//LEE:: segmentation for video images
void Masek::segmentiris(Masek::IMAGE *eyeimage, int *circleiris, int *circlepupil, double *imagewithnoise, int eyelidon, int highlighton, int highlightvalue)
{
int lpupilradius, upupilradius, lirisradius, uirisradius, reflecthres;
double scaling;
int rowi, coli, ri, rowp, colp, rp, oldrowp;
double rowid, colid, rid, rowpd, colpd, rpd;
int irl, iru, icl, icu;
int imgsize[2];
IMAGE* imagepupil, *topeyelid, *bottomeyelid;
int i, j, k, m;
int linecount;
double *lines;
int *xl, *yl;
int *y2;
int yla;
//% define range of pupil & iris radii
//LEE:Video Data
//lpupilradius = 25;
//lpupilradius = 22;
//in small pupil, 12, 20 works very well.
//in big pupil, 20, 55
//the best result 14, 42;
lpupilradius = 14;//
upupilradius = 42;
lirisradius = 62;
uirisradius = 78;
/* //%CASIA
lpupilradius = 28;
upupilradius = 75;
lirisradius = 80;
uirisradius = 150;*/
/*% %LIONS
% lpupilradius = 32;
% upupilradius = 85;
% lirisradius = 145;
% uirisradius = 169;
*/
//% define scaling factor to speed up Hough transform
scaling = 0.4;
reflecthres = 240;
//reflecthres = 100;
//% find the iris boundary
findcircle(eyeimage, lirisradius, uirisradius, scaling, 2, 0.20, 0.19, 1.00, 0.00, &rowi, &coli,&ri);
//LEE:
//findcircle(eyeimage, lirisradius, uirisradius, scaling, 2, 0.19, 0.13, 1.00, 0.00, &rowi, &coli,&ri);
//findcircle(eyeimage, lirisradius, uirisradius, scaling, 2, 0.19, 0.11, 1.00, 0.00, &rowi, &coli,&ri);
/*rowi = 215;
coli = 345;
ri = 115;*/
/*rowi = 235;
coli = 275;
ri = 117;*/
circleiris[0] = rowi;
circleiris[1] = coli;
circleiris[2] = ri;
printf("iris is %d %d %d\n", rowi, coli, ri);
rowid = (double)rowi;
colid = (double)coli;
rid = (double)ri;
irl = roundND(rowid-rid);
iru = roundND(rowid+rid);
icl = roundND(colid-rid);
icu = roundND(colid+rid);
imgsize[0] = eyeimage->hsize[0];
imgsize[1] = eyeimage->hsize[1];
if (irl < 1 )
irl = 1;
if (icl < 1)
icl = 1;
if (iru > imgsize[0])
iru = imgsize[0];
if (icu > imgsize[1])
icu = imgsize[1];
printf("irl is %d, icl is %d iru is %d, icu is %d\n", irl , icl, iru, icu);
//% to find the inner pupil, use just the region within the previously
//% detected iris boundary
imagepupil = (IMAGE*) malloc (sizeof(IMAGE));
imagepupil->hsize[0] = iru-irl+1;
imagepupil->hsize[1] = icu-icl+1;
imagepupil->data = (unsigned char*)malloc(sizeof(unsigned char)*imagepupil->hsize[0]*imagepupil->hsize[1]);
for (i = irl-1, k=0; i<iru; i++,k++)
{
for (j = icl-1, m=0; j<icu; j++, m++)
imagepupil->data[k*imagepupil->hsize[1]+m] = eyeimage->data[i*eyeimage->hsize[1]+j];
}
//printimage(imagepupil, "imagepupil.txt");
//%find pupil boundary
findcircle(imagepupil, lpupilradius, upupilradius ,0.6,2,0.25,0.25,1.00,1.00, &rowp, &colp, &rp);
//LEE:
//findcircle(imagepupil, lpupilradius, upupilradius ,0.6,2,0.25,0.21,1.00,1.00, &rowp, &colp, &rp);
//findcircle(imagepupil, lpupilradius, upupilradius ,0.6,2,0.26,0.24,1.00,1.00, &rowp, &colp, &rp);//Best
//findcircle(imagepupil, lpupilradius, upupilradius ,0.6,2,0.26,0.25,1.00,1.00, &rowp, &colp, &rp);//Best
printf("1st: pupil is %d %d %d\n", rowp, colp, rp);
oldrowp = rowp;
rowpd = (double)rowp;
colpd = (double)colp;
rpd = (double)rp;
rowpd = (double)irl + rowp;
colpd = (double)icl + colp;
rowp = roundND(rowpd);
colp = roundND(colpd);
circlepupil[0] = rowp;
circlepupil[1] = colp;
circlepupil[2] = rp;
printf("2nd: pupil is %d %d %d\n", rowp, colp, rp);
//% set up array for recording noise regions
//% noise pixels will have NaN values
for (i = 0; i<eyeimage->hsize[0]*eyeimage->hsize[1]; i++)
imagewithnoise[i] = eyeimage->data[i];
if (eyelidon==1)
{
//%find top eyelid
topeyelid = (IMAGE*)malloc(sizeof(IMAGE));
topeyelid->hsize[0] = oldrowp-rp;
topeyelid->hsize[1] = imagepupil->hsize[1];
topeyelid->data = (unsigned char*) malloc(sizeof(unsigned char)*topeyelid->hsize[0]*topeyelid->hsize[1]);
if (topeyelid->hsize[0]>0 && topeyelid->hsize[1]>0)
{
for (i = 0; i<(oldrowp-rp)*imagepupil->hsize[1]; i++)
topeyelid->data[i] = imagepupil->data[i];
linecount = findline(topeyelid, &lines);
}
else
linecount=0;
if (linecount > 0)
{
xl = (int*)malloc(sizeof(int)*topeyelid->hsize[1]);
yl = (int*)malloc(sizeof(int)*topeyelid->hsize[1]);
linescoords(lines, topeyelid->hsize[0], topeyelid->hsize[1], xl, yl);
yla = -1;
for (i = 0; i<topeyelid->hsize[1]; i++)
{
yl[i] = yl[i]+irl-1;
xl[i]=xl[i]+icl-1;
if (yla<yl[i])
yla = yl[i];
imagewithnoise[(yl[i]-1)*eyeimage->hsize[1]+xl[i]-1] = sqrt((double)-1); // Lee: added cast
}
y2 = (int*)malloc(sizeof(int)*yla);
for (i = 0; i<yla; i++)
{
y2[i] = i+1;
for (j = 0; j<topeyelid->hsize[1]; j++)
imagewithnoise[(y2[i]-1)*eyeimage->hsize[1]+xl[j]-1] = sqrt((double)-1); // Lee: added cast
}
free (xl);
free (yl);
free(y2);
free(lines);
}
//%find bottom eyelid
bottomeyelid = (IMAGE*)malloc(sizeof(IMAGE));
bottomeyelid->hsize[0] = imagepupil->hsize[0]-(oldrowp+rp)+1;
bottomeyelid->hsize[1] = imagepupil->hsize[1];
bottomeyelid->data = (unsigned char*) malloc(sizeof(unsigned char)*bottomeyelid->hsize[0]*bottomeyelid->hsize[1]);
if (bottomeyelid->hsize[0]>0 && bottomeyelid->hsize[1]>0)
{
memcpy(bottomeyelid->data, &imagepupil->data[(oldrowp+rp-1)*imagepupil->hsize[1]], bottomeyelid->hsize[0]*bottomeyelid->hsize[1]);
linecount = findline(bottomeyelid, &lines);
}
else
linecount=0;
if (linecount > 0)
{
xl = (int*)malloc(sizeof(int)*bottomeyelid->hsize[1]);
yl = (int*)malloc(sizeof(int)*bottomeyelid->hsize[1]);
linescoords(lines, bottomeyelid->hsize[0], bottomeyelid->hsize[1], xl, yl);
/*fid = fopen("x1.txt", "w");
for (i=0; i<bottomeyelid->hsize[1]; i++)
fprintf(fid, "%d %d\n", i+1, xl[i]);
fclose(fid);
fid = fopen("y1.txt", "w");
for (i=0; i<bottomeyelid->hsize[1]; i++)
fprintf(fid, "%d %d\n", i+1, yl[i]);
fclose(fid);*/
yla = eyeimage->hsize[0];
for (i = 0; i<bottomeyelid->hsize[1]; i++)
{
yl[i] = yl[i]+irl+oldrowp+rp-2;
xl[i]=xl[i]+icl-1;
if ( yla>yl[i])
yla = yl[i];
imagewithnoise[(yl[i]-1)*eyeimage->hsize[1]+xl[i]-1] = sqrt((double)-1); // Lee: added cast
}
y2 = (int*)malloc(sizeof(int)*(eyeimage->hsize[0]-yla+1));
for (i = yla-1; i<eyeimage->hsize[0]; i++)
{
y2[i-yla+1] = i+1;
for (j = 0; j<bottomeyelid->hsize[1]; j++)
imagewithnoise[(y2[i-yla+1]-1)*eyeimage->hsize[1]+xl[j]-1] = sqrt((double)-1); // Lee: added cast
}
free (xl);
free (yl);
free(y2);
free(lines);
}
free(topeyelid->data);
free(topeyelid);
free(bottomeyelid->data);
free(bottomeyelid);
}
/*fid = fopen("imagewithnoise.txt", "w");
for (i = 0; i<eyeimage->hsize[0]; i++)
for (j = 0; j<eyeimage->hsize[1]; j++)
{
if (gccport::_isnan(imagewithnoise[i*eyeimage->hsize[1]+j]))
fprintf(fid, "%d %d NaN\n", i+1, j+1);
else
fprintf(fid, "%d %d %f\n", i+1, j+1, imagewithnoise[i*eyeimage->hsize[1]+j]);
}
fclose(fid);
*/
/*%For CASIA, eliminate eyelashes by thresholding
%ref = eyeimage < 100;
%coords = find(ref==1);
%imagewithnoise(coords) = NaN;
*/
if (highlighton==1)
{
for (i = 0; i<eyeimage->hsize[0]*eyeimage->hsize[1]; i++)
if (eyeimage->data[i]>highlightvalue)
imagewithnoise[i] = sqrt((double)-1); // Lee: added cast
}
free(imagepupil->data);
free(imagepupil);
}
int Masek::segmentiris_iridian(Masek::IMAGE *eyeimage, char *gndfilename, int *circleiris, int *circlepupil, double *imagewithnoise, int eyelidon, int highlighton, int highlightvalue)
{
int lpupilradius, upupilradius, lirisradius, uirisradius, reflecthres;
double scaling;
int rowi, coli, ri, rowp, colp, rp, oldrowp;
double rowid, colid, rid;//LEE: delete rowpd, colpd, rpd;
int irl, iru, icl, icu;
int imgsize[2];
IMAGE* imagepupil, *topeyelid, *bottomeyelid;
int i, j, k, m;
int linecount;
double *lines;
int *xl, *yl;
int *y2;
int yla;
// int iris_xpart[8], iris_ypart[8], iris_valid[8], pupil_xpart[8], pupil_ypart[8], pupil_valid[8];//LEE:
// char buffer[100];//LEE:
FILE *gndfile;
// char tmpchar;//LEE:
// int count;//LEE:
// int tmpr;//LEE:
// double a, b;
// int left, right, hasnoise;//LEE:
//% define range of pupil & iris radii
/* //LEE:Video Data
lpupilradius = 25;
upupilradius = 58;
lirisradius = 62;
uirisradius = 78;*/
/* //LEE:Video Data
lpupilradius = 12;
upupilradius = 58;
lirisradius = 60;
uirisradius = 80;*/
//%CASIA
lpupilradius = 28;
upupilradius = 75;
lirisradius = 80;
uirisradius = 150;
/*% %LIONS
% lpupilradius = 32;
% upupilradius = 85;
% lirisradius = 145;
% uirisradius = 169;
*/
//% define scaling factor to speed up Hough transform
scaling = 0.4;
reflecthres = 240;
//read in iris and pupil boundaries.
gndfile = fopen(gndfilename, "r");
if (gndfile==NULL)
{
printf("could not open gndfile %s \n", gndfilename);
return -1;
}
fscanf(gndfile, "%d %d %d %d %d %d",&rowi, &coli, &ri, &rowp, &colp, &rp);
fclose(gndfile);
//% find the iris boundary
circleiris[0] = rowi;
circleiris[1] = coli;
circleiris[2] = ri;
//printf("iris is %d %d %d\n", rowi, coli, ri);
rowid = (double)rowi;
colid = (double)coli;
rid = (double)ri;
irl = roundND(rowid-rid);
iru = roundND(rowid+rid);
icl = roundND(colid-rid);
icu = roundND(colid+rid);
imgsize[0] = eyeimage->hsize[0];
imgsize[1] = eyeimage->hsize[1];
if (irl < 1 )
irl = 1;
if (icl < 1)
icl = 1;
if (iru > imgsize[0])
iru = imgsize[0];
if (icu > imgsize[1])
icu = imgsize[1];
//printf("irl is %d, icl is %d iru is %d, icu is %d\n", irl , icl, iru, icu);
//% to find the inner pupil, use just the region within the previously
//% detected iris boundary
imagepupil = (IMAGE*) malloc (sizeof(IMAGE));
imagepupil->hsize[0] = iru-irl+1;
imagepupil->hsize[1] = icu-icl+1;
imagepupil->data = (unsigned char*)malloc(sizeof(unsigned char)*imagepupil->hsize[0]*imagepupil->hsize[1]);
for (i = irl-1, k=0; i<iru; i++,k++)
{
for (j = icl-1, m=0; j<icu; j++, m++)
imagepupil->data[k*imagepupil->hsize[1]+m] = eyeimage->data[i*eyeimage->hsize[1]+j];
}
//printimage(imagepupil, "imagepupil.txt");
//%find pupil boundary
//findcircle(imagepupil, lpupilradius, upupilradius ,0.6,2,0.25,0.25,1.00,1.00, &rowp, &colp, &rp);
//printf("pupil is %d %d %d\n", rowp, colp, rp);
oldrowp = rowp-irl;
/*rowpd = (double)rowp;
colpd = (double)colp;
rpd = (double)rp;
rowpd = (double)irl + rowp;
colpd = (double)icl + colp;
rowp = roundND(rowpd);
colp = roundND(colpd);
*/
circlepupil[0] = rowp;
circlepupil[1] = colp;
circlepupil[2] = rp;
//printf("pupil is %d %d %d\n", rowp, colp, rp);
//% set up array for recording noise regions
//% noise pixels will have NaN values
for (i = 0; i<eyeimage->hsize[0]*eyeimage->hsize[1]; i++)
imagewithnoise[i] = eyeimage->data[i];
if (eyelidon==1)
{
//%find top eyelid
topeyelid = (IMAGE*)malloc(sizeof(IMAGE));
topeyelid->hsize[0] = oldrowp-rp;
topeyelid->hsize[1] = imagepupil->hsize[1];
topeyelid->data = (unsigned char*) malloc(sizeof(unsigned char)*topeyelid->hsize[0]*topeyelid->hsize[1]);
if (topeyelid->hsize[0]>0 && topeyelid->hsize[1]>0)
{
for (i = 0; i<(oldrowp-rp)*imagepupil->hsize[1]; i++)
topeyelid->data[i] = imagepupil->data[i];
linecount = findline(topeyelid, &lines);
}
else
linecount=0;
if (linecount > 0)
{
xl = (int*)malloc(sizeof(int)*topeyelid->hsize[1]);
yl = (int*)malloc(sizeof(int)*topeyelid->hsize[1]);
linescoords(lines, topeyelid->hsize[0], topeyelid->hsize[1], xl, yl);
yla = -1;
for (i = 0; i<topeyelid->hsize[1]; i++)
{
yl[i] = yl[i]+irl-1;
xl[i]=xl[i]+icl-1;
if (yla<yl[i])
yla = yl[i];
imagewithnoise[(yl[i]-1)*eyeimage->hsize[1]+xl[i]-1] = sqrt((double)-1); // Lee: added cast
}
y2 = (int*)malloc(sizeof(int)*yla);
for (i = 0; i<yla; i++)
{
y2[i] = i+1;
for (j = 0; j<topeyelid->hsize[1]; j++)
imagewithnoise[(y2[i]-1)*eyeimage->hsize[1]+xl[j]-1] = sqrt((double)-1); // Lee: added cast
}
free (xl);
free (yl);
free(y2);
free(lines);
}
//%find bottom eyelid
bottomeyelid = (IMAGE*)malloc(sizeof(IMAGE));
bottomeyelid->hsize[0] = imagepupil->hsize[0]-(oldrowp+rp)+1;
bottomeyelid->hsize[1] = imagepupil->hsize[1];
bottomeyelid->data = (unsigned char*) malloc(sizeof(unsigned char)*bottomeyelid->hsize[0]*bottomeyelid->hsize[1]);
if (bottomeyelid->hsize[0]>0 && bottomeyelid->hsize[1]>0)
{
memcpy(bottomeyelid->data, &imagepupil->data[(oldrowp+rp-1)*imagepupil->hsize[1]], bottomeyelid->hsize[0]*bottomeyelid->hsize[1]);
linecount = findline(bottomeyelid, &lines);
}
else
linecount=0;
if (linecount > 0)
{
xl = (int*)malloc(sizeof(int)*bottomeyelid->hsize[1]);
yl = (int*)malloc(sizeof(int)*bottomeyelid->hsize[1]);
linescoords(lines, bottomeyelid->hsize[0], bottomeyelid->hsize[1], xl, yl);
/*fid = fopen("x1.txt", "w");
for (i=0; i<bottomeyelid->hsize[1]; i++)
fprintf(fid, "%d %d\n", i+1, xl[i]);
fclose(fid);
fid = fopen("y1.txt", "w");
for (i=0; i<bottomeyelid->hsize[1]; i++)
fprintf(fid, "%d %d\n", i+1, yl[i]);
fclose(fid);*/
yla = eyeimage->hsize[0];
for (i = 0; i<bottomeyelid->hsize[1]; i++)
{
yl[i] = yl[i]+irl+oldrowp+rp-2;
xl[i]=xl[i]+icl-1;
if ( yla>yl[i])
yla = yl[i];
imagewithnoise[(yl[i]-1)*eyeimage->hsize[1]+xl[i]-1] = sqrt((double)-1); // Lee: added cast
}
y2 = (int*)malloc(sizeof(int)*(eyeimage->hsize[0]-yla+1));
for (i = yla-1; i<eyeimage->hsize[0]; i++)
{
y2[i-yla+1] = i+1;
for (j = 0; j<bottomeyelid->hsize[1]; j++)
imagewithnoise[(y2[i-yla+1]-1)*eyeimage->hsize[1]+xl[j]-1] = sqrt((double)-1); // Lee: added cast
}
free (xl);
free (yl);
free(y2);
free(lines);
}
free(topeyelid->data);
free(topeyelid);
free(bottomeyelid->data);
free(bottomeyelid);
}
/*fid = fopen("imagewithnoise.txt", "w");
for (i = 0; i<eyeimage->hsize[0]; i++)
for (j = 0; j<eyeimage->hsize[1]; j++)
{
if (gccport::_isnan(imagewithnoise[i*eyeimage->hsize[1]+j]))
fprintf(fid, "%d %d NaN\n", i+1, j+1);
else
fprintf(fid, "%d %d %f\n", i+1, j+1, imagewithnoise[i*eyeimage->hsize[1]+j]);
}
fclose(fid);
*/
/*%For CASIA, eliminate eyelashes by thresholding
%ref = eyeimage < 100;
%coords = find(ref==1);
%imagewithnoise(coords) = NaN;
*/
if (highlighton==1)
{
for (i = 0; i<eyeimage->hsize[0]*eyeimage->hsize[1]; i++)
if (eyeimage->data[i]>highlightvalue)
imagewithnoise[i] = sqrt((double)-1);
}
free(imagepupil->data);
free(imagepupil);
printf("leaving segmentiris\n");
return 0;
}
void Masek::normaliseiris(Masek::filter *image, int xiris, int yiris, int riris,
int xpupil, int ypupil, int rpupil,
char *eyeimage_filename,
int radpixels, int angulardiv,
Masek::filter *polar_array, Masek::IMAGE *polar_noise)
{
//global DIAGPATH
int radiuspixels;
int angledivisions;
double r;
double *theta, *b, xcosmat, xsinmat, rmat;
filter xo, yo;
int i, j;
double x_iris, y_iris, r_iris, x_pupil, y_pupil, r_pupil, ox, oy;
int sgn;
double phi;
double a;
//FILE *fid;
//IMAGE tmpimage;
int *x, *y, *xp, *yp;
int len;
double sum, avg;
int count;
//printfilter(image, "image.txt");
radiuspixels = radpixels + 2;
angledivisions = angulardiv-1;
theta = (double*)malloc(sizeof(double)*(angledivisions+1));
for (i = 0; i<angledivisions+1; i++)
theta[i] = 2*i*PI/angledivisions;
x_iris = (double)xiris;
y_iris = (double)yiris;
r_iris = (double)riris;
x_pupil = (double)xpupil;
y_pupil = (double)ypupil;
r_pupil = (double)rpupil;
//% calculate displacement of pupil center from the iris center
ox = x_pupil - x_iris;
oy = y_pupil - y_iris;
if (ox <= 0)
sgn = -1;
else if (ox > 0)
sgn = 1;
if (ox==0 && oy > 0)
sgn = 1;
//a = ones(1,angledivisions+1)* (ox^2 + oy^2);
a = ox*ox+oy*oy;
//% need to do something for ox = 0
if (ox == 0)
phi = PI/2;
else
phi = atan(oy/ox);
b = (double*)malloc(sizeof(double)*(angledivisions+1));
xo.hsize[0] = (radiuspixels-2);
xo.hsize[1] = angledivisions+1;
xo.data = (double*)malloc(sizeof(double)*(angledivisions+1)*(radiuspixels-2));
yo.hsize[0] = (radiuspixels-2);
yo.hsize[1] = angledivisions+1;
yo.data = (double*)malloc(sizeof(double)*(angledivisions+1)*(radiuspixels-2));
//% calculate radius around the iris as a function of the angle
for (i = 0; i<angledivisions+1; i++)
{
b[i] = sgn*cos(PI - phi - theta[i]);
r = sqrt(a)*b[i]+sqrt(a*b[i]*b[i]-(a-r_iris*r_iris));
r -= r_pupil;
//% calculate cartesian location of each data point around the circular iris
//% region
xcosmat = cos(theta[i]);
xsinmat = sin(theta[i]);
/*% exclude values at the boundary of the pupil iris border, and the iris scelra border
% as these may not correspond to areas in the iris region and will introduce noise.
%
% ie don't take the outside rings as iris data.*/
for (j = 0; j<radiuspixels; j++)
{
rmat = r*j/(radiuspixels-1);
rmat += r_pupil;
if (j>0 && j<radiuspixels-1)
{
xo.data[(j-1)*(angledivisions+1)+i] = rmat*xcosmat+x_pupil;
yo.data[(j-1)*(angledivisions+1)+i] = -rmat*xsinmat+y_pupil;
}
}
}
/*
% extract intensity values into the normalised polar representation through
% interpolation
[x,y] = meshgrid(1:size(image,2),1:size(image,1)); */
interp2(image, &xo, &yo, polar_array);
//% create noise array with location of NaNs in polar_array
polar_noise->hsize[0] = polar_array->hsize[0];
polar_noise->hsize[1] = polar_array->hsize[1];
polar_noise->data = (unsigned char*)malloc(sizeof(unsigned char)*polar_noise->hsize[0]*polar_noise->hsize[1]);
memset(polar_noise->data, 0, polar_noise->hsize[0]*polar_noise->hsize[1]);
count=0;
for (i = 0; i<polar_noise->hsize[0]*polar_noise->hsize[1]; i++)
{
if (isnan(polar_array->data[i])) // Lee: renamed from "isnan"
{
polar_noise->data[i] = 1;
count++;
}
else
{
polar_noise->data[i] = 0;
polar_array->data[i] = polar_array->data[i]/255;
}
}
//printfilter(polar_array, "polar.txt");
//printimage(polar_noise, "polar_noise.txt");
//% start diagnostics, writing out eye image with rings overlayed
//% get rid of outling points in order to write out the circular pattern
for (i = 0; i<xo.hsize[0]*xo.hsize[1]; i++)
{
if (xo.data[i]>image->hsize[1])
xo.data[i] = image->hsize[1];
else if (xo.data[i]<1)
xo.data[i] = 1;
xo.data[i] = roundND(xo.data[i]);
}
for (i = 0; i<yo.hsize[0]*yo.hsize[1]; i++)
{
if (yo.data[i]>image->hsize[0])
yo.data[i] = image->hsize[0];
else if (yo.data[i]<1)
yo.data[i] = 1;
yo.data[i] = roundND(yo.data[i]);
}
/*tmpimage.hsize[0] = image->hsize[0];
tmpimage.hsize[1] = image->hsize[1];
tmpimage.data = (unsigned char*)malloc(sizeof(unsigned char)*tmpimage.hsize[0]*tmpimage.hsize[1]);
for (i = 0; i<tmpimage.hsize[0]*tmpimage.hsize[1]; i++)
{
if (_isnan(image->data[i])) // Lee: renamed from "isnan"
tmpimage.data[i] = 0;
else
tmpimage.data[i] = (int)image->data[i];
}*/
/*for (i = 0; i<yo.hsize[0]*yo.hsize[1]; i++)
tmpimage.data[(int)((yo.data[i]-1)*tmpimage.hsize[1]+(xo.data[i])-1)] = 255;
*/
//%get pixel coords for circle around iris
len = circlecoords(x_iris,y_iris,r_iris,image->hsize, -1, &x, &y);
//ind2 = sub2ind(size(image),double(y),double(x));
/*fid = fopen("xy.txt", "w");
for (i = 0; i<len; i++)
{
fprintf(fid, "%d %d %d\n", i+1, x[i], y[i]);
tmpimage.data[(y[i]-1)*tmpimage.hsize[1]+(x[i]-1)] = 255;
}
fclose(fid);*/
//%get pixel coords for circle around pupil
len = circlecoords(x_pupil,y_pupil,r_pupil,image->hsize, -1, &xp, &yp);
/*for (i = 0; i<len; i++)
tmpimage.data[(yp[i]-1)*tmpimage.hsize[1]+(xp[i]-1)] = 255;*/
//printimage(&tmpimage, "tmpimage.txt");
/*% write out rings overlaying original iris image
%w = cd;
%cd(DIAGPATH);
imwrite(image,[eyeimage_filename,'-normal.jpg'],'jpg');
%cd(w);
% end diagnostics
*/
//%replace NaNs before performing feature encoding
sum = 0;
for (i = 0; i<polar_array->hsize[0]*polar_array->hsize[1]; i++)
{
if (isnan(polar_array->data[i])) // Lee: renamed from "isnan"
sum+=0.5;
else
sum+=polar_array->data[i];
}
avg = sum/(polar_array->hsize[0]*polar_array->hsize[1]);
for (i = 0; i<polar_array->hsize[0]*polar_array->hsize[1]; i++)
{
if (isnan(polar_array->data[i]))
//polar_array->data[i] = sqrt((double)-1);//LEE:added
polar_array->data[i] = avg;
}
free(xp);
free(yp);
free(x);
free(y);
free(theta);
free(b);
free(xo.data);
free(yo.data);
//printfilter(polar_array, "polar_array.txt");
}
