MetadataTools.h

/*
 * #%L
 * OME-BIOFORMATS C++ library for image IO.
 * Copyright © 2006 - 2015 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
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * The views and conclusions contained in the software and documentation are
 * those of the authors and should not be interpreted as representing official
 * policies, either expressed or implied, of any organization.
 * #L%
 */

#include <string>

#include <ome/bioformats/FormatReader.h>
#include <ome/bioformats/Types.h>

#include <ome/common/filesystem.h>

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

#include <ome/xml/model/enums/DimensionOrder.h>

#ifndef OME_BIOFORMATS_METADATATOOLS_H
#define OME_BIOFORMATS_METADATATOOLS_H

namespace ome
{
  namespace bioformats
  {

    // Use overloaded functions for creating identifiers since
    // pre-C++11 compilers don't support the C99 stdarg interface.

    std::string
    createID(std::string const&  type,
             dimension_size_type idx);

    std::string
    createID(std::string const&  type,
             dimension_size_type idx1,
             dimension_size_type idx2);

    std::string
    createID(std::string const&  type,
             dimension_size_type idx1,
             dimension_size_type idx2,
             dimension_size_type idx3);

    std::string
    createID(std::string const&  type,
             dimension_size_type idx1,
             dimension_size_type idx2,
             dimension_size_type idx3,
             dimension_size_type idx4);

    ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
    createOMEXMLMetadata(ome::common::xml::dom::Document& document);

    ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
    createOMEXMLMetadata(const boost::filesystem::path& file);

    ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
    createOMEXMLMetadata(const std::string& text);

    ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
    createOMEXMLMetadata(std::istream& stream);

    ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
    createOMEXMLMetadata(const FormatReader& reader,
                         bool                doPlane = false,
                         bool                doImageName = true);


    ome::compat::shared_ptr< ::ome::xml::meta::MetadataRoot>
    createOMEXMLRoot(const std::string& document);

    ome::compat::shared_ptr< ::ome::xml::meta::OMEXMLMetadata>
    getOMEXMLMetadata(ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>& retrieve);

    std::string
    getOMEXML(::ome::xml::meta::OMEXMLMetadata& omexml,
              bool                              validate = true);

    bool
    validateOMEXML(const std::string& document);

    void
    fillMetadata(::ome::xml::meta::MetadataStore& store,
                 const FormatReader&              reader,
                 bool                             doPlane = false,
                 bool                             doImageName = true);

    void
    fillMetadata(::ome::xml::meta::MetadataStore&                          store,
                 const std::vector<ome::compat::shared_ptr<CoreMetadata> > seriesList,
                 bool                                                      doPlane = false);

    void
    fillAllPixels(::ome::xml::meta::MetadataStore& store,
                  const FormatReader&              reader);

    void
    fillPixels(::ome::xml::meta::MetadataStore& store,
               const FormatReader&              reader);

    void
    fillPixels(::ome::xml::meta::MetadataStore& store,
               const CoreMetadata&              seriesMetadata,
               dimension_size_type              series);

    void
    addMetadataOnly(::ome::xml::meta::OMEXMLMetadata& omexml,
                    dimension_size_type               series,
                    bool                              resolve = true);

    Modulo
    getModuloAlongZ(const ::ome::xml::meta::OMEXMLMetadata& omexml,
                    dimension_size_type                     image);

    Modulo
    getModuloAlongT(const ::ome::xml::meta::OMEXMLMetadata& omexml,
                    dimension_size_type                     image);

    Modulo
    getModuloAlongC(const ::ome::xml::meta::OMEXMLMetadata& omexml,
                    dimension_size_type                     image);

    Modulo
    getModulo(const ::ome::xml::meta::OMEXMLMetadata& omexml,
              const std::string&                      tag,
              dimension_size_type                     image);

    void
    verifyMinimum(::ome::xml::meta::MetadataRetrieve& retrieve,
                  dimension_size_type                 series = 0U);

    void
    removeBinData(::ome::xml::meta::OMEXMLMetadata& omexml);

    void
    removeChannels(::ome::xml::meta::OMEXMLMetadata& omexml,
                   dimension_size_type               image,
                   dimension_size_type               sizeC);

    MetadataMap
    getOriginalMetadata(::ome::xml::meta::OMEXMLMetadata& omexml);

    void
    fillOriginalMetadata(::ome::xml::meta::OMEXMLMetadata& omexml,
                         const MetadataMap&                metadata);

    bool
    defaultCreationDateEnabled();

    std::string
    getModelVersion();

    std::string
    getModelVersion(ome::common::xml::dom::Document& document);

    std::string
    getModelVersion(const std::string& document);

    std::string
    transformToLatestModelVersion(const std::string& document);

    void
    defaultCreationDateEnabled(bool enabled);

    void
    setDefaultCreationDate(::ome::xml::meta::MetadataStore& store,
                           dimension_size_type              series,
                           const boost::filesystem::path&   id);

    ome::xml::model::enums::DimensionOrder
    createDimensionOrder(const std::string& order);

    storage_size_type
    pixelSize(const ::ome::xml::meta::MetadataRetrieve& meta,
              dimension_size_type                       series);

    storage_size_type
    pixelSize(const ::ome::xml::meta::MetadataRetrieve& meta);


    storage_size_type
    significantPixelSize(const ::ome::xml::meta::MetadataRetrieve& meta,
                         dimension_size_type                       series);

    storage_size_type
    significantPixelSize(const ::ome::xml::meta::MetadataRetrieve& meta);

  }
}

#endif // OME_BIOFORMATS_METADATATOOLS_H

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