Using MB-System and USGS MIPS with Humminbird files

Official Firmware, Side Image Viewers, Map Overlays, 3rd Party Apps, etc..
Jbretel
Posts: 2
Joined: Wed Nov 18, 2009 4:57 pm
Location: United Kingdom

Post by Jbretel » Thu Nov 19, 2009 12:20 pm

Hi Barb,

Yeah - my idea was to remove ALL electrical feedback from the HB unit (Fridges, winches, etc) but sounds like you got it nailed.

Hmmm - the spec is pretty low on the old laptop (it used to creak with Win 2000) - I have an old (newer) PC that might be better - 3gb ram and 1.7 processor - it's gotta beat trying to get unix to function correctly on a windows platform (always a compromise) - plus I haven't loaded up linux for ages - might be fun to see what's new in ubuntu !!

Just as well its winter here, and the sea is boiling like a cauldron - gotta have projects for the long dark evenings !!!

Hey - maybe I can load an external harddrive to my main PC and run Linux on that yeah - dual boot setup ?

I'm off to troll the Linux forums.

JB.

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

linux installs

Post by oceanecology » Thu Nov 19, 2009 1:02 pm

Hi Jeremy:

I hear you about the long winter nights!! Looks like we'll be out working this December - sheltered waters, but an adventure none the less.

We don't have as much problem with electrical feedback on our ship - no fridge at the moment, and everything else runs off hydraulics. So this is probably why we aren't having more problems with noise (other than the alternators!).

Lot's of people use dual boot systems with Linux. Some of them have very small footprints - Puppy Linux, for example, can be booted off a jumpdrive or CD.

I am very happy with my Cygwin install - some people claim it is a bit slow compared to a full Linux operating system, but it has worked really well for me. My main reason for going this route is that I use alot of Windows software, such as ArcGIS, which cannot run on Linux. When I use Cygwin, I can smoothly move data from one system to the other without shutting down and rebooting or having to run two separate computers and transfer data between them.

Cheers,
Barb

bigkahuna
Posts: 30
Joined: Wed Nov 11, 2009 10:39 am
Location: Outer Banks of North Carolina

Post by bigkahuna » Thu Nov 19, 2009 7:01 pm

@JB - Ubuntu has probably improved immensely since you last tried it. Dual boot installation is a breeze, doesn't even require repartitioning anymore, and hardware configuration is almost as easy as my Mac. I bought my wife a 15" Dell notebook this summer that had Ubuntu pre-installed and it immediately recognized our HP printer and scanner. Last time I used Linux was a couple years ago and couldn't believe how much better it's gotten.

When I started to read the installation instructions for MB-System the first thing I thought was to run it from Ubuntu also, except since I've got a Mac I'll set it up on a virtual machine with Parallels Desktop.

@oceanecology - I've been following this thread with great interest. Thank you for sharing this information. I also come from the research community (formerly with NOAA, Univ. Hawaii and Univ. Washington) and now work in undersea robotics. I've been very impressed with what a sub $1K HB side scanner can do, so much so I plan on buying one before year's end. MB-System and DrDepth give me the perfect excuse to buy a new toy. ;)

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

Updated installation instructions

Post by oceanecology » Tue Jan 19, 2010 8:26 pm

Hi all:

New updates are out again, and I have updated my installation instructions for Cygwin, USGS MIPS, and MB-System.

Lot's of improvements and a few fixes:
  • Cygwin has been updated from 1.5 to 1.7 - a big jump with some significant changes and improvements.
  • The installation instructions are for the newest version of GMT with HDF5 support (this was disabled in the last install).
  • I've changed the GUI for GMT (the one I'm using now is more flexible, and iGMT won't work with GMT 4.5.1).
  • MB-System has been updated - it is now compatible with GMT 4.5.1 and has a number of new features, including the ability to do tidal corrections.
  • I've managed to get USGS MIPS fully functional again (some components were disabled before as a result of updates to Cygwin).
The instructions can be dowloaded at http://www.oceanecology.ca/software.htm.

Cheers,
Barb

Quagdop
Posts: 2
Joined: Wed Feb 10, 2010 8:13 am
Location: Frankfort, KY

Using Sidescan Calculator

Post by Quagdop » Wed Feb 10, 2010 9:14 am

Hi Barb,

Thanks for the great software and cygwin instructionals. I work for the KY Dept. of Fish and Wildlife and we are using side-scan for search&rescue, habitat mapping, etc. I have managed to use MIPS a little but I find the Linux interface a little challenging. I guess I spent too many years working with DOS. I used MIPS under Poseidon for a while, but I am trying to set up cygwin now. I do a lot of work with ArcGIS so it is handier to work on a windows computer.

Anyway, I was using Sidescan Calculator to parse an SON file to get the data into ArcMap. When I use the export to XYZ it works fine, but the coordinates only have 4 significant digits. They are correct, but in most cases, I need 6 digits for adequate resolution. I hope that higher resolution data is available in the SON file.

Would it be possible to increase the number of digits in the export? I tried converting to an SLG file and parsing that out, but Lowrance uses a funky coordinate system based on distance from the Equator and the Prime Meridian.

Let me know what you think and thanks again for all the assistance you have provided this forum!

Don

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

Significant digits

Post by oceanecology » Wed Feb 10, 2010 12:17 pm

Hi Don:

I’m glad that you are finding the MIPS stuff useful! Thank you!

I too work with ArcMap alot, and find that having MIPS (and many other programs) installed on Cygwin makes the transfer of data between a Linux environment and a Windows environment nearly transparent. Having worked with separate (and dual boot) systems before, this is really great!

With respect to the decimal place output in the SidescanCalculator, it simply outputs the raw data as a double. All calculations within the program are done using double format, so there should be no inadvertent truncating of the data. In my test runs with the program, I commonly get 4 to 6 decimal places depending on the inputted values (zero values at the end of a decimal are not printed).

The truncated values you are receiving makes me think that the Humminbird unit is not receiving the GPS signal properly. I have had this problem before with our units. For example, our DGPS can be a bit flakey and produces bad check sums at the end of its NMEA sentences. The Humminbird unit will check to see if each sentence has the correct checksum, and will ignore bad sentences. This causes two things to happen. Firstly, we get a lot of “skips” in our positional data (the Humminbird unit can be set up to interpolate between skips, but I’m not sure if this interpolation gets recorded in the SON file). Secondly, since our DGPS puts out both a high accuracy and a low accuracy positional sentence, and the high accuracy one is the one most likely to get gibbled, the position defaults to low accuracy (2 to 4 decimal places rather than 6). I now know to watch for this problem, and in our case, a simple reset of the DGPS clears the problem and everything is okay after that. I’m not sure if this is the problem that you are having, but it is worth looking into. Also, different pieces of equipment are more sensitive to this problem than others, depending on whether or not they pay attention to the checksum. For example, our navigational software (Nobeltec) never looks at the checksums and will always give the high accuracy positional information even when the Humminbird (or other instruments) which are checking the checksum values defaults to low accuracy (all from the same DGPS signal with a splitter).

I hope this helps. Let me know how it goes!

Cheers,
Barb

Quagdop
Posts: 2
Joined: Wed Feb 10, 2010 8:13 am
Location: Frankfort, KY

Thanks for the info!

Post by Quagdop » Thu Feb 11, 2010 6:33 pm

Hi Barb,

Thanks for clearing that up. I'll have to look at a larger data sample. It looks like our best bet is to have a logger hooked up to capture the NMEA direct. I prefer to have the raw data and do my own editing. I was going to use the output for Dr Depth, but we can use the track data for that.

I succeeded in setting up MIPS under Cygwin on my netbook. It is nice to run it on WinXP, but I kind of miss the GUI I had with Poseidon. I still have a few bugs to work out, like an XWin that doesn't like to close gracefully, but its fully functional. I may try MB-system next.

Thanks Again!

Don

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

Logging GPS data

Post by oceanecology » Thu Feb 11, 2010 7:07 pm

Hi Don:

I usually log all my nmea data separately as well - it provides a good backup in case one of my other software programs is misbehaving!! I use Franson GpsGate, as it has a built in multiplexing function (I can run several instruments into the USB ports on my computer and log them all at 1 second intervals).

I had problems with the XWin .bat file that came with the new Cygwin install as well. I believe my newest installation notes cover a way of getting around it.

Good luck with MB-system - it is very powerful, but a bit more complex and less self-explanatory than MIPS.

Cheers,
Barb

ageo
Posts: 22
Joined: Tue Dec 18, 2007 3:34 pm
Location: Florida.USA

Problem installing MIPS

Post by ageo » Sat Aug 21, 2010 3:08 pm

Barb,

Following your instructions I was able to install MB-systems and the associated software needed to process the Humminbird data. I was able to process a test set and after I fine tune some settings on our 797 my images should be a little better.

I WISH TO THANK YOU FOR THOSE INSTRUCTIONS!!

I want to improve the imagery from the side sonar and I am trying to install MIPS. I am getting the following errors when I try to install MIPS.

">>> Building applystr
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lg2c
collect2: ld returned 1 exit status
>>> Compiling binmap
>>> Building binmap
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lg2c
collect2: ld returned 1 exit status"

And these errors continue throughout the remainder of the build. Any help would be wonderful.

Thanks

AGEO

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

Installing MIPS

Post by oceanecology » Sat Aug 21, 2010 6:27 pm

Hi Ageo:

Under the instructions for installing Cygwin, make sure that you have done Step (7):

7. Start Cygwin. At the Cygwin prompt, type the following:

ln -s /lib/gcc/i686-pc-cygwin/3.4.4/libg2c.a /lib/gcc/i686-pc-cygwin/4.3.4/libg2c.a

Exit from Cygwin.


This should resolve any issues with the -lg2c errors.

I will be posting some new instructions for processing using MIPS shortly that have a few new tips and ideas.

Cheers,
Barb

ageo
Posts: 22
Joined: Tue Dec 18, 2007 3:34 pm
Location: Florida.USA

lg2c error still showing up

Post by ageo » Sat Aug 21, 2010 8:43 pm

Hi Barb,

I typed in the soft link that you provided at the cygwin prompt and then exited the cygwin prompt. I must have previously typed in that command because it told me that the symbolic link already existed. I went ahead and opened the Xterm window and tried the installation again and still received the same error. Still not sure of the problem.

Thanks
AGEO

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

MIPS installation

Post by oceanecology » Sat Aug 21, 2010 8:57 pm

Hi Ageo:

Please check to see what versions of gcc you have installed and let me know.

Cheers,
Barb

ageo
Posts: 22
Joined: Tue Dec 18, 2007 3:34 pm
Location: Florida.USA

GCC version

Post by ageo » Sat Aug 21, 2010 9:12 pm

Barb,

Again thanks for taking the time to assist me in getting MIPS installed.

I checked which version of GCC I have installed and it is version 4.3.4.

Thanks

AGEO

ageo
Posts: 22
Joined: Tue Dec 18, 2007 3:34 pm
Location: Florida.USA

GCC version

Post by ageo » Sat Aug 21, 2010 9:14 pm

Barb,

It is funny how the program compiles and builds all the way up to the image processing part of MIPS. that is where I start getting the error messages.


AGEO

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

Software updates

Post by oceanecology » Mon Aug 30, 2010 9:34 pm

Hi all:

I've updated my SideScanCalculator software. Problems with the accuracy of the latitude and longitude outputs have been corrected.

I've also posted updated instructions for using USGS MIPS to create mosaics from Humminbird sidescan data.

Software can be downloaded from

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

Cheers,
Barb

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