OMETIFFReader.h

/*
 * #%L
 * OME-BIOFORMATS C++ library for image IO.
 * Copyright © 2015 - 2016 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.
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#ifndef OME_BIOFORMATS_IN_OMETIFFREADER_H
#define OME_BIOFORMATS_IN_OMETIFFREADER_H

#include <ome/bioformats/in/MinimalTIFFReader.h>
#include <ome/bioformats/tiff/ImageJMetadata.h>

#include <ome/common/log.h>

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

namespace ome
{

  namespace xml
  {
    namespace meta
    {
      class OMEXMLMetadata;
    }
  }

  namespace bioformats
  {
    namespace in
    {

      class OMETIFFReader : public ::ome::bioformats::detail::FormatReader
      {
        using detail::FormatReader::isThisType;
        using ::ome::bioformats::FormatReader::getOptimalTileWidth;
        using ::ome::bioformats::FormatReader::getOptimalTileHeight;

      protected:
        ome::common::Logger logger;

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

        typedef std::map<boost::filesystem::path, boost::filesystem::path> invalid_file_map;

        typedef std::map<boost::filesystem::path, ome::compat::shared_ptr<ome::bioformats::tiff::TIFF> > tiff_map;

        uuid_file_map files;

        invalid_file_map invalidFiles;

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

        boost::filesystem::path metadataFile;

        std::vector<boost::filesystem::path> usedFiles;

        bool hasSPW;

      public:
        OMETIFFReader();

        virtual
        ~OMETIFFReader();

        // Documented in superclass.
        bool
        isSingleFile(const boost::filesystem::path& id) const;

        // Documented in superclass.
        bool
        isThisType(const boost::filesystem::path& name,
                   bool                           open) const;

      protected:
        // Documented in superclass.
        bool
        isFilenameThisTypeImpl(const boost::filesystem::path& name) const;

        // Documented in superclass.
        void
        getLookupTable(dimension_size_type plane,
                       VariantPixelBuffer& buf) const;

        // Documented in superclass.
        void
        openBytesImpl(dimension_size_type plane,
                      VariantPixelBuffer& buf,
                      dimension_size_type x,
                      dimension_size_type y,
                      dimension_size_type w,
                      dimension_size_type h) const;

        const ome::compat::shared_ptr<const tiff::IFD>
        ifdAtIndex(dimension_size_type plane) const;

        void
        addTIFF(const boost::filesystem::path& tiff);

        const ome::compat::shared_ptr<const ome::bioformats::tiff::TIFF>
        getTIFF(const boost::filesystem::path& tiff) const;

        void
        closeTIFF(const boost::filesystem::path& tiff);

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

        const std::vector<std::string>&
        getDomains() const;

        // Documented in superclass.
        const std::vector<boost::filesystem::path>
        getSeriesUsedFiles(bool noPixels) const;

        // Documented in superclass.
        FormatReader::FileGroupOption
        fileGroupOption(const std::string& id);

        // Documented in superclass.
        dimension_size_type
        getOptimalTileWidth(dimension_size_type channel) const;

        // Documented in superclass.
        dimension_size_type
        getOptimalTileHeight(dimension_size_type channel) const;

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

      private:
        void
        findUsedFiles(const ome::xml::meta::OMEXMLMetadata& meta,
                      const boost::filesystem::path&        currentId,
                      const boost::filesystem::path&        currentDir,
                      const boost::optional<std::string>&   currentUUID);

        void
        getAcquisitionDates(const ome::xml::meta::OMEXMLMetadata&                                  meta,
                            std::vector<boost::optional<ome::xml::model::primitives::Timestamp> >& timestamps);

        void
        cleanMetadata(ome::xml::meta::OMEXMLMetadata& meta);

        dimension_size_type
        seriesFileSamplesPerPixel(const ome::xml::meta::OMEXMLMetadata&    meta,
                                  ome::xml::meta::BaseMetadata::index_type series);

        void
        seriesIndexStart(const ome::xml::meta::OMEXMLMetadata&                             meta,
                         ome::xml::meta::BaseMetadata::index_type                          series,
                         boost::optional<ome::xml::model::primitives::NonNegativeInteger>& zIndexStart,
                         boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tIndexStart,
                         boost::optional<ome::xml::model::primitives::NonNegativeInteger>& cIndexStart);

        bool
        getTiffDataValues(const ome::xml::meta::OMEXMLMetadata&                             meta,
                          ome::xml::meta::BaseMetadata::index_type                          series,
                          ome::xml::meta::BaseMetadata::index_type                          tiffData,
                          boost::optional<ome::xml::model::primitives::NonNegativeInteger>& tdIFD,
                          ome::xml::model::primitives::NonNegativeInteger&                  numPlanes,
                          ome::xml::model::primitives::NonNegativeInteger&                  firstZ,
                          ome::xml::model::primitives::NonNegativeInteger&                  firstT,
                          ome::xml::model::primitives::NonNegativeInteger&                  firstC);

        void
        fixOMEROMetadata(ome::xml::meta::OMEXMLMetadata&          meta,
                         ome::xml::meta::BaseMetadata::index_type series);

        void
        fixDimensions(ome::xml::meta::BaseMetadata::index_type series);

      public:
        ome::compat::shared_ptr< ome::xml::meta::MetadataStore>
        getMetadataStoreForConversion();

        ome::compat::shared_ptr< ome::xml::meta::MetadataStore>
        getMetadataStoreForDisplay();
      };


    }
  }
}

#endif // OME_BIOFORMATS_IN_OMETIFFREADER_H

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