/*=========================================================================

   Program:   ParaView
   Module:    hdf5Reader.cxx

   Copyright (c) 2005,2006 Sandia Corporation, Kitware Inc.
   All rights reserved.

   ParaView is a free software; you can redistribute it and/or modify it
   under the terms of the ParaView license version 1.2.

   See License_v1.2.txt for the full ParaView license.
   A copy of this license can be obtained by contacting
   Kitware Inc.
   28 Corporate Drive
   Clifton Park, NY 12065
   USA

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 AUTHORS 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.

=========================================================================*/

/*-------------------------------------------------------------------------
   Copyright (c) 2022 Verein zur Foerderung der Software openCFS
-------------------------------------------------------------------------*/

#include <algorithm>
#include <cassert>
#include <iostream>

#include <vtksys/SystemTools.hxx>

#include "hdf5Reader.h" // same directory

namespace H5CFS
{

//-----------------------------------------------------------------------------
Hdf5Reader::~Hdf5Reader()
{
  this->CloseFile();
}

//-----------------------------------------------------------------------------
void Hdf5Reader::CloseFile()
{
  if (this->MainFile != -1)
  {
    H5Gclose(this->MainRoot);
    H5Fclose(this->MainFile);
    this->MainFile = -1;
  }
}

//-----------------------------------------------------------------------------
void Hdf5Reader::LoadFile(const std::string& fileName)
{
  this->CloseFile();

  this->FileName = vtksys::SystemTools::CollapseFullPath(fileName); // normalize
  this->BaseDir =
    vtksys::SystemTools::GetParentDirectory(this->FileName); // used to load external results

  // open file and store main group and mesh group
  this->MainFile = H5Fopen(this->FileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
  if (this->MainFile < 0)
  {
    throw std::runtime_error(std::string("cannot open file ") + this->FileName);
  }

  this->MainRoot = H5CFS::OpenGroup(this->MainFile, "/");
  this->MeshRoot = H5CFS::OpenGroup(this->MainRoot, "Mesh");

  // check for use of external files (uint to bool)
  this->HasExternalFiles =
    H5CFS::ReadAttribute<unsigned int>(this->MainRoot, "Results/Mesh", "ExternalFiles") != 0;

  // read general mesh information
  this->ReadMeshStatusInformations();
}

//-----------------------------------------------------------------------------
unsigned int Hdf5Reader::GetDimension() const
{
  return H5CFS::ReadAttribute<unsigned int>(this->MeshRoot, "Dimension");
}

//-----------------------------------------------------------------------------
unsigned int Hdf5Reader::GetGridOrder() const
{
  auto quadelems = H5CFS::ReadAttribute<unsigned int>(this->MeshRoot, "Elements", "QuadraticElems");
  return quadelems == 1 ? 2 : 1;
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetNodeCoordinates(std::vector<std::vector<double>>& coords) const
{
  hid_t nodeGroup = H5CFS::OpenGroup(this->MeshRoot, "Nodes");

  // read nodal coordinates
  std::vector<double> coordVec;
  H5CFS::ReadArray(nodeGroup, "Coordinates", coordVec);

  assert(coordVec.size() / 3 == H5CFS::GetArrayDims(nodeGroup, "Coordinates")[0]);
  assert(coordVec.size() % 3 == 0); // division by 3 has no rest

  const unsigned int numNodes = static_cast<unsigned int>(coordVec.size() / 3);
  coords.resize(numNodes);
  unsigned int index = 0;
  for (auto& coord : coords)
  {
    coord.resize(3);
    coord[0] = coordVec[index];
    coord[1] = coordVec[index + 1];
    coord[2] = coordVec[index + 2];
    index += 3;
  }

  H5Gclose(nodeGroup);
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetElements(
  std::vector<H5CFS::ElemType>& types, std::vector<std::vector<unsigned int>>& connect) const
{
  std::vector<unsigned int> dim = H5CFS::GetArrayDims(this->MeshRoot, "Elements/Connectivity");
  unsigned int numElems = dim[0];        // number of elements
  unsigned int numNodesPerElem = dim[1]; // maximum number of nodes per elements

  // read element types
  std::vector<int> elemTypes;
  H5CFS::ReadArray(this->MeshRoot, "Elements/Types", elemTypes);

  // read nodes per element
  std::vector<unsigned int> globConnect;
  H5CFS::ReadArray(this->MeshRoot, "Elements/Connectivity", globConnect);

  // add element definition
  types.resize(numElems);
  connect.resize(numElems);
  auto it1 = globConnect.begin();
  auto it2 = it1;
  for (unsigned int i = 0; i < numElems; i++)
  {
    it2 = it1 + NUM_ELEM_NODES[elemTypes[i]];
    connect[i] = std::vector<unsigned int>(it1, it2);
    types[i] = static_cast<H5CFS::ElemType>(elemTypes[i]);
    it1 += numNodesPerElem;
  }
}

//-----------------------------------------------------------------------------
const std::vector<unsigned int>& Hdf5Reader::GetElementsOfRegion(const std::string& regionName)
{
  if (std::find(this->RegionNames.begin(), this->RegionNames.end(), regionName) ==
    this->RegionNames.end())
  {
    throw std::runtime_error(std::string("no elements present for region ") + regionName);
  }

  return this->RegionElems[regionName];
}

//-----------------------------------------------------------------------------
const std::vector<unsigned int>& Hdf5Reader::GetNodesOfRegion(const std::string& regionName)
{
  if (std::find(this->RegionNames.begin(), this->RegionNames.end(), regionName) ==
    this->RegionNames.end())
  {
    throw std::runtime_error(std::string("no nodes present for region ") + regionName);
  }

  return this->RegionNodes[regionName];
}

//-----------------------------------------------------------------------------
const std::vector<unsigned int>& Hdf5Reader::GetNamedNodes(const std::string& name)
{
  if (std::find(this->NodeNames.begin(), this->NodeNames.end(), name) == this->NodeNames.end() &&
    std::find(this->ElementNames.begin(), this->ElementNames.end(), name) ==
      this->ElementNames.end())
  {
    throw std::runtime_error(std::string("no nodes present for named entity ") + name);
  }

  return this->EntityNodes[name];
}

//-----------------------------------------------------------------------------
const std::vector<unsigned int>& Hdf5Reader::GetNamedElements(const std::string& name)
{
  if (std::find(this->ElementNames.begin(), this->ElementNames.end(), name) ==
    this->ElementNames.end())
  {
    throw std::runtime_error(std::string("no elements present for named entity ") + name);
  }

  return this->EntityElems[name];
}

//-----------------------------------------------------------------------------
const std::vector<unsigned int>& Hdf5Reader::GetEntities(EntityType type, const std::string& name)
{
  bool isRegion = (std::find(this->RegionNames.begin(), this->RegionNames.end(), name) !=
    this->RegionNames.end());

  if (type == H5CFS::NODE)
  {
    return isRegion ? this->GetNodesOfRegion(name) : this->GetNamedNodes(name);
  }

  if (type == H5CFS::ELEMENT)
  {
    return isRegion ? this->GetElementsOfRegion(name) : this->GetNamedElements(name);
  }

  assert(type == H5CFS::SURF_ELEM);
  return this->GetNamedElements(name);
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetNumberOfMultiSequenceSteps(
  std::map<unsigned int, H5CFS::AnalysisType>& analysis,
  std::map<unsigned int, unsigned int>& numSteps, bool isHistory) const
{
  analysis.clear();
  numSteps.clear();

  // search for all MultiStep_n with n >= 1 and very often 1 in either
  // - /Results/History (history results are (scalar) region results
  //  - /Results/Mesh for the common nodes and elements results (almost always present)
  std::string key = "/Results/" + std::string(isHistory ? "History" : "Mesh");
  hid_t baseGroup = H5CFS::OpenGroup(this->MainRoot, key, false); // no exception
  if (baseGroup < 0)
  {
    // group does not exist, hence don't add anything.
    // nothing to close, we may exit
    return;
  }

  // next count the MultiStep_n
  H5G_info_t info = H5CFS::GetInfo(baseGroup);
  std::set<unsigned int> msStepNumbers;
  for (hsize_t i = 0; i < info.nlinks; i++)
  {
    // get name
    std::string actName = H5CFS::GetObjNameByIdx(baseGroup, i);

    // cut away "MultiStep_"-substring and convert  into int
    // we don't want to use boost::erase_all and std has no nice replacement
    char* no_str = vtksys::SystemTools::RemoveChars(actName.c_str(), "MultiStep_");
    std::string numOnly(no_str);
    msStepNumbers.insert(std::stoi(numOnly));
    delete[] no_str;

    // try to find all single multisequence steps and related analysis strings
    for (auto it : msStepNumbers)
    {
      hid_t actMsGroup = H5CFS::GetMultiStepGroup(this->MainRoot, it, isHistory);

      // get analysis string
      std::string actAnalysisString = H5CFS::ReadAttribute<std::string>(actMsGroup, "AnalysisType");
      auto actMsNumSteps = H5CFS::ReadAttribute<unsigned int>(actMsGroup, "LastStepNum");
      H5CFS::AnalysisType actAnalysis = H5CFS::NO_ANALYSIS_TYPE;
      if (actAnalysisString == "static")
      {
        actAnalysis = H5CFS::STATIC;
      }
      else if (actAnalysisString == "transient")
      {
        actAnalysis = H5CFS::TRANSIENT;
      }
      else if (actAnalysisString == "harmonic" || actAnalysisString == "multiharmonic")
      {
        actAnalysis = H5CFS::HARMONIC;
      }
      else if (actAnalysisString == "eigenFrequency")
      {
        actAnalysis = H5CFS::EIGENFREQUENCY;
      }
      else if (actAnalysisString == "buckling")
      {
        actAnalysis = H5CFS::BUCKLING;
      }
      else if (actAnalysisString == "eigenValue")
      {
        actAnalysis = H5CFS::EIGENVALUE;
      }
      else
      {
        throw std::runtime_error("Unknown analysis type found in hdf file: " + actAnalysisString);
      }
      analysis[it] = actAnalysis;
      numSteps[it] = actMsNumSteps;

      H5Gclose(actMsGroup);
    }
  }
  H5Gclose(baseGroup);
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetStepValues(unsigned int sequenceStep, const std::string& infoName,
  std::map<unsigned int, double>& steps, bool isHistory) const
{
  // open corresponding multistep group
  hid_t msGroup = H5CFS::GetMultiStepGroup(this->MainRoot, sequenceStep, isHistory);

  // open result description
  std::string key = "ResultDescription/" + std::string(infoName);
  hid_t resGroup = H5CFS::OpenGroup(msGroup, key);

  // read stepValues and stepNumbers
  std::vector<double> values;
  std::vector<unsigned int> numbers;
  H5CFS::ReadArray(resGroup, "StepNumbers", numbers);
  H5CFS::ReadArray(resGroup, "StepValues", values);

  // sanity check: both vectors need to have the same dimension
  if (values.size() != numbers.size())
  {
    throw std::runtime_error("There are not as many stepnumbers as stepvalues");
  }

  // copy to steps-array
  // make it robust to handle old optimization files which are corrupt
  // stop reading if the value is not larger than the last
  steps.clear();
  for (size_t i = 0; i < numbers.size(); ++i)
  {
    steps[numbers[i]] = values[i];
  }

  H5Gclose(resGroup);
  H5Gclose(msGroup);
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetResultTypes(unsigned int sequenceStep,
  std::vector<std::shared_ptr<H5CFS::ResultInfo>>& infos, bool isHistory) const
{
  // open ms group and 'Result Description' subgroup
  hid_t msGroup = H5CFS::GetMultiStepGroup(this->MainRoot, sequenceStep, isHistory);
  hid_t resInfoGroup = H5CFS::OpenGroup(msGroup, "ResultDescription");
  H5G_info_t gi = H5CFS::GetInfo(resInfoGroup);

  infos.clear();
  for (hsize_t i = 0; i < gi.nlinks; i++)
  {
    // iterate over all entries and assemble the result info object

    // create new H5CFS::ResultInfo objects
    std::shared_ptr<H5CFS::ResultInfo> pi(new H5CFS::ResultInfo());
    pi->name = H5CFS::GetObjNameByIdx(resInfoGroup, i);
    hid_t resGroup = H5CFS::OpenGroup(resInfoGroup, pi->name);

    pi->unit = H5CFS::ReadDataSet<std::string>(resGroup, "Unit");
    pi->entryType = static_cast<EntryType>(H5CFS::ReadDataSet<unsigned int>(resGroup, "EntryType"));
    pi->listType = static_cast<EntityType>(H5CFS::ReadDataSet<unsigned int>(resGroup, "DefinedOn"));
    pi->isHistory = isHistory;
    H5CFS::ReadArray(resGroup, "DOFNames", pi->dofNames);

    // perform consistency check
    if (pi->name.empty())
    {
      throw std::runtime_error("Result has no proper name");
    }

    if (pi->entryType == H5CFS::UNKNOWN)
    {
      throw std::runtime_error("Result '" + pi->name + "' has no proper EntryType");
    }

    if (pi->dofNames.empty())
    {
      throw std::runtime_error("Result '" + pi->name + "' has no degrees of freedoms");
    }

    // now, run over all regions and create for each region a new result info
    std::vector<std::string> entities;
    H5CFS::ReadArray(resGroup, "EntityNames", entities);

    for (const std::string& region : entities)
    {
      std::shared_ptr<H5CFS::ResultInfo> actInfo(new H5CFS::ResultInfo(*pi));
      actInfo->listName = region;
      infos.push_back(actInfo);
    }
    H5Gclose(resGroup);
  }
  H5Gclose(resInfoGroup);
  H5Gclose(msGroup);
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetMeshResult(unsigned int sequenceStep, unsigned int stepNum, Result* result)
{
  // open step group, open specific result subgroup (or external file)
  hid_t stepGroup = H5CFS::GetStepGroup(this->MainRoot, sequenceStep, stepNum);

  // check, if results are stored at external file location
  hid_t extFile = 0;
  if (this->HasExternalFiles)
  {
    std::string extFileString = H5CFS::ReadAttribute<std::string>(stepGroup, "ExtHDF5FileName");
    // construct the path with BaseDir. Convert makes sure this is also nice for Windows
    std::string extFileNameComplete =
      vtksys::SystemTools::ConvertToOutputPath(BaseDir + "/" + extFileString);
    extFile = H5Fopen(extFileNameComplete.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
    if (extFile < 0)
    {
      throw std::runtime_error(std::string("cannot open external file ") + extFileNameComplete);
    }

    // replace old step group by new one
    H5Gclose(stepGroup);
    stepGroup = H5CFS::OpenGroup(extFile, "/");
  }

  // determine region for this results
  std::string groupName = result->resultInfo->name + "/" + result->resultInfo->listName + "/";

  switch (result->resultInfo->listType)
  {
    case H5CFS::NODE:
      groupName += "Nodes";
      break;
    case H5CFS::ELEMENT:
    case H5CFS::SURF_ELEM:
      groupName += "Elements";
      break;
    default:
      throw std::runtime_error(
        "unknown mesh result type " + std::to_string(result->resultInfo->listType));
  }

  hid_t resGroup = H5CFS::OpenGroup(stepGroup, groupName);

  // read data array
  std::vector<double> realVals;
  H5CFS::ReadArray(resGroup, "Real", realVals);

  std::vector<unsigned int> idx;
  const unsigned int numDofs = static_cast<const unsigned int>(result->resultInfo->dofNames.size());
  std::vector<unsigned int> entities =
    this->GetEntities(result->resultInfo->listType, result->resultInfo->listName);
  const unsigned int numEntities = static_cast<const unsigned int>(entities.size());
  const unsigned int resVecSize = static_cast<const unsigned int>(numEntities * numDofs);

  // copy data array to result object
  // REAL part
  std::vector<double>& resRealVec = result->realVals;
  resRealVec.resize(resVecSize);
  for (unsigned int i = 0; i < numEntities; i++)
  {
    for (unsigned int iDof = 0; iDof < numDofs; iDof++)
    {
      resRealVec[i * numDofs + iDof] = realVals[i * numDofs + iDof];
    }
  }

  // check if also imaginaryinary values are present
  H5G_info_t info = H5CFS::GetInfo(resGroup);
  if (info.nlinks > 1)
  {
    result->isComplex = true;
    std::vector<double> imaginaryVals;
    H5CFS::ReadArray(resGroup, "Imag", imaginaryVals);
    std::vector<double>& resImagVec = result->imaginaryVals;
    resImagVec.resize(resVecSize);
    for (unsigned int i = 0; i < numEntities; i++)
    {
      for (unsigned int iDof = 0; iDof < numDofs; iDof++)
      {
        resImagVec[i * numDofs + iDof] = imaginaryVals[i * numDofs + iDof];
      }
    }
  }
  else
  {
    result->isComplex = false;
  }

  H5Gclose(resGroup);
  H5Gclose(stepGroup);
  if (this->HasExternalFiles)
  {
    H5Fclose(extFile);
  }
}

//-----------------------------------------------------------------------------
void Hdf5Reader::GetHistoryResult(
  unsigned int sequenceStep, const std::string& entityId, Result* result) const
{
  // open multisequence group
  hid_t msGroup =
    H5CFS::GetMultiStepGroup(this->MainRoot, sequenceStep, true); // true for isHistory

  // open group for specific result
  hid_t resGroup = H5CFS::OpenGroup(msGroup, result->resultInfo->name);

  // determine from definedOn type the correct string representation of the subgroup
  H5CFS::EntityType definedOn = result->resultInfo->listType;

  std::string entityTypeString = H5CFS::MapUnknownTypeAsString(definedOn);
  hid_t entityGroup = H5CFS::OpenGroup(resGroup, entityTypeString);
  hid_t entGroup = H5CFS::OpenGroup(entityGroup, entityId);

  // read single part of array and set it in the result vector
  H5CFS::ReadArray(entGroup, "Real", result->realVals);
  H5G_info_t info = H5CFS::GetInfo(entGroup);
  if (info.nlinks > 1)
  {
    result->isComplex = true;
    H5CFS::ReadArray(entGroup, "Imag", result->imaginaryVals);
  }
  else
  {
    result->isComplex = false;
  }

  H5Gclose(entGroup);
  H5Gclose(entityGroup);
  H5Gclose(resGroup);
  H5Gclose(msGroup);
}

//-----------------------------------------------------------------------------
void Hdf5Reader::ReadMeshStatusInformations()
{
  H5CFS::ReadAttribute(this->MeshRoot, "Nodes", "NumNodes", this->NumNodes);
  H5CFS::ReadAttribute(this->MeshRoot, "Elements", "NumElems", this->NumElems);

  // read region names and dimensions
  hid_t regionGroup = H5CFS::OpenGroup(this->MeshRoot, "Regions");
  H5G_info_t info = H5CFS::GetInfo(regionGroup);

  this->RegionNames.clear();
  for (hsize_t i = 0; i < info.nlinks; i++)
  {
    // get name
    std::string actName = H5CFS::GetObjNameByIdx(regionGroup, i);
    this->RegionNames.push_back(actName);

    hid_t actRegion = H5CFS::OpenGroup(regionGroup, actName);

    RegionDims[actName] = H5CFS::ReadAttribute<unsigned int>(actRegion, "Dimension");

    // read elem numbers for this region
    H5CFS::ReadArray(actRegion, "Elements", this->RegionElems[actName]);

    // read node numbers for this region
    H5CFS::ReadArray(actRegion, "Nodes", this->RegionNodes[actName]);

    H5Gclose(actRegion);
  }
  H5Gclose(regionGroup);

  // groups are named nodes/elements
  // we are a little tolerant w.r.t. groups
  hid_t groups = H5Gopen(this->MeshRoot, "Groups", H5P_DEFAULT);
  if (groups >= 0)
  {
    H5G_info_t groupsInfo = H5CFS::GetInfo(groups);

    this->NodeNames.clear();
    this->ElementNames.clear();

    for (hsize_t ig = 0; ig < groupsInfo.nlinks; ig++)
    {
      // get name of group
      std::string actName = H5CFS::GetObjNameByIdx(groups, ig);

      // open entitygroup and get number of different entity types
      // (nodes, elements) it is defined on
      hid_t actEntityGroup = H5CFS::OpenGroup(groups, actName);

      H5G_info_t actEntityInfo = H5CFS::GetInfo(actEntityGroup);

      // check all children of the act group for "Elements"
      bool hasElems = false;
      for (hsize_t it = 0; it < actEntityInfo.nlinks && !hasElems; it++)
      {
        if (H5CFS::GetObjNameByIdx(actEntityGroup, it) == "Elements")
        {
          hasElems = true;
        }
      }

      if (hasElems)
      {
        this->ElementNames.push_back(actName);

        // read nodes and elements from file and add to grid
        H5CFS::ReadArray(actEntityGroup, "Nodes", this->EntityNodes[actName]);
        H5CFS::ReadArray(actEntityGroup, "Elements", this->EntityElems[actName]);
      }
      else
      {
        this->NodeNames.push_back(actName);

        // read nodes from file and add to grid
        H5CFS::ReadArray(actEntityGroup, "Nodes", this->EntityNodes[actName]);
      }
      H5Gclose(actEntityGroup);
    } // end loop over entity groups

    H5Gclose(groups);
  }
}

} // end of namespace H5CFS
