void demo05020_1() {
int x = 1;
int y = 99;
printf("x:%2d, y:%2d\n", x, y);
swap_2(&x, &y);
printf("x:%2d, y:%2d\n", x, y);
}
int main(int argc, char *argv[])
{
int rv, len, nblocks, done = 0;
char * data = NULL;
if ( (rv = get_opts(&gopts, argc, argv)) != 0 )
return rv;
/* register interrupt trap */
signal(SIGTERM, cleanup); /* so need global variables */
signal(SIGINT, cleanup);
/* open or set input file */
if( gopts.in_fname )
{
gcontr.infd = open(gopts.in_fname, O_RDONLY);
if( gcontr.infd < 0 )
{
fprintf(stderr,"** failed to open infile '%s'\n",gopts.in_fname);
return 1;
}
}
else
gcontr.infd = 0; /* stdin */
/* allocate data block */
data = (char *)malloc(gopts.block_len * sizeof(char));
if( !data )
{
fprintf(stderr,"** failed to alloc %d bytes for block\n",
gopts.block_len);
return 1;
}
if( gopts.swap == 2 ) swap_2(data, gopts.block_len/2);
else if( gopts.swap == 4 ) swap_4(data, gopts.block_len/4);
if( (rv = open_serial(&gopts, &gcontr)) != 0 )
return rv;
nblocks = 0;
while(! done && (gopts.nblocks <= 0 || nblocks < gopts.nblocks) )
{
len = set_data(&gopts, &gcontr, data);
if( len > 0 ) done = send_serial(&gopts, &gcontr, data, len);
else done = 1;
nblocks++;
if( gopts.ms_sleep ) ms_sleep(gopts.ms_sleep);
}
free(data);
close_ports();
if(gopts.debug) fprintf(stderr,"-d wrote %d blocks of data\n",nblocks);
return 0;
}
static void convert_cell(
unsigned char *out_cell, const DCELL in_cell,
int is_fp, int bytes, int swap_flag)
{
if (is_fp) {
switch (bytes) {
case 4:
*(float *) out_cell = (float) in_cell;
break;
case 8:
*(double *) out_cell = (double) in_cell;
break;
}
}
else {
switch (bytes) {
case 1:
*(unsigned char *) out_cell = (unsigned char) in_cell;
break;
case 2:
*(short *) out_cell = (short) in_cell;
break;
case 4:
*(int *) out_cell = (int) in_cell;
break;
#ifdef HAVE_LONG_LONG_INT
case 8:
*(long long *) out_cell = (long long) in_cell;
break;
#endif
}
}
if (swap_flag) {
switch (bytes) {
case 1: break;
case 2: swap_2(out_cell); break;
case 4: swap_4(out_cell); break;
case 8: swap_8(out_cell); break;
}
}
}
static void read_cell(DCELL *out_cell, int is_integer, int is_signed, int bytes,
int byte_swap) {
if (fread(in_cell, bytes, 1, fp) != 1)
G_fatal_error(_("Error reading binary data"));
if (byte_swap) {
switch (bytes) {
case 1:
break;
case 2:
swap_2(in_cell);
break;
case 4:
swap_4(in_cell);
break;
case 8:
swap_8(in_cell);
break;
}
}
if (!is_integer) {
switch (bytes) {
case 4:
*out_cell = (DCELL) *(float *) in_cell;
break;
case 8:
*out_cell = (DCELL) *(double *) in_cell;
break;
}
} else if (is_signed) {
switch (bytes) {
case 1:
*out_cell = (DCELL) *(signed char *) in_cell;
break;
case 2:
*out_cell = (DCELL) *(short *) in_cell;
break;
case 4:
*out_cell = (DCELL) *(int *) in_cell;
break;
#ifdef HAVE_LONG_LONG_INT
case 8:
*out_cell = (DCELL) *(long long *) in_cell;
break;
#endif
}
} else {
switch (bytes) {
case 1:
*out_cell = (DCELL) *(unsigned char *) in_cell;
break;
case 2:
*out_cell = (DCELL) *(unsigned short *) in_cell;
break;
case 4:
*out_cell = (DCELL) *(unsigned int *) in_cell;
break;
#ifdef HAVE_LONG_LONG_INT
case 8:
*out_cell = (DCELL) *(unsigned long long *) in_cell;
break;
#endif
}
}
}
int main( int argc , char *argv[] )
{
FILE *imfile ;
int length , skip , swap=0 , gg ;
char orients[8] , str[8] ;
int nx , ny , bpp , cflag , hdroff , verb=0 , iarg=1 ;
/*------ help? ------*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: ge_header [-verb] file ...\n"
"Prints out information from the GE image header of each file.\n"
"Options:\n"
" -verb: Print out some probably useless extra stuff.\n"
) ;
exit(0) ;
}
if( strcmp(argv[iarg],"-verb") == 0 ){ verb++ ; iarg++ ; }
if( strcmp(argv[iarg],"-verb") == 0 ){ verb++ ; iarg++ ; }
/*----- loop over input files -----*/
for( gg=iarg ; gg < argc ; gg++ ){
imfile = fopen( argv[gg] , "r" ) ;
if( imfile == NULL ){
printf("-----------------------------------\n"
"Can't open file %s\n" ,
argv[gg] ) ;
continue ; /* skip to next file */
}
fseek( imfile , 0L , SEEK_END ) ; /* get the length of the file */
length = ftell( imfile ) ; /* (the AJ way) */
if( length < 1024 ){
printf("-----------------------------------\n"
"File %s is too short to be an image\n" ,
argv[gg] ) ;
fclose(imfile) ; continue ;
}
/*--- 03 Dec 2001: check for GEMS format file "IMGF" ---*/
/*[[[ Information herein from Medical Image Format FAQ ]]]*/
strcpy(str,"JUNK") ; /* initialize string */
rewind(imfile) ;
fread(str,1,4,imfile) ; /* check for "IMGF" at start of file */
if( str[0]=='I' && str[1]=='M' && str[2]=='G' && str[3]=='F' ){ /* good */
/*-- read next 5 ints (after the "IMGF" string) --*/
fread( &skip , 4,1, imfile ) ; /* offset into file of image data */
fread( &nx , 4,1, imfile ) ; /* x-size */
fread( &ny , 4,1, imfile ) ; /* y-size */
fread( &bpp , 4,1, imfile ) ; /* bits per pixel (should be 16) */
fread( &cflag, 4,1, imfile ) ; /* compression flag (1=uncompressed)*/
/*-- check if nx is funny --*/
if( nx < 0 || nx > 8192 ){ /* have to byte swap these 5 ints */
swap = 1 ; /* flag to swap data, too */
swap_4(&skip); swap_4(&nx); swap_4(&ny); swap_4(&bpp); swap_4(&cflag);
if( nx < 0 || nx > 8192 || ny < 0 || ny > 8192 ){
printf("-----------------------------------\n"
"File %s: illegal nx hand/or ny in header\n" ,
argv[gg] ) ;
fclose(imfile) ; continue ;
}
} else {
swap = 0 ; /* data is ordered for this CPU */
}
printf("-----------------------------------\n"
"File %s\n"
" nx=%d ny=%d skip=%d swap=%s compressed=%s bits-per-pixel=%d\n",
argv[gg] , nx , ny , skip ,
(swap) ? "YES" : "NO" ,
(cflag==1) ? "NO" : "YES" ,
bpp
) ;
/*-- try to read image header data as well --*/
length = fseek( imfile , 148L , SEEK_SET ) ; /* magic GEMS offset */
if( length == 0 ){ /* seek was good */
fread( &hdroff , 4,1 , imfile ) ; /* location of image header */
if( swap ) swap_4(&hdroff) ;
if( hdroff > 0 ){ /* read from image header */
float dx,dy,dz, xyz[9], xx,yy,zz, tr ; int itr, ii,jj,kk ;
/*-- get voxel grid sizes --*/
fseek( imfile , hdroff+26 , SEEK_SET ) ; /* dz */
fread( &dz , 4,1 , imfile ) ;
fseek( imfile , hdroff+50 , SEEK_SET ) ; /* dx and dy */
fread( &dx , 4,1 , imfile ) ;
fread( &dy , 4,1 , imfile ) ;
if( swap ){ swap_4(&dx); swap_4(&dy); swap_4(&dz); }
printf(" dx=%g dy=%g dz=%g" , dx,dy,dz ) ;
/* grid orientation: from 3 sets of LPI corner coordinates: */
/* xyz[0..2] = top left hand corner of image (TLHC) */
/* xyz[3..5] = top right hand corner of image (TRHC) */
/* xyz[6..8] = bottom right hand corner of image (BRHC) */
/* GEMS coordinate orientation here is LPI */
fseek( imfile , hdroff+154 , SEEK_SET ) ; /* another magic number */
fread( xyz , 4,9 , imfile ) ;
if( swap ){
swap_4(xyz+0); swap_4(xyz+1); swap_4(xyz+2);
swap_4(xyz+3); swap_4(xyz+4); swap_4(xyz+5);
swap_4(xyz+6); swap_4(xyz+7); swap_4(xyz+8);
}
/* x-axis orientation */
/* ii determines which spatial direction is x-axis */
/* and is the direction that has the biggest change */
/* between the TLHC and TRHC */
dx = fabs(xyz[3]-xyz[0]) ; ii = 1 ;
dy = fabs(xyz[4]-xyz[1]) ; if( dy > dx ){ ii=2; dx=dy; }
dz = fabs(xyz[5]-xyz[2]) ; if( dz > dx ){ ii=3; }
dx = xyz[ii+2]-xyz[ii-1] ; if( dx < 0. ){ ii = -ii; }
switch( ii ){
case 1: orients[0]= 'L'; orients[1]= 'R'; break; /* Left to Right */
case -1: orients[0]= 'R'; orients[1]= 'L'; break; /* Right to Left */
case 2: orients[0]= 'P'; orients[1]= 'A'; break; /* Posterior to Anterior */
case -2: orients[0]= 'A'; orients[1]= 'P'; break; /* Anterior to Posterior */
case 3: orients[0]= 'I'; orients[1]= 'S'; break; /* Inferior to Superior */
case -3: orients[0]= 'S'; orients[1]= 'I'; break; /* Superior to Inferior */
default: orients[0]='\0'; orients[1]='\0'; break; /* should never happen */
}
/* y-axis orientation */
/* jj determines which spatial direction is y-axis */
/* and is the direction that has the biggest change */
/* between the BRHC and TRHC */
dx = fabs(xyz[6]-xyz[3]) ; jj = 1 ;
dy = fabs(xyz[7]-xyz[4]) ; if( dy > dx ){ jj=2; dx=dy; }
dz = fabs(xyz[8]-xyz[5]) ; if( dz > dx ){ jj=3; }
dx = xyz[jj+5]-xyz[jj+2] ; if( dx < 0. ){ jj = -jj; }
switch( jj ){
case 1: orients[2] = 'L'; orients[3] = 'R'; break;
case -1: orients[2] = 'R'; orients[3] = 'L'; break;
case 2: orients[2] = 'P'; orients[3] = 'A'; break;
case -2: orients[2] = 'A'; orients[3] = 'P'; break;
case 3: orients[2] = 'I'; orients[3] = 'S'; break;
case -3: orients[2] = 'S'; orients[3] = 'I'; break;
default: orients[2] ='\0'; orients[3] ='\0'; break;
}
orients[4] = '\0' ; /* terminate orientation string */
kk = 6 - abs(ii)-abs(jj) ; /* which spatial direction is z-axis */
/* where 1=LR, 2=PA, 3=IS */
/* (can't tell orientation from 1 slice) */
zz = xyz[kk-1] ; /* z-coordinate of this slice */
xx = xyz[abs(ii)-1] ;
yy = xyz[abs(jj)-1] ;
printf(" zoff=%g orient=%s xoff=%g yoff=%g",
zz,orients,xx,yy ) ;
/*-- get TR in seconds --*/
fseek( imfile , hdroff+194 , SEEK_SET ) ;
fread( &itr , 4,1 , imfile ) ; /* note itr is an int */
if( swap ) swap_4(&itr) ;
tr = 1.0e-6 * itr ; /* itr is in microsec */
printf(" TR=%gs",tr) ;
/*-- get TE in milliseconds --*/
fseek( imfile , hdroff+202 , SEEK_SET ) ;
fread( &itr , 4,1 , imfile ) ; /* itr is an int, in microsec */
if( swap ) swap_4(&itr) ;
printf(" TE=%gms",1.0e-3*itr) ;
/*-- end of image header printouts --*/
printf("\n") ;
/*-- verbosity? --*/
if( verb )
printf(" TLHC= %g %g %g\n"
" TRHC= %g %g %g\n"
" BRHC= %g %g %g\n" ,
xyz[0],xyz[1],xyz[2],xyz[3],xyz[4],xyz[5],xyz[6],xyz[7],xyz[8] ) ;
/*-- date/time stamp */
if( verb ){
int dt1 , dt2 ; short in1,in2 ;
fseek( imfile , hdroff+10 , SEEK_SET ) ;
fread( &in1 , 2,1 , imfile ) ;
fread( &in2 , 2,1 , imfile ) ;
fread( &dt1 , 4,1 , imfile ) ;
fread( &dt2 , 4,1 , imfile ) ;
if( swap ){ swap_4(&dt1);swap_4(&dt2);swap_2(&in1);swap_2(&in2); }
printf(" image date/time stamps=%d,%d series#=%d im#=%d\n",dt1,dt2,in1,in2) ;
} /* end of philately */
} /* end of actually reading image header */
} /* end of trying to read image header */
/* maybe read series header */
if( verb > 1 ){
int dt1 , dt2 ; short in1,in2 ;
fseek( imfile , 140L , SEEK_SET ) ;
fread( &hdroff , 4,1 , imfile ) ; /* location of series header */
if( swap ) swap_4(&hdroff) ;
if( hdroff > 0 ){
fseek( imfile , hdroff+10 , SEEK_SET ) ;
fread( &in1 , 2,1 , imfile ) ;
fread( &dt1 , 4,1 , imfile ) ;
fread( &dt2 , 4,1 , imfile ) ;
if( swap ){ swap_4(&dt1);swap_4(&dt2);swap_2(&in1); }
printf(" series date/time stamps=%d,%d series#=%d\n",dt1,dt2,in1) ;
}
} /* end of series header */
/*****************************************************************
To actually read image data, do something like this:
int npix=nx*ny , nb=bpp/8 ;
data = malloc(nb*npix) ;
fseek( imfile , skip , SEEK_SET ) ;
fread( data , 1 , nb*npix , imfile ) ;
if( swap ){ switch( nb ){
case 2: swap_twobytes ( npix , data ); break;
case 4: swap_fourbytes( npix , data ); break;
} }
The latter 2 swap functions are in mri_swapbytes.c
******************************************************************/
} else { /*-------------- not a GEMS file --------------*/
printf("-----------------------------------\n"
"File %s is not a GE image file [doesn't start with IMGF]\n" ,
argv[gg] ) ;
}
fclose(imfile) ; /* done with this file */
} /* end of loop over input files */
exit(0) ;
}
