EST_DMatrix.cc

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 /*************************************************************************/
 /*                                                                       */
 /*                     Author :  Simon King                              */
 /*                     Date   :  February 1999                           */
 /* --------------------------------------------------------------------- */
 /*          Double matrix class - copied from DMatrix !                  */
 /*                                                                       */
 /*************************************************************************/

#include <cstdlib>
#include <cstdio>
#include <fstream>
#include <sstream>
#include <cmath>
#include <climits>
#include "EST_String.h"
#include "EST_types.h"
#include "EST_FileType.h"
#include "EST_Option.h"
#include "EST_DMatrix.h"
#include "EST_cutils.h"  // for swap functions 
#include "EST_Token.h"
#include "rateconv.h"

using namespace std;

EST_String EST_DMatrix::default_file_type = "est_ascii";

EST_DMatrix::EST_DMatrix(const EST_DMatrix &a, int b)
:EST_TSimpleMatrix<double>(a.num_rows(), a.num_columns())
{
    double vv = 0.0;
    if (b < 0)
    return;
    if (b == 0)
    fill(vv);
}

EST_DMatrix & EST_DMatrix::operator+=(const EST_DMatrix &a)
{
    ssize_t i, j;
    if (a.num_columns() != num_columns())
    {
    cerr <<"Matrix addition error: bad number of columns\n";
    return *this;
    }
    if (a.num_rows() != num_rows())
    {
    cerr <<"Matrix addition error: bad number of rows\n";
    return *this;
    }
    for (i = 0; i < num_rows(); ++i)
    for (j = 0; j < num_columns(); ++j)
        a_no_check(i, j) += a.a_no_check(i,j);

    return *this;
}

EST_DMatrix & EST_DMatrix::operator-=(const EST_DMatrix &a)
{
    ssize_t i, j;
    if (a.num_columns() != num_columns())
    {
    cerr <<"Matrix subtraction error: bad number of columns\n";
    return *this;
    }
    if (a.num_rows() != num_rows())
    {
    cerr <<"Matrix subtraction error: bad number of rows\n";
    return *this;
    }
    for (i = 0; i < num_rows(); ++i)
    for (j = 0; j < num_columns(); ++j)
        a_no_check(i, j) -= a.a_no_check(i,j);

    return *this;
}

EST_DMatrix & EST_DMatrix::operator*=(const double f)
{

    ssize_t i,j;
    for (i = 0; i < num_rows(); ++i)
    for (j = 0; j < num_columns(); ++j)
        a_no_check(i, j) *= f;

    return *this;
}

EST_DMatrix & EST_DMatrix::operator/=(const double f)
{

    ssize_t i,j;
    for (i = 0; i < num_rows(); ++i)
    for (j = 0; j < num_columns(); ++j)
        a_no_check(i, j) /= f;

    return *this;
}

EST_DMatrix operator+(const EST_DMatrix &a, const EST_DMatrix &b)
{
    EST_DMatrix ab;
    ssize_t i, j;
    if (a.num_columns() != b.num_columns())
    {
    cerr <<"Matrix addition error: bad number of columns\n";
    return ab;
    }
    if (a.num_rows() != b.num_rows())
    {
    cerr <<"Matrix addition error: bad number of rows\n";
    return ab;
    }
    ab.resize(a.num_rows(), a.num_columns());
    for (i = 0; i < a.num_rows(); ++i)
    for (j = 0; j < a.num_columns(); ++j)
        ab.a_no_check(i, j) = a.a_no_check(i, j) + b.a_no_check(i, j);

    return ab;
}

EST_DMatrix operator-(const EST_DMatrix &a,const EST_DMatrix &b)
{
    EST_DMatrix ab;
    ssize_t i, j;

    if (a.num_columns() != b.num_columns())
    {
    cerr <<"Matrix subtraction error: bad number of columns:" <<
        a.num_columns() << " and " << b.num_columns() << endl;
    return ab;
    }
    if (a.num_rows() != b.num_rows())
    {
    cerr <<"Matrix subtraction error: bad number of rows\n";
    return ab;
    }
    ab.resize(a.num_rows(), a.num_columns());
    for (i = 0; i < a.num_rows(); ++i)
    for (j = 0; j < a.num_columns(); ++j)
        ab.a_no_check(i, j) = a.a_no_check(i, j) - b.a_no_check(i, j);

    return ab;
}

EST_DMatrix operator*(const double x, const EST_DMatrix &a)
{
    return a*x;
}

EST_DMatrix operator*(const EST_DMatrix &a, const double x)
{
    EST_DMatrix b(a, 0);
    ssize_t i, j;

    for (i = 0; i < a.num_rows(); ++i)
    for (j = 0; j < a.num_columns(); ++j)
        b.a_no_check(i,j) = a.a_no_check(i,j) * x;

    return b;
}

EST_DVector operator*(const EST_DMatrix &a, const EST_DVector &v)
{    
    // treat the vector as a column vector
    // multiply each row of the matrix in turn by the vector

    EST_DVector b;
    b.resize(a.num_rows());
    
    if(a.num_columns() != v.n())
    {
    cerr <<"Matrix-vector multiplication error: matrix rows != vector size"
         << endl;
    return b;
    }

    ssize_t i, j;
    for (i = 0; i < a.num_rows(); ++i){
    b[i] = 0.0;
    for (j = 0; j < a.num_columns(); ++j)
        b.a_no_check(i) += a.a_no_check(i,j) * v.a_no_check(j);
    }
    return b;
}

EST_DVector operator+(const EST_DVector &a, const EST_DVector &b)
{
    EST_DVector ab;
    ssize_t i;
    if (a.length() != b.length())
    {
    cerr <<"Vector addition error: mismatched lengths\n";
    return ab;
    }

    ab.resize(a.length());
    for (i = 0; i < a.length(); ++i)
    ab.a_no_check(i) = a.a_no_check(i) + b.a_no_check(i);

    return ab;
}

EST_DVector operator-(const EST_DVector &a, const EST_DVector &b)
{
    EST_DVector ab;
    ssize_t i;
    if (a.length() != b.length())
    {
    cerr <<"Vector subtraction error: mismatched lengths\n";
    return ab;
    }

    ab.resize(a.length());
    for (i = 0; i < a.length(); ++i)
    ab.a_no_check(i) = a.a_no_check(i) - b.a_no_check(i);

    return ab;
}


EST_DVector operator*(const EST_DVector &v,const EST_DMatrix &a)
{    
    // treat the vector as a row vector
    // multiply the vector by each column of the matrix in turn

    EST_DVector b;
    b.resize(a.num_columns());
    
    if(a.num_columns() != v.n())
    {
    cerr <<"Matrix-vector multiplication error: matrix rows != vector size"
         << endl;
    return b;
    }

    ssize_t i, j;
    for (j = 0; j < a.num_columns(); ++j){
    b[j] = 0.0;
    for (i = 0; i < a.num_rows(); ++i)
        b.a_no_check(i) += a.a_no_check(i,j) * v.a_no_check(j);
    }
    return b;
}


#if 0
EST_DMatrix operator/(const EST_DMatrix &a, double x)
{
    return (a * (1/x));
}
#endif

EST_DMatrix operator*(const EST_DMatrix &a, const EST_DMatrix &b)
{
    EST_DMatrix ab;
    multiply(a,b,ab);
    return ab;
}

void multiply(const EST_DMatrix &a, const EST_DMatrix &b, EST_DMatrix &ab)
{

    if (a.num_columns() != b.num_rows())
    {
    cerr <<"Matrix multiply error: a.num_columns() != b.num_rows()\n";
    return;
    }

    ab.resize(a.num_rows(), b.num_columns());
    ssize_t i, j, k, n;
    n = a.num_columns();    // could also be b.num_rows()
    
    for (i = 0; i < a.num_rows(); ++i)
    for (k = 0; k < b.num_columns(); ++k)
    {
        ab.a_no_check(i, k) = 0.0;
        for (j = 0; j < n; ++j)
        ab.a_no_check(i, k) += 
            a.a_no_check(i, j) * b.a_no_check(j, k);
    }
}

void EST_DMatrix::copyin(double **inx, ssize_t rows, ssize_t cols)
{
    ssize_t i, j;

    resize(rows, cols);

    for (i = 0; i < rows; ++i)
    for (j = 0; j < cols; ++j)
        a_no_check(i,j) = inx[i][j];
    
}

EST_write_status EST_DMatrix::save(const EST_String &filename,
                   const EST_String &type)
{

    if ((type == "est_ascii") || (type == "est_binary"))
    return est_save(filename,type);
    else
    {   // the old stuff raw unheadered
    ssize_t i, j;
    ostream *outf;
    if (filename == "-")
        outf = &cout;
    else
        outf = new ofstream(filename);

    outf->precision(25);
    if (!(*outf))
    {
        cerr << "DMatrix: can't open file \"" << filename 
        <<"\" for writing" << endl;
        return misc_write_error;
    }
    
    for (i = 0; i < num_rows(); ++i)
    {
        for (j = 0; j < num_columns(); ++j)
        *outf << a_no_check(i,j) << " ";
        *outf << endl;
    }
    
    if (outf != &cout)
        delete outf;
    
    return write_ok;
    }
}

EST_write_status EST_DMatrix::est_save(const EST_String &filename,
                       const EST_String &type)
{
    // Binary save with short header for byte swap and sizes
    ssize_t i,j;
    FILE *fd;

    /* size_t does not have a ISO C++ printf format specifier (%zd is
     * not standard for C++ 1998 nor C++ 2003). We use a workaround. */
    std::stringstream tmpstring;
    std::string tmpstring2;

    if (filename == "-")
    fd = stdout;
    else if ((fd = fopen(filename, "wb")) == NULL)
    {
    cerr << "EST_DMatrix: binsave: failed to open \"" << filename << 
        "\" for writing" << endl;
    return misc_write_error;
    }

    fprintf(fd,"EST_File dmatrix\n");
    fprintf(fd,"version 1\n");
    if (type == "est_binary")
    {
    fprintf(fd,"DataType binary\n");
    if (EST_LITTLE_ENDIAN)
        fprintf(fd,"ByteOrder LittleEndian\n");
    else
        fprintf(fd,"ByteOrder BigEndian\n");
    }
    else
    fprintf(fd,"DataType ascii\n");

    tmpstring.str("");
    tmpstring << num_rows();
    tmpstring2 = tmpstring.str();
    fprintf(fd,"rows %s\n", tmpstring2.c_str());
    tmpstring.str("");
    tmpstring << num_columns();
    tmpstring2 = tmpstring.str();
    fprintf(fd,"columns %s\n", tmpstring2.c_str());

    fprintf(fd,"EST_Header_End\n");

    if (type == "est_binary")
    {
    for (i = 0; i < num_rows(); ++i)
        for (j=0; j < num_columns(); j++)
        if (fwrite(&a_no_check(i,j),sizeof(double),1,fd) != 1)
        {
            cerr << "EST_DMatrix: binsave: failed to write row " 
            << i << " column " << j 
                << " to \"" << filename << "\"" << endl;
            if (fd != stdout) fclose(fd);
            return misc_write_error;
        }
    }
    else
    {   // est_ascii
    for (i = 0; i < num_rows(); ++i)
    {
        for (j=0; j < num_columns(); j++)
        fprintf(fd,"%.25f ",a_no_check(i,j));
        fprintf(fd,"\n");
    }
    }
    
    if (fd != stdout)
    fclose(fd);

    return write_ok;
}

EST_read_status EST_DMatrix::est_load(const EST_String &filename)
{

  // ascii/binary load with short header for byte swap and sizes
  ssize_t i,j,k;
  int rows, cols, swap;
  EST_TokenStream ts;
  EST_read_status r;
  EST_EstFileType t;
  EST_Option hinfo;
  bool ascii;
    
  if (((filename == "-") ? ts.open(cin) : ts.open(filename)) != 0)
    {
      cerr << "DMatrix: can't open DMatrix input file " 
       << filename << endl;
      return misc_read_error;
    }
  if ((r = read_est_header(ts, hinfo, ascii, t)) != format_ok)
    return r;
    if (t != est_file_dmatrix)
      return misc_read_error;
    if (hinfo.ival("version") != 1)
      {
    cerr << "DMatrix load: " << ts.pos_description() <<
      " wrong version of DMatrix format expected 1 but found " <<
      hinfo.ival("version") << endl;
    return misc_read_error;
      }
    rows = hinfo.ival("rows");
    cols = hinfo.ival("columns");
    resize(rows,cols);
    
    if (ascii)
      {   // an ascii file
    for (i = 0; i < num_rows(); ++i)
      {
        for (j = 0; j < num_columns(); ++j)
          a_no_check(i,j) = atof(ts.get().string());
        if (!ts.eoln())
          {
        cerr << "DMatrix load: " << ts.pos_description() <<
          " missing end of line at end of row " << i << endl;
        return misc_read_error;
          }
      }
      }
    else
      {   // a binary file
    double *buff;
    if ((EST_BIG_ENDIAN && (hinfo.sval("ByteOrder")=="LittleEndian")) ||
        (EST_LITTLE_ENDIAN && (hinfo.sval("ByteOrder") == "BigEndian")))
      swap = TRUE;
    else
      swap = FALSE;
    
    buff = walloc(double,rows*cols);
    // A single read is *much* faster than multiple reads
    if (ts.fread(buff,sizeof(double),rows*cols) != rows*cols)
      {
        cerr << "EST_DMatrix: binload: short file in \""  
         << filename << "\"" << endl;
        wfree(buff);
        return misc_read_error;
      }
    if (swap)
      swap_bytes_double(buff,rows*cols);
    for (k = i = 0; i < num_rows(); ++i)
      for (j = 0; j < num_columns(); ++j)
        a_no_check(i,j) = buff[k++];
    wfree(buff);
      }
    
    ts.close();
    return read_ok;
}

EST_read_status EST_DMatrix::load(const EST_String &filename)
{
    EST_read_status r;

    if ((r = est_load(filename)) == format_ok)
    return r;
    else if (r == wrong_format)
    {   // maybe its an ancient ascii file
    EST_TokenStream ts, tt;
    EST_StrList sl;
    ssize_t i, j, n_rows=0, n_cols=0;
    EST_String t;
    EST_Litem *p;
    if (((filename == "-") ? ts.open(cin) : ts.open(filename)) != 0)
    {
        cerr << "Can't open DMatrix file " << filename << endl;
        return misc_read_error;
    }
    // set up the character constant values for this stream
    ts.set_SingleCharSymbols(";");
    
    // first read in as list
    for (n_rows = 0; !ts.eof(); ++n_rows)
        sl.append(ts.get_upto_eoln().string());

    if (n_rows > 0)
    {
        tt.open_string(sl.first());
        for (n_cols = 0; !tt.eof(); ++n_cols)
        tt.get().string();
    }

    // resize track and copy values in
    resize(n_rows, n_cols);
    
    for (p = sl.head(), i = 0; p != 0; ++i, p = p->next())
    {
        tt.open_string(sl(p));
        for (j = 0; !tt.eof(); ++j)
        a_no_check(i,j) = atof(tt.get().string());
        if (j != n_cols)
        {
        cerr << "Wrong number of points in row " << i << endl;
        cerr << "Expected " << n_cols << " got " << j << endl;
        return misc_read_error;
        }
    }
    return format_ok;
    }
    else
    return r;

    return format_ok;
}

EST_read_status EST_DVector::est_load(const EST_String &filename)
{    
  // ascii/binary load with short header for byte swap and sizes
  ssize_t i,k;
  int l, swap;
  EST_TokenStream ts;
  EST_read_status r;
  EST_EstFileType t;
  EST_Option hinfo;
  bool ascii;
    
  if (((filename == "-") ? ts.open(cin) : ts.open(filename)) != 0)
    {
      cerr << "DVector: can't open DVector input file " 
       << filename << endl;
      return misc_read_error;
    }
  if ((r = read_est_header(ts, hinfo, ascii, t)) != format_ok)
    return r;
    if (t != est_file_dvector)
      return misc_read_error;
    if (hinfo.ival("version") != 1)
      {
    cerr << "DVector load: " << ts.pos_description() <<
      " wrong version of DVector format expected 1 but found " <<
      hinfo.ival("version") << endl;
    return misc_read_error;
      }
    l = hinfo.ival("length");
    resize(l);
    
    if (ascii)
      {   // an ascii file
    for (i = 0; i < length(); ++i)
      a_no_check(i) = atof(ts.get().string());
      }
    else
      {   // a binary file
    double *buff;
    if ((EST_BIG_ENDIAN && (hinfo.sval("ByteOrder")=="LittleEndian")) ||
        (EST_LITTLE_ENDIAN && (hinfo.sval("ByteOrder") == "BigEndian")))
      swap = TRUE;
    else
      swap = FALSE;
    
    buff = walloc(double,l);
    // A single read is *much* faster than multiple reads
    if (ts.fread(buff,sizeof(double),l) != l)
      {
        cerr << "EST_DVector: binload: short file in \""  
         << filename << "\"" << endl;
         wfree(buff);
        return misc_read_error;
      }
    if (swap)
      swap_bytes_double(buff,l);
    for (k = i = 0; i < length(); ++i)
      a_no_check(i) = buff[k++];
    wfree(buff);
      }
    
    ts.close();
    return read_ok;
}

EST_read_status EST_DVector::load(const EST_String &filename)
{    

    EST_read_status r;

    if ((r = est_load(filename)) == format_ok)
    return r;
    else if (r == wrong_format)
    {   // maybe its an ancient ascii file
      EST_TokenStream ts;
      EST_String s;
      int i;

      i = 0;
      
      if (((filename == "-") ? ts.open(cin) : ts.open(filename)) != 0)
    {
      cerr << "can't open vector input file " << filename << endl;
      return misc_read_error;
    }
      ts.set_SingleCharSymbols(";");
      
      while (!ts.eof())
    {
      ts.get();
      ++i;
    }
      resize(i);
      
      ts.close();
      if (((filename == "-") ? ts.open(cin) : ts.open(filename)) != 0)
    {
      cerr << "can't open vector input file " << filename << endl;
      return misc_read_error;
    }
      
      for (i = 0; !ts.eof(); ++i)
    {
      s = ts.get().string();
      (*this)[i] = atof(s);  // actually returns double
    }
      ts.close();
      return format_ok;
    }
    else
      return r;

    return format_ok;

}


EST_DVector & EST_DVector::operator+=(const EST_DVector &s)
{
    ssize_t i;
    if(n() != s.n()){
    cerr << "Cannot elementwise add vectors of differing lengths" 
        << endl;
    return *this;
    }
    
    for (i = 0; i < n(); ++i)
    (*this)[i] += s(i);

    
    return *this;
}


EST_DVector& EST_DVector::operator*=(const EST_DVector &s)
{
    if(n() != s.n()){
    cerr << "Cannot elementwise multiply vectors of differing lengths" 
        << endl;
    return *this;
    }

    for (ssize_t i = 0; i < n(); ++i)
    (*this)[i] *= s(i);

    return *this;
}

EST_DVector& EST_DVector::operator*=(const double f)
{
    for (ssize_t i = 0; i < n(); ++i)
    (*this)[i] *= f;

    return *this;
}

double operator*(const EST_DVector &v1, const EST_DVector &v2)
{
  if(v1.length() != v2.length())
    {
      cerr << "Can't do vector dot prod  - differing vector sizes !" << endl;
      return 0;
    }
  double p=0;
  for (ssize_t i = 0; i < v1.length(); ++i)
      p += v1.a_no_check(i) * v2.a_no_check(i);

    return p;
}


EST_DVector& EST_DVector::operator/=(const double f)
{
    for (ssize_t i = 0; i < n(); ++i)
    (*this)[i] /= f;

    return *this;
}


EST_write_status EST_DVector::save(const EST_String &filename,
                   const EST_String &type)
{

    if ((type == "est_ascii") || (type == "est_binary"))
    return est_save(filename,type);
    else
    {   // the old stuff raw unheadered
    ssize_t i;
    ostream *outf;
    if (filename == "-")
        outf = &cout;
    else
        outf = new ofstream(filename);

    outf->precision(25);
    if (!(*outf))
    {
        cerr << "DVector: can't open file \"" << filename 
        <<"\" for writing" << endl;
        return misc_write_error;
    }
    
    for (i = 0; i < length(); ++i)
        *outf << a_no_check(i) << " ";
    *outf << endl;
    
    if (outf != &cout)
        delete outf;
    
    return write_ok;
    }
}

EST_write_status EST_DVector::est_save(const EST_String &filename,
                      const EST_String &type)
{
    // Binary save with short header for byte swap and sizes
    ssize_t i;
    std::stringstream tmpstring;
    std::string tmpstring2;
    FILE *fd;
    if (filename == "-")
    fd = stdout;
    else if ((fd = fopen(filename, "wb")) == NULL)
    {
    cerr << "EST_DVector: binsave: failed to open \"" << filename << 
        "\" for writing" << endl;
    return misc_write_error;
    }

    fprintf(fd,"EST_File dvector\n");
    fprintf(fd,"version 1\n");
    if (type == "est_binary")
    {
    fprintf(fd,"DataType binary\n");
    if (EST_LITTLE_ENDIAN)
        fprintf(fd,"ByteOrder LittleEndian\n");
    else
        fprintf(fd,"ByteOrder BigEndian\n");
    }
    else
    fprintf(fd,"DataType ascii\n");

    tmpstring.str("");
    tmpstring << length();
    tmpstring2 = tmpstring.str();
    fprintf(fd,"length %s\n", tmpstring2.c_str());
    fprintf(fd,"EST_Header_End\n");

    if (type == "est_binary")
    {
    for (i = 0; i < length(); ++i)
        if (fwrite(&a_no_check(i),sizeof(double),1,fd) != 1)
        {
        cerr << "EST_DVector: binsave: failed to write item " 
             << i << " to \"" << filename << "\"" << endl;
        if (fd != stdout) fclose(fd);
        return misc_write_error;
        }
    }
    else
    {   // est_ascii
    for (i = 0; i < length(); ++i)
        fprintf(fd,"%.25f ",a_no_check(i));
    fprintf(fd,"\n");
    }
    
    if (fd != stdout)
    fclose(fd);

    return write_ok;
}