#define IFM_VERSION "version 3.3a (March 22, 2005)"
static char g_history[] =
"----------------------------------------------------------------------\n"
" history:\n"
"\n"
" 1.0 November 21, 2002\n"
" - initial release\n"
"\n"
" 1.1 November 27, 2002\n"
" - renamed from Hfile to Imon (I-file monitor)\n"
"\n"
" 1.2 November 27, 2002\n"
" - after N idle mid-run TRs, print warning message\n"
" - added '-nice INCR' option\n"
" - added BEEP on error\n"
" - replaced '-status' with '-quiet', so '-debug 1' is default\n"
" - no fatal error during volume search, try to recover\n"
" - display that the user should use <ctrl-c> to quit\n"
" - adjust globbing to be '...[0-9][02468]?/I.*' (or w/[13579])\n"
"\n"
" 1.3 December 13, 2002\n"
" - compile as standalone (include mcw_glob, but not mcw_malloc)\n"
" - added l_THD_filesize (local copy of THD_filesize)\n"
" - removed dependance on mrilib.h and r_idisp.h\n"
"\n"
" 2.0 January 15, 2003\n"
" - rtfeedme feature\n"
" o added -rt option: pass data to afni as collected\n"
" o added -host option: specify afni host for real-time\n"
" o added -swap option: byte swap pairs before sending to afni\n"
" o created realtime.[ch] for all RT processing functions\n"
" o (see gAC struct and ART_ functions)\n"
" - actually read and store images (to be sent to afni)\n"
" - moved function declarations to Imon.c (from Imon.h)\n"
"\n"
" 2.1 January 27, 2003\n"
" - added '-nt VOLUMES_PER_RUN' option (for checking stalled runs)\n"
"\n"
" 2.2 February 2, 2003\n"
" - allow IFM_MAX_GE_FAILURES file reading failures\n"
"\n"
" 2.3 February 14, 2003\n"
" - added -start_file option\n"
" - created opts_t struct for user options\n"
"\n"
" 2.4 February 18, 2003\n"
" - added DRIVE_AFNI command to open a graph window\n"
" - added -drive_afni option\n"
" - added NOTE command to append Imon command to any new dataset\n"
"\n"
" 2.5 February 20, 2003\n"
" - deal better with missing first slice of first volume\n"
" - make each DRIVE_AFNI command separate\n"
"\n"
" 2.6 March 25, 2003\n"
" - added -GERT_Reco2 option\n"
" - RT: only send good volumes to afni\n"
" - RT: added -rev_byte_order option\n"
" - RT: also open relevant image window\n"
" - RT: mention starting file in NOTE command\n"
"\n"
" 2.7 June 25, 2003\n"
" - added axes offsets (see xorg and realtime.c: XYZFIRST)\n"
"\n"
" 2.8 June 27, 2003\n"
" - BYTEORDER is now operational in plug_realtime\n"
" - implemented -rev_byte_order option\n"
"\n"
" 2.9 July 27, 2003\n"
" - wrap unknown printed strings in NULL check\n"
" - only print newer files in debug check\n"
"\n"
" 2.10 August 5, 2003\n"
" - added '-sp SLICE_PATTERN' option (see spat and opts.sp)\n"
"\n"
" 2.11 August 14, 2003\n"
" - added '-quit' option\n"
" - changed CHECK_NULL_STR() output to (NULL) (to see when used)\n"
" - change exit status to 0 (why the heck did I use 1?)\n"
" - allow I.* or i.* filename expansions\n"
"\n"
" 3.0 August 20, 2003\n"
" - It seems that the GE scanners may write the files for a volume\n"
" out of order. To handle that possibility, volume_match() will\n"
" re-test any volume for error conditions (separated by sleep()).\n"
" Errors will be reported only if they persist (i.e. the scanner\n"
" is not still working on the volume).\n"
"\n"
" 3.1 September 02, 2003\n"
" - Add option '-od OUTPUT_DIRECTORY' for the GERT_Reco2 case.\n"
"\n"
" 3.2 January 13, 2004\n"
" - added '-zorder ORDER' option to specify slice timing in the\n"
" real-time mode (the real-time default is now 'alt')\n"
" - added '-hist' option for history display\n"
"\n"
" 3.3 February 13, 2004\n"
" - added '-rt_cmd' option for passing commands to the realtime plugin\n"
" (this option may be used multiple times)\n"
" - '-drive_cmd' option can now be used multiple times\n"
" - realtime.c: changed default zorder back to seq\n"
" (affects slice order in the RT plugin)\n"
" - realtime.c: passed list of drive and rt commands to RT plugin\n"
" - added add_to_string_list() and empty_string_list()\n"
"\n"
" 3.3a March 22, 2005 - removed all tabs\n"
" 3.3b May 16, 2005 - incorporate some Dimon changes\n"
" 3.4 July 5, 2005 - removed tabs\n"
"----------------------------------------------------------------------\n";
/*----------------------------------------------------------------------
* todo:
*
* - add -full_prefix option
*----------------------------------------------------------------------
*/
/*----------------------------------------------------------------------
* Imon - monitor real-time aquisition of I-files
*
* This program is intended to be run during a scanning session
* on a GE scanner, to monitor the collection of I-files. The
* user will be notified of any missing slice or any slice that
* is aquired out of order.
*
* It is recommended that the user runs 'Imon' before scanning
* begins, and then watches for error messages during the
* scanning session. The user should terminate the program
* whey they are done with all runs.
*
* At the present time, the user must use <ctrl-c> to terminate
* the program.
*
* usage: Imon [options] -start_dir DIR
*
* examples: Imon -start_dir 003
* Imon -help
* Imon -version
* Imon -start_dir 003 -GERT_Reco2
* Imon -start_dir 003 -debug 2
* Imon -start_dir 003 -nt 120
* Imon -start_dir 003 -rt -host pickle -swap
* Imon -start_dir 003 -rt -host pickle -rev_byte_order
*----------------------------------------------------------------------
*/
#include <stdio.h>
#include <ctype.h>
#include <dirent.h>
#include <errno.h>
#include <math.h>
#include <signal.h>
#include <stdlib.h>
#include <string.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include "Imon.h"
#include "l_mcw_glob.h"
#include "thd_iochan.h"
#include "realtime.h"
#define IFM_PROG_NAME "Imon"
/*----------------------------------------------------------------------*/
/* static function declarations */
static int add_to_string_list ( string_list * list, char * str );
static int alloc_x_im ( im_store_t * is, int bytes );
static int check_error ( int * retry, float tr, char * note );
static int check_im_byte_order ( int * order, vol_t * v, param_t * p );
static int check_im_store_space( im_store_t * is, int num_images );
static int check_stalled_run ( int run, int seq_num, int naps, int nap_time );
static int complete_orients_str( vol_t * v, param_t * p );
static int create_gert_script ( stats_t * s, opts_t * opts );
static int dir_expansion_form ( char * sin, char ** sexp );
static int empty_string_list ( string_list * list, int free_mem );
static int find_first_volume ( vol_t * v, param_t * p, ART_comm * ac );
static int find_fl_file_index ( param_t * p, char * file );
static int find_more_volumes ( vol_t * v, param_t * p, ART_comm * ac );
static int find_next_zoff ( param_t * p, int start, float zoff );
static int init_extras ( param_t * p, ART_comm * ac );
static int init_options ( param_t * p, ART_comm * a, int argc,
char * argv[] );
static int nap_time_from_tr ( float tr );
static int path_to_dir_n_suffix( char * dir, char * suff, char * path );
static int read_ge_files ( param_t * p, int start, int max );
static int read_ge_image ( char * pathname, finfo_t * fp,
int get_image, int need_memory );
static int scan_ge_files ( param_t * p, int next, int nfiles );
static int set_nice_level ( int level );
static int set_volume_stats ( param_t * p, stats_t * s, vol_t * v );
static int show_run_stats ( stats_t * s );
static int str_char_count ( char * str, int len, char target );
static int swap_4 ( void * ptr );
static void hf_signal ( int signum );
/* volume scanning */
static int volume_match ( vol_t * vin, vol_t * vout, param_t * p, int start );
static int volume_search ( vol_t * V, param_t * p, int start, int maxsl,
int * fl_start );
/* information functions */
static int idisp_hf_opts_t ( char * info, opts_t * opt );
static int idisp_hf_param_t ( char * info, param_t * p );
static int idisp_hf_vol_t ( char * info, vol_t * v );
static int idisp_ge_extras ( char * info, ge_extras * E );
static int idisp_ge_header_info ( char * info, ge_header_info * I );
static int idisp_im_store_t ( char * info, im_store_t * is );
static int usage ( char * prog, int level );
/* local copy of AFNI function */
static unsigned long l_THD_filesize( char * pathname );
/*----------------------------------------------------------------------*/
#define MAIN
/***********************************************************************/
/* globals */
IFM_debug gD; /* debug information */
param_t gP; /* main parameter struct */
stats_t gS; /* general run information */
ART_comm gAC; /* afni communication struct */
/***********************************************************************/
int main( int argc, char * argv[] )
{
ART_comm * ac = &gAC; /* access AFNI comm as local */
param_t * p = &gP; /* access the global as local */
vol_t baseV; /* base volume - first scanned */
int ret_val;
/* validate inputs and init options structure */
if ( (ret_val = init_options( p, ac, argc, argv )) != 0 )
return ret_val;
if ( (ret_val = init_extras( p, ac )) != 0 )
return ret_val;
if ( (ret_val = find_first_volume( &baseV, p, ac )) != 0 )
return ret_val;
if ( (ret_val = find_more_volumes( &baseV, p, ac )) != 0 )
return ret_val;
return 0;
}
/***********************************************************************/
/*----------------------------------------------------------------------
* find_first_volume: scan p->flist for a complete volume
*
* This function runs until either a volume is located, or an
* error occurs.
*
* return: 0 : on success
* else : error
*----------------------------------------------------------------------
*/
static int find_first_volume( vol_t * v, param_t * p, ART_comm * ac )
{
int max_im_alloc = IFM_MAX_IM_ALLOC;
int ret_val;
int fl_start = 0; /* starting offset into the current flist */
if ( gD.level > 0 ) /* status */
fprintf( stderr, "-- scanning for first volume\n" );
ret_val = 0;
while ( ret_val == 0 )
{
ret_val = read_ge_files( p, fl_start, max_im_alloc );
if ( ret_val > 0 )
{
ret_val = volume_search( v, p, 0, 0, &fl_start );
if ( ret_val == -1 ) /* try to recover from a data error */
ret_val = 0;
if ( (ret_val == 0) && (p->nused > (max_im_alloc / 2)) )
{
/* If we don't have a volume yet, but have used "too much"
* of our available memory, request more, making sure there
* is enough for a volume, despite the previous max_im_alloc
* limitation.
*/
max_im_alloc *= 2;
}
}
if ( ret_val == 0 ) /* we are not done yet */
{
if ( gD.level > 0 ) /* status */
fprintf( stderr, "." );
sleep( 4 ); /* nap time! */
}
else if ( ret_val > 0 ) /* success - we have a volume! */
{
if ( gD.level > 0 )
{
fprintf( stderr, "\n-- first volume found\n" );
if ( gD.level > 1 )
{
idisp_hf_vol_t( "first volume : ", v );
idisp_hf_param_t( "first vol - new params : ", p );
}
}
/* make sure there is enough memory for bad volumes */
if ( p->nalloc < (4 * v->nim) )
{
p->nalloc = 4 * v->nim;
p->flist = (finfo_t *)realloc( p->flist,
p->nalloc*sizeof(finfo_t) );
if ( p->flist == NULL )
{
fprintf( stderr, "** FFV: failure to allocate %d finfo_t "
"structs!\n", p->nalloc );
return -1;
}
if ( gD.level > 1 )
idisp_hf_param_t( "++ final realloc of flist : ", p );
}
/* use this volume to complete the geh.orients string */
if ( complete_orients_str( v, p ) < 0 )
return -1;
/* use this volume to note the byte order of image data */
if ( check_im_byte_order( &ac->byte_order, v, p ) < 0 )
return -1;
/* if wanted, verify afni link, send image info and first volume */
if ( ac->state == ART_STATE_TO_OPEN )
ART_open_afni_link( ac, 5, 0, gD.level );
if ( ac->state == ART_STATE_TO_SEND_CTRL )
ART_send_control_info( ac, v, gD.level );
if ( ac->state == ART_STATE_IN_USE )
ART_send_volume( ac, v, gD.level );
if ( gD.level > 1 )
{
ART_idisp_ART_comm( "-- first vol ", ac );
idisp_im_store_t( "-- first vol ", &p->im_store );
}
}
else
return ret_val; /* fatal error condition */
}
if ( ret_val > 0 )
return 0;
else
return ret_val;
}
/*----------------------------------------------------------------------
* find_more_volumes: given first volume, keep scanning for others
*
* This function runs until a fatal error occurs.
*
* return: 0 : on success
* else : error
*----------------------------------------------------------------------
*/
static int find_more_volumes( vol_t * v0, param_t * p, ART_comm * ac )
{
vol_t vn;
int ret_val, done;
int run, seq_num, next_im;
int fl_index; /* current index into p->flist */
int naps; /* keep track of consecutive naps */
int nap_time; /* sleep time, in seconds */
if ( v0 == NULL || p == NULL )
{
fprintf( stderr, "error: IFM:FMV() lacking parameters\n" );
return -1;
}
done = 0;
naps = 0;
run = v0->run;
seq_num = v0->seq_num = 1; /* set first seq_num to 1 */
fl_index = v0->fn_n + 1; /* start looking past first volume */
next_im = v0->fn_n + 1; /* for read_ge_files() */
nap_time = nap_time_from_tr( v0->geh.tr );
if ( gD.level > 0 ) /* status */
{
fprintf( stderr, "-- scanning for additional volumes...\n" );
fprintf( stderr, "-- run %d: %d ", run, seq_num );
}
/* give stats when user quits */
signal( SIGTERM, hf_signal );
signal( SIGINT, hf_signal );
if ( set_volume_stats( p, &gS, v0 ) )
return -1;
while ( ! done )
{
/* check all of the volumes we've already scanned in */
ret_val = 1;
while ( (ret_val == 1) || (ret_val == -1) )
{
ret_val = volume_match( v0, &vn, p, fl_index );
if ( ret_val < -1 ) /* bail out on fatal error */
return ret_val;
if ( (ret_val == 1) || (ret_val == -1) )
{
if ( gD.level > 2 )
idisp_hf_vol_t( "-- new volume: ", &vn );
fl_index += vn.nim; /* note the new position */
next_im = vn.fn_n + 1; /* for read_ge_files() */
if ( vn.run != run ) /* new run? */
{
/* pass run and seq_num before they are updated */
if ( ac->state == ART_STATE_IN_USE )
ART_send_end_of_run( ac, run, seq_num, gD.level );
run = vn.run; /* reset */
seq_num = 1;
if ( gD.level > 0 )
fprintf( stderr, "\n-- run %d: %d ", run, seq_num );
}
else
{
seq_num++;
if ( gD.level > 0 )
fprintf( stderr, "%d ", seq_num );
}
vn.seq_num = seq_num;
if ( set_volume_stats( p, &gS, &vn ) )
return -1;
if ( complete_orients_str( &vn, p ) < 0 )
return -1;
if ( ac->state == ART_STATE_TO_SEND_CTRL )
ART_send_control_info( ac, &vn, gD.level );
/* only send good volumes to afni - 2003.03.10 */
if ( (ac->state == ART_STATE_IN_USE) && (ret_val == 1) )
ART_send_volume( ac, &vn, gD.level );
naps = 0; /* reset on existing volume */
}
}
/* now we need new data - skip past last file name index */
ret_val = read_ge_files( p, next_im, p->nalloc );
fl_index = 0; /* reset flist index */
while ( (ret_val >= 0 ) && /* no fatal error, and */
(ret_val < v0->nim) ) /* didn't see full volume yet */
{
if ( naps > 0 )
{
if ( p->opts.quit ) /* then we are outta here */
{
if ( ac->state == ART_STATE_IN_USE )
ART_send_end_of_run( ac, run, seq_num, gD.level );
show_run_stats( &gS );
return 0;
}
/* continue, regardless */
if ( check_stalled_run( run, seq_num, naps, nap_time ) > 0 )
if ( ac->state == ART_STATE_IN_USE )
ART_send_end_of_run( ac, run, seq_num, gD.level );
if ( gD.level > 0 ) /* status */
fprintf( stderr, ". " );
}
sleep( nap_time ); /* wake after a couple of TRs */
naps ++;
ret_val = read_ge_files( p, next_im, p->nalloc );
}
if ( ret_val < 0 ) /* aaaaagh! panic! wet pants! */
{
fprintf( stderr, "\n** failure: IFM:RGF fatal error\n" );
return -1;
}
}
return 0; /* success */
}
/*----------------------------------------------------------------------
* volume_search: scan p->flist for a complete volume
*
* - start should be at the expected beginning of a volume!
* - *fl_start may be returned as a new starting index into fnames
*
* return: -2 : on programming error
* -1 : on data error
* 0 : on success - no volume yet
* 1 : on success - volume read
*----------------------------------------------------------------------
*/
static int volume_search(
vol_t * V, /* volume to fill */
param_t * p, /* master structure */
int start, /* starting index into p->flist */
int maxsl, /* max number of slices to check */
int * fl_start ) /* return new fnames search point */
{
finfo_t * fp;
float z_orig, delta, dz, prev_z;
int bound; /* upper bound on image slice */
int next;
int run0, run1; /* run numbers, for comparison */
int first = start; /* first image (start or s+1) */
int last; /* final image in volume */
if ( V == NULL || p == NULL || p->flist == NULL || start < 0 )
{
fprintf( stderr, "failure: FNV: bad parameter data\n" );
return -2;
}
/* note the bound on the slice index */
if ( (maxsl <= 0) || ((maxsl + first) >= p->nused) )
bound = p->nused;
else
bound = first + maxsl;
if ( (bound - first) < 4 ) /* not enough data to work with */
return 0;
delta = p->flist[first+1].geh.zoff - p->flist[first].geh.zoff;
run0 = p->flist[first ].geh.uv17;
run1 = p->flist[first+1].geh.uv17;
/* if apparent 1-slice volume, skip and start over */
if ( (fabs(delta) < IFM_EPSILON) || (run1 != run0) )
{
if ( gD.level > 1 )
fprintf( stderr, "-- skipping single slice volume <%s>\n",
p->fnames[p->flist[first].index] );
first++;
delta = p->flist[first+1].geh.zoff - p->flist[first].geh.zoff;
run0 = run1;
if ( fabs(delta) < IFM_EPSILON )
{
fprintf( stderr, "Error: 3 slices with 0 delta, beginning with"
"file <%s>\n", p->fnames[p->flist[start].index] );
*fl_start = p->flist[start+2].index;
return -1;
}
}
fp = p->flist + first; /* initialize flist posn */
z_orig = fp->geh.zoff; /* note original position */
/* set current values at position (first+1) */
fp++;
prev_z = fp->geh.zoff;
run1 = fp->geh.uv17;
dz = delta;
/* scan for volume break */
next = first + 2; /* next z to look at */
while ( (next < bound) && (fabs(dz - delta) < IFM_EPSILON) &&
(run1 == run0) )
{
fp++; /* good index so get new values */
dz = fp->geh.zoff - prev_z;
run1 = fp->geh.uv17;
prev_z = fp->geh.zoff;
next++;
}
last = next - 2; /* note final image in volume */
if ( fabs(fp->geh.zoff - p->flist[first].geh.zoff) < IFM_EPSILON )
{
/* Current location is same as first, we have a volume! */
/* So deltas are consistent from slice 'first' to slice 'last'. */
V->geh = p->flist[first].geh; /* copy GE structure */
V->gex = p->flist[first].gex; /* copy GE extras */
V->nim = last - first + 1;
V->fl_1 = first;
V->fn_1 = p->flist[first].index;
V->fn_n = p->flist[last].index;
strncpy( V->first_file, p->fnames[V->fn_1], IFM_MAX_FLEN );
strncpy( V->last_file, p->fnames[V->fn_n], IFM_MAX_FLEN );
V->z_first = p->flist[first].geh.zoff;
V->z_last = p->flist[last].geh.zoff;
V->z_delta = delta;
V->seq_num = -1; /* uninitialized */
V->run = V->geh.uv17;
return 1;
}
else if ( (fabs(dz - delta) < IFM_EPSILON) && (run1 == run0) )
return 0; /* we did not finish a volume */
else if ( dz * delta < 0.0 )
{
/* We have gone in the wrong direction. This means that the
* starting slice was not the first in the volume. Try restarting
* from the current position.
*/
fprintf( stderr, "\n"
"*************************************************\n"
"Error: missing slice(s) in first volume!\n"
" attempting to re-start at file: %s\n"
"*************************************************\n",
p->fnames[p->flist[last+1].index] );
*fl_start = p->flist[last+1].index;
}
else /* right direction, but bad delta */
{
/* the next slice does not match the original - interleaving? */
int testc;
for ( testc = next - 1; testc < bound; testc++ )
if ( abs( p->flist[first].geh.zoff -
p->flist[testc].geh.zoff ) < IFM_EPSILON )
{
/* aaaaagh! we are missing data from the first volume! */
/* print error, and try to skip this volume */
fprintf( stderr, "\n"
"*************************************************\n"
"Error: missing slice in first volume!\n"
" detected at file: %s\n"
" re-starting at file: %s\n"
"*************************************************\n",
p->fnames[p->flist[last+1].index],
p->fnames[p->flist[testc].index] );
/* try to skip this volume and recover */
*fl_start = p->flist[testc].index;
return -1;
}
/* we didn't find the original zoff, wait for more files */
return 0;
}
return -1; /* thank you, come again */
}
/*----------------------------------------------------------------------
* volume_match: scan p->flist for a matching volume
*
* - start should be at the expected beginning of a volume!
*
* return: -2 : fatal error
* -1 : recoverable data error
* 0 : on success - no volume yet
* 1 : on success - volume read
*----------------------------------------------------------------------
*/
static int volume_match( vol_t * vin, vol_t * vout, param_t * p, int start )
{
static int retry = 1; /* v2.12 */
finfo_t * fp;
finfo_t * fp_test;
float z;
int count, next_start = -1;
int missing = 0;
if ( vin == NULL || vout == NULL ||
p == NULL || p->flist == NULL || start < 0 )
{
fprintf( stderr, "failure: FMV: bad parameter data\n" );
return -2;
}
if ( (p->nused - start) < vin->nim ) /* enough files to scan? */
return 0;
/* now 'everything' should match */
fp = p->flist+start;
for ( count = 0; count < vin->nim - 1; count++ ) /* last is separate */
{
z = vin->z_first + count * vin->z_delta; /* note expected z */
if ( fabs( z - fp->geh.zoff ) > IFM_EPSILON )
{
/* slice is either missing or out of order */
fp_test = fp + 1; /* check next image */
if ( fabs( z + vin->z_delta - fp_test->geh.zoff ) < IFM_EPSILON )
{
/* report the error? v2.12 */
if ( !check_error(&retry, vin->geh.tr, "slice out of order") )
return 0;
/* next slice as expected, so current is out of order */
/* nothing to do but warn the user and continue */
IFM_BIG_ERROR_MESG( "slice out of order!",
p->fnames[fp->index], z, fp->geh.zoff,
fp->geh.uv17, count + 1, vin->nim );
}
else if ( fabs(z + vin->z_delta - fp->geh.zoff) < IFM_EPSILON )
{
/* current slice matches next expected - slice missing */
/* report the error? */
if ( !check_error(&retry, vin->geh.tr, "slice missing") )
return 0;
/* nothing to do but note error, warn user and continue */
missing++;
IFM_BIG_ERROR_MESG( "slice missing!",
p->fnames[fp->index], z, fp->geh.zoff,
fp->geh.uv17, count + 1, vin->nim );
count++; /* attempt to continue by skipping this slice */
}
else /* unknown error - find start of next volume */
{
/* search for a next starting point */
next_start = find_next_zoff( p, start+count, vin->z_first );
if ( next_start < 0 ) /* come back and try again later */
return 0;
else
{
/* report error? */
if ( !check_error(&retry, vin->geh.tr, "vol toasted") )
return 0;
IFM_BIG_ERROR_MESG( "volume severely toasted!",
p->fnames[fp->index], z, fp->geh.zoff,
fp->geh.uv17, count + 1, vin->nim );
break; /* terminate for loop and try to recover */
}
}
}
fp++;
}
z = vin->z_first + count * vin->z_delta; /* note expected z */
if ( count >= vin->nim ) /* missed second to last slice */
next_start = start + vin->nim - missing;
else if ( (next_start < 0) && (fabs( z - fp->geh.zoff ) > IFM_EPSILON) )
{
/* check last slice - count and fp should be okay*/
if ( (p->nused - start) <= vin->nim ) /* no more images to check */
return 0; /* wait for more data */
fp_test = fp + 1; /* check next image */
if ( fabs( vin->z_first - fp_test->geh.zoff ) < IFM_EPSILON )
{
/* next image starts next run, slice is probably out of order */
/* report error? */
if ( !check_error(&retry, vin->geh.tr, "last slice out of order") )
return 0;
IFM_BIG_ERROR_MESG( "last slice out of order!",
p->fnames[fp->index], z, fp->geh.zoff,
fp->geh.uv17, count + 1, vin->nim );
}
else if ( fabs(vin->z_first - fp->geh.zoff) < IFM_EPSILON )
{
/* this image starts next run, slice is missing */
/* report error? */
if ( !check_error(&retry, vin->geh.tr, "last slice missing") )
return 0;
missing++;
IFM_BIG_ERROR_MESG( "last slice missing!",
p->fnames[fp->index], z, fp->geh.zoff,
fp->geh.uv17, count + 1, vin->nim );
}
else /* unknown error - find start of next volume */
{
/* search for a next starting point */
next_start = find_next_zoff( p, start+count+1, vin->z_first );
if ( next_start < 0 ) /* come back and try again later */
return 0;
else
{
/* report error? */
if ( !check_error(&retry, vin->geh.tr, "Vol toasted") )
return 0;
IFM_BIG_ERROR_MESG( "Volume severely toasted!",
p->fnames[fp->index], z, fp->geh.zoff,
fp->geh.uv17, count + 1, vin->nim );
}
}
}
if ( next_start < 0)
next_start = start + vin->nim - missing;
if ( retry == 0 && gD.level > 0 ) /* v2.12 */
fprintf(stderr," (retry OK - no errors)\n");
retry = 1; /* next error gets two tries - v2.12 */
/* fill volume structure */
vout->geh = p->flist[start].geh;
vout->gex = p->flist[start].gex;
vout->nim = next_start - start;
vout->fl_1 = start;
vout->fn_1 = p->flist[start].index;
vout->fn_n = p->flist[start+vout->nim-1].index;
strncpy( vout->first_file, p->fnames[vout->fn_1], IFM_MAX_FLEN );
strncpy( vout->last_file, p->fnames[vout->fn_n], IFM_MAX_FLEN );
vout->z_first = vin->z_first;
vout->z_last = vin->z_last;
vout->z_delta = vin->z_delta;
vout->seq_num = -1; /* uninitialized */
vout->run = vout->geh.uv17;
if ( vout->nim != vin->nim )
return -1;
else
return 1;
}
/*----------------------------------------------------------------------
* check_error: only report error on second failure v2.12
*
* return: < 0 : on programming error
* 0 : do not report error yet
* 1 : report error
*----------------------------------------------------------------------
*/
static int check_error( int * retry, float tr, char * note )
{
if ( !retry )
return -1;
if ( *retry == 1 )
{
/* let user know we're checking */
if ( gD.level > 0 )
fprintf(stderr," (volume retry test for warning '%s'...)\n",
CHECK_NULL_STR(note));
*retry = 0;
sleep( nap_time_from_tr(tr) );
return 0;
}
/* so calling function should print error */
*retry = 2;
return 1;
}
/*----------------------------------------------------------------------
* read_ge_files:
*
* - sanity checks
* - read_directory (free any old file expansion list)
* - decide number of files to scan (max == 0 implies the rest)
* - allocate necessary p->flist memory
* - read GE structures
*
* return: < 0 : on error
* files read : on success
*----------------------------------------------------------------------
*/
static int read_ge_files(
param_t * p, /* parameter scruct */
int start, /* index of next file to scan from */
int max ) /* max number of files to scan */
{
int n2scan; /* number of files to actually scan */
int next = start; /* initialize next index to start */
if ( p == NULL )
{
fputs( "failure: RAF: no param_t struct\n", stderr );
return -1;
}
/* clear away old file list */
if ( p->fnames != NULL )
{
if ( p->nfiles <= 0 )
{
fputs( "failure: RAF: fnames does not match nfiles\n", stderr );
return -1;
}
MCW_free_expand( p->nfiles, p->fnames );
p->fnames = NULL;
}
/* get files */
MCW_file_expand( 1, &p->glob_dir, &p->nfiles, &p->fnames );
/* if next is 0, search for any first_file */
if ( (next == 0 ) && (p->opts.start_file != NULL) )
{
next = find_fl_file_index( p, p->opts.start_file );
if ( next < 0 ) /* if not found, try again later */
{
if ( gD.level > 0 ) /* inform the user */
{
static int attempts = 0;
if ( attempts == 0 )
fprintf(stderr, "-- still searching for start_file, '%s'\n",
p->opts.start_file );
attempts++;
}
return 0;
}
}
if ( gD.level > 3 )
{
int fnum;
for ( fnum = next; fnum < p->nfiles; fnum++ )
printf( "file %4d: %s\n", fnum, p->fnames[fnum] );
}
if ( p->nfiles <= 0 )
return 0;
/* set the number of files to scan - if max is usable, use it */
if ( (max > 0) && (max <= (p->nfiles - next)) )
n2scan = max; /* scan next max files */
else
n2scan = p->nfiles - next; /* scan rest of files */
/* do we need/want more memory? */
if ( (n2scan > p->nalloc) || (max > p->nalloc) )
{
int nalloc;
/* allow a request to allocate 'max' entries */
nalloc = (n2scan >= max) ? n2scan : max;
p->flist = (finfo_t *)realloc( p->flist, nalloc * sizeof(finfo_t) );
if ( p->flist == NULL )
{
fprintf(stderr, "failure to allocate %d finfo_t structs\n", nalloc);
return -1;
}
p->nalloc = nalloc;
if ( gD.level > 1 )
{
idisp_hf_param_t( "++ realloc of flist : ", p );
fprintf( stderr, "-- n2scan = %d, max = %d\n", n2scan, max );
}
}
p->nused = scan_ge_files( p, next, n2scan );
if ( gD.level > 2 )
idisp_hf_param_t( "end read_ge_files : ", p );
/* may be negative for an error condition */
return p->nused;
}
/*----------------------------------------------------------------------
* scan_ge_files:
*
* Starting at index 'next' of 'fnames', scan 'nfiles' files,
* filling the 'flist' array.
*----------------------------------------------------------------------
*/
static int scan_ge_files (
param_t * p, /* general parameter structure */
int next, /* index of next file to scan */
int nfiles ) /* number of files to scan */
{
finfo_t * fp;
int im_num, fnum;
int files_read, rv;
int need_M; /* do we need image memory? */
if ( nfiles <= 0 )
return 0;
if ( check_im_store_space( &p->im_store, nfiles ) < 0 )
return -1;
p->im_store.nused = 0;
/* scan from 'next' to 'next + nfiles - 1' */
for ( im_num = 0, fnum = next, fp = p->flist;
im_num < nfiles;
im_num++, fnum++, fp++ )
{
if ( im_num < p->im_store.nalloc ) /* then we have image memory */
{
fp->image = p->im_store.im_ary[im_num];
need_M = 0;
}
else /* get it from read_ge_image */
{
fp->image = NULL;
need_M = 1;
}
rv = read_ge_image( p->fnames[fnum], fp, 1, need_M );
/* don't lose any allocated memory, regardless of the return value */
if ( (need_M == 1) && (fp->image != NULL) )
{
p->im_store.im_ary[im_num] = fp->image;
p->im_store.nalloc++;
/* note the size of the image and get memory for x_im */
if ( p->im_store.im_size == 0 )
{
if ( alloc_x_im( &p->im_store, fp->bytes ) < 0 )
return -1;
}
if ( gD.level > 1 )
fprintf( stderr, "++ allocated image %d at address %p\n",
im_num, p->im_store.im_ary[im_num] );
}
if ( (rv != 0) || (fp->geh.good != 1) )
{
static int read_failure = -1; /* last read_ge_image failure */
static int fail_count = 0; /* get multiple tries to succeed */
/* on first failure, note file and set fail_count to 1 */
if ( read_failure != fnum )
{
read_failure = fnum;
fail_count = 1;
}
else
fail_count++;
/* after too many failure, we give up */
if ( fail_count > IFM_MAX_GE_FAILURES )
{
fprintf( stderr, "\n** failure: cannot read GE header for "
"file <%s>\n", p->fnames[fnum] );
return -1;
}
/* we failed, but will try again later - maybe inform user */
if ( gD.level > 1 )
fprintf( stderr, "\n-- (%d) failures to read GE header for "
"file <%s>, trying again...\n",
fail_count, p->fnames[fnum] );
break;
}
else
{
p->im_store.nused++; /* keep track of used images */
fp->index = fnum; /* store index into fnames array */
if ( gD.level > 2 )
{
idisp_ge_header_info( p->fnames[fp->index], &fp->geh );
idisp_ge_extras( p->fnames[fp->index], &fp->gex );
}
}
}
/* even on failure, this non-negative integer is accurate */
files_read = fnum - next;
if ( gD.level > 1 )
printf( "-- scanned %d GE files, from <%s> to <%s>\n",
files_read, p->fnames[next], p->fnames[next+files_read-1] );
return files_read;
}
/*----------------------------------------------------------------------
* init_options:
*
* 1. check usage: Imon -start_dir DIR
* 2. do initial allocation of data structures
*----------------------------------------------------------------------
*/
static int init_options( param_t * p, ART_comm * A, int argc, char * argv[] )
{
int ac, errors = 0;
if ( p == NULL )
return 2;
if ( argc < 2 )
{
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
/* basic initialization of data structures */
memset( p, 0, sizeof(*p) ); /* parameters */
memset( &gD, 0, sizeof(gD) ); /* debug struct */
memset( &gS, 0, sizeof(gS) ); /* stats struct */
memset( A, 0, sizeof(gAC) ); /* afni comm struct */
ART_init_AC_struct( A ); /* init for no real-time comm */
A->param = p; /* store the param_t pointer */
empty_string_list( &p->opts.drive_list, 0 );
empty_string_list( &p->opts.rt_list, 0 );
/* debug level 1 is now the default - by order of Wen-Ming :) */
gD.level = 1;
for ( ac = 1; ac < argc; ac++ )
{
if ( ! strncmp( argv[ac], "-debug", 4 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -debug LEVEL\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.debug = atoi(argv[ac]);
gD.level = p->opts.debug;
if ( gD.level < 0 || gD.level > IFM_MAX_DEBUG )
{
fprintf( stderr, "error: debug level must be in [0,%d]\n",
IFM_MAX_DEBUG );
errors++;
}
}
else if ( ! strncmp( argv[ac], "-GERT_Reco2", 7 ) )
{
p->opts.gert_reco = 1; /* output script at the end */
}
else if ( ! strncmp( argv[ac], "-help", 5 ) )
{
usage( IFM_PROG_NAME, IFM_USE_LONG );
return 1;
}
else if ( ! strncmp( argv[ac], "-hist", 5 ) )
{
usage( IFM_PROG_NAME, IFM_USE_HIST );
return 1;
}
else if ( ! strncmp( argv[ac], "-nice", 4 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -nice INCREMENT\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.nice = atoi(argv[ac]);
if ( (p->opts.nice < IFM_MIN_NICE_INC) ||
(p->opts.nice > IFM_MAX_NICE_INC) )
{
fprintf( stderr, "error: nice incrment must be in [%d,%d]\n",
IFM_MIN_NICE_INC, IFM_MAX_NICE_INC );
errors++;
}
}
else if ( ! strncmp( argv[ac], "-nt", 3 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -nt VOLUMES_PER_RUN\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.nt = atoi(argv[ac]);
if ( p->opts.nt < 0 || p->opts.nt > IFM_MAX_NT )
{
fprintf( stderr,
"option usage: -nt VOLUMES_PER_RUN\n"
" error: VOLUMES_PER_RUN must be in [%d,%d]\n",
0, IFM_MAX_NT );
errors++;
}
}
else if ( ! strncmp( argv[ac], "-od", 3 ) ||
! strncmp( argv[ac], "-gert_outdir", 9 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -gert_outdir OUTPUT_DIR\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.gert_outdir = argv[ac];
}
else if ( ! strncmp( argv[ac], "-quiet", 6 ) )
{
/* only go quiet if '-debug' option has not changed it */
if ( gD.level == IFM_DEBUG_DEFAULT )
gD.level = 0;
}
else if ( ! strncmp( argv[ac], "-quit", 5 ) )
{
p->opts.quit = 1;
}
else if ( ! strncmp( argv[ac], "-sp", 3 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -sp PATTERN\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.sp = argv[ac];
}
else if ( ! strncmp( argv[ac], "-start_dir", 8 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -start_dir DIRECTORY\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.start_dir = argv[ac];
}
else if ( ! strncmp( argv[ac], "-start_file", 8 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -start_file DIR/FIRST_FILE\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.start_file = argv[ac];
}
else if ( ! strncmp( argv[ac], "-version", 2 ) )
{
usage( IFM_PROG_NAME, IFM_USE_VERSION );
return 1;
}
/* real-time options */
else if ( ! strncmp( argv[ac], "-drive_afni", 6 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -drive_afni COMMAND\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
if ( add_to_string_list( &p->opts.drive_list, argv[ac] ) != 0 )
{
fprintf(stderr,"** failed add '%s' to drive_list\n",argv[ac]);
return 1;
}
}
else if ( ! strncmp( argv[ac], "-host", 4 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -host HOSTNAME\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
p->opts.host = argv[ac]; /* note and store the user option */
strncpy( A->host, argv[ac], ART_NAME_LEN-1 );
A->host[ART_NAME_LEN-1] = '\0'; /* just to be sure */
}
else if ( ! strncmp( argv[ac], "-rev_byte_order", 4 ) )
{
p->opts.rev_bo = 1; /* note to send reverse byte order */
}
else if ( ! strncmp( argv[ac], "-rt_cmd", 6 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -rt_cmd COMMAND\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
if ( add_to_string_list( &p->opts.rt_list, argv[ac] ) != 0 )
{
fprintf(stderr,"** failed add '%s' to rt_list\n",argv[ac]);
return 1;
}
}
else if ( ! strncmp( argv[ac], "-rt", 3 ) )
{
A->state = ART_STATE_TO_OPEN; /* real-time is open for business */
p->opts.rt = 1; /* just note the user option */
}
else if ( ! strncmp( argv[ac], "-swap", 5 ) )
{
A->swap = 1; /* do byte swapping before sending */
p->opts.swap = 1; /* just note the user option */
}
else if ( ! strncmp( argv[ac], "-zorder", 6 ) )
{
if ( ++ac >= argc )
{
fputs( "option usage: -zorder ORDER\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
A->zorder = argv[ac];
}
else
{
fprintf( stderr, "error: invalid option <%s>\n\n", argv[ac] );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
}
if ( errors > 0 ) /* check for all minor errors before exiting */
{
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
if ( p->opts.start_dir == NULL )
{
fputs( "error: missing '-start_dir DIR' option\n", stderr );
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
if ( p->opts.rev_bo && p->opts.swap )
{
fprintf( stderr, "error: options '-rev_byte_order' and '-swap' "
"cannot both be used\n");
usage( IFM_PROG_NAME, IFM_USE_SHORT );
return 1;
}
if ( A->zorder )
{
if ( strcmp(A->zorder, "alt") && strcmp(A->zorder, "seq") )
{
fprintf(stderr,"** order '%s' is invalid for '-zorder' option,\n"
" must be either 'alt' or 'seq'\n", A->zorder);
return -1;
}
}
/* done processing argument list */
if ( dir_expansion_form( p->opts.start_dir, &p->glob_dir ) != 0 )
return 2;
/* save command arguments to add as a NOTE to any AFNI datasets */
p->opts.argv = argv;
p->opts.argc = argc;
p->ftype = IFM_IM_FTYPE_GEMS5; /* 27 May 2005 */
if ( gD.level > 1 )
{
idisp_hf_opts_t ( "end init_options : ", &p->opts );
idisp_hf_param_t( "end init_options : ", p );
}
if ( gD.level > 0 )
fprintf( stderr, "\n%s running, use <ctrl-c> to quit...\n\n",
IFM_PROG_NAME );
return 0;
}
/*----------------------------------------------------------------------
* initialize:
* - nice level
* - afni communications
* - verify that any passed 'start_file' "matches" 'start_dir'
* (for now, just do this by comparing directory depth)
*----------------------------------------------------------------------
*/
static int init_extras( param_t * p, ART_comm * ac )
{
if ( p->opts.nice && set_nice_level(p->opts.nice) )
return 1;
if ( ac->state == ART_STATE_TO_OPEN ) /* open afni comm link */
{
atexit( ART_exit );
ac->mode = AFNI_OPEN_CONTROL_MODE;
ART_open_afni_link( ac, 2, 1, gD.level );
}
/* check directory depth of start_file against glob_dir */
if ( p->opts.start_file != NULL )
{
char * sf = p->opts.start_file;
char * gd = p->glob_dir;
int flevel = str_char_count( sf, strlen(sf), (char)'/' );
/* check whether the number of slashes match */
if ( flevel != str_char_count( gd, strlen(gd), (char)'/' ) )
{
fprintf( stderr,
"** warning : relative path to : '-start_dir %s'\n"
" does not seem to match : '-start_file %s'\n"
" (so 'start_file' may never be found)\n\n",
p->opts.start_file, p->opts.start_dir );
}
else if ( gD.level > 1 )
fprintf( stderr, "-- '-start_file %s' and\n"
" '-start_dir %s' match at dir level %d\n",
p->opts.start_file, p->opts.start_dir, flevel );
}
return 0;
}
/*----------------------------------------------------------------------
* set_nice_level - set to given "nice" value
*
* returns: 0 : success
* else : failure
*----------------------------------------------------------------------
*/
static int set_nice_level( int level )
{
int rv;
rv = nice( level );
if ( rv != 0 )
{
if ( level < 0 )
fprintf( stderr, "error: only root may decrement nice value\n"
" (errno = %d, rv = %d)\n", errno, rv );
else
fprintf( stderr,
"error: failure to adjust nice by %d\n"
" (errno = %d, rv = %d)\n", level, errno, rv );
}
else if ( gD.level > 1 )
fprintf( stderr, "-- nice value incremented by %d\n", level );
return rv;
}
/*------------------------------------------------------------
* dir_expansion_form
*
* sin : must be in the form "...0[01]n", where n is a digit
* (note that "...0[01]n/..." is okay)
* sexp : memory is allocated for the output string of the
* form: "...[0-9][02468]n/I.*"
*
* returns: 0 : on success
* else : error
*------------------------------------------------------------
*/
int dir_expansion_form( char * sin, char ** sexp )
{
char * out;
char * cp;
char d0, d1, d2; /* the three relevant digits */
int len;
if ( (sin == NULL) || (sexp == NULL) )
return -1;
*sexp = NULL;
len = strlen(sin);
out = (char *)malloc((len + IFM_PAD_LEN) * sizeof(char));
if ( out == NULL )
{
fprintf( stderr, "failure: dir_expansion_form malloc\n" );
return -1;
}
*sexp = out; /* save resulting malloc'd address */
strcpy( out,sin );
cp = out + len - 1; /* point to end */
/* we'd better find 0[01]n - ignore the rest??? */
while ( (cp > (out+2)) && !isdigit( *cp ) )
cp--;
if ( !isdigit(*cp) ) /* didn't find even one */
{
fprintf( stderr, "error: dir <%s> is not of the form 00n (e.g. 003)\n",
sin );
free(out);
return -1;
}
cp -= 2; /* should be first zero */
d0 = cp[0]; /* note the three digits */
d1 = cp[1];
d2 = cp[2];
if ( (d0 != '0') || /* first is not a zero */
( (d1 != '0') && (d1 != '1')) ) /* second is not 0 or 1 */
{
fprintf( stderr, "error: dir <%s> is not of the form 0[01]n"
" (e.g. 003)\n", sin );
free(out);
return -1;
}
/* woohooo! we're good to go! */
/* set to "...[0-9][02468]n/I.*" (or with [13579]) */
strcpy( cp, "[0-9]" ); /* add and skip "[0-9]" */
cp += strlen( "[0-9]" );
if ( d1 == '0' ) /* adding 2 to each */
strcpy( cp, "[02468]" );
else
strcpy( cp, "[13579]" );
cp += strlen( "[02468]" );
*cp++ = d2; /* insert final digit */
/* allow either I.* or i.* - v2.11 */
strcpy( cp, "/[Ii].*" ); /* the big finish */
return 0;
}
/*----------------------------------------------------------------------
* read_ge_image (basically from Ifile.c, but use file_tool.c version)
*
* returns: 0 : success
* < 0 : failure
*----------------------------------------------------------------------
*/
static int read_ge_image( char * pathname, finfo_t * fp,
int get_image, int need_memory )
{
ge_header_info * hi = &fp->geh;
FILE *imfile ;
int length , skip , swap=0 ;
char orients[8] , str[8] ;
int nx , ny , bpp , cflag , hdroff ;
float uv17 = -1.0;
if( hi == NULL ) return -1; /* bad */
hi->good = 0 ; /* not good yet */
if( pathname == NULL ||
pathname[0] == '\0' ) return -1; /* bad */
length = l_THD_filesize( pathname ) ;
if( length < 1024 ) return -1; /* bad */
imfile = fopen( pathname , "r" ) ;
if( imfile == NULL ) return -1; /* bad */
strcpy(str,"JUNK") ; /* initialize string */
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' ){ /* bad */
fclose(imfile) ; return -2;
}
/*-- 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);
} else {
swap = 0 ; /* data is ordered for this CPU */
}
if( nx < 0 || nx > 8192 || ny < 0 || ny > 8192 ){ /* bad */
fclose(imfile) ; return -1;
}
hi->nx = nx ;
hi->ny = ny ;
if( skip+2*nx*ny > length || /* file is too short */
skip <= 0 || /* bizarre */
cflag != 1 || /* data is compressed */
bpp != 16 ){
fclose(imfile); return -1; /* data is not shorts */
}
/*-- try to read image header data as well --*/
fseek( imfile , 148L , SEEK_SET ) ; /* magic GEMS offset */
fread( &hdroff , 4,1 , imfile ) ; /* location of image header */
if( swap ) swap_4(&hdroff) ;
if( hdroff > 0 && hdroff+256 < length ){ /* can read from image header */
float dx,dy,dz, xyz[9], zz ; 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); }
hi->dx = dx ; hi->dy = dy ; hi->dz = 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;
case -1: orients[0]= 'R'; orients[1]= 'L'; break;
case 2: orients[0]= 'P'; orients[1]= 'A'; break;
case -2: orients[0]= 'A'; orients[1]= 'P'; break;
case 3: orients[0]= 'I'; orients[1]= 'S'; break;
case -3: orients[0]= 'S'; orients[1]= 'I'; break;
default: orients[0]='\0'; orients[1]='\0'; break;
}
/* 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 */
hi->zoff = zz ;
strcpy(hi->orients,orients) ;
/* similarly (with zoff), store x and y origins in ge_extras */
/* 2003 Jun 25 [rickr] */
fp->gex.xorg = xyz[abs(ii)-1];
fp->gex.yorg = xyz[abs(jj)-1];
/*-- 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) ;
hi->tr = 1.0e-6 * itr ; /* itr is in microsec */
/*-- 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) ;
hi->te = 1.0e-6 * itr ;
/* zmodify: get User Variable 17, a likely indicator of a new scan,
* info by S. Marrett, location from S. Inati's matlab function
* GE_readHeaderImage.m
*/
/* printf ("\nuv17 = \n"); */
fseek ( imfile , hdroff+272+202, SEEK_SET ) ;
fread( &uv17 , 4, 1 , imfile ) ;
if( swap ) swap_4(&uv17) ;
/* printf ("%d ", (int)uv17); */
hi->uv17 = (int)uv17;
/* printf ("\n"); */
/* store the ge_extra info */
fp->gex.bpp = bpp;
fp->gex.cflag = cflag;
fp->gex.hdroff = hdroff;
fp->gex.skip = skip;
fp->gex.swap = swap;
fp->gex.kk = kk;
memcpy( fp->gex.xyz, xyz, sizeof(xyz) );
hi->good = 1 ; /* this is a good file */
} /* end of actually reading image header */
/* read image in as well */
if ( get_image )
{
int elements = hi->nx * hi->ny;
fp->bytes = elements * 2; /* bpp == 16 */
if ( need_memory )
fp->image = malloc( fp->bytes );
if ( fp->image == NULL )
{
fprintf(stderr, "** RGI: no memory for %d byte image\n", fp->bytes);
hi->good = 0;
return -1;
}
fseek ( imfile, skip, SEEK_SET );
if ( fread( fp->image , 2, elements, imfile ) != elements )
{
fprintf( stderr, "** RGI: failed to read %d shorts from %s\n",
elements, pathname );
hi->good = 0; /* signal file problem */
return -1;
}
}
fclose(imfile);
return 0;
}
/*------------------------------------------------------------
* Reverse the order of the 4 bytes at this address.
*------------------------------------------------------------
*/
static int swap_4( void * ptr ) /* destructive */
{
unsigned char * addr = ptr;
addr[0] ^= addr[3]; addr[3] ^= addr[0]; addr[0] ^= addr[3];
addr[1] ^= addr[2]; addr[2] ^= addr[1]; addr[1] ^= addr[2];
return 0;
}
/*------------------------------------------------------------
* print out the contents of the im_store_t struct
*------------------------------------------------------------
*/
static int idisp_im_store_t( char * info, im_store_t * is )
{
if ( info )
fputs( info, stdout );
if ( is == NULL )
{
printf( "idisp_im_store_t: is == NULL\n" );
return -1;
}
printf( "im_store_t struct at %p :\n"
" (nalloc, nused) = (%d, %d)\n"
" (ary_len, im_size) = (%d, %d)\n"
" (im_ary, x_im) = (%p, %p)\n",
is, is->nalloc, is->nused,
is->ary_len, is->im_size, is->im_ary, is->x_im );
return 0;
}
/*------------------------------------------------------------
* print out the contents of the param_t struct
*------------------------------------------------------------
*/
static int idisp_hf_param_t( char * info, param_t * p )
{
if ( info )
fputs( info, stdout );
if ( p == NULL )
{
printf( "idisp_hf_param_t: p == NULL\n" );
return -1;
}
printf( "param_t struct at %p :\n"
" ftype =%d\n"
" (nused, nalloc) = (%d, %d)\n"
" flist = %p\n"
" glob_dir = %s\n"
" nfiles = %d\n"
" fnames = %p\n",
p, p->ftype, p->nused, p->nalloc, p->flist,
CHECK_NULL_STR(p->glob_dir),
p->nfiles, p->fnames );
return 0;
}
/*------------------------------------------------------------
* print out the contents of the opts_t struct
*------------------------------------------------------------
*/
static int idisp_hf_opts_t( char * info, opts_t * opt )
{
if ( info )
fputs( info, stdout );
if ( opt == NULL )
{
printf( "idisp_hf_opts_t: opt == NULL\n" );
return -1;
}
printf( "opts_t struct at %p :\n"
" start_file = %s\n"
" start_dir = %s\n"
" sp = %s\n"
" gert_outdir = %s\n"
" (argv, argc) = (%p, %d)\n"
" (nt, nice) = (%d, %d)\n"
" (debug, gert_reco) = (%d, %d)\n"
" quit = %d\n"
" (rt, swap, rev_bo) = (%d, %d, %d)\n"
" host = %s\n"
" drive_list(u,a,p) = %d, %d, %p\n"
" rt_list (u,a,p) = %d, %d, %p\n",
opt,
CHECK_NULL_STR(opt->start_file),
CHECK_NULL_STR(opt->start_dir),
CHECK_NULL_STR(opt->sp),
CHECK_NULL_STR(opt->gert_outdir),
opt->argv, opt->argc,
opt->nt, opt->nice,
opt->debug, opt->gert_reco, opt->quit,
opt->rt, opt->swap, opt->rev_bo,
CHECK_NULL_STR(opt->host),
opt->drive_list.nused, opt->drive_list.nalloc, opt->drive_list.str,
opt->rt_list.nused, opt->rt_list.nalloc, opt->rt_list.str
);
return 0;
}
/*------------------------------------------------------------
* print out the contents of the vol_t struct
*------------------------------------------------------------
*/
static int idisp_hf_vol_t( char * info, vol_t * v )
{
if ( info )
fputs( info, stdout );
if ( v == NULL )
{
printf( "idisp_hf_vol_t: v == NULL\n" );
return -1;
}
printf( "vol_t struct at %p :\n"
" nim = %d\n"
" (fl_1, fn_1, fn_n) = (%d, %d, %d)\n"
" first_file = %s\n"
" last_file = %s\n"
" (z_first, z_last) = (%f, %f)\n"
" z_delta = %f\n"
" (seq_num, run) = (%d, %d)\n",
v, v->nim, v->fl_1, v->fn_1, v->fn_n,
v->first_file, v->last_file,
v->z_first, v->z_last, v->z_delta,
v->seq_num, v->run );
idisp_ge_header_info( info, &v->geh );
idisp_ge_extras( info, &v->gex );
return 0;
}
/*------------------------------------------------------------
* Display the contents of the ge_extras struct.
* (copied from file_tool.c)
*------------------------------------------------------------
*/
static int idisp_ge_extras( char * info, ge_extras * E )
{
if ( info )
fputs( info, stdout );
if ( E == NULL )
{
printf( "idisp_ge_extras: E == NULL\n" );
return -1;
}
printf( "ge_extras at %p :\n"
" bpp = %d\n"
" cflag = %d\n"
" hdroff = %d\n"
" skip = %d\n"
" swap = %d\n"
" kk = %d\n"
" xorg = %f\n"
" yorg = %f\n"
" (xyz0,xyz1,xyz2) = (%f,%f,%f)\n"
" (xyz3,xyz4,xyz5) = (%f,%f,%f)\n"
" (xyz6,xyz7,xyz8) = (%f,%f,%f)\n",
E, E->bpp, E->cflag, E->hdroff, E->skip, E->swap, E->kk,
E->xorg, E->yorg,
E->xyz[0], E->xyz[1], E->xyz[2],
E->xyz[3], E->xyz[4], E->xyz[5],
E->xyz[6], E->xyz[7], E->xyz[8]
);
return 0;
}
/*------------------------------------------------------------
* Display the contents of the ge_header_info struct.
* (copied from file_tool.c)
*------------------------------------------------------------
*/
static int idisp_ge_header_info( char * info, ge_header_info * I )
{
if ( info )
fputs( info, stdout );
if ( I == NULL )
{
printf( "idisp_ge_header_info: I == NULL\n" );
return -1;
}
printf( "ge_header_info at %p :\n"
" good = %d\n"
" (nx,ny) = (%d,%d)\n"
" uv17 = %d\n"
" (dx,dy,dz) = (%f,%f,%f)\n"
" zoff = %f\n"
" (tr,te) = (%f,%f)\n"
" orients = %-8s\n",
I, I->good, I->nx, I->ny, I->uv17,
I->dx, I->dy, I->dz, I->zoff, I->tr, I->te,
CHECK_NULL_STR(I->orients)
);
return 0;
}
/*----------------------------------------------------------------------
* usage
*----------------------------------------------------------------------
*/
static int usage ( char * prog, int level )
{
if ( level == IFM_USE_SHORT )
{
fprintf( stderr,
"usage: %s [options] -start_dir DIR\n"
"usage: %s -help\n",
prog, prog );
return 0;
}
else if ( level == IFM_USE_LONG )
{
printf(
"\n"
"%s - monitor real-time acquisition of I-files\n"
"\n"
" This program is intended to be run during a scanning session\n"
" on a GE scanner, to monitor the collection of I-files. The\n"
" user will be notified of any missing slice or any slice that\n"
" is aquired out of order.\n"
"\n"
" It is recommended that the user runs '%s' just after the\n"
" scanner is first prepped, and then watches for error messages\n"
" during the scanning session. The user should terminate the\n"
" program whey they are done with all runs.\n"
"\n"
" Note that '%s' can also be run separate from scanning, either\n"
" to verify the integrity of I-files, or to create a GERT_Reco2\n"
" script, which is used to create AFNI datasets.\n"
"\n"
" At the present time, the user must use <ctrl-c> to terminate\n"
" the program.\n"
"\n"
" ---------------------------------------------------------------\n"
" usage: %s [options] -start_dir DIR\n"
"\n"
" ---------------------------------------------------------------\n"
" examples (no real-time options):\n"
"\n"
" %s -start_dir 003\n"
" %s -help\n"
" %s -start_dir 003 -GERT_reco2 -quit\n"
" %s -start_dir 003 -nt 120 -start_file 043/I.901\n"
" %s -debug 2 -nice 10 -start_dir 003\n"
"\n"
" examples (with real-time options):\n"
"\n"
" %s -start_dir 003 -rt\n"
" %s -start_dir 003 -rt -host pickle\n"
" %s -start_dir 003 -nt 120 -rt -host pickle\n"
"\n"
" ** detailed real-time example:\n"
"\n"
" This example scans data starting from directory 003, expects\n"
" 160 repetitions (TRs), and invokes the real-time processing,\n"
" sending data to a computer called some.remote.computer.name\n"
" (where afni is running, and which considers THIS computer to\n"
" be trusted - see the AFNI_TRUSTHOST environment variable).\n"
"\n"
" Multiple DRIVE_AFNI commands are passed through '-drive_afni'\n"
" options, one requesting to open an axial image window, and\n"
" another requesting an axial graph, with 160 data points.\n"
"\n"
" See README.driver for acceptable DRIVE_AFNI commands.\n"
"\n"
" Also, multiple commands specific to the real-time plugin are\n"
" passed via the '-rt_cmd' options. The 'REFIX command sets the\n"
" prefix for the datasets output by afni. The GRAPH_XRANGE and\n"
" GRAPH_YRANGE commands set the graph dimensions for the 3D\n"
" motion correction graph (only). And the GRAPH_EXPR command\n"
" is used to replace the 6 default motion correction graphs with\n"
" a single graph, according to the given expression, the square\n"
" root of the average squared entry of the 3 rotaion parameters,\n"
" roll, pitch and yaw, ignoring the 3 shift parameters, dx, dy\n"
" and dz.\n"
"\n"
" See README.realtime for acceptable DRIVE_AFNI commands.\n"
"\n"
" %s \\\n"
" -start_dir 003 \\\n"
" -nt 160 \\\n"
" -rt \\\n"
" -host some.remote.computer.name \\\n"
" -drive_afni 'OPEN_WINDOW axialimage' \\\n"
" -drive_afni 'OPEN_WINDOW axialgraph pinnum=160' \\\n"
" -rt_cmd 'PREFIX eat.more.cheese' \\\n"
" -rt_cmd 'GRAPH_XRANGE 160' \\\n"
" -rt_cmd 'GRAPH_YRANGE 1.02' \\\n"
" -rt_cmd 'GRAPH_EXPR sqrt((d*d+e*e+f*f)/3)' \n"
"\n"
" ---------------------------------------------------------------\n"
" notes:\n"
"\n"
" - Once started, this program exits only when a fatal error\n"
" occurs (single missing or out of order slices are not\n"
" considered fatal).\n"
"\n"
" ** This has been modified. The '-quit' option tells Imon\n"
" to terminate once it runs out of new data to use.\n"
"\n"
" - To terminate this program, use <ctrl-c>.\n"
"\n"
" ---------------------------------------------------------------\n"
" main option:\n"
"\n"
" -start_dir DIR : (REQUIRED) specify starting directory\n"
"\n"
" e.g. -start_dir 003\n"
"\n"
" The starting directory, DIR, must be of the form 00n,\n"
" where n is a digit. The program then monitors all\n"
" directories of the form ??n, created by the GE scanner.\n"
"\n"
" For instance, with the option '-start_dir 003', this\n"
" program watches for new directories 003, 023, 043, etc.\n"
"\n"
" ---------------------------------------------------------------\n"
" real-time options:\n"
"\n"
" -rt : specify to use the real-time facility\n"
"\n"
" With this option, the user tells '%s' to use the real-time\n"
" facility, passing each volume of images to an existing\n"
" afni process on some machine (as specified by the '-host'\n"
" option). Whenever a new volume is aquired, it will be\n"
" sent to the afni program for immediate update.\n"
"\n"
" Note that afni must also be started with the '-rt' option\n"
" to make use of this.\n"
"\n"
" Note also that the '-host HOSTNAME' option is not required\n"
" if afni is running on the same machine.\n"
"\n"
" -drive_afni CMND : send 'drive afni' command, CMND\n"
"\n"
" e.g. -drive_afni 'OPEN_WINDOW axialimage'\n"
"\n"
" This option is used to pass a single DRIVE_AFNI command\n"
" to afni. For example, 'OPEN_WINDOW axialimage' will open\n"
" such an axial view window on the afni controller.\n"
"\n"
" Note: the command 'CMND' must be given in quotes, so that\n"
" the shell will send it as a single parameter.\n"
"\n"
" Note: this option may be used multiple times.\n"
"\n"
" See README.driver for more details.\n"
"\n"
" -host HOSTNAME : specify the host for afni communication\n"
"\n"
" e.g. -host mycomputer.dot.my.network\n"
" e.g. -host 127.0.0.127\n"
" e.g. -host mycomputer\n"
" the default host is 'localhost'\n"
"\n"
" The specified HOSTNAME represents the machine that is\n"
" running afni. Images will be sent to afni on this machine\n"
" during the execution of '%s'.\n"
"\n"
" Note that the enviroment variable AFNI_TRUSTHOST must be\n"
" set on the machine running afni. Set this equal to the\n"
" name of the machine running Imon (so that afni knows to\n"
" accept the data from the sending machine).\n"
"\n"
" -rev_byte_order : pass the reverse of the BYTEORDER to afni\n"
"\n"
" Reverse the byte order that is given to afni. In case the\n"
" detected byte order is not what is desired, this option\n"
" can be used to reverse it.\n"
"\n"
" See the (obsolete) '-swap' option for more details.\n"
"\n"
" -rt_cmd COMMAND : send COMMAND(s) to realtime plugin\n"
"\n"
" e.g. -rt_cmd 'GRAPH_XRANGE 120'\n"
" e.g. -rt_cmd 'GRAPH_XRANGE 120 \\n GRAPH_YRANGE 2.5'\n"
"\n"
" This option is used to pass commands to the realtime\n"
" plugin. For example, 'GRAPH_XRANGE 120' will set the\n"
" x-scale of the motion graph window to 120 (repetitions).\n"
"\n"
" Note: the command 'COMMAND' must be given in quotes, so\n"
" that the shell will send it as a single parameter.\n"
"\n"
" Note: this option may be used multiple times.\n"
"\n"
" See README.realtime for more details.\n"
"\n"
" -swap (obsolete) : swap data bytes before sending to afni\n"
"\n"
" Since afni may be running on a different machine, the byte\n"
" order may differ there. This option will force the bytes\n"
" to be reversed, before sending the data to afni.\n"
"\n"
" ** As of version 3.0, this option should not be necessary.\n"
" '%s' detects the byte order of the image data, and then\n"
" passes that information to afni. The realtime plugin\n"
" will (now) decide whether to swap bytes in the viewer.\n"
"\n"
" If for some reason the user wishes to reverse the order\n"
" from what is detected, '-rev_byte_order' can be used.\n"
"\n"
" -zorder ORDER : slice order over time\n"
"\n"
" e.g. -zorder alt\n"
" e.g. -zorder seq\n"
" the default is 'alt'\n"
"\n"
" This options allows the user to alter the slice\n"
" acquisition order in real-time mode, simliar to the slice\n"
" pattern of the '-sp' option. The main differences are:\n"
" o only two choices are presently available\n"
" o the syntax is intentionally different (from that\n"
" of 'to3d' or the '-sp' option)\n"
"\n"
" ORDER values:\n"
" alt : alternating in the Z direction (over time)\n"
" seq : sequential in the Z direction (over time)\n"
"\n"
" ---------------------------------------------------------------\n"
" other options:\n"
"\n"
" -debug LEVEL : show debug information during execution\n"
"\n"
" e.g. -debug 2\n"
" the default level is 1, the domain is [0,3]\n"
" the '-quiet' option is equivalent to '-debug 0'\n"
"\n"
" -help : show this help information\n"
"\n"
" -hist : display a history of program changes\n"
"\n"
" -nice INCREMENT : adjust the nice value for the process\n"
"\n"
" e.g. -nice 10\n"
" the default is 0, and the maximum is 20\n"
" a superuser may use down to the minimum of -19\n"
"\n"
" A positive INCREMENT to the nice value of a process will\n"
" lower its priority, allowing other processes more CPU\n"
" time.\n"
"\n"
" -nt VOLUMES_PER_RUN : set the number of time points per run\n"
"\n"
" e.g. -nt 120\n"
"\n"
" With this option, if a run stalls before the specified\n"
" VOLUMES_PER_RUN is reached (notably including the first\n"
" run), the user will be notified.\n"
"\n"
" Without this option, %s will compute the expected number\n"
" of time points per run based on the first run (and will\n"
" allow the value to increase based on subsequent runs).\n"
" Therefore %s would not detect a stalled first run.\n"
"\n"
" -quiet : show only errors and final information\n"
"\n"
" -quit : quit when there is no new data\n"
"\n"
" With this option, the program will terminate once a delay\n"
" in new data occurs. This is most appropriate to use when\n"
" the image files have already been collected.\n"
"\n"
" -start_file S_FILE : have %s process starting at S_FILE\n"
"\n"
" e.g. -start_file 043/I.901\n"
"\n"
" With this option, any earlier I-files will be ignored\n"
" by %s. This is a good way to start processing a later\n"
" run, if it desired not to look at the earlier data.\n"
"\n"
" In this example, all files in directories 003 and 023\n"
" would be ignored, along with everything in 043 up through\n"
" I.900. So 043/I.901 might be the first file in run 2.\n"
"\n"
" -version : show the version information\n"
"\n"
" ---------------------------------------------------------------\n"
" GERT_Reco2 options:\n"
"\n"
" -GERT_Reco2 : output a GERT_Reco2 script\n"
"\n"
" Create a script called 'GERT_Reco2', similar to the one\n"
" that Ifile creates. This script may be run to create the\n"
" AFNI datasets corresponding to the I-files.\n"
"\n"
" -gert_outdir OUTPUT_DIR : set output directory in GERT_Reco2\n"
"\n"
" e.g. -gert_outdir subject_A7\n"
" e.g. -od subject_A7\n"
" the default is '-gert_outdir afni'\n"
"\n"
" This will add '-od OUTPUT_DIR' to the @RenamePanga command\n"
" in the GERT_Reco2 script, creating new datasets in the\n"
" OUTPUT_DIR directory, instead of the 'afni' directory.\n"
"\n"
" -sp SLICE_PATTERN : set output slice pattern in GERT_Reco2\n"
"\n"
" e.g. -sp alt-z\n"
" the default is 'alt+z'\n"
"\n"
" This options allows the user to alter the slice\n"
" acquisition pattern in the GERT_Reco2 script.\n"
"\n"
" See 'to3d -help' for more information.\n"
"\n"
" ---------------------------------------------------------------\n"
"\n"
" Author: R. Reynolds - %s\n"
"\n"
" (many thanks to R. Birn)\n"
"\n",
prog, prog, prog, prog,
prog, prog, prog, prog, prog, prog, prog, prog, prog,
prog, prog, prog, prog, prog, prog, prog,
IFM_VERSION
);
return 0;
}
else if ( level == IFM_USE_HIST )
{
fputs( g_history, stdout );
return 0;
}
else if ( level == IFM_USE_VERSION )
{
printf( "%s: %s, compile date: %s\n",
prog, IFM_VERSION, __DATE__ );
return 0;
}
fprintf( stderr, "error: usage() called with illegal level <%d>\n", level );
return -1;
}
/* ----------------------------------------------------------------------
* signal handler
* ----------------------------------------------------------------------
*/
static void hf_signal( int signum )
{
switch ( signum )
{
default :
fprintf( stderr, "\nError: received unknown signal, %d\n",
signum );
break;
case SIGINT :
case SIGTERM :
show_run_stats( &gS );
break;
}
exit(0);
}
/* ----------------------------------------------------------------------
* set_volume_stats
* ----------------------------------------------------------------------
*/
static int set_volume_stats( param_t * p, stats_t * s, vol_t * v )
{
run_t * rp; /* for a little speed, this will be called often */
if ( v == NULL || v->seq_num < 0 || v->run < 0 )
{
fprintf( stderr, "failure: SVS - insufficient data\n\n" );
idisp_hf_vol_t ( "-- VOLUME FAILURE INFO : ", v );
}
/* initialize the stats structure */
if ( s->nalloc == 0 )
{
s->runs = (run_t *)calloc( IFM_STAT_ALLOC, sizeof(run_t) );
if ( s->runs == NULL )
{
fprintf( stderr, "failure: cannot allocate space for run info\n" );
return -1;
}
/* first time caller - fill initial stats info */
s->slices = v->nim;
s->z_first = v->z_first;
s->z_last = v->z_last;
s->z_delta = v->z_delta;
s->nalloc = IFM_STAT_ALLOC;
s->nused = 0;
s->nvols = gP.opts.nt; /* init with any user input value */
if ( gD.level > 1 )
fprintf( stderr, "\n-- svs: init alloc - vol %d, run %d, file %s\n",
v->seq_num, v->run, v->first_file );
}
if ( v->run >= s->nalloc ) /* run is 0-based */
{
/* make space for many more runs - we don't want to do this often */
s->runs = (run_t *)realloc( s->runs, (v->run + IFM_STAT_ALLOC) *
sizeof(run_t) );
if ( s->runs == NULL )
{
fprintf( stderr, "failure: cannot realloc space for run info\n" );
return -1;
}
s->nalloc = v->run + IFM_STAT_ALLOC;
/* zero out any new memory */
memset( s->runs + s->nused, 0, (s->nalloc - s->nused)*sizeof(run_t) );
if ( gD.level > 1 )
fprintf( stderr,
"\n-- svs: realloc (%d entries) - vol %d, run %d, file %s\n",
s->nalloc, v->seq_num, v->run, v->first_file );
}
/* we have memory - the current run number is an index into runs */
rp = s->runs + v->run;
if ( s->nused < v->run+1 )
s->nused = v->run+1;
if ( rp->volumes == 0 )
strncpy( rp->f1name, v->first_file, IFM_MAX_FLEN );
rp->volumes = v->seq_num;
/* update nvols (if the user did not specify it and it is small) */
if ( (p->opts.nt <= 0) && (s->nvols < v->seq_num) )
s->nvols = v->seq_num;
if ( gD.level > 2 )
fprintf( stderr, "\n-- svs: run %d, seq_num %d\n", v->run, v->seq_num );
return 0;
}
/* ----------------------------------------------------------------------
* Create a gert_reco script.
*
* Note - stats struct parameters have been checked.
* ----------------------------------------------------------------------
*/
static int create_gert_script( stats_t * s, opts_t * opts )
{
FILE * fp;
char * spat; /* slice acquisition pattern */
char cdir[4], csuff[IFM_SUFFIX_LEN];
int num_valid, c;
/* if the user did not give a slice pattern string, use the default */
spat = opts->sp ? opts->sp : IFM_SLICE_PAT;
for ( c = 0, num_valid = 0; c < s->nused; c++ )
if ( s->runs[c].volumes > 0 )
num_valid++;
if ( num_valid == 0 )
{
fprintf( stderr, "-- no runs to use for '%s'\n", IFM_GERT_SCRIPT );
return 0;
}
if ( (fp = fopen( IFM_GERT_SCRIPT, "w" )) == NULL )
{
fprintf( stderr, "failure: cannot open '%s' for writing, "
"check permissions\n", IFM_GERT_SCRIPT );
return -1;
}
/* output text casually, uh, borrowed from Ifile.c */
fprintf( fp,
"#!/bin/tcsh\n"
"\n"
"# This script was automatically generated by '%s'.\n"
"# The script format was, uh, borrowed from Ziad's Ifile.c.\n"
"#\n"
"# Please modify the following options for your own evil uses.\n"
"\n"
"set OutlierCheck = '-oc' # use '' to skip outlier check\n"
"set OutPrefix = 'OutBrick' # prefix for datasets\n"
"set OutputDir = '-od %s' # where to put output datasets\n"
"\n"
"\n",
IFM_PROG_NAME,
opts->gert_outdir ? opts->gert_outdir : "afni"
);
for ( c = 0; c < s->nused; c++ )
if ( s->runs[c].volumes > 0 )
{
if ( path_to_dir_n_suffix(cdir, csuff, s->runs[c].f1name) < 0 )
{
fclose( fp );
return -1;
}
fprintf( fp, "@RenamePanga %s %s %d %d $OutPrefix "
"-sp %s $OutlierCheck $OutputDir\n",
cdir, csuff, s->slices, s->runs[c].volumes, spat );
}
fputc( '\n', fp );
fclose( fp );
/* now make it an executable */
system( "chmod u+x " IFM_GERT_SCRIPT );
return 0;
}
/* ----------------------------------------------------------------------
* - show statistics from the runs
* - output any requested GERT_Reco2 file
* ----------------------------------------------------------------------
*/
static int show_run_stats( stats_t * s )
{
int c;
if ( s == NULL )
{
fprintf( stderr, "failure, SRS - no stats struct!\n" );
return -1;
}
if ( s->nalloc <= 0 || s->nused <= 0 )
return 0;
printf( "\n\n"
"final run statistics:\n"
" volume info :\n"
" slices : %d\n"
" z_first : %.4f\n"
" z_last : %.4f\n"
" z_delta : %.4f\n"
"\n",
s->slices, s->z_first, s->z_last, s->z_delta );
for ( c = 0; c < s->nused; c++ )
{
if ( s->runs[c].volumes > 0 )
printf( " run #%4d : volumes = %3d, first file = %s\n",
c, s->runs[c].volumes, s->runs[c].f1name );
}
putchar( '\n' );
if ( gP.opts.gert_reco )
(void)create_gert_script( s, &gP.opts );
fflush( stdout );
return 0;
}
/* ----------------------------------------------------------------------
* given tr, compute a sleep time of approximate 2*TR
* ----------------------------------------------------------------------
*/
static int nap_time_from_tr( float tr )
{
float tr2 = 2 * tr;
if ( tr2 < 1 )
return 1;
if ( tr2 > 10 )
return 10; /* ??? tres big */
return( (int)(tr2 + 0.9) ); /* basically, use ceiling */
}
/* ----------------------------------------------------------------------
* find_next_zoff
*
* Given p->flist, search from index start for an image with
* geh.zoff equal to zoff.
*
* return index : upon succes (start <= index <= p->nused)
* -1 : not found
* -2 : error
* ----------------------------------------------------------------------
*/
static int find_next_zoff( param_t * p, int start, float zoff )
{
int count;
if ( (p == NULL) || (start < 0) )
return -2;
if ( start > p->nused ) /* say not found */
return -1;
for ( count = start; count <= p->nused; count++ )
if ( fabs( zoff - p->flist[count].geh.zoff ) < IFM_EPSILON )
return count; /* found! */
return -1;
}
/* ----------------------------------------------------------------------
* Given: run > 0
* seq_num > 0
* naps
*
* If naps is too big, and the run is incomplete, print an obnoxious
* warning message to the user.
*
* notes: - print only 1 warning message per seq_num, per run
* - prev_run and prev_seq_num are for the previously found volume
*
* returns:
* 2 : run is stalled - message printed
* 1 : apparent end of a run
* 0 : no stall, or if a message has already been printed
* -1 : function failure
* ----------------------------------------------------------------------
*/
static int check_stalled_run ( int run, int seq_num, int naps, int nap_time )
{
static int func_failure = 0;
static int prev_run = -1;
static int prev_seq = -1;
if ( func_failure != 0 )
return 0;
if ( ( run < 1 ) || ( seq_num < 1 ) || ( naps <= IFM_MAX_RUN_NAPS ) )
return 0;
/* verify that we have already taken note of the previous volume */
if ( (((gS.nused + 1) < run) || (gS.runs[run].volumes < seq_num)) &&
( func_failure == 0 ) )
{
fprintf( stderr, "** warning: CSR - stats inconsistancy!\n" );
func_failure = 1;
return -1;
}
if ( seq_num < gS.nvols ) /* are we done with the run yet? */
{
/* if we haven't printed before, this is the first stalled case */
if ( (run != prev_run) || (seq_num != prev_seq) )
{
fprintf( stderr, "\007\n"
"****************************************************\n"
"Warning: run seems to be stalled\n"
"\n"
" run : %d\n"
" TRs completed : %d (of %d)\n"
" approximate idle time : %d seconds\n"
" first file of this run : %s\n"
"****************************************************\n",
run, seq_num, gS.nvols,
naps*nap_time, gS.runs[run].f1name );
prev_run = run;
prev_seq = seq_num;
return 2;
}
}
/* else (we are done) */
else if ( (run != prev_run) || (seq_num != prev_seq) )
{
/* this is our first visit, note the fact */
prev_run = run;
prev_seq = seq_num;
return 1;
}
return 0;
}
/*-------------------------------------------------------*/
/*! Return the file length (-1 if file not found). */
/* (local copy from thd_filestuff.c */
static unsigned long l_THD_filesize( char * pathname )
{
static struct stat buf ; int ii ;
if( pathname == NULL ) return -1 ;
ii = stat( pathname , &buf ) ; if( ii != 0 ) return -1 ;
return buf.st_size ;
}
/* ----------------------------------------------------------------------
* Make sure im_ary has enough memory for num_images pointers.
*
* return -1 : on error
* 0 : nothing needed
* 1 : memory successfully created
* ----------------------------------------------------------------------
*/
static int check_im_store_space( im_store_t * is, int num_images )
{
if ( (is == NULL) || (num_images <= 0) )
{
fprintf( stderr, "** CISS: invalid parameters (%p,%d)\n",
is, num_images );
return -1;
}
if ( is->ary_len >= num_images )
return 0;
/* so we need memory */
if ( gD.level > 2 )
fprintf( stderr, "++ allocating %d image pointers (was %d)\n",
num_images, is->ary_len );
is->im_ary = realloc(is->im_ary, num_images * sizeof(void *));
if ( is->im_ary == NULL )
{
fprintf( stderr, "** failure: cannot allocate %d image pointers\n",
num_images );
return -1;
}
is->ary_len = num_images;
return 1;
}
/* ----------------------------------------------------------------------
* Set the im_size and allocate memory for x_im.
*
* return -1 : on error
* 0 : success
* ----------------------------------------------------------------------
*/
static int alloc_x_im( im_store_t * is, int bytes )
{
if ( (is == NULL) || (bytes <= 0) )
{
fprintf( stderr, "** bad params to AXI (%p,%d)\n", is, bytes );
return -1;
}
is->im_size = bytes;
if ( (is->x_im = malloc( bytes )) == NULL )
{
fprintf( stderr, "** AXI: failed to malloc %d bytes for x_im\n",
bytes );
return -1;
}
if ( gD.level > 1 )
fprintf( stderr, "++ allocating %d bytes for is->x_im\n", bytes );
return 0;
}
/* ----------------------------------------------------------------------
* Determine the byte order of the image.
*
* Note our byte order (LSB_FIRST or MSB_FIRST).
* If gex.swap is set, reverse it. If user wants opposite, reverse it.
*
* return 0 : success
* -1 : on error
* ----------------------------------------------------------------------
*/
static int check_im_byte_order( int * order, vol_t * v, param_t * p )
{
int one = 1;
if ( (order == NULL) || (v == NULL) || (p == NULL) )
{
fprintf( stderr, "** invalid paramters to CIBO (%p,%p,%p)\n",
order, v, p );
return -1;
}
/* note the order for the current system */
*order = (*(char *)&one == 1) ? LSB_FIRST : MSB_FIRST;
if ( gD.level > 1 )
fprintf( stderr, "-- system order is %s, ",
(*order == MSB_FIRST) ? "MSB_FIRST" : "LSB_FIRST" );
/* are the images the opposite of this? does the user want the opposite? */
if ( p->flist[v->fl_1].gex.swap ^ p->opts.rev_bo )
*order = LSB_FIRST + MSB_FIRST - *order; /* for entertainment */
if ( gD.level > 1 )
fprintf( stderr, "image order is %s\n",
(*order == MSB_FIRST) ? "MSB_FIRST" : "LSB_FIRST" );
return 0;
}
/* ----------------------------------------------------------------------
* Use gex.kk to figure out the z orientation, and complete
* the v->geh.orients string.
*
* orient(kk) = { LR, if kk = 1
* { PA, if kk = 2
* { IS, if kk = 3
*
* return 0 : success
* -1 : on error
* ----------------------------------------------------------------------
*/
static int complete_orients_str( vol_t * v, param_t * p )
{
int kk;
if ( (v == NULL) || (p == NULL) )
{
fprintf( stderr, "** invalid paramters to COS (%p,%p)\n", v, p );
return -1;
}
kk = p->flist[v->fl_1].gex.kk;
switch( kk )
{
case 1: /* LR */
if ( v->z_delta > 0 )
{
v->geh.orients[4] = 'L';
v->geh.orients[5] = 'R';
}
else
{
v->geh.orients[4] = 'R';
v->geh.orients[5] = 'L';
}
break;
case 2: /* PA */
if ( v->z_delta > 0 )
{
v->geh.orients[4] = 'P';
v->geh.orients[5] = 'A';
}
else
{
v->geh.orients[4] = 'A';
v->geh.orients[5] = 'P';
}
break;
case 3: /* IS */
if ( v->z_delta > 0 )
{
v->geh.orients[4] = 'I';
v->geh.orients[5] = 'S';
}
else
{
v->geh.orients[4] = 'S';
v->geh.orients[5] = 'I';
}
break;
default:
{
fprintf(stderr, "** COS failure: kk (%d) out of [1,3] range\n", kk);
return -1;
}
}
v->geh.orients[6] = '\0';
return 0;
}
/* ----------------------------------------------------------------------
* return the index of 'file' in the directory list
*
* return -1 : failed to find it
* else : index
* ----------------------------------------------------------------------
*/
static int find_fl_file_index( param_t * p, char * file )
{
char ** nlp;
int index;
if ( (p == NULL) || (file == NULL) )
return 0;
for ( index = 0, nlp = p->fnames; index < p->nfiles; index++, nlp++ )
if ( ! strcmp( *nlp, file ) )
return index;
return -1;
}
/* ----------------------------------------------------------------------
* return the number of occurances of 'target' in 'str' of length 'len'
* ----------------------------------------------------------------------
*/
static int str_char_count( char * str, int len, char target )
{
char * cp;
char * last = str + len;
int num = 0;
if ( (str == NULL) || (len <= 0) )
return 0;
for ( cp = str; cp < last; cp++ )
if ( *cp == target )
num++;
return num;
}
/* ----------------------------------------------------------------------
* Given path, find dir and suff.
*
* dir - 3 character starting directory (e.g. 003)
* suff - 10 char (max) trailing I-file suffix (e.g. 017, for I.017)
* path - first file in run (e.g. 003/I.017)
*
* return 0 : success
* -1 : failure
* ----------------------------------------------------------------------
*/
static int path_to_dir_n_suffix( char * dir, char * suff, char * path )
{
char * cp, *cp2;
if ( (dir == NULL) || (suff == NULL) || (path == NULL) )
{
fprintf( stderr, "failure: PTDNS - invalid params (%p,%p,%p)\n",
dir, suff, path );
return -1;
}
/* find last '.' */
for ( cp = path + strlen(path) - 1; (*cp != '.') && (cp > path); cp-- )
;
if ( *cp != '.' )
{
fprintf( stderr, "failure: cannot find suffix in '%s'\n", path );
return -1;
}
else if ( strlen( cp ) > IFM_SUFFIX_LEN ) /* '.' not included */
{
fprintf( stderr, "failure: suffix too long in '%s'\n", path );
return -1;
}
strcpy( suff, cp+1 ); /* copy null-terminated suffix */
/* make sure all characters are digits (treat as string, not int) */
for ( cp2 = suff; (*cp2 != '\0') && isdigit(*cp2); cp2++ )
;
if ( *cp2 != '\0' )
{
fprintf( stderr, "failure: suffix not integer in '%s'\n", path );
return -1;
}
/* now get dir prefix - should be nnn/I.mmm */
cp -= 5;
if ( ( cp < path ) || /* we should have a directory here */
( ! isdigit( cp[0] ) ) || /* then 3 digits */
( ! isdigit( cp[1] ) ) ||
( ! isdigit( cp[2] ) ) ||
( cp[3] != '/' ) ||
( cp[4] != 'I' ) )
{
fprintf( stderr, "failure: PTDNS - ill-formed path '%s'\n", path );
return -1;
}
/* we are set, just copy the data */
strncpy( dir, cp, 3 );
dir[3] = '\0';
return 0;
}
/* ----------------------------------------------------------------------
* Add given string (pointer) to list. v3.3 [rickr]
*
* return 0 : success
* -1 : failure (realloc)
* ----------------------------------------------------------------------
*/
static int add_to_string_list( string_list * list, char * str )
{
if ( !list || !str )
return -1;
/* if needed, just add 10 at a time to nalloc (they're only pointers) */
if ( list->nalloc == 0 || (list->nalloc <= list->nused) )
{
list->nalloc += 10;
list->str = (char **)realloc(list->str, list->nalloc*sizeof(char *));
if ( !list->str )
{
fprintf(stderr,"** failed to allocate for %d (char *)s\n",
list->nalloc);
return -1;
}
}
list->str[list->nused] = str;
list->nused++;
return 0;
}
/* ----------------------------------------------------------------------
* If free_mem, free memory. Set contents as empty. v3.3 [rickr]
* ----------------------------------------------------------------------
*/
static int empty_string_list( string_list * list, int free_mem )
{
if ( list->str && free_mem )
free( list->str );
list->str = NULL;
list->nalloc = 0;
list->nused = 0;
return 0;
}
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