MarketIO.h
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1 // This file is part of Eigen, a lightweight C++ template library
2 // for linear algebra.
3 //
4 // Copyright (C) 2011 Gael Guennebaud <gael.guennebaud@inria.fr>
5 // Copyright (C) 2012 Desire NUENTSA WAKAM <desire.nuentsa_wakam@inria.fr>
6 //
7 // This Source Code Form is subject to the terms of the Mozilla
8 // Public License v. 2.0. If a copy of the MPL was not distributed
9 // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10 
11 #ifndef EIGEN_SPARSE_MARKET_IO_H
12 #define EIGEN_SPARSE_MARKET_IO_H
13 
14 #include <iostream>
15 #include <vector>
16 
17 namespace Eigen {
18 
19 namespace internal
20 {
21  template <typename Scalar, typename StorageIndex>
22  inline void GetMarketLine (const char* line, StorageIndex& i, StorageIndex& j, Scalar& value)
23  {
24  std::stringstream sline(line);
25  sline >> i >> j >> value;
26  }
27 
28  template<> inline void GetMarketLine (const char* line, int& i, int& j, float& value)
29  { std::sscanf(line, "%d %d %g", &i, &j, &value); }
30 
31  template<> inline void GetMarketLine (const char* line, int& i, int& j, double& value)
32  { std::sscanf(line, "%d %d %lg", &i, &j, &value); }
33 
34  template<> inline void GetMarketLine (const char* line, int& i, int& j, std::complex<float>& value)
35  { std::sscanf(line, "%d %d %g %g", &i, &j, &numext::real_ref(value), &numext::imag_ref(value)); }
36 
37  template<> inline void GetMarketLine (const char* line, int& i, int& j, std::complex<double>& value)
38  { std::sscanf(line, "%d %d %lg %lg", &i, &j, &numext::real_ref(value), &numext::imag_ref(value)); }
39 
40  template <typename Scalar, typename StorageIndex>
41  inline void GetMarketLine (const char* line, StorageIndex& i, StorageIndex& j, std::complex<Scalar>& value)
42  {
43  std::stringstream sline(line);
44  Scalar valR, valI;
45  sline >> i >> j >> valR >> valI;
46  value = std::complex<Scalar>(valR,valI);
47  }
48 
49  template <typename RealScalar>
50  inline void GetVectorElt (const std::string& line, RealScalar& val)
51  {
52  std::istringstream newline(line);
53  newline >> val;
54  }
55 
56  template <typename RealScalar>
57  inline void GetVectorElt (const std::string& line, std::complex<RealScalar>& val)
58  {
59  RealScalar valR, valI;
60  std::istringstream newline(line);
61  newline >> valR >> valI;
62  val = std::complex<RealScalar>(valR, valI);
63  }
64 
65  template<typename Scalar>
66  inline void putMarketHeader(std::string& header,int sym)
67  {
68  header= "%%MatrixMarket matrix coordinate ";
69  if(internal::is_same<Scalar, std::complex<float> >::value || internal::is_same<Scalar, std::complex<double> >::value)
70  {
71  header += " complex";
72  if(sym == Symmetric) header += " symmetric";
73  else if (sym == SelfAdjoint) header += " Hermitian";
74  else header += " general";
75  }
76  else
77  {
78  header += " real";
79  if(sym == Symmetric) header += " symmetric";
80  else header += " general";
81  }
82  }
83 
84  template<typename Scalar, typename StorageIndex>
85  inline void PutMatrixElt(Scalar value, StorageIndex row, StorageIndex col, std::ofstream& out)
86  {
87  out << row << " "<< col << " " << value << "\n";
88  }
89  template<typename Scalar, typename StorageIndex>
90  inline void PutMatrixElt(std::complex<Scalar> value, StorageIndex row, StorageIndex col, std::ofstream& out)
91  {
92  out << row << " " << col << " " << value.real() << " " << value.imag() << "\n";
93  }
94 
95 
96  template<typename Scalar>
97  inline void putVectorElt(Scalar value, std::ofstream& out)
98  {
99  out << value << "\n";
100  }
101  template<typename Scalar>
102  inline void putVectorElt(std::complex<Scalar> value, std::ofstream& out)
103  {
104  out << value.real() << " " << value.imag()<< "\n";
105  }
106 
107 } // end namespace internal
108 
109 inline bool getMarketHeader(const std::string& filename, int& sym, bool& iscomplex, bool& isvector)
110 {
111  sym = 0;
112  iscomplex = false;
113  isvector = false;
114  std::ifstream in(filename.c_str(),std::ios::in);
115  if(!in)
116  return false;
117 
118  std::string line;
119  // The matrix header is always the first line in the file
120  std::getline(in, line); eigen_assert(in.good());
121 
122  std::stringstream fmtline(line);
123  std::string substr[5];
124  fmtline>> substr[0] >> substr[1] >> substr[2] >> substr[3] >> substr[4];
125  if(substr[2].compare("array") == 0) isvector = true;
126  if(substr[3].compare("complex") == 0) iscomplex = true;
127  if(substr[4].compare("symmetric") == 0) sym = Symmetric;
128  else if (substr[4].compare("Hermitian") == 0) sym = SelfAdjoint;
129 
130  return true;
131 }
132 
133 template<typename SparseMatrixType>
134 bool loadMarket(SparseMatrixType& mat, const std::string& filename)
135 {
136  typedef typename SparseMatrixType::Scalar Scalar;
137  typedef typename SparseMatrixType::StorageIndex StorageIndex;
138  std::ifstream input(filename.c_str(),std::ios::in);
139  if(!input)
140  return false;
141 
142  char rdbuffer[4096];
143  input.rdbuf()->pubsetbuf(rdbuffer, 4096);
144 
145  const int maxBuffersize = 2048;
146  char buffer[maxBuffersize];
147 
148  bool readsizes = false;
149 
151  std::vector<T> elements;
152 
153  Index M(-1), N(-1), NNZ(-1);
154  Index count = 0;
155  while(input.getline(buffer, maxBuffersize))
156  {
157  // skip comments
158  //NOTE An appropriate test should be done on the header to get the symmetry
159  if(buffer[0]=='%')
160  continue;
161 
162  if(!readsizes)
163  {
164  std::stringstream line(buffer);
165  line >> M >> N >> NNZ;
166  if(M > 0 && N > 0)
167  {
168  readsizes = true;
169  mat.resize(M,N);
170  mat.reserve(NNZ);
171  }
172  }
173  else
174  {
175  StorageIndex i(-1), j(-1);
176  Scalar value;
178 
179  i--;
180  j--;
181  if(i>=0 && j>=0 && i<M && j<N)
182  {
183  ++count;
184  elements.push_back(T(i,j,value));
185  }
186  else
187  std::cerr << "Invalid read: " << i << "," << j << "\n";
188  }
189  }
190 
191  mat.setFromTriplets(elements.begin(), elements.end());
192  if(count!=NNZ)
193  std::cerr << count << "!=" << NNZ << "\n";
194 
195  input.close();
196  return true;
197 }
198 
199 template<typename VectorType>
200 bool loadMarketVector(VectorType& vec, const std::string& filename)
201 {
202  typedef typename VectorType::Scalar Scalar;
203  std::ifstream in(filename.c_str(), std::ios::in);
204  if(!in)
205  return false;
206 
207  std::string line;
208  int n(0), col(0);
209  do
210  { // Skip comments
211  std::getline(in, line); eigen_assert(in.good());
212  } while (line[0] == '%');
213  std::istringstream newline(line);
214  newline >> n >> col;
215  eigen_assert(n>0 && col>0);
216  vec.resize(n);
217  int i = 0;
218  Scalar value;
219  while ( std::getline(in, line) && (i < n) ){
221  vec(i++) = value;
222  }
223  in.close();
224  if (i!=n){
225  std::cerr<< "Unable to read all elements from file " << filename << "\n";
226  return false;
227  }
228  return true;
229 }
230 
231 template<typename SparseMatrixType>
232 bool saveMarket(const SparseMatrixType& mat, const std::string& filename, int sym = 0)
233 {
234  typedef typename SparseMatrixType::Scalar Scalar;
235  typedef typename SparseMatrixType::RealScalar RealScalar;
236  std::ofstream out(filename.c_str(),std::ios::out);
237  if(!out)
238  return false;
239 
240  out.flags(std::ios_base::scientific);
241  out.precision(std::numeric_limits<RealScalar>::digits10 + 2);
242  std::string header;
243  internal::putMarketHeader<Scalar>(header, sym);
244  out << header << std::endl;
245  out << mat.rows() << " " << mat.cols() << " " << mat.nonZeros() << "\n";
246  int count = 0;
247  for(int j=0; j<mat.outerSize(); ++j)
248  for(typename SparseMatrixType::InnerIterator it(mat,j); it; ++it)
249  {
250  ++ count;
251  internal::PutMatrixElt(it.value(), it.row()+1, it.col()+1, out);
252  }
253  out.close();
254  return true;
255 }
256 
257 template<typename VectorType>
258 bool saveMarketVector (const VectorType& vec, const std::string& filename)
259 {
260  typedef typename VectorType::Scalar Scalar;
261  typedef typename VectorType::RealScalar RealScalar;
262  std::ofstream out(filename.c_str(),std::ios::out);
263  if(!out)
264  return false;
265 
266  out.flags(std::ios_base::scientific);
267  out.precision(std::numeric_limits<RealScalar>::digits10 + 2);
268  if(internal::is_same<Scalar, std::complex<float> >::value || internal::is_same<Scalar, std::complex<double> >::value)
269  out << "%%MatrixMarket matrix array complex general\n";
270  else
271  out << "%%MatrixMarket matrix array real general\n";
272  out << vec.size() << " "<< 1 << "\n";
273  for (int i=0; i < vec.size(); i++){
274  internal::putVectorElt(vec(i), out);
275  }
276  out.close();
277  return true;
278 }
279 
280 } // end namespace Eigen
281 
282 #endif // EIGEN_SPARSE_MARKET_IO_H
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@ Symmetric
Definition: Constants.h:227
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Definition: Eigen/src/Core/MathFunctions.h:1267
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#define eigen_assert(x)
Definition: Macros.h:1037
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void GetVectorElt(const std::string &line, RealScalar &val)
Definition: MarketIO.h:50
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bool loadMarketVector(VectorType &vec, const std::string &filename)
Definition: MarketIO.h:200
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bool saveMarketVector(const VectorType &vec, const std::string &filename)
Definition: MarketIO.h:258
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Definition: MarketIO.h:66
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Definition: Eigen/src/Core/MathFunctions.h:1239
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A small structure to hold a non zero as a triplet (i,j,value).
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void putVectorElt(Scalar value, std::ofstream &out)
Definition: MarketIO.h:97
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void GetMarketLine(const char *line, StorageIndex &i, StorageIndex &j, Scalar &value)
Definition: MarketIO.h:22
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Definition: MarketIO.h:85
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m row(1)
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bool saveMarket(const SparseMatrixType &mat, const std::string &filename, int sym=0)
Definition: MarketIO.h:232
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bool getMarketHeader(const std::string &filename, int &sym, bool &iscomplex, bool &isvector)
Definition: MarketIO.h:109
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Definition: MarketIO.h:134
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The Index type as used for the API.
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