/*
* Read a plane out of an ICS file. The buffer is malloc'd, xsize and ysize
* are set to the image size. The data type is always uint8. You need to free()
* the data block when you're done.
*/
Ics_Error IcsLoadPreview (char const* filename, size_t planenumber, void** dest,
size_t* xsize, size_t* ysize)
{
ICSDECL;
ICS* ics;
size_t bufsize;
size_t xs, ys;
void* buf;
ICSXR( IcsOpen (&ics, filename, "r") );
xs = ics->Dim[0].Size;
ys = ics->Dim[1].Size;
bufsize = xs*ys;
buf = malloc(bufsize);
ICSTR( buf == NULL, IcsErr_Alloc );
error = IcsGetPreviewData (ics, buf, bufsize, planenumber);
ICSXA( IcsClose(ics) );
if (error == IcsErr_Ok) {
*dest = buf;
*xsize = xs;
*ysize = ys;
}
else {
free (buf);
}
return error;
}
int main(int argc, char **argv)
{
Ics_Error icserr;
ICS* ics;
size_t dims[ICS_MAXDIM];
int ndims;
int i,j;
Ics_DataType dt;
char fname[32];
char cmdlin[256];
/* TODO */
pix_type *prev; /* previous frame */
unsigned char *buf; /* 8-bit buffer */
int startframe,endframe;
int emin,emax;
if(argc < 2){
printf("usage: extract <filename>.ics [startframe [endframe]] [-e cutoff]\n");
printf("the -e option enhances the contrast using histogram analysis.\n");
printf("TODO: enabled by default, cutoff=16\n");
printf("example: extract livecell.ics 30 35 e\n");
printf("extracts all frames if start frame not specified\n");
return 0;
}
/* Open file */
icserr = IcsOpen(&ics, argv[1], "r");
ICS_CHECK(icserr);
#ifdef DEBUG_PRINT
printf("ics file loaded.\n");
#endif
/* Sniff out file; make sure it is compatible with our prog */
icserr = IcsGetLayout(ics, &dt, &ndims, dims);
ICS_CHECK(icserr);
if(dt != Ics_uint16){
printf("Sorry, image modes other than 16-bit (unsigned) ");
printf("not supported at the moment.\n");
return 0;
}
/* number of frames specified */
startframe = 0;
endframe = dims[3];
if(argc >= 3){
startframe = strtol(argv[2],NULL,0);
if(startframe > dims[3]) startframe = dims[3];
if(startframe < 0){
printf("Start frame number must be non-negative.\n");
return 1;
}
if(argc >= 4){
endframe = strtol(argv[3],NULL,0);
if(endframe < startframe){
printf("End frame number must be greater than start.\n");
return 2;
}
if(endframe > dims[3]) endframe = dims[3];
}
}
#ifdef DEBUG_PRINT
printf("dimensions: ");
for(i=0;i<ndims;i++)
printf("%ld ", dims[i]);
printf("data type: %d \n", dt);
#endif
/* TODO: warning if dimensions look non-standard */
/* allocate space before reading */
/* Only allocate for one frame; allows images with many frames
* to be loaded without much memory, unlike some programs
* (I'm looking at you, ics_opener/ImageJ ! */
prev = malloc(dims[1]*dims[2]*sizeof(pix_type));
buf = malloc(dims[1]*dims[2]*sizeof(unsigned char));
if((!prev)||(!buf))
{
printf("Couldn't allocate enough memory.\n");
return 1;
}
printf("tracking...\n");
/* read sequentially from file. */
/* Each call to IcsGetDataBlock proceeds from the end of the last */
for(i=0;i<endframe;i++){
icserr = IcsGetDataBlock(ics, prev, dims[1]*dims[2]*2);
ICS_CHECK(icserr);
if(i>=startframe){
printf("frame %d\n", i);
//for(j=0;j<dims[1]*dims[2];j++)
//buf[j] = prev[j]; >> 4;
/* normalize all images to first output frame */
if(i==startframe) edr(prev, dims[1], dims[2], &emin, &emax);
normalize(prev, buf, dims[1], dims[2], emin, emax);
sprintf(fname, "frame_%04d.png", i);
export_8bit_pgm(buf, dims[1], dims[2], "tmp.pgm");
//alib_savebitmap(fname, buf, dims[1], dims[2], 8, 1);
sprintf(cmdlin, "pnmtopng -compression 1 < tmp.pgm > %s", fname, fname);
system(cmdlin);
}
}
/* no need to free memory; that's just silly */
IcsClose(ics);
return 0;
}
int main(int argc, char **argv)
{
Ics_Error icserr;
ICS* ics;
size_t dims[ICS_MAXDIM];
int ndims;
int i,j;
Ics_DataType dt;
/* TODO */
pix_type *prev; /* previous frame */
unsigned char *buf; /* 8-bit buffer */
int startframe,endframe;
int *tmp1,*tmp2,*var,*sob;
int xmark[2],ymark[2];
unsigned char *wsh;
FILE *comf;
char fname[64],cmdlin[128];
if(argc < 4){
printf("usage: nucfollow <filename>.ics <x> <y> [startframe [endframe]] [-e cutoff]\n");
printf("(x,y) is the coordinate of the nucleus at first iteration.\n");
printf("example: nucfollow livecell.ics 400 300 30\n");
printf("extracts all frames if start frame not specified\n");
return 0;
}
/* Open file */
icserr = IcsOpen(&ics, argv[1], "r");
ICS_CHECK(icserr);
#ifdef DEBUG_PRINT
printf("ics file loaded.\n");
#endif
/* Sniff out file; make sure it is compatible with our prog */
icserr = IcsGetLayout(ics, &dt, &ndims, dims);
ICS_CHECK(icserr);
if(dt != Ics_uint16){
printf("Sorry, image modes other than 16-bit (unsigned) ");
printf("not supported at the moment.\n");
return 0;
}
/* marker */
xmark[0] = 10;
ymark[0] = 10;
xmark[1] = strtol(argv[2],NULL,0);
ymark[1] = strtol(argv[3],NULL,0);
/* number of frames specified */
startframe = 0;
endframe = 1;
if(argc >= 5){
startframe = strtol(argv[4],NULL,0);
if(startframe > dims[3]) startframe = dims[3];
if(startframe < 0){
printf("Start frame number must be non-negative.\n");
return 1;
}
if(argc >= 6){
endframe = strtol(argv[5],NULL,0);
if(endframe < startframe){
printf("End frame number must be greater than start.\n");
return 2;
}
if(endframe > dims[3]) endframe = dims[3];
} else {
endframe = startframe+1;
}
}
#ifdef DEBUG_PRINT
printf("dimensions: ");
for(i=0;i<ndims;i++)
printf("%ld ", dims[i]);
printf("data type: %d \n", dt);
#endif
/* TODO: warning if dimensions look non-standard */
/* allocate space before reading */
/* Only allocate for one frame; allows images with many frames
* to be loaded without much memory, unlike some programs
* (I'm looking at you, ics_opener/ImageJ ! */
prev = malloc(dims[1]*dims[2]*sizeof(pix_type));
buf = malloc(dims[1]*dims[2]*sizeof(unsigned char));
tmp1 = (int *)malloc(dims[1]*dims[2]*sizeof(int));
tmp2 = (int *)malloc(dims[1]*dims[2]*sizeof(int));
var = (int *)malloc(dims[1]*dims[2]*sizeof(int));
sob = (int *)malloc(dims[1]*dims[2]*sizeof(int));
wsh = (unsigned char*)malloc(dims[1]*dims[2]*sizeof(int));
if((!prev)||(!buf)||(!tmp1)||(!tmp2)||(!var)||(!sob)||(!wsh))
{
printf("Couldn't allocate enough memory.\n");
return 1;
}
/* open CoM file for output */
comf = fopen("comf.txt","w");
if(!comf){
printf("error: couldn't open comf.txt to write center of mass data!\n");
return 22;
}
fprintf(comf,"frame x y\n"); /* legend */
printf("tracking...\n");
/* read sequentially from file. */
/* Each call to IcsGetDataBlock proceeds from the end of the last */
for(i=0;i<endframe;i++){
icserr = IcsGetDataBlock(ics, prev, dims[1]*dims[2]*2);
ICS_CHECK(icserr);
if(i <startframe) continue;
/* we are at the desired frame sequence. */
/* variance filter */
printf("frame %d\n", i);
printf(" Variance filter...\n");
#if 0
if(variance(prev,var,tmp1,tmp2,dims[1],dims[2],1.0,4.0,12))
printf("Variance filter error!\n");
#endif
fast_variance(prev, var, tmp1, dims[1], dims[2]);
printf(" Cusp blur...\n");
blur_cusp(var,tmp1,dims[1],dims[2],230);
/*printf("Diffusion blur...\n");
blur_diffuse(var,tmp2,dims[1],dims[2]);
blur_diffuse(tmp2,var,dims[1],dims[2]);
*/
int maxo;
maxo=0;
for(j=0;j<dims[1]*dims[2];j++) if(var[j]>maxo) maxo=var[j];
printf(" maxo: %d\n", maxo);
printf(" Sobel edge detection...\n");
sobel(var, sob, dims[1], dims[2]);
/* reduce the output of sobel before watershed;
* this greatly reduces processing time */
/* TODO: infer this from the actual histographic data */
for(j=0;j<dims[1]*dims[2];j++) sob[j] /= 10;
for(j=0;j<dims[1]*dims[2];j++) if(sob[j]>255) sob[j]=255;
printf(" watershed assembly...\n");
if(watershed_rep(sob, wsh, tmp1, dims[1], dims[2], xmark, ymark, 2, buf, 8, 8.0)){
printf(" error during watershed!\n");
return 1;
}
/* print center of mass to file */
fprintf(comf,"%d %d %d\n", i, xmark[1], ymark[1]);
/* modify mark */
if(center_of_mass(buf, dims[1], dims[2], 8, xmark+1, ymark+1)){
printf(" zero identified regions!\n aborting.\n");
break; /* abort so we can at least see the results */
}
/* output superimposed image */
for(j=0;j<dims[1]*dims[2];j++)
wsh[j] = prev[j] >> 4;
hardedge(buf, wsh, dims[1], dims[2]);
sprintf(fname,"vesw_sup_%04d.pgm",i);
export_8bit_pgm(wsh, dims[1], dims[2], fname);
sprintf(cmdlin,"pnmtopng < %s > vesw_sup_%04d.png\nrm %s\n", fname, i, fname);
if(system(cmdlin)){
printf("Error during NetPbm invoke!\n");
return 55;
}
}
buf[ymark[1]*dims[1] + xmark[1]]=255-buf[ymark[1]*dims[1] + xmark[1]]; /* mark next CoM */
export_8bit_pgm(buf, dims[1], dims[2], "vesw.pgm");
for(j=0;j<dims[1]*dims[2];j++) buf[j] = var[j]/64;
export_8bit_pgm(buf, dims[1], dims[2], "ve.pgm");
for(j=0;j<dims[1]*dims[2];j++) buf[j] = sob[j]/8;
export_8bit_pgm(buf, dims[1], dims[2], "ves.pgm");
fclose(comf);
/* no need to free memory; that's just silly */
IcsClose(ics);
return 0;
}
