MatlabWorkspace.h

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// This file is part of libigl, a simple c++ geometry processing library.
// 
// Copyright (C) 2013 Alec Jacobson <alecjacobson@gmail.com>
// 
// This Source Code Form is subject to the terms of the Mozilla Public License 
// v. 2.0. If a copy of the MPL was not distributed with this file, You can 
// obtain one at http://mozilla.org/MPL/2.0/.
#ifndef IGL_MATLAB_MATLAB_WORKSPACE_H
#define IGL_MATLAB_MATLAB_WORKSPACE_H
 
#include <Eigen/Dense>
#include <Eigen/Sparse>
 
#include <mat.h>
 
#include <string>
#include <vector>
 
namespace igl
{
  namespace matlab
  {
    class MatlabWorkspace
    {
      private:
        std::vector<std::string> names;
        std::vector<mxArray*> data;
      public:
        MatlabWorkspace();
        ~MatlabWorkspace();
        inline void clear();
        inline bool write(const std::string & path) const;
        inline bool read(const std::string & path);
        template <typename DerivedM>
        inline MatlabWorkspace& save(
          const Eigen::MatrixBase<DerivedM>& M,
          const std::string & name);
        template <typename MT>
        inline MatlabWorkspace& save(
          const Eigen::SparseMatrix<MT>& M,
          const std::string & name);
        template <typename ScalarM>
        inline MatlabWorkspace& save(
          const std::vector<std::vector<ScalarM> > & vM,
          const std::string & name);
        template <typename ScalarV>
        inline MatlabWorkspace& save(
          const std::vector<ScalarV> & vV,
          const std::string & name);
        template <typename Q>
        inline MatlabWorkspace& save(
          const Eigen::Quaternion<Q> & q,
          const std::string & name);
        inline MatlabWorkspace& save(
          const double d,
          const std::string & name);
        template <typename DerivedM>
        inline MatlabWorkspace& save_index(
          const Eigen::DenseBase<DerivedM>& M,
          const std::string & name);
        template <typename ScalarM>
        inline MatlabWorkspace& save_index(
          const std::vector<std::vector<ScalarM> > & vM,
          const std::string & name);
        template <typename ScalarV>
        inline MatlabWorkspace& save_index(
          const std::vector<ScalarV> & vV,
          const std::string & name);
        template <typename DerivedM>
        inline bool find( 
          const std::string & name,
          Eigen::PlainObjectBase<DerivedM>& M);
        template <typename MT>
        inline bool find( 
          const std::string & name,
          Eigen::SparseMatrix<MT>& M);
        inline bool find( 
          const std::string & name,
          double & d);
        inline bool find( 
          const std::string & name,
          int & v);
        template <typename DerivedM>
        inline bool find_index( 
          const std::string & name,
          Eigen::PlainObjectBase<DerivedM>& M);
    };
  }
}
 
// Implementation
 
// Be sure that this is not compiled into libigl.a
// http://stackoverflow.com/a/3318993/148668
 
// IGL
#include "igl/list_to_matrix.h"
 
// MATLAB
#include "mat.h"
 
// STL
#include <iostream>
#include <algorithm>
#include <vector>
 
inline igl::matlab::MatlabWorkspace::MatlabWorkspace():
  names(),
  data()
{
}
 
inline igl::matlab::MatlabWorkspace::~MatlabWorkspace()
{
  // clean up data
  clear();
}
 
inline void igl::matlab::MatlabWorkspace::clear()
{
  for_each(data.begin(),data.end(),&mxDestroyArray);
  data.clear();
  names.clear();
}
 
inline bool igl::matlab::MatlabWorkspace::write(const std::string & path) const
{
  MATFile * mat_file = matOpen(path.c_str(), "w");
  if(mat_file == NULL)
  {
    fprintf(stderr,"Error opening file %s\n",path.c_str());
    return false;
  }
  assert(names.size() == data.size());
  // loop over names and data
  for(int i = 0;i < (int)names.size(); i++)
  {
    // Put variable as LOCAL variable
    int status = matPutVariable(mat_file,names[i].c_str(), data[i]);
    if(status != 0) 
    {
      std::cerr<<"^MatlabWorkspace::save Error: matPutVariable ("<<names[i]<<
        ") failed"<<std::endl;
      return false;
    } 
  }
  if(matClose(mat_file) != 0)
  {
    fprintf(stderr,"Error closing file %s\n",path.c_str());
    return false;
  }
  return true;
}
 
inline bool igl::matlab::MatlabWorkspace::read(const std::string & path)
{
 
  MATFile * mat_file;
 
  mat_file = matOpen(path.c_str(), "r");
  if (mat_file == NULL) 
  {
    std::cerr<<"Error: failed to open "<<path<<std::endl;
    return false;
  }
 
  int ndir;
  const char ** dir = (const char **)matGetDir(mat_file, &ndir);
  if (dir == NULL) {
    std::cerr<<"Error reading directory of file "<< path<<std::endl;
    return false;
  }
  mxFree(dir);
 
  // Must close and reopen
  if(matClose(mat_file) != 0)
  {
    std::cerr<<"Error: failed to close file "<<path<<std::endl;
    return false;
  }
  mat_file = matOpen(path.c_str(), "r");
  if (mat_file == NULL) 
  {
    std::cerr<<"Error: failed to open "<<path<<std::endl;
    return false;
  }
  
 
  /* Read in each array. */
  for (int i=0; i<ndir; i++) 
  {
    const char * name;
    mxArray * mx_data = matGetNextVariable(mat_file, &name);
    if (mx_data == NULL) 
    {
      std::cerr<<"Error: matGetNextVariable failed in "<<path<<std::endl;
      return false;
    } 
    const int dims = mxGetNumberOfDimensions(mx_data);
    assert(dims == 2);
    if(dims != 2)
    {
      fprintf(stderr,"Variable '%s' has %d ≠ 2 dimensions. Skipping\n",
          name,dims);
      mxDestroyArray(mx_data);
      continue;
    }
    // don't destroy
    names.push_back(name);
    data.push_back(mx_data);
  }
 
  if(matClose(mat_file) != 0)
  {
    std::cerr<<"Error: failed to close file "<<path<<std::endl;
    return false;
  }
 
  return true;
}
 
// Treat everything as a double
template <typename DerivedM>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
  const Eigen::MatrixBase<DerivedM>& M,
  const std::string & name)
{
  const int m = M.rows();
  const int n = M.cols();
  mxArray * mx_data = mxCreateDoubleMatrix(m,n,mxREAL);
  data.push_back(mx_data);
  names.push_back(name);
  // Copy data immediately
  // Use Eigen's map and cast to copy
  Eigen::Map< Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> > 
    map(mxGetPr(mx_data),m,n);
  map = M.template cast<double>();
  return *this;
}
 
// Treat everything as a double
template <typename MT>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
  const Eigen::SparseMatrix<MT>& M,
  const std::string & name)
{
  const int m = M.rows();
  const int n = M.cols();
  // THIS WILL NOT WORK FOR ROW-MAJOR
  assert(n==M.outerSize());
  const int nzmax = M.nonZeros();
  mxArray * mx_data = mxCreateSparse(m, n, nzmax, mxREAL);
  data.push_back(mx_data);
  names.push_back(name);
  // Copy data immediately
  double * pr = mxGetPr(mx_data);
  mwIndex * ir = mxGetIr(mx_data);
  mwIndex * jc = mxGetJc(mx_data);
 
  // Iterate over outside
  int k = 0;
  for(int j=0; j<M.outerSize();j++)
  {
    jc[j] = k;
    // Iterate over inside
    for(typename Eigen::SparseMatrix<MT>::InnerIterator it (M,j); it; ++it)
    {
      pr[k] = it.value();
      ir[k] = it.row();
      k++;
    }
  }
  jc[M.outerSize()] = k;
 
  return *this;
}
 
template <typename ScalarM>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
  const std::vector<std::vector<ScalarM> > & vM,
  const std::string & name)
{
  Eigen::MatrixXd M;
  list_to_matrix(vM,M);
  return this->save(M,name);
}
 
template <typename ScalarV>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
  const std::vector<ScalarV> & vV,
  const std::string & name)
{
  Eigen::MatrixXd V;
  list_to_matrix(vV,V);
  return this->save(V,name);
}
 
template <typename Q>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
  const Eigen::Quaternion<Q> & q,
  const std::string & name)
{
  Eigen::Matrix<Q,1,4> qm;
  qm(0,0) = q.w();
  qm(0,1) = q.x();
  qm(0,2) = q.y();
  qm(0,3) = q.z();
  return save(qm,name);
}
 
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
  const double d,
  const std::string & name)
{
  Eigen::VectorXd v(1);
  v(0) = d;
  return save(v,name);
}
 
template <typename DerivedM>
inline igl::matlab::MatlabWorkspace& 
  igl::matlab::MatlabWorkspace::save_index(
    const Eigen::DenseBase<DerivedM>& M,
    const std::string & name)
{
  DerivedM Mp1 = M;
  Mp1.array() += 1;
  return this->save(Mp1,name);
}
 
template <typename ScalarM>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save_index(
  const std::vector<std::vector<ScalarM> > & vM,
  const std::string & name)
{
  Eigen::MatrixXd M;
  list_to_matrix(vM,M);
  return this->save_index(M,name);
}
 
template <typename ScalarV>
inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save_index(
  const std::vector<ScalarV> & vV,
  const std::string & name)
{
  Eigen::MatrixXd V;
  list_to_matrix(vV,V);
  return this->save_index(V,name);
}
 
template <typename DerivedM>
inline bool igl::matlab::MatlabWorkspace::find( 
  const std::string & name,
  Eigen::PlainObjectBase<DerivedM>& M)
{
  const int i = std::find(names.begin(), names.end(), name)-names.begin();
  if(i>=(int)names.size())
  {
    return false;
  }
  assert(i<=(int)data.size());
  mxArray * mx_data = data[i];
  assert(!mxIsSparse(mx_data));
  assert(mxGetNumberOfDimensions(mx_data) == 2);
  //cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
  const int m = mxGetM(mx_data);
  const int n = mxGetN(mx_data);
  // Handle vectors: in the sense that anything found becomes a column vector,
  // whether it was column vector, row vector or matrix
  if(DerivedM::IsVectorAtCompileTime)
  {
    assert(m==1 || n==1 || (m==0 && n==0));
    M.resize(m*n,1);
  }else
  {
    M.resize(m,n);
  }
  assert(mxGetNumberOfElements(mx_data) == M.size());
  // Use Eigen's map and cast to copy
  M = Eigen::Map< Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> > 
    (mxGetPr(mx_data),M.rows(),M.cols()).cast<typename DerivedM::Scalar>();
  return true;
}
 
template <typename MT>
inline bool igl::matlab::MatlabWorkspace::find( 
  const std::string & name,
  Eigen::SparseMatrix<MT>& M)
{
  const int i = std::find(names.begin(), names.end(), name)-names.begin();
  if(i>=(int)names.size())
  {
    return false;
  }
  assert(i<=(int)data.size());
  mxArray * mx_data = data[i];
  // Handle boring case where matrix is actually an empty dense matrix
  if(mxGetNumberOfElements(mx_data) == 0)
  {
    M.resize(0,0);
    return true;
  }
  assert(mxIsSparse(mx_data));
  assert(mxGetNumberOfDimensions(mx_data) == 2);
  //cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
  const int m = mxGetM(mx_data);
  const int n = mxGetN(mx_data);
  // TODO: It should be possible to directly load the data into the sparse
  // matrix without going through the triplets
  // Copy data immediately
  double * pr = mxGetPr(mx_data);
  mwIndex * ir = mxGetIr(mx_data);
  mwIndex * jc = mxGetJc(mx_data);
  vector<Eigen::Triplet<MT> > MIJV;
  const int nnz = mxGetNzmax(mx_data);
  MIJV.reserve(nnz);
  // Iterate over outside
  int k = 0;
  for(int j=0; j<n;j++)
  {
    // Iterate over inside
    while(k<(int)jc[j+1])
    {
      //cout<<ir[k]<<" "<<j<<" "<<pr[k]<<endl;
      assert((int)ir[k]<m);
      assert((int)j<n);
      MIJV.push_back(Eigen::Triplet<MT >(ir[k],j,pr[k]));
      k++;
    }
  }
  M.resize(m,n);
  M.setFromTriplets(MIJV.begin(),MIJV.end());
 
  return true;
}
 
inline bool igl::matlab::MatlabWorkspace::find( 
  const std::string & name,
  int & v)
{
  const int i = std::find(names.begin(), names.end(), name)-names.begin();
  if(i>=(int)names.size())
  {
    return false;
  }
  assert(i<=(int)data.size());
  mxArray * mx_data = data[i];
  assert(!mxIsSparse(mx_data));
  assert(mxGetNumberOfDimensions(mx_data) == 2);
  //cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
  assert(mxGetNumberOfElements(mx_data) == 1);
  copy(
    mxGetPr(mx_data),
    mxGetPr(mx_data)+mxGetNumberOfElements(mx_data),
    &v);
  return true;
}
 
inline bool igl::matlab::MatlabWorkspace::find( 
  const std::string & name,
  double & d)
{
  const int i = std::find(names.begin(), names.end(), name)-names.begin();
  if(i>=(int)names.size())
  {
    return false;
  }
  assert(i<=(int)data.size());
  mxArray * mx_data = data[i];
  assert(!mxIsSparse(mx_data));
  assert(mxGetNumberOfDimensions(mx_data) == 2);
  //cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
  assert(mxGetNumberOfElements(mx_data) == 1);
  copy(
    mxGetPr(mx_data),
    mxGetPr(mx_data)+mxGetNumberOfElements(mx_data),
    &d);
  return true;
}
 
template <typename DerivedM>
inline bool igl::matlab::MatlabWorkspace::find_index( 
  const std::string & name,
  Eigen::PlainObjectBase<DerivedM>& M)
{
  if(!find(name,M))
  {
    return false;
  }
  M.array() -= 1;
  return true;
}
 
 
//template <typename Data>
//bool igl::matlab::MatlabWorkspace::save(const Data & M, const std::string & name)
//{
//  using namespace std;
//  // If I don't know the type then I can't save it
//  std::cerr<<"^MatlabWorkspace::save Error: Unknown data type. "<<
//    name<<" not saved."<<std::endl;
//  return false;
//}
 
#endif