00613 {
00614     static int been_here = 0;           /* on an error, we may come back */
00615 
00616     if ( been_here == 0 )
00617     {
00618         iochan_close(gAC.ioc);
00619         fprintf( stderr, "ART_exit: closing afni control channel\n" );
00620         been_here = 1;
00621     }
00622 
00623     return;
00624 }

00632 {
00633     if ( info )
00634         fputs( info, stdout );
00635 
00636     if ( ac == NULL )
00637     {
00638         printf( "ART_idisp_ART_comm: ac == NULL\n" );
00639         return -1;
00640     }
00641 
00642     printf( "ART_comm struct at %p :\n"
00643             "   (state, mode)   = (%d, %d)\n"
00644             "   (use_tcp, swap) = (%d, %d)\n"
00645             "   byte_order      = %d\n"
00646             "   zorder          = %s\n"
00647             "   host            = %s\n"
00648             "   ioc_name        = %s\n"
00649             "   (ioc, param)    = (0x%p, 0x%p)\n",
00650             ac, ac->state, ac->mode, ac->use_tcp, ac->swap, ac->byte_order,
00651             CHECK_NULL_STR(ac->zorder), CHECK_NULL_STR(ac->host),
00652             CHECK_NULL_STR(ac->ioc_name), ac->ioc, ac->param );
00653 
00654     return 0;
00655 }

00340 {
00341     if ( ac == NULL )
00342         return -1;
00343 
00344     ac->state       = ART_STATE_NO_USE;
00345     ac->mode        = 0;
00346     ac->use_tcp     = 1;
00347     ac->swap        = 0;
00348     ac->zorder      = NULL;
00349     strcpy( ac->host, "localhost" );
00350     ac->ioc_name[0] = '\0';
00351     ac->ioc         = NULL;
00352     ac->param       = NULL;
00353 
00354     return 0;
00355 }

00289 {
00290     int rv = 0, count;
00291 
00292     if ( ac == NULL )
00293         return -1;
00294 
00295     if ( debug > 1 )
00296         fprintf( stderr, "-- starting I/O to afni\n" );
00297 
00298     if ( ac->state != ART_STATE_TO_OPEN )
00299         return 0;
00300 
00301     for ( count = 0;
00302           (count < num_tries) && (rv == 0) && (ac->mode != AFNI_CONTINUE_MODE);
00303           count++ )
00304     {
00305         rv = ART_start_io( ac, debug );
00306         iochan_sleep(100);              /* even on success, give afni time */
00307     }
00308 
00309     if ( ac->mode == AFNI_CONTINUE_MODE )       /* afni comm is ready! */
00310     {
00311         if ( debug > 0 )
00312             fprintf( stderr, "++ comm link to afni established at <%s>\n",
00313                      ac->host );
00314         ac->state = ART_STATE_TO_SEND_CTRL;
00315     }
00316     else if ( (rv == 0) && again )
00317     {
00318         if ( debug > 0 )
00319         {
00320             fprintf( stderr, "** failed to connect to afni at '%s' - "
00321                      "will try again later\n", ac->host );
00322         }
00323     }
00324     else                        /* bad news - give up on afni communication */
00325     {
00326         fprintf( stderr, "** failed to connect to afni at '%s' - "
00327                  "GIVING UP!\n", ac->host );
00328         ac->state = ART_STATE_NO_USE;
00329     }
00330 
00331     return rv;
00332 }

00363 {
00364     char tbuf[ART_TBUF_LEN];          /* temporary buffer for adding to buf */
00365     int  rv;
00366 
00367     if ( (ac == NULL) || (v == NULL) )
00368     {
00369         fprintf( stderr, "failure: ASCI called with invalid parameters\n" );
00370         ac->state = ART_STATE_NO_USE;
00371         return -1;
00372     }
00373 
00374     if ( (ac->state != ART_STATE_TO_SEND_CTRL) ||
00375          (ac->mode  != AFNI_CONTINUE_MODE) )
00376         return 0;
00377 
00378     ac->buf[0] = '\0';                      /* init message buffer to empty */
00379 
00380     /* data organization style */
00381     strcpy( tbuf, "ACQUISITION_TYPE 2D+zt" );
00382     ART_ADD_TO_BUF( ac->buf, tbuf );
00383 
00384     /* slice order */
00385     if ( ac->zorder )
00386         sprintf( tbuf, "ZORDER %s", ac->zorder);
00387     else
00388         strcpy( tbuf, "ZORDER seq" );   /* back to seq for now  [v3.3 rickr] */
00389     ART_ADD_TO_BUF( ac->buf, tbuf );
00390 
00391     /* timing pattern, this may also come from image files - rcr */
00392     if ( ac->param->opts.sp )
00393     {
00394         sprintf( tbuf, "TPATTERN %s", ac->param->opts.sp );
00395         ART_ADD_TO_BUF( ac->buf, tbuf );
00396     }
00397 
00398     /* volume time step */
00399     sprintf( tbuf, "TR %f", v->geh.tr );
00400     ART_ADD_TO_BUF( ac->buf, tbuf );
00401 
00402     /* volume dimensions */
00403     sprintf( tbuf, "XYFOV %f %f %f", fabs(v->geh.nx * v->geh.dx),
00404                                      fabs(v->geh.ny * v->geh.dy),
00405                                      fabs(v->nim    * v->z_delta) );
00406     ART_ADD_TO_BUF( ac->buf, tbuf );
00407 
00408     /* matrix sizes */
00409     sprintf( tbuf, "XYMATRIX %d %d %d", v->geh.nx, v->geh.ny, v->nim );
00410     ART_ADD_TO_BUF( ac->buf, tbuf );
00411 
00412     /* data type - no mrilib.h, and don't duplicate MRI_TYPE_name list */
00413     strcpy( tbuf, "DATUM short" );
00414     ART_ADD_TO_BUF( ac->buf, tbuf );
00415 
00416     /* axes orientations */
00417     sprintf( tbuf, "XYZAXES %c-%c %c-%c %c-%c",
00418                            v->geh.orients[0], v->geh.orients[1],
00419                            v->geh.orients[2], v->geh.orients[3],
00420                            v->geh.orients[4], v->geh.orients[5] );
00421     ART_ADD_TO_BUF( ac->buf, tbuf );
00422 
00423     /* volume offsets                          2003 June 25 [rickr] */
00424     /* now, base on param->ftype               2005 May  16 [rickr] */
00425     if( ac->param->ftype == IFM_IM_FTYPE_GEMS5 )
00426     {
00427         char o0 = v->geh.orients[0];    /* for ease of typing later */
00428         char o2 = v->geh.orients[2];
00429         char o4 = v->geh.orients[4];
00430         int  sx, sy, sz;                /* directional sign values  */
00431 
00432         /* Note - the LPI directions are negatives in GEMS 5.x files, */
00433         /*        so when one of those is the origin, negate it.      */
00434 
00435         /* rcr - this must rely on 0,0,0 being within the volume - fix it */
00436 
00437         /* just note o_i directions in s_i */
00438         if ( o0 == 'L' || o0 == 'P' || o0 == 'I' ) sx = -1; else sx = 1;
00439         if ( o2 == 'L' || o2 == 'P' || o2 == 'I' ) sy = -1; else sy = 1;
00440         if ( o4 == 'L' || o4 == 'P' || o4 == 'I' ) sz = -1; else sz = 1;
00441 
00442         /* note - we do not use a dz/2 offset, as we have slice locations */
00443         sprintf(tbuf,"XYZFIRST %f %f %f",
00444             sx * v->gex.xorg - v->geh.dx/2.0,
00445             sy * v->gex.yorg - v->geh.dy/2.0,
00446             sz * v->z_first );
00447 
00448         ART_ADD_TO_BUF( ac->buf, tbuf );
00449     }
00450     else if( ac->param->ftype == IFM_IM_FTYPE_DICOM )  /* 16 May 2005 */
00451     {
00452         char o0 = v->geh.orients[0];    /* for ease of typing later */
00453         char o2 = v->geh.orients[2];
00454         char o4 = v->geh.orients[4];
00455 
00456         /* if the files were DICOM, then the origin should be accurate */
00457         /* (so pick code based on sign, and remove sign)               */
00458 
00459         sprintf(tbuf,"XYZFIRST %f%c %f%c %f%c",
00460                 fabs(v->gex.xorg), orient_side_rai(v->gex.xorg, o0),
00461                 fabs(v->gex.yorg), orient_side_rai(v->gex.yorg, o2),
00462                 fabs(v->z_first),  orient_side_rai(v->z_first,  o4));
00463         ART_ADD_TO_BUF( ac->buf, tbuf );
00464     }
00465 
00466     /* BYTEORDER interface - send if swap flag is not set */
00467     if ( ! ac->swap )
00468     {
00469         sprintf( tbuf, "BYTEORDER %s", (ac->byte_order == LSB_FIRST) ?
00470                  "LSB_FIRST" : "MSB_FIRST" );
00471         ART_ADD_TO_BUF( ac->buf, tbuf );
00472     }
00473 
00474     /* DRIVE_AFNI interface - open afni windows */
00475     {
00476         char * graph_win;                       /* graph window to open */
00477         char * image_win;                       /* image window to open */
00478         char   o4 = v->geh.orients[4];          /* note last axis       */
00479         int    nt = ac->param->opts.nt;         /* note user defined nt */
00480 
00481         if ( (o4 == 'R') || (o4 == 'r') || (o4 == 'L') || (o4 == 'l') )
00482         {
00483             graph_win = "sagittalgraph";
00484             image_win = "sagittalimage";
00485         }
00486         else if ( (o4 == 'I') || (o4 == 'i') || (o4 == 'S') || (o4 == 's') )
00487         {
00488             graph_win = "axialgraph";
00489             image_win = "axialimage";
00490         }
00491         else
00492         {
00493             graph_win = "coronalgraph";
00494             image_win = "coronalimage";
00495         }
00496         
00497         /* open image and graph window - possibly adding pinnum */
00498         sprintf(tbuf, "DRIVE_AFNI OPEN_WINDOW %s\n"
00499                       "DRIVE_AFNI OPEN_WINDOW %s", image_win, graph_win );
00500 
00501         if ( nt > 0 )
00502             sprintf( tbuf+strlen(tbuf), " pinnum=%d", nt );
00503 
00504         ART_ADD_TO_BUF( ac->buf, tbuf );
00505     }
00506 
00507     /* pass along any user specified realtime command(s)    v3.2 [rickr] */
00508     if ( ac->param->opts.rt_list.str )
00509     {
00510         string_list * list = &ac->param->opts.rt_list;
00511         char        * cp;
00512         int           ns;
00513 
00514         for ( ns = 0; ns < list->nused; ns++ )
00515         {
00516             strncpy( tbuf, list->str[ns], 256 );
00517 
00518             /* sneaky... change any "\n" pairs to '\n' */
00519             for ( cp = tbuf; cp < (tbuf + strlen(tbuf) - 1); cp++ )
00520                 if ( cp[0] == '\\' && cp[1] == 'n' )
00521                 {
00522                     cp[0] = ' ';
00523                     cp[1] = '\n';
00524                     cp++;
00525                 }
00526 
00527             ART_ADD_TO_BUF( ac->buf, tbuf );
00528         }
00529     }
00530 
00531     /* pass along any user specified drive command(s) */
00532     if ( ac->param->opts.drive_list.str )
00533     {
00534         string_list * list = &ac->param->opts.drive_list;
00535         char        * cp;
00536         int           ns;
00537 
00538         for ( ns = 0; ns < list->nused; ns++ )
00539         {
00540             sprintf( tbuf, "DRIVE_AFNI %s", list->str[ns] );
00541 
00542             /* sneaky... change any "\n" pairs to '\n' */
00543             for ( cp = tbuf; cp < (tbuf + strlen(tbuf) - 1); cp++ )
00544                 if ( cp[0] == '\\' && cp[1] == 'n' )
00545                 {
00546                     cp[0] = ' ';
00547                     cp[1] = '\n';
00548                     cp++;
00549                 }
00550 
00551             ART_ADD_TO_BUF( ac->buf, tbuf );
00552         }
00553     }
00554 
00555     /* NOTE interface - add a note to the dataset: the actual Imon command */
00556     {
00557         int count, len, tot_len;
00558 
00559         /* form-feeds will be replaced with newlines in plug_realtime */
00560         sprintf( tbuf, "NOTE created remotely via real-time afni\f"
00561                  "    starting with file : '%s'\f"
00562                  "    creation command   :",
00563                  v->first_file );
00564         tot_len = strlen( tbuf );
00565 
00566         for ( count = 0; count < ac->param->opts.argc; count++ )
00567         {
00568             len = strlen( ac->param->opts.argv[count] );
00569 
00570             /* are we out of space? */
00571             if ( tot_len + len + 5 >= ART_TBUF_LEN )
00572             {
00573                 strcat( tbuf, " ..." );
00574                 break;
00575             }
00576 
00577             strcat( tbuf, " " );
00578             strcat( tbuf, ac->param->opts.argv[count] );
00579         }
00580         
00581         ART_ADD_TO_BUF( ac->buf, tbuf );
00582     }
00583 
00584     if ( debug > 1 )
00585         fprintf( stderr, "++ dataset control info for afni:\n   %s", ac->buf );
00586     if ( (debug > 0) && (strlen(ac->buf) > (ART_TBUF_LEN * 0.8)) )
00587         fprintf(stderr,"** warning: ac->buf len uses %d of %d bytes\n",
00588                 (int)strlen(ac->buf), ART_TBUF_LEN);
00589 
00590     rv = iochan_sendall( ac->ioc, ac->buf, strlen(ac->buf)+1 );
00591 
00592     if ( rv < 0 )
00593     {
00594         fprintf( stderr, "** failure to send control info to afni\n" );
00595         ac->state = ART_STATE_NO_USE;
00596 
00597         return -1;
00598     }
00599 
00600     ac->state = ART_STATE_IN_USE;                 /* declaration of success */
00601 
00602     iochan_sleep(50);                             /* give afni some time    */
00603 
00604     return 0;
00605 }

00183 {
00184     static int   prev_run = -1;
00185     static int   prev_seq = -1;
00186     char       * image;
00187 
00188     if ( ac->state != ART_STATE_IN_USE )
00189         return 0;
00190 
00191     if ( (run != prev_run) || (seq != prev_seq) )
00192     {
00193         prev_run = run;
00194         prev_seq = seq;
00195 
00196         image = (char *)ac->param->im_store.x_im;
00197 
00198         if ( image == NULL )
00199         {
00200             fprintf( stderr, "** failure: x_im is NULL\n"
00201                              "   - closing afni connection\n" );
00202 
00203             ac->state = ART_STATE_NO_USE;
00204             ART_exit();
00205             return -1;
00206         }
00207 
00208         strcpy( image, ART_COMMAND_MARKER );
00209         image[ART_COMMAND_MARKER_LEN] = '\0';
00210 
00211         if ( iochan_sendall( ac->ioc, image, ac->param->im_store.im_size ) < 0 )
00212         {
00213             fprintf( stderr, "** failed to transmit EOR to afni @ %s\n"
00214                              "   - closing afni connection\n", ac->host );
00215 
00216             ac->state = ART_STATE_NO_USE;
00217             ART_exit();
00218             return -1;
00219         }
00220 
00221         if ( debug > 1 )
00222             fprintf( stderr, "-- EOR: end of run signal (%d,%d)\n", run, seq );
00223 
00224         /* we will need to send new control info to afni */
00225         ac->state = ART_STATE_TO_SEND_CTRL;
00226 
00227         iochan_sleep(50);                         /* give afni some time    */
00228 
00229         return 1;
00230     }
00231 
00232     return 0;
00233 }

00241 {
00242     char * image;
00243     int    slice, bytes;
00244 
00245     if ( ac == NULL || v == NULL )
00246     {
00247         fprintf( stderr, "failure: ASV called with invalid arguments!\n" );
00248         return -1;
00249     }
00250 
00251     if ( ac->state != ART_STATE_IN_USE )
00252         return 0;
00253 
00254     /* send one complete volume */
00255 
00256     bytes = ac->param->im_store.im_size;
00257 
00258     for ( slice = 0; slice < v->nim; slice++ )
00259     {
00260         image = (char *)ac->param->im_store.im_ary[v->fl_1 + slice];
00261 
00262         if ( ac->swap )              /* maybe we must swap the bytes first */
00263             swap_2( image, bytes/2 );
00264 
00265         if ( iochan_sendall( ac->ioc, image, bytes ) < 0 )
00266         {
00267             fprintf( stderr, "** failed to transmit data to afni @ %s\n"
00268                              "   - closing afni connection\n", ac->host );
00269 
00270             ac->state = ART_STATE_NO_USE;
00271             ART_exit();
00272             return -1;
00273         }
00274     }
00275 
00276     if ( debug > 2 )
00277         fprintf( stderr, "++ sent images from volume (%d:%d) to host %s\n",
00278                  v->run, v->seq_num, ac->host );
00279 
00280     return 0;
00281 }

00048 {
00049    int ii ;
00050 
00051    /***** Check for illegal conditions *****/
00052 
00053    if( ac->mode <= 0 || ac->mode == AFNI_CONTINUE_MODE ) return 0 ;
00054 
00055    /***** If we are at the first time in,
00056           try to open a control socket to talk to AFNI *****/
00057 
00058    if( ac->mode == AFNI_OPEN_CONTROL_MODE ){
00059 
00060       sprintf( ac->ioc_name , "tcp:%s:%d" , ac->host , AFNI_CONTROL_PORT ) ;
00061 
00062       if( debug > 1 )
00063          fprintf(stderr,"Opening control channel %s to AFNI.\n",ac->ioc_name) ;
00064 
00065       ac->ioc = iochan_init( ac->ioc_name , "w" ) ;
00066 
00067       if( ac->ioc == NULL ){
00068          fprintf(stderr,"Can't open control channel %s to AFNI!\a\n",
00069                  ac->ioc_name) ;
00070          return -1;
00071       } else {
00072          if( debug > 1 )
00073              fprintf(stderr,"Entering AFNI_WAIT_CONTROL_MODE.\n") ;
00074 
00075          /* begin waiting for AFNI connection */
00076          ac->mode = AFNI_WAIT_CONTROL_MODE ;
00077       }
00078    }
00079 
00080    /***** Check if the control socket is connected to AFNI *****/
00081 
00082    if( ac->mode == AFNI_WAIT_CONTROL_MODE ){
00083 
00084       ii = iochan_writecheck( ac->ioc , 1 ) ;  /* Check; wait at most 1 msec */
00085 
00086       /** if ii == 0, then the channel is still pending,
00087           so do nothing; otherwise, take some action.    **/
00088 
00089       if( ii < 0 ){
00090          fprintf(stderr,"Control channel to AFNI failed!\n") ;
00091          IOCHAN_CLOSENOW(ac->ioc) ;
00092          ac->mode = 0 ;                    /* disable AFNI */
00093          return -1;
00094       } else if( ii > 0 ){
00095          if( debug > 1 )
00096          {
00097             fprintf(stderr,"Control channel connected to AFNI.");
00098             fprintf(stderr,"  Entering AFNI_OPEN_DATA_MODE.\n") ;
00099          }
00100 
00101          ac->mode = AFNI_OPEN_DATA_MODE ;  /* prepare to send data to AFNI */
00102       }
00103    }
00104 
00105    /***** Send the control information, which says
00106           how we will talk to AFNI in the future (shmem or TCP/IP),
00107           then close the control channel and open this new data channel *****/
00108 
00109    if( ac->mode == AFNI_OPEN_DATA_MODE ){
00110 
00111       /* decide name of data channel: it can be TCP/IP or shared memory */
00112 
00113       if ( ac->use_tcp )
00114          sprintf(ac->ioc_name,"tcp:%s:%d",ac->host,AFNI_TCP_PORT) ;
00115 
00116       strcpy(ac->buf, ac->ioc_name) ;     /* tell AFNI where to read data */
00117 
00118       if( debug > 1 )
00119          fprintf(stderr,"Sending control information to AFNI:\n%s\n",ac->buf) ;
00120 
00121       ii = iochan_sendall( ac->ioc , ac->buf , strlen(ac->buf)+1 ) ;
00122 
00123       /** A negative return is bad news **/
00124 
00125       if( ii < 0 ){
00126          fprintf(stderr,"Transmission of control data to AFNI failed!\a\n") ;
00127          IOCHAN_CLOSENOW(ac->ioc) ;
00128          ac->mode = 0 ;
00129          return -1;
00130       } else {
00131          /* wait for control data to clear */
00132          while( ! iochan_clearcheck(ac->ioc,2) )
00133             iochan_sleep(2) ;
00134          IOCHAN_CLOSENOW(ac->ioc) ;                 /* close control channel */
00135 
00136          if( debug > 1 )
00137             fprintf(stderr,"Opening data channel %s to AFNI.\n",ac->ioc_name) ;
00138 
00139          ac->ioc = iochan_init( ac->ioc_name , "w" ) ; /* open data channel */
00140          if( ac->ioc == NULL ){
00141             fprintf(stderr,"Can't open data channel %s to AFNI!\a\n",
00142                     ac->ioc_name) ;
00143             ac->mode = 0 ;
00144             return -1;
00145          } else {
00146             if( debug > 1 ) fprintf(stderr,"Entering AFNI_CATCHUP_MODE.\n") ;
00147             ac->mode = AFNI_CATCHUP_MODE ;
00148          }
00149       }
00150    }
00151 
00152    /***** Wait for the data channel to be connected to AFNI,
00153           and then send any images that are reconstructed and ready to go *****/
00154 
00155    if( ac->mode == AFNI_CATCHUP_MODE ){
00156 
00157       ii = iochan_writecheck( ac->ioc , 1 ) ;  /* wait at most 1 msec */
00158       if( ii < 0 ){
00159          fprintf(stderr,
00160                  "AFNI data channel aborted before any data was sent!\a\n") ;
00161          IOCHAN_CLOSENOW(ac->ioc) ;
00162          ac->mode = 0 ;
00163          return -1;
00164       } else if( ii > 0 ){                      /* can now send data to AFNI! */
00165          ac->mode = AFNI_CONTINUE_MODE ;
00166 
00167         if ( debug > 1 )
00168             fprintf(stderr,"Entering AFNI_CONTINUE_MODE.\n");
00169       }
00170    }
00171 
00172    return 0;
00173 }

00680 {
00681     int d = toupper(dir);
00682 
00683     if ( d == 'R' || d == 'L' ) return( coord < 0 ? 'R' : 'L' );
00684     if ( d == 'A' || d == 'P' ) return( coord < 0 ? 'A' : 'P' );
00685     if ( d == 'I' || d == 'S' ) return( coord < 0 ? 'I' : 'S' );
00686 }

00663 {
00664     unsigned char * addr = ptr;
00665     int             count;
00666 
00667     for ( count = 0; count < npairs; count++ )
00668     {
00669         addr[0] ^= addr[1]; addr[1] ^= addr[0]; addr[0] ^= addr[1];
00670         addr += 2;
00671     }
00672 
00673     return 0;
00674 }