// This function makes a ppm file from the MSP and displays 'nl' detected landmarks.
//im: the input image
//lmx and lmy: are pointers to nl size arrays including the (x,y) for the nl landmarks
//ppmfile: the output file name
void mspPPM(SHORTIM im, int *ii, int *jj, int nl, const char *ppmfile)
{
int colourflag;
// unsigned char colour[3]={0xFF,0xFF,0x00};
// unsigned char colour[3]={0x00,0xFF,0x00};
unsigned char colour[3]={0xFF,0xFF,0xFF};
unsigned char *imgTemp;
FILE *fp;
int kk=im.nz/2;
/*size of the mark*/
int d=4;
float temp;
imgTemp=(unsigned char *)calloc(im.nv,sizeof(unsigned char));
int low, high;
setLowHigh(im.v+kk*im.np, im.nx*im.ny, &low, &high, 1.0);
for(int i=0;i<im.nv;i++)
{
if( im.v[i] >= high ) temp=255.0;
else temp=im.v[i]*255.0/high;
imgTemp[i]=(unsigned char)temp;
}
fp=fopen(ppmfile,"w");
if(fp==NULL) file_open_error(ppmfile);
/*Write the header part of the PPM file*/
fprintf(fp,"P6\n");
fprintf(fp,"%d %d\n", im.nx, im.ny);
fprintf(fp,"255\n");
for (int j=0;j<im.ny;j++)
{
for(int i=0;i<im.nx;i++)
{
for(int m=0;m<nl;m++)
{
//uncomment to save in different colours
// if(m==3) { colour[0]=255; colour[1]=0; colour[2]=0; }
// else if(m==1) { colour[0]=0; colour[1]=255; colour[2]=0; }
// else if(m==2) { colour[0]=0; colour[1]=0; colour[2]=255; }
// else if(m==0) { colour[0]=0; colour[1]=255; colour[2]=191; }
// else if(m==4) { colour[0]=0; colour[1]=128; colour[2]=255; }
// else if(m==5) { colour[0]=255; colour[1]=0; colour[2]=255; }
// else if(m==6) { colour[0]=255; colour[1]=128; colour[2]=0; }
// else if(m==7) { colour[0]=255; colour[1]=255; colour[2]=0; }
if( (i==ii[m] && jj[m]-d<j && j<jj[m]+d) || (j==jj[m] && ii[m]-d<i && i<ii[m]+d) )
{
fwrite(colour,1,3,fp);
colourflag=1;
}
}
if(colourflag==0)
{
fwrite(imgTemp+im.np*kk+im.nx*j+i,1,1,fp);
fwrite(imgTemp+im.np*kk+im.nx*j+i,1,1,fp);
fwrite(imgTemp+im.np*kk+im.nx*j+i,1,1,fp);
}
colourflag=0;
}
}
fclose(fp);
if(opt_png)
{
char *pngfilename;
char *cmnd;
int L;
L = strlen(ppmfile);
pngfilename = (char *)calloc(L,sizeof(char));
cmnd = (char *)calloc(2*L+128,sizeof(char)); // 128 is plenty :)
stpcpy(pngfilename, ppmfile);
pngfilename[L-1]='g';
pngfilename[L-2]='n';
pngfilename[L-3]='p';
sprintf(cmnd,"pnmtopng %s > %s",ppmfile,pngfilename);
if(opt_png) system(cmnd);
free(pngfilename);
free(cmnd);
}
if(opt_ppm==NO) remove(ppmfile);
delete imgTemp;
}
//im: the input image
//nx,ny,nz: size of the image
//lm[3]: coordinate of the landmark (satrting from 0)
//ppmfile: name of the ppmfile as the output
void makePPM(SHORTIM im, int *lm, const char *ppmfile)
{
unsigned char yellow[3]={0xFF,0xFF,0x00};
unsigned char *imgTemp;
FILE *fp;
int nv=im.nx*im.ny*im.nz;
int np=im.nx*im.ny;
int ii=lm[0];
int jj=lm[1];
int kk=lm[2];
float temp;
imgTemp=(unsigned char *)calloc(nv,sizeof(unsigned char));
int low, high;
setLowHigh(im.v, nv, &low, &high);
for(int i=0;i<nv;i++)
{
if( im.v[i] >= high ) temp=255.0;
else temp=im.v[i]*255.0/high;
imgTemp[i]=(unsigned char)temp;
}
fp=fopen(ppmfile,"w");
/*Write the header part of the PPM file*/
fprintf(fp,"P6\n");
fprintf(fp,"# x=%d, y=%d, z=%d\n", ii, jj, kk);
fprintf(fp,"%d %d\n", im.nx+im.nz+im.nz, im.ny);
fprintf(fp,"255\n");
/*Write the data part of the PPM file*/
for (int j=0,ik=0;j<im.ny & ik<im.nx;j++,ik++)
{
for(int i=0;i<im.nx;i++)
{
if(i==ii | j==jj) fwrite(yellow,1,3,fp);
else {
fwrite(imgTemp+np*kk+im.nx*j+i,1,1,fp);
fwrite(imgTemp+np*kk+im.nx*j+i,1,1,fp);
fwrite(imgTemp+np*kk+im.nx*j+i,1,1,fp);
}
}
for(int k=0;k<im.nz;k++)
{
if(j==jj | k==kk) fwrite(yellow,1,3,fp);
else {
fwrite(imgTemp+np*k+im.nx*j+ii,1,1,fp);
fwrite(imgTemp+np*k+im.nx*j+ii,1,1,fp);
fwrite(imgTemp+np*k+im.nx*j+ii,1,1,fp);
}
}
for(int k=0;k<im.nz;k++)
{
if(ik==ii | k==kk) fwrite(yellow,1,3,fp);
else {
fwrite(imgTemp+np*k+im.nx*jj+ik,1,1,fp);
fwrite(imgTemp+np*k+im.nx*jj+ik,1,1,fp);
fwrite(imgTemp+np*k+im.nx*jj+ik,1,1,fp);
}
}
}
fclose(fp);
delete imgTemp;
}
char *find_foreground_mask(short *im, int nv, int nb, int nclass, int niter, short *thresh)
{
char *mask;
double *hist;
double *mean;
double *var;
double *p;
double *fit;
short *label;
FILE *fp;
int low,high,v;
int bw;
int T;
int nbv;
mask=(char *)calloc(nv,sizeof(char));
nbv=0;
for(int i=0; i<nv; i++) if(im[i]>0) nbv++;
mean = (double *)calloc(nclass,sizeof(double));
var = (double *)calloc(nclass,sizeof(double));
p = (double *)calloc(nclass,sizeof(double));
fit = (double *)calloc(nb,sizeof(double));
label = (short *)calloc(nb,sizeof(short));
if(mean==NULL || var==NULL || p==NULL || fit==NULL || label==NULL)
{
printf("\nMemory allocation problem in 'find_foreground_mask'\n");
return(NULL);
}
{
short *im_mskd;
int k=0;
im_mskd = (short *)calloc(nbv,sizeof(short));
if(im_mskd==NULL)
{
printf("\nMemory allocation problem for 'im_mskd', aborting ...\n");
exit(0);
}
for(int i=0; i<nv; i++) if(im[i]>0) im_mskd[k++]=im[i];
setLowHigh(im_mskd, nbv, &low, &high, 0.01);
hist=findHistogram(im_mskd, nbv, nb, low, high, &bw);
free(im_mskd);
}
for(int b=0; b<nb; b++) hist[b]/=nbv;
EMFIT1d(hist, fit, label, nb, mean, var, p, nclass, niter);
T=0;
for(int b=1; b<nb-1; b++)
if( fit[b-1]>fit[b] && fit[b+1]>fit[b] )
{
T=b;
break;
}
*thresh=0;
for(int i=0;i<nv;i++)
if(im[i]>0)
{
v = im[i];
if(v<=low) v=0;
else if(v>=high) v=high-low;
else v-=low;
v = (int)(v/bw);
if(v==T && im[i] > *thresh ) *thresh=im[i];
}
for(int i=0;i<nv;i++) if(im[i] <= *thresh) mask[i]=0; else mask[i]=1;
free(mean);
free(var);
free(p);
free(fit);
free(label);
free(hist);
return(mask);
}