mitkMultiLabelIOHelper.h

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/*============================================================================
 
The Medical Imaging Interaction Toolkit (MITK)
 
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
 
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
 
============================================================================*/
 
#ifndef mitkMultiLabelIOHelper_h
#define mitkMultiLabelIOHelper_h
 
#include <mitkLabel.h>
 
#include <mitkLabelSetImage.h>
 
#include <itkSmartPointer.h>
#include <nlohmann/json.hpp>
 
#include <MitkMultilabelExports.h>
 
namespace tinyxml2
{
  class XMLDocument;
  class XMLElement;
}
 
namespace itk
{
  class MetaDataDictionary;
}
 
namespace mitk
{
  const constexpr char* const PROPERTY_NAME_TIMEGEOMETRY_TYPE = "org.mitk.timegeometry.type";
  const constexpr char* const PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS = "org.mitk.timegeometry.timepoints";
  const constexpr char* const PROPERTY_KEY_TIMEGEOMETRY_TYPE = "org_mitk_timegeometry_type";
  const constexpr char* const PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS = "org_mitk_timegeometry_timepoints";
  const constexpr char* const PROPERTY_KEY_UID = "org_mitk_uid";
 
  class MITKMULTILABEL_EXPORT MultiLabelIOHelper
  {
  public:
    static bool SaveMultiLabelSegmentationPreset(const std::string &presetFilename,
                                        const mitk::MultiLabelSegmentation *inputSegmentation);
 
    static bool LoadMultiLabelSegmentationPreset(const std::string &presetFilename,
                                        mitk::MultiLabelSegmentation *inputSegmentation);
 
    static itk::SmartPointer<mitk::Label> LoadLabelFromXMLDocument(const tinyxml2::XMLElement *labelElem);
 
    static tinyxml2::XMLElement *GetLabelAsXMLElement(tinyxml2::XMLDocument &doc, const Label *label);
 
    static tinyxml2::XMLElement *PropertyToXMLElement(tinyxml2::XMLDocument& doc, const std::string &key, const BaseProperty *property);
 
    static bool PropertyFromXMLElement(std::string &key, itk::SmartPointer<mitk::BaseProperty> &prop, const tinyxml2::XMLElement *elem);
 
    static int GetIntByKey(const itk::MetaDataDictionary& dic, const std::string& key);
    static std::string GetStringByKey(const itk::MetaDataDictionary& dic, const std::string& key);
 
    struct MITKMULTILABEL_EXPORT LabelGroupMetaData
    {
      std::string name;
      LabelVector labels;
      PropertyList::Pointer properties; // For custom group properties
 
      LabelGroupMetaData();
      LabelGroupMetaData(const std::string& groupName, const LabelVector& groupLabels);
      LabelGroupMetaData(const std::string& groupName, const LabelVector& groupLabels, PropertyList* groupProperties);
      ~LabelGroupMetaData() = default;
    };
 
 
    using GroupFileNameCallback = std::function<std::string(const mitk::MultiLabelSegmentation*, mitk::MultiLabelSegmentation::GroupIndexType)>;
    using LabelFileNameCallback = std::function<std::string(const mitk::MultiLabelSegmentation*, mitk::MultiLabelSegmentation::LabelValueType)>;
    using LabelFileValueCallback = std::function<mitk::MultiLabelSegmentation::LabelValueType(const mitk::MultiLabelSegmentation*, mitk::MultiLabelSegmentation::LabelValueType)>;
 
    static nlohmann::json SerializeMultLabelGroupsToJSON(const mitk::MultiLabelSegmentation* inputSegmentation,
      GroupFileNameCallback groupFileNameCallback = nullptr ,
      LabelFileNameCallback labelFileNameCallback = nullptr,
      LabelFileValueCallback labelFileValueCallback = nullptr);
 
    static std::vector<LabelGroupMetaData> DeserializeMultiLabelGroupsFromJSON(const nlohmann::json& listOfLabelGroups);
 
    static nlohmann::json SerializeLabelToJSON(const Label* label);
 
    static mitk::Label::Pointer DeserializeLabelFromJSON(const nlohmann::json& labelJson);
 
    static nlohmann::json SerializeLabelPropertyToJSON(const BaseProperty* property);
 
    template<typename TValueType>
    static bool GetValueFromJson(const nlohmann::json& labelJson, const std::string& key, TValueType& value)
    {
      if (labelJson.find(key) != labelJson.end())
      {
        try
        {
          value = labelJson[key].get<TValueType>();
          return true;
        }
        catch (...)
        {
          MITK_ERROR << "Unable to read label information from json. Value has wrong type. Failed key: " << key << "; invalid value: " << labelJson[key].dump();
          throw;
        }
      }
      return false;
    }
 
    static void RemoveMetaPropertiesFromLabel(Label* label);
 
    static LabelVector CloneLabelsWithoutMetaProperties(const LabelVector& labels);
 
  private:
    MultiLabelIOHelper() = delete;
  };
}
 
#endif