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

  Program:   ITK-SNAP
  Module:    $RCSfile: ImageCoordinateGeometry.cxx,v $
  Language:  C++
  Date:      $Date: 2009/10/12 19:05:56 $
  Version:   $Revision: 1.4 $
  Copyright (c) 2007 Paul A. Yushkevich
  
  This file is part of ITK-SNAP 

  ITK-SNAP 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.

  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/>.

  -----

  Copyright (c) 2003 Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.  See the above copyright notices for more information. 

=========================================================================*/
#include "ImageCoordinateGeometry.h"
#include "IRISException.h"

const char ImageCoordinateGeometry::m_RAICodes[3][2] = {
  {'R', 'L'},
  {'A', 'P'},
  {'I', 'S'}};

ImageCoordinateGeometry::AxisDirectionDescriptionMap
ImageCoordinateGeometry::m_AxisDirectionDescriptionMap;

ImageCoordinateGeometry
::ImageCoordinateGeometry()
{
  // By default all transforms are identity.  Nothing to do here
  m_ImageToAnatomyTransform = ImageCoordinateTransform::New();

  for(int i = 0; i < 3; i++)
    {
    m_AnatomyToDisplayTransform[i] = ImageCoordinateTransform::New();
    m_ImageToDisplayTransform[i] = ImageCoordinateTransform::New();
    m_DisplayToImageTransform[i] = ImageCoordinateTransform::New();
    }
}

void
ImageCoordinateGeometry
::SetGeometry(DirectionMatrix imageDirection,
              const IRISDisplayGeometry &dispGeom,
              const Vector3ui &imageSize)
{
  // Store the image direction matrix
  m_ImageDirectionCosineMatrix = imageDirection; 

  // Keep a copy of the display-to-anatomy geometry
  m_DisplayGeometry = dispGeom;

  // Remap the direction matrix to an RAI code
  std::string imageAnatomyRAICode = 
    ConvertDirectionMatrixToClosestRAICode(m_ImageDirectionCosineMatrix);  

  // Check the code
  if(!IsRAICodeValid(imageAnatomyRAICode))
    throw IRISException("Image has an invalid orientation (code %s)",
                        imageAnatomyRAICode.c_str());

  // We can easily compute the image to anatomy transform
  m_ImageToAnatomyTransform->SetTransform(
    ConvertRAIToCoordinateMapping(imageAnatomyRAICode.c_str()),imageSize);

  // Compute the size of the anatomy image in its coordinates
  Vector3ui szAnatomy = m_ImageToAnatomyTransform->TransformSize(imageSize);

  // Compute the anatomy to display transform
  for(unsigned int slice=0;slice < 3;slice++)
    {
    // Get the display to anatomy RAI code for this slice
    const char *displayAnatomyRAICode = m_DisplayGeometry.DisplayToAnatomyRAI[slice].c_str();

    // Make sure the code is valid
    assert(IsRAICodeValid(displayAnatomyRAICode));

    m_AnatomyToDisplayTransform[slice]->SetTransform(
          InvertMappingVector(ConvertRAIToCoordinateMapping(displayAnatomyRAICode)),
          szAnatomy);

    // Compute the combined transform
    m_AnatomyToDisplayTransform[slice]->ComputeProduct(
          m_ImageToAnatomyTransform, m_ImageToDisplayTransform[slice]);

    // Compute the opposite direction transform
    m_ImageToDisplayTransform[slice]->ComputeInverse(
          m_DisplayToImageTransform[slice]);
    }
}

bool 
ImageCoordinateGeometry
::IsRAICodeValid(const std::string &rai)
{
  if(rai.size() != 3)
    return false;

  // Check the validity of the RAI code - no repetition
  // is allowed
  bool rl = false,ap = false,is = false;
  for (int i=0;i<3;i++) 
    {
    switch (rai[i]) 
      {
      case 'r' :
      case 'R' :
      case 'l' :
      case 'L' :
        rl = true;break;
      case 'a' :
      case 'A' :
      case 'p' :
      case 'P' :
        ap = true;break;
      case 'i' :
      case 'I' :
      case 's' :
      case 'S' :
        is = true;break;
      default:
        return false;
      }
    }

  // All three should have been encountered!
  return rl && ap && is;
}

ImageCoordinateGeometry::AxisDirectionDescriptionMap
&ImageCoordinateGeometry::GetAxisDirectionDescriptionMap()
{
  if(m_AxisDirectionDescriptionMap.size() == 0)
    {
    m_AxisDirectionDescriptionMap[R_TO_L] = "Right to Left";
    m_AxisDirectionDescriptionMap[L_TO_R] = "Left to Right";
    m_AxisDirectionDescriptionMap[A_TO_P] = "Anterior to Posterior";
    m_AxisDirectionDescriptionMap[P_TO_A] = "Posterior to Anterior";
    m_AxisDirectionDescriptionMap[I_TO_S] = "Inferior to Superior";
    m_AxisDirectionDescriptionMap[S_TO_I] = "Superior to Inferior";
    }

  return m_AxisDirectionDescriptionMap;
}

ImageCoordinateGeometry::AxisDirection
ImageCoordinateGeometry::ConvertRAILetterToAxisDirection(char letter)
{
  ImageCoordinateGeometry::AxisDirection axisDirection;

  switch(letter)
    {
    case 'r' :
    case 'R' : axisDirection = R_TO_L;break;
    case 'l' :
    case 'L' : axisDirection = L_TO_R;break;
    case 'a' :
    case 'A' : axisDirection = A_TO_P;break;
    case 'p' :
    case 'P' : axisDirection = P_TO_A;break;
    case 'i' :
    case 'I' : axisDirection = I_TO_S;break;
    case 's' :
    case 'S' : axisDirection = S_TO_I;break;
    default  : axisDirection = INVALID_DIRECTION;
    }
  return(axisDirection);
}

char ImageCoordinateGeometry
::ConvertAxisDirectionToRAILetter(ImageCoordinateGeometry::AxisDirection dir)
{
  switch(dir)
    {
    case R_TO_L: return 'R';
    case L_TO_R: return 'L';
    case A_TO_P: return 'A';
    case P_TO_A: return 'P';
    case I_TO_S: return 'I';
    case S_TO_I: return 'S';
    default:
      assert(0);
      return (char) 0;
    }
}

Vector3i
ImageCoordinateGeometry
::ConvertRAIToCoordinateMapping(const std::string &rai)
{
  assert(IsRAICodeValid(rai));
  
  Vector3i result;

  for(unsigned int i=0;i<3;i++)
    {
    result[i] = (int) ConvertRAILetterToAxisDirection(rai[i]);
    assert(result[i] != INVALID_DIRECTION);
    }

  return result;
}


std::string 
ImageCoordinateGeometry
::ConvertDirectionMatrixToClosestRAICode(DirectionMatrix mat)
{
  // RAI codes for cardinal directions
  const static std::string rai_start("RAI"), rai_end("LPS");
  std::string rai_out("...");

  for(size_t i = 0; i < 3; i++)
    {
    // Get the direction of the i-th voxel coordinate
    vnl_vector<double> dir_i = mat.get_column(i);

    // Get the maximum angle with any axis
    double maxabs_i = dir_i.inf_norm();
    for(size_t off = 0; off < 3; off++)
      {
      // This trick allows us to visit (i,i) first, so that if one of the
      // direction cosines makes the same angle with two of the axes, we 
      // can still assign a valid RAI code
      size_t j = (i + off) % 3;

      // Is j the best-matching direction?
      if(fabs(dir_i[j]) == maxabs_i)
        {
        rai_out[i] = dir_i[j] > 0 ? rai_start[j] : rai_end[j];
        break;
        }
      }
    }
      
  return rai_out;
}

ImageCoordinateGeometry::DirectionMatrix
ImageCoordinateGeometry::ConvertRAICodeToDirectionMatrix(
    const std::string &rai)
{
  // Check the RAI code
  assert(IsRAICodeValid(rai.c_str()));

  // An identity matrix, for pulling out rows
  Matrix3d eye;
  eye.set_identity();

  // Create the output direction matrix
  DirectionMatrix dm(3, 3);

  // Apply the RAI code
  for(size_t i = 0; i < 3; i++)
    {
    for(size_t j = 0; j < 3; j++)
      {
      for(size_t k = 0; k < 2; k++)
        {
        if(toupper(rai[i]) == m_RAICodes[j][k])
          {
          dm.set_column(i, (k==0 ? 1.0 : -1.0) * eye.get_row(j).as_ref());
          }
        }
      }
    }

  return dm;
}

bool
ImageCoordinateGeometry
::IsDirectionMatrixOblique(DirectionMatrix mat)
{
  for(size_t i = 0; i < 3; i++)
    for(size_t j = 0; j < 3; j++)
      if(fabs(mat[i][j]) > 0 && fabs(mat[i][j]) < 1)
        return true;
  return false;
}


Vector3i
ImageCoordinateGeometry
::InvertMappingVector(const Vector3i &map)
{
  Vector3i inv;

  for(int i=0;i<3;i++)
    {
    if(map[i] > 0)
      inv[map[i]-1] = i+1;
    else
      inv[-1-map[i]] = -i-1;
    }

  return inv;
}
