Ken Mankoff Feed Conglomerate

KenMankoff: Mars Geology

Sun, 18 Jul 2010 18:54:54 GMT

Data from the U.S.G.S. PIGWAD site converted to display in Google Mars. View the KML layer or the legend (also available through the layer).

Mars Geology

@conference{skinner2006digital,
  title={{Digital renovation of the atlas of Mars
         1: 15,000,000-scale global geologic series maps}},
  author={Skinner Jr, JA and Hare, TM and Tanaka, KL},
  booktitle={37th Annual Lunar and Planetary Science Conference},
  volume={37},
  pages={2331},
  year={2006}
}

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KenMankoff: A Radio Interview

Sat, 17 Jul 2010 18:31:45 GMT

I am still learning how to interact with the media and press. It is good to practice on radio where I only have to worry about speaking and not everything else that comes with television.

Last month I was interviewed by the NewlyGreens and it aired on WPSC 88.7 out of Wayne, NJ broadcasting over New Jersey and New York.

You can listen to the interview here.

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KenMankoff: Ice Melts

Wed, 30 Jun 2010 15:16:27 GMT

Nature’s best thermometer, perhaps its most sensitive and unambiguous indicator of climate change, is ice. Ice asks no questions, presents no arguments, reads no newspapers, listens to no debates. It is not burdened by ideology and carries no political baggage as it changes from solid to liquid. It just melts.

– Henry Pollack, PhD. A World Without Ice.

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KenMankoff: Vertical Data in Google Earth

Sat, 15 May 2010 03:10:22 GMT

Google Earth does not officially support vertical curtains of data. However, it does support buildings with images on the side. If you are willing to stretch the definition of a building, you can put any vertical data you like into KML. This implementation was inspired by the Goddard Earth Science (GES) Data and Information Service Center (DISC) sample files for CloudSat, CALIPSO, and Aqua.

If you use IDL and would like to image your data in Google Earth, be it points, lines, regions, surface images, or vertical data, you should be using my IDL interface to the KML API.

Vertical Data in Google Earth

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KenMankoff: GLIMMER Ice Shelf Modeling (OS X HowTo)

Sat, 15 May 2010 01:17:15 GMT

A new beta version of the Community Ice Sheet Model, Glimmer-CISM, has been released. Below are instructions to compile and run it on OS X.

# build NetCDF
export CFLAGS=-m32
export FFLAGS=-m32
./configure --prefix=/Users/mankoff/local/netcdf-4.1.1 \
          --disable-cxx --disable-curl  --disable-dap
make && make install
say netCDF done

# build GLIMMER
cd ~/local/src/
wget http://download.berlios.de/glimmer-cism/glimmer-1.7.0.tar.gz
tar zxvf glimmer-1.7.0.tar.gz
cd glimmer-1.7.0/

# OS X has issues with 32 and 64 bit libraries.
# The -m32 flag forces 32 bit compilation.
# The following should be one long line:
./configure --prefix=/Users/mankoff/local/glimmer-1.7.0 \
     --with-netcdf=/Users/mankoff/local/netcdf-4.0.1 \
     FC=gfortran F77=gfortran CFLAGS=-m32

make
make install
say GLIMMER done

There are a few ways to test the installation. The source folder provides a test folder:

export PATH=/Users/mankoff/local/glimmer-1.7.0/bin:$PATH
cd ~/local/src/glimmer-1.7.0/tests/shelf
python circular-shelf.py circular-shelf.PP.config
python confined-shelf.py confined-shelf.PP.config
say GLIMMER Test Done # Takes a while. Turn up your volume

Running the above command will result in NetCDF files being created in the output/ subdirectory. You can view the contents of example.nc with most any generic NetCDF viewer. While theses tests run over a given period of time, the output only has one time stored. If you want to see an evolution of the ice shelf, older test suites available from the previous code repository site should be used:

cd ~/tmp/
wget http://forge.nesc.ac.uk/download.php/200/glimmer-example-0.6.tar.gz
tar zxvf glimmer-example-0.6.tar.gz
cd glimmer-example-0.6/
~/local/glimmer-1.7.0/bin/glide_launch.py ./example.config
say done

Examine the output file example.nc to see ice sheet evolution over time. Basal melt is shown below:

@article{Rutt:2009,
  Author = {Ian C. Rutt and Nicholas R. J. Hulton and Antony J. Payne},
  Title = {{The Glimmer community ice sheet model}},
  Year = {2009}}
  Journal = {J. Geophys. Res.},
  Volume = {114},
  Number = {F2},

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KenMankoff: Optical Character Recognition HowTo

Sat, 08 May 2010 01:34:48 GMT

Optical character recognition (OCR) is useful for converting images of text into normal computer text that you can edit, copy, paste and search. With OCR software you can convert old image-based PDFs to text. About 95% of words from a cleanly scanned PDF using a modern font are correctly recognized. Of the ~ 1 in 20 that confuse the algorithm, about half are easily corrected with a spell checker, and the remaining must be manually adjusted.

Google has made the tesseract OCR code they use for Google Books available. They don’t officially support OS X. Below are instructions to get tesseract-ocr running on OS X. As usual, Developer Tools (XCode) needs to be installed.

A slightly simpler installation does not use LibTIFF, but in this case you can only convert single page and uncompressed TIFF files. As PDFs are usually multiple pages, it is worth it to install and compile with LibTIFF.

# prepare dependencies
fink install libtiff libtiff-shlibs

# fetch
svn checkout http://tesseract-ocr.googlecode.com/svn/trunk/ tesseract-svn
cd tesseract-svn

# compile
./runautoconf
export CXXFLAGS=-m32 # Force 32-bit architecture
./configure --prefix=/Users/mankoff/local/tesseract/ --with-libtiff=/sw/lib
make
make install

# test run
~/local/tesseract/bin/tesseract image.tif out # run it
say Tesseract finished # might take a while. Turn on your speaker.
gn Finished Tesseract # alias gn='growlnotify -s -m'
less out.txt # check

Notes:

Here is a sample image for testing
The image must be in TIF format.
The extension must be have one “f”: TIF or tif not TIFF.
Images and complex equations are not handled

I tried to run tesseract on my handwriting and it could not decode it. I wrote a simple sentence as clearly as possible, took a photo:

The Quick Brown Fox

And the result was:

THE ®.U\(.K
[awww Fox
TUMPED oval
#IE uxzv ooé

It got “THE” and “Fox” and most of JUMPED. However, tesseract supports full training so if you need to convert your notes read the documentation and post what your learn below.

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KenMankoff: Earthquakes

Fri, 23 Apr 2010 19:39:52 GMT

I came across a database of earthquakes from 1960 to almost present. I converted it from the existing form to KML so it can be seen in both Google Earth and Google Maps. Both views incorporate a temporal component.

For the Google Earth view, magnitude as been encoded as pin size and depth has been encoded as height above the Earth. A few interesting regions where the deep quakes occur, such as east of the Andes, pop out.

Earthquakes

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KenMankoff: Iceland’s Root

Thu, 22 Apr 2010 04:58:44 GMT

Iceland's Root

Image appears to be related to Wolfe et al. (1997). Also available in Schubert and Turcotte below the discussion. Image found at LDEO.

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KenMankoff: Pine Island Glacier Publication TimeMap

Fri, 19 Mar 2010 17:31:38 GMT

In which I present a rough geo-spatial-temporal map of Pine Island Glacier (PIG) publications.

Geo-spatial-temporal time-map of Pine Island Glacier (PIG) publications

Usage: Drag the time bars to the left or right to change the time period displayed. Navigate the map as you would any Google Map: drag to pan, zoom in (double-click, scroll mouse, or use the control on the side), or zoom out (scroll, control). Click on an item in the timeline or area in the map to get more information.

Legend: Each publication is tagged by last name of first author and publication year. Each publication is placed in the timeline at or spanning the years covered by the research or the years in which the data was collected. These dates are based on a quick skim of the articles and may have errors. Exact dates were often not given in which case rough guesses for the month range were used. Modeling studies that used future unspecified dates start at 2015 and go from there some amount into the future.

Each publication was also skimmed to see the geospatial region covered by the article, and this point, line, or area is shown on the map. Regions are rough estimates. Studies that covered the whole Antarctic continent including PIG are just given a large area around the PIG drainage basin.

Future Work

Improve the geospatial component so that the more precise region of study is highlighted.
Encode extra information, such as using color and/or icons to denote, for example study type (modeling, geophysical, oceanographic, etc.)
Allow individual articles to be turned on and off. Right now so many get turned on during the 1990-2005 range that you cannot see anything in the map
Link to PDFs for downloads
Build an interface for anyone to submit their own articles (with time and place meta-data).

Lessons learned: Publication lists are full of typos. Even though I use software tools to manage lists of papers and citations from Google Scholar or ISI, I found dozens of typos (and different versions of names). I’m sure some remain even now that I did not find. Triple-check your bibliography.

I’m sure I’m missing some relevant articles. Please let me know of any omissions and errors.

Thanks

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KenMankoff: Building a Software/Hardware Environment for Research

Mon, 15 Mar 2010 08:25:17 GMT

Sometimes I get asked what software/hardware systems I recommend for research. Below is my standard advice. I am a scientific programmer and student and my day-to-day tasks involve research, data analysis, scientific programming, and writing. Data sets might include satellite images, model output, GPS, seismic, and a variety of other data. Data domains are ocean, atmosphere, and/or ice. I travel a lot, either from home to the office or to the field (which might mean months on a boat with no internet connection). Therefore I try to have a setup that supports high performance computing (HPC) on a laptop.

Purchase

Get a MacBook Pro.

If you need the extreme computing power of a quad-core desktop then you might consider the Mac Pro, but ideally you’d use the MacBook Pro and ssh into your local supercomputer or cluster. If you travel a lot and don’t need a lot of disk space you might consider a Macbook Air.

Computer

Get the 13 inch model. This makes traveling easier and maximizes battery life. Since you’ll have an external monitor at your desktop, even the 17 inch laptop will have a small screen in comparison, so you might as well go for portability.

Other specifications:

Minimum CPU.
Maximum hard drive space.
Minimum RAM from Apple.
Go get the maximum possible RAM from http://crucial.com 8GB is nice.

Peripherals

One External monitor.
Two backup disks, equal in size to your internal disk. Ideally one would be the Apple TimeCapsule, but this is quite expensive, so USB or FireWire disks will suffice. Keep one at home and one at the office. Set a calendar reminder to plug into each one at least once a week if you don’t do it every night by habit.
Two adapter cables (one for VGA one for DVI) so you can connect to external monitors and/or projectors.
A USB key to quickly transfer files

Optional Peripherals

External mouse
External keyboard
Wacom tablet (to help with RSI and/or artwork)
Headphones to tune out office mates
A USB hub so you can plug in more than 2 peripherals
A Firewire 400 to 800 adapter if you have old firewire drives not supported by the new laptop interface

Software

The following software list should allow you to write code in almost any language you choose, and to access, display, and analyze almost any data set. The following software will also help you manage your PDF library and write papers.

Official Apple Software

You must install the Apple “Developer Tools” package that is an optional install on the OS X disk provided with your computer. You know you have installed it if you have a “/Developer” folder at the root of your disk.

The Apple iWork suite is nice. It is nicer than MS Office for OS X and provides Pages, Keynote, and Numbers as equivalents to Word, PowerPoint, and Excel. Free alternatives to iWork and Office are Google Docs and Open Office. Or LaTeX for documents, CSV for spreadsheets, and Beamer for presentations.

3rd Party OS X Software

A partial list of useful 3rd party OS X software follows. Drop any of these words into your favorite search engine to get a download link. Software that cost money is starred*.

Adium (For IM, Google Talk, etc.)
AntiRSI (Reminds you to take a break from typing)
Aquamacs (A good code editor)
BibDesk or Mendeley (Manage your PDF library and references)
Celestia (Fly through the universe)
Cyberduck (FTP/SFTP)
DoubleTake* (or Hugin) (Stitch together panoramic photos)
Enthought Python Distribution (EPD) (One-stop shopping for all your Python needs)
Firefox (Browse the web)
Fluid (Make Gmail (or any other site) a stand-alone desktop application)
GeoMapApp (Geospatial data browser)
Gimp (Edit images)
GoogleEarth
GrandPerspective (Find out where disk space is getting used)
Graphviz (Flowcharts)
Growl (sleek uniform system notices)
IDL*
Jumpcut (Global clipboard buffer)
LaTeXiT
MATLAB*
MacFUSE (make any computer appear like a local folder via ssh)
MenuMeters (monitor your system status in the menubar)
Mouse Locator (never lose your pointer even on a big screen)
ODV (Ocean Data Viewer)
OmniGraphSketcher* (Make pretty charts)
PDF to Keynote (Convert PDFs to Keynote slides)
Qgis (A free GIS application)
Quicksilver (Use your keyboard for everything. Be efficient)
Sim Daltonism (Simulate color-blind and color-deficiencies so you know your graphs will be readable by everyone, and even print to grayscale well)
Skim (An enhanced PDF reader if you find Preview.app lacking)
Stellarium (See the stars)
SuperDuper!* (Clone a disk for backup, although Time Machine is probably good enough)
Sysquake (For control or robotics applications)
Vapor (or Visit) (Advanced visualization software)

From the above list, I want to stress the following:

A good PDF manager is essential for research and writing. Use BibDesk, Mendeley, or Zotero or CiteULike.
Firefox is a decent web browser, but what makes it very useful are the extensions and customization it allows:
- Smart bookmarks can make searching any website a breeze. For example you could just type “gsch keywords” as a shortcut for Google Scholar.
- Useful extensions are: DownloadHelper, DownThemAll!, Firefox PDF Plugin for Mac OS X, Flashblock, Permit Cookies, Tab Mix Plus, TabSwitcher, Tree Style Tab, Zotero.
Jumpcut is amazing.
Fluid will change the way you use your web browser. If you use FaceBook or Gmail or have some other website that is persistently open in your browser, make it a stand-alone application with its own icon, and free your browser for browsing.
You might notice no mention of Adobe.
- For basic image work, I use Gimp or GraphicsMagick instead of PhotoShop.
- For posters I use Pages, Keynote, Beamer, or Powerpoint rather than Illustrator.
- For PDFs I use Preview or Skim rather than Acrobat.

Unix Software

Much of the following unix-based software will only work if the Apple Developer tools is installed as suggested above.

The main system that provides access to a variety of unix tools is fink. (OS X is code-named Darwin, and Darwin is linked to Galapagos finches, and fink is the German word for finch, and the main developer of fink is German).

If you prefer not to use fink, you can probably get many of your HPC tools installed via double-clicking. This might be easier, but your choices will be limited compared to fink, and you won’t have one environment that lets you manage all of the software. However, if all you need is one FORTRAN compiler, or one LaTeX installation, then you might want to search through the pages listed in the Other Resources section below.

Fink

Download and install fink. Follow the default options, but then enable the “unstable” tree to get access to a whole lot of additional (perfectly stable) software.

Once fink is installed and set up, you want to use it to install your favorite unix tools. You can find things to install with the “list” command, like this: “fink list fortran”. I find the following tools quite useful, but I like to geo-tag images and write presentations in LaTeX…

fink install base-files bash bash-completion contacts coreutils daemonic ddclient detex exiftags exiv2 fuse g77 gcc44 ghostscript gmt gpsbabel graphicsmagick ispell latex-beamer launch lynx minicom mpack ncarg ncftp ncview proj pstree psutils r-base smartmontools tesseract texlive-base texlive-texmf tree unzip watch wget xtermcontrol

Due to dependency bloat, I prefer graphicsmagick to imagemagick, and avoid using “gv” altogether. Instead of gv I use the less user-friendly “gs” from ghostview, let Preview.app convert it to PDF, or manually convert it to pdf with “ps2pdf”. Again due to dependency bloat, Octave and gnuplot are two of the few “unix” tools that I install without fink, instead using the OS X HPC page listed at the bottom.

Not Fink

Not everything is available in Fink. I have found the following non-fink-packaged software useful:

csv2latex (convert CSV files to LaTeX tables)
gpicsync (geotag and produce KML files of photos)
ViewPoints (multivariate data exploration tool)

Customizing

Now that the software is installed, you’ll need to spend some time customizing it. The following key areas should be customized for efficiency:

Your bash prompt (.bash_profile)
Bash aliases (.bash_profile)
Emacs/Aquamacs (.emacs)
SSH (.ssh/config) and ssh keys

With a bit of effort adjusting the above files you can, for example, log into your remote machines with just two keystrokes, one of them being the return key.

Windows and Other Operating Systems

If you want to run Windows and/or other flavors of Linux (OS X being based on BSD), you can easily do so. You have four main choices: BootCamp, VMWare, Parallels, or VirtualBox, and some minor choices: Crossover, Wine, etc.

Use VirtualBox to host your Windows installation as a local disk image. Do not use the Apple BootCamp.

If you need to run Windows by itself, and want to use some of the tools mentioned in this page in Linux in Windows, you have a few options. The most popular is a Linux Live CD (try Ubuntu). Less popular but easier (no CD required) is andLinux. Download, double-click, install like regular Windows software, reboot, and you’ll have a bash shell icon on your desktop.

Extra Hardware

If you program hardware via serial ports you’ll need a USB to Serial adapter. Keyspan makes the best ones. You’ll also want to make sure minicom is installed (fink install minicom).
If you use Google Earth a lot you will be grateful to invest in a 3D Connexion 6-DOF mouse.
If you want more than 1 external monitor, the best solution is a new breed of USB-based monitors. You can have, I think, as many as you like.
If you read a lot of papers an eBook might be a good investment. The only one big enough at the time of this writing to display PDFs as images is the Kindle DX. If you can wait 6 months to a year there should be some good competition and even laptops that have screens that switch to e-ink mode when dimmed.

UCSC Specific Tips

UCSC provides licenses for MATLAB and ENVI (which includes IDL). You can run these for free when you are on the campus network (although I think you have to be wired, or on the “cruznet secure” network, not on the general cruznet network.).

If you want to run the software from home you can set up a VPN. This makes your computer appear as though it is on the UCSC network, even though you can be anywhere in the world. The VPN is also beneficial as it lets you access libraries and journals as though you are on campus, making it easy to download papers into BibDesk.

Other Resources and Alternatives

http://hpc.sourceforge.net/
http://www.atmos.washington.edu/~salathe/osx_unix/
http://www.macresearch.org/
http://www.osxgnu.org/
You can use Darwin Ports instead of fink: http://darwinports.com/