Posts Tagged ‘ mapping ’
I saw this link on Kurt’s blog – I didn’t even know about the Ocean Bytes blog before.
Reson Seabat 8101 on Ocean Bytes blog
Brian Kidd is an oceanographic technician aboard the R/V Hugh R. Sharp, and in these two videos, he’s being interviewed about the 8101 system. In the first part, he describes the monitoring and display station, and in the second part, he talks more about the wet side – the transducer and mounting assembly.
It seems like the next logical step, in a way – I’ve already got GMT and MB-System. Might as well try out the GRASS free GIS software. I just downloaded it using sudo apt-get install grass in Ubuntu. And it looks like there’s a pretty easy installer for Mac also.
This screenshot is from the Ubuntu version – don’t get too excited though – the cool display is due to Compiz-Fusion, not GRASS. But the overall effect is impressive. (Nice to know that I’m more concerned with how the UI looks than the functionality of the program).
Thanks for the tip, Kurt!!
I guess this is probably a painfully obvious solution to anyone who knows what they’re doing, but it turns out I was missing the link to GDAL in my install_makefiles script. There’s a line in there that looks like this:
$LFLAGS = "-L$NETCDFLIBDIR -lm -lnetcdf";
It should have had a link to GDAL like this:
$LFLAGS = "-L$NETCDFLIBDIR -lm -lnetcdf -lgdal";
So it worked! It ran with no errors, and seemed to build correctly. So one step closer! I then continued along the instructions to setting the .bashrc file. I had left out one line before, so I added it, and then ran:
$ source .bashrc
To test my GMT and MBSystem installs, I tried:
$ psxy
$ man psxy
$ mbgrid
$ man mbgrid
Since I don’t know how to use GMT and MBSystem yet, I don’t know if these did what they were supposed to. But it seemed like they did, except for mbgrid, which came up with an error: “Unable to open data list file: datalist.mb-1“. But at least it recognized mbgrid as a command and tried to do something!
Ah, finally, I’m getting somewhere! 
Jonathan Beaudoin, an old friend of mine from UNB, has recently moved down to UNH… and he’s got a blog! Yay for nerdy blogs! Check it out here: 2bitbrain.blogspot.com. It’s totally on my Google Reader list, as of 5 minutes ago.
Jonathan does some really neat research, and is a fantastic combination of computer scientist/hydrographer /general smarty-pants, so I’m looking forward to following his adventures as he moves into mac-land.
Well. I honestly am not sure what fixed my problems, but the good news is, the GMT install went smoothly, and I now have a fully functional GMT + GDAL install. And I’m ready for MB-System!
So I basically sat down tonight, for the first time in ages, prepared to dig into GMT/GDAL again, armed with advice from both Kurt and Monica on how I might fix things. (or at least begin a fruitful investigation into why it wasn’t working). So to get back up to speed, I wanted to display the errors that I’d been seeing before. The problems would arise when I tried installing GMT using the command
sudo sh install_gmt GMTparam.txt
Where GMTparam.txt is the input file that I carefully prepared on the GMT download site. I was previously getting all sorts of errors telling me that all of my GDAL functions were undefined. I ran the GMT installer again, and, lo and behold, it just worked. I suspect it had something to do with me rebooting the system. Is it possible that I hadn’t rebooted after my last GDAL re-install? Maybe. And maybe it needed to reboot to recognize the changes? I’m not sure. But I’m happy that I can finally move on. It feels good.
Yeah – thanks, Val!
Square Dancing Article from The New York Times
This article made me smile – it gives a fun description of the Pythagorean theorem. Yay, geometry! My favorite is the part where the author tells where the word geometry comes from geo (earth) and metry (measurement) – geometry was originally used in solving problems of land measurement. This makes me happy to be a surveyor
Last night I didn’t finish installing GMT because I wanted to make sure I had access to GDAL (Geospatial Data Abstraction Library). I got it by running sudo apt-get install gdal-bin. I am not entirely certain if that was the right thing to do. And if it does install GDAL, I’m not sure what version it will be. (I think it’s 1.5?)
It installed and I ran the GMT install file again, this time choosing the GDAL option and specifying the appropriate path. Seemed like it worked at first…but I now think I’m worse off than ever…
I think maybe my problem is that I don’t know where my installed folders are going. I just found this little hint:
sudo updatedb
locate gdal
This command returned a ton of lines – I guess that means I have a lot of files and folders on my computer that contain the string “gdal” in their title. Anyway, this was enough to show me where to find my elusive GDAL directory. (it’s in /usr/share/, it’s called /gdal15).
I also tried to use this to find my netcdf directory, since that was also giving me similar errors during GMT installation. But there are so many netcdf files and folders that I don’t know which one is the installation folder. I need to figure out how to install things where I want them.
I finally just ran install_gmt without the GDAL option. I think it went okay, except for a bunch of warnings and errors at the end about “gmt_support” and the triangulate function.
*sigh* … I still have a lot to figure out. I’m at that stage where every question I ask raises about 10 new questions.
After all of the problems I had with the NetCDF portion of my GMT install yesterday, it seems like I ought to figure out what NetCDF is. Here’s the description, quoted directly from the Unidata Program Center in Boulder, Colorado:
NetCDF (network Common Data Form) is a set of interfaces for array-oriented data access and a freely-distributed collection of data access libraries for C, Fortran, C++, Java, and other languages. The netCDF libraries support a machine-independent format for representing scientific data. Together, the interfaces, libraries, and format support the creation, access, and sharing of scientific data.
NetCDF data is:
Self-Describing. A netCDF file includes information about the data it contains.
Portable. A netCDF file can be accessed by computers with different ways of storing integers, characters, and floating-point numbers.
Scalable. A small subset of a large dataset may be accessed efficiently.
Appendable. Data may be appended to a properly structured netCDF file without copying the dataset or redefining its structure.
Sharable. One writer and multiple readers may simultaneously access the same netCDF file.
Archivable. Access to all earlier forms of netCDF data will be supported by current and future versions of the software.
The netCDF software was developed by Glenn Davis, Russ Rew, Ed Hartnett, John Caron, Steve Emmerson, and Harvey Davies at the Unidata Program Center in Boulder, Colorado, with contributions from many other netCDF users.
(Warning: This is a long, and probably confusing post. Read at your own risk!)
My life for the last 7 years has basically revolved around oceans and maps in one way or another. Since I’m now trying to embrace the wonderful world of open source, I thought it would be a good idea to combine my passions and finally figure out GMT and MB System. I thought this tutorial on installing MB-System on Ubuntu would be helpful, but I was doing something wrong and couldn’t even get past the very first step.
So the way it works is that on the GMT home page, you can use a form to automatically generate a script that you can save as a text file and use as an argument to the install_gmt command. I tried to do this for (literally) hours. I kept getting an error message about how it couldn’t find my netcdf directory. So a couple of minutes ago, I finally ran the install_gmt script without the GMTparams.txt argument, and I think I got a little further. It installed the necessary netcdf stuff, appeared to be installing GMT, and then gave me errors about not being able to find some files or directories. I think that the errors were all related to a missing GDAL directory. The GDAL thing is an optional feature that you can set up during installation that is supposed to allow you to create geo-tiffs. But I think I must haave set it up wrong…
So in the end, I am not certain whether I successfully installed GMT or not. But it’s now getting too late, and I’m too tired to figure it out. To be be continued…
**** a bit later *****
Ah-ha! I started the installation again found this little tidbit:
GMT offers experimental and optional support for other grid formats
and plotting of geotiffs via GDAL. To use this option you must already
have the GDAL library and include files installed.
I think this means it’s getting late and I’m starting to miss obvious things. More tomorrow!