,
                uInt memoryInMB = 64,
                Bool allowOverwrite=False,
                            Bool zeroBlanks=False);
 
    // Convert a Casacore image to a FITS file.
    // <ul>
    //   <li> <src>return</src> True if the conversion succeeds, False 
    //        otherwise.
    //   <li> <src>error</src> will be set if the conversion fails.
    //   <li> <src>image</src> The image to convert.
    //   <li> <src>fitsName</src> If the name is "-" (the minus character), 
    //        then write to stdout Always writes to the primary array.
    //   <li> <src>memoryInMB</src>. Setting this to zero will result in
    //        row-by-row copying, otherwise it will attempt to with as large
    //        a chunk-size as possible, while fitting in the desired memory.
    //   <li> <src>preferVelocity</src>Write a velocity primary spectral axis
    //        if possible.
    //   <li> <src>opticalVelocity</src>If writing a velocity, use the optical
    //        definition (otherwise use radio).
    //   <li> <src>BITPIX, minPix, maxPix</src>
    //        BITPIX can presently be set to -32 or 16 only. When BITPIX is
    //        16 it will write BSCALE and BZERO into the FITS file. If minPix
    //        is greater than maxPix the minimum and maximum pixel values
    //        will be determined from the array, otherwise the supplied
    //        values will be used and pixels outside that range will be
    //        truncated to the minimum and maximum pixel values (note that
    //        this truncation does not occur for BITPIX=-32).
    //   <li> <src>allowOverwrite</src> If True, allow fitsName to be 
    //        overwritten if it already exists.
    //   <li> <src>degenerateLast</src> If True, axes of length 1 will be written
    //        last to the header.
    //   <li> <src>preferWavelength</src> If True, write a wavelength primary axis.
    //   <li> <src>airWavelength</src> If True and <src>preferWavelength</src> is True write
    //        an air wavelength primary axis.
    //   <li> <src>origin</src> gives the origin, i.e., the name of the package.
    //        If empty, it defaults to "casacore-"getVersion().
    //   </ul>
    // <group>
    static Bool ImageToFITS(String &error,
                            ImageInterface<Float> &image,
                            const String &fitsName,
                            uInt memoryInMB = 64,
                            Bool preferVelocity = True,
                            Bool opticalVelocity = True,
                            Int BITPIX=-32,
                            Float minPix = 1.0, Float maxPix = -1.0,
                            Bool allowOverwrite=False,
                            Bool degenerateLast=False,
                            Bool verbose=True,
                            Bool stokesLast=False,
                            Bool preferWavelength=False,
                            Bool airWavelength=False,
                            const String& origin = String(),
                            Bool history=True);
    static Bool ImageHeaderToFITS(String &error,
                                  ImageFITSHeaderInfo& fhi,
                                  const ImageInterface<Float> &image,
                                  Bool preferVelocity = True,
                                  Bool opticalVelocity = True,
                                  Int BITPIX=-32,
                                  Float minPix = 1.0, Float maxPix = -1.0,
                                  Bool degenerateLast=False,
                                  Bool verbose=True,
                                  Bool stokesLast=False,
                                  Bool preferWavelength=False,
                                  Bool airWavelength=False,
                                  Bool primHead = True,
                                  Bool allowAppend = True,
                                  const String& origin = String(),
                                  Bool history=True);
    // </group>
 
    // Helper function - used to calculate a cursor appropriate for the
    // desired memory use. It's not intended that application programmers
    // call this, but you may if it's useful to you.
    static IPosition copyCursorShape(String &report,
                     const IPosition &shape, 
                     uInt imagePixelSize,
                     uInt fitsPixelSize,
                     uInt memoryInMB);
 
    // Recover CoordinateSystem from header.
    // Used keywords are removed from header and the unused ones returned
    // in a Record for ease of use.
    // Degenerate axes may be added to shape if needed.
    static CoordinateSystem getCoordinateSystem (Int& imageType,
                                                 RecordInterface& headerRec,
                                                 const Vector<String>& header,
                                                 LogIO& os, uInt whichRep,
                                                 IPosition& shape,
                                                 Bool dropStokes);
 
    // Recover ImageInfo from header. Used keywords are removed from header
    static ImageInfo getImageInfo (RecordInterface& header);
 
    // Recover brightness unit from header.
    // Used keywords are removed from header.
    static Unit getBrightnessUnit (RecordInterface& header, LogIO& os);
 
    // Recover history from FITS file keyword list into logger.
    static void restoreHistory (LoggerHolder& logger,
                                ConstFitsKeywordList& kw);
                   
    // Parse header record and set MiscInfo
    static Bool extractMiscInfo (RecordInterface& miscInfo,
                                 const RecordInterface& header);
 
    // Read the BEAMS table if present and add the restoring beams to
    // <src>info</src>.
    static void readBeamsTable (ImageInfo& info, const String& filename,
                                const DataType type);
 
  private:
 
    // Put a CASA image to an opened FITS image
    // Parameters as in "ImageToFITS". In addition:
    // <ul>
    //   <li> <src>output</src> The FITS output to write to.
    //   <li> <src>primHead</src> Write to a primary HDU.
    //   <li> <src>allowAppend</src> Allow to append extension HDU's.
    // </ul>
    static Bool ImageToFITSOut (String &error, LogIO &os,
                                const ImageInterface<Float> &image,
                                FitsOutput *output, uInt memoryInMB = 64,
                                Bool preferVelocity = True,
                                Bool opticalVelocity = True,
                                Int BITPIX=-32,
                                Float minPix = 1.0, Float maxPix = -1.0,
                                Bool degenerateLast=False,
                                Bool verbose=True,
                                Bool stokesLast=False,
                                Bool preferWavelength=False,
                                Bool airWavelength=False,
                                Bool primHead=True,
                                Bool allowAppend=False,
                                const String& origin = String(),
                                Bool history=True);
 
    // Put a CASA image with quality coordinate
    // to an opened FITS file
    // Parameters as in "ImageToFITS". In addition:
    // <ul>
    //   <li> <src>output</src> The FITS output to write to.
    // </ul>
    static Bool QualImgToFITSOut (String &error,
                                  LogIO &os,
                                  ImageInterface<Float> &image,
                                  FitsOutput *outfile,
                                  uInt memoryInMB,
                                  Bool preferVelocity,
                                  Bool opticalVelocity,
                                  Int BITPIX, Float minPix, Float maxPix,
                                  Bool degenerateLast,
                                  Bool verbose, Bool stokesLast,
                                  Bool preferWavelength,
                                  Bool airWavelength,
                                  const String& origin,
                                  Bool history);
 
    // If existing, remove the file, symlink, or directory given by
    // <src>outFile</src>. It is only removed if allowOverwrite=True.
    // An exception (using argument outName) is thrown if the file could
    // not be removed.
    static Bool removeFile (String& error, const File& outFile,
                            const String& outName, Bool allowOverwrite);
 
    // Create an open FITS file with the name given
    static Bool openFitsOutput (String &error, FitsOutput *(&openFitsOutput),
                                const String &fitsName,
                                const Bool &allowOverwrite);
 
 
    static void _writeBeamsTable (FitsOutput *const &outfile,
                                  const ImageInfo& info);
 
  };
 
 
  // <summary>
  // This class is an internal class for ImageFITSConverter.
  // </summary>
 
  // <use visibility=local>
 
  // <synopsis>
  // This class is an internal class used to implement 
  // ImageFitsConverter::FITSToImage - in particular, it has the code which
  // is dependent on the various types (BITPIX values).
  // </synopsis>
  template<class HDUType> class ImageFITSConverterImpl
  {
  public:
    static void FITSToImage(ImageInterface<Float> *&newImage,
                            String &error,
                            const String &newImageName,
                            const uInt whichRep,
                            HDUType &fitsImage,
                            const String& fitsFilename,
                            const DataType dataType,
                            const uInt memoryInMB = 64,
                            const Bool zeroBlanks=False);
  };
 
 
} //# NAMESPACE CASACORE - END
 
#ifndef CASACORE_NO_AUTO_TEMPLATES
#include <casacore/images/Images/ImageFITSConverter.tcc>
#endif //# CASACORE_NO_AUTO_TEMPLATES
 
#endif