#include "ismrmrd/xml.h"
#include "ismrmrd/version.h"
#include "pugixml.hpp"
#include <cstdlib>

namespace ISMRMRD
{
  //Utility Functions for deserializing Header
  EncodingSpace parse_encoding_space(pugi::xml_node& n, const char* child) 
  {
    EncodingSpace e;
    pugi::xml_node encodingSpace = n.child(child);
    pugi::xml_node matrixSize = encodingSpace.child("matrixSize");
    pugi::xml_node fieldOfView_mm = encodingSpace.child("fieldOfView_mm");
    
    if (!matrixSize) {
      throw std::runtime_error("matrixSize not found in encodingSpace");
    } else {
      e.matrixSize.x = std::atoi(matrixSize.child_value("x"));
      e.matrixSize.y = std::atoi(matrixSize.child_value("y"));
      e.matrixSize.z = std::atoi(matrixSize.child_value("z"));
    }

    if (!fieldOfView_mm) {
      throw std::runtime_error("fieldOfView_mm not found in encodingSpace");
    } else {
      e.fieldOfView_mm.x = std::atof(fieldOfView_mm.child_value("x"));
      e.fieldOfView_mm.y = std::atof(fieldOfView_mm.child_value("y"));
      e.fieldOfView_mm.z = std::atof(fieldOfView_mm.child_value("z"));
    }

    return e;
  }
  
  Optional<Limit> parse_encoding_limit(pugi::xml_node& n, const char* child) 
  {
    Optional<Limit> o;
    pugi::xml_node nc = n.child(child);
    
    if (nc) {
      Limit l;
      l.minimum = std::atoi(nc.child_value("minimum"));
      l.maximum = std::atoi(nc.child_value("maximum"));
      l.center = std::atoi(nc.child_value("center"));
      o = l;
    }

    return o;
  }

  std::string parse_string(pugi::xml_node& n, const char* child) 
  {
    std::string r(n.child_value(child));
    if (r.size() == 0) throw std::runtime_error("Null length string");
    return r;
  }

  Optional<std::string> parse_optional_string(pugi::xml_node& n, const char* child)
  {
    std::string s(n.child_value(child));
    Optional<std::string> r;
    if (s.size()) r = s;
    return r;
  }

  Optional<float> parse_optional_float(pugi::xml_node& n, const char* child)
  {
    Optional<float> r;
    pugi::xml_node nc = n.child(child);
    if (nc) {
      r = std::atof(nc.child_value());
    }
    return r;
  }

  Optional<long> parse_optional_long(pugi::xml_node& n, const char* child) {
    Optional<long> r;
    pugi::xml_node nc = n.child(child);
    if (nc) {
      r = std::atol(nc.child_value());
    }
    return r;
  }

  Optional<unsigned short> parse_optional_ushort(pugi::xml_node& n, const char* child) {
    Optional<unsigned short> r;
    pugi::xml_node nc = n.child(child);
    if (nc) {
      r = static_cast<unsigned short>(std::atoi(nc.child_value()));
    }
    return r;
  }

  std::vector<float> parse_vector_float(pugi::xml_node& n, const char* child) 
  {
    std::vector<float> r;
    
    pugi::xml_node nc = n.child(child);

    while (nc) {
      float f = std::atof(nc.child_value());
      r.push_back(f);
      nc = nc.next_sibling(child);
    }
    
    return r;
  }

  std::vector<std::string> parse_vector_string(pugi::xml_node& n, const char* child)
  {
    std::vector<std::string> r;
    pugi::xml_node nc = n.child(child);
    while (nc) {
      std::string s = nc.child_value();
      r.push_back(s);
      nc = nc.next_sibling(child);
    }
    return r;
  }

  std::vector<UserParameterLong> parse_user_parameter_long(pugi::xml_node& n, const char* child) 
  {
    std::vector<UserParameterLong> r;
    pugi::xml_node nc = n.child(child);
    while (nc) {
      UserParameterLong v;
      pugi::xml_node name = nc.child("name");
      pugi::xml_node value = nc.child("value");

      if (!name || !value) {
	throw std::runtime_error("Malformed user parameter (long)");
      }

      v.name = std::string(name.child_value());
      v.value = std::atoi(value.child_value());

      r.push_back(v);

      nc = nc.next_sibling(child);
    }
    return r;
  }

  std::vector<UserParameterDouble> parse_user_parameter_double(pugi::xml_node& n, const char* child) 
  {
    std::vector<UserParameterDouble> r;
    pugi::xml_node nc = n.child(child);
    while (nc) {
      UserParameterDouble v;
      pugi::xml_node name = nc.child("name");
      pugi::xml_node value = nc.child("value");

      if (!name || !value) {
	throw std::runtime_error("Malformed user parameter (double)");
      }

      char buffer[10000];
      memcpy(buffer,name.child_value(),strlen(name.child_value())+1);
      v.name = name.child_value();
      v.value = std::atof(value.child_value());

      r.push_back(v);

      nc = nc.next_sibling(child);
    }
   
    return r;
  }

  std::vector<UserParameterString> parse_user_parameter_string(pugi::xml_node& n, const char* child) 
  {
    std::vector<UserParameterString> r;
    pugi::xml_node nc = n.child(child);
    while (nc) {
      UserParameterString v;
      pugi::xml_node name = nc.child("name");
      pugi::xml_node value = nc.child("value");

      if (!name || !value) {
	throw std::runtime_error("Malformed user parameter (string)");
      }

      v.name = std::string(name.child_value());
      v.value = std::string(value.child_value());

      r.push_back(v);

      nc = nc.next_sibling(child);
    }
   
    return r;
  }

  //End of utility functions for deserializing header

  void deserialize(const char* xml, IsmrmrdHeader& h) 
  {
    pugi::xml_document doc;
    pugi::xml_parse_result result = doc.load(xml);
    
    if (!result) {
      throw std::runtime_error("Unable to load ISMRMRD XML header");
    }

    pugi::xml_node root = doc.child("ismrmrdHeader");

    if (root) {
      pugi::xml_node subjectInformation = root.child("subjectInformation");
      pugi::xml_node studyInformation = root.child("studyInformation");
      pugi::xml_node measurementInformation = root.child("measurementInformation");
      pugi::xml_node acquisitionSystemInformation = root.child("acquisitionSystemInformation");
      pugi::xml_node experimentalConditions = root.child("experimentalConditions");
      pugi::xml_node encoding = root.child("encoding");
      pugi::xml_node sequenceParameters = root.child("sequenceParameters");
      pugi::xml_node userParameters = root.child("userParameters");

      // Parsing version
      h.version = parse_optional_long(root, "version");
      
      //Parsing experimentalConditions
      if (!experimentalConditions) {
	throw std::runtime_error("experimentalConditions not defined in ismrmrdHeader");
      } else {
	ExperimentalConditions e;
	e.H1resonanceFrequency_Hz = std::atoi(experimentalConditions.child_value("H1resonanceFrequency_Hz"));
	h.experimentalConditions = e;
      }
      
      //Parsing encoding section
      if (!encoding) {
	throw std::runtime_error("encoding section not found in ismrmrdHeader");
      } else {
	while (encoding) {
	  Encoding e;
	  
	  try {
	    e.encodedSpace = parse_encoding_space(encoding,"encodedSpace");
	    e.reconSpace = parse_encoding_space(encoding,"reconSpace");
	  } catch (std::runtime_error& e) {
	    std::cout << "Unable to parse encoding section: " << e.what() << std::endl;
	    throw;
	  }

	  pugi::xml_node encodingLimits = encoding.child("encodingLimits");
	  
	  if (!encodingLimits) {
	    throw std::runtime_error("encodingLimits not found in encoding section");
	  } else {
	    e.encodingLimits.kspace_encoding_step_0 = parse_encoding_limit(encodingLimits,"kspace_encoding_step_0");
	    e.encodingLimits.kspace_encoding_step_1 = parse_encoding_limit(encodingLimits,"kspace_encoding_step_1");
	    e.encodingLimits.kspace_encoding_step_2 = parse_encoding_limit(encodingLimits,"kspace_encoding_step_2");
	    e.encodingLimits.average                = parse_encoding_limit(encodingLimits,"average");
	    e.encodingLimits.slice                  = parse_encoding_limit(encodingLimits,"slice");
	    e.encodingLimits.contrast               = parse_encoding_limit(encodingLimits,"contrast");
	    e.encodingLimits.phase                  = parse_encoding_limit(encodingLimits,"phase");
	    e.encodingLimits.repetition             = parse_encoding_limit(encodingLimits,"repetition");
	    e.encodingLimits.set                    = parse_encoding_limit(encodingLimits,"set");
	    e.encodingLimits.segment                = parse_encoding_limit(encodingLimits,"segment");
	  }
	  
	  pugi::xml_node trajectory = encoding.child("trajectory");
	  if (!trajectory) {
	    throw std::runtime_error("trajectory not found in encoding section");
	  } else {
	    e.trajectory = std::string(encoding.child_value("trajectory"));
	  }

	  pugi::xml_node trajectoryDescription = encoding.child("trajectoryDescription");
	  
	  if (trajectoryDescription) {
	    TrajectoryDescription traj;
	    try {
	      traj.identifier = parse_string(trajectoryDescription,"identifier");
	      traj.userParameterLong = 
		parse_user_parameter_long(trajectoryDescription, "userParameterLong");
	      traj.userParameterDouble = 
		parse_user_parameter_double(trajectoryDescription, "userParameterDouble");
	      traj.comment = parse_optional_string(trajectoryDescription, "comment");
	      e.trajectoryDescription = traj;
	    } catch (std::runtime_error& e) {
	      std::cout << "Error parsing trajectory description" << std::endl;
	      throw;
	    }
	    
	  }

	  pugi::xml_node parallelImaging = encoding.child("parallelImaging");
	  if (parallelImaging) {
	    ParallelImaging info;
	    
	    pugi::xml_node accelerationFactor = parallelImaging.child("accelerationFactor");
	    if (!accelerationFactor) {
	      throw std::runtime_error("Unable to accelerationFactor section in parallelImaging");
	    } else {
	      info.accelerationFactor.kspace_encoding_step_1 = static_cast<unsigned short>(std::atoi(accelerationFactor.child_value("kspace_encoding_step_1")));
	      info.accelerationFactor.kspace_encoding_step_2 = static_cast<unsigned short>(std::atoi(accelerationFactor.child_value("kspace_encoding_step_2")));
	    }
	    
	    info.calibrationMode = parse_optional_string(parallelImaging,"calibrationMode");
	    info.interleavingDimension = parse_optional_string(parallelImaging,"interleavingDimension");
	    e.parallelImaging = info;
	  }

	  e.echoTrainLength = parse_optional_long(encoding, "echoTrainLength");

	  h.encoding.push_back(e);
	  encoding = encoding.next_sibling("encoding");
	}

      }

      if (subjectInformation) {
	SubjectInformation info;
	info.patientName = parse_optional_string(subjectInformation, "patientName");
	info.patientWeight_kg = parse_optional_float(subjectInformation, "patientWeight_kg");
	info.patientID = parse_optional_string(subjectInformation, "patientID");
	info.patientBirthdate = parse_optional_string(subjectInformation, "patientBirthdate");
	info.patientGender = parse_optional_string(subjectInformation, "patientGender");
	h.subjectInformation = info;
      }

      if (studyInformation) {
	StudyInformation info;
	info.studyDate = parse_optional_string(studyInformation,"studyDate");
	info.studyTime = parse_optional_string(studyInformation,"studyTime");
	info.studyID = parse_optional_string(studyInformation,"studyID");
	info.accessionNumber = parse_optional_long(studyInformation,"accessionNumber");
	info.referringPhysicianName = parse_optional_string(studyInformation,"referringPhysicianName");
	info.studyDescription = parse_optional_string(studyInformation,"studyDescription");
	info.studyInstanceUID = parse_optional_string(studyInformation,"studyInstanceUID");
	h.studyInformation = info;
      }

      if (measurementInformation) {
	MeasurementInformation info;
	info.measurementID = parse_optional_string(measurementInformation,"measurementID");
	info.seriesDate = parse_optional_string(measurementInformation, "seriesDate");
	info.seriesTime = parse_optional_string(measurementInformation, "seriesTime");
	info.patientPosition = parse_string(measurementInformation, "patientPosition");
	info.initialSeriesNumber = parse_optional_long(measurementInformation, "initialSeriesNumber");
	info.protocolName = parse_optional_string(measurementInformation, "protocolName");
	info.seriesDescription = parse_optional_string(measurementInformation, "seriesDescription");
	
	pugi::xml_node measurementDependency = measurementInformation.child("measurementDependency");
	while (measurementDependency) {
	  try {
	    MeasurementDependency d;
	    d.measurementID = parse_string(measurementDependency,"measurementID");
	    d.dependencyType = parse_string(measurementDependency,"dependencyType");
	    info.measurementDependency.push_back(d);
	  } catch (std::runtime_error& e) {
	    std::cout << "Error parsing measurement dependency: " << e.what() << std::endl;
	    throw;
	  } 
	  measurementDependency = measurementDependency.next_sibling("measurementDependency");
	}

	info.seriesInstanceUIDRoot = parse_optional_string(measurementInformation,"seriesInstanceUIDRoot");
	info.frameOfReferenceUID = parse_optional_string(measurementInformation,"frameOfReferenceUID");

	//This part of the schema is totally messed up and needs to be fixed, but for now we will just read it. 
	pugi::xml_node ri = measurementInformation.child("referencedImageSequence");
	if (ri) {
	  pugi::xml_node ric = ri.child("referencedSOPInstanceUID");
	  while (ric) {
	    ReferencedImageSequence r;
	    r.referencedSOPInstanceUID = ric.child_value();
	    info.referencedImageSequence.push_back(r);
	    ric = ric.next_sibling("referencedSOPInstanceUID");
	  }
	}

	h.measurementInformation = info;
      }

      if (acquisitionSystemInformation) {
	AcquisitionSystemInformation info;
	info.systemVendor = parse_optional_string(acquisitionSystemInformation, "systemVendor");
	info.systemModel = parse_optional_string(acquisitionSystemInformation, "systemModel");
	info.systemFieldStrength_T = parse_optional_float(acquisitionSystemInformation, "systemFieldStrength_T");
	info.relativeReceiverNoiseBandwidth = parse_optional_float(acquisitionSystemInformation, "relativeReceiverNoiseBandwidth");
	info.receiverChannels = parse_optional_ushort(acquisitionSystemInformation, "receiverChannels");
	pugi::xml_node coilLabel = acquisitionSystemInformation.child("coilLabel");
	while (coilLabel) {
	  CoilLabel l;
	  l.coilNumber = std::atoi(coilLabel.child_value("coilNumber"));
	  l.coilName = parse_string(coilLabel, "coilName");
	  info.coilLabel.push_back(l);
	  coilLabel = coilLabel.next_sibling("coilLabel");
	}
	info.institutionName = parse_optional_string(acquisitionSystemInformation, "institutionName");
	info.stationName = parse_optional_string(acquisitionSystemInformation, "stationName");

	h.acquisitionSystemInformation = info;
      }

      if (sequenceParameters) {
	SequenceParameters p;
	p.TR = parse_vector_float(sequenceParameters,"TR");
	p.TE = parse_vector_float(sequenceParameters,"TE");
	p.TI = parse_vector_float(sequenceParameters,"TI");
	p.flipAngle_deg = parse_vector_float(sequenceParameters, "flipAngle_deg");

	h.sequenceParameters = p;
      }

      if (userParameters) {
	UserParameters p;
 	p.userParameterLong = parse_user_parameter_long(userParameters,"userParameterLong");
 	p.userParameterDouble = parse_user_parameter_double(userParameters,"userParameterDouble");
 	p.userParameterString = parse_user_parameter_string(userParameters,"userParameterString");
 	p.userParameterBase64 = parse_user_parameter_string(userParameters,"userParameterBase64");
	h.userParameters = p;
      }
    } else {
      throw std::runtime_error("Root node 'ismrmrdHeader' not found");
    }

  }


  //Utility functions for serialization
  void to_string_val(const std::string& v, std::string& o)
  {
    o = v;
  }

  void to_string_val(const float& v, std::string& o)
  {
    char buffer[256];
    sprintf(buffer,"%f",v);
    o = std::string(buffer);
  }

  void to_string_val(const double& v, std::string& o)
  {
    char buffer[256];
    sprintf(buffer,"%f",v);
    o = std::string(buffer);
  }

  void to_string_val(const unsigned short& v, std::string& o)
  {
    char buffer[256];
    sprintf(buffer,"%d",v);
    o = std::string(buffer);
  }

  void to_string_val(const long& v, std::string& o)
  {
    char buffer[256];
    sprintf(buffer,"%ld",v);
    o = std::string(buffer);
  }

  template <class T> void append_optional_node(pugi::xml_node& n, const char* child, const Optional<T>& v) 
  {
    if (v) {
      pugi::xml_node n2 = n.append_child(child);
      std::string v_as_string;
      to_string_val(*v, v_as_string);
      n2.append_child(pugi::node_pcdata).set_value(v_as_string.c_str());
    }
  } 
  
  template <class T> void append_node(pugi::xml_node& n, const char* child, const T& v) 
  {
    pugi::xml_node n2 = n.append_child(child);
    std::string v_as_string;
    to_string_val(v, v_as_string);
    n2.append_child(pugi::node_pcdata).set_value(v_as_string.c_str());
  } 

  void append_encoding_space(pugi::xml_node& n, const char* child, const EncodingSpace& s) 
  {
    pugi::xml_node n2 = n.append_child(child);
    pugi::xml_node n3 = n2.append_child("matrixSize");
    append_node(n3,"x",s.matrixSize.x);
    append_node(n3,"y",s.matrixSize.y);
    append_node(n3,"z",s.matrixSize.z);
    n3 = n2.append_child("fieldOfView_mm");
    append_node(n3,"x",s.fieldOfView_mm.x);
    append_node(n3,"y",s.fieldOfView_mm.y);
    append_node(n3,"z",s.fieldOfView_mm.z);
  }
  
  void append_encoding_limit(pugi::xml_node& n, const char* child, const Optional<Limit>& l) 
  {
    if (l) {
      pugi::xml_node n2 = n.append_child(child);
      append_node(n2,"minimum",l->minimum);
      append_node(n2,"maximum",l->maximum);
      append_node(n2,"center",l->center);
    }
  }

  template <class T> 
  void append_user_parameter(pugi::xml_node& n, const char* child, 
			     const std::vector<T>& v) 
  {
    for (size_t i = 0; i < v.size(); i++) {
      pugi::xml_node n2 = n.append_child(child);
      append_node(n2,"name",v[i].name);
      append_node(n2,"value",v[i].value);
    }
  }

  //End utility functions for serialization

  void serialize(const IsmrmrdHeader& h, std::ostream& o)
  {
    pugi::xml_document doc;
    pugi::xml_node root = doc.append_child();
    pugi::xml_node n1,n2,n3;
    pugi::xml_attribute a;

    root.set_name("ismrmrdHeader");

    a = root.append_attribute("xmlns");
    a.set_value("http://www.ismrm.org/ISMRMRD");

    a = root.append_attribute("xmlns:xsi");
    a.set_value("http://www.w3.org/2001/XMLSchema-instance");
  
    a = root.append_attribute("xmlns:xs");
    a.set_value("http://www.w3.org/2001/XMLSchema");
    
    a = root.append_attribute("xsi:schemaLocation");
    a.set_value("http://www.ismrm.org/ISMRMRD ismrmrd.xsd");

    if (h.version) {
      if (*h.version != ISMRMRD_XMLHDR_VERSION) {
        throw std::runtime_error("XML header version does not match library schema version.");
      }
      append_optional_node(root,"version",h.version);
    }
    
    if (h.subjectInformation) {
      n1 = root.append_child();
      n1.set_name("subjectInformation");
      append_optional_node(n1,"patientName",h.subjectInformation->patientName);
      append_optional_node(n1,"patientWeight_kg",h.subjectInformation->patientWeight_kg);
      append_optional_node(n1,"patientID",h.subjectInformation->patientID);
      append_optional_node(n1,"patientBirthdate",h.subjectInformation->patientBirthdate);
      append_optional_node(n1,"patientGender",h.subjectInformation->patientGender);
    }

    if (h.studyInformation) {
      n1 = root.append_child();
      n1.set_name("studyInformation");
      append_optional_node(n1,"studyDate",h.studyInformation->studyDate);
      append_optional_node(n1,"studyTime",h.studyInformation->studyTime);
      append_optional_node(n1,"studyID",h.studyInformation->studyID);
      append_optional_node(n1,"accessionNumber",h.studyInformation->accessionNumber);
      append_optional_node(n1,"referringPhysicianName",h.studyInformation->referringPhysicianName);
      append_optional_node(n1,"studyDescription",h.studyInformation->studyDescription);
      append_optional_node(n1,"studyInstanceUID",h.studyInformation->studyInstanceUID);
    }

    if (h.measurementInformation) {
      n1 = root.append_child();
      n1.set_name("measurementInformation");
      append_optional_node(n1,"measurementID",h.measurementInformation->measurementID);
      append_optional_node(n1,"seriesDate",h.measurementInformation->seriesDate);
      append_optional_node(n1,"seriesTime",h.measurementInformation->seriesTime);
      append_node(n1,"patientPosition",h.measurementInformation->patientPosition);
      append_optional_node(n1,"initialSeriesNumber",h.measurementInformation->initialSeriesNumber);
      append_optional_node(n1,"protocolName",h.measurementInformation->protocolName);
      append_optional_node(n1,"seriesDescription",h.measurementInformation->seriesDescription);

      for (size_t i = 0; i < h.measurementInformation->measurementDependency.size(); i++) {
	n2 = n1.append_child();
	n2.set_name("measurementDependency");
	append_node(n2,"dependencyType",h.measurementInformation->measurementDependency[i].dependencyType);
	append_node(n2,"measurementID",h.measurementInformation->measurementDependency[i].measurementID);
      }
      
      append_optional_node(n1,"seriesInstanceUIDRoot",h.measurementInformation->seriesInstanceUIDRoot);
      append_optional_node(n1,"frameOfReferenceUID",h.measurementInformation->frameOfReferenceUID);
      
      //TODO: Sort out stuff with this referenced image sequence. This is all messed up. 
      if (h.measurementInformation->referencedImageSequence.size()) {
	n2 = n1.append_child("referencedImageSequence");
	for (size_t i = 0; i < h.measurementInformation->referencedImageSequence.size(); i++) {
	  append_node(n2,"referencedSOPInstanceUID", h.measurementInformation->referencedImageSequence[i].referencedSOPInstanceUID);
	}
      }
      

    }

    if (h.acquisitionSystemInformation) {
      n1 = root.append_child();
      n1.set_name("acquisitionSystemInformation");
      append_optional_node(n1,"systemVendor",h.acquisitionSystemInformation->systemVendor);
      append_optional_node(n1,"systemModel",h.acquisitionSystemInformation->systemModel);
      append_optional_node(n1,"systemFieldStrength_T",h.acquisitionSystemInformation->systemFieldStrength_T);
      append_optional_node(n1,"relativeReceiverNoiseBandwidth",h.acquisitionSystemInformation->relativeReceiverNoiseBandwidth);
      append_optional_node(n1,"receiverChannels",h.acquisitionSystemInformation->receiverChannels);
      for (size_t i = 0; i < h.acquisitionSystemInformation->coilLabel.size(); i++) {
	n2 = n1.append_child();
	n2.set_name("coilLabel");
	append_node(n2,"coilNumber",h.acquisitionSystemInformation->coilLabel[i].coilNumber);
	append_node(n2,"coilName",h.acquisitionSystemInformation->coilLabel[i].coilName);
      }
      append_optional_node(n1,"institutionName",h.acquisitionSystemInformation->institutionName);
      append_optional_node(n1,"stationName",h.acquisitionSystemInformation->stationName);
    }

    n1 = root.append_child();
    n1.set_name("experimentalConditions");
    append_node(n1,"H1resonanceFrequency_Hz", h.experimentalConditions.H1resonanceFrequency_Hz);

    if (!h.encoding.size()) {
      throw std::runtime_error("Encoding array is empty. Invalid ISMRMRD header structure");
    }

    for (size_t i = 0; i < h.encoding.size(); i++) {
      n1 = root.append_child("encoding");
      append_encoding_space(n1,"encodedSpace",h.encoding[i].encodedSpace);
      append_encoding_space(n1,"reconSpace",h.encoding[i].reconSpace);
      n2 = n1.append_child("encodingLimits");
      append_encoding_limit(n2,"kspace_encoding_step_0",h.encoding[i].encodingLimits.kspace_encoding_step_0);
      append_encoding_limit(n2,"kspace_encoding_step_1",h.encoding[i].encodingLimits.kspace_encoding_step_1);
      append_encoding_limit(n2,"kspace_encoding_step_2",h.encoding[i].encodingLimits.kspace_encoding_step_2);
      append_encoding_limit(n2,"average",h.encoding[i].encodingLimits.average);
      append_encoding_limit(n2,"slice",h.encoding[i].encodingLimits.slice);
      append_encoding_limit(n2,"contrast",h.encoding[i].encodingLimits.contrast);
      append_encoding_limit(n2,"phase",h.encoding[i].encodingLimits.phase);
      append_encoding_limit(n2,"repetition",h.encoding[i].encodingLimits.repetition);
      append_encoding_limit(n2,"set",h.encoding[i].encodingLimits.set);
      append_encoding_limit(n2,"segment",h.encoding[i].encodingLimits.segment);
      append_node(n1,"trajectory",h.encoding[i].trajectory);
      
      if (h.encoding[i].trajectoryDescription) {
	n2 = n1.append_child("trajectoryDescription");
	append_node(n2,"identifier",h.encoding[i].trajectoryDescription->identifier);
	append_user_parameter(n2,"userParameterLong",h.encoding[i].trajectoryDescription->userParameterLong); 
	append_user_parameter(n2,"userParameterDouble",h.encoding[i].trajectoryDescription->userParameterDouble); 
	append_optional_node(n2,"comment",h.encoding[i].trajectoryDescription->comment);
      }

      if (h.encoding[i].parallelImaging) {
	n2 = n1.append_child("parallelImaging");
	n3 = n2.append_child("accelerationFactor");
	append_node(n3,"kspace_encoding_step_1",h.encoding[i].parallelImaging->accelerationFactor.kspace_encoding_step_1);
	append_node(n3,"kspace_encoding_step_2",h.encoding[i].parallelImaging->accelerationFactor.kspace_encoding_step_2);
	append_optional_node(n2, "calibrationMode", h.encoding[i].parallelImaging->calibrationMode);
	append_optional_node(n2, "interleavingDimension", h.encoding[i].parallelImaging->interleavingDimension);
      }

      append_optional_node(n1, "echoTrainLength", h.encoding[i].echoTrainLength);

    }

    if (h.sequenceParameters) {
      n1 = root.append_child("sequenceParameters");
      if (!h.sequenceParameters->TR.size()) {
	throw std::runtime_error("TR section of sequenceParameters does not contain any values");
      }
      if (!h.sequenceParameters->TE.size()) {
	throw std::runtime_error("TE section of sequenceParameters does not contain any values");
      }

      for (size_t i = 0; i < h.sequenceParameters->TR.size(); i++) {
	append_node(n1,"TR",h.sequenceParameters->TR[i]);
      }
      for (size_t i = 0; i < h.sequenceParameters->TE.size(); i++) {
	append_node(n1,"TE",h.sequenceParameters->TE[i]);
      }
      for (size_t i = 0; i < h.sequenceParameters->TI.size(); i++) {
	append_node(n1,"TI",h.sequenceParameters->TI[i]);
      }
      for (size_t i = 0; i < h.sequenceParameters->flipAngle_deg.size(); i++) {
	append_node(n1,"flipAngle_deg",h.sequenceParameters->flipAngle_deg[i]);
      }
    }

    if (h.userParameters) {
      n1 = root.append_child("userParameters");
      append_user_parameter(n1,"userParameterLong",h.userParameters->userParameterLong);
      append_user_parameter(n1,"userParameterDouble",h.userParameters->userParameterDouble);
      append_user_parameter(n1,"userParameterString",h.userParameters->userParameterString);
      append_user_parameter(n1,"userParameterBase64",h.userParameters->userParameterBase64);
    }

    doc.save(o);
  }


}
