OMETIFFWriter.h

/*
 * #%L
 * OME-FILES C++ library for image IO.
 * Copyright © 2006 - 2014 Open Microscopy Environment:
 *   - Massachusetts Institute of Technology
 *   - National Institutes of Health
 *   - University of Dundee
 *   - Board of Regents of the University of Wisconsin-Madison
 *   - Glencoe Software, Inc.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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 * POSSIBILITY OF SUCH DAMAGE.
 *
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 * #L%
 */

#ifndef OME_FILES_OUT_OMETIFFWRITER_H
#define OME_FILES_OUT_OMETIFFWRITER_H

#include <boost/filesystem/path.hpp>

#include <ome/files/detail/FormatWriter.h>
#include <ome/files/detail/OMETIFF.h>

#include <ome/common/log.h>

#include <ome/xml/meta/OMEXMLMetadata.h>

namespace ome
{
  namespace files
  {
    namespace tiff
    {

      class TIFF;
      class IFD;

    }

    namespace out
    {

      class OMETIFFWriter : public ::ome::files::detail::FormatWriter
      {
      protected:
        ome::common::Logger logger;

        typedef std::map<boost::filesystem::path, std::string> file_uuid_map;

        // In the Java reader, this is uuids + ifdCounts
        struct TIFFState
        {
          std::string uuid;
          std::shared_ptr<ome::files::tiff::TIFF> tiff;
          dimension_size_type ifdCount;

          TIFFState(std::shared_ptr<ome::files::tiff::TIFF>& tiff);

          ~TIFFState();
        };

        typedef std::map<boost::filesystem::path, TIFFState> tiff_map;

        // In the Java reader, this is imageLocations.
        struct SeriesState
        {
          std::vector<detail::OMETIFFPlane> planes;
        };

        typedef std::vector<SeriesState> series_list;

        boost::filesystem::path baseDir;

        file_uuid_map files;

        // Mutable to allow opening TIFFs when const.
        mutable tiff_map tiffs;

        tiff_map::iterator currentTIFF;

        std::string flags;
        
        series_list seriesState;

        std::shared_ptr<::ome::xml::meta::MetadataRetrieve> originalMetadataRetrieve;

        std::shared_ptr<ome::xml::meta::OMEXMLMetadata> omeMeta;

      private:
        boost::optional<bool> bigTIFF;

      public:
        OMETIFFWriter();

        virtual
        ~OMETIFFWriter();

        // Documented in superclass.
        void
        setId(const boost::filesystem::path& id);

        // Documented in superclass.
        void
        close(bool fileOnly = false);

        using FormatWriter::saveBytes;

        // Documented in superclass.
        void
        setSeries(dimension_size_type series) const;

        // Documented in superclass.
        void
        setPlane(dimension_size_type plane) const;

      protected:
        void
        nextIFD() const;

        void
        setupIFD() const;

      public:
        // Documented in superclass.
        void
        saveBytes(dimension_size_type plane,
                  VariantPixelBuffer& buf,
                  dimension_size_type x,
                  dimension_size_type y,
                  dimension_size_type w,
                  dimension_size_type h);

      private:
        void
        fillMetadata();

        std::string
        getOMEXML(const boost::filesystem::path& id);

        void
        saveComment(const boost::filesystem::path& id,
                    const std::string&             xml);

        // Java getUUID unimplemented; see uuid member of TIFFState.

        // Java planeCount() unimplemented; use getImageCount()
        // instead.  Note the java implementation special-cases
        // certain behaviour such as interleaving for certain pixel
        // types; here the caller can specify exactly what they want.

      public:
        void
        setBigTIFF(boost::optional<bool> big = true);

        boost::optional<bool>
        getBigTIFF() const;
      };

    }
  }
}

#endif // OME_FILES_OUT_OMETIFFWRITER_H

/*
 * Local Variables:
 * mode:C++
 * End:
 */