/** Copy one time frame (1..dimt) from 4D image to 3D short int volume.
* Svol can be but need not to be allocated.
*
* @param img image structure
* @param svol short volume structure
* @param frame frame number [1..number of frames]
* @return 0 if ok, 1 invalid image status, 2 invalid input
*/
int img2svol(IMG *img, SVOL *svol, int frame) {
int ret;
unsigned short int zi, yi, xi, fi;
float fmin, fmax, g;
if(VOL_TEST) printf("img2svol(img, %d, svol)\n", frame);
/* Check input */
if(svol==NULL) return(1);
svol->statmsg=_volStatusMessage[1];
if(img->status!=IMG_STATUS_OCCUPIED) return(1);
if(frame<1 || img->dimt<frame) return(2);
if(svol->status==IMG_STATUS_UNINITIALIZED) return(1);
/* Allocate memory (if needed) for volume */
ret=svolAllocate(svol, img->dimz, img->dimy, img->dimx);
if(ret) return(ret);
/* Copy data */
fi=frame-1;
svol->orientation=img->orientation;
svol->sizex=img->sizex; svol->sizey=img->sizey; svol->sizez=img->sizez;
ret=imgFrameMinMax(img, frame, &fmin, &fmax); if(ret) return(10+ret);
if(fabs(fmin)>fabs(fmax)) g=fabs(fmin); else g=fabs(fmax);
if(g!=0) g=32766./g; else g=1.0;
for(zi=0; zi<svol->dimz; zi++)
for(yi=0; yi<svol->dimy; yi++)
for(xi=0; xi<svol->dimx; xi++)
svol->v[zi][yi][xi]=(short int)temp_roundf(g*img->m[zi][yi][xi][fi]);
svol->scale_factor=1.0/g;
return(0);
}
/*!
* Write one PET frame from IMG data struct into Analyze 7.5 database file.
* This function can be called repeatedly to write all frames one at a time
* to conserve memory. This function does not write SIF.
*
* @param dbname name of file where IMG contents will be written.
* If file does not exist, it is created.
* Make sure to delete existing file, unless you want to add data
* @param frame_to_write PET frame number (1..frameNr) which will be written:
* If set to 0, frame data will be written to an existing or new PET file as
* a new frame, never overwriting existing data.
* If >0, then frame data is written as specified frame number, overwriting
* any data existing with the same frame number
* @param img pointer to the IMG data struct
* @param frame_index IMG frame index (0..dimt-1) which will be written
* @param fmin minimum pixel value in all frames that will be written;
* used only when writing the first frame
* @param fmax maximum pixel value in all frames that will be written;
* used only when writing the first frame
* @return errstatus, which is STATUS_OK (0) when call was successful,
* and >0 in case of an error.
*/
int imgWriteAnalyzeFrame(
const char *dbname, int frame_to_write, IMG *img, int frame_index,
float fmin, float fmax
) {
IMG test_img;
int ret=0, pxlNr, zi, xi, yi, little;
FILE *fp;
short int *sdata=NULL, *sptr;
char datfile[FILENAME_MAX], hdrfile[FILENAME_MAX], siffile[FILENAME_MAX];
ANALYZE_DSR dsr;
float scale_factor=1.0;
if(IMG_TEST) printf("\nimgWriteAnalyzeFrame(%s, %d, *img, %d, %g, %g)\n",
dbname, frame_to_write, frame_index, fmin, fmax);
/*
* Check the input
*/
if(dbname==NULL) return STATUS_FAULT;
if(img==NULL) return STATUS_FAULT;
if(img->status!=IMG_STATUS_OCCUPIED) return STATUS_FAULT;
if(frame_to_write<0) return STATUS_FAULT;
if(frame_index<0 || frame_index>=img->dimt) return STATUS_FAULT;
if(img->_fileFormat!=IMG_ANA_L && img->_fileFormat!=IMG_ANA)
return STATUS_FAULT;
/*
* If database does not exist, then create it with new header,
* and if it does exist, then read and check header information.
* Create or edit header to contain correct frame nr.
* Determine the global scaling factor.
*/
imgInit(&test_img);
if(anaDatabaseExists(dbname, hdrfile, datfile, siffile)==0) { // not existing
/* Create database filenames */
sprintf(hdrfile, "%s.hdr", dbname);
sprintf(datfile, "%s.img", dbname);
sprintf(siffile, "%s.sif", dbname);
/* Set main header */
imgSetAnalyzeHeader(img, dbname, &dsr, fmin, fmax);
if(frame_to_write==0) frame_to_write=1;
dsr.dime.dim[4]=frame_to_write;
scale_factor=dsr.dime.funused1;
if(fabs(scale_factor)>1.0E-20) scale_factor=1.0/scale_factor;
/* Write Analyze header */
ret=anaWriteHeader(hdrfile, &dsr);
if(ret && IMG_TEST) printf("anaWriteHeader() := %d\n", ret);
if(ret) return STATUS_CANTWRITEHEADERFILE;
/* Remove datafile if necessary */
if(access(datfile, 0) != -1) remove(datfile);
} else { /* database does exist */
/* Read header information for checking */
ret=imgReadAnalyzeHeader(dbname, &test_img);
if(ret!=0) {imgEmpty(&test_img); return ret;}
/* Check that file format is the same */
if(img->_fileFormat!=test_img._fileFormat || img->type!=test_img.type) {
imgEmpty(&test_img); return STATUS_WRONGFILETYPE;}
/* Check that matrix sizes are the same */
if(img->dimz!=test_img.dimz || img->dimx!=test_img.dimx ||
img->dimy!=test_img.dimy) {
imgEmpty(&test_img); return STATUS_VARMATSIZE;}
imgEmpty(&test_img);
/* Read the header, set new frame number, and write it back */
/* Get also the scale factor */
if((ret=anaReadHeader(hdrfile, &dsr))!=0) return STATUS_NOMAINHEADER;
scale_factor=1.0/dsr.dime.funused1;
if(frame_to_write==0) frame_to_write=dsr.dime.dim[4]+1;
if(dsr.dime.dim[4]<frame_to_write) {
if(dsr.dime.dim[4]+1<frame_to_write) return STATUS_MISSINGMATRIX;
dsr.dime.dim[4]=frame_to_write;
}
if((ret=anaWriteHeader(hdrfile, &dsr))!=0) return STATUS_NOWRITEPERM;
}
if(IMG_TEST>2) {
printf("frame_to_write := %d\n", frame_to_write);
printf("hdrfile := %s\n", hdrfile);
printf("datfile := %s\n", datfile);
printf("siffile := %s\n", siffile);
}
/* Allocate memory for matrix short int data (one plane) */
pxlNr=img->dimx*img->dimy;
sdata=(short int*)malloc(pxlNr*sizeof(short int));
if(sdata==NULL) return STATUS_NOMEMORY;
/* Open datafile, not removing possible old contents */
if(frame_to_write==1) fp=fopen(datfile, "wb"); else fp=fopen(datfile, "r+b");
if(fp==NULL) {free(sdata); return STATUS_CANTWRITEIMGFILE;}
/* Move file pointer to the place of current frame */
if(fseek(fp, (frame_to_write-1)*pxlNr*img->dimz*sizeof(short int),
SEEK_SET)!=0) {
free(sdata); fclose(fp); return STATUS_MISSINGMATRIX;}
little=little_endian();
/* Copy, scale and write data plane-by-plane */
if(anaFlipping()==0) {
for(zi=0; zi<img->dimz; zi++) {
sptr=sdata;
/*printf("plane := %d\n scale_factor := %g\n", zi+1, scale_factor);*/
for(yi=img->dimy-1; yi>=0; yi--) for(xi=img->dimx-1; xi>=0; xi--) {
*sptr=temp_roundf(scale_factor*img->m[zi][yi][xi][frame_index]); sptr++;
}
/* Change byte order if necessary */
sptr=sdata; if(little!=dsr.little) swabip(sptr, pxlNr*sizeof(short int));
/* Write image data */
sptr=sdata;
if(fwrite(sptr, sizeof(short int), pxlNr, fp) != pxlNr) {
free(sdata); fclose(fp); return STATUS_CANTWRITEIMGFILE;
}
}
} else {
for(zi=img->dimz-1; zi>=0; zi--) {
sptr=sdata;
for(yi=img->dimy-1; yi>=0; yi--) for(xi=img->dimx-1; xi>=0; xi--) {
*sptr=temp_roundf(scale_factor*img->m[zi][yi][xi][frame_index]); sptr++;
}
/* Change byte order if necessary */
sptr=sdata; if(little!=dsr.little) swabip(sptr, pxlNr*sizeof(short int));
/* Write image data */
sptr=sdata;
if(fwrite(sptr, sizeof(short int), pxlNr, fp) != pxlNr) {
free(sdata); fclose(fp); return STATUS_CANTWRITEIMGFILE;
}
}
}
free(sdata);
fclose(fp);
return STATUS_OK;
}
/**
* Copy header information in IMG struct into Analyze 7.5 header struct.
* Min, max, and scale factor are set here and they apply to all frames.
*
* @return errstatus, which is STATUS_OK (0) when call was successful,
* and >0 in case of an error.
*/
int imgSetAnalyzeHeader(
/** pointer to IMG struct from which header information is read */
IMG *img,
/** Analyze 7.5 database name */
const char *dbname,
/** pointer to Analyze header struct to be filled */
ANALYZE_DSR *dsr,
/** minimum pixel value in all frames that will be written */
float fmin,
/** maximum pixel value in all frames that will be written */
float fmax
) {
struct tm *st;
char *cptr;
float g;
if(IMG_TEST) printf("\nimgSetAnalyzeHeader(*img, %s, *dsr, %g, %g)\n",
dbname, fmin, fmax);
/* Check the input */
if(img==NULL) return STATUS_FAULT;
if(img->status!=IMG_STATUS_INITIALIZED && img->status!=IMG_STATUS_OCCUPIED)
return STATUS_FAULT;
imgSetStatus(img, STATUS_FAULT);
if(dsr==NULL) return STATUS_FAULT;
/* Byte order */
if(img->_fileFormat==IMG_ANA_L) dsr->little=1; else dsr->little=0;
/* Header key */
memset(&dsr->hk, 0, sizeof(ANALYZE_HEADER_KEY));
memset(&dsr->dime, 0, sizeof(ANALYZE_HEADER_IMGDIM));
memset(&dsr->hist, 0, sizeof(ANALYZE_HEADER_HISTORY));
dsr->hk.sizeof_hdr=348;
strcpy(dsr->hk.data_type, "");
cptr=strrchr(dbname, '/'); if(cptr==NULL) cptr=strrchr(dbname, '\\');
if(cptr!=NULL) cptr++; if(cptr==NULL) cptr=(char*)dbname;
strncpy(dsr->hk.db_name, cptr, 17);
dsr->hk.extents=16384;
dsr->hk.regular='r';
/* Image dimension */
dsr->dime.dim[0]=4;
dsr->dime.dim[1]=img->dimx;
dsr->dime.dim[2]=img->dimy;
dsr->dime.dim[3]=img->dimz;
dsr->dime.dim[4]=img->dimt;
dsr->dime.datatype=ANALYZE_DT_SIGNED_SHORT;
dsr->dime.bitpix=16;
dsr->dime.pixdim[0]=0.0;
dsr->dime.pixdim[1]=img->sizex;
dsr->dime.pixdim[2]=img->sizey;
dsr->dime.pixdim[3]=img->sizez;
dsr->dime.pixdim[4]=0.0;
dsr->dime.funused1=0.0; /* Scale factor is set later */
/* dsr.dime.funused2=img->zoom; */ /* Reconstruction zoom */
dsr->dime.funused3=img->isotopeHalflife;
/* Data history */
if(img->decayCorrection==IMG_DC_CORRECTED)
strcpy(dsr->hist.descrip, "Decay corrected.");
else if(img->decayCorrection==IMG_DC_NONCORRECTED)
strcpy(dsr->hist.descrip, "No decay correction.");
else
strcpy(dsr->hist.descrip, "");
if(strlen(img->studyNr)>0 && strcmp(img->studyNr, ".")!=0)
strncpy(dsr->hist.scannum, img->studyNr, 10);
else
strcpy(img->studyNr, "");
st=localtime(&img->scanStart);
if(st!=NULL) {
strftime(dsr->hist.exp_date, 10, "%Y%m%d", st);
strftime(dsr->hist.exp_time, 10, "%H:%M:%S", st);
} else {
strcpy(dsr->hist.exp_date, "19000101");
strcpy(dsr->hist.exp_time, "00:00:00");
}
/* Determine and set scale factor and cal_min & cal_max */
if(fmin<fmax) {
dsr->dime.cal_min=fmin; dsr->dime.cal_max=fmax;
} else { /* not given in function call, try to find those here */
if(img->status==IMG_STATUS_OCCUPIED &&
imgMinMax(img, &dsr->dime.cal_min, &dsr->dime.cal_max)==0) {}
else return STATUS_FAULT;
}
if(fabs(dsr->dime.cal_min) > fabs(dsr->dime.cal_max)) g=fabs(dsr->dime.cal_min);
else g = fabs(dsr->dime.cal_max);
/* if(fabs(dsr->dime.cal_min)>fabs(dsr->dime.cal_max))
g=fabs(dsr->dime.cal_min); */
/* else g=fabs(dsr->dime.cal_max); */
if(g<1E-20) g=1.0; else g=32767./g; dsr->dime.funused1=1.0/g;
/* Set header glmin & glmax */
dsr->dime.glmin=temp_roundf(fmin*g); dsr->dime.glmax=temp_roundf(fmax*g);
/* printf("glmin=%d\n", dsr->dime.glmin); */
/* printf("glmax=%d\n", dsr->dime.glmax); */
imgSetStatus(img, STATUS_OK);
return STATUS_OK;
}
/*!
* Write Analyze 7.5 image.
* Analyze database name must be given with path. Path must exist.
* Image and header files with .img and .hdr extensions are created.
* Existing files are overwritten.
* anaFlipping() determines whether image is flipped in z-direction;
* image is always flipped in x,y-directions.
* Byte order is determined based on _fileFormat field.
*
* @param dbname analyze database name with path, without extension
* @param img pointer to IMG data
* @return 0 if ok, 1 invalid input, 2 invalid image status (image not occupied),
* 3 failed to resolve extreme values (min and max),
* 12 failed to allocate temp memory, 14 failed to open file for writing,
* 15 failed to write data, 21 failed to write header, and
* sets IMG->statmsg in case of error
*/
int imgWriteAnalyze(const char *dbname, IMG *img) {
FILE *fp;
int ret, fi, pi, xi, yi, little;
float g;
ANALYZE_DSR dsr;
char datfile[FILENAME_MAX], hdrfile[FILENAME_MAX], siffile[FILENAME_MAX];
const char *cptr;
int pxlNr=0;
struct tm *st;
short int *sdata, *sptr, smin, smax;
SIF sif;
if(IMG_TEST) printf("imgWriteAnalyze(%s, *img)\n", dbname);
/* Check the arguments */
imgSetStatus(img, STATUS_OK);
if(img==NULL || img->status!=IMG_STATUS_OCCUPIED) {
imgSetStatus(img, STATUS_FAULT); return(2);}
if(dbname==NULL || !dbname[0]) {imgSetStatus(img, STATUS_FAULT); return(1);}
/* Make the image and header filenames */
strcpy(datfile, dbname); strcat(datfile, ".img");
strcpy(hdrfile, dbname); strcat(hdrfile, ".hdr");
strcpy(siffile, dbname); strcat(siffile, ".sif");
/*
* Fill Analyze header
*/
if(img->_fileFormat==IMG_ANA_L) dsr.little=1; else dsr.little=0;
/* Header key */
memset(&dsr.hk, 0, sizeof(ANALYZE_HEADER_KEY));
memset(&dsr.dime, 0, sizeof(ANALYZE_HEADER_IMGDIM));
memset(&dsr.hist, 0, sizeof(ANALYZE_HEADER_HISTORY));
dsr.hk.sizeof_hdr=348;
strcpy(dsr.hk.data_type, "");
cptr=strrchr(dbname, '/'); if(cptr==NULL) cptr=strrchr(dbname, '\\');
if(cptr!=NULL) cptr++; if(cptr==NULL) cptr=dbname;
strncpy(dsr.hk.db_name, cptr, 17);
dsr.hk.extents=16384;
dsr.hk.regular='r';
/* Image dimension */
dsr.dime.dim[0]=4;
dsr.dime.dim[1]=img->dimx;
dsr.dime.dim[2]=img->dimy;
dsr.dime.dim[3]=img->dimz;
dsr.dime.dim[4]=img->dimt;
dsr.dime.datatype=ANALYZE_DT_SIGNED_SHORT;
dsr.dime.bitpix=16;
dsr.dime.pixdim[0]=0.0;
dsr.dime.pixdim[1]=img->sizex;
dsr.dime.pixdim[2]=img->sizey;
dsr.dime.pixdim[3]=img->sizez;
dsr.dime.pixdim[4]=0.0;
dsr.dime.funused1=0.0; /* Scale factor is set later */
/* dsr.dime.funused2=img->zoom; */ /* Reconstruction zoom */
dsr.dime.funused3=img->isotopeHalflife;
/* Data history */
if(img->decayCorrection==IMG_DC_CORRECTED)
strcpy(dsr.hist.descrip, "Decay corrected.");
else if(img->decayCorrection==IMG_DC_NONCORRECTED)
strcpy(dsr.hist.descrip, "No decay correction.");
else
strcpy(dsr.hist.descrip, "");
if(strlen(img->studyNr)>0 && strcmp(img->studyNr, ".")!=0)
strncpy(dsr.hist.scannum, img->studyNr, 10);
else
strcpy(dsr.hist.scannum, "");
st=localtime(&img->scanStart);
if(st!=NULL) {
strftime(dsr.hist.exp_date, 10, "%Y-%m-%d", st);
strftime(dsr.hist.exp_time, 10, "%H:%M:%S", st);
} else {
strncpy(dsr.hist.exp_date, "1900-01-01", 10);
strncpy(dsr.hist.exp_time, "00:00:00", 10);
}
/*
* Scale data to short int range
* Determine and set scale factor and cal_min & cal_max
*/
if(IMG_TEST) printf("scaling data to short ints\n");
ret=imgMinMax(img, &dsr.dime.cal_min, &dsr.dime.cal_max);
if(ret) {imgSetStatus(img, STATUS_FAULT); return(3);}
if(fabs(dsr.dime.cal_min)>fabs(dsr.dime.cal_max)) g=fabs(dsr.dime.cal_min);
else g=fabs(dsr.dime.cal_max);
if(g<1E-20) g=1.0; else g=32767./g; dsr.dime.funused1=1.0/g;
if(IMG_TEST) printf("min=%g max=%g scale_factor=%g\n",
dsr.dime.cal_min, dsr.dime.cal_max, dsr.dime.funused1);
/* Allocate memory for short int array */
pxlNr=(img->dimx)*(img->dimy)*(img->dimz);
sdata=malloc(pxlNr*sizeof(short int));
if(sdata==NULL) {
imgSetStatus(img, STATUS_NOMEMORY);
return 12;
}
/* Open image data file for write */
if((fp=fopen(datfile, "wb")) == NULL) {
imgSetStatus(img, STATUS_CANTWRITEIMGFILE);
free(sdata);
return 14;
}
/* Copy and write image matrix data to short int array */
/* Data is written one frame at a time */
smin=smax=temp_roundf(g*img->m[0][0][0][0]);
for(fi=0; fi<img->dimt; fi++) {
sptr=sdata;
if(anaFlipping()==0) {
for(pi=0; pi<img->dimz; pi++)
for(yi=img->dimy-1; yi>=0; yi--)
for(xi=img->dimx-1; xi>=0; xi--) {
*sptr=temp_roundf(g*img->m[pi][yi][xi][fi]);
if(*sptr>smax) smax=*sptr; else if(*sptr<smin) smin=*sptr;
sptr++;
}
} else {
for(pi=img->dimz-1; pi>=0; pi--)
for(yi=img->dimy-1; yi>=0; yi--)
for(xi=img->dimx-1; xi>=0; xi--) {
*sptr=temp_roundf(g*img->m[pi][yi][xi][fi]);
if(*sptr>smax) smax=*sptr; else if(*sptr<smin) smin=*sptr;
sptr++;
}
}
/* Change byte order if necessary */
little=little_endian();
if(little!=dsr.little)
swabip(sdata, pxlNr*sizeof(short int));
/* Write image data */
if(fwrite(sdata, 2, pxlNr, fp) != pxlNr) {
imgSetStatus(img, STATUS_CANTWRITEIMGFILE);
free(sdata); fclose(fp);
return 15;
}
}
/* Done writing */
fclose(fp);
free(sdata);
if(IMG_TEST) printf("smin=%d smax=%d\n", smin, smax);
/* Set header glmin & glmax */
dsr.dime.glmin=smin; dsr.dime.glmax=smax;
/* Write Analyze header */
ret=anaWriteHeader(hdrfile, &dsr);
if(ret) {
imgSetStatus(img, STATUS_CANTWRITEHEADERFILE);
return 21;
}
imgSetStatus(img, STATUS_OK);
/* Otherwise ready, but check if SIF should/can be written */
sifInit(&sif);
/* Try to read existing SIF */
ret=sifRead(siffile, &sif);
if(ret==0) { // SIF could be read
if(sif.frameNr==img->dimt) {
/* If size matches, then update the contents, but keep counts, in case
previous SIF comes with actual count info from scanner */
ret=img2sif(img, &sif, 1, 1, 0, IMG_TEST-2);
} else {
/* otherwise create SIF contents */
ret=img2sif(img, &sif, 1, 1, 2, IMG_TEST-2);
}
} else {
/* otherwise create SIF contents */
ret=img2sif(img, &sif, 1, 1, 2, IMG_TEST-2);
}
if(ret!=0) {
/* SIF data could not be made: do not give error, just do not write it */
if(IMG_TEST>0) printf("SIF contents could not be filled.\n");
return 0;
}
/* Write SIF */
ret=sifWrite(&sif, siffile);
if(ret!=0) {
/* SIF could not be written: do not give error, just do not write it */
if(IMG_TEST>0)
fprintf(stderr, "Error: SIF could not be written (%d).\n", ret);
}
imgSetStatus(img, STATUS_OK);
return 0;
}
/** The matrix is filled with 0's (outside of ROI), 1's (on the ROI border),
* and 2's (inside the ROI border).
* If ROI extends outside image borders, those points are ignored.
* Matrix coordinates are up-to-bottom and left-to-right.
\return Function returns 0, if everything is OK.
*/
int roiOnOff(
/** Definitions for one region-of-interest */
ROI *roi,
/** Image matrix x dimension */
int dimx,
/** Image matrix y dimension */
int dimy,
/** Image reconstruction zoom */
float zoom,
/** Allocated memory for output matrix[dimx][dimy] */
char **m
) {
int i, j, n, *x, *y, pos_x, pos_y, *fx, *fy;
float f;
/* Check the parameters */
if(roi==NULL || dimx<2 || dimy<2 || zoom<1.0e-6 || m==NULL) {
strcpy(roierrmsg, "invalid arguments for roiOnOff()");
return(1);
}
/* Make scaled ROI points */
strcpy(roierrmsg, "out of memory");
if((x=malloc(roi->point_nr*sizeof(int)))==NULL) return(2);
if((y=malloc(roi->point_nr*sizeof(int)))==NULL) {
free((char*)x); return(2);}
f=roi->zoom; if(f<=0.0) f=1.0;
pos_x=(int)temp_roundf(((float)roi->pos_x)/f);
pos_y=(int)temp_roundf(((float)roi->pos_y)/f);
f=roi->zoom*(roi->recon_zoom/zoom); if(f<=0.0) f=1.0;
for(i=0; i<roi->point_nr; i++) {
x[i]=pos_x+(int)temp_roundf((float)roi->x[i]/f);
y[i]=pos_y+(int)temp_roundf((float)roi->y[i]/f);
}
/* Fill the gaps between points */
n=roiFillGaps(x, y, roi->point_nr, &fx, &fy);
if(n<1) {
strcpy(roierrmsg, "cannot fill the gaps in ROI border");
free((char*)x); free((char*)y); return(3);
}
/* Set matrix */
for(i=0; i<dimy; i++) for(j=0; j<dimx; j++) m[j][i]=(char)0;
for(i=0; i<n; i++) if(fx[i]>=0 && fx[i]<dimx && fy[i]>=0 && fy[i]<dimy)
m[fx[i]][fy[i]]=(char)1;
/* Fill the inside of ROI */
for(i=0; i<dimy; i++) if(m[0][i]==0) m[0][i]=2; else break;
for(i=dimy-1; i>=0; i--) if(m[0][i]==0) m[0][i]=2; else break;
for(i=0; i<dimy; i++) if(m[dimx-1][i]==0) m[dimx-1][i]=2; else break;
for(i=dimy-1; i>=0; i--) if(m[dimx-1][i]==0) m[dimx-1][i]=2; else break;
for(i=0; i<dimx; i++) if(m[i][0]==0) m[i][0]=2; else break;
for(i=dimx-1; i>=0; i--) if(m[i][0]==0) m[i][0]=2; else break;
for(i=0; i<dimx; i++) if(m[i][dimy-1]==0) m[i][dimy-1]=2; else break;
for(i=dimx-1; i>=0; i--) if(m[i][dimy-1]==0) m[i][dimy-1]=2; else break;
for(i=0; i<dimy; i++) for(j=0; j<dimx; j++) {
if(m[j][i]!=2) continue;
if(i>0 && m[j][i-1]==0) {m[j][i-1]=2; j=-1; i-=2; continue;}
if(j>0 && m[j-1][i]==0) {m[j-1][i]=2; j-=2; continue;}
if(j+1<dimx) {if(m[j+1][i]!=1) m[j+1][i]=2;}
if(i+1<dimy) {if(m[j][i+1]!=1) m[j][i+1]=2;}
m[j][i]=3;
}
for(i=0; i<dimy; i++) for(j=0; j<dimx; j++)
if(m[j][i]==0) m[j][i]=2; else if(m[j][i]>1) m[j][i]=0;
//if(m[j][i]<2) m[j][i]=1; else m[j][i]=0;
/* Free memory */
free((char*)x); free((char*)y);
free((char*)fx); free((char*)fy);
return(0);
}
/** Fills the gaps between ROI points; join them with new points.
* Allocates memory for new point data in fx and fy.
\return Returns the number of new points or =< 0, if error.
*/
int roiFillGaps(int *x, int *y, int nr, int **ffx, int **ffy)
{
int i, j, x1, x2=0, y1, y2=0, dx, dy, nx, ny, *fx, *fy, n;
float k;
/* Check data */
if(nr<1) return(0);
/* Allocate memory for new data */
if((fx=malloc(nr*sizeof(int)))==NULL) return -1;
if((fy=malloc(nr*sizeof(int)))==NULL) {free((char*)fx); return -1;}
/* Process from first to last (last->first is done already) */
for(i=1, n=j=0; i<nr; i++) {
x1=x[i-1]; x2=x[i]; y1=y[i-1]; y2=y[i]; dx=x2-x1; dy=y2-y1;
fx[j]=x1; fy[j++]=y1;
if(abs(dx)<2 && abs(dy)<2) continue;
if(abs(dx)>=abs(dy)) {
k=(float)dy/(float)dx;
if(x2>x1)
for(nx=x1+1; nx<x2; nx++) {
ny=y1+(int)temp_roundf(k*(nx-x1));
fx[j]=nx; fy[j++]=ny; n++;
if((fx=(int*)realloc((char*)fx, (nr+n)*sizeof(int)))==NULL) {
free((char*)fy); return -1;}
if((fy=(int*)realloc((char*)fy, (nr+n)*sizeof(int)))==NULL) {
free((char*)fx); return -1;}
}
else
for(nx=x1-1; nx>x2; nx--) {
ny=y1+(int)temp_roundf(k*(nx-x1));
fx[j]=nx; fy[j++]=ny; n++;
if((fx=(int*)realloc((char*)fx, (nr+n)*sizeof(int)))==NULL) {
free((char*)fy); return -1;}
if((fy=(int*)realloc((char*)fy, (nr+n)*sizeof(int)))==NULL) {
free((char*)fx); return -1;}
}
} else {
k=(float)dx/(float)dy;
if(y2>y1)
for(ny=y1+1; ny<y2; ny++) {
nx=x1+(int)temp_roundf(k*(ny-y1));
fx[j]=nx; fy[j++]=ny; n++;
if((fx=(int*)realloc((char*)fx, (nr+n)*sizeof(int)))==NULL) {
free((char*)fy); return -1;}
if((fy=(int*)realloc((char*)fy, (nr+n)*sizeof(int)))==NULL) {
free((char*)fx); return -1;}
}
else
for(ny=y1-1; ny>y2; ny--) {
nx=x1+(int)temp_roundf(k*(ny-y1));
fx[j]=nx; fy[j++]=ny; n++;
if((fx=(int*)realloc((char*)fx, (nr+n)*sizeof(int)))==NULL) {
free((char*)fy); return -1;}
if((fy=(int*)realloc((char*)fy, (nr+n)*sizeof(int)))==NULL) {
free((char*)fx); return -1;}
}
}
}
fx[j]=x2; fy[j++]=y2; n=j;
*ffx=fx; *ffy=fy;
return(n);
}
/*!
* Write ECAT 6.3 sinogram matrix header and data
*
* @param fp target file pointer
* @param matnum matrix number [1..number of matrixes]
* @param h Ecat 6.3 scan header
* @param fdata matrix data
* @return 0 if ok, 1 invalid input, 3 invalid matrix dimension,
* 4 invalid block number, 5 failed to allocate memory for data,
* 8 failed to resolve next block number, 10 cannot write sub header,
* 13 failed to write data
*/
int ecat63WriteScanMatrix(FILE *fp, int matnum, ECAT63_scanheader *h, float *fdata) {
int i, nxtblk, blkNr, data_size, pxlNr, ret;
float *fptr, fmin, fmax, g, f;
char *mdata, *mptr;
short int *sptr;
if(ECAT63_TEST) printf("ecat63WriteScanMatrix(fp, %d, h, data)\n", matnum);
if(fp==NULL || matnum<1 || h==NULL || fdata==NULL) {
sprintf(ecat63errmsg, "invalid function parameter.\n");
return(1);
}
/* nr of pixels */
pxlNr=h->dimension_1*h->dimension_2;
if(pxlNr<1) {
sprintf(ecat63errmsg, "invalid matrix dimension.\n");
return(3);
}
/* How much memory is needed for ALL pixels */
data_size=pxlNr*ecat63pxlbytes(h->data_type);
/* block nr taken by all pixels */
blkNr=(data_size+MatBLKSIZE-1)/MatBLKSIZE; if(blkNr<1) {
sprintf(ecat63errmsg, "invalid block number.\n");
return(4);
}
/* Allocate memory for matrix data */
mdata=(char*)calloc(blkNr, MatBLKSIZE); if(mdata==NULL) {
sprintf(ecat63errmsg, "out of memory.\n");
return(5);
}
/* Search for min and max for calculation of scale factor */
fptr=fdata; fmin=fmax=*fptr;
for(i=0; i<pxlNr; i++, fptr++) {
if(*fptr>fmax) fmax=*fptr; else if(*fptr<fmin) fmin=*fptr;
}
if(fabs(fmin)>fabs(fmax)) g=fabs(fmin); else g=fabs(fmax);
if(g>0) f=32766./g; else f=1.0;
/* Check if pixels values can be left as such with scale_factor = 1 */
fptr=fdata;
if(f>=1.0 && ecat63_is_scaling_needed(g, fptr, pxlNr)==0) f=1.0;
/* Scale matrix data to shorts */
h->scale_factor=1.0/f;
sptr=(short int*)mdata; fptr=fdata;
for(i=0; i<pxlNr; i++, sptr++, fptr++) *sptr=(short int)temp_roundf(f*(*fptr));
/* Set header short min & max */
h->scan_min=(short int)temp_roundf(f*fmin);
h->scan_max=(short int)temp_roundf(f*fmax);
/* Get block number for matrix header and data */
nxtblk=ecat63Matenter(fp, matnum, blkNr); if(nxtblk<1) {
sprintf(ecat63errmsg, "cannot determine matrix block (%d).\n", -nxtblk);
free(mdata); return(8);
}
if(ECAT63_TEST>2) printf(" block=%d fmin=%g fmax=%g\n", nxtblk, fmin, fmax);
/* Write header */
ret=ecat63WriteScanheader(fp, nxtblk, h); if(ret) {
sprintf(ecat63errmsg, "cannot write subheader (%d).\n", ret);
free(mdata); return(10);
}
/* Write matrix data */
mptr=mdata;
ret=ecat63WriteMatdata(fp, nxtblk+1, mptr, pxlNr, ecat63pxlbytes(h->data_type));
free(mdata);
if(ret) {
sprintf(ecat63errmsg, "cannot write matrix data (%d).\n", ret);
return(13);
}
return(0);
}
