00001 /*****************************************************************************
00002    Major portions of this software are copyrighted by the Medical College
00003    of Wisconsin, 1994-2000, and are released under the Gnu General Public
00004    License, Version 2.  See the file README.Copyright for details.
00005 ******************************************************************************/
00006    
00007 #include "mrilib.h"
00008 
00009 int main( int argc , char * argv[] )
00010 {
00011    char prefix[255]="obi-wan-kenobi" , fname[255] ;
00012    int datum = -1 ;
00013    int iarg = 1 ;
00014    int gnim , nx , ny , nz , kz ;
00015    char ** gname ;
00016    MRI_IMARR * arr ;
00017    MRI_IMAGE * im , * qim ;
00018    FILE * fp ;
00019 
00020    /***** help? *****/
00021 
00022    if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
00023       printf(
00024        "Usage: imstack [options] image_filenames ...\n"
00025        "Stacks up a set of 2D images into one big file (a la MGH).\n"
00026        "Options:\n"
00027        "  -datum type   Converts the output data file to be 'type',\n"
00028        "                  which is either 'short' or 'float'.\n"
00029        "                  The default type is the type of the first image.\n"
00030        "  -prefix name  Names the output files to be 'name'.b'type' and 'name'.hdr.\n"
00031        "                  The default name is 'obi-wan-kenobi'.\n"
00032       ) ;
00033 
00034       exit(0) ;
00035    }
00036 
00037    machdep() ;
00038 
00039    /***** scan for option *****/
00040 
00041    while( iarg < argc && argv[iarg][0] == '-' ){
00042 
00043       /*** -datum ***/
00044 
00045       if( strcmp(argv[iarg],"-datum") == 0 ){
00046          if( ++iarg >= argc ){
00047             fprintf(stderr,"-datum needs a type!\n") ; exit(1) ;
00048          }
00049          if( strcmp(argv[iarg],"short") == 0 ){
00050             datum = MRI_short ;
00051          } else if( strcmp(argv[iarg],"float") == 0 ){
00052             datum = MRI_float ;
00053          } else {
00054             fprintf(stderr,"-datum %s is illegal!\n",argv[iarg]) ; exit(1) ;
00055          }
00056          iarg++ ; continue ;
00057       }
00058 
00059       /*** -prefix ***/
00060 
00061       if( strcmp(argv[iarg],"-prefix") == 0 ){
00062          if( ++iarg >= argc ){
00063             fprintf(stderr,"-prefix needs a name!\n") ; exit(1) ;
00064          }
00065          strcpy(prefix,argv[iarg]) ;
00066          iarg++ ; continue ;
00067       }
00068 
00069       /*** ERROR ***/
00070 
00071       fprintf(stderr,"Unrecognized option: %s\n",argv[iarg]) ; exit(1) ;
00072    }
00073 
00074    /***** Check if any filenames left *****/
00075 
00076    if( iarg >= argc ){
00077       fprintf(stderr,"No input image filenames?!\n") ; exit(1) ;
00078    }
00079 
00080    /***** Perform filename expansion on the input list *****/
00081 
00082    MCW_warn_expand(1) ;
00083    MCW_file_expand( argc - iarg , argv + iarg , &gnim , &gname ) ;
00084    MCW_warn_expand(0) ;
00085 
00086    if( gnim < 1 ){
00087       fprintf(stderr,"Filename expansion fails on input filenames?!\n") ; exit(1) ;
00088    }
00089 
00090    /***** Read all files *****/
00091 
00092    arr = mri_read_many_files( gnim , gname ) ;
00093    if( arr == NULL || IMARR_COUNT(arr) <= 0 ){
00094       fprintf(stderr,"Can't read input files?!\n") ; exit(1) ;
00095    }
00096    MCW_free_expand( gnim , gname ) ;
00097    fprintf(stderr,"Read in %d 2D slices\n",IMARR_COUNT(arr)) ;
00098 
00099    /***** Set output datum, if not already fixed *****/
00100 
00101    if( datum < 0 ){
00102       datum = IMARR_SUBIMAGE(arr,0)->kind ;
00103 
00104       if( datum != MRI_short && datum != MRI_float ){
00105          fprintf(stderr,"Input image type is %s -- you must use -datum!\n",
00106                  MRI_TYPE_name[datum]) ;
00107          exit(1) ;
00108       }
00109    }
00110 
00111    /***** Check images for equal sizes *****/
00112 
00113    nx = IMARR_SUBIMAGE(arr,0)->nx ;
00114    ny = IMARR_SUBIMAGE(arr,0)->ny ;
00115    nz = IMARR_COUNT(arr) ;
00116 
00117    for( kz=1 ; kz < nz ; kz++ ){
00118       if( IMARR_SUBIMAGE(arr,kz)->nx != nx ||
00119           IMARR_SUBIMAGE(arr,kz)->ny != ny   ){
00120 
00121          fprintf(stderr,"All images must be the same size (%d x %d)\n",nx,ny) ;
00122          exit(1) ;
00123       }
00124    }
00125 
00126    /***** Write the output brick *****/
00127 
00128    sprintf(fname,"%s.b%s",prefix,MRI_TYPE_name[datum]) ;
00129    fp = fopen( fname , "w" ) ;
00130    if( fp == NULL ){
00131       fprintf(stderr,"Can't open output file %s\n",fname) ; exit(1) ;
00132    }
00133 
00134    for( kz=0 ; kz < nz ; kz++ ){
00135 
00136       im = IMARR_SUBIMAGE(arr,kz) ;
00137       if( im->kind != datum ) qim = mri_to_mri( datum , im ) ;
00138       else                    qim = im ;
00139 
00140       fwrite( mri_data_pointer(qim) , qim->pixel_size , qim->nx * qim->ny , fp ) ;
00141 
00142       if( qim != im ) mri_free(qim) ;
00143       mri_free(im);
00144    }
00145    fclose( fp ) ;
00146    fprintf(stderr,"Wrote output brick %s\n",fname) ;
00147 
00148    /***** Write the output header *****/
00149 
00150    sprintf(fname,"%s.hdr",prefix) ;
00151    fp = fopen( fname , "w" ) ;
00152    if( fp == NULL ){
00153       fprintf(stderr,"Can't open output file %s\n",fname) ; exit(1) ;
00154    }
00155 
00156    fprintf( fp , "%d %d %d 0\n" , nx,ny,nz ) ;
00157    fclose(fp) ;
00158    fprintf(stderr,"Wrote output header %s: %d %d %d\n",fname,nx,ny,nz) ;
00159 
00160    exit(0) ;
00161 }