MRI_IMAGE *mri_new( int nx , int ny , MRI_TYPE kind )
{
MRI_IMAGE *newim ;
newim = mri_new_7D_generic( nx,ny , 1,1,1,1,1 , kind , TRUE ) ;
return newim ;
}
MRI_IMAGE *mri_new_vol_empty( int nx , int ny , int nz , MRI_TYPE kind )
{
MRI_IMAGE *newim ;
newim = mri_new_7D_generic( nx,ny,nz , 1,1,1,1 , kind , FALSE ) ;
return newim ;
}
/*-------------------------------------------------------------------------
* read data into image array, based on mosaic (fill image and image array)
* (from mri_read_dicom.c 22 Dec 2010 [rickr]
*
* - fp : open file pointer (input/output)
* - im : current image (output)
* - imar : mosaic image array (output)
* - flip_slices: whether to reverse slice order (output)
* - mi : mosaic info (input)
* - datum : type for image array (input)
* - bpp : bytes per pixel (input)
* - kor : slice direction orientation (input)
* - swap : whether to byte swap data (input)
* - dx,y,z : slice dimensions (input)
* - dt : TR, if > 0 (input)
*
* return 0 on success
* 1 on error
*/
int read_mosaic_data( FILE *fp, MRI_IMAGE *im, MRI_IMARR *imar,
int * flip_slices, Siemens_extra_info *mi, int datum, int bpp, int kor,
int swap, float dx, float dy, float dz, float dt)
{ /*-- 28 Oct 2002: is a 2D mosaic --*******************/
char * dar=NULL, * iar ;
int nvox, yy, xx, nxx, ii, jj, slice ;
int mos_nx, mos_ny, mos_nz, mos_ix, mos_iy, mosaic_num;
int verb = g_dicom_ctrl.verb; /* typing ease, default level is 1 */
ENTRY("read_mosaic_data");
if( !mi->good ) {
if( verb ) fprintf(stderr,"** apply_z_orient but not mosaic");
RETURN(1);
}
/* determine if slices should be reversed */
*flip_slices = flip_slices_mosaic(mi, kor);
/* just to make it a little easier to read */
mos_nx = mi->mos_nx; mos_ny = mi->mos_ny;
mos_ix = mi->mos_ix; mos_iy = mi->mos_ix; /* always square */
mos_nz = mos_ix * mos_iy ; /* number of slices in mosaic */
if( verb > 1 )
fprintf(stderr, "-- read_mosaic_data flip_slices %d "
"mos_nx,ny,nz = %d,%d,%d mos_ix = %d\n",
*flip_slices,mos_nx,mos_ny,mos_nz, mos_ix);
mosaic_num = mi->mosaic_num;
nvox = mos_nx*mos_ny*mos_nz ; /* total number of voxels */
if( g_dicom_ctrl.read_data ) {
dar = (char*)calloc(bpp,nvox) ; /* make space for super-image */
if(dar==NULL) { /* exit if can't allocate memory */
ERROR_message("Could not allocate memory for mosaic volume");
RETURN(1);
}
fread( dar , bpp , nvox , fp ) ; /* read data directly into it */
if( swap ){ /* swap bytes? */
switch( bpp ){
default: break ;
case 2: swap_twobytes ( nvox, dar ) ; break ; /* short */
case 4: swap_fourbytes( nvox, dar ) ; break ; /* int, float */
case 8: swap_fourbytes( 2*nvox, dar ) ; break ; /* complex */
}
}
}
/* load data from dar into images */
nxx = mos_nx * mos_ix ; /* # pixels per mosaic line */
for (ii=0;ii<mosaic_num;ii++) {
/* find right slice - may be reading the series of slices backwards */
if(*flip_slices) slice = mosaic_num - ii -1;
else slice = ii;
xx = slice % mos_ix; /* xx,yy are indices for position in mosaic matrix */
yy = slice / mos_iy;
/* im = mri_new( mos_nx , mos_ny , datum ) ; */
im = mri_new_7D_generic(mos_nx,mos_ny, 1,1,1,1,1, datum,
g_dicom_ctrl.read_data);
if( !im ) {
fprintf(stderr,"** RMD: failed to allocate %d voxel image\n",
mos_nx * mos_ny);
RETURN(1);
}
/* if reading data, actually copy data into MRI image */
if( g_dicom_ctrl.read_data ) {
iar = mri_data_pointer( im ) ; /* sub-image array */
for( jj=0 ; jj < mos_ny ; jj++ ) /* loop over rows inside sub-image */
memcpy( iar + jj*mos_nx*bpp ,
dar + xx*mos_nx*bpp + (jj+yy*mos_ny)*nxx*bpp ,
mos_nx*bpp ) ;
}
if( dx > 0.0 && dy > 0.0 && dz > 0.0 ){
im->dx = dx; im->dy = dy; im->dz = dz; im->dw = 1.0;
}
if( dt > 0.0 ) im->dt = dt ;
if( swap ) im->was_swapped = 1 ;
ADDTO_IMARR(imar,im) ;
} /* end of ii sub-image loop */
if( dar )
free(dar); /* don't need no more; copied all data out of it now */
/* truncate zero images out of tail of mosaic */
if( mosaic_num < IMARR_COUNT(imar) )
TRUNCATE_IMARR(imar,mosaic_num) ;
if( verb > 1 )
fprintf(stderr,"\nmri_read_dicom Mosaic: mos_nx=%d mos_ny=%d mos_ix=%d"
" mos_iy=%d slices=%d\n",
mos_nx,mos_ny,mos_ix,mos_iy,IMARR_COUNT(imar)) ;
/* MCHECK ; */
RETURN(0);
}