KenMankoff

Mars Geology

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}
}

A Radio Interview

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.

Ice Melts

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.

Vertical Data in Google Earth

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

GLIMMER Ice Shelf Modeling (OS X HowTo)

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},

Optical Character Recognition HowTo

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.

Earthquakes

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

Iceland’s Root

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.

Pine Island Glacier Publication TimeMap

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

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Building a Software/Hardware Environment for Research

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.

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