/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2013 Medical Physics Department, CHU of Liege,
 * Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * In addition, as a special exception, the copyright holders of this
 * program give permission to link the code of its release with the
 * OpenSSL project's "OpenSSL" library (or with modified versions of it
 * that use the same license as the "OpenSSL" library), and distribute
 * the linked executables. You must obey the GNU General Public License
 * in all respects for all of the code used other than "OpenSSL". If you
 * modify file(s) with this exception, you may extend this exception to
 * your version of the file(s), but you are not obligated to do so. If
 * you do not wish to do so, delete this exception statement from your
 * version. If you delete this exception statement from all source files
 * in the program, then also delete it here.
 * 
 * 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
 * General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 **/


#include "RadiotherapyRestApi.h"

#include "ServerToolbox.h"

#define RETRIEVE_CONTEXT(call)                          \
  OrthancRestApi& contextApi =                          \
    dynamic_cast<OrthancRestApi&>(call.GetContext());   \
  ServerContext& context = contextApi.GetContext()


// DICOM tags for RT-STRUCT

#define REFERENCED_STUDY_SEQUENCE "0008,1110"
#define REFERENCED_SOP_INSTANCE_UID "0008,1155"
#define FRAME_OF_REFERENCE_UID "0020,0052"
#define REFERENCED_FRAME_OF_REFERENCE_SEQUENCE "3006,0010"
#define STRUCTURE_SET_ROI_SEQUENCE "3006,0020"
#define ROI_NUMBER "3006,0022"
#define ROI_NAME "3006,0026"
#define ROI_GENERATION_ALGORITHM "3006,0036"
#define ROI_CONTOUR_SEQUENCE "3006,0039"
#define REFERENCED_ROI_NUMBER "3006,0084"
#define ROI_DISPLAY_COLOR "3006,002a"
#define CONTOUR_SEQUENCE "3006,0040"
#define CONTOUR_IMAGE_SEQUENCE "3006,0016"
#define CONTOUR_GEOMETRIC_TYPE "3006,0042"
#define NUMBER_OF_CONTOUR_POINTS "3006,0046"
#define CONTOUR_DATA "3006,0050"
#define CONTOUR_SLAB_THICKNESS "3006,0044"


namespace Orthanc
{
  static bool CheckSeriesModality(Json::Value& study,
                                  Json::Value& series,
                                  Json::Value& content,
                                  ServerContext& context,
                                  const std::string& seriesId,
                                  const std::string& modality)
  {
    if (!context.GetIndex().LookupResource(series, seriesId, ResourceType_Series))
    {
      return false;
    }

    // Retrieve the parent study
    std::string studyId = series["ParentStudy"].asString();
    if (!context.GetIndex().LookupResource(study, studyId, ResourceType_Study))
    {
      return false;
    }

    // Check the modality and that there is a single instance inside the series
    if (!series["MainDicomTags"].isMember("Modality") ||
        series["MainDicomTags"]["Modality"].asString() != modality ||
        series["Instances"].size() != 1)
    {
      return false;
    }

    // Retrieve the instance data
    std::string instanceId = series["Instances"][0].asString();

    Json::Value info;
    context.ReadJson(content, instanceId);

    return true;
  }


  static bool ContourToPoints(Json::Value& result,
                              const Json::Value& source)
  {
    std::vector<std::string> points;
    Toolbox::Split(points, source.asString(), '\\');

    if (points.size() % 3 != 0)
    {
      return false;
    }

    result = Json::arrayValue;

    for (size_t k = 0; k < points.size(); k += 3)
    {
      Json::Value p = Json::arrayValue;

      try
      {
        p.append(boost::lexical_cast<float>(points[k]));
        p.append(boost::lexical_cast<float>(points[k + 1]));
        p.append(boost::lexical_cast<float>(points[k + 2]));
      }
      catch (boost::bad_lexical_cast)
      {
        return false;
      }

      result.append(p);
    }

    return true;
  }


  static bool GetRtStructuresInfo(Json::Value& study,
                                  Json::Value& series,
                                  Json::Value& content,
                                  std::string& frameOfReference,
                                  ServerContext& context,
                                  const std::string& seriesId)
  {
    if (!CheckSeriesModality(study, series, content, context, seriesId, "RTSTRUCT"))
    {
      return false;
    }

    // Check that the "ReferencedStudySequence" is the same as the parent study.
    if (!content.isMember(REFERENCED_STUDY_SEQUENCE) ||
        content[REFERENCED_STUDY_SEQUENCE]["Value"].size() != 1 ||
        !content[REFERENCED_STUDY_SEQUENCE]["Value"][0].isMember(REFERENCED_SOP_INSTANCE_UID) ||
        content[REFERENCED_STUDY_SEQUENCE]["Value"][0][REFERENCED_SOP_INSTANCE_UID]["Value"].asString() != 
        study["MainDicomTags"]["StudyInstanceUID"].asString())
    {
      return false;
    }

    // Lookup for the frame of reference. Orthanc does not support
    // RTSTRUCT with multiple frames of reference.
    if (!content.isMember(REFERENCED_FRAME_OF_REFERENCE_SEQUENCE) ||
        content[REFERENCED_FRAME_OF_REFERENCE_SEQUENCE]["Value"].size() != 1 ||
        !content[REFERENCED_FRAME_OF_REFERENCE_SEQUENCE]["Value"][0].isMember(FRAME_OF_REFERENCE_UID))
    {
      return false;
    }

    frameOfReference = content[REFERENCED_FRAME_OF_REFERENCE_SEQUENCE]["Value"][0][FRAME_OF_REFERENCE_UID]["Value"].asString();

    return true;
  }


  static bool GetRtStructuresRoi(Json::Value& result,
                                 Json::Value& contourSequence,
                                 std::string& instanceId,
                                 ServerContext& context,
                                 const std::string& seriesId,
                                 const std::string& roiNumber)
  {
    Json::Value study, series, content;
    std::string frameOfReference;

    if (!GetRtStructuresInfo(study, series, content, frameOfReference, context, seriesId))
    {
      return false;
    }

    if (!content.isMember(STRUCTURE_SET_ROI_SEQUENCE) ||
        !content.isMember(ROI_CONTOUR_SEQUENCE))
    {
      return false;
    }

    instanceId = series["Instances"][0].asString();

    bool found = false;

    for (Json::Value::ArrayIndex i = 0; i < content[STRUCTURE_SET_ROI_SEQUENCE]["Value"].size(); i++)
    {
      const Json::Value& roi = content[STRUCTURE_SET_ROI_SEQUENCE]["Value"][i];

      if (roi.isMember(ROI_NUMBER) &&
          roi.isMember(ROI_NAME) &&
          roi[ROI_NUMBER]["Value"].asString() == roiNumber)
      {
        result["InternalIndex"] = i;
        result["Number"] = boost::lexical_cast<unsigned int>(roiNumber);
        result["Name"] = roi[ROI_NAME]["Value"].asString();
        result["GenerationAlgorithm"] = roi[ROI_GENERATION_ALGORITHM]["Value"].asString();
        found = true;
      }
    }

    if (!found)
    {
      return false;
    }

    for (Json::Value::ArrayIndex i = 0; i < content[ROI_CONTOUR_SEQUENCE]["Value"].size(); i++)
    {
      const Json::Value& contour = content[ROI_CONTOUR_SEQUENCE]["Value"][i];

      if (contour.isMember(REFERENCED_ROI_NUMBER) &&
          contour.isMember(ROI_DISPLAY_COLOR) &&
          contour.isMember(CONTOUR_SEQUENCE) &&
          contour[REFERENCED_ROI_NUMBER]["Value"].asString() == roiNumber)
      {
        std::vector<std::string> color;
        Toolbox::Split(color, contour[ROI_DISPLAY_COLOR]["Value"].asString(), '\\');

        result["DisplayColor"] = Json::arrayValue;
        if (color.size() != 3)
        {
          return false;
        }

        for (size_t k = 0; k < color.size(); k++)
        {
          try
          {
            result["DisplayColor"].append(boost::lexical_cast<int>(color[k]));
          }
          catch (boost::bad_lexical_cast)
          {
            return false;
          }
        }

        contourSequence = contour[CONTOUR_SEQUENCE]["Value"];

        return true;
      }
    }

    return false;
  }


  static void GetRtStructuresInfo(RestApi::GetCall& call)
  {
    RETRIEVE_CONTEXT(call);

    Json::Value study, series, content;
    std::string frameOfReference;
    if (GetRtStructuresInfo(study, series, content, frameOfReference, context, call.GetUriComponent("id", "")))
    {
      Json::Value result;

      result["Study"] = study["ID"];


      // Lookup the series with the same frame of reference inside this study
      result["RelatedSeries"] = Json::arrayValue;

      for (Json::Value::ArrayIndex i = 0; i < study["Series"].size(); i++)
      {
        Json::Value otherSeries;
        if (context.GetIndex().LookupResource(otherSeries, study["Series"][i].asString(), ResourceType_Series) &&
            otherSeries["Instances"].size() > 0)
        {
          Json::Value info;
          context.ReadJson(info, otherSeries["Instances"][0].asString());

          if (info.isMember(FRAME_OF_REFERENCE_UID))
          {
            result["RelatedSeries"].append(study["Series"][i].asString());
          }
        }
      }


      call.GetOutput().AnswerJson(result);
    }
  }


  static void GetRtStructuresListOfROIs(RestApi::GetCall& call)
  {
    RETRIEVE_CONTEXT(call);

    Json::Value study, series, content;
    std::string frameOfReference;
    if (GetRtStructuresInfo(study, series, content, frameOfReference, context, call.GetUriComponent("id", "")))
    {
      Json::Value result(Json::arrayValue);

      if (content.isMember(STRUCTURE_SET_ROI_SEQUENCE))
      {
        for (Json::Value::ArrayIndex i = 0; i < content[STRUCTURE_SET_ROI_SEQUENCE]["Value"].size(); i++)
        {
          if (content[STRUCTURE_SET_ROI_SEQUENCE]["Value"][i].isMember(ROI_NUMBER))
          {
            result.append(boost::lexical_cast<int>(content[STRUCTURE_SET_ROI_SEQUENCE]["Value"][i][ROI_NUMBER]["Value"].asString()));
          }
        }
      }

      call.GetOutput().AnswerJson(result);
    }
  }


  static void GetRtStructuresROI(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour;
     std::string instanceId;

     if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       roi.removeMember("InternalIndex");
       call.GetOutput().AnswerJson(roi);
     }
  }


  static void GetRtStructuresROIPoints(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour;
     std::string instanceId;

     if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       Json::Value result = Json::arrayValue;

       for (Json::Value::ArrayIndex i = 0; i < contour.size(); i++)
       {
         if (contour[i][CONTOUR_GEOMETRIC_TYPE]["Value"].asString() == "POINT")
         {
           Json::Value p;
           if (ContourToPoints(p, contour[i][CONTOUR_DATA]["Value"].asString()) &&
               p.size() == 1)
           {
             result.append(p[0]);
           }
         }
       }

       call.GetOutput().AnswerJson(result);
     }
  }


  static void GetRtStructuresListOfClosedPlanars(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour;
     std::string instanceId;

     if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       Json::Value result = Json::arrayValue;

       for (Json::Value::ArrayIndex i = 0; i < contour.size(); i++)
       {
         if (contour[i].isMember(CONTOUR_IMAGE_SEQUENCE) &&
             contour[i].isMember(CONTOUR_GEOMETRIC_TYPE) &&
             contour[i].isMember(NUMBER_OF_CONTOUR_POINTS) &&
             contour[i].isMember(CONTOUR_DATA) &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"].size() == 1 &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0].isMember(REFERENCED_SOP_INSTANCE_UID) &&
             contour[i][CONTOUR_GEOMETRIC_TYPE]["Value"].asString() == "CLOSED_PLANAR")
         {
           result.append(i);
         }
       }

       call.GetOutput().AnswerJson(result);
     }
  }


  static void GetRtStructuresSingleClosedPlanar(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour;
     std::string instanceId;

     if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       unsigned int index = boost::lexical_cast<unsigned int>(call.GetUriComponent("polygon", ""));

       boost::mutex::scoped_lock lock(context.GetDicomFileMutex());
       ParsedDicomFile& dicom = context.GetDicomFile(instanceId);

       ParsedDicomFile::SequencePath path;
       path.push_back(std::make_pair(DicomTag(0x3006, 0x0039 /* ROIContourSequence */), roi["InternalIndex"].asInt()));
       path.push_back(std::make_pair(DicomTag(0x3006, 0x0040 /* ContourSequence */), index));
        
       Json::Value result;
       std::string contourData;
       std::string numberOfPoints;

       if (dicom.GetTagValue(contourData, path, DicomTag(0x3006, 0x0050 /* ContourData */)) &&
           dicom.GetTagValue(numberOfPoints, path, DicomTag(0x3006, 0x0046 /* NumberOfContourPoints */)) &&
           ContourToPoints(result, contourData) &&
           result.size() == boost::lexical_cast<unsigned int>(numberOfPoints))
       {
         call.GetOutput().AnswerJson(result);
       }
     }
  }


  static void GetRtStructuresClosedPlanarThickness(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour;
     std::string instanceId;

     if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       unsigned int index = boost::lexical_cast<unsigned int>(call.GetUriComponent("polygon", ""));

       if (contour[index].isMember(CONTOUR_SLAB_THICKNESS))
       {
         std::cout <<contour[index][CONTOUR_SLAB_THICKNESS] << std::endl;
         call.GetOutput().AnswerBuffer(contour[index][CONTOUR_SLAB_THICKNESS]["Value"].asString(), "text/plain");
       }
       else
       {
         // TODO - No slab thickness is explicitely specified: Should we
         // fallback to the thickness of the instance?
       }
     }
  }


  static void GetRtStructuresInstanceOfClosedPlanar(RestApi::GetCall& call)
  {
    RETRIEVE_CONTEXT(call);

    Json::Value roi, contour;
    std::string instanceId;

    if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                           call.GetUriComponent("id", ""),
                           call.GetUriComponent("roi", "")))
    {
      unsigned int index = boost::lexical_cast<unsigned int>(call.GetUriComponent("polygon", ""));

      if (contour[index].isMember(CONTOUR_IMAGE_SEQUENCE) &&
          contour[index][CONTOUR_IMAGE_SEQUENCE]["Value"].size() == 1 &&
          contour[index][CONTOUR_IMAGE_SEQUENCE]["Value"][0].isMember(REFERENCED_SOP_INSTANCE_UID))
      {
        std::string uid = contour[index][CONTOUR_IMAGE_SEQUENCE]["Value"][0][REFERENCED_SOP_INSTANCE_UID]["Value"].asString();

        std::list<std::string> instance;
        context.GetIndex().LookupTagValue(instance, DICOM_TAG_SOP_INSTANCE_UID, uid);

        Json::Value result;
        if (instance.size() == 1 &&
            context.GetIndex().LookupResource(result, instance.front(), ResourceType_Instance))
        {
          call.GetOutput().AnswerJson(result);
        }
      }
    }
  }


  static void GetRtStructuresListOfInstances(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour;
     std::string instanceId;

     if (GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       Json::Value result = Json::arrayValue;

       for (Json::Value::ArrayIndex i = 0; i < contour.size(); i++)
       {
         if (contour[i].isMember(CONTOUR_IMAGE_SEQUENCE) &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"].size() == 1 &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0].isMember(REFERENCED_SOP_INSTANCE_UID))
         {
           std::string uid = contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0][REFERENCED_SOP_INSTANCE_UID]["Value"].asString();

           std::list<std::string> instance;
           context.GetIndex().LookupTagValue(instance, DICOM_TAG_SOP_INSTANCE_UID, uid);

           if (instance.size() == 1)
           {
             result.append(instance.front());
           }
         }
       }

       call.GetOutput().AnswerJson(result);
     }
  }



  static void GetRtStructuresClosedPlanarsOfInstance(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour, instance;
     std::string instanceId;

     if (context.GetIndex().LookupResource(instance, call.GetUriComponent("instance", ""), ResourceType_Instance) &&
         GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       boost::mutex::scoped_lock lock(context.GetDicomFileMutex());
       ParsedDicomFile& dicom = context.GetDicomFile(instanceId);

       Json::Value result = Json::arrayValue;

       for (Json::Value::ArrayIndex i = 0; i < contour.size(); i++)
       {
         if (contour[i].isMember(CONTOUR_DATA) &&
             contour[i].isMember(CONTOUR_IMAGE_SEQUENCE) &&
             contour[i].isMember(NUMBER_OF_CONTOUR_POINTS) &&
             contour[i].isMember(CONTOUR_GEOMETRIC_TYPE) &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"].size() == 1 &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0].isMember(REFERENCED_SOP_INSTANCE_UID) &&
             contour[i][CONTOUR_GEOMETRIC_TYPE]["Value"].asString() == "CLOSED_PLANAR")
         {
           std::string uid = contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0][REFERENCED_SOP_INSTANCE_UID]["Value"].asString();

           if (uid == instance["MainDicomTags"]["SOPInstanceUID"].asString())
           {
             ParsedDicomFile::SequencePath path;
             path.push_back(std::make_pair(DicomTag(0x3006, 0x0039 /* ROIContourSequence */), roi["InternalIndex"].asInt()));
             path.push_back(std::make_pair(DicomTag(0x3006, 0x0040 /* ContourSequence */), i));
        
             Json::Value points;
             std::string contourData;
             std::string numberOfPoints;

             if (dicom.GetTagValue(contourData, path, DicomTag(0x3006, 0x0050 /* ContourData */)) &&
                 dicom.GetTagValue(numberOfPoints, path, DicomTag(0x3006, 0x0046 /* NumberOfContourPoints */)) &&
                 ContourToPoints(points, contourData) &&
                 points.size() == boost::lexical_cast<unsigned int>(numberOfPoints))
             {
               result.append(points);
             }             
           }
         }
       }

       call.GetOutput().AnswerJson(result);
     }
  }



  static void GetRtStructuresPointsOfInstance(RestApi::GetCall& call)
  {
     RETRIEVE_CONTEXT(call);

     Json::Value roi, contour, instance;
     std::string instanceId;

     if (context.GetIndex().LookupResource(instance, call.GetUriComponent("instance", ""), ResourceType_Instance) &&
         GetRtStructuresRoi(roi, contour, instanceId, context, 
                            call.GetUriComponent("id", ""),
                            call.GetUriComponent("roi", "")))
     {
       Json::Value result = Json::arrayValue;

       for (Json::Value::ArrayIndex i = 0; i < contour.size(); i++)
       {
         if (contour[i].isMember(CONTOUR_DATA) &&
             contour[i].isMember(CONTOUR_IMAGE_SEQUENCE) &&
             contour[i].isMember(CONTOUR_GEOMETRIC_TYPE) &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"].size() == 1 &&
             contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0].isMember(REFERENCED_SOP_INSTANCE_UID) &&
             contour[i][CONTOUR_GEOMETRIC_TYPE]["Value"].asString() == "POINT")
         {
           std::string uid = contour[i][CONTOUR_IMAGE_SEQUENCE]["Value"][0][REFERENCED_SOP_INSTANCE_UID]["Value"].asString();

           if (uid == instance["MainDicomTags"]["SOPInstanceUID"].asString())
           {
             Json::Value p;
             if (ContourToPoints(p, contour[i][CONTOUR_DATA]["Value"].asString()) &&
                 p.size() == 1)
             {
               result.append(p[0]);
             }
           }
         }
       }

       call.GetOutput().AnswerJson(result);
     }
  }




  RadiotherapyRestApi::RadiotherapyRestApi(ServerContext& context) : OrthancRestApi(context)
  {
    Register("/series/{id}/rt-structures", GetRtStructuresInfo);
    Register("/series/{id}/rt-structures/roi", GetRtStructuresListOfROIs);
    Register("/series/{id}/rt-structures/roi/{roi}/info", GetRtStructuresROI);
    Register("/series/{id}/rt-structures/roi/{roi}/points", GetRtStructuresROIPoints);
    Register("/series/{id}/rt-structures/roi/{roi}/closed-planar", GetRtStructuresListOfClosedPlanars);
    Register("/series/{id}/rt-structures/roi/{roi}/closed-planar/{polygon}/vertices", GetRtStructuresSingleClosedPlanar);
    Register("/series/{id}/rt-structures/roi/{roi}/closed-planar/{polygon}/thickness", GetRtStructuresClosedPlanarThickness);
    Register("/series/{id}/rt-structures/roi/{roi}/closed-planar/{polygon}/instance", GetRtStructuresInstanceOfClosedPlanar);
    Register("/series/{id}/rt-structures/roi/{roi}/instances", GetRtStructuresListOfInstances);
    Register("/series/{id}/rt-structures/roi/{roi}/instances/{instance}/closed-planar", GetRtStructuresClosedPlanarsOfInstance);
    Register("/series/{id}/rt-structures/roi/{roi}/instances/{instance}/points", GetRtStructuresPointsOfInstance);
  }

}


//  curl http://localhost:8042/series/0b9e2bb2-605a59aa-f27c0260-9cc4faf6-9d8bf457/rt-structures
//  curl http://localhost:8042/series/ef041e6b-c855e775-f7e0f7fe-dc3c17dc-533cb8c5/rt-structures