The guide describes the process of taking raw .XTF files logged in Isis, adjusting the imagery using slant range correction and also using some of the image processing tools available in Isis. Then producing a merged image in TritonMap. Finally the export of that image to a GeoTIFF file.
The guide may be read as a whole from start to finish or use the following links to jump to a particular topic.
Isis can store the all the settings used and will keep those settings until reset, when starting a new project it is a very good idea to begin with Isis in its default condition.
Start Isis and click Configuration>Reset to factory config:
You will be asked to confirm,
Hit OK
Hit OK again, and Isis will re-start.
When the main screen has returned hit the green arrow to select a file for playback:
The standard Windows open file dialog, select a file and hit Open
Isis immediately configures the screen for the type of data in the XTF file and starts playing back the file. The type of data in the sample here contains both MutliBeam data and Sidescan sonar data. We are not interested in the Multibeam data right now so close the True 3D display and the Bathymetry 2D view, and maximize Vertical Waterfall (Sidescan) window, use the X and Max buttons as shown:
Isis will display just the Sidescan waterfall window:
We can see in the example that the data are very dark, Right-Click anywhere in the main waterfall window to open the Waterfall Display dialog, we will use the Threshold slider.
Reduce the Threshold to make the image lighter:
Hit OK, the Isis waterfall display should change to a lighter image:
The data in these files have not been bottom tracked - note the red bottom track line at the center of the waterfall. The next task is to bottom track the data. The bottom track may have been done during acquisition of the data, however it is not unusual to have to re-track the bottom to create a good quality mosaic. Good bottom tracking is important for accurate Slant Correction of the data before Mosaicing.
The bottom tracking gate has a couple of settings that need to be adjusted to correctly track the bottom. The bottom track tells Isis the altitude of the towfish above the bottom and is used by the slant range correction algorithm.
At the lower right side of the Isis display find the window labeled Bottom Track Primary Towfish. Use the Method dropdown menu to select the Amplitude option. Amplitude tracking is the most common method and gives a good result for the majority of data types, there are other options also available Gradient, Manual and P&C these are covered under Advanced Bottom tracking
The first control hat needs to be set is the Holdoff:
The Holdoff setting is used to prevent the tracking gate from locking to the tail end of the sonar transmission pulse or to noise in the water column, you should take a look at all the lines in the survey and choose a value that is less than the smallest distance from the towfish to the bottom on any line in the survey, in the example the water column is very clean with no noise and so we have set the value just high enough to prevent the gate from locking to the transmission pulse.
The other main control is Level, this setting determines how large a change in signal is needed to trigger the tracking gate, moving the slider to the Right increases the required signal level:
However, if the setting is too high the gate move "deeper" into the data:
Moving the slider to the left reduces the required signal level to trigger the gate:
However, if the slider is moved too far to the left the gate may sit somewhere in the water column:
For most data sets the correct setting will be around 25% (the default) and the result should be a bottom track line that closely follows the bottom profile:
The other slider, Channel in the TVG dialog box allows us to use a different channel for bottom tracking, the starboard channel may be "cleaner" with less noise than the port channel.
Once we have a good setting we may want to save the new altitude values back into the original .XTF files. To do this check the box Save newly tracked altitude to original file.
A red flashing box warns you that you altering the data in the original .XTF file:
Once this has been done for all the files in the data set, don't forget to set the Method slider back to Off so that Isis will use the new attitude read from the file:
To turn on slant range correction Right click once more in the waterfall display to open the Waterfall display dialog:
Click OK
When the file is played back the water column has been removed (see above) - the port and starboard Sidescan channels are now continuous.
Time Varying Gain is a basic correction for the variation of sonar signal strength with time. All sonars incorporate some form of TVG that is already applied to the data before it appears in Isis, however Isis also has the ability to apply some extra TVG. In the image above notice that the data near the center (nadir) of the waterfall is darker, we may not be able to see some features in this area so we may want to try and improve things a little. In the Bottom Track Primary Towfish window click the TVG button:
The TVG window opens alongside the main waterfall window:
The settings shown work well for the data in the sample:
Custom - use the Custom settings dialog which allows us to change the shape of the applied TVG curve using either the small dialog boxes or dragging the curve with the mouse.
First return - apply the setting from the point where the bottom track has detected the bottom. (You must have performed the bottom track procedure already described).
We see a considerable improvement in the data, note however that there will always be some inconsistencies around nadir due to the stretching of the data in that area.
At this point we should save our settings, if Isis id re-started the TVG, Bottom track and other settings will be retained.
Click Configure>Save Setup...
Hit OK to save, the next time Isis starts it will return with all settings.
The settings that have been saved applied only to the line that we decided to choose as our starting point, a "typical line" from the survey. It is necessary to check that all the other lines in the survey display properly and that none have, for example, large changes in signal strength that might cause us to revise our TVG or threshold settings. We cannot adjust these settings for each line; we must come up with average settings that work best for the whole survey. In areas where there are extreme changes in Sidescan signal strength it may be necessary to break the area into different mosaics with different gain settings for each area. In the writers experience this requirement is rare.
There are two methods to process the navigation for the mosaic, one uses a built in Kalman filter the other allows the user to specify the navigation smoothing via the Isis coverage map, the following describes the second, "Coverage Map" method
The imagery is transferred from Isis to the mosaic exactly as it appears in the Isis waterfall window, whatever processing has been done is preserved in the final mosaic.
From the Isis menu choose Tools>Coverage map and Mosaic:
The coverage map and mosaic dialog opens:
Choose Full Delphmap mosaic, and uncheck the option Start Delphmap to display...
Two windows will open:
We are interested in Isis -Coverage Map for the moment. We are going to mosaic all the lines in the survey so we have to set up Isis to play back all lines one after the other.
In Isis hit the Green playback button:
And choose the first line that was recorded in the survey (note this is actual time the file was originally logged, not necessarily the time on the file as seen in explorer)
Hit Open and Isis will start playing back that file, hit the <spacebar> to pause the playback.
In Isis hit File>At end of File>Go To next file in time:
Hit the <spacebar> again to unpause and Isis will playback all the files in the folder one after the other in the order they were originally acquired. You will see the track of those lines being displayed in the Coverage Map window, when the last line has been displayed the following message will be displayed:
Hit Exit and look at the coverage Map window,
Click Zoom > Best Fit to center the lines in the window:
The display is a representation of the towfish track and heading based on the CMG (Course Made Good). There are other options to use the vehicle's or towfish heading sensor. In this image you can see that due to small jumps in navigation the heading lines are displaced in some cases.
Now click Nav>Smooth Navigation:
The Smooth Navigation window opens.
For conventional Sidescan data from a towed fish some navigation smoothing is always needed to generate a coherent image. The default 9 point boxcar filter has proved to work well in most cases, also the default speed limits seem good. You may of course alter these settings.
It has been found that with Sidescan data from modern AUVs where the navigation can be very accurate and has perhaps been processed in a navigation computer, the smoothing algorithms can induced errors, in that special case the best option is to set the number of points to smooth to 1, (no smoothing).
You may click Smooth Now to see the effect of the navigation smoothing in the coverage map window, you can also click Smooth Now more than once to get extra smoothing. However the best course of action here is to apply the minimum amount of smoothing to get a consistent track in the coverage map. Click UnSmooth to restore the raw position.
Smoothed track ready for Mosaicing. When you click Close in the Smooth Navigation dialog, the following message is displayed:
Click Yes unless you want to add more lines.
To take advantage of a new feature in this version of TargetPro that improves the accuracy and co-registration of imagery and contact positions you must Save the smoothed coverage map points to an ASCII text file:
When TargetPro is later used to acquire full-resolution Targets from the Isis waterfall they will then use the same navigation used to create the mosaic, for details on this important update to TargetPro see this document.
Return to the Delph Mosaic and DTM dialog box and click Set Projection and Bounding Box:
The Map and Projections dialog is displayed:
By default we assume that the navigation data are in Lat/Long related to the WGS84 datum, then the Mosaicing engine will read the navigation, automatically selecting the correct UTM Grid Zone.
If the navigation data are in some other coordinate system you will need to setup the correct parameters using the Change buttons both for the Input Projection (the coordinate system used in the .XTF files) and for the Output Projection (the coordinate system for your project).
NOTE: You must visit the Map and Projection dialog at least once for any project. If you do not, the projection information will not be stored in the header of the .DDS_VIF file, and TritonMap will not be able to display the image.
The default resolution for the mosaic image is 1m. For most sidescan data this is rather poor, a value of 0.25m is a good starting point:
The resolution is the size of one pixel in the final image, beware of making this value very small, increasing the resolution from 1m to 0.25m increases the size of the mosaic file by a factor of 16x - going beyond that resolution for a large area can make the resultant file very large and may be difficult to display.
Hit OK to close the Map and Projection dialog box when everything has been set.
Return to the Delph Mosaic and DTM dialog and click More Options:
The dialog expands:
Recall that in this example we are going to use the smoothed navigation from the Coverage Map, check the box Use Nav from Coverage Map.
If you want to apply a layback check Apply Layback to nav in mosaic. For details of how this option works see Layback
Also check the box Build Sidescan Mosaic:
note the message and click Start Mosaic:
If slant range correction is not turned on in Isis you will get this message:
in almost all cases you need to click Yes to turn on slant range correction for your mosaic.
The Select geocoded image filename dialog opens, you must enter a name for your mosaic, note that the file name extension is .DDS_VIF, this is the file format that is read by Delphmap.
Hit Save.
Note the messages in the Delph Mosaic and DTM dialog "Successfully started mosaic" and "Data scrolled in the waterfall...."
Shift the focus back to the main Isis window by clicking on the Isis title bar, and hit the <spacebar> again to unpause the playback.
The Mosaic window should start updating as shown while the image is being created. The Coverage map window will update with a white line showing progress:
When Isis reaches the end of the available XTF files in that folder the following dialog will appear:
Hit EXIT
Back in the Delph Mosaic and DTM dialog hit Done. This is important, until you hit Done the image file has not been closed, be SURE you hit done before proceeding.
At this time you may want to save the navigation in an ASCII text file, if you need to return to this data set you can quickly load the smoothed navigation data from that file using the Load coverage points option.
As this is a new project it is a good idea to reset to factory settings, start TritonMap and Click Settings>Reset to Factory settings:
Click OK to confirm:
When the main window returns click on Settings>All Settings:
Click the ... button to browse to the folder (Working Folder) where you saved your .DDS_VIF file after Mosaicing:
Click OK, back in the main TritonMap window click Project>Save As:
And enter a name for your project:
Hit Save
Click Project>Insert Layer(s):
If you have your .DDS_VIF files in the correct (Project) folder you should see two files that were generated during the Mosaicing process, first select the file with the .DDS_VIF extension:
Hit Open
TritonMap first asks you to confirm the name of this layer (you may change it if you wish):
Hit OK, TritonMap displays the Sidescan Sonar mosaic created earlier:
Hit File>Import Layer again and choose the other file _track.DDS_VOB:
Hit Open, after confirming the layer name, TritonMap displays the trackline information that was also generated when the mosaic was created.
Left click on the + signs in the tree view to see more information about the two layers. Note that the Mosaic image itself is an Image Layer while _track line is a Vector layer.
Right click on the image layer name to allow the image to be Hidden or Displayed:
Trackline only:
Save the project by hitting Project>Save, the next time you want to open the project, start TritonMap and hit Project>Open Project and choose the .DMP file:
It may be useful to have information about your project to go along with the files you will export, hit Project>Project Information:
TritonMap displays some projection and coordinate information, you may also want save this to an ASCII file by hitting Export to an ASCII file:
To export either of the two layers, right click on the layer name:
And choose Export As...
Note that the export format for the Image layer is GeoTIFF, and
For the Trackline the format is DXF.
The exported file will be an internally referenced GeoTIFF file with meter coordinates in whatever projection the user set up as the "Project Output" projection, see Choosing the correct projection and Datum In some cases the Projection and/or datum may not be supported by the internal GeoTIFF tags that are available, at the time of the export the user will be advised of this and the alternative TIFF format should be used. In both cases the Arc GIS World File .TFW is generated to allow the import of the image into other applications.
World file details
Here is a typical "World File" and the definitions of the various lines, it is a simple ASCII text file:
20.17541308822119
0.000000000000000
0.000000000000000
-20.17541308822119
424178.11472601280548
4313415.90726399607956
And here’s what these six values represent (the values must be in this order in the file)
20.17541308822119 The dimension of a pixel in map units in the x direction (the x-scale)
0.000000000000000 Rotation term for a row. (rarely used )
0.000000000000000 Rotation term for a column (rarely used)
-20.17541308822119 The dimension of a pixel in map units in the y direction (the y-scale)
424178.11472601280548 The x coordinate of the center of the upper-left pixel in map units.
4313415.90726399607956 The y coordinate of the center of the upper-left pixel in map units.
Note that the y-scale is the negative value of the x-scale. This is to account for the differences between the origins of the image and non-image data. Arc View’s image-to-world transformation is a six-parameter affine transformation. If you want to see the formula Arc View uses, search the on-line help index for “world files”
The exported file will be a .DXF file (AutoCAD R-1/2) format. DXF files hold no projection information; the coordinates in the file will be meters in the chosen projection. In this case the Project Information file will be essential.