USGS MIPS Strips Processing Documentation

USGS MIPS Strips Processing Documentation

This is an XWindows application program that creates and executes a batch file for processing sidescan sonar images through a sequence of programs within the USGS MIPS package. The processing sequence is meant to take a sidescan sonar image/strip whose navigation file has been "cleaned up" and process it to the point where it can be used as input to SNRGEOM and then digitally mosaicked with other strips.

Batch files, such as the one generated by Strips, can also be created using a text editor; however, by using Strips the user is interactively guided step-by-step in the selection of files to be processed, programs to be run, program parameters, and specific batch file options. Once the required information is supplied by the user, Strips creates and executes a batch file for the selected image files. Once the selected images/files have been processed a new set of input images/files can easily be selected and processed using the same sequence and parameters set up during the initial pass. This interaction between the user and Strips not only allows a user to quickly and interactively create a batch file and start processing his/her data, but also allows various versions of the same sequence to be easily modified and executed (i.e., the various processing steps in the sequence are variable and easily turned on or off).

Processing in General

Within the USGS MIPS Sonar package and the Strips program there are two general image processing areas addressed. The two general categories of processing areas are radiometric and geometric corrections and are applied to sidescan sonar data to help obtain the most information possible. The radiometric processing involves shading corrections and noise removal procedures and deal with changing the Digital Number (DN ) assigned to a given pixel . The programs SNRSHADE and SHADE remove low frequency shading problems in the across-track direction. The noise removal procedure allows for the removal of speckle/high frequency noise that may appear in sonar images as either short horizontal lines or isolated pixels. The program DESTRIPE is used to remove either horizontal or vertical striping/banding that may be present.

The above combination of programs improves the overall appearance of a sidescan sonar image; in addition, the appearance of nadir can also be improved. The USGS MIPS Nadir Fix procedure was developed to subdue the blockiness and high contrast appearance of nadir relative to the rest of the sonar image. Also, if broad band striping exists at nadir, it can be minimized as well. Some or all of these radiometric corrections can be applied, but keep in mind that they do not neccessarily all need to be used on a given set of data.

The next main category of processing is geometric corrections; they are applied to sidescan sonar images to correct for geometric distortion in both the along- and across-track directions. When processing sonar images that will be geometrically projected and/or digitally mosaicked the program SLR2GR MUST be run (i.e., it is NOT optional). SLR2GR corrects for both the water column offset and slant range (across-track) geometry problems. To correct for the change in the ship's speed (along-track) and to adjust for any aspect ratio distortions between the along- and across-track directions the program DELTAV is used.

Input File Selection

The first step is to select the sonar image files that are to be processed; this must be done before a batch file can be created. The number of images/files to be processed can be from one to ten; during the initial set up phase it is best to use only one file. The images to be processed are selected using the "Select" button from the File pull-down menu, which shows a dialog box or window, allowing the user to specify/select the sonar image files to be processed. The selection of files can be accomplished in one of two ways: 1) the user can manually type in the filenames, or 2) the user can use the "Select" button to select sonar image filenames through the use of a file selection box (point and click, similar to how other USGS MIPS programs select files). The Strips procedure currently allows a maximum of 10 unsigned 8-bit or signed 16-bit sonar image files to be selected and processed at any one time.

The Strips processing procedure helps make both the program and parameter selection for the strip processing sequence more automatic and helps the user to interactively set up which programs/steps are to be included in the strip processing sequence for the given data set. Many of the required parameters for the individual programs are automatically selected for you based on the bit-type, number of samples, and pulse repetition rate of the first sidescan sonar image to be processed. The procedure sets up automatic defaults, which can be changed by the user and compares the first image/set of image information against that of the other sonar images to be processed later. Doing this ensures that all the images to be processed using the selected parameters and sequence have the same image characteristics (i.e., same number of samples, bit-type and pulse repetition rate;--- collected by the same instrument with the same settings).

The programs

The following programs and set of programs are currently available to be included or excluded from the Strips processing procedure. Each of these programs have two buttons that are side-by-side; the first is a toggle button and the second a push button.

The toggle button is used to select whether or not the given program will be part of the processing sequence. Clicking the button once will select/turn-on the given program (text on push button becomes unstipled) while clicking it a second time turns the selection off (i.e., text on push button becomes stipled and takes the program out of the processing sequence). The push button displays a dialog box that shows the selected default values for that given program and allows the user to select/enter different values for the given program.

SNRSHADE

This program applies beam-angle shading corrections and the automatically selected default values for the various parameters are:

  * ADDITIVE shading correction
  * AVERAGE for left and right normalization factors
  * MINIMUM valid DN is 1 and -32767 for unsigned byte and
    signed word images, respectively
  * MAXIMUM valid DN is 254 and 32766 for unsigned byte and
    signed word images, respectively

See SNRSHADE documentation for more details.

SHADE

This program corrects vertical shading problems and the automatically selected values for the various parameters are:

  * ADDITIVE shading correction
  * AVERAGE normalization factor
  * STARTING LINE for collecting statistics is 1
  * ENDING LINE for collecting statistics is the 
    number of lines in the file

See SHADE documentation for more details.

NOISE REMOVAL

This procedure is used to remove noise that appears in the image as short horizontal lines or isolated pixels (Monterey Bay data had this type of noise). A speckle/high frequency noise removal type procedure is used. The general sequence is:

  - apply a small high pass filter (HPF) to be used to 
    identify the high frequencies that have large DN changes
    with its neighboring pixels

  - use the HPF image with MIN and MAX values to stencil/set 
    to zero pixels in the sidescan sonar image with the large 
    DN differences 

  - use a low pass filter zeroes (LPFZ) to fill-in the holes
    created in the stenciling process

The default parameters are:

HPF
---
  * NUMBER OF LINES in high pass filter is 7
  * NUMBER OF SAMPLES in high pass filter is 1
  * valid LOW DN for high pass filter is 1 and 
    -32767 for unsigned byte and signed word 
    images, respectively

STENCIL
------
  * MIN is ???
  * MAX is ???

  Note: MIN and MAX do not currently have defaults, 
        therefore, they must be determined by the user.
        For Monterey Bay use 104 and 136, respectively.

LPFZ
----
  * NUMBER OF LINES in LPFZ filter is 7
  * NUMBER OF SAMPLES in LPFZ filter is 1
  * valid LOW DN for LPFZ filter is 1 and -32767 
    for unsigned byte and signed word images,
    respectively

SLR2GR

This program converts sonar images from a slant-range to a ground-range geometry and the automatically selected default values for the various parameters are:

  * across-track PIXEL RESOLUTION is based on the 
    pulse repetition rate of the sonar device and 
    is chosen such that the output image will have 
    1000 samples 
  * NEAR RANGE depression angle is 90.0
  * FAR RANGE depression angle is 0.5
  * left and right side water column pixel OFFSETS are 0

See SLR2GR documentation for more details.

SHADE
This Shade is identical to the one above and is included here also to allow the user to insert it either before or after SLR2GR (See previous Shade description). Depending on the data and vertical striping it may generate better results either before or after SLR2GR.

DESTRIPE

This program removes horizontal striping in an image and the automatically selected values for the various parameters are:

  * NUMBER OF LINES in low pass filter is 11
  * NUMBER OF SAMPLES in low pass filter is 101
  * valid LOW DN is 1 and -32767 for unsigned byte and 
    signed word images, respectively
  * valid HIGH DN is 254 and 32766 for unsigned byte 
    and signed word images, respectively

  * NUMBER OF LINES in high pass filter is 1
  * NUMBER OF SAMPLES in high pass filter is 101
  * valid LOW DN is 1 and -32767 for unsigned byte and
    signed word images, respectively
  * valid HIGH DN is 254 and 32766 for unsigned byte and
    signed word images, respectively

See DESTRIPE documentation for more details.

NADIR FIX

See USGS MIPS Sidescan Sonar Automatic Nadir Fix Procedure for details.

BROAD NADIR RADIOMETRIC IMPROVEMENT AND MATCHING

This is an additional destripe added to the processing sequence to minimize broad vertical band striping in the nadir area. The automatically selected default values for the various parameters are:

  * NUMBER OF LINES in low pass filter is 301 
  * NUMBER OF SAMPLES in low pass filter is 301
  * valid LOW DN is 1 and -32767 for unsigned byte and 
    signed word images, respectively
  * valid HIGH DN is 254 and 32766 for unsigned byte 
    and signed word images, respectively

  * NUMBER OF LINES in high pass filter is 301 
  * NUMBER OF SAMPLES in high pass filter is 31
  * valid LOW DN is 1 and -32767 for unsigned byte and
    signed word images, respectively
  * valid HIGH DN is 254 and 32766 for unsigned byte and
    signed word images, respectively

DELTAV
This program corrects for along-track geometric distortions in sidescan sonar images. The default pixel resolution used is that given for the across-track resolution in the program Slr2gr above. If Slr2gr is not in the selected processing sequence Strips will automatically calculate a default value. The default value will be based on the pulse repetition rate stored in the image headers and on generating an output image that has 1000 samples.
See DELTAV documentation for more details.

In general, the strip processing results using the automatically selected defaults will be acceptable for the quick-look/off the ship processing, however, they will often also be acceptable for part of the final processing sequence. The main parameter that needs to be selected and can make the difference between a shipboard versus final mosaic is the spatial resolution of the ouptut image in the program SLR2GR. Currently, the default output resolution is chosen so that the output image has 1000 samples. If a higher resolution is desired the pixel resolution parameter needed by the program SLR2GR must be modified (i.e., do not keep the default value automatically selected for you; enter the desired value).

As indicated by the arrows (between programs) on the main Strips window, the order of these programs is important. Selecting the programs Snrshade and Shade means that the program Snrshade will be run before Shade; if Snrshade and Slr2gr are selected while Shade is not means that Snrshade will be run first and Slr2gr second, while skipping the program Shade altogether.

As noted earlier, the geometric corrections in the procedure should be applied to the sonar image before being geometrically projected and/or digitally mosaicked. Therefore, the default starting sequence includes the programs SLR2GR and DELTAV whenever a new file or set of files are selected.

Batch file options

The following options may be selected from the Options pull-down menu and can be used to customize the strips processing batch file created by Strips.

Defaults
This option allows a user to reset all the currently selected parameters back to the automatically selected defaults. Currently the user may reset parameters back to standard 8-bit, standard 16-bit, or user default parameters. Standard 8-bit and 16-bit defaults refers to parameters being reset back to Strips specific defaults for 8-bit unsigned byte and 16-bit signed word images, respectively. User defaults refer to the values read from the user selected Strips processing parameter file restored from an earlier/initial pass.
Output to screen
This option allows the user to specify whether or not the current command/program being executed in the batch file should be displayed to the screen. If set, the user is shown what program in the batch file processing sequence is currently running. The default is to output to the screen.
Intermediate files
This option allows the user to specify whether or not to save the processed results from each individual program. For example, if the processing sequence is Snrshade -> Shade -> Slr2gr and this option is set, the files created from the three programs are saved. If this option is not selected, the output image files of Snrshade and Shade are automatically deleted. The default is to not save intermediate files once they are no longer needed -- this will minimize the amount of disk storage required during the processing (i.e., only the final processed results are saved).
Processing directory
This option allows the user to specify an alternate disk and/or directory for the processed results to be stored. For example, all the input files can be on a disk called WORK1 and the user wants to save the processed results and intermediate files on WORK2 because there is not enough room on WORK1. Using this option the pathname for WORK2 can be entered to allow the user to perform strip processing using the images on WORK1 and storing the intermediate and final results on WORK2. The default is to use the disk and directory that the input file is on to store the results generated by the strips processing procedure.

Creating and Executing the Batch File

Once the user has performed the following:

  * selected input image filenames

  * selected the programs to be included in the Strips 
    processing sequence

  * entered desired parameters for each program selected or 
    accepted the automatically selected default values

  * selected appropriate options

then the button labeled "Execute" can be used to tell Strips to create the batch file and start executing the individual programs on the selected input images. When this button is selected, the user is prompted to enter a name for the batch file to be created. Once entered, the batch file is created and submitted to the operating system as a batch file (it runs as a background process allowing the user to conduct other work). Note that once this batch file is created and executed, it physically exists in the directory from which Strips was run. The file can be visually inspected, printed out or executed at a later time. The batch filename extensions used by Strips are ".com" under the VMS operating system and ".csh" for UNIX.

If the user changes his or her mind and decides that they want to cancel the batch file already in execution, the following should be done to terminate the batch file:

for VMS

  - type in SHOW QUEUE

  - get the entry number for the batch file in execution

  - type in STOP/ENTRY=##

    where ## is the entry number obtained earlier

for UNIX

  - type in ps

  - get the PID (process ID) for the batch file in execution

  - type in kill ##

    where ## is the PID obtained earlier

Saving a Strips processing parameter file

Selecting the "Save params" button from the File pull-down menu allows the user to create a file that contains the options selected (programs chosen and parameters used for each program) for a particular Strips session. By saving this information to a params file, the user can rerun the exact same procedure at a later time without having to reselect all the options/parameters (to process a different set of images all that is required is that the image files to be processed be selected and the EXECUTE button pushed). If "Save params" is selected, the user is prompted for a filename in which to store this information (Strips automatically concatenates a ".params" extension to the filename entered here if one is not specified). NOTE that this file is not the batch file but is a file used specifically to set up programs and parameter information to be used in a future Strips session. This filename must be given during a different Strips session later to identify it as the file containing the desired processing sequence and parameter information (see next section).

Restoring a Strips processing parameter file

Selecting the "Restore params" button from the File pull-down menu allows the user to restore all the options and parameter information saved from a previous Strips session. Simply select the "Restore params" button, select the filename of the Strips processing parameter file previously saved (as identified in the section right above this one), select input filenames and execute the batch file. By default, the file selection box searches for files with a ".params" extension, if a file was previously saved with a different extension, the user must use the file selection box's filter option (i.e., changing the filter from "*.params" to "*.options" allows the user to select any file saved with the ".options" extension).

Exiting Strips

Clicking on the button labeled "Exit" from the File pull-down menu terminates the execution of Strips but does not affect the execution of the batch file already being executed (if any).