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SRE2D-for.CPP
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SRE2D-for.CPP
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#define _CRT_SECURE_NO_WARNINGS
// This file contains sourcecode distributed as freeware.
// The intellectual property of the sourcecode is shown
// here to belong to Carlo Ciulla.
// Disclaimer:
// The website here named www.sourcecodewebsiteCarloCiulla.com 2013 [1] does not intend
// to convey the meaning of profit making for what pertains to the content
// provided. --->>> Instead, when the content is downloaded, the user(s) are
// kindly invited to donate money to charity organizations involved in
// helping people in need of food and water. <<<---
// The Novel Re-sampling Locations have been sized to be a fraction of
// the pixel size. The programs presented here confirm both concepts and
// implications brought to knowledge through the unifying theory [1].
// Reference:
// [1] Carlo Ciulla "Improved Signal and Image Interpolation in Biomedical Applications:
// The Case of Magnetic Resonance Imaging (MRI)." Medical Information Science
// Reference - IGI Global Publisher - March 2009; ISBN: 978 - 160566202 - 2.
// Project Title: Bivariate Linear (Bivariate Linear SRE-based Interpolation)
#include < iostream >
#include < fstream >
#include < ostream >
#include < string >
#include < io.h >
#include < dos.h >
#include < conio.h >
#include < stdlib.h >
#include < sstream >
#include < stdio.h >
#include < iomanip >
#include < istream >
#include < math.h >
#define NSCALE 0.1
#define ESCALE 0.1
#define TH 0
using namespace std;
class SRE2D2013 {
int n1; // matrix size x
int n2; // matrix size y
public:
int getNofPixelsX(void) { return this->n1; };
int getNofPixelsY(void) { return this->n2; };
void setNofPixelsX(int x) { this->n1 = x; };
void setNofPixelsY(int y) { this->n2 = y; };
public:
struct data {
double **fMRI; // pointer to the matrix entry
double **scaledfMRI; // pointer to the matrix entry
double **Xsre; // pointer to the matrix entry
double **Ysre; // pointer to the matrix entry
double **shifted_fMRI; // pointer to the matrix entry
double **SE; // pointer to the matrix entry
double **DELTA; // pointer to the matrix entry
double **the_SRE_shifted_fMRI; // pointer to the matrix entry
double **SE_SRE; // pointer to the matrix entry
double **X_recomputed; // pointer to the matrix entry
double **Y_recomputed; // pointer to the matrix entry
double **X_recomputed_scaled; // pointer to the matrix entry
double **Y_recomputed_scaled; // pointer to the matrix entry
double **ICF; // pointer to the matrix entry
}*pointer; // pointer to the matrices
public:
SRE2D2013(int x, int y) : n1(x), n2(y) { };// constructor
void allocateData();
~SRE2D2013() { } // destructor
};
void SRE2D2013::allocateData() { // allocate data
// (1) allocate struct 'data' (begin)
pointer = new data;
pointer->fMRI = new double*[this->n1];
pointer->scaledfMRI = new double*[this->n1];
pointer->Xsre = new double*[this->n1];
pointer->Ysre = new double*[this->n1];
pointer->shifted_fMRI = new double*[this->n1];
pointer->SE = new double*[this->n1];
pointer->DELTA = new double*[this->n1];
pointer->the_SRE_shifted_fMRI = new double*[this->n1];
pointer->SE_SRE = new double*[this->n1];
pointer->X_recomputed = new double*[this->n1];
pointer->Y_recomputed = new double*[this->n1];
pointer->X_recomputed_scaled = new double*[this->n1];
pointer->Y_recomputed_scaled = new double*[this->n1];
pointer->ICF = new double*[this->n1];
for( int v=0; v < this->n1; v++ ) { // (1)
pointer->fMRI[v] = new double[this->n2];
pointer->scaledfMRI[v] = new double[this->n2];
pointer->Xsre[v] = new double[this->n2];
pointer->Ysre[v] = new double[this->n2];
pointer->shifted_fMRI[v] = new double[this->n2];
pointer->SE[v] = new double[this->n2];
pointer->DELTA[v] = new double[this->n2];
pointer->the_SRE_shifted_fMRI[v] = new double[this->n2];
pointer->SE_SRE[v] = new double[this->n2];
pointer->X_recomputed[v] = new double[this->n2];
pointer->Y_recomputed[v] = new double[this->n2];
pointer->X_recomputed_scaled[v] = new double[this->n2];
pointer->Y_recomputed_scaled[v] = new double[this->n2];
pointer->ICF[v] = new double[this->n2];
} // (1) allocate struct 'data' (end)
// (2) initialize (begin)
for( int v=0; v < this->n1; v++ ) { // (a)
for( int f=0; f < this->n2 ; f++ ) { // (b)
pointer->fMRI[v][f] = (double)0.0;
pointer->scaledfMRI[v][f] = (double)0.0;
pointer->Xsre[v][f] = (double)0.0;
pointer->Ysre[v][f] = (double)0.0;
pointer->shifted_fMRI[v][f] = (double)0.0;
pointer->SE[v][f] = (double)0.0;
pointer->DELTA[v][f] = (double)0.0;
pointer->the_SRE_shifted_fMRI[v][f] = (double)0.0;
pointer->SE_SRE[v][f] = (double)0.0;
pointer->X_recomputed[v][f] = (double)0.0;
pointer->Y_recomputed[v][f] = (double)0.0;
pointer->X_recomputed_scaled[v][f] = (double)0.0;
pointer->Y_recomputed_scaled[v][f] = (double)0.0;
pointer->ICF[v][f] = (double)0.0;
} //(b)
} //(a)
// (2) initialize (end)
} // allocate data
int main ( int argc, char * argv[] ) {
char outputFile[128]="SRE2D-for.log";
FILE * savedata;
double MAX = 5000000000000000000.0;
if (argc < 8) { std::cout << endl;
std::cout << "Please type the image file name" << endl;
std::cout << "Please make sure that the image format is Analyze 'double': 64 bits real" << endl;
std::cout << "Before running the program, please make sure that the image is padded of 'n >= 1'";
std::cout << "number of pixels along X and Y" << endl;
std::cout << "Please enter the number of pixels along the X direction (integer)" << endl;
std::cout << "Please enter the number of pixels along the Y direction (integer)" << endl;
std::cout << "Please enter the pixel size along the X direction (double)" << endl;
std::cout << "Please enter the pixel size along the Y direction (double)" << endl;
std::cout << "Please enter that 'n >= 1' number of pixels along X and Y which will pad the image" << endl;
std::cout << "Some data will be lost if you enter a value of n which is greater than" << endl;
std::cout << "the actual number of pixels along X and Y which was used to pad the image" << endl;
std::cout << "before running the program." << endl;
std::cout << "Please type 'n' to scale the Image Data or 'e' to exponentialize the Image Data" << endl;
std::cout << endl;
exit(0); }
else { // run the program (begin)
if ((savedata = fopen(outputFile,"w"))==NULL)
{
std::cout << "Cannot open output file, Now Exit..." << endl;
} else { // processing (begin)
int n1 = atoi(argv[2]);
int n2 = atoi(argv[3]);
double XPixelSize = atof(argv[4]);
double YPixelSize = atof(argv[5]);
char imageFileName[128];
int PAD = atoi(argv[6]);
unsigned char Fyn = 'n';
Fyn = *argv[7];
if ( PAD < 1 ) { // if test PAD
std::cout << "Please make sure to pad the image with 'n >= 1' number of pixels along X and Y" << endl;
fprintf(savedata,"%s\n", "Please make sure to pad the image with 'n >= 1' number of pixels along X and Y");
fclose(savedata);
exit(0);
} // if test PAD
sprintf(imageFileName, "%s", argv[1]);
std::cout << endl;
std::cout << "The image file name is: " << imageFileName << endl;
std::cout << "The number of pixels along the X direction is: " << atoi(argv[2]) << endl;
std::cout << "The number of pixels along the Y direction is: " << atoi(argv[3]) << endl;
std::cout << "The pixel size along the X direction is: " << atof(argv[4]) << endl;
std::cout << "The pixel size along the Y direction is: " << atof(argv[5]) << endl;
std::cout << "The 'n' number of pixels along X and Y which you entered to pad the image is: " << atoi(argv[6]) << endl;
std::cout << "Some data will be lost if you enter a value of n which is greater than" << endl;
std::cout << "the actual number of pixels along X and Y which was used to pad the image" << endl;
std::cout << "before running the program." << endl;
if ( tolower(Fyn) == 'e' )
std::cout << "The program exponentialize the Image Data before processing: " << Fyn << endl;
else if ( tolower(Fyn) == 'n' )
std::cout << "The program scales the Image Data before processing: " << Fyn << endl;
std::cout << endl;
fprintf(savedata,"%s%s\n", "The image file name is: " , imageFileName);
fprintf(savedata,"%s%d\n", "The number of pixels along the X direction is: ", n1);
fprintf(savedata,"%s%d\n", "The number of pixels along the Y direction is: ", n2);
fprintf(savedata,"%s%lf\n", "The pixel size along the X direction is: ", XPixelSize);
fprintf(savedata,"%s%lf\n", "The pixel size along the Y direction is: ", YPixelSize);
fprintf(savedata,"%s%d\n", "The 'n' number of pixels along X and Y which you entered to pad the image is: ", PAD);
fprintf(savedata,"%s\n", "Some data will be lost if you enter a value of n which is greater than");
fprintf(savedata,"%s\n", "the actual number of pixels along X and Y which was used to pad the image");
fprintf(savedata,"%s\n", "before running the program.");
if ( tolower(Fyn) == 'e' )
fprintf(savedata,"%s%c\n", "The program exponentialize the Image Data before processing: ", Fyn);
else if ( tolower(Fyn) == 'n' )
fprintf(savedata,"%s%c\n", "The program scales the Image Data before processing: ", Fyn);
fprintf(savedata,"\n");
double STEP_A = (double)0.0;
double STEP_MX = (double)0.0;
double STEP_MY = (double)0.0;
double x_misplacement_X = (double)0.01;
double y_misplacement_Y = (double)0.01;
double theta = (double)0.01;
SRE2D2013 SRE(n1,n2);
SRE.allocateData();
/// read image file (begin)
FILE * pf;
if ((pf = fopen(imageFileName,"rb+"))==NULL)
{
std::cout << "Cannot open file: " << imageFileName << endl;
fprintf(savedata,"%s%s\n", "Cannot open file: " , imageFileName );
exit(0);
} else { // else
double number;
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
fread(&number,sizeof(double),1,pf);
SRE.pointer->fMRI[i1][i2] = (double)number;
SRE.pointer->scaledfMRI[i1][i2] = (double)number;
} // x dim
} // y dim
fclose (pf);
} // else
/// read image file (end)
std::cout << "Image data loaded" << endl;
fprintf(savedata, "%s\t %s\t %s\t\t %s\t\t %s\n", "misplacement_X", "misplacement_Y", "SE", "SRE SE", "SE Difference");
fprintf(savedata,"\n");
std::cout << "Now Computing..." << endl;
std::cout << "Image data loaded" << endl;
double max=-MAX;
double min=MAX;
// make decision as to if standarzize or scale the Image data (begin)
if ( tolower(Fyn) == 'e' ) {
double Std = 0, Average = 0;
long int counting = 0;
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
Average += (double) SRE.pointer->fMRI[i1][i2];
counting++;
}
} // y dim
} // x dim
Average /= ((double)counting);
counting = 0;
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
Std = (double)Std + ((double) (Average - SRE.pointer->fMRI[i1][i2]) *
(Average - SRE.pointer->fMRI[i1][i2]) );
counting++;
}
} // y dim
} // x dim
Std = (double) sqrt( (double) Std / ((double)counting) );
// standardize (begin)
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
SRE.pointer->scaledfMRI[i1][i2] = (double) ESCALE * ( (double) exp((double) (SRE.pointer->fMRI[i1][i2] - Average) / Std) );
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->scaledfMRI[i1][i2] = (double)0.0;
}
} // y dim
} // x dim
// standardize (end)
} else if ( tolower(Fyn) == 'n' )
{ // make decision as to if standarzize or scale the Image data
/// compute max and min of data (begin)
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if( SRE.pointer->fMRI[i1][i2] > (double)max )
max = (double)SRE.pointer->fMRI[i1][i2];
if( SRE.pointer->fMRI[i1][i2] < (double)min )
min = (double)SRE.pointer->fMRI[i1][i2];
} // y dim
} // x dim
/// compute max and min of data (end)
// scale (begin)
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
if ( max == min ) SRE.pointer->scaledfMRI[i1][i2] = (double)0.0;
else SRE.pointer->scaledfMRI[i1][i2] = (double) NSCALE *
(double) fabs ( (min - SRE.pointer->fMRI[i1][i2]) / (min - max) );
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->scaledfMRI[i1][i2] = (double)0.0;
}
} // y dim
} // x dim
// scale (end)
std::cout << "Image data scaled" << endl;
} // make decision as to if standarzize or scale the Image data (end)
// compute XSRE and YSRE (begin)
double omega;
int XNEI = 1;
for (int i1=0; i1 < n1-1; i1++) {// x dim
for (int i2=0; i2 < n2-1; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) { /// if threshold
omega = ((double) SRE.pointer->scaledfMRI[i1+1][i2+1] + SRE.pointer->scaledfMRI[i1][i2] -
SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2+1] );
if ( ((double)SRE.pointer->scaledfMRI[i1][i2+1] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega != 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2+1] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega == 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2+1] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega != 0.0 )
SRE.pointer->Xsre[i1][i2] = ((double) -2.0 * (SRE.pointer->scaledfMRI[i1][i2+1] - SRE.pointer->scaledfMRI[i1][i2] ) / omega);
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2+1] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega == 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)1.0; // de L'Hopital
if ( ((double)SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega != 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega == 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega != 0.0 )
SRE.pointer->Ysre[i1][i2] = ((double) -2.0 * (SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) / omega);
else if ( ((double)SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega == 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)1.0; // de L'Hopital
/// calculate last horizontal/vertical stripe of signal (begin)
if ( i1 >= 1 && i2 == ((int)n1 - PAD - XNEI) )
{ // if
if ( (double)SRE.pointer->scaledfMRI[i1][i2] > TH ) {
omega = ((double) SRE.pointer->scaledfMRI[i1-1][i2-1] + SRE.pointer->scaledfMRI[i1][i2] -
SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2-1] );
if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega != 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega == 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega != 0.0 )
SRE.pointer->Xsre[i1][i2] = ((double) -2.0 * (SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) / omega);
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega == 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)1.0; // de L'Hopital
if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega != 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega == 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega != 0.0 )
SRE.pointer->Ysre[i1][i2] = ((double) -2.0 * (SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) / omega);
else if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega == 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)1.0; // de L'Hopital
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->Xsre[i1][i2] = (double)0.0;
SRE.pointer->Ysre[i1][i2] = (double)0.0;
}
} // if
if ( i1 == ((int)n1 - PAD - XNEI) && i2 >= 1 )
{ // if
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
omega = ((double) SRE.pointer->scaledfMRI[i1-1][i2-1] + SRE.pointer->scaledfMRI[i1][i2] -
SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2-1] );
if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega != 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega == 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega != 0.0 )
SRE.pointer->Xsre[i1][i2] = ((double) -2.0 * (SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) / omega);
else if ( ((double)SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega == 0.0 )
SRE.pointer->Xsre[i1][i2] = (double)1.0; // de L'Hopital
if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega != 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega == 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)0.0;
else if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) != 0.0 && (double)omega != 0.0 )
SRE.pointer->Ysre[i1][i2] = ((double) -2.0 * (SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) / omega);
else if ( ((double)SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) == 0.0 && (double)omega == 0.0 )
SRE.pointer->Ysre[i1][i2] = (double)1.0; // de L'Hopital
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->Xsre[i1][i2] = (double)0.0;
SRE.pointer->Ysre[i1][i2] = (double)0.0;
}
} // if
/// calculate last vertical stripe of signal (end)
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) { /// if threshold
SRE.pointer->Xsre[i1][i2] = (double)0.0;
SRE.pointer->Ysre[i1][i2] = (double)0.0;
} /// if threshold
} // y dim
} // x dim
// calculate SRE (end)
std::cout << "XSRE and YSRE calculated" << endl;
//---> major for loop (begin) <---//
for (int step = 1; step <= 100; step++) {
double misplacement_X = ((double)1.0 - ( cos( (double)theta + STEP_A) + sin( (double)theta + STEP_A) ) + (double)x_misplacement_X + (double)STEP_MX);
double misplacement_Y = ((double)1.0 - (-sin( (double)theta + STEP_A) + cos( (double)theta + STEP_A) ) + (double)y_misplacement_Y + (double)STEP_MY);
misplacement_X = ((double)misplacement_X/XPixelSize);
misplacement_Y = ((double)misplacement_Y/YPixelSize);
//////////////////***********/////////////////////
// Above formula scales the misplacement to the //
// pixel size the same way the following formula //
// would do: (min - misplacement)/(min - max) //
//////////////////***********//////////////////////
// scale X_sre (begin)
max=-MAX;
min=MAX;
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
if( SRE.pointer->Xsre[i1][i2] > (double)max ) max = (double)SRE.pointer->Xsre[i1][i2];
if( SRE.pointer->Xsre[i1][i2] < (double)min ) min = (double)SRE.pointer->Xsre[i1][i2];
}
} // y dim
} // x dim
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
if ( max == min ) SRE.pointer->Xsre[i1][i2] = (double)0.0;
else SRE.pointer->Xsre[i1][i2] = (double) misplacement_X *
(double) fabs ( (min - SRE.pointer->Xsre[i1][i2]) / (min - max) );
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->Xsre[i1][i2] = (double)0.0;
}
} // y dim
} // x dim
// scale X_sre (end)
// scale Y_sre (begin)
max=-MAX;
min=MAX;
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
if( SRE.pointer->Ysre[i1][i2] > (double)max ) max = (double)SRE.pointer->Ysre[i1][i2];
if( SRE.pointer->Ysre[i1][i2] < (double)min ) min = (double)SRE.pointer->Ysre[i1][i2];
}
} // y dim
} // x dim
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
if ( max == min ) SRE.pointer->Ysre[i1][i2] = (double)0.0;
else SRE.pointer->Ysre[i1][i2] = (double) misplacement_Y *
(double) fabs ( (min - SRE.pointer->Ysre[i1][i2]) / (min - max) );
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->Ysre[i1][i2] = (double)0.0;
}
} // y dim
} // x dim
// scale Y_sre (end)
// shift the image of the given misplacement (begin)
for (int i1=0; i1 < n1-1; i1++) {// x dim
for (int i2=0; i2 < n2-1; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
SRE.pointer->shifted_fMRI[i1][i2] = (double) SRE.pointer->fMRI[i1][i2] +
misplacement_X * ( SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) +
misplacement_Y * ( SRE.pointer->scaledfMRI[i1][i2+1] - SRE.pointer->scaledfMRI[i1][i2] ) +
misplacement_X * misplacement_Y * ( SRE.pointer->scaledfMRI[i1+1][i2+1] + SRE.pointer->scaledfMRI[i1][i2] -
SRE.pointer->scaledfMRI[i1+1][i2] - SRE.pointer->scaledfMRI[i1][i2+1] ) ;
/// calculate last horizontal/vertical stripe of signal (begin)
if ( i1 >= 1 && i2 == ((int)n1 - PAD - XNEI) )
{ // if
SRE.pointer->shifted_fMRI[i1][i2] = (double) SRE.pointer->fMRI[i1][i2] +
misplacement_X * ( SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) +
misplacement_Y * ( SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) +
misplacement_X * misplacement_Y * ( SRE.pointer->scaledfMRI[i1-1][i2-1] + SRE.pointer->scaledfMRI[i1][i2] -
SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2-1] ) ;
} // if
if ( i1 == ((int)n1 - PAD - XNEI) && i2 >= 1 )
{ // if
SRE.pointer->shifted_fMRI[i1][i2] = (double) SRE.pointer->fMRI[i1][i2] +
misplacement_X * ( SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2] ) +
misplacement_Y * ( SRE.pointer->scaledfMRI[i1][i2-1] - SRE.pointer->scaledfMRI[i1][i2] ) +
misplacement_X * misplacement_Y * ( SRE.pointer->scaledfMRI[i1-1][i2-1] + SRE.pointer->scaledfMRI[i1][i2] -
SRE.pointer->scaledfMRI[i1-1][i2] - SRE.pointer->scaledfMRI[i1][i2-1] ) ;
} // if
/// calculate last vertical stripe of signal (end)
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->shifted_fMRI[i1][i2] = (double)0.0;
}
} // y dim
} // x dim
// shift the image of the given misplacement (end)
std::cout << "Image data shifted" << endl;
// compute SE (begin)
double SE_sum = 0.0;
long int counter = 0;
for (int i1=0; i1 < n1; i1++) {// x dim
for (int i2=0; i2 < n2; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
counter++;
SRE.pointer->SE[i1][i2] = (double) sqrt( ( SRE.pointer->fMRI[i1][i2] - SRE.pointer->shifted_fMRI[i1][i2] ) *
( SRE.pointer->fMRI[i1][i2] - SRE.pointer->shifted_fMRI[i1][i2] ) );
SE_sum = SRE.pointer->SE[i1][i2] + SE_sum;
}
} // y dim
} // x dim
// compute SE (end)
std::cout << "SE with no SRE is: " << ((double)SE_sum / (counter)) << endl;
std::cout << endl;
double errorSE = ((double)SE_sum / (counter));
/// compute DELTA and recomputed_X and recomputed_Y (begin)
double k, s;
for (int i1=0; i1 < n1-1; i1++) {// x dim
for (int i2=0; i2 < n2-1; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
k = (double) SRE.pointer->fMRI[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 2.0 ) *
( SRE.pointer->fMRI[i1+1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 2.0 ) *
( SRE.pointer->fMRI[i1][i2+1] - SRE.pointer->fMRI[i1][i2] ) +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 4.0 ) *
( SRE.pointer->fMRI[i1+1][i2+1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1+1][i2] - SRE.pointer->fMRI[i1][i2+1] ) ;
s = (double) SRE.pointer->fMRI[i1][i2] * ( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 2.0 ) * ( SRE.pointer->fMRI[i1+1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 2.0 ) * ( SRE.pointer->fMRI[i1][i2+1] - SRE.pointer->fMRI[i1][i2] ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 4.0 ) *
( SRE.pointer->fMRI[i1+1][i2+1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1+1][i2] - SRE.pointer->fMRI[i1][i2+1] ) ;
/// calculate last horizontal/vertical stripe of signal (begin)
if ( i1 >= 1 && i2 == ((int)n1 - PAD - XNEI) )
{ // if
k = (double) SRE.pointer->fMRI[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 2.0 ) *
( SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 2.0 ) *
( SRE.pointer->fMRI[i1][i2-1] - SRE.pointer->fMRI[i1][i2] ) +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 4.0 ) *
( SRE.pointer->fMRI[i1-1][i2-1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2-1] ) ;
s = (double) SRE.pointer->fMRI[i1][i2] * ( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 2.0 ) * ( SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 2.0 ) * ( SRE.pointer->fMRI[i1][i2-1] - SRE.pointer->fMRI[i1][i2] ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 4.0 ) *
( SRE.pointer->fMRI[i1-1][i2-1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2-1] ) ;
} // if
if ( i1 == ((int)n1 - PAD - XNEI) && i2 >= 1 )
{ // if
k = (double) SRE.pointer->fMRI[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 2.0 ) *
( SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 2.0 ) *
( SRE.pointer->fMRI[i1][i2-1] - SRE.pointer->fMRI[i1][i2] ) +
( SRE.pointer->Xsre[i1][i2] * SRE.pointer->Xsre[i1][i2] * SRE.pointer->Ysre[i1][i2] * SRE.pointer->Ysre[i1][i2] / 4.0 ) *
( SRE.pointer->fMRI[i1-1][i2-1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2-1] ) ;
s = (double) SRE.pointer->fMRI[i1][i2] * ( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 2.0 ) * ( SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 2.0 ) * ( SRE.pointer->fMRI[i1][i2-1] - SRE.pointer->fMRI[i1][i2] ) +
( ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) * ( SRE.pointer->Xsre[i1][i2] - misplacement_X ) *
( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) * ( SRE.pointer->Ysre[i1][i2] - misplacement_Y ) / 4.0 ) *
( SRE.pointer->fMRI[i1-1][i2-1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1-1][i2] - SRE.pointer->fMRI[i1][i2-1] ) ;
} // if
/// calculate last vertical stripe of signal (end)
if ( (double)s == 0.0 && (double)k == 0.0 ) SRE.pointer->DELTA[i1][i2] = (double)1.0; // de l'Hopital
else if ( (double)s == 0.0 && (double)k != 0.0 ) SRE.pointer->DELTA[i1][i2] = (double)0.0;
else if ( (double)s != 0.0 && (double)k == 0.0 ) SRE.pointer->DELTA[i1][i2] = (double)0.0;
else if ( (double)s != 0.0 && (double)k != 0.0 ) SRE.pointer->DELTA[i1][i2] = (double)s/k;
} else if ( (double)SRE.pointer->fMRI[i1][i2] <= TH ) {
SRE.pointer->DELTA[i1][i2] = (double)0.0;
}
} // y dim
} // x dim
// compute DELTA (end)
std::cout << "DELTA calculated" << endl;
// calculate ICF (begin)
std::cout << "Compute Intensity-Curvature Functional" << endl;
for (int i1=0; i1 < n1-1; i1++) {// x dim
for (int i2=0; i2 < n2-1; i2++) { // y dim
if ( (double)SRE.pointer->fMRI[i1][i2] > TH ) {
k = (double) SRE.pointer->fMRI[i1][i2] * misplacement_X * misplacement_Y +
( misplacement_X * misplacement_Y * misplacement_X / 2.0) *
( SRE.pointer->fMRI[i1+1][i2] - SRE.pointer->fMRI[i1][i2] ) +
( misplacement_X * misplacement_Y * misplacement_Y / 2.0) *
( SRE.pointer->fMRI[i1][i2+1] - SRE.pointer->fMRI[i1][i2] ) +
( misplacement_X * misplacement_X * misplacement_Y * misplacement_Y / 4.0) *
( SRE.pointer->fMRI[i1+1][i2+1] + SRE.pointer->fMRI[i1][i2] - SRE.pointer->fMRI[i1+1][i2] - SRE.pointer->fMRI[i1][i2+1] );
s = (double) SRE.pointer->fMRI[i1][i2] * misplacement_X * misplacement_Y;
if ( (double)s == 0.0 && (double)k == 0.0 ) SRE.pointer->ICF[i1][i2] = (double)1.0; // de l'Hopital
else if ( (double)s == 0.0 && (double)k != 0.0 ) SRE.pointer->ICF[i1][i2] = (double)0.0;
else if ( (double)s != 0.0 && (double)k == 0.0 ) SRE.pointer->ICF[i1][i2] = (double)0.0;
else if ( (double)s != 0.0 && (double)k != 0.0 ) SRE.pointer->ICF[i1][i2] = (double)s/k;