reSortOMG

Description

reSortOMG is a utility designed to reorder an OMG-HDCS merged file that has profiles out of chronological or ping number sequence. This can occur due to various reasons during data acquisition or post-processing, especially with systems like KMALL where data packets might not arrive in strict order.

The tool reads the entire merged file, extracts time and ping number information for each profile, sorts this information, and then rewrites the merged file in the correct order.

Usage 

reSortOMG <input_omg_file(.merged)> [OPTIONS]

Arguments

Option Description  
<input_omg_file(.merged)> Required. The path to the input OMG-HDCS merged file. This file will not be modified directly; a new sorted file will be created.  
-AUV_draft (Not implemented in the provided code, but present in USAGE) This option likely has to do with AUV-specific draft calculations or handling but its effect on sorting is not shown.  
-v Enable verbose output.  

How It Works

  1. Input Reading: Opens the input merged file for reading.
  2. Summary Header Reading: Reads the summary header to get the total number of profiles.
  3. Index Creation:
    • Allocates memory for an array of pingindex structures, one for each profile.
    • Iterates through each profile in the original merged file.
    • For each profile, it reads the profile.pingNo and profile.timeOffset and stores them along with the original profile’s index (origpingnum) into the pingindex array.
  4. Order Check: During the index creation, it also checks if there are any profiles where profile.timeOffset is less than the last_timeOffset, indicating out-of-order data.
  5. Sorting: If out-of-order profiles are detected (nobackward > 0):
    • It performs a bubble sort (or similar comparison sort) on the pingindex array based on the timeOffset field. This ensures that the pingindex array now contains the original profile numbers in chronological order.
    • It reports the number of passes and swaps made during the sort to a .sort.stats file.
  6. Output File Creation:
    • A new output file is created with the name input_omg_file.sorted.
    • The summary header from the original file is dumped to the new sorted file.
    • It then iterates through the sorted pingindex array. For each entry in this array, it reads the corresponding original profile and its raw beams from the input file (using pI[i].origpingnum) and writes them to the new .sorted file.
  7. No Sort Scenario: If no backward time steps are detected, it prints a message indicating that it’s not bothering to write out a sorted file.
  8. Cleanup: Closes all open files and frees allocated memory.

Output Files

  • <input_omg_file_prefix>.sorted: A new OMG-HDCS merged file with profiles sorted chronologically.
  • <input_omg_file_prefix>.sort.stats: An ASCII file containing statistics about the sorting process.

Dependencies

  • OMG_HDCS_jversion.h: For OMG-HDCS data structures.
  • support.h: For general utility functions and error handling.

Notes

Sorting merged files chronologically is crucial for ensuring proper processing by other tools that rely on sequential data (e.g., motion compensation, tide correction, or data cleaning algorithms that look at adjacent pings). This tool provides a robust way to correct out-of-order data, particularly from newer data acquisition systems. The tool creates a new file, ensuring the integrity of the original.