refoROSS

Description

refoROSS is a utility designed to convert HYPACK-formatted ROSS data (from systems like ROSS profilers or SeaBat 9001) into the OMG-HDCS (Ocean Mapping Group - Hydrographic Data Conversion System) merged file format. It parses ASCII data containing bathymetry, navigation, heading (GYR), and heave/roll/pitch (HCP) records, and then maps them to the corresponding OMG-HDCS structures.

This tool is essential for integrating ROSS data into the OMG processing pipeline, enabling further analysis and visualization with other OMG tools. It can also output a simplified “spitout” file for basic review.

Usage 

refoROSS <infile> <outfile_prefix> [-9001] [-leapyear] [-spitout <azifile>] [-v]

Arguments

| Option | Description | |—|—| | <infile> | Required. Path to the input HYPACK-formatted ROSS data file. | | <outfile_prefix> | Required. Prefix for the output OMG-HDCS files. The tool will generate: * <outfile_prefix>.merged: The main OMG-HDCS merged file. * <outfile_prefix>.nav: Binary navigation file. * <outfile_prefix>.gyro: Binary gyro (heading) attitude file. * <outfile_prefix>.orientation: Binary heave/roll/pitch attitude file. * <outfile_prefix>.fix: Binary fix data. | | -9001 | Specifies that the input data is from a SeaBat 9001 system (instead of a ROSS profiler). This changes beam configuration. | | -leapyear | Accounts for a leap year when calculating Julian Day. | | -spitout <azifile> | Creates a simplified “spitout” file (.fix) and uses an external azimuth file (azifile). | | -v | Enable verbose output. |

How It Works

  1. Initialization: Parses command-line arguments, setting input/output filenames and various flags (sonar_type, leap_flag, spitout_flag). Initializes OMG-HDCS structures (OMG_HDCS_summary_header, OMG_HDCS_profile_header, OMG_HDCS_beam, OMG_HDCS_summary_attitude, OMG_HDCS_attitude).
  2. File Opening: Opens the input HYPACK file for reading. Opens output files (.merged, .nav, .gyro, .orientation, .fix) as needed.
  3. OMG Summary Header Initialization: Initializes summary (for merged data) with fileVersion, toolType (ROSS_Profiler or Seabat9001), and numDepths.
  4. Record Processing Loop: Reads the input HYPACK file line by line:
    • Line ID Parsing: Identifies the record type by a 3-character ID (e.g., “TND”, “DEV”, “PRD”, “GYR”, “POS”, “RAW”, “ECM”, “HCP”, “SB2”, “EC1”).
    • Timestamp Parsing (“TND” record): Extracts date and time, converting it to Julian Day and a Unix timestamp (day_time).
    • Device Parameters (“PRD” record): Extracts beam across, along, and draft offsets for ROSS profiler.
    • Gyro Data (“GYR” record): Extracts heading and calls dump_GYRO() to write an OMG_HDCS_attitude record to the .gyro file.
    • Navigation Data (“RAW” record): Extracts centre_lat, centre_lon, and creates a jcu_nav_rec. Writes it to the .nav file.
    • Heave/Roll/Pitch Data (“HCP” record): Extracts heave, roll, pitch and calls dump_HRP() to write an OMG_HDCS_attitude record to the .orientation file.
    • ROSS Swath Data (“ECM” record): Extracts depth and nobeams and calls dump_ROSS_swath() to write a profile of across, along, depth data to the .merged file.
    • SeaBat 9001 Swath Data (“SB2” record): Extracts soundvel, range, codes and calls dump_9001_swath() to write a profile of across, along, depth data to the .merged file.
    • Spitout Mode (-spitout): If enabled, it writes a simplified format to the .fix file.
  5. Cleanup: Closes all open files.

Helper Functions

dump_GYRO()

Writes heading data to the .gyro file.

  • Initializes gyr_summary for the first gyro record.
  • Populates gyr_att with heading and writes it to gyrfile.

dump_HRP()

Writes heave, roll, pitch data to the .orientation file.

  • Initializes hrp_summary for the first HRP record.
  • Populates hrp_att with heave, roll, pitch and writes it to hrpfile.

dump_9001_swath()

Writes SeaBat 9001 swath data to the .merged file.

  • Initializes summary for the first swath record.
  • Populates profile with time, position, attitude (derived), and various sonar settings.
  • Populates beams with calculated acrossTrack, alongTrack, observedDepth based on range and array_angle.
  • Writes profile and beams to depfile.

dump_ROSS_swath()

Writes ROSS profiler swath data to the .merged file.

  • Initializes summary for the first swath record.
  • Populates profile with time, position, and (empty) attitude data.
  • Populates beams with acrossTrack, alongTrack, observedDepth based on extracted data.
  • Writes profile and beams to depfile.

Output Files

  • <outfile_prefix>.merged: OMG-HDCS merged file.
  • <outfile_prefix>.nav: Binary navigation file.
  • <outfile_prefix>.gyro: Binary gyro (heading) attitude file.
  • <outfile_prefix>.orientation: Binary heave/roll/pitch attitude file.
  • <outfile_prefix>.fix: Simplified output file (if -spitout).