/*-------------------------------------------------------------------- * The MB-system: mbclean.c 2/26/93 * $Id: mbclean.c 2227 2015-02-05 21:12:31Z caress $ * * Copyright (c) 1993-2015 by * David W. Caress (caress@mbari.org) * Monterey Bay Aquarium Research Institute * Moss Landing, CA 95039 * and Dale N. Chayes (dale@ldeo.columbia.edu) * Lamont-Doherty Earth Observatory * Palisades, NY 10964 * * See README file for copying and redistribution conditions. *--------------------------------------------------------------------*/ /* * mbclean identifies and flags artifacts in swath sonar bathymetry data. * The edit events are output to an edit save file which can be applied * to the data by the program mbprocess. * Several algorithms are available for identifying artifacts; multiple * algorithmscan be applied in a single pass. The most commonly used * approach is to identify artifacts based on excessive bathymetric * slopes. If desired, mbclean will also flag beams associated with * "rails" where outer beams have smaller acrosstrack distances than * more inner beams (-Q option). Low and high bounds on acceptable depth * values can be set; depth values outside the acceptable range will be * flagged. The acceptable depth ranges can either be absolute (-B option), relative * to the local median depth (-A option) or defined by low and high fractions * of the local median depth (-G option). A set number of outer beams can also be * flagged. * The order in which the flagging algorithms are applied is as follows: * 1. Flag specified number of outer beams (-X option). * 2. Flag soundings outside specified acceptable * depth range (-B option). * 3. Flag soundings outside acceptable depth range using * fractions of local median depth (-G option). * 4. Flag soundings outside acceptable depth range using * deviation from local median depth (-A option). * 5. Flag soundings associated with excessive slopes * (-C option or default). * 6. Zap "rails" (-Q option). * 7. Flag all soundings in pings with too few * good soundings (-U option). * * * Author: D. W. Caress * Date: February 26, 1993 (buffered i/o version) * Date: January 19, 2001 (edit save file version) * * Acknowledgments: * This program is based to a large extent on the program mbcleanx * by Alberto Malinverno (formerly at L-DEO, now at Schlumberger), * which was in turn based on the original program mbclean (v. 1.0) * by David Caress. * */ /* standard include files */ #include #include #include #include #include #include #include /* mbio include files */ #include "mb_status.h" #include "mb_format.h" #include "mb_define.h" #include "mb_io.h" #include "mb_swap.h" #include "mb_process.h" /* local defines */ #define MBCLEAN_FLAG_ONE 1 #define MBCLEAN_FLAG_BOTH 2 #define MBCLEAN_ZERO_ONE 3 #define MBCLEAN_ZERO_BOTH 4 /* MBIO buffer size default */ #define MBCLEAN_BUFFER_DEFAULT 500 /* edit action defines */ #define MBCLEAN_NOACTION 0 /* ping structure definition */ struct mbclean_ping_struct { int time_i[7]; double time_d; int multiplicity; double navlon; double navlat; double speed; double heading; int beams_bath; char *beamflag; char *beamflagorg; double *bath; double *bathacrosstrack; double *bathalongtrack; double *bathx; double *bathy; }; /* bad beam identifier structure definition */ struct bad_struct { int flag; int ping; int beam; double bath; }; /* edit output function */ int mbclean_save_edit(int verbose, FILE *sofp, double time_d, int beam, int action, int *error); static char rcs_id[] = "$Id: mbclean.c 2227 2015-02-05 21:12:31Z caress $"; /*--------------------------------------------------------------------*/ int main (int argc, char **argv) { char program_name[] = "MBCLEAN"; char help_message[] = "MBCLEAN identifies and flags artifacts in swath sonar bathymetry data\nBad beams are indentified based on one simple criterion only: \nexcessive bathymetric slopes. The default input and output streams \nare stdin and stdout."; char usage_message[] = "mbclean [-Amax -Blow/high -Cslope/unit -Dmin/max \n" "\t-Fformat -Gfraction_low/fraction_high -Iinfile -Krange_min \n" "\t-Llonflip -Mmode -Ooutfile -Pmin_speed/max_speed -Q -Rmaxheadingrate \n" "\t-Sspike_slope/mode/format -Ttolerance -Wwest/east/south/north \n" "\t-Xbeamsleft/beamsright -Ydistanceleft/distanceright -Z\n\t-V -H]\n\n"; extern char *optarg; int errflg = 0; int c; int help = 0; int flag = 0; /* MBIO status variables */ int status; int verbose = 0; int error = MB_ERROR_NO_ERROR; char *message = NULL; /* swath file locking variables */ int uselockfiles; int lock_status; int locked; int lock_purpose; mb_path lock_program; mb_path lock_cpu; mb_path lock_user; char lock_date[25]; /* MBIO read control parameters */ int read_datalist = MB_NO; char read_file[MB_PATH_MAXLINE]; char swathfile[MB_PATH_MAXLINE]; char swathfileread[MB_PATH_MAXLINE]; void *datalist; int look_processed = MB_DATALIST_LOOK_UNSET; int oktoprocess; double file_weight; int format; int formatread; int variable_beams; int traveltime; int beam_flagging; int pings; int lonflip; double bounds[4]; int btime_i[7]; int etime_i[7]; double btime_d; double etime_d; double speedmin; double timegap; double distance; double altitude; double sonardepth; int beams_bath; int beams_amp; int pixels_ss; double *amp; double *ss; double *ssacrosstrack; double *ssalongtrack; /* mbio read and write values */ void *mbio_ptr = NULL; int kind; struct mbclean_ping_struct ping[3]; int nrec, irec; int pingsread; struct bad_struct bad[2]; int find_bad; int nfiletot = 0; int ndatatot = 0; int ndepthrangetot = 0; int nminrangetot = 0; int nfractiontot = 0; int nspeedtot = 0; int nzeropostot = 0; int ndeviationtot = 0; int nouterbeamstot = 0; int nouterdistancetot = 0; int nrailtot = 0; int nlong_acrosstot=0; //2010/03/07 DY int nmintot = 0; int nbadtot = 0; int nspiketot = 0; int nflagtot = 0; int nunflagtot = 0; int nzerotot = 0; int nflagesftot = 0; int nunflagesftot = 0; int nzeroesftot = 0; int ndata = 0; int ndepthrange = 0; int nminrange = 0; int nfraction = 0; int nspeed = 0; int nzeropos = 0; int nrangepos = 0; int ndeviation = 0; int nouterbeams = 0; int nouterdistance = 0; int nrail = 0; int nlong_across=0; //2010/03/07 DY int nmax_heading_rate=0; //2010/04/27 DY int nmax_heading_ratetot=0; //2010/04/27 DY int nmin = 0; int nbad = 0; int nspike = 0; int nflag = 0; int nunflag = 0; int nzero = 0; int nflagesf = 0; int nunflagesf = 0; int nzeroesf = 0; char comment[MB_COMMENT_MAXLINE]; int check_slope = MB_NO; double slopemax = 1.0; int check_spike = MB_NO; double spikemax = 1.0; int spike_mode = 1; int slope_form = 0; double distancemin = 0.01; double distancemax = 0.25; int mode = MBCLEAN_FLAG_ONE; int zap_beams = MB_NO; int zap_beams_right = 0; int zap_beams_left = 0; int zap_distance = MB_NO; double zap_distance_right = 0.0; double zap_distance_left = 0.0; int zap_rails = MB_NO; int zap_long_across = MB_NO; //2010/03/07 DY int zap_max_heading_rate = MB_NO; //2010/04/27 DY int check_range = MB_NO; double depth_low; double depth_high; int check_range_min = MB_NO; double range_min; int check_fraction = MB_NO; double fraction_low; double fraction_high; int check_speed_good = MB_NO; int check_zero_position = MB_NO; int check_position_bounds = MB_NO; double speed_low; double speed_high; double west,east,south,north; int check_deviation = MB_NO; double deviation_max; int check_num_good_min = MB_NO; int num_good_min; int num_good; int action; /* rail processing variables */ int center; double lowdist; //2010/03/07 DY changed these to doubles double highdist; double backup_dist = 0; //2010/04/27 DY /* max acrosstrack filter variable 2010/03/07 DY */ double max_acrosstrack = 120; /* max heading_rate variable 2010/04/27 DY */ double max_heading_rate; double last_heading = 0.0; double last_time = 0.0; /* slope processing variables */ double mtodeglon; double mtodeglat; double headingx; double headingy; int nlist; double *list = NULL; double median = 0.0; double dd; double dd2; double slope; double slope2; /* fix_edit_timestamps variables */ int fix_edit_timestamps = MB_NO; double tolerance = 0.0; /* save file control variables */ int esffile_open = MB_NO; char esffile[MB_PATH_MAXLINE]; struct mb_esf_struct esf; /* processing variables */ int read_data; int start, done; int i, j, k, n, p, b; /* get current default values */ status = mb_defaults(verbose,&format,&pings,&lonflip,bounds, btime_i,etime_i,&speedmin,&timegap); status = mb_uselockfiles(verbose,&uselockfiles); /* reset all defaults but the format and lonflip */ pings = 1; bounds[0] = -360.; bounds[1] = 360.; bounds[2] = -90.; bounds[3] = 90.; btime_i[0] = 1962; btime_i[1] = 2; btime_i[2] = 21; btime_i[3] = 10; btime_i[4] = 30; btime_i[5] = 0; btime_i[6] = 0; etime_i[0] = 2062; etime_i[1] = 2; etime_i[2] = 21; etime_i[3] = 10; etime_i[4] = 30; etime_i[5] = 0; etime_i[6] = 0; speedmin = 0.0; timegap = 1000000000.0; strcpy(read_file, "datalist.mb-1"); /* process argument list */ while ((c = getopt(argc, argv, "VvHhA:a:B:b:C:c:D:d:E:e:F:f:G:g:K:k:L:l:I:i:M:m:Q:q:P:p:R:r:S:s:T:t:U:u:W:w:X:x:Y:y:Zz")) != -1) { switch (c) { case 'H': case 'h': help++; break; case 'V': case 'v': verbose++; break; case 'A': case 'a': sscanf (optarg,"%lf", &deviation_max); check_deviation = MB_YES; flag++; break; case 'B': case 'b': sscanf (optarg,"%lf/%lf", &depth_low,&depth_high); check_range = MB_YES; flag++; break; case 'C': case 'c': slope_form = 0; sscanf (optarg,"%lf/%d", &slopemax, &slope_form); check_slope = MB_YES; if (slope_form == 1) slopemax = tan(slopemax); else if (slope_form == 2) slopemax = tan(DTR * slopemax); flag++; break; case 'D': case 'd': sscanf (optarg,"%lf/%lf", &distancemin, &distancemax); flag++; break; case 'E': //2010/03/07 DY added the max acrosstrack filter case 'e': sscanf (optarg,"%lf", &max_acrosstrack); zap_long_across = MB_YES; flag++; break; case 'F': case 'f': sscanf (optarg,"%d", &format); flag++; break; case 'G': case 'g': sscanf (optarg,"%lf/%lf", &fraction_low,&fraction_high); check_fraction = MB_YES; flag++; break; case 'K': case 'k': sscanf (optarg,"%lf", &range_min); check_range_min = MB_YES; flag++; break; case 'I': case 'i': sscanf (optarg,"%s", read_file); flag++; break; case 'L': case 'l': sscanf (optarg,"%d", &lonflip); flag++; break; case 'M': case 'm': sscanf (optarg,"%d", &mode); flag++; break; case 'P': case 'p': sscanf (optarg,"%lf/%lf", &speed_low,&speed_high); check_speed_good = MB_YES; flag++; break; case 'Q': case 'q': zap_rails = MB_YES; backup_dist = 0.0; sscanf (optarg,"%lf", &backup_dist); flag++; break; case 'R': case 'r': zap_max_heading_rate = MB_YES; sscanf (optarg,"%lf", &max_heading_rate); flag++; break; case 'S': case 's': slope_form = 0; sscanf (optarg,"%lf/%d/%d", &spikemax, &spike_mode, &slope_form); check_spike = MB_YES; if (2 == slope_form) spikemax = tan(DTR * spikemax); if (1 == slope_form) spikemax = tan(spikemax); flag++; break; case 'T': case 't': fix_edit_timestamps = MB_YES; sscanf (optarg,"%lf", &tolerance); flag++; break; case 'U': case 'u': sscanf (optarg,"%d", &num_good_min); check_num_good_min = MB_YES; flag++; break; case 'W': case 'w': check_position_bounds = MB_YES; sscanf (optarg,"%lf/%lf/%lf/%lf",&west,&east,&south,&north); flag++; break; case 'X': case 'x': n = sscanf (optarg,"%d/%d", &zap_beams_left, &zap_beams_right); if (n == 1) zap_beams_right = zap_beams_left; zap_beams = MB_YES; flag++; break; case 'Y': case 'y': n = sscanf (optarg,"%lf/%lf", &zap_distance_left, &zap_distance_right); if (n == 1) zap_distance_right = zap_distance_left; if (zap_distance_left > 0.0) zap_distance_left = -zap_distance_left; if (zap_distance_right < 0.0) zap_distance_right = -zap_distance_right; zap_distance = MB_YES; flag++; break; case 'Z': case 'z': check_zero_position = MB_YES; flag++; break; case '?': errflg++; } } /* if error flagged then print it and exit */ if (errflg) { fprintf(stderr,"usage: %s\n", usage_message); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); error = MB_ERROR_BAD_USAGE; exit(error); } /* turn on slope checking if nothing else is to be used */ if (check_slope == MB_NO && zap_beams == MB_NO && zap_distance == MB_NO && zap_rails == MB_NO && check_spike == MB_NO && check_range == MB_NO && check_fraction == MB_NO && check_speed_good == MB_NO && check_deviation == MB_NO && check_num_good_min == MB_NO && check_position_bounds == MB_NO && check_zero_position == MB_NO && fix_edit_timestamps == MB_NO) check_slope = MB_YES; /* print starting message */ if (verbose == 1 || help) { fprintf(stderr,"\nProgram %s\n",program_name); fprintf(stderr,"Version %s\n",rcs_id); fprintf(stderr,"MB-system Version %s\n",MB_VERSION); } /* print starting debug statements */ if (verbose >= 2) { fprintf(stderr,"\ndbg2 Program <%s>\n",program_name); fprintf(stderr,"dbg2 Version %s\n",rcs_id); fprintf(stderr,"dbg2 MB-system Version %s\n",MB_VERSION); fprintf(stderr,"dbg2 Control Parameters:\n"); fprintf(stderr,"dbg2 verbose: %d\n",verbose); fprintf(stderr,"dbg2 help: %d\n",help); fprintf(stderr,"dbg2 pings: %d\n",pings); fprintf(stderr,"dbg2 lonflip: %d\n",lonflip); fprintf(stderr,"dbg2 bounds[0]: %f\n",bounds[0]); fprintf(stderr,"dbg2 bounds[1]: %f\n",bounds[1]); fprintf(stderr,"dbg2 bounds[2]: %f\n",bounds[2]); fprintf(stderr,"dbg2 bounds[3]: %f\n",bounds[3]); fprintf(stderr,"dbg2 btime_i[0]: %d\n",btime_i[0]); fprintf(stderr,"dbg2 btime_i[1]: %d\n",btime_i[1]); fprintf(stderr,"dbg2 btime_i[2]: %d\n",btime_i[2]); fprintf(stderr,"dbg2 btime_i[3]: %d\n",btime_i[3]); fprintf(stderr,"dbg2 btime_i[4]: %d\n",btime_i[4]); fprintf(stderr,"dbg2 btime_i[5]: %d\n",btime_i[5]); fprintf(stderr,"dbg2 btime_i[6]: %d\n",btime_i[6]); fprintf(stderr,"dbg2 etime_i[0]: %d\n",etime_i[0]); fprintf(stderr,"dbg2 etime_i[1]: %d\n",etime_i[1]); fprintf(stderr,"dbg2 etime_i[2]: %d\n",etime_i[2]); fprintf(stderr,"dbg2 etime_i[3]: %d\n",etime_i[3]); fprintf(stderr,"dbg2 etime_i[4]: %d\n",etime_i[4]); fprintf(stderr,"dbg2 etime_i[5]: %d\n",etime_i[5]); fprintf(stderr,"dbg2 etime_i[6]: %d\n",etime_i[6]); fprintf(stderr,"dbg2 speedmin: %f\n",speedmin); fprintf(stderr,"dbg2 timegap: %f\n",timegap); fprintf(stderr,"dbg2 data format: %d\n",format); fprintf(stderr,"dbg2 input file: %s\n",read_file); fprintf(stderr,"dbg2 mode: %d\n",mode); fprintf(stderr,"dbg2 zap_beams: %d\n",zap_beams); fprintf(stderr,"dbg2 zap_beams_left: %d\n",zap_beams_left); fprintf(stderr,"dbg2 zap_beams_right: %d\n",zap_beams_right); fprintf(stderr,"dbg2 zap_distance: %d\n",zap_distance); fprintf(stderr,"dbg2 zap_distance_left: %f\n",zap_distance_left); fprintf(stderr,"dbg2 zap_distance_right: %f\n",zap_distance_right); fprintf(stderr,"dbg2 zap_rails: %d\n",zap_rails); fprintf(stderr,"dbg2 backup_dist: %f\n",backup_dist); fprintf(stderr,"dbg2 zap_max_heading_rate: %d\n",zap_max_heading_rate); fprintf(stderr,"dbg2 max_heading_rate: %f\n",max_heading_rate); fprintf(stderr,"dbg2 check_slope: %d\n",check_slope); fprintf(stderr,"dbg2 maximum slope: %f\n",slopemax); fprintf(stderr,"dbg2 check_spike: %d\n",check_spike); fprintf(stderr,"dbg2 maximum spike: %f\n",spikemax); fprintf(stderr,"dbg2 spike mode: %d\n",spike_mode); fprintf(stderr,"dbg2 minimum dist: %f\n",distancemin); fprintf(stderr,"dbg2 minimum dist: %f\n",distancemax); fprintf(stderr,"dbg2 check_range: %d\n",check_range); fprintf(stderr,"dbg2 depth_low: %f\n",depth_low); fprintf(stderr,"dbg2 depth_high: %f\n",depth_high); fprintf(stderr,"dbg2 check_fraction: %d\n",check_fraction); fprintf(stderr,"dbg2 fraction_low: %f\n",fraction_low); fprintf(stderr,"dbg2 fraction_high: %f\n",fraction_high); fprintf(stderr,"dbg2 check_deviation: %d\n",check_deviation); fprintf(stderr,"dbg2 check_num_good_min: %d\n",check_num_good_min); fprintf(stderr,"dbg2 num_good_min: %d\n",num_good_min); fprintf(stderr,"dbg2 zap_long_across: %d\n",zap_long_across); fprintf(stderr,"dbg2 max_acrosstrack: %f\n",max_acrosstrack); fprintf(stderr,"dbg2 fix_edit_timestamps: %d\n",fix_edit_timestamps); fprintf(stderr,"dbg2 tolerance: %f\n",tolerance); fprintf(stderr,"dbg2 check_speed_good: %d\n",check_speed_good); fprintf(stderr,"dbg2 speed_low: %f\n",speed_low); fprintf(stderr,"dbg2 speed_high: %f\n",speed_high); fprintf(stderr,"dbg2 check_position_bounds:%d\n",check_position_bounds); fprintf(stderr,"dbg2 check_zero_position: %d\n",check_zero_position); } /* if help desired then print it and exit */ if (help) { fprintf(stderr,"\n%s\n",help_message); fprintf(stderr,"\nusage: %s\n", usage_message); exit(error); } /* get format if required */ if (format == 0) mb_get_format(verbose,read_file,NULL,&format,&error); /* determine whether to read one file or a list of files */ if (format < 0) read_datalist = MB_YES; /* open file list */ if (read_datalist == MB_YES) { if ((status = mb_datalist_open(verbose,&datalist, read_file,look_processed,&error)) != MB_SUCCESS) { error = MB_ERROR_OPEN_FAIL; fprintf(stderr,"\nUnable to open data list file: %s\n", read_file); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } if ((status = mb_datalist_read(verbose,datalist, swathfile,&format,&file_weight,&error)) == MB_SUCCESS) read_data = MB_YES; else read_data = MB_NO; } /* else copy single filename to be read */ else { strcpy(swathfile, read_file); read_data = MB_YES; } /* loop over all files to be read */ while (read_data == MB_YES) { oktoprocess = MB_YES; /* check format and get format flags */ if ((status = mb_format_flags(verbose,&format, &variable_beams, &traveltime, &beam_flagging, &error)) != MB_SUCCESS) { mb_error(verbose,error,&message); fprintf(stderr,"\nMBIO Error returned from function regarding input format %d:\n%s\n",format,message); fprintf(stderr,"\nFile <%s> skipped by program <%s>\n", swathfile,program_name); oktoprocess = MB_NO; status = MB_SUCCESS; error = MB_ERROR_NO_ERROR; } /* check that clean mode is allowed for the specified data format */ if (beam_flagging == MB_NO && mode <= 2) { fprintf(stderr,"\nMBIO format %d does not allow flagging of bad data \nas negative numbers (specified by cleaning mode %d).\n",format,mode); fprintf(stderr,"\nCopy the data to another format or set the cleaning mode to zero \nbad data values (-M3 or -M4).\n"); fprintf(stderr,"\nFile <%s> skipped by program <%s>\n", swathfile,program_name); oktoprocess = MB_NO; } /* try to lock file */ if (uselockfiles == MB_YES) status = mb_pr_lockswathfile(verbose, swathfile, MBP_LOCK_EDITBATHY, program_name, &error); else { lock_status = mb_pr_lockinfo(verbose, swathfile, &locked, &lock_purpose, lock_program, lock_user, lock_cpu, lock_date, &error); /* if locked get lock info */ if (error == MB_ERROR_FILE_LOCKED) { fprintf(stderr, "\nFile %s locked but lock ignored\n", swathfile); fprintf(stderr, "File locked by <%s> running <%s>\n", lock_user, lock_program); fprintf(stderr, "on cpu <%s> at <%s>\n", lock_cpu, lock_date); error = MB_ERROR_NO_ERROR; } } /* if locked let the user know file can't be opened */ if (status == MB_FAILURE) { /* if locked get lock info */ if (error == MB_ERROR_FILE_LOCKED) { lock_status = mb_pr_lockinfo(verbose, swathfile, &locked, &lock_purpose, lock_program, lock_user, lock_cpu, lock_date, &error); fprintf(stderr, "\nUnable to open input file:\n"); fprintf(stderr, " %s\n", swathfile); fprintf(stderr, "File locked by <%s> running <%s>\n", lock_user, lock_program); fprintf(stderr, "on cpu <%s> at <%s>\n", lock_cpu, lock_date); } /* else if unable to create lock file there is a permissions problem */ else if (error == MB_ERROR_OPEN_FAIL) { fprintf(stderr, "Unable to create lock file\n"); fprintf(stderr, "for intended input file:\n"); fprintf(stderr, " %s\n", swathfile); fprintf(stderr, "-Likely permissions issue\n"); } /* reset error and status */ oktoprocess = MB_NO; status = MB_SUCCESS; error = MB_ERROR_NO_ERROR; } /* proceed if file locked and format ok */ if (oktoprocess == MB_YES) { /* check for "fast bathymetry" or "fbt" file */ strcpy(swathfileread, swathfile); formatread = format; mb_get_fbt(verbose, swathfileread, &formatread, &error); /* initialize reading the input swath sonar file */ if ((status = mb_read_init( verbose,swathfileread,formatread,pings,lonflip,bounds, btime_i,etime_i,speedmin,timegap, &mbio_ptr,&btime_d,&etime_d, &beams_bath,&beams_amp,&pixels_ss,&error)) != MB_SUCCESS) { mb_error(verbose,error,&message); fprintf(stderr,"\nMBIO Error returned from function :\n%s\n",message); fprintf(stderr,"\nMultibeam File <%s> not initialized for reading\n",swathfile); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } /* initialize and increment counting variables */ ndata = 0; ndepthrange = 0; nminrange = 0; nfraction = 0; nspeed = 0; nzeropos = 0; nrangepos = 0; ndeviation = 0; nouterbeams = 0; nouterdistance = 0; nrail = 0; nlong_across=0; //2010/03/07 DY nmin = 0; nbad = 0; nspike = 0; nflag = 0; nunflag = 0; nzero = 0; nflagesf = 0; nunflagesf = 0; nzeroesf = 0; /* give the statistics */ if (verbose >= 0) { fprintf(stderr,"\nProcessing %s\n",swathfileread); } /* allocate memory for data arrays */ for (i=0;i<3;i++) { ping[i].beamflag = NULL; ping[i].beamflagorg = NULL; ping[i].bath = NULL; ping[i].bathacrosstrack = NULL; ping[i].bathalongtrack = NULL; ping[i].bathx = NULL; ping[i].bathy = NULL; if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(char), (void **)&ping[i].beamflag, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(char), (void **)&ping[i].beamflagorg, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&ping[i].bath, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&ping[i].bathacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&ping[i].bathalongtrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&ping[i].bathx, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&ping[i].bathy, &error); } amp = NULL; ss = NULL; ssacrosstrack = NULL; ssalongtrack = NULL; list = NULL; if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_AMPLITUDE, sizeof(double), (void **)&, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ss, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ssacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ssalongtrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, 4 * sizeof(double), (void **)&list, &error); /* if error initializing memory then quit */ if (error != MB_ERROR_NO_ERROR) { mb_error(verbose,error,&message); fprintf(stderr,"\nMBIO Error allocating data arrays:\n%s\n",message); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } /* now deal with old edit save file */ if (status == MB_SUCCESS) { /* reset message */ fprintf(stderr, "Sorting old edits...\n"); /* handle esf edits */ status = mb_esf_load(verbose, swathfile, MB_YES, MB_YES, esffile, &esf, &error); if (status == MB_SUCCESS && esf.esffp != NULL) esffile_open = MB_YES; if (status == MB_FAILURE && error == MB_ERROR_OPEN_FAIL) { esffile_open = MB_NO; fprintf(stderr, "\nUnable to open new edit save file %s\n", esf.esffile); } else if (status == MB_FAILURE && error == MB_ERROR_MEMORY_FAIL) { esffile_open = MB_NO; fprintf(stderr, "\nUnable to allocate memory for edits in esf file %s\n", esf.esffile); } /* reset message */ fprintf(stderr, "%d old edits sorted...\n",esf.nedit); } /* read */ done = MB_NO; start = 0; nrec = 0; fprintf(stderr, "Processing data...\n"); while (done == MB_NO) { if (verbose > 1) fprintf(stderr,"\n"); /* read next record */ error = MB_ERROR_NO_ERROR; status = mb_get(verbose, mbio_ptr,&kind,&pingsread, ping[nrec].time_i,&ping[nrec].time_d, &ping[nrec].navlon,&ping[nrec].navlat, &ping[nrec].speed,&ping[nrec].heading, &distance,&altitude,&sonardepth, &ping[nrec].beams_bath,&beams_amp,&pixels_ss, ping[nrec].beamflag,ping[nrec].bath,amp, ping[nrec].bathacrosstrack,ping[nrec].bathalongtrack, ss,ssacrosstrack,ssalongtrack, comment, &error); if (verbose >= 2) { fprintf(stderr,"\ndbg2 current data status:\n"); fprintf(stderr,"dbg2 kind: %d\n",kind); fprintf(stderr,"dbg2 status: %d\n",status); fprintf(stderr,"dbg2 ndata: %d\n",ndata); fprintf(stderr,"dbg2 nrec: %d\n",nrec); fprintf(stderr,"dbg2 nflagesf: %d\n",nflagesf); fprintf(stderr,"dbg2 nunflagesf: %d\n",nunflagesf); fprintf(stderr,"dbg2 nzeroesf: %d\n",nzeroesf); fprintf(stderr,"dbg2 nouterbeams: %d\n",nouterbeams); fprintf(stderr,"dbg2 nouterdistance: %d\n",nouterdistance); fprintf(stderr,"dbg2 nmin: %d\n",nmin); fprintf(stderr,"dbg2 ndepthrange: %d\n",ndepthrange); fprintf(stderr,"dbg2 nminrange: %d\n",nminrange); fprintf(stderr,"dbg2 nfraction: %d\n",nfraction); fprintf(stderr,"dbg2 nspeed: %d\n",nspeed); fprintf(stderr,"dbg2 nzeropos: %d\n",nzeropos); fprintf(stderr,"dbg2 nrangepos: %d\n",nrangepos); fprintf(stderr,"dbg2 ndeviation: %d\n",ndeviation); fprintf(stderr,"dbg2 nrail: %d\n",nrail); fprintf(stderr,"dbg2 nlong_across: %d\n",nlong_across); fprintf(stderr,"dbg2 nbad: %d\n",nbad); fprintf(stderr,"dbg2 npike; %d\n",nspike); fprintf(stderr,"dbg2 nflag: %d\n",nflag); fprintf(stderr,"dbg2 nunflag: %d\n",nunflag); fprintf(stderr,"dbg2 nzero: %d\n",nzero); } if (status == MB_SUCCESS && kind == MB_DATA_DATA) { /* check for multiple pings with the same time stamps */ if (nrec > 0 && ping[nrec].time_d == ping[nrec-1].time_d) { ping[nrec].multiplicity = ping[nrec-1].multiplicity + 1; } else { ping[nrec].multiplicity = 0; } /* save original beamflags */ for (i=0;i= 2) { fprintf(stderr,"\ndbg2 center beam locations:\n"); for (j=0;j MB_ERROR_NO_ERROR) { done = MB_YES; } /* process a record */ if (nrec > 0) { /* get record to process */ if (nrec >= 2) irec = 1; else if (nrec == 1) irec = 0; /* get center beam */ center = ping[irec].beams_bath / 2; /* zap outer beams by number if requested */ if (zap_beams == MB_YES) { for (i=0;i= 1) fprintf(stderr,"x: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nouterbeams++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; nouterbeams++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } for (i=0;i= 1) fprintf(stderr,"x: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], j,ping[irec].bath[j]); if (mode <= 2) { ping[irec].beamflag[j] = MB_FLAG_FLAG + MB_FLAG_FILTER; nouterbeams++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, j + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[j] = MB_FLAG_NULL; nouterbeams++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, j + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } /* zap outer beams by distance if requested */ if (zap_distance == MB_YES) { for (i=0;i= zap_distance_right)) { find_bad = MB_YES; if (verbose >= 1) fprintf(stderr,"y: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nouterdistance++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; nouterdistance++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } /* check for speed range if requested */ if(check_speed_good == MB_YES) { if (ping[irec].speed > speed_high || ping[irec].speed < speed_low) { if (verbose >= 1) fprintf(stderr,"p: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].speed); for (i=0;ieast || ping[irec].navlatnorth) { if (verbose >= 1) fprintf(stderr,"w: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %f %f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,mtodeglon,mtodeglat); for (i=0;i= 1) fprintf(stderr,"z: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %f %f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,mtodeglon,mtodeglat); for (i=0;i depth_high)) { if (verbose >= 1) fprintf(stderr,"b: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); find_bad = MB_YES; if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; ndepthrange++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; ndepthrange++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } /* check depths for minimum range if requested (replacement for Dana Yoerger test) */ if (check_range_min == MB_YES) { for (i=0;i= 1) fprintf(stderr,"k: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); find_bad = MB_YES; if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nminrange++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; nminrange++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } /* check for max heading rate if requested */ if (zap_max_heading_rate == MB_YES) { double dh, heading_rate; dh = (ping[irec].heading-last_heading); if(dh > 180)dh -=360; if(dh < -180)dh +=360; heading_rate = dh/(ping[irec].time_d-last_time); //printf("heading rate is: %f\n",heading_rate); last_time = ping[irec].time_d; last_heading = ping[irec].heading; for (i=0;i max_heading_rate) { if (verbose >= 1) fprintf(stderr,"r: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); find_bad = MB_YES; if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nmax_heading_rate++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; nmax_heading_rate++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } /* zap rails if requested */ if (zap_rails == MB_YES) { /* flag all beams with acrosstrack distance less than the maximum out to that beam */ lowdist = 0.0; highdist = 0.0; for (j=center;j= 1) fprintf(stderr,"q: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); find_bad = MB_YES; if (mode <= 2) { ping[irec].beamflag[j] = MB_FLAG_FLAG + MB_FLAG_FILTER; nrail++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, j + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[j] = MB_FLAG_NULL; nrail++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, j + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } else highdist = ping[irec].bathacrosstrack[j]; k = center - (j - center) - 1; if (mb_beam_ok(ping[irec].beamflag[k]) && ping[irec].bathacrosstrack[k] >= lowdist + backup_dist) { find_bad = MB_YES; if (verbose >= 1) fprintf(stderr,"q: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); if (mode <= 2) { ping[irec].beamflag[k] = MB_FLAG_FLAG + MB_FLAG_FILTER; nrail++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, k + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[k] = MB_FLAG_NULL; nrail++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, k + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } else lowdist = ping[irec].bathacrosstrack[k]; } /* printf("%d %d xtrack: %.2f lowdist=%.2lf %d\n",irec,k,ping[irec].bathacrosstrack[k], lowdist,ping[irec].beamflag[k]); */ } // if zap_rails==yes /* zap long acrosstrack if requested */ if (zap_long_across == MB_YES) { for (j=0;j max_acrosstrack) { find_bad = MB_YES; if (verbose >= 1) fprintf(stderr,"e: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i]); if (mode <= 2) { ping[irec].beamflag[j] = MB_FLAG_FLAG + MB_FLAG_FILTER; nlong_across++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, j + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[j] = MB_FLAG_NULL; nlong_across++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, j + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } /* do tests that require looping over all available beams */ if (check_fraction == MB_YES || check_deviation == MB_YES || check_spike == MB_YES || check_slope == MB_YES) { for (i=0;i= 2) { fprintf(stderr,"\ndbg2 depth statistics:\n"); fprintf(stderr,"dbg2 number: %d\n",nlist); fprintf(stderr,"dbg2 minimum depth: %f\n",list[0]); fprintf(stderr,"dbg2 median depth: %f\n",median); fprintf(stderr,"dbg2 maximum depth: %f\n",list[nlist-1]); } /* check fractional deviation from median if desired */ if (check_fraction == MB_YES && median > 0.0) { if (ping[irec].bath[i]/median < fraction_low || ping[irec].bath[i]/median > fraction_high) { if (verbose >= 1) fprintf(stderr,"f: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i],median); find_bad = MB_YES; if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nfraction++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; nfraction++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } /* check absolute deviation from median if desired */ if (check_deviation == MB_YES && median > 0.0) { if (fabs(ping[irec].bath[i] - median) > deviation_max) { if (verbose >= 1) fprintf(stderr,"a: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %8.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i],median); find_bad = MB_YES; if (mode <= 2) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; ndeviation++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { ping[irec].beamflag[i] = MB_FLAG_NULL; ndeviation++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } /* check spikes - acrosstrack */ if (check_spike == MB_YES && 0 != (spike_mode & 1) && median > 0.0 && i > 0 && i < ping[irec].beams_bath -1 && mb_beam_ok(ping[irec].beamflag[i-1]) && mb_beam_ok(ping[irec].beamflag[i+1])) { dd = sqrt((ping[irec].bathx[i-1] - ping[irec].bathx[i]) *(ping[irec].bathx[i-1] - ping[irec].bathx[i]) + (ping[irec].bathy[i-1] - ping[irec].bathy[i]) *(ping[irec].bathy[i-1] - ping[irec].bathy[i])); if (dd > distancemin * median && dd <= distancemax * median) { slope = (ping[irec].bath[i-1] - ping[irec].bath[i])/dd; dd2 = sqrt((ping[irec].bathx[i+1] - ping[irec].bathx[i]) *(ping[irec].bathx[i+1] - ping[irec].bathx[i]) + (ping[irec].bathy[i+1] - ping[irec].bathy[i]) *(ping[irec].bathy[i+1] - ping[irec].bathy[i])); if (dd2 > distancemin * median && dd2 <= distancemax * median) { slope2 = (ping[irec].bath[i] - ping[irec].bath[i+1])/dd2; if ((slope > spikemax && slope2 < -spikemax) || (slope2 > spikemax && slope < -spikemax)) { nspike++; nflag++; if (mode == MBCLEAN_FLAG_ONE || mode == MBCLEAN_FLAG_BOTH) { ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else if (mode == MBCLEAN_ZERO_ONE || mode == MBCLEAN_ZERO_BOTH) { ping[irec].beamflag[i] = MB_FLAG_NULL; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } if (verbose >= 1) { if (verbose >= 2) fprintf(stderr,"\n"); fprintf(stderr,"s: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %8.2f %6.2f %6.2f %6.2f %6.2f\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i],median,slope,slope2,dd,dd2); } } } } } /* check spikes - alongtrack */ if (check_spike == MB_YES && nrec == 3 && 0 != (spike_mode & 2) && mb_beam_ok(ping[0].beamflag[i]) && mb_beam_ok(ping[2].beamflag[i])) { dd = sqrt((ping[0].bathx[i] - ping[1].bathx[i]) *(ping[0].bathx[i] - ping[1].bathx[i]) + (ping[0].bathy[i] - ping[1].bathy[i]) *(ping[0].bathy[i] - ping[1].bathy[i])); if (dd > distancemin * median && dd <= distancemax * median) { slope = (ping[0].bath[i] - ping[1].bath[i])/dd; dd2 = sqrt((ping[2].bathx[i] - ping[1].bathx[i]) *(ping[2].bathx[i] - ping[1].bathx[i]) + (ping[2].bathy[i] - ping[1].bathy[i]) *(ping[2].bathy[i] - ping[1].bathy[i])); if (dd2 > distancemin * median && dd2 <= distancemax * median) { slope2 = (ping[1].bath[i] - ping[2].bath[i])/dd2; if ((slope > spikemax && slope2 < -spikemax) || (slope2 > spikemax && slope < -spikemax)) { nspike++; nflag++; if (mode == MBCLEAN_FLAG_ONE || mode == MBCLEAN_FLAG_BOTH) { ping[1].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; mb_ess_save(verbose, &esf, ping[1].time_d, i + ping[1].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else if (mode == MBCLEAN_ZERO_ONE || mode == MBCLEAN_ZERO_BOTH) { ping[1].beamflag[i] = MB_FLAG_NULL; mb_ess_save(verbose, &esf, ping[1].time_d, i + ping[1].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } if (verbose >= 1) { if (verbose >= 2) fprintf(stderr,"\n"); fprintf(stderr,"s: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %8.2f %6.2f %6.2f %6.2f %6.2f\n", ping[1].time_i[0], ping[1].time_i[1], ping[1].time_i[2], ping[1].time_i[3], ping[1].time_i[4], ping[1].time_i[5], ping[1].time_i[6], i,ping[1].bath[i],median,slope,slope2,dd,dd2); } } } } } /* check slopes - loop over each of the beams in the current ping */ if (check_slope == MB_YES && nrec == 3 && median > 0.0) for (j=0;j 0.0 && dd <= distancemax * median) slope = fabs((ping[j].bath[k] - ping[1].bath[i])/dd); else slope = 0.0; if (slope > slopemax && dd > distancemin * median) { find_bad = MB_YES; if (mode == MBCLEAN_FLAG_BOTH) { bad[0].flag = MB_YES; bad[0].ping = j; bad[0].beam = k; bad[0].bath = ping[j].bath[k]; bad[1].flag = MB_YES; bad[1].ping = 1; bad[1].beam = i; bad[1].bath = ping[1].bath[i]; ping[j].beamflag[k] = MB_FLAG_FLAG + MB_FLAG_FILTER; ping[1].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nbad++; nflag = nflag + 2; mb_ess_save(verbose, &esf, ping[j].time_d, k + ping[j].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); mb_ess_save(verbose, &esf, ping[1].time_d, i + ping[1].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else if (mode == MBCLEAN_FLAG_ONE) { if (fabs((double)ping[j].bath[k]-median) > fabs((double)ping[1].bath[i]-median)) { bad[0].flag = MB_YES; bad[0].ping = j; bad[0].beam = k; bad[0].bath = ping[j].bath[k]; bad[1].flag = MB_NO; ping[j].beamflag[k] = MB_FLAG_FLAG + MB_FLAG_FILTER; mb_ess_save(verbose, &esf, ping[j].time_d, k + ping[j].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { bad[0].flag = MB_YES; bad[0].ping = 1; bad[0].beam = i; bad[0].bath = ping[1].bath[i]; bad[1].flag = MB_NO; ping[1].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; mb_ess_save(verbose, &esf, ping[1].time_d, i + ping[1].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } nbad++; nflag++; } else if (mode == MBCLEAN_ZERO_BOTH) { bad[0].flag = MB_YES; bad[0].ping = j; bad[0].beam = k; bad[0].bath = ping[j].bath[k]; bad[1].flag = MB_YES; bad[1].ping = 1; bad[1].beam = i; bad[1].bath = ping[1].bath[i]; ping[j].beamflag[k] = MB_FLAG_NULL; ping[1].beamflag[i] = MB_FLAG_NULL; nbad++; nzero = nzero + 2; mb_ess_save(verbose, &esf, ping[j].time_d, k + ping[j].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); mb_ess_save(verbose, &esf, ping[1].time_d, i + ping[1].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } else if (mode == MBCLEAN_ZERO_ONE) { if (fabs((double)ping[j].bath[k]-median) > fabs((double)ping[1].bath[i]-median)) { bad[0].flag = MB_YES; bad[0].ping = j; bad[0].beam = k; bad[0].bath = ping[j].bath[k]; bad[1].flag = MB_NO; ping[j].beamflag[k] = MB_FLAG_NULL; mb_ess_save(verbose, &esf, ping[j].time_d, k + ping[j].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } else { bad[0].flag = MB_YES; bad[0].ping = 1; bad[0].beam = i; bad[0].bath = ping[1].bath[i]; bad[1].flag = MB_NO; ping[1].beamflag[i] = MB_FLAG_NULL; mb_ess_save(verbose, &esf, ping[1].time_d, i + ping[1].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } nbad++; nzero++; } } if (verbose >= 1 && slope > slopemax && dd > distancemin * median && bad[0].flag == MB_YES) { p = bad[0].ping; b = bad[0].beam; if (verbose >= 2) fprintf(stderr,"\n"); fprintf(stderr,"s: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %8.2f %6.2f %6.2f\n", ping[p].time_i[0], ping[p].time_i[1], ping[p].time_i[2], ping[p].time_i[3], ping[p].time_i[4], ping[p].time_i[5], ping[p].time_i[6], b,bad[0].bath,median,slope,dd); } if (verbose >= 1 && slope > slopemax && dd > distancemin * median && bad[1].flag == MB_YES) { p = bad[1].ping; b = bad[1].beam; if (verbose >= 2) fprintf(stderr,"\n"); fprintf(stderr,"s: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %8.2f %6.2f %6.2f\n", ping[p].time_i[0], ping[p].time_i[1], ping[p].time_i[2], ping[p].time_i[3], ping[p].time_i[4], ping[p].time_i[5], ping[p].time_i[6], b,bad[1].bath,median,slope,dd); } } } } } } } /* check for minimum number of good depths on each side of swath */ if (check_num_good_min == MB_YES && num_good_min > 0) { /* do port */ num_good = 0; for (i=0;i= 1) fprintf(stderr,"n: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %3d %3d\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i], num_good, num_good_min); ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nmin++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else if (mb_beam_ok(ping[irec].beamflag[i])) { if (verbose >= 1) fprintf(stderr,"n: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %3d %3d\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i], num_good, num_good_min); ping[irec].beamflag[i] = MB_FLAG_NULL; nmin++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } /* do starboard */ num_good = 0; for (i=center+1;i= 1) fprintf(stderr,"n: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %3d %3d\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i], num_good, num_good_min); ping[irec].beamflag[i] = MB_FLAG_FLAG + MB_FLAG_FILTER; nmin++; nflag++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else if (mb_beam_ok(ping[irec].beamflag[i])) { if (verbose >= 1) fprintf(stderr,"n: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f %3d %3d\n", ping[irec].time_i[0], ping[irec].time_i[1], ping[irec].time_i[2], ping[irec].time_i[3], ping[irec].time_i[4], ping[irec].time_i[5], ping[irec].time_i[6], i,ping[irec].bath[i], num_good, num_good_min); ping[irec].beamflag[i] = MB_FLAG_NULL; nmin++; nzero++; mb_ess_save(verbose, &esf, ping[irec].time_d, i + ping[irec].multiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } } } } /* write out edits from completed pings */ if ((status == MB_SUCCESS && nrec == 3) || done == MB_YES) { if (done == MB_YES) k = nrec; else k = 1; for (irec=0;irec= 4) status = mb_memory_list(verbose,&error); /* increment the total counting variables */ nfiletot++; ndatatot += ndata; nflagesftot += nflagesf; nunflagesftot += nunflagesf; nzeroesftot += nzeroesf; ndepthrangetot += ndepthrange; nminrangetot += nminrange; nfractiontot += nfraction; ndeviationtot += ndeviation; nouterbeamstot += nouterbeams; nouterdistancetot += nouterdistance; nrailtot += nrail; nlong_acrosstot += nlong_across; nmax_heading_ratetot += nmax_heading_rate; nmintot += nmin; nbadtot += nbad; nspiketot += nspike; nflagtot += nflag; nunflagtot += nunflag; nzerotot += nzero; /* give the statistics */ if (verbose >= 0) { fprintf(stderr,"%d bathymetry data records processed\n",ndata); if (esf.nedit > 0) { fprintf(stderr,"%d beams flagged in old esf file\n",nflagesf); fprintf(stderr,"%d beams unflagged in old esf file\n",nunflagesf); fprintf(stderr,"%d beams zeroed in old esf file\n",nzeroesf); } fprintf(stderr,"%d beams zapped by beam number\n",nouterbeams); fprintf(stderr,"%d beams zapped by distance\n",nouterdistance); fprintf(stderr,"%d beams zapped for too few good beams in ping\n",nmin); fprintf(stderr,"%d beams out of acceptable depth range\n",ndepthrange); fprintf(stderr,"%d beams less than minimum range\n",nminrange); fprintf(stderr,"%d beams out of acceptable fractional depth range\n",nfraction); fprintf(stderr,"%d beams out of acceptable speed range\n",nspeed); fprintf(stderr,"%d beams have zero position (lat/lon)\n",nzeropos); fprintf(stderr,"%d beams exceed acceptable deviation from median depth\n",ndeviation); fprintf(stderr,"%d bad rail beams identified\n",nrail); fprintf(stderr,"%d long acrosstrack beams identified\n",nlong_across); fprintf(stderr,"%d max heading rate pings identified\n",nmax_heading_rate); fprintf(stderr,"%d excessive slopes identified\n",nbad); fprintf(stderr,"%d excessive spikes identified\n",nspike); fprintf(stderr,"%d beams flagged\n",nflag); fprintf(stderr,"%d beams unflagged\n",nunflag); fprintf(stderr,"%d beams zeroed\n",nzero); } } /* figure out whether and what to read next */ if (read_datalist == MB_YES) { if ((status = mb_datalist_read(verbose,datalist, swathfile,&format,&file_weight,&error)) == MB_SUCCESS) read_data = MB_YES; else read_data = MB_NO; } else { read_data = MB_NO; } /* end loop over files in list */ } if (read_datalist == MB_YES) mb_datalist_close(verbose,&datalist,&error); /* give the total statistics */ if (verbose >= 0) { fprintf(stderr,"\nMBclean Processing Totals:\n"); fprintf(stderr,"-------------------------\n"); fprintf(stderr,"%d total swath data files processed\n",nfiletot); fprintf(stderr,"%d total bathymetry data records processed\n",ndatatot); fprintf(stderr,"%d total beams flagged in old esf files\n",nflagesftot); fprintf(stderr,"%d total beams unflagged in old esf files\n",nunflagesftot); fprintf(stderr,"%d total beams zeroed in old esf files\n",nzeroesftot); fprintf(stderr,"%d total beams zapped by beam number\n",nouterbeamstot); fprintf(stderr,"%d total beams zapped by distance\n",nouterdistancetot); fprintf(stderr,"%d total beams zapped for too few good beams in ping\n",nmintot); fprintf(stderr,"%d total beams out of acceptable depth range\n",ndepthrangetot); fprintf(stderr,"%d total beams less than minimum range\n",nminrangetot); fprintf(stderr,"%d total beams out of acceptable fractional depth range\n",nfractiontot); fprintf(stderr,"%d total beams out of acceptable speed range\n",nspeedtot); fprintf(stderr,"%d total beams zero position (lat/lon)\n",nzeropostot); fprintf(stderr,"%d total beams exceed acceptable deviation from median depth\n",ndeviationtot); fprintf(stderr,"%d total bad rail beams identified\n",nrailtot); fprintf(stderr,"%d total long acrosstrack beams identified\n",nlong_acrosstot); fprintf(stderr,"%d total max heading rate beams identified\n",nmax_heading_ratetot); fprintf(stderr,"%d total excessive spikes identified\n",nspiketot); fprintf(stderr,"%d total excessive slopes identified\n",nbadtot); fprintf(stderr,"%d total beams flagged\n",nflagtot); fprintf(stderr,"%d total beams unflagged\n",nunflagtot); fprintf(stderr,"%d total beams zeroed\n",nzerotot); } /* set program status */ status = MB_SUCCESS; /* check memory */ if (verbose >= 4) status = mb_memory_list(verbose,&error); /* print output debug statements */ if (verbose >= 2) { fprintf(stderr,"\ndbg2 Program <%s> completed\n", program_name); fprintf(stderr,"dbg2 Ending status:\n"); fprintf(stderr,"dbg2 status: %d\n",status); } /* end it all */ exit(error); } /*--------------------------------------------------------------------*/ int mbclean_save_edit(int verbose, FILE *sofp, double time_d, int beam, int action, int *error) { /* local variables */ char *function_name = "mbclean_save_edit"; int status = MB_SUCCESS; /* print input debug statements */ if (verbose >= 2) { fprintf(stderr,"\ndbg2 MBIO function <%s> called\n", function_name); fprintf(stderr,"dbg2 Input arguments:\n"); fprintf(stderr,"dbg2 sofp: %p\n",(void *)sofp); fprintf(stderr,"dbg2 time_d: %f\n",time_d); fprintf(stderr,"dbg2 beam: %d\n",beam); fprintf(stderr,"dbg2 action: %d\n",action); } /* write out the edit */ fprintf(stderr,"OUTPUT EDIT: %f %d %d\n",time_d,beam,action); if (sofp != NULL) { #ifdef BYTESWAPPED mb_swap_double(&time_d); beam = mb_swap_int(beam); action = mb_swap_int(action); #endif if (fwrite(&time_d, sizeof(double), 1, sofp) != 1) { status = MB_FAILURE; *error = MB_ERROR_WRITE_FAIL; } if (status == MB_SUCCESS && fwrite(&beam, sizeof(int), 1, sofp) != 1) { status = MB_FAILURE; *error = MB_ERROR_WRITE_FAIL; } if (status == MB_SUCCESS && fwrite(&action, sizeof(int), 1, sofp) != 1) { status = MB_FAILURE; *error = MB_ERROR_WRITE_FAIL; } } /* print output debug statements */ if (verbose >= 2) { fprintf(stderr,"\ndbg2 MBIO function <%s> completed\n", function_name); fprintf(stderr,"dbg2 Return values:\n"); fprintf(stderr,"dbg2 error: %d\n",*error); fprintf(stderr,"dbg2 Return status:\n"); fprintf(stderr,"dbg2 status: %d\n",status); } /* return */ return(status); } /*--------------------------------------------------------------------*/