Using MB-System and USGS MIPS with Humminbird files

Official Firmware, Side Image Viewers, Map Overlays, 3rd Party Apps, etc..
oceanecology
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Location: Prince Rupert, BC, Canada

MB System

Post by oceanecology » Thu Mar 05, 2009 11:32 pm

Yes, I have another conversion program for MB System which is just in the testing phase. I'm hoping to post that in the next month or so.

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camalama
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Location: St. Charles, MO
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Post by camalama » Wed Mar 11, 2009 12:02 pm

I am working very hard to install per your instructions dated 2/5/09 but have run into some difficulty. When installing GMT I get the following errors and nothing is added to the GMT/bin directory.

Code: Select all

---> Begin GMT 4.4.0 installation <---

---> Run configure to create makegmt.macros and gmt_notposix.h

./configure --prefix=/usr/local/gmt/GMT4.4.0 --bindir=/usr/local/gmt/GMT4.4.0/bi
n --libdir=/usr/local/gmt/GMT4.4.0/lib --includedir=/usr/local/gmt/GMT4.4.0/incl
ude    --enable-netcdf=/usr/local/netcdf-3.6.3 --enable-octave=yes    --enable-t
riangle    --mandir=/usr/local/gmt/GMT4.4.0/man --docdir=/usr/local/gmt/GMT4.4.0
/share --datadir=/usr/local/gmt/GMT4.4.0/share --enable-update=
gmt_init.c: In function `GMT_setmode':
gmt_init.c:5917: warning: implicit declaration of function `setmode'
triangle.c: In function `insertvertex':
triangle.c:8422: warning: ISO C forbids conversion of function pointer to object
 pointer type
greenspline.c: In function `svdcmp':
greenspline.c:1672: warning: 'nm' might be used uninitialized in this function
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../i686-pc-cygwin/bin/ld: cannot find
 -loctave
collect2: ld returned 1 exit status
make[2]: *** [grdinfo.mex] Error 1
make[1]: *** [mex] Error 2
make: *** [suppl] Error 2
Any help would be appreciated.
Cameron
2009 Skeeter ZX190 Yamaha 175
997cSI Dash Interlinked to 787c2i Bow with Weather Sense

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

Installing GMT

Post by oceanecology » Wed Mar 11, 2009 12:40 pm

Hi Cameron:

It looks like you have two different GMT installs on your computer (GMT 4.4.0 and GMT 4.3.2). This is confusing the system - it is looking for files in the wrong directory. I would recommend that you remove both installs and start fresh with the most current version.

Cheers,
Barb

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camalama
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Location: St. Charles, MO
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Post by camalama » Wed Mar 11, 2009 12:48 pm

It does seem that way, but I have only installed the latest version (4.4.0). I hate to scrap all this work, I'm nearly to the end of your instructions. Oh well. I guess it wasn't meant to be. Is there other software that will take the sonar files and convert them into mosaics? All I want to be able to do is overlay these on Google Earth to share with friends when we plan our fishing trips.
Cameron
2009 Skeeter ZX190 Yamaha 175
997cSI Dash Interlinked to 787c2i Bow with Weather Sense

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

Post by oceanecology » Wed Mar 11, 2009 1:21 pm

Hi Cameron:

You probably wouldn't need to start over from scratch - just remove the GMT component. Unlike windows, the installs for each component are quite separate on Linux, and you can often remove one install without affecting the others. Also check out your environmental variables and make sure your GMTHOME variable is pointing to the correct directory (see 3(d) in the instructions). If you are using a different version of GMT from the one I used, you will need to set this to the correct version (e.g. 4.4.0 instead of 4.3.1).

With respect to other mosaicing software - I have looked extensively for other open source, freeware, or cheap mosaicing software, but have had no success. Most mosaicing software costs thousands of dollars (up to $5,000 or even $10,000) - which is why I have worked so much on the MIPS and MB System solutions.

Cheers,
Barb

bradhamptonkc7mrp
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Joined: Tue Nov 11, 2008 11:52 am
Location: central washington state

Post by bradhamptonkc7mrp » Mon Mar 23, 2009 6:47 pm

your images are very impressive, i saw the first ones that looked like a single pass and thought I was one up on you guys then saw the ones with several passes doh! I have been croping out my data fields then using photo editing software to stitch them together into a panoramic I can only do so many images at a time befor I run out of PC resources.
I would love to say have an out line of my lake of intrest and put together a bunch of scans on the map in there corect location and orentation.

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

MBSConverter and processing

Post by oceanecology » Thu Mar 26, 2009 10:23 pm

I finally got back to work on this project!! I now have a converter that will take the XTF file generated by son2xtf and convert it into something that can be read by MB-System. I have posted the software and the instructions for its use on my web site:

http://www.oceanecology.ca/software.htm

I have also updated the installation instructions for MB-System (I am now using the most recent Beta version which has better filtering functions).

So .... what have I learned from all of this??

Both MIPS and MB-System are quite different in how they handle the data. MIPS produces a very nice quality sharp mosaic with lots of detail. However, it loses all the depth and navigational data when the final end-product image is generated. This means that it cannot be used to generate 3D images, and it needs to be re-georeferenced if you want to plot the image on a map.

MB-System also has it pros and cons. It can generate a sidescan plot (an un-mosaiced, but georeferenced image) quite quickly (see below).

Image

However, on the other hand, MB-System produces a much lower resolution mosaic image (see below).

Image

This is largely the result of MB-System's heavy dependency on high quality bathymetric data being available. Generally, MB-System is used to process data which has both sidescan (or amplitude) values as well as accurate depth values (usually from a multibeam system). The positive features about this mosaic are that it still retains both depth and navigational information in the data file. Thus, the file can be viewed in a 3D viewer (e.g., iView3D, a free viewer from Fledermaus). This can be a lot of fun!!

Image

It can also be easily uploaded to Google Earth.

Image

Note that there are some projection inaccuracies in the Google Earth image - I'm not sure if this is a result of the way Google Earth is doing the projection, or whether the original data had relatively low accuracy GPS information.

That's all for now! I hope some of you find this useful!

Cheers,
Barb

bradhamptonkc7mrp
Posts: 24
Joined: Tue Nov 11, 2008 11:52 am
Location: central washington state

Post by bradhamptonkc7mrp » Sat Mar 28, 2009 12:55 pm

your software is looking very exciting, many of the programs I have looked at were not user frendly at all and required some one with a degreen in cartrogropyh and surveying just to do the most basic operations.
I am a diver in central washington and love to scan for things to dive but I have a favorite lake and have scanned miles of the shore line it is a deep lake and most things below 200feet are not usefull for me.
the DrDepth software is nice but requires you to run over every foot of lake bottom to build a map.
I have an object in a river I have been trying to figure out what it is for a couple years now, some day I will just have to dive the thing but in a 3mph river can be interesting.
I have tried scanning it from differant sides and differant ranges I think I could be some old railroad equipment, we had a big explosion some years back.
some of the cross currant scans are suewed due to crabbing acrost the river.
I imaging you are getting more and more people wanting you to process there scans.
I'll have to give your software a try.
brad

diver651
Posts: 45
Joined: Thu Nov 29, 2007 1:07 pm
Location: Cincinnati

CYGWIN installtion issues

Post by diver651 » Wed May 06, 2009 1:36 pm

Barb,

I am attempting to follow your instructions for the software installations as detailed in your "Sidescan and Multibeam Processing Using Cygwin on Windows XPPro" and am running into some issues.

The first is that when selecting the packages you have listed, I am unable to locate a number of them. Most of them are the "xorg" packages. there appears to have been some update to Cygwin/X that removes some of these. Might you have any insight into the correct replacements, or updated directions?

Secondly, when attempting to make the changes described in section 2 C, I am apparently unable to access the GUI you are referring to from the properties tab of the directory. The only security tab I find is the "sharing and security" tab, but nothing under the properies tab. Any idea what I might be doing wrong?

Thanks for whatever insight you can provide.

Mike

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

New software updates

Post by oceanecology » Thu Jul 16, 2009 10:09 pm

Hi to all those experiencing problems with Cygwin's upgrades!!!

Sorry to have taken so long to get back to this project! Cygwin has indeed undergone some major revisions, particularly in the Xwin components. This has pretty much made my old instructions useless, as things have been moved to new directories, and there are no longer any xorg packages. However, I have managed to update my installation instructions (current as of yesterday), so if anyone wants to brave the installations again, things should go more smoothly.

With respect to finding the "security" tab, apparently this is only required if your computer has an NTFS formatted hard drive. If your drive is FAT32 formatted, skip this step (I have changed this in my updated installation instructions).

I have also updated all my conversion programs - they have a few more bells and whistles, and there is now support for the 262/455 side imaging transducer which many of us are using in salt water.

Another addition is a conversion program to take SON files from the 967 3D units to an MB-System format, for anyone who is working with the multibeam stuff.

Everything is still available on my website:

http://www.oceanecology.ca/software.htm

Hope this helps those who have struggled along with me so far!

Cheers,
Barb

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

Further updates to installation instructions

Post by oceanecology » Sat Jul 18, 2009 6:21 pm

Hi all:

Looks like GMT just came out with its newest update (GMT4.5.0) a day ago. Unfortunately, MB-System seems to have a conflict with this. If you were using my instruction from before and downloaded GMT4.4.0 - great! If not, I have posted some new and improved instructions explaining how to download GMT4.4.0 now that the auto-install method only serves up GMT4.5.0!

Instructions can be found at:

http://www.oceanecology.ca/software.htm

Cheers,
Barb

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

Another conversion program

Post by oceanecology » Sat Jul 18, 2009 10:46 pm

Hi all:

Here's another little bit of fun that I have been working on. It's a little catch-all conversion program that reads a Humminbird SI SON file. Much of it is still in the testing phase, but some of you may find it interesting.

The program is called SideScanCalculator, and it performs a variety of calculations on a SON file, including (1) conversion to an SLG file for viewing in SonarViewer, (2) creation of an XYZ (lat, long, depth) text file, (3) calculation of bottom roughness and hardness, (4) calculation of fish abundance, and (5) calculation of macrophyte height.

It can be downloaded at

http://www.oceanecology.ca/software.htm

Cheers,
Barb

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

More updates and some wreck hunting

Post by oceanecology » Wed Sep 02, 2009 2:26 pm

Hi all:

Just posted some recent updates for the MipsConverter, MBSConverter, and SideScanCalculator. For the MipsConverter and MBSConverter, I added an additional function which allows you to set the range value for conversion to a manually chosen value. This has proven useful for trimming files where the maximum depth used during recording exceeded the sidescan range (120 m or so) and garbage was recorded outside this range. For the SideScanCalculator, I fixed a problem with memory allocation which was causing the program to crash when loading large files. The updates can be found on our website:

http://www.oceanecology.ca/software.htm

On another note, for those who are interested in wreck hunting, we just finished taking some side scan images of the USAT Brigadier General M. G. Zalinski, a wreck which can be found in Grenville Channel, BC. The location, story, and side scan images of the wreck are posted on our website:

http://www.oceanecology.ca/zalinski.htm

The project made for some interesting research, as the ship was a "forgotten" US Army transport ship which was carrying a load of bombs when she went down. The Canadian government is now looking into the possibility of removing the fuel and munitions from the wreck, possibly by 2010.

Some other notes of interest regarding issues that have been talked about in this forum:

1. Range settings
Correct range settings are absolutely crucial if you want to be able to mosaic the data. Both the downward looking sonar and sidescan sonar must be firing at the same frequency, which means they both have to be set for the same maximum range. This can be done by setting the "Max Depth" value on the unit (which sets the range value for the recording). However, if the "Max Depth" value exceeds the maximum range of the sidescan (120 m or so), or if the unit is unable to lock onto the bottom within the "Max Depth", bizarre, and often erroneous, values will be recorded in the SON files. As a result, you will probably have little luck getting MBSystem or MIPS to process the data.

2. Alternator noise
We've had serious problems with alternator noise. We've installed noise reduction filters on both our alternators (we have a 24V and 12V system), and on the power supply to the Humminbird unit. While these help, we have discovered that one of our alternators (on the 12V system) is producing a loud (and very irritating) RF signal. Our next step will be to disassemble the alternator and clean the brushes to see if this will help.

Cheers,
Barb

Jbretel
Posts: 2
Joined: Wed Nov 18, 2009 4:57 pm
Location: United Kingdom

Alternator Noise

Post by Jbretel » Wed Nov 18, 2009 5:23 pm

Hi Barb,

I have previously struggled with noise affecting Sonar in the past (both on my Garmin units and Humminbird 3D and 987c SI units).

It's probably the one single thing that reduces quality of sonar - yet is least addressed.

I have gotten around this (after much trial and error) by the following solution - which works perfectly by the way.

I run a separate battery for the electronics, and have installed a double-pole heavy duty isolation switch (easily available from almost every chandlers) which links this 2nd battery to my "main" battery (and the charging system with the "noisy" alternators and all other electronic gubbins).

When I'm running out to dive sites and not using the depth sounders for anything other than navigation, I have the Double Pole switch set so that the motors alternator charges both batteries (circuit connected).

When I'm ready to troll for bottom scanning purposes I simply turn the double pole switch "off".

This cuts both Positive and Neutral connections from the main battery and isolates the GPS from any potential interference within the main boat electrics wiring (fridges etc).

The fact that the circuit is only "cut" between the two batteries (and not the unit) means that the unit does not turn off or on, and coverage is seamless (powering on and off in choppy seas and obtaining a position fix in a 21ft bouncing boat is a pain - I know coz I've tried).

The battery does not necessarily need to be a substantial affair - just one large enough to run for as long as you need to troll (a decent 12v motorcycle battery can suffice) - but it's one sure way of guaranteeing zero noise / feedback affecting your unit.

Hope this helps some people improve their sonar recordings.

And the MIPS and MB-System S/W looks very good - I've an old laptop that I could reformat to unix and load ubuntu or similar onto just for the image processing, this should be ok yeah ?

Regards,

Jeremy

oceanecology
Posts: 40
Joined: Mon Aug 25, 2008 5:22 pm
Location: Prince Rupert, BC, Canada

Post by oceanecology » Wed Nov 18, 2009 7:45 pm

Hi Jeremy:

Thanks for the helpful hints on reducing alternator noise!

Ultimately, we discovered that one of the noise-reducing filters on our 12V alternator was fried. When we replaced it with a new one, the noise magcially disappeared! Those filters are amazing!

We also considered putting in a switch to shut off the 12 V alternator when we wanted really noise-free recording. This is similar to your idea - isolating the system from any alternator noise.

As for using an old computer for processing - it may work okay. I know that some of the Linux installs are very light and fast (good for older computers with slower processors and less memory). The actual data crunching does take some brain-power from your computer, but if you are willing to wait abit for a slower computer, it will probably work fine.

Cheers,
Barb

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