/*-------------------------------------------------------------------- * The MB-system: mbpreprocess.c 1/8/2014 * $Id: mbpreprocess.c 2230 2015-02-19 00:39:00Z caress $ * * Copyright (c) 2014-2015 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. *--------------------------------------------------------------------*/ /* * MBpreprocess handles preprocessing of swath sonar data as part of setting * up an MB-System processing structure for a dataset. * * This program replaces the several format-specific preprocessing programs * found in MB-System version 5 releases with a single program for version 6. * * Author: D. W. Caress * Date: January 8, 2014 * * */ /* source file version string */ static char version_id[] = "$Id: mbpreprocess.c 2230 2015-02-19 00:39:00Z caress $"; /* standard include files */ #include #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_aux.h" /* local defines */ #define MBPREPROCESS_ALLOC_CHUNK 1000 #define MBPREPROCESS_MERGE_OFF 0 #define MBPREPROCESS_MERGE_FILE 1 #define MBPREPROCESS_MERGE_ASYNC 2 #define MBPREPROCESS_TIMESHIFT_OFF 0 #define MBPREPROCESS_TIMESHIFT_FILE 1 #define MBPREPROCESS_TIMESHIFT_CONSTANT 2 #define MBPREPROCESS_TIMESHIFT_APPLY_NONE 0x00 #define MBPREPROCESS_TIMESHIFT_APPLY_NAV 0x01 #define MBPREPROCESS_TIMESHIFT_APPLY_SENSORDEPTH 0x02 #define MBPREPROCESS_TIMESHIFT_APPLY_HEADING 0x04 #define MBPREPROCESS_TIMESHIFT_APPLY_ALTITUDE 0x08 #define MBPREPROCESS_TIMESHIFT_APPLY_ATTITUDE 0x10 #define MBPREPROCESS_TIMESHIFT_APPLY_ALL_ANCILLIARY 0x7F #define MBPREPROCESS_TIMESHIFT_APPLY_SURVEY 0x80 #define MBPREPROCESS_TIMESHIFT_APPLY_ALL 0xFF /*--------------------------------------------------------------------*/ int main (int argc, char **argv) { char program_name[] = "mbpreprocess"; char help_message[] = "mbpreprocess handles preprocessing of swath sonar data as part of setting up an MB-System processing structure for a dataset.\n"; char usage_message[] = "mbpreprocess --verbose --help --merge-nav-from-file=file"; extern char *optarg; int option_index; int errflg = 0; int c; int help = 0; /* MBIO status variables */ int status = MB_SUCCESS; int verbose = 0; int error = MB_ERROR_NO_ERROR; char *message; /* command line option definitions */ /* mbpreprocess --verbose * --help * --input=datalist * --format=format_id * --nav_file=file * --nav_file_format=format_id * --nav_async=record_kind * --sensordepth_file=file * --sensordepth_file_format=format_id * --sensordepth_async=record_kind * --heading_file=file * --heading_file_format=format_id * --heading_async=record_kind * --altitude_file=file * --altitude_file_format=format_id * --altitude_async=record_kind * --attitude_file=file * --attitude_file_format=format_id * --attitude_async=record_kind * --timeshift_file=file * --timeshift_constant=value * --timeshift_apply_nav=boolean * --timeshift_apply_sensordepth=boolean * --timeshift_apply_heading=boolean * --timeshift_apply_attitude=boolean * --timeshift_apply_all_ancilliary=boolean * --timeshift_apply_survey=boolean * --timeshift_apply_all=boolean * --sensor_offset_file=offset_file * --sonar_offsets=offset_x/offset_y/offset_z/offset_heading/offset_roll/offset_pitch * --vru_offsets=offset_x/offset_y/offset_z/offset_heading/offset_roll/offset_pitch * --navigation_offsets=offset_x/offset_y/offset_z/offset_heading/offset_roll/offset_pitch * --no_change_survey */ static struct option options[] = { {"verbose", no_argument, NULL, 0}, {"help", no_argument, NULL, 0}, {"verbose", no_argument, NULL, 0}, {"input", required_argument, NULL, 0}, {"format", required_argument, NULL, 0}, {"nav_file", required_argument, NULL, 0}, {"nav_file_format", required_argument, NULL, 0}, {"nav_async", required_argument, NULL, 0}, {"sensordepth_file", required_argument, NULL, 0}, {"sensordepth_file_format", required_argument, NULL, 0}, {"sensordepth_async", required_argument, NULL, 0}, {"heading_file", required_argument, NULL, 0}, {"heading_file_format", required_argument, NULL, 0}, {"heading_async", required_argument, NULL, 0}, {"altitude_file", required_argument, NULL, 0}, {"altitude_file_format", required_argument, NULL, 0}, {"altitude_async", required_argument, NULL, 0}, {"attitude_file", required_argument, NULL, 0}, {"attitude_file_format", required_argument, NULL, 0}, {"attitude_async", required_argument, NULL, 0}, {"timeshift_file", required_argument, NULL, 0}, {"timeshift_constant", required_argument, NULL, 0}, {"timeshift_apply_nav", no_argument, NULL, 0}, {"timeshift_apply_sensordepth", no_argument, NULL, 0}, {"timeshift_apply_heading", no_argument, NULL, 0}, {"timeshift_apply_attitude", no_argument, NULL, 0}, {"timeshift_apply_all_ancilliary", no_argument, NULL, 0}, {"timeshift_apply_survey", no_argument, NULL, 0}, {"timeshift_apply_all", no_argument, NULL, 0}, {"sensor_offset_file", required_argument, NULL, 0}, {"sonar_offsets", required_argument, NULL, 0}, {"vru_offsets", required_argument, NULL, 0}, {"navigation_offsets", required_argument, NULL, 0}, {"no_change_survey", no_argument, NULL, 0}, {NULL, 0, NULL, 0} }; /* asynchronous navigation, heading, attitude data */ int nav_mode = MBPREPROCESS_MERGE_OFF; mb_path nav_file; int nav_file_format = 0; int nav_async = MB_DATA_DATA; int nav_num = 0; int nav_alloc = 0; double *nav_time_d = NULL; double *nav_navlon = NULL; double *nav_navlat = NULL; double *nav_speed = NULL; int sensordepth_mode = MBPREPROCESS_MERGE_OFF; mb_path sensordepth_file; int sensordepth_file_format = 0; int sensordepth_async = MB_DATA_DATA; int sensordepth_num = 0; int sensordepth_alloc = 0; double *sensordepth_time_d = NULL; double *sensordepth_sensordepth = NULL; int heading_mode = MBPREPROCESS_MERGE_OFF; mb_path heading_file; int heading_file_format = 0; int heading_async = MB_DATA_DATA; int heading_num = 0; int heading_alloc = 0; double *heading_time_d = NULL; double *heading_heading = NULL; int altitude_mode = MBPREPROCESS_MERGE_OFF; mb_path altitude_file; int altitude_file_format = 0; int altitude_async = MB_DATA_DATA; int altitude_num = 0; int altitude_alloc = 0; double *altitude_time_d = NULL; double *altitude_altitude = NULL; int attitude_mode = MBPREPROCESS_MERGE_OFF; mb_path attitude_file; int attitude_file_format = 0; int attitude_async = MB_DATA_DATA; int attitude_num = 0; int attitude_alloc = 0; double *attitude_time_d = NULL; double *attitude_roll = NULL; double *attitude_pitch = NULL; double *attitude_heave = NULL; int timeshift_mode = MBPREPROCESS_TIMESHIFT_OFF; mb_u_char timeshift_apply = MBPREPROCESS_TIMESHIFT_APPLY_NONE; mb_path timeshift_file; int timeshift_format = 0; int timeshift_num = 0; int timeshift_alloc = 0; double *timeshift_time_d = NULL; double *timeshift_timeshift = NULL; double timeshift_constant = 0.0; mb_path offset_file; int sonar_offset_mode = MB_NO; double sonar_offset_x = 0.0; double sonar_offset_y = 0.0; double sonar_offset_z = 0.0; double sonar_offset_heading = 0.0; double sonar_offset_roll = 0.0; double sonar_offset_pitch = 0.0; int vru_offset_mode = MB_NO; double vru_offset_x = 0.0; double vru_offset_y = 0.0; double vru_offset_z = 0.0; double vru_offset_heading = 0.0; double vru_offset_roll = 0.0; double vru_offset_pitch = 0.0; int navigation_offset_mode = MB_NO; double navigation_offset_x = 0.0; double navigation_offset_y = 0.0; double navigation_offset_z = 0.0; double navigation_offset_heading = 0.0; double navigation_offset_roll = 0.0; double navigation_offset_pitch = 0.0; int no_change_survey = MB_NO; int timestamp_changed = MB_NO; int nav_changed = MB_NO; int heading_changed = MB_NO; int sensordepth_changed = MB_NO; int altitude_changed = MB_NO; int attitude_changed = MB_NO; /* MBIO read control parameters */ int read_datalist = MB_NO; int read_data; mb_path read_file; void *datalist; int look_processed = MB_DATALIST_LOOK_UNSET; double file_weight; int format = 0; int iformat; int oformat; 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; mb_path ifile; mb_path ofile; mb_path fileroot; int beams_bath; int beams_amp; int pixels_ss; int obeams_bath; int obeams_amp; int opixels_ss; /* MBIO read values */ void *imbio_ptr = NULL; void *ombio_ptr = NULL; void *istore_ptr = NULL; int kind; int time_i[7]; double time_d; double navlon; double navlat; double speed; double heading; double distance; double altitude; double sensordepth; double draft; double roll; double pitch; double heave; char *beamflag = NULL; double *bath = NULL; double *bathacrosstrack = NULL; double *bathalongtrack = NULL; double *amp = NULL; double *ss = NULL; double *ssacrosstrack = NULL; double *ssalongtrack = NULL; char comment[MB_COMMENT_MAXLINE]; double navlon_org; double navlat_org; double speed_org; double heading_org; double altitude_org; double sensordepth_org; double draft_org; double roll_org; double pitch_org; double heave_org; double depth_offset_use, depth_offset_org, depth_offset_change; double range, alphar, betar; double lever_x, lever_y, lever_z; double headingx, headingy, mtodeglon, mtodeglat; /* arrays for asynchronous data accessed using mb_extract_nnav() */ int nanavmax = MB_NAV_MAX; int nanav; int atime_i[7*MB_NAV_MAX]; double atime_d[MB_NAV_MAX]; double alon[MB_NAV_MAX]; double alat[MB_NAV_MAX]; double aspeed[MB_NAV_MAX]; double aheading[MB_NAV_MAX]; double asensordepth[MB_NAV_MAX]; double aroll[MB_NAV_MAX]; double apitch[MB_NAV_MAX]; double aheave[MB_NAV_MAX]; /* counts of records read and written */ int n_rf_data = 0; int n_rf_comment = 0; int n_rf_nav = 0; int n_rf_nav1 = 0; int n_rf_nav2 = 0; int n_rf_nav3 = 0; int n_rf_att = 0; int n_rf_att1 = 0; int n_rf_att2 = 0; int n_rf_att3 = 0; int n_rt_data = 0; int n_rt_comment = 0; int n_rt_nav = 0; int n_rt_nav1 = 0; int n_rt_nav2 = 0; int n_rt_nav3 = 0; int n_rt_att = 0; int n_rt_att1 = 0; int n_rt_att2 = 0; int n_rt_att3 = 0; int n_wf_data = 0; int n_wf_comment = 0; int n_wf_nav = 0; int n_wf_nav1 = 0; int n_wf_nav2 = 0; int n_wf_nav3 = 0; int n_wf_att = 0; int n_wf_att1 = 0; int n_wf_att2 = 0; int n_wf_att3 = 0; int n_wt_data = 0; int n_wt_comment = 0; int n_wt_nav = 0; int n_wt_nav1 = 0; int n_wt_nav2 = 0; int n_wt_nav3 = 0; int n_wt_att = 0; int n_wt_att1 = 0; int n_wt_att2 = 0; int n_wt_att3 = 0; int testformat; int interp_status = MB_SUCCESS; int interp_error = MB_ERROR_NO_ERROR; double timeshift; int jsurvey = 0; int jnav = 0; int jsensordepth = 0; int jheading = 0; int jaltitude = 0; int jattitude = 0; int i, j, n; /* get current default values */ status = mb_defaults(verbose,&format,&pings,&lonflip,bounds, btime_i,etime_i,&speedmin,&timegap); /* set default input to datalist.mb-1 */ strcpy (read_file, "datalist.mb-1"); /* process argument list */ while ((c = getopt_long(argc, argv, "", options, &option_index)) != -1) switch (c) { /* long options all return c=0 */ case 0: /* verbose */ if (strcmp("verbose", options[option_index].name) == 0) { verbose++; } /* help */ else if (strcmp("help", options[option_index].name) == 0) { help = MB_YES; } /*------------------------------------------------------- * Define input file and format (usually a datalist) */ /* input */ else if (strcmp("input", options[option_index].name) == 0) { strcpy(read_file, optarg); } /* format */ else if (strcmp("format", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &format); } /*------------------------------------------------------- * Define source of navigation - could be an external file * or an internal asynchronous record */ /* nav_file */ else if (strcmp("nav_file", options[option_index].name) == 0) { strcpy(nav_file, optarg); nav_mode = MBPREPROCESS_MERGE_FILE; } /* nav_file_format */ else if (strcmp("nav_file_format", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &nav_file_format); } /* nav_async */ else if (strcmp("nav_async", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &nav_async); if (n == 1) nav_mode = MBPREPROCESS_MERGE_ASYNC; } /*------------------------------------------------------- * Define source of sensordepth - could be an external file * or an internal asynchronous record */ /* sensordepth_file */ else if (strcmp("sensordepth_file", options[option_index].name) == 0) { strcpy(sensordepth_file, optarg); sensordepth_mode = MBPREPROCESS_MERGE_FILE; } /* sensordepth_file_format */ else if (strcmp("sensordepth_file_format", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &sensordepth_file_format); } /* sensordepth_async */ else if (strcmp("sensordepth_async", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &sensordepth_async); if (n == 1) sensordepth_mode = MBPREPROCESS_MERGE_ASYNC; } /*------------------------------------------------------- * Define source of heading - could be an external file * or an internal asynchronous record */ /* heading_file */ else if (strcmp("heading_file", options[option_index].name) == 0) { strcpy(heading_file, optarg); heading_mode = MBPREPROCESS_MERGE_FILE; } /* heading_file_format */ else if (strcmp("heading_file_format", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &heading_file_format); } /* heading_async */ else if (strcmp("heading_async", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &heading_async); if (n == 1) heading_mode = MBPREPROCESS_MERGE_ASYNC; } /*------------------------------------------------------- * Define source of altitude - could be an external file * or an internal asynchronous record */ /* altitude_file */ else if (strcmp("altitude_file", options[option_index].name) == 0) { strcpy(altitude_file, optarg); altitude_mode = MBPREPROCESS_MERGE_FILE; } /* altitude_file_format */ else if (strcmp("altitude_file_format", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &altitude_file_format); } /* altitude_async */ else if (strcmp("altitude_async", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &altitude_async); if (n == 1) altitude_mode = MBPREPROCESS_MERGE_ASYNC; } /*------------------------------------------------------- * Define source of attitude - could be an external file * or an internal asynchronous record */ /* attitude_file */ else if (strcmp("attitude_file", options[option_index].name) == 0) { strcpy(attitude_file, optarg); attitude_mode = MBPREPROCESS_MERGE_FILE; } /* attitude_file_format */ else if (strcmp("attitude_file_format", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &attitude_file_format); } /* attitude_async */ else if (strcmp("attitude_async", options[option_index].name) == 0) { n = sscanf(optarg, "%d", &attitude_async); if (n == 1) attitude_mode = MBPREPROCESS_MERGE_ASYNC; } /*------------------------------------------------------- * Define source of timeshift - could be an external file * or single value. Also define which data the timeshift model * will be applied to - nav, sensordepth, heading, attitude, * or all. */ /* timeshift_file */ else if (strcmp("timeshift_file", options[option_index].name) == 0) { strcpy(timeshift_file, optarg); timeshift_mode = MBPREPROCESS_TIMESHIFT_FILE; } /* timeshift_constant */ else if (strcmp("timeshift_constant", options[option_index].name) == 0) { n = sscanf(optarg, "%lf", ×hift_constant); if (n == 1) timeshift_mode = MBPREPROCESS_TIMESHIFT_CONSTANT; } /* timeshift_apply_nav */ else if (strcmp("timeshift_apply_nav", options[option_index].name) == 0) { timeshift_apply = timeshift_apply | MBPREPROCESS_TIMESHIFT_APPLY_NAV; } /* timeshift_apply_sensordepth */ else if (strcmp("timeshift_apply_sensordepth", options[option_index].name) == 0) { timeshift_apply = timeshift_apply | MBPREPROCESS_TIMESHIFT_APPLY_SENSORDEPTH; } /* timeshift_apply_heading */ else if (strcmp("timeshift_apply_heading", options[option_index].name) == 0) { timeshift_apply = timeshift_apply | MBPREPROCESS_TIMESHIFT_APPLY_HEADING; } /* timeshift_apply_attitude */ else if (strcmp("timeshift_apply_attitude", options[option_index].name) == 0) { timeshift_apply = timeshift_apply | MBPREPROCESS_TIMESHIFT_APPLY_ATTITUDE; } /* timeshift_apply_altitude */ else if (strcmp("timeshift_apply_altitude", options[option_index].name) == 0) { timeshift_apply = timeshift_apply | MBPREPROCESS_TIMESHIFT_APPLY_ATTITUDE; } /* timeshift_apply_all_ancilliary */ else if (strcmp("timeshift_apply_all_ancilliary", options[option_index].name) == 0) { timeshift_apply = MBPREPROCESS_TIMESHIFT_APPLY_ALL_ANCILLIARY; } /* timeshift_apply_survey */ else if (strcmp("timeshift_apply_survey", options[option_index].name) == 0) { timeshift_apply = MBPREPROCESS_TIMESHIFT_APPLY_SURVEY; } /* timeshift_apply_all */ else if (strcmp("timeshift_apply_all", options[option_index].name) == 0) { timeshift_apply = MBPREPROCESS_TIMESHIFT_APPLY_ALL; } /* sensor_offset_file */ else if (strcmp("sensor_offset_file", options[option_index].name) == 0) { } /* sonar_offsets */ else if (strcmp("sonar_offsets", options[option_index].name) == 0) { n = sscanf(optarg, "%lf/%lf/%lf/%lf/%lf/%lf", &sonar_offset_x,&sonar_offset_y,&sonar_offset_z, &sonar_offset_heading,&sonar_offset_roll,&sonar_offset_pitch); if (n == 6) sonar_offset_mode = MB_YES; } /* vru_offsets */ else if (strcmp("vru_offsets", options[option_index].name) == 0) { n = sscanf(optarg, "%lf/%lf/%lf/%lf/%lf/%lf", &vru_offset_x,&vru_offset_y,&vru_offset_z, &vru_offset_heading,&vru_offset_roll,&vru_offset_pitch); if (n == 6) sonar_offset_mode = MB_YES; } /* navigation_offsets */ else if (strcmp("navigation_offsets", options[option_index].name) == 0) { n = sscanf(optarg, "%lf/%lf/%lf/%lf/%lf/%lf", &navigation_offset_x,&navigation_offset_y,&navigation_offset_z, &navigation_offset_heading,&navigation_offset_roll,&navigation_offset_pitch); if (n == 6) sonar_offset_mode = MB_YES; } /* no_change_survey */ else if (strcmp("no_change_survey", options[option_index].name) == 0) { no_change_survey = MB_YES; } 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,"Source File Version %s\n",version_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",version_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 format: %d\n",format); 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 read_file: %s\n",read_file); fprintf(stderr,"dbg2 nav_mode: %d\n",nav_mode); fprintf(stderr,"dbg2 nav_file: %s\n",nav_file); fprintf(stderr,"dbg2 nav_file_format: %d\n",nav_file_format); fprintf(stderr,"dbg2 nav_async: %d\n",nav_async); fprintf(stderr,"dbg2 sensordepth_mode: %d\n",sensordepth_mode); fprintf(stderr,"dbg2 sensordepth_file: %s\n",sensordepth_file); fprintf(stderr,"dbg2 sensordepth_file_format: %d\n",sensordepth_file_format); fprintf(stderr,"dbg2 sensordepth_async: %d\n",sensordepth_async); fprintf(stderr,"dbg2 heading_mode: %d\n",heading_mode); fprintf(stderr,"dbg2 heading_file: %s\n",heading_file); fprintf(stderr,"dbg2 heading_file_format: %d\n",heading_file_format); fprintf(stderr,"dbg2 heading_async: %d\n",heading_async); fprintf(stderr,"dbg2 altitude_mode: %d\n",altitude_mode); fprintf(stderr,"dbg2 altitude_file: %s\n",altitude_file); fprintf(stderr,"dbg2 altitude_file_format: %d\n",altitude_file_format); fprintf(stderr,"dbg2 altitude_async: %d\n",altitude_async); fprintf(stderr,"dbg2 attitude_mode: %d\n",attitude_mode); fprintf(stderr,"dbg2 attitude_file: %s\n",attitude_file); fprintf(stderr,"dbg2 attitude_file_format: %d\n",attitude_file_format); fprintf(stderr,"dbg2 attitude_async: %d\n",attitude_async); fprintf(stderr,"dbg2 timeshift_mode: %d\n",timeshift_mode); fprintf(stderr,"dbg2 timeshift_file: %s\n",timeshift_file); fprintf(stderr,"dbg2 timeshift_format: %d\n",timeshift_format); fprintf(stderr,"dbg2 timeshift_apply: %x\n",timeshift_apply); fprintf(stderr,"dbg2 offset_file: %s\n",offset_file); fprintf(stderr,"dbg2 sonar_offset_mode: %d\n",sonar_offset_mode); fprintf(stderr,"dbg2 sonar_offset_x: %f\n",sonar_offset_x); fprintf(stderr,"dbg2 sonar_offset_y: %f\n",sonar_offset_y); fprintf(stderr,"dbg2 sonar_offset_z: %f\n",sonar_offset_z); fprintf(stderr,"dbg2 sonar_offset_heading: %f\n",sonar_offset_heading); fprintf(stderr,"dbg2 sonar_offset_roll: %f\n",sonar_offset_roll); fprintf(stderr,"dbg2 sonar_offset_pitch: %f\n",sonar_offset_pitch); fprintf(stderr,"dbg2 vru_offset_mode: %d\n",vru_offset_mode); fprintf(stderr,"dbg2 vru_offset_x: %f\n",vru_offset_x); fprintf(stderr,"dbg2 vru_offset_y: %f\n",vru_offset_y); fprintf(stderr,"dbg2 vru_offset_z: %f\n",vru_offset_z); fprintf(stderr,"dbg2 vru_offset_heading: %f\n",vru_offset_heading); fprintf(stderr,"dbg2 vru_offset_roll: %f\n",vru_offset_roll); fprintf(stderr,"dbg2 vru_offset_pitch: %f\n",vru_offset_pitch); fprintf(stderr,"dbg2 navigation_offset_mode: %d\n",navigation_offset_mode); fprintf(stderr,"dbg2 navigation_offset_x: %f\n",navigation_offset_x); fprintf(stderr,"dbg2 navigation_offset_y: %f\n",navigation_offset_y); fprintf(stderr,"dbg2 navigation_offset_z: %f\n",navigation_offset_z); fprintf(stderr,"dbg2 navigation_offset_heading: %f\n",navigation_offset_heading); fprintf(stderr,"dbg2 navigation_offset_roll: %f\n",navigation_offset_roll); fprintf(stderr,"dbg2 navigation_offset_pitch: %f\n",navigation_offset_pitch); fprintf(stderr,"dbg2 no_change_survey: %d\n",no_change_survey); } /* 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); } /* load ancilliary data from external files if requested */ if (nav_mode == MBPREPROCESS_MERGE_FILE) { mb_loadnavdata(verbose, nav_file, nav_file_format, lonflip, &nav_num, &nav_alloc, &nav_time_d, &nav_navlon, &nav_navlat, &nav_speed, &error); if (verbose > 0) fprintf(stderr,"%d navigation records loaded from file %s\n", nav_num, nav_file); } if (sensordepth_mode == MBPREPROCESS_MERGE_FILE) { mb_loadsensordepthdata(verbose, sensordepth_file, sensordepth_file_format, &sensordepth_num, &sensordepth_alloc, &sensordepth_time_d, &sensordepth_sensordepth, &error); if (verbose > 0) fprintf(stderr,"%d sensordepth records loaded from file %s\n", sensordepth_num, sensordepth_file); } if (heading_mode == MBPREPROCESS_MERGE_FILE) { mb_loadheadingdata(verbose, heading_file, heading_file_format, &heading_num, &heading_alloc, &heading_time_d, &heading_heading, &error); if (verbose > 0) fprintf(stderr,"%d heading records loaded from file %s\n", heading_num, heading_file); } if (altitude_mode == MBPREPROCESS_MERGE_FILE) { mb_loadaltitudedata(verbose, altitude_file, altitude_file_format, &altitude_num, &altitude_alloc, &altitude_time_d, &altitude_altitude, &error); if (verbose > 0) fprintf(stderr,"%d altitude records loaded from file %s\n", altitude_num, altitude_file); } if (attitude_mode == MBPREPROCESS_MERGE_FILE) { mb_loadattitudedata(verbose, attitude_file, attitude_file_format, &attitude_num, &attitude_alloc, &attitude_time_d, &attitude_roll, &attitude_pitch, &attitude_heave, &error); if (verbose > 0) fprintf(stderr,"%d attitude records loaded from file %s\n", heading_num, heading_file); } if (timeshift_mode == MBPREPROCESS_MERGE_FILE) { mb_loadtimeshiftdata(verbose, timeshift_file, timeshift_format, ×hift_num, ×hift_alloc, ×hift_time_d, ×hift_timeshift, &error); if (verbose > 0) fprintf(stderr,"%d timeshift records loaded from file %s\n", heading_num, heading_file); } /*-------------------------------------------------------------------*/ /* Do first pass through the data collecting ancilliary data from the desired source records */ /* 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, ifile,&iformat,&file_weight,&error)) == MB_SUCCESS) read_data = MB_YES; else read_data = MB_NO; } /* else copy single filename to be read */ else { strcpy(ifile, read_file); iformat = format; read_data = MB_YES; } /* loop over all files to be read */ while (read_data == MB_YES) { if (verbose > 0) fprintf(stderr,"\nPass 1: Opening file %s %d\n", ifile, iformat); /* initialize reading the swath file */ if ((status = mb_read_init( verbose,ifile,iformat,pings,lonflip,bounds, btime_i,etime_i,speedmin,timegap, &imbio_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",ifile); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } beamflag = NULL; bath = NULL; amp = NULL; bathacrosstrack = NULL; bathalongtrack = NULL; ss = NULL; ssacrosstrack = NULL; ssalongtrack = NULL; if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(char), (void **)&beamflag, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&bath, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_AMPLITUDE, sizeof(double), (void **)&, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&bathacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&bathalongtrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ss, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ssacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_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); } /* zero file count records */ n_rf_data = 0; n_rf_comment = 0; n_rf_nav = 0; n_rf_nav1 = 0; n_rf_nav2 = 0; n_rf_nav3 = 0; n_rf_att = 0; n_rf_att1 = 0; n_rf_att2 = 0; n_rf_att3 = 0; /* read data */ while (error <= MB_ERROR_NO_ERROR) { /* reset error */ error = MB_ERROR_NO_ERROR; /* read next data record */ status = mb_get_all(verbose,imbio_ptr,&istore_ptr,&kind, time_i,&time_d,&navlon,&navlat, &speed,&heading, &distance,&altitude,&sensordepth, &beams_bath,&beams_amp,&pixels_ss, beamflag,bath,amp,bathacrosstrack,bathalongtrack, ss,ssacrosstrack,ssalongtrack, comment,&error); /* some nonfatal errors do not matter */ if (error < MB_ERROR_NO_ERROR && error > MB_ERROR_UNINTELLIGIBLE) { error = MB_ERROR_NO_ERROR; status = MB_SUCCESS; } /* print debug statements */ if (verbose >= 2) { fprintf(stderr,"\ndbg2 Data record read in program <%s>\n", program_name); fprintf(stderr,"dbg2 kind: %d\n",kind); fprintf(stderr,"dbg2 error: %d\n",error); fprintf(stderr,"dbg2 status: %d\n",status); } /* count records */ if (kind == MB_DATA_DATA) { n_rf_data++; n_rt_data++; } else if (kind == MB_DATA_COMMENT) { n_rf_comment++; n_rt_comment++; } else if (kind == MB_DATA_NAV) { n_rf_nav++; n_rt_nav++; } else if (kind == MB_DATA_NAV1) { n_rf_nav1++; n_rt_nav1++; } else if (kind == MB_DATA_NAV2) { n_rf_nav2++; n_rt_nav2++; } else if (kind == MB_DATA_NAV3) { n_rf_nav3++; n_rt_nav3++; } else if (kind == MB_DATA_ATTITUDE) { n_rf_att++; n_rt_att++; } else if (kind == MB_DATA_ATTITUDE1) { n_rf_att1++; n_rt_att1++; } else if (kind == MB_DATA_ATTITUDE2) { n_rf_att2++; n_rt_att2++; } else if (kind == MB_DATA_ATTITUDE3) { n_rf_att3++; n_rt_att3++; } /* look for nav if not externally defined */ if (status == MB_SUCCESS && nav_mode == MBPREPROCESS_MERGE_ASYNC && kind == sensordepth_async) { /* extract nav data */ status = mb_extract_nnav(verbose, imbio_ptr, istore_ptr, nanavmax, &kind, &nanav, atime_i, atime_d, alon, alat, aspeed, aheading, asensordepth, aroll, apitch, aheave, &error); /* allocate memory if needed */ if (status == MB_SUCCESS && nanav > 0 && nav_num + nanav >= nav_alloc) { nav_alloc += MAX(MBPREPROCESS_ALLOC_CHUNK, nanav); status = mb_reallocd(verbose,__FILE__,__LINE__,nav_alloc*sizeof(double),(void **)&nav_time_d,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,nav_alloc*sizeof(double),(void **)&nav_navlon,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,nav_alloc*sizeof(double),(void **)&nav_navlat,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,nav_alloc*sizeof(double),(void **)&nav_speed,&error); 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); } } /* copy the nav data */ if (status == MB_SUCCESS && nanav > 0) { for (i=0;i 0.0 && alon[i] != 0.0 && alat[i] != 0.0) { nav_time_d[nav_num] = atime_d[i]; nav_navlon[nav_num] = alon[i]; nav_navlat[nav_num] = alat[i]; nav_speed[nav_num] = aspeed[i]; nav_num++; } } } } /* look for sensordepth if not externally defined */ if (status == MB_SUCCESS && sensordepth_mode == MBPREPROCESS_MERGE_ASYNC && kind == sensordepth_async) { /* extract sensordepth data */ status = mb_extract_nnav(verbose, imbio_ptr, istore_ptr, nanavmax, &kind, &nanav, atime_i, atime_d, alon, alat, aspeed, aheading, asensordepth, aroll, apitch, aheave, &error); /* allocate memory if needed */ if (status == MB_SUCCESS && nanav > 0 && sensordepth_num + nanav >= sensordepth_alloc) { sensordepth_alloc += MAX(MBPREPROCESS_ALLOC_CHUNK, nanav); status = mb_reallocd(verbose,__FILE__,__LINE__,sensordepth_alloc*sizeof(double),(void **)&sensordepth_time_d,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,sensordepth_alloc*sizeof(double),(void **)&sensordepth_sensordepth,&error); 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); } } /* copy the sensordepth data */ if (status == MB_SUCCESS && nanav > 0) { for (i=0;i 0 && heading_num + nanav >= heading_alloc) { heading_alloc += MAX(MBPREPROCESS_ALLOC_CHUNK, nanav); status = mb_reallocd(verbose,__FILE__,__LINE__,heading_alloc*sizeof(double),(void **)&heading_time_d,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,heading_alloc*sizeof(double),(void **)&heading_heading,&error); 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); } } /* copy the heading data */ if (status == MB_SUCCESS && nanav > 0) { for (i=0;i= altitude_alloc) { altitude_alloc += MBPREPROCESS_ALLOC_CHUNK; status = mb_reallocd(verbose,__FILE__,__LINE__,altitude_alloc*sizeof(double),(void **)&altitude_time_d,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,altitude_alloc*sizeof(double),(void **)&altitude_altitude,&error); 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); } } /* copy the altitude data */ if (status == MB_SUCCESS) { altitude_time_d[altitude_num] = time_d; altitude_altitude[altitude_num] = altitude; altitude_num++; } } /* look for attitude if not externally defined */ if (status == MB_SUCCESS && attitude_mode == MBPREPROCESS_MERGE_ASYNC && kind == attitude_async) { /* extract attitude data */ status = mb_extract_nnav(verbose, imbio_ptr, istore_ptr, nanavmax, &kind, &nanav, atime_i, atime_d, alon, alat, aspeed, aheading, asensordepth, aroll, apitch, aheave, &error); /* allocate memory if needed */ if (status == MB_SUCCESS && nanav > 0 && attitude_num + nanav >= attitude_alloc) { attitude_alloc += MAX(MBPREPROCESS_ALLOC_CHUNK, nanav); status = mb_reallocd(verbose,__FILE__,__LINE__,attitude_alloc*sizeof(double),(void **)&attitude_time_d,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,attitude_alloc*sizeof(double),(void **)&attitude_roll,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,attitude_alloc*sizeof(double),(void **)&attitude_pitch,&error); status = mb_reallocd(verbose,__FILE__,__LINE__,attitude_alloc*sizeof(double),(void **)&attitude_heave,&error); 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); } } /* copy the attitude data */ if (status == MB_SUCCESS && nanav > 0) { for (i=0;i 0) { fprintf(stderr,"Pass 1: Records read from input file %s\n", ifile); fprintf(stderr," %d survey records\n", n_rf_data); fprintf(stderr," %d comment records\n", n_rf_comment); fprintf(stderr," %d nav records\n", n_rf_nav); fprintf(stderr," %d nav1 records\n", n_rf_nav1); fprintf(stderr," %d nav2 records\n", n_rf_nav2); fprintf(stderr," %d nav3 records\n", n_rf_nav3); fprintf(stderr," %d att records\n", n_rf_att); fprintf(stderr," %d att1 records\n", n_rf_att1); fprintf(stderr," %d att2 records\n", n_rf_att2); fprintf(stderr," %d att3 records\n", n_rf_att3); } /* close the swath file */ status = mb_close(verbose,&imbio_ptr,&error); /* figure out whether and what to read next */ if (read_datalist == MB_YES) { if ((status = mb_datalist_read(verbose,datalist, ifile,&iformat,&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); /* output data counts */ if (verbose > 0) { fprintf(stderr,"\n-----------------------------------------------\n"); fprintf(stderr,"Pass 1: Total records read from all input files:\n"); fprintf(stderr," %d survey records\n", n_rt_data); fprintf(stderr," %d comment records\n", n_rt_comment); fprintf(stderr," %d nav records\n", n_rt_nav); fprintf(stderr," %d nav1 records\n", n_rt_nav1); fprintf(stderr," %d nav2 records\n", n_rt_nav2); fprintf(stderr," %d nav3 records\n", n_rt_nav3); fprintf(stderr," %d att records\n", n_rt_att); fprintf(stderr," %d att1 records\n", n_rt_att1); fprintf(stderr," %d att2 records\n", n_rt_att2); fprintf(stderr," %d att3 records\n", n_rt_att3); fprintf(stderr,"Pass 1: Asynchronous data available for merging:\n"); fprintf(stderr," %d navigation data (mode:%d)\n", nav_num, nav_mode); fprintf(stderr," %d sensordepth data (mode:%d)\n", sensordepth_num, sensordepth_mode); fprintf(stderr," %d heading data (mode:%d)\n", heading_num, heading_mode); fprintf(stderr," %d altitude data (mode:%d)\n", altitude_num, altitude_mode); fprintf(stderr," %d attitude data (mode:%d)\n", attitude_num, attitude_mode); fprintf(stderr," %d timeshift data (mode:%d)\n", timeshift_num, timeshift_mode); fprintf(stderr,"-----------------------------------------------\n"); } /* end first pass through data */ /*-------------------------------------------------------------------*/ /* Apply any specified timeshift to the chosen data */ if (timeshift_mode != MBPREPROCESS_TIMESHIFT_OFF) { /* if no affected data have been specified apply timeshift to all */ if (timeshift_apply == MBPREPROCESS_TIMESHIFT_APPLY_NONE) timeshift_apply = MBPREPROCESS_TIMESHIFT_APPLY_ALL_ANCILLIARY; /* apply timeshift to nav data */ if (timeshift_apply & MBPREPROCESS_TIMESHIFT_APPLY_NAV) { if (timeshift_mode == MBPREPROCESS_TIMESHIFT_FILE) { j = 0; for (i=0;i Terminated\n", program_name); exit(error); } if ((status = mb_datalist_read(verbose,datalist, ifile,&iformat,&file_weight,&error)) == MB_SUCCESS) read_data = MB_YES; else read_data = MB_NO; } /* else copy single filename to be read */ else { strcpy(ifile, read_file); iformat = format; read_data = MB_YES; } /* loop over all files to be read */ while (read_data == MB_YES) { /* get output format - in some cases this may be a * different, generally extended format * more suitable for processing than the original */ if (iformat == MBF_EMOLDRAW || iformat == MBF_EM12IFRM || iformat == MBF_EM12DARW || iformat == MBF_EM300RAW || iformat == MBF_EM300MBA) oformat = MBF_EM300MBA; else if (iformat == MBF_EM710RAW || iformat == MBF_EM710MBA) oformat = MBF_EM710MBA; else oformat = iformat; /* figure out the output file name */ status = mb_get_format(verbose, ifile, fileroot, &testformat, &error); sprintf(ofile, "%s.mb%d", fileroot, oformat); if (strcmp(ifile,ofile) == 0) sprintf(ofile, "%sr.mb%d", fileroot, oformat); if (verbose > 0) fprintf(stderr,"\nPass 2: Opening input file: %s %d\n", ifile, iformat); /* initialize reading the input file */ if ((status = mb_read_init( verbose,ifile,iformat,pings,lonflip,bounds, btime_i,etime_i,speedmin,timegap, &imbio_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",ifile); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } if (verbose > 0) fprintf(stderr,"Pass 2: Opening output file: %s %d\n", ofile, oformat); /* initialize writing the output swath file */ if ((status = mb_write_init( verbose,ofile,oformat,&ombio_ptr, &obeams_bath,&obeams_amp,&opixels_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 writing\n",ofile); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } beamflag = NULL; bath = NULL; amp = NULL; bathacrosstrack = NULL; bathalongtrack = NULL; ss = NULL; ssacrosstrack = NULL; ssalongtrack = NULL; if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(char), (void **)&beamflag, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&bath, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_AMPLITUDE, sizeof(double), (void **)&, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&bathacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_BATHYMETRY, sizeof(double), (void **)&bathalongtrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ss, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_ptr, MB_MEM_TYPE_SIDESCAN, sizeof(double), (void **)&ssacrosstrack, &error); if (error == MB_ERROR_NO_ERROR) status = mb_register_array(verbose, imbio_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); } /* zero file count records */ n_rf_data = 0; n_rf_comment = 0; n_rf_nav = 0; n_rf_nav1 = 0; n_rf_nav2 = 0; n_rf_nav3 = 0; n_rf_att = 0; n_rf_att1 = 0; n_rf_att2 = 0; n_rf_att3 = 0; n_wf_data = 0; n_wf_comment = 0; n_wf_nav = 0; n_wf_nav1 = 0; n_wf_nav2 = 0; n_wf_nav3 = 0; n_wf_att = 0; n_wf_att1 = 0; n_wf_att2 = 0; n_wf_att3 = 0; /* ------------------------------- */ /* write comments to output file */ /* ------------------------------- */ /* start read+process,+output loop */ while (error <= MB_ERROR_NO_ERROR) { /* reset error */ status = MB_SUCCESS; error = MB_ERROR_NO_ERROR; /* read next data record */ status = mb_get_all(verbose,imbio_ptr,&istore_ptr,&kind, time_i,&time_d,&navlon_org,&navlat_org, &speed_org,&heading_org, &distance,&altitude_org,&sensordepth_org, &beams_bath,&beams_amp,&pixels_ss, beamflag,bath,amp,bathacrosstrack,bathalongtrack, ss,ssacrosstrack,ssalongtrack, comment,&error); /* some nonfatal errors do not matter */ if (error < MB_ERROR_NO_ERROR && error > MB_ERROR_UNINTELLIGIBLE) { error = MB_ERROR_NO_ERROR; status = MB_SUCCESS; } /* count records */ if (kind == MB_DATA_DATA) { n_rf_data++; n_rt_data++; } else if (kind == MB_DATA_COMMENT) { n_rf_comment++; n_rt_comment++; } else if (kind == MB_DATA_NAV) { n_rf_nav++; n_rt_nav++; } else if (kind == MB_DATA_NAV1) { n_rf_nav1++; n_rt_nav1++; } else if (kind == MB_DATA_NAV2) { n_rf_nav2++; n_rt_nav2++; } else if (kind == MB_DATA_NAV3) { n_rf_nav3++; n_rt_nav3++; } else if (kind == MB_DATA_ATTITUDE) { n_rf_att++; n_rt_att++; } else if (kind == MB_DATA_ATTITUDE1) { n_rf_att1++; n_rt_att1++; } else if (kind == MB_DATA_ATTITUDE2) { n_rf_att2++; n_rt_att2++; } else if (kind == MB_DATA_ATTITUDE3) { n_rf_att3++; n_rt_att3++; } timestamp_changed = MB_NO; nav_changed = MB_NO; heading_changed = MB_NO; sensordepth_changed = MB_NO; attitude_changed = MB_NO; /* apply preprocessing to survey data records */ if (status == MB_SUCCESS && (kind == MB_DATA_DATA || kind == MB_DATA_SUBBOTTOM_MCS || kind == MB_DATA_SUBBOTTOM_CNTRBEAM || kind == MB_DATA_SUBBOTTOM_SUBBOTTOM || kind == MB_DATA_SIDESCAN2 || kind == MB_DATA_SIDESCAN3 || kind == MB_DATA_WATER_COLUMN)) { /* call mb_extract_nav to get attitude */ status = mb_extract_nav(verbose, imbio_ptr, istore_ptr, &kind, time_i, &time_d, &navlon_org, &navlat_org, &speed_org, &heading_org, &draft_org, &roll_org, &pitch_org, &heave_org, &error); /* call mb_extract_altitude to get altitude */ status = mb_extract_altitude(verbose, imbio_ptr, istore_ptr, &kind, &sensordepth_org, &altitude_org, &error); /* save the original values */ navlon = navlon_org; navlat = navlat_org; speed = speed_org; heading = heading_org; altitude = altitude_org; sensordepth = sensordepth_org; draft = draft_org; roll = roll_org; pitch = pitch_org; heave = heave_org; /* apply timeshift to survey data */ if (timeshift_apply & MBPREPROCESS_TIMESHIFT_APPLY_SURVEY) { if (timeshift_mode == MBPREPROCESS_TIMESHIFT_FILE) { interp_status = mb_linear_interp(verbose, timeshift_time_d-1, timeshift_timeshift-1, timeshift_num, time_d, ×hift, &jsurvey, &interp_error); time_d += timeshift; } else if (timeshift_mode == MBPREPROCESS_TIMESHIFT_CONSTANT) { time_d += timeshift_constant; } timestamp_changed = MB_YES; } /* get nav sensordepth heading attitude values for record timestamp */ if (nav_num > 0) { interp_status = mb_linear_interp_longitude(verbose, nav_time_d-1, nav_navlon-1, nav_num, time_d, &navlon, &jnav, &interp_error); interp_status = mb_linear_interp_latitude(verbose, nav_time_d-1, nav_navlat-1, nav_num, time_d, &navlat, &jnav, &interp_error); interp_status = mb_linear_interp(verbose, nav_time_d-1, nav_speed-1, nav_num, time_d, &speed, &jnav, &interp_error); nav_changed = MB_YES; } if (sensordepth_num > 0) { interp_status = mb_linear_interp(verbose, sensordepth_time_d-1, sensordepth_sensordepth-1, sensordepth_num, time_d, &sensordepth, &jsensordepth, &interp_error); sensordepth_changed = MB_YES; } if (heading_num > 0) { interp_status = mb_linear_interp_heading(verbose, heading_time_d-1, heading_heading-1, heading_num, time_d, &heading, &jheading, &interp_error); heading_changed = MB_YES; } if (altitude_num > 0) { interp_status = mb_linear_interp(verbose, altitude_time_d-1, altitude_altitude-1, altitude_num, time_d, &altitude, &jaltitude, &interp_error); altitude_changed = MB_YES; } if (attitude_num > 0) { interp_status = mb_linear_interp(verbose, attitude_time_d-1, attitude_roll-1, attitude_num, time_d, &roll, &jattitude, &interp_error); interp_status = mb_linear_interp(verbose, attitude_time_d-1, attitude_pitch-1, attitude_num, time_d, &pitch, &jattitude, &interp_error); interp_status = mb_linear_interp(verbose, attitude_time_d-1, attitude_heave-1, attitude_num, time_d, &heave, &jattitude, &interp_error); attitude_changed = MB_YES; } if (sensordepth_num > 0 || attitude_num > 0) { draft = sensordepth - heave; } /* attempt to execute a preprocess function for these data */ //status = mb_preprocess(verbose, imbio_ptr, istore_ptr, // time_d, navlon, navlat, speed, // heading, sensordepth, // roll, pitch, heave, &error); status = MB_FAILURE; /* If a predefined preprocess function does not exist for * this format then standard preprocessing will be done * 1) Replace time tag, nav, attitude * 2) if attitude values changed rotate bathymetry accordingly * 3) if any values changed reinsert the data */ if (status == MB_FAILURE) { /* reset status and error */ status = MB_SUCCESS; error = MB_ERROR_NO_ERROR; /* if sensor offsets have been defined, apply lever arm correction */ if (sonar_offset_mode == MB_YES || vru_offset_mode == MB_YES || navigation_offset_mode == MB_YES) { /* do lever arm calculation with sensor offsets */ mb_lever(verbose, sonar_offset_x, sonar_offset_y, sonar_offset_z, vru_offset_x, vru_offset_y, vru_offset_z, navigation_offset_x, navigation_offset_y, navigation_offset_z, pitch, roll, &lever_x, &lever_y, &lever_z, &error); //fprintf(stderr,"LEVER: roll:%f pitch:%f lever: %f %f %f\n", roll, pitch, lever_x, lever_y, lever_z); /* get local translation between lon lat degrees and meters */ mb_coor_scale(verbose,navlat,&mtodeglon,&mtodeglat); headingx = sin(DTR*heading); headingy = cos(DTR*heading); /* apply position offsets */ if (sonar_offset_x != 0.0 || sonar_offset_y != 0.0) { navlon += headingy * sonar_offset_x * mtodeglon + headingx * sonar_offset_y * mtodeglon; navlat+= -headingx * sonar_offset_x * mtodeglat + headingy * sonar_offset_y * mtodeglat; nav_changed = MB_YES; //fprintf(stderr,"HEADING: %f %f %f POSITION OFFSET: meters: %f %f lonlat: %f %f ", //heading, headingx, headingy, //sonar_offset_x, sonar_offset_y, //headingy * sonar_offset_x * mtodeglon + headingx * sonar_offset_y * mtodeglon, //-headingx * sonar_offset_x * mtodeglat + headingy * sonar_offset_y * mtodeglat); } if (sonar_offset_z != 0.0) { sensordepth -= sonar_offset_z; sensordepth_changed = MB_YES; //fprintf(stderr,"SENSORDEPTH OFFSET: %f ",-sonar_offset_z); } /* apply lever arm calculation */ if (lever_x != 0.0 || lever_y != 0.0) { navlon += headingy * lever_x * mtodeglon + headingx * lever_y * mtodeglon; navlat+= -headingx * lever_x * mtodeglat + headingy * lever_y * mtodeglat; nav_changed = MB_YES; //fprintf(stderr,"LEVER ARM XY OFFSET: meters: %f %f lonlat: %f %f ", //lever_x, lever_y, //headingy * lever_x * mtodeglon + headingx * lever_y * mtodeglon, //-headingx * lever_x * mtodeglat + headingy * lever_y * mtodeglat); } if (lever_z != 0.0) { sensordepth -= lever_z; sensordepth_changed = MB_YES; //fprintf(stderr,"LEVER ARM Z OFFSET: %f ",-lever_z); } //if (sonar_offset_x != 0.0 || sonar_offset_y != 0.0 || sonar_offset_z != 0.0 //|| lever_x != 0.0 || lever_y != 0.0 || lever_z != 0.0) //fprintf(stderr,"\n"); } /* if attitude changed apply rigid rotations to the bathymetry */ if (attitude_changed == MB_YES) { /* add heave and draft */ depth_offset_use = heave + draft; depth_offset_org = heave + draft_org; /* loop over the beams */ for (i=0;i= 5) { fprintf(stderr,"\ndbg5 Depth value to be calculated in program <%s>:\n",program_name); fprintf(stderr,"dbg5 kind: %d\n",kind); fprintf(stderr,"dbg5 beam: %d\n",i); fprintf(stderr,"dbg5 xtrack: %f\n",bathacrosstrack[i]); fprintf(stderr,"dbg5 ltrack: %f\n",bathalongtrack[i]); fprintf(stderr,"dbg5 depth: %f\n",bath[i]); } /* strip off heave + draft */ bath[i] -= depth_offset_org; /* get range and angles in roll-pitch frame */ range = sqrt(bath[i] * bath[i] + bathacrosstrack[i] * bathacrosstrack[i] + bathalongtrack[i] * bathalongtrack[i]); if (fabs(range) < 0.001) { alphar = 0.0; betar = 0.5 * M_PI; } else { alphar = asin(MAX(-1.0, MIN(1.0, (bathalongtrack[i] / range)))); betar = acos(MAX(-1.0, MIN(1.0, (bathacrosstrack[i] / range / cos(alphar))))); } if (bath[i] < 0.0) betar = 2.0 * M_PI - betar; /* apply roll pitch corrections */ betar += DTR * (roll - roll_org); alphar += DTR * (pitch - pitch_org); /* recalculate bathymetry */ bath[i] = range * cos(alphar) * sin(betar); bathalongtrack[i] = range * sin(alphar); bathacrosstrack[i] = range * cos(alphar) * cos(betar); /* add heave and draft back in */ bath[i] += depth_offset_use; /* output some debug messages */ if (verbose >= 5) { fprintf(stderr,"\ndbg5 Depth value calculated in program <%s>:\n",program_name); fprintf(stderr,"dbg5 kind: %d\n",kind); fprintf(stderr,"dbg5 beam: %d\n",i); fprintf(stderr,"dbg5 xtrack: %f\n",bathacrosstrack[i]); fprintf(stderr,"dbg5 ltrack: %f\n",bathalongtrack[i]); fprintf(stderr,"dbg5 depth: %f\n",bath[i]); } } } } /* recalculate bathymetry by changes to sensor depth */ else if (sensordepth_changed == MB_YES) { /* get draft change */ depth_offset_change = draft - draft_org; /* fprintf(stderr, "time:%f drafts:%f %f lever:%f depth_offset_change:%f\n", time_d, draft, draft_org, lever_heave, depth_offset_change);*/ /* loop over the beams */ for (i=0;i= 5) { fprintf(stderr,"\ndbg5 Depth value calculated in program <%s>:\n",program_name); fprintf(stderr,"dbg5 kind: %d\n",kind); fprintf(stderr,"dbg5 beam: %d\n",i); fprintf(stderr,"dbg5 xtrack: %f\n",bathacrosstrack[i]); fprintf(stderr,"dbg5 ltrack: %f\n",bathalongtrack[i]); fprintf(stderr,"dbg5 depth: %f\n",bath[i]); } } } /*fprintf(stderr, "time:%4.4d/%2.2d/%2.2d %2.2d:%2.2d:%2.2d.%6.6d draft:%f depth_offset_change:%f\n", time_i[0], time_i[1], time_i[2], time_i[3], time_i[4], time_i[5], time_i[6], draft, depth_offset_change);*/ } /* insert navigation */ if (nav_changed == MB_YES || heading_changed == MB_YES || sensordepth_changed == MB_YES || attitude_changed == MB_YES) { status = mb_insert_nav(verbose, imbio_ptr, istore_ptr, time_i, time_d, navlon, navlat, speed, heading, draft, roll, pitch, heave, &error); } /* insert altitude */ if (altitude_changed == MB_YES) { status = mb_insert_altitude(verbose, imbio_ptr, istore_ptr, sensordepth, altitude, &error); if (status == MB_FAILURE) { status = MB_SUCCESS; error = MB_ERROR_NO_ERROR; } } /* if attitude changed apply rigid rotations to the bathymetry */ if (no_change_survey == MB_NO && (attitude_changed == MB_YES || sensordepth_changed == MB_YES)) { status = mb_insert(verbose,imbio_ptr, istore_ptr, kind, time_i, time_d, navlon, navlat, speed, heading, beams_bath,beams_amp,pixels_ss, beamflag, bath, amp, bathacrosstrack, bathalongtrack, ss, ssacrosstrack, ssalongtrack, comment, &error); } } } /* write some data */ if (error == MB_ERROR_NO_ERROR) { status = mb_put_all(verbose,ombio_ptr, istore_ptr,MB_NO,kind, time_i,time_d, navlon,navlat,speed,heading, obeams_bath,obeams_amp,opixels_ss, beamflag,bath,amp,bathacrosstrack,bathalongtrack, ss,ssacrosstrack,ssalongtrack, comment,&error); if (status != MB_SUCCESS) { mb_error(verbose,error,&message); fprintf(stderr,"\nMBIO Error returned from function :\n%s\n",message); fprintf(stderr,"\nMultibeam Data Not Written To File <%s>\n",ofile); fprintf(stderr,"\nProgram <%s> Terminated\n", program_name); exit(error); } /* count records */ if (kind == MB_DATA_DATA) { n_wf_data++; n_wt_data++; } else if (kind == MB_DATA_COMMENT) { n_wf_comment++; n_wt_comment++; } else if (kind == MB_DATA_NAV) { n_wf_nav++; n_wt_nav++; } else if (kind == MB_DATA_NAV1) { n_wf_nav1++; n_wt_nav1++; } else if (kind == MB_DATA_NAV2) { n_wf_nav2++; n_wt_nav2++; } else if (kind == MB_DATA_NAV3) { n_wf_nav3++; n_wt_nav3++; } else if (kind == MB_DATA_ATTITUDE) { n_wf_att++; n_wt_att++; } else if (kind == MB_DATA_ATTITUDE1) { n_wf_att1++; n_wt_att1++; } else if (kind == MB_DATA_ATTITUDE2) { n_wf_att2++; n_wt_att2++; } else if (kind == MB_DATA_ATTITUDE3) { n_wf_att3++; n_wt_att3++; } } } /* end read+process+output data loop */ /* --------------------------------- */ /* output data counts */ if (verbose > 0) { fprintf(stderr,"Pass 2: Records read from input file %s\n", ifile); fprintf(stderr," %d survey records\n", n_rf_data); fprintf(stderr," %d comment records\n", n_rf_comment); fprintf(stderr," %d nav records\n", n_rf_nav); fprintf(stderr," %d nav1 records\n", n_rf_nav1); fprintf(stderr," %d nav2 records\n", n_rf_nav2); fprintf(stderr," %d nav3 records\n", n_rf_nav3); fprintf(stderr," %d att records\n", n_rf_att); fprintf(stderr," %d att1 records\n", n_rf_att1); fprintf(stderr," %d att2 records\n", n_rf_att2); fprintf(stderr," %d att3 records\n", n_rf_att3); fprintf(stderr,"Pass 2: Records written to output file %s\n", ofile); fprintf(stderr," %d survey records\n", n_wf_data); fprintf(stderr," %d comment records\n", n_wf_comment); fprintf(stderr," %d nav records\n", n_wf_nav); fprintf(stderr," %d nav1 records\n", n_wf_nav1); fprintf(stderr," %d nav2 records\n", n_wf_nav2); fprintf(stderr," %d nav3 records\n", n_wf_nav3); fprintf(stderr," %d att records\n", n_wf_att); fprintf(stderr," %d att1 records\n", n_wf_att1); fprintf(stderr," %d att2 records\n", n_wf_att2); fprintf(stderr," %d att3 records\n", n_wf_att3); } /* close the input swath file */ status = mb_close(verbose,&imbio_ptr,&error); /* close the output swath file */ status = mb_close(verbose,&ombio_ptr,&error); /* generate inf fnv and fbt files */ if (status == MB_SUCCESS) status = mb_make_info(verbose, MB_YES, ofile, oformat, &error); /* figure out whether and what to read next */ if (read_datalist == MB_YES) { if ((status = mb_datalist_read(verbose,datalist, ifile,&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); /* output data counts */ if (verbose > 0) { fprintf(stderr,"\nPass 2: Total records read from all input files\n"); fprintf(stderr," %d survey records\n", n_rt_data); fprintf(stderr," %d comment records\n", n_rt_comment); fprintf(stderr," %d nav records\n", n_rt_nav); fprintf(stderr," %d nav1 records\n", n_rt_nav1); fprintf(stderr," %d nav2 records\n", n_rt_nav2); fprintf(stderr," %d nav3 records\n", n_rt_nav3); fprintf(stderr," %d att records\n", n_rt_att); fprintf(stderr," %d att1 records\n", n_rt_att1); fprintf(stderr," %d att2 records\n", n_rt_att2); fprintf(stderr," %d att3 records\n", n_rt_att3); fprintf(stderr,"Pass 2: Total records written to all output files\n"); fprintf(stderr," %d survey records\n", n_wt_data); fprintf(stderr," %d comment records\n", n_wt_comment); fprintf(stderr," %d nav records\n", n_wt_nav); fprintf(stderr," %d nav1 records\n", n_wt_nav1); fprintf(stderr," %d nav2 records\n", n_wt_nav2); fprintf(stderr," %d nav3 records\n", n_wt_nav3); fprintf(stderr," %d att records\n", n_wt_att); fprintf(stderr," %d att1 records\n", n_wt_att1); fprintf(stderr," %d att2 records\n", n_wt_att2); fprintf(stderr," %d att3 records\n", n_wt_att3); } /* end second pass through data */ /*-------------------------------------------------------------------*/ /* deallocate nav, sensordepth, heading, attitude, and timeshift arrays */ if (nav_alloc > 0) { status = mb_freed(verbose,__FILE__,__LINE__,(void **)&nav_time_d,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&nav_navlon,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&nav_navlat,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&nav_speed,&error); } if (sensordepth_alloc > 0) { status = mb_freed(verbose,__FILE__,__LINE__,(void **)&sensordepth_time_d,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&sensordepth_sensordepth,&error); } if (heading_alloc > 0) { status = mb_freed(verbose,__FILE__,__LINE__,(void **)&heading_time_d,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&heading_heading,&error); } if (attitude_alloc > 0) { status = mb_freed(verbose,__FILE__,__LINE__,(void **)&attitude_time_d,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&attitude_roll,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&attitude_pitch,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)&attitude_heave,&error); } if (timeshift_alloc > 0) { status = mb_freed(verbose,__FILE__,__LINE__,(void **)×hift_time_d,&error); status = mb_freed(verbose,__FILE__,__LINE__,(void **)×hift_timeshift,&error); } /* 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); } /*--------------------------------------------------------------------*/