/**
 * Stone of Orthanc
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2020 Osimis S.A., Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Affero General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program 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
 * Affero General Public License for more details.
 * 
 * You should have received a copy of the GNU Affero General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 **/


#include "DicomStructureSetLoader.h"

#include "../Scene2D/PolylineSceneLayer.h"
#include "../StoneException.h"
#include "../Toolbox/GeometryToolbox.h"

#include <Core/Toolbox.h>

#include <algorithm>

namespace OrthancStone
{

#if 0
  void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap)
  {
    using namespace std;
    //ios_base::fmtflags state = o.flags();
    //o.flags(ios::right | ios::hex);
    //o << "(" << setfill('0') << setw(4) << tag.GetGroup()
    //  << "," << setw(4) << tag.GetElement() << ")";
    //o.flags(state);
    Json::Value val;
    dicomMap.Serialize(val);
    o << val;
    //return o;
  }
#endif

  // implementation of IInstanceLookupHandler that uses Orthanc REST API calls to retrive the 
  // geometry of referenced instances
  class DicomStructureSetLoader::RestInstanceLookupHandler : public DicomStructureSetLoader::IInstanceLookupHandler,
    public LoaderStateMachine
  {
  public:
    static boost::shared_ptr<RestInstanceLookupHandler > Create(DicomStructureSetLoader& loader)
    {
      boost::shared_ptr<RestInstanceLookupHandler> obj(new RestInstanceLookupHandler(loader));
      obj->LoaderStateMachine::PostConstructor();
      return obj;
    }

  protected:
    RestInstanceLookupHandler(DicomStructureSetLoader& loader) 
      : LoaderStateMachine(loader.loadersContext_)
      , loader_(loader)
    {
    }

    virtual void RetrieveReferencedSlices(const std::set<std::string>& nonEmptyInstances) ORTHANC_OVERRIDE;

  private:
    // these subclasses hold the loading state
    class AddReferencedInstance;   // 2nd state
    class LookupInstance;          // 1st state

    DicomStructureSetLoader& loader_;
  };

  class DicomStructureSetLoader::RestInstanceLookupHandler::AddReferencedInstance : public LoaderStateMachine::State
  {
  private:
    std::string instanceId_;
      
  public:
    AddReferencedInstance(DicomStructureSetLoader& that,
                          const std::string& instanceId) :
      State(that),
      instanceId_(instanceId)
    {
    }

    virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
    {
      Json::Value tags;
      message.ParseJsonBody(tags);
        
      Orthanc::DicomMap dicom;
      dicom.FromDicomAsJson(tags);

      DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
    
      loader.AddReferencedSlice(dicom);
    }
  };


  // State that converts a "SOP Instance UID" to an Orthanc identifier
  class DicomStructureSetLoader::RestInstanceLookupHandler::LookupInstance : public LoaderStateMachine::State
  {
  private:
    std::string  sopInstanceUid_;
      
  public:
    LookupInstance(DicomStructureSetLoader& that,
                   const std::string& sopInstanceUid) :
      State(that),
      sopInstanceUid_(sopInstanceUid)
    {
    }

    virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
    {
      DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();

      Json::Value lookup;
      message.ParseJsonBody(lookup);

      if (lookup.type() != Json::arrayValue ||
          lookup.size() != 1 ||
          !lookup[0].isMember("Type") ||
          !lookup[0].isMember("Path") ||
          lookup[0]["Type"].type() != Json::stringValue ||
          lookup[0]["ID"].type() != Json::stringValue ||
          lookup[0]["Type"].asString() != "Instance")
      {
        std::stringstream msg;
        msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = ";
        for (OrthancStone::OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin();
             it != message.GetAnswerHeaders().end(); ++it)
        {
          msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n";
        }
        const std::string msgStr = msg.str();
        LOG(ERROR) << msgStr;
        throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);          
      }

      const std::string instanceId = lookup[0]["ID"].asString();

      {
        std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
        command->SetHttpHeader("Accept-Encoding", "gzip");
        std::string uri = "/instances/" + instanceId + "/tags";
        command->SetUri(uri);
        command->AcquirePayload(new AddReferencedInstance(loader, instanceId));
        Schedule(command.release());
      }
    }
  };

  void DicomStructureSetLoader::RestInstanceLookupHandler::RetrieveReferencedSlices(
    const std::set<std::string>& nonEmptyInstances)
  {
    for (std::set<std::string>::const_iterator it = nonEmptyInstances.begin(); 
         it != nonEmptyInstances.end(); 
         ++it)
    {
      std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
      command->SetUri("/tools/lookup");
      command->SetMethod(Orthanc::HttpMethod_Post);
      command->SetBody(*it);
      command->AcquirePayload(new LookupInstance(loader_, *it));
      Schedule(command.release());
    }
  }

  class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State
  {
  public:
    LoadStructure(DicomStructureSetLoader& that) :
    State(that)
    {
    }
    
    virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
    {
      DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();

      // Set the actual structure set content
      {
        OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer());

        loader.content_.reset(new OrthancStone::DicomStructureSet(dicom));
      }

      // initialize visibility flags
      SetDefaultStructureVisibility();

      // retrieve the (non-empty) referenced instances (the CT slices containing the corresponding structures)
      // Some (admittedly invalid) Dicom files have empty values in the 
      // 0008,1155 tag. We try our best to cope with this.
      // this is why we use `nonEmptyInstances` and not `instances`
      std::set<std::string> instances;
      std::set<std::string> nonEmptyInstances;

      // this traverses the polygon collection for all structures and retrieve the SOPInstanceUID of 
      // the referenced instances
      loader.content_->GetReferencedInstances(instances);

      for (std::set<std::string>::const_iterator
        it = instances.begin(); it != instances.end(); ++it)
      {
        std::string instance = Orthanc::Toolbox::StripSpaces(*it);
        if(instance != "")
          nonEmptyInstances.insert(instance);
      }

      loader.RetrieveReferencedSlices(nonEmptyInstances);
    }

    void SetDefaultStructureVisibility()
    {
      DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();

      size_t structureCount = loader.content_->GetStructuresCount();

      loader.structureVisibility_.resize(structureCount);
      bool everythingVisible = false;
      if ((loader.initiallyVisibleStructures_.size() == 1)
          && (loader.initiallyVisibleStructures_[0].size() == 1)
          && (loader.initiallyVisibleStructures_[0][0] == '*'))
      {
        everythingVisible = true;
      }

      for (size_t i = 0; i < structureCount; ++i)
      {
        // if a single "*" string is supplied, this means we want everything 
        // to be visible...
        if (everythingVisible)
        {
          loader.structureVisibility_.at(i) = true;
        }
        else
        {
          // otherwise, we only enable visibility for those structures whose 
          // names are mentioned in the initiallyVisibleStructures_ array
          const std::string& structureName = loader.content_->GetStructureName(i);

          std::vector<std::string>::iterator foundIt =
            std::find(
              loader.initiallyVisibleStructures_.begin(),
              loader.initiallyVisibleStructures_.end(),
              structureName);
          std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end();
          if (foundIt != endIt)
            loader.structureVisibility_.at(i) = true;
          else
            loader.structureVisibility_.at(i) = false;
        }
      }
    }

    private:


  };
    

  class DicomStructureSetLoader::Slice : public IExtractedSlice
  {
  private:
    const OrthancStone::DicomStructureSet&  content_;
    uint64_t                  revision_;
    bool                      isValid_;
    std::vector<bool>         visibility_;
      
  public:
    /**
    The visibility vector must either:
    - be empty
    or
    - contain the same number of items as the number of structures in the 
      structure set.
    In the first case (empty vector), all the structures are displayed.
    In the second case, the visibility of each structure is defined by the 
    content of the vector at the corresponding index.
    */
    Slice(const OrthancStone::DicomStructureSet& content,
          uint64_t revision,
          const OrthancStone::CoordinateSystem3D& cuttingPlane,
          std::vector<bool> visibility = std::vector<bool>()) 
      : content_(content)
      , revision_(revision)
      , visibility_(visibility)
    {
      ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount())
        || (visibility_.size() == 0u));

      bool opposite;

      const OrthancStone::Vector normal = content.GetNormal();
      isValid_ = (
        OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) ||
        OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) ||
        OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY()));
    }
      
    virtual bool IsValid()
    {
      return isValid_;
    }

    virtual uint64_t GetRevision()
    {
      return revision_;
    }

    virtual OrthancStone::ISceneLayer* CreateSceneLayer(
      const OrthancStone::ILayerStyleConfigurator* configurator,
      const OrthancStone::CoordinateSystem3D& cuttingPlane)
    {
      assert(isValid_);

      std::unique_ptr<OrthancStone::PolylineSceneLayer> layer(new OrthancStone::PolylineSceneLayer);
      layer->SetThickness(2);

      for (size_t i = 0; i < content_.GetStructuresCount(); i++)
      {
        if ((visibility_.size() == 0) || visibility_.at(i))
        {
          const OrthancStone::Color& color = content_.GetStructureColor(i);

#ifdef USE_BOOST_UNION_FOR_POLYGONS 
          std::vector< std::vector<OrthancStone::Point2D> > polygons;

          if (content_.ProjectStructure(polygons, i, cuttingPlane))
          {
            for (size_t j = 0; j < polygons.size(); j++)
            {
              PolylineSceneLayer::Chain chain;
              chain.resize(polygons[j].size());

              for (size_t k = 0; k < polygons[j].size(); k++)
              {
                chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y);
    }

              layer->AddChain(chain, true /* closed */, color);
  }
        }
#else
          std::vector< std::pair<OrthancStone::Point2D, OrthancStone::Point2D> > segments;

          if (content_.ProjectStructure(segments, i, cuttingPlane))
          {
            for (size_t j = 0; j < segments.size(); j++)
            {
              OrthancStone::PolylineSceneLayer::Chain chain;
              chain.resize(2);

              chain[0] = OrthancStone::ScenePoint2D(segments[j].first.x, segments[j].first.y);
              chain[1] = OrthancStone::ScenePoint2D(segments[j].second.x, segments[j].second.y);

              layer->AddChain(chain, false /* NOT closed */, color);
            }
          }
#endif        
        }
      }

      return layer.release();
    }
  };
    

  DicomStructureSetLoader::DicomStructureSetLoader(
    OrthancStone::ILoadersContext& loadersContext) 
    : LoaderStateMachine(loadersContext)
    , loadersContext_(loadersContext)
    , revision_(0)
    , countProcessedInstances_(0)
    , countReferencedInstances_(0)
    , structuresReady_(false)
  {
    // the default handler to retrieve slice geometry is RestInstanceLookupHandler
    instanceLookupHandler_ = RestInstanceLookupHandler::Create(*this);
  }
    
  boost::shared_ptr<OrthancStone::DicomStructureSetLoader> DicomStructureSetLoader::Create(OrthancStone::ILoadersContext& loadersContext)
  {
    boost::shared_ptr<DicomStructureSetLoader> obj(
      new DicomStructureSetLoader(
        loadersContext));
    obj->LoaderStateMachine::PostConstructor();
    return obj;
  }

  void DicomStructureSetLoader::AddReferencedSlice(const Orthanc::DicomMap& dicom)
  {
    content_->AddReferencedSlice(dicom);
    countProcessedInstances_ ++;
    assert(countProcessedInstances_ <= countReferencedInstances_);

    revision_++;
    SetStructuresUpdated();

    if (countProcessedInstances_ == countReferencedInstances_)
    {
      // All the referenced instances have been loaded, finalize the RT-STRUCT
      content_->CheckReferencedSlices();
      revision_++;
      SetStructuresReady();
    }
  }

  void DicomStructureSetLoader::RetrieveReferencedSlices(const std::set<std::string>& nonEmptyInstances)
  {
    // we set the number of referenced instances. This allows to know, in the method above, when we're done
    countReferencedInstances_ = static_cast<unsigned int>(nonEmptyInstances.size());
    instanceLookupHandler_->RetrieveReferencedSlices(nonEmptyInstances);
  }

  void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display)
  {
    structureVisibility_.at(structureIndex) = display;
    revision_++;
  }

  DicomStructureSetLoader::~DicomStructureSetLoader()
  {
    LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()";
  }

  void DicomStructureSetLoader::LoadInstance(
    const std::string& instanceId, 
    const std::vector<std::string>& initiallyVisibleStructures)
  {
    Start();
      
    instanceId_ = instanceId;
    initiallyVisibleStructures_ = initiallyVisibleStructures;

    {
      std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
      command->SetHttpHeader("Accept-Encoding", "gzip");

      std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";

      command->SetUri(uri);
      command->AcquirePayload(new LoadStructure(*this));
      Schedule(command.release());
    }
  }

  void DicomStructureSetLoader::LoadInstanceFullVisibility(const std::string& instanceId)
  {
    std::vector<std::string> initiallyVisibleStructures;
    initiallyVisibleStructures.push_back("*"); // wildcard to make all structure sets visible
    LoadInstance(instanceId, initiallyVisibleStructures);
  }

  OrthancStone::IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const OrthancStone::CoordinateSystem3D& cuttingPlane)
  {
    if (content_.get() == NULL)
    {
      // Geometry is not available yet
      return new OrthancStone::IVolumeSlicer::InvalidSlice;
    }
    else
    {
      return new Slice(*content_, revision_, cuttingPlane, structureVisibility_);
    }
  }

  void DicomStructureSetLoader::SetStructuresUpdated()
  {
    BroadcastMessage(DicomStructureSetLoader::StructuresUpdated(*this));
  }

  void DicomStructureSetLoader::SetStructuresReady()
  {
    ORTHANC_ASSERT(!structuresReady_);
    structuresReady_ = true;
    BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this));
  }

  bool DicomStructureSetLoader::AreStructuresReady() const
  {
    return structuresReady_;
  }

}