/*-------------------------------------------------------------------- * The MB-system: mbneptune2esf.c 2004/11/11 * $Id: mbneptune2esf.c 1917 2012-01-10 19:25:33Z caress $ * * Copyright (c) 2004-2012 by * Gordon Keith * CSIRO Marine Research * Castray Esplanade * Battery Point TAS 7000 * Australia * 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. *--------------------------------------------------------------------*/ /* * MBneptune2esf reads a binstat_?.rules file generated by manually cleaning * data using the correlation plot in the binstat tool of the neptune sofware * written by Kongsberg Simrad and writes these edits in an mbsystem esf file. * The purpose of this tool is to allow data cleaning done using neptune to * be carried into the mbsystem environment - thus making neptune a more useful * tool. * * MBneptune2esf applies all the manual edits in the rules file given to those * of the input files it recognises as matching the original lines. * A line is considered to match if the line name contained in the rules file * (e.g. 0002_20000408_221415) is part of the file name of the data file * (e.g. 0002_20000408_221415.mb57). * * Swath line files should be converted to format 57 using mbcopy before * using this program, as format 56 does not have the ability to flag data * (although it can be zeroed). * * Data flagged by rules generated in binstat is not flagged by this program - * only manually flagged data is flagged. * * Author: G. J. Keith * Date: 11 November 2004 * * Acknowledgments: * This program is based on a skeleton derived from mbclean. * * $Log: mbneptune2esf.c,v $ * Revision 5.5 2008/09/11 20:20:14 caress * Checking in updates made during cruise AT15-36. * * Revision 5.4 2006/01/18 15:17:00 caress * Added stdlib.h include. * * Revision 5.3 2005/11/05 01:07:54 caress * Programs changed to register arrays through mb_register_array() rather than allocating the memory directly with mb_realloc() or mb_malloc(). * * Revision 5.2 2005/03/25 04:43:02 caress * Standardized the string lengths used for filenames and comment data. * * Revision 5.1 2004/12/18 01:38:52 caress * Working towards release 5.0.6. * * Revision 5.0 2004/12/02 06:40:49 caress * New program submitted by Gordon Keith. * * */ /* standard include files */ #include #include #include #include #include #include #include /* mbio include files */ #include "../../include/mb_status.h" #include "../../include/mb_format.h" #include "../../include/mb_define.h" #include "../../include/mb_io.h" #include "../../include/mb_swap.h" #include "../../include/mb_process.h" #include "../../include/mbsys_simrad2.h" /* length of line name nnnn_yyyymmdd_hhmmss = 20 */ #define LINE_NAME_LENGTH 20 #define LINE_NAME_BUFFER LINE_NAME_LENGTH + 1 /* use MB-System memory allocation functions */ #define USE_MB_MALLOC 1 /* list of flagged beams */ struct neptune_beam_list { int beam; struct neptune_beam_list *next; }; /* ping tree structure */ struct neptune_ping_tree { int ping; struct neptune_ping_tree *prev; struct neptune_ping_tree *next; struct neptune_beam_list *beams; }; /* line tree structure */ struct neptune_line_tree { char name[LINE_NAME_BUFFER]; struct neptune_line_tree *prev; struct neptune_line_tree *next; struct neptune_ping_tree *pings; }; /* ping structure definition */ struct mbclean_ping_struct { int time_i[7]; double time_d; 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; }; /* function prototypes */ int mbclean_save_edit(int verbose, FILE *sofp, double time_d, int beam, int action, int *error); int find_line(int verbose, char* line_name, struct neptune_line_tree **node, int create, struct neptune_line_tree **result, int *nlines, int *error); int find_ping(int verbose, int ping, struct neptune_ping_tree **node, int create, struct neptune_ping_tree **result, int *error); int line_array(struct neptune_line_tree *line, struct neptune_line_tree ***array, int *n); int print_pings(FILE *output, struct neptune_ping_tree *node); int free_pings(int verbose, struct neptune_ping_tree **node, int *error); static char rcs_id[] = "$Id: mbneptune2esf.c 1917 2012-01-10 19:25:33Z caress $"; /*--------------------------------------------------------------------*/ int main (int argc, char **argv) { char program_name[] = "mbneptune2esf"; char help_message[] = "mbneptune2esf reads a Simrad Neptune BinStat rules files and a list of MB-Systems data files\nand applies the flags in the rules file to the esf file of the coresponding line"; char usage_message[] = "mbneptune2esf [-Rrules -Fformat -Iinfile -Ooutfile -V -H]"; 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; /* MBIO read control parameters */ int read_datalist = MB_NO; char read_file[MB_PATH_MAXLINE]; char swathfile[MB_PATH_MAXLINE]; void *datalist; int look_processed = MB_DATALIST_LOOK_UNSET; double file_weight; int format; 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; struct mb_io_struct *mb_io_ptr; struct mbsys_simrad2_struct *store; struct mbsys_simrad2_ping_struct *sim_ping; int kind; struct mbclean_ping_struct cur_ping; int pingsread; int nfiletot = 0; int ndatatot = 0; int nflagtot = 0; int nzerotot = 0; int nflagesftot = 0; int nunflagesftot = 0; int nzeroesftot = 0; int ndata = 0; int nflag = 0; int nzero = 0; int nflagesf = 0; int nunflagesf = 0; int nzeroesf = 0; char comment[MB_COMMENT_MAXLINE]; int mode = 1; int action; /* rules file */ char rulesfile[MB_PATH_MAXLINE]; struct neptune_line_tree *rule_lines = NULL; int no_lines = 0; FILE *rules_fp; int rules_done; int rule_level; int usable_rule; int nscan; int nlines; int npings; int nbeams; int used; int bytes; char buffer[MB_PATH_MAXLINE]; char word[MB_PATH_MAXLINE]; char buff[MB_PATH_MAXLINE]; char beams_buff[MB_PATH_MAXLINE]; char line_name[MB_PATH_MAXLINE]; int nlen; int slen; int ping_no; int beam_no; struct neptune_line_tree **lines; struct neptune_line_tree *line; struct neptune_ping_tree *ping; struct neptune_beam_list *beam; char *buffer_ptr; int output_file_set = MB_NO; char output_file[MB_PATH_MAXLINE]; FILE *output; /* save file control variables */ int esffile_open = MB_NO; char esffile[MB_PATH_MAXLINE]; struct mb_esf_struct esf; /* processing variables */ int pingmultiplicity; double time_d_lastping; int read_data; int start, done; int i, j, k; /* get current default values */ status = mb_defaults(verbose,&format,&pings,&lonflip,bounds, btime_i,etime_i,&speedmin,&timegap); /* 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"); strcpy(rulesfile, "-"); /* process argument list */ while ((c = getopt(argc, argv, "VvHhF:f:I:i:M:m:O:o:R:r:")) != -1) switch (c) { case 'H': case 'h': help++; break; case 'V': case 'v': verbose++; break; case 'F': case 'f': sscanf (optarg,"%d", &format); flag++; break; case 'I': case 'i': sscanf (optarg,"%s", read_file); flag++; break; case 'M': case 'm': sscanf (optarg,"%d", &mode); flag++; break; case 'O': case 'o': sscanf (optarg,"%s", output_file); output_file_set = MB_YES; flag++; break; case 'R': case 'r': sscanf (optarg,"%s", rulesfile); 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); } /* 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); } /* 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); } /* read rules */ if (0 == strncmp("-",rulesfile,2)) rules_fp =stdin; else if ((rules_fp = fopen(rulesfile,"r")) == NULL) { fprintf(stderr,"\nUnable to open rules file %s\n",rulesfile); fprintf(stderr,"\nusage: %s\n", usage_message); exit(error); } rules_done = MB_NO; usable_rule = MB_NO; rule_level = 0; status = MB_SUCCESS; while (MB_NO == rules_done) { /* skip till we find a rule */ while (MB_NO == rules_done && MB_NO == usable_rule) { buffer_ptr = fgets(buffer,MB_PATH_MAXLINE,rules_fp); if (buffer_ptr != buffer) rules_done = MB_YES; else { nscan = sscanf(buffer, "%s",word); if (1 == nscan && ')' == word[0]) rule_level--; else if (1 == nscan && '(' == word[0] && ')' != word[1]) { rule_level++; if (2 == rule_level) { nscan = sscanf(buffer, "%s %s",buff,word); if (2 == nscan && 0 == strncmp(word,"LINES_PING_BEAM_RULE",20)) usable_rule = MB_YES; } } } } /* read a rule */ if (MB_NO == rules_done) { buffer_ptr = fgets(buffer,MB_PATH_MAXLINE,rules_fp); if (buffer_ptr != buffer) { rules_done = MB_YES; status = MB_FAILURE; error = MB_ERROR_EOF; } else { if (MB_SUCCESS == status && 2 != sscanf(buffer,"%s %d",word,&nlines)) status = MB_FAILURE; if (MB_SUCCESS == status && 0 != strncmp(word,"NO_OF_LINES",11)) status = MB_FAILURE; if (MB_SUCCESS == status) for(i = 0; i < nlines; i++) { if (buffer != fgets(buffer,MB_PATH_MAXLINE,rules_fp)) status = MB_FAILURE; if (MB_SUCCESS == status && 2 != sscanf(buffer,"%s '%s'",word,line_name)) status = MB_FAILURE; if (MB_SUCCESS == status && 0 != strncmp(word,"LINE_NAME",9)) status = MB_FAILURE; if (MB_SUCCESS == status) status = find_line(verbose,line_name,&rule_lines,MB_YES,&line,&no_lines,&error); if (buffer != fgets(buffer,MB_PATH_MAXLINE,rules_fp)) status = MB_FAILURE; if (MB_SUCCESS == status && 2 != sscanf(buffer,"%s %d",word,&npings)) status = MB_FAILURE; if (MB_SUCCESS == status && 0 != strncmp(word,"NO_OF_PINGS",11)) status = MB_FAILURE; if (MB_SUCCESS == status) for(j = 0; j < npings; j++) { if (buffer != fgets(buffer,MB_PATH_MAXLINE,rules_fp)) status = MB_FAILURE; if (MB_SUCCESS == status && 5 > sscanf(buffer,"%s %d %s %d %s %n", word,&ping_no,buff,&nbeams,beams_buff,&used)) status = MB_FAILURE; if (MB_SUCCESS == status && (0 != strncmp(word,"PING",4) || 0 != strncmp(buff,"NO_OF_BEAMS",11) || 0 != strncmp(beams_buff,"BEAMS",5))) status = MB_FAILURE; if (MB_SUCCESS == status) status = find_ping(verbose,ping_no,&(line->pings),MB_YES,&ping,&error); beam = ping->beams; if (NULL != beam) { while (NULL != beam->next) beam = beam->next; } if (MB_SUCCESS == status) for (k = 0; k < nbeams; k++) { if (MB_SUCCESS == status && 1 > sscanf(&buffer[used],"%d %n", &beam_no,&bytes)) status = MB_FAILURE; used += bytes; if (NULL == beam) { #ifdef USE_MB_MALLOC status = mb_mallocd(verbose,__FILE__,__LINE__,sizeof(struct neptune_beam_list),(void **)&(ping->beams),&error); #else ping->beams = malloc(sizeof(struct neptune_beam_list)); #endif beam = ping->beams; } else { #ifdef USE_MB_MALLOC status = mb_mallocd(verbose,__FILE__,__LINE__,sizeof(struct neptune_beam_list),(void **)&(beam->next),&error); #else beam->next = malloc(sizeof(struct neptune_beam_list)); #endif beam = beam->next; } beam->beam = beam_no; beam->next = NULL; } } } if (MB_FAILURE == status && 1<= verbose) { fprintf(stderr,"Failed to understand line: \n%s",buffer); } status = MB_SUCCESS; } } } /* put lines in an array */ status = mb_mallocd(verbose,__FILE__,__LINE__,no_lines * sizeof(void*),(void **)&lines,&error); i = 0; line_array(rule_lines,&lines,&i); /* output rules found */ if (MB_YES == output_file_set) { if (0 == strncmp("-",output_file,2)) output = stdout; else output = fopen(output_file, "w"); if (output != NULL) { for (i = 0; i < no_lines; i++) { fprintf(output, "%s\n", lines[i]->name); print_pings(output, lines[i]->pings); } } } /* 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) { usable_rule = MB_NO; /* check if this file matches any lines */ if (MBF_EM300RAW == format || MBF_EM300MBA == format) for (i = 0; i < no_lines; i++) { strcpy(line_name,lines[i]->name); nlen = strlen(line_name); slen = strlen(swathfile); for (j = 0 ; j <= slen-nlen; j++) if (0 == strncmp(line_name,&swathfile[j],nlen)) { usable_rule = MB_YES; line = lines[i]; j = slen; i = no_lines; } } if (MB_YES == usable_rule) { /* 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,"\nProgram <%s> Terminated\n", program_name); exit(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 (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,"\nProgram <%s> Terminated\n", program_name); exit(error); } /* initialize reading the input swath sonar file */ if ((status = mb_read_init( verbose,swathfile,format,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; nflag = 0; nzero = 0; nflagesf = 0; nunflagesf = 0; nzeroesf = 0; /* give the statistics */ if (verbose >= 0) { fprintf(stderr,"\nProcessing %s\n",swathfile); } /* allocate memory for data arrays */ cur_ping.beamflag = NULL; cur_ping.beamflagorg = NULL; cur_ping.bath = NULL; cur_ping.bathacrosstrack = NULL; cur_ping.bathalongtrack = NULL; cur_ping.bathx = NULL; cur_ping.bathy = NULL; if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(char), (void **)&cur_ping.beamflag, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(char), (void **)&cur_ping.beamflagorg, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&cur_ping.bath, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&cur_ping.bathacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&cur_ping.bathalongtrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&cur_ping.bathx, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, mbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&cur_ping.bathy, &error); amp = NULL; ss = NULL; ssacrosstrack = NULL; ssalongtrack = 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 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; time_d_lastping = 0.0; 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, cur_ping.time_i,&cur_ping.time_d, &cur_ping.navlon,&cur_ping.navlat, &cur_ping.speed,&cur_ping.heading, &distance,&altitude,&sonardepth, &cur_ping.beams_bath,&beams_amp,&pixels_ss, cur_ping.beamflag,cur_ping.bath,amp, cur_ping.bathacrosstrack,cur_ping.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 nflagesf: %d\n",nflagesf); fprintf(stderr,"dbg2 nunflagesf: %d\n",nunflagesf); fprintf(stderr,"dbg2 nzeroesf: %d\n",nzeroesf); fprintf(stderr,"dbg2 nflag: %d\n",nflag); fprintf(stderr,"dbg2 nzero: %d\n",nzero); } if (status == MB_SUCCESS && kind == MB_DATA_DATA) { /* save original beamflags */ for (i=0;istore_data; sim_ping = (struct mbsys_simrad2_ping_struct *) store->ping; /* get ping no */ ping_no = sim_ping ->png_count; /* if ping in rules get it and flag beams */ if (MB_SUCCESS == find_ping(verbose,ping_no,&line->pings,MB_NO,&ping,&error)) { beam = ping->beams; while (NULL != beam) { beam_no = beam->beam; if (mb_beam_ok(cur_ping.beamflag[beam_no])) { if (verbose >= 1) fprintf(stderr,"z: %4d %2d %2d %2.2d:%2.2d:%2.2d.%6.6d %4d %8.2f\n", cur_ping.time_i[0], cur_ping.time_i[1], cur_ping.time_i[2], cur_ping.time_i[3], cur_ping.time_i[4], cur_ping.time_i[5], cur_ping.time_i[6], i,cur_ping.bath[beam_no]); if (mode <= 2) { cur_ping.beamflag[beam_no] = MB_FLAG_FLAG + MB_FLAG_FILTER; nflag++; mb_ess_save(verbose, &esf, cur_ping.time_d, beam_no + pingmultiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_FILTER, &error); } else { cur_ping.beamflag[beam_no] = MB_FLAG_NULL; nzero++; mb_ess_save(verbose, &esf, cur_ping.time_d, beam_no + pingmultiplicity * MB_ESF_MULTIPLICITY_FACTOR, MBP_EDIT_ZERO, &error); } } beam = beam->next; } /* write out edits from completed pings */ if (status == MB_SUCCESS || done == MB_YES) { for (i=0;i MB_ERROR_NO_ERROR) { done = MB_YES; } } /* close the files */ status = mb_close(verbose,&mbio_ptr,&error); /* close edit save file */ status = mb_esf_close(verbose, &esf, &error); /* update mbprocess parameter file */ if (esffile_open == MB_YES) { /* update mbprocess parameter file */ status = mb_pr_update_format(verbose, swathfile, MB_YES, format, &error); status = mb_pr_update_edit(verbose, swathfile, MBP_EDIT_ON, esffile, &error); } /* check memory */ if (verbose >= 4) status = mb_memory_list(verbose,&error); /* increment the total counting variables */ nfiletot++; ndatatot += ndata; nflagesftot += nflagesf; nunflagesftot += nunflagesf; nzeroesftot += nzeroesf; nflagtot += nflag; 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 flagged\n",nflag); fprintf(stderr,"%d beams zeroed\n",nzero); } } /* if usable_rule */ /* 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 flagged\n",nflagtot); fprintf(stderr,"%d total beams zeroed\n",nzerotot); } /* set program status */ status = MB_SUCCESS; /* free memory associated with lines. */ for (i=0; i < no_lines; i++) { free_pings(verbose, &lines[i]->pings, &error); #ifdef USE_MB_MALLOC mb_freed(verbose,__FILE__,__LINE__,(void **) &lines[i], &error); #else free(lines[i]); #endif } /* 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: %lu\n",(size_t)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); } /*--------------------------------------------------------------------*/ int find_line(int verbose, char* line_name, struct neptune_line_tree **node, int create, struct neptune_line_tree **result, int *nlines, int *error) { int status = MB_SUCCESS; int comp; if (NULL == *node) { if (MB_NO == create) return MB_FAILURE; #ifdef USE_MB_MALLOC status = mb_mallocd(verbose,__FILE__,__LINE__,sizeof(struct neptune_line_tree), (void **)result,error); #else *result = malloc(sizeof(struct neptune_line_tree)); #endif if (MB_SUCCESS == status) { strncpy((*result)->name,line_name,LINE_NAME_LENGTH); (*result)->name[LINE_NAME_LENGTH] =0; (*result)->prev = NULL; (*result)->next = NULL; (*result)->pings = NULL; (*nlines)++; *node = *result; } return status; } comp = strncmp(line_name,(*node)->name,LINE_NAME_LENGTH); if (0 == comp) { *result = *node; return status; } if (0 > comp) return find_line(verbose, line_name, &((*node)->prev), create, result, nlines, error); return find_line(verbose, line_name, &((*node)->next), create, result, nlines, error); } /*--------------------------------------------------------------------*/ int find_ping(int verbose, int ping, struct neptune_ping_tree **node, int create, struct neptune_ping_tree **result, int *error) { int status = MB_SUCCESS; if (NULL == *node) { if (MB_NO == create) return MB_FAILURE; #ifdef USE_MB_MALLOC status = mb_mallocd(verbose,__FILE__,__LINE__,sizeof(struct neptune_ping_tree), (void **)result,error); #else *result = malloc(sizeof(struct neptune_ping_tree)); #endif if (MB_SUCCESS == status) { (*result)->ping = ping; (*result)->prev = NULL; (*result)->next = NULL; (*result)->beams = NULL; *node = *result; } return status; } if (ping == (*node)->ping) { *result = *node; return status; } if ((*node)->ping > ping) return find_ping(verbose, ping, &((*node)->prev), create, result, error); return find_ping(verbose, ping, &((*node)->next), create, result, error); } /*--------------------------------------------------------------------*/ int line_array(struct neptune_line_tree *line, struct neptune_line_tree ***array, int *n) { if (NULL == line) return MB_SUCCESS; line_array(line->prev,array,n); (*array)[(*n)++] = line; line_array(line->next,array,n); return MB_SUCCESS; } /*--------------------------------------------------------------------*/ int print_pings(FILE *output, struct neptune_ping_tree *node) { struct neptune_beam_list *beam; if (NULL == node) return MB_SUCCESS; print_pings(output, node->prev); fprintf(output, "\tPing %d beams: ", node->ping); beam = node->beams; while (NULL != beam) { fprintf(output, " %d", beam->beam); beam = beam->next; } fprintf(output, "\n"); print_pings(output, node->next); return MB_SUCCESS; } /*--------------------------------------------------------------------*/ int free_pings(int verbose, struct neptune_ping_tree **node, int *error) { struct neptune_beam_list *beam; struct neptune_beam_list *nextbeam; if (NULL == *node) return MB_SUCCESS; free_pings(verbose,&(*node)->prev,error); free_pings(verbose,&(*node)->next,error); beam = (*node)->beams; while (NULL != beam) { nextbeam = beam->next; #ifdef USE_MB_MALLOC mb_freed(verbose,__FILE__,__LINE__,(void **) &beam, error); #else free(beam); #endif beam = nextbeam; } #ifdef USE_MB_MALLOC mb_freed(verbose,__FILE__,__LINE__,(void **) node, error); #else free(*node); #endif return MB_SUCCESS; } /*--------------------------------------------------------------------*/