miscmaths.cc

/*  miscmaths.cc

    Mark Jenkinson, Mark Woolrich, Christian Beckmann, Tim Behrens and Matthew Webster, FMRIB Image Analysis Group

    Copyright (C) 1999-2009 University of Oxford  */

/*  CCOPYRIGHT  */

// Miscellaneous maths functions
#define NOMINMAX
#include <cstdlib>
#include <cmath>
#include <algorithm>
#include "miscmaths.h"
#include "miscprob.h"
#include "stdlib.h"
#include "newmatio.h"

using namespace std;

namespace MISCMATHS {

  // The following lines are ignored by the current SGI compiler
  //  (version egcs-2.91.57)
  // A temporary fix of including the std:: in front of all abs() etc
  //  has been done for now
  using std::abs;
  using std::sqrt;
  using std::exp;
  using std::log;
  //  using std::pow;
  using std::atan2;


  string size(const Matrix& mat)
  {
    string str = num2str(mat.Nrows())+"*"+num2str(mat.Ncols());
        
    return str;
  }


  float Sinc(const float x) {
    if (fabs(x)<1e-9) {
      return 1-x*x*M_PI*M_PI/6.0;
    } else {
      return sin(M_PI*x)/(M_PI*x);
    }
  }

  double Sinc(const double x) {
    if (fabs(x)<1e-9) {
      return 1-x*x*M_PI*M_PI/6.0;
    } else {
      return sin(M_PI*x)/(M_PI*x);
    }
  }

  // General string/IO functions
  bool isNumber( const string& input)
  {
    if (input.size()==0) return false;
    char *pend;
    strtod(input.c_str(),&pend);
    if (*pend!='\0') return false;
    return true; 
  } 

  // Use this to skip all lines that contain non-numeric entries, and return the first line starting with a number
  //  and the file pointer is reset to the beginning of the first line that starts with a number
  string skip_alpha(ifstream& fs) 
  {
    string cline;
    while (!fs.eof()) {
      streampos curpos = fs.tellg();
      // read a line, then turn it into a stream in order to read out the first token
      getline(fs,cline);
      cline += " "; // force extra entry in parsing (ensure at least one token is read)
      istringstream ss(cline.c_str());
      string firstToken="";
      ss >> firstToken; // Put first non-whitespace sequence into firstToken
      if (isNumber(firstToken)) {
	if (fs.eof()) { fs.clear(); }  // should only be executed if the file had no valid line terminators
	fs.seekg(curpos); 
	return cline;
      }
    }
    return "";
  }

  ReturnMatrix read_ascii_matrix(int nrows, int ncols, const string& filename)
  {
    return read_ascii_matrix(filename,nrows,ncols);
  }


  ReturnMatrix read_ascii_matrix(const string& filename, int nrows, int ncols)
  {
    Matrix mat(nrows,ncols);
    mat = 0.0;
  
    if ( filename.size()<1 ) return mat;
    ifstream fs(filename.c_str());
    if (!fs) { 
      cerr << "Could not open matrix file " << filename << endl;
      return mat;
    }
    mat = read_ascii_matrix(fs,nrows,ncols);
    fs.close();
    mat.Release();
    return mat;
  }

  ReturnMatrix read_ascii_matrix(int nrows, int ncols, ifstream& fs)
  {
    return read_ascii_matrix(fs, nrows, ncols);
  }

  ReturnMatrix read_ascii_matrix(ifstream& fs, int nrows, int ncols)
  {
    Matrix mat(nrows,ncols);
    mat = 0.0;
    string ss="";
    double newnum;

    ss = skip_alpha(fs);
    for (int r=1; r<=nrows; r++) {
      istringstream sline(ss.c_str());
      for (int c=1; c<=ncols; c++) {
	sline >> newnum;
	if ( sline.eof() ) {
	  throw Exception("Could not find enough numbers in matrix file");
	}
	mat(r,c) = newnum;
      }						
      getline(fs,ss);  // this is processed now, so move the stream past it
      ss = skip_alpha(fs);
    }
    mat.Release();
    return mat;
  }

  
  ReturnMatrix read_ascii_matrix(const string& filename)
  {
    Matrix mat;
    if ( filename.size()<1 ) return mat;
    ifstream fs(filename.c_str());
    if (!fs) { 
      cerr << "Could not open matrix file " << filename << endl;
      mat.Release();
      return mat;
    }
    mat = read_ascii_matrix(fs);
    fs.close();
    mat.Release();
    return mat;
  }


  ReturnMatrix read_ascii_matrix(ifstream& fs)
  {
    int nRows(0), nColumns(0);
    string currentLine;
    // skip initial non-numeric lines
    //  and count the number of columns in the first numeric line
    currentLine = skip_alpha(fs);
    currentLine += " ";
    {
      istringstream ss(currentLine.c_str());
      string dummyToken="";
      while (!ss.eof()) {
	nColumns++;
	ss >> dummyToken;
      }
    }
    nColumns--;

    // count the number of lines that start with a number (don't worry if they don't have enough numbers at this stage)
    do {
      getline(fs,currentLine);
      currentLine += " "; // force extra entry in parsing
      istringstream ss(currentLine.c_str()); 
      string firstToken("");
      ss >> firstToken; //Put first non-whitespace sequence into cc
      if (isNumber(firstToken)) nRows++;  // add new row to matrix
    } while (!fs.eof());
    
    // now know the size of matrix
    fs.clear();
    fs.seekg(0,ios::beg);    
    return read_ascii_matrix(fs,nRows,nColumns);

  }

#define BINFLAG 42

  ReturnMatrix read_binary_matrix(const string& filename)
  {
    Matrix mres;