KenMankoff

BUBBLES And A Fish

Bubbles is a small ROV built from a kit with a customized camera mount for looking up at ice from below and down at the bottom. Her construction was motivated by some underwater footage of bed load transport due to wave action.

BUBBLES is an acronym for some combination of the words Bubbles the Underwater Undersea Blue Bathymetric Basal Buoyant Little Liquid Exploration Submersible or Submarine.

Bubble was previously deployed in a hot-tub and in Younger Lagoon, Santa Cruz, CA, as test sites. Recently Bubbles went swimming under the ice-covered Silver Lake near Kirkwood, CA. Due to the late season, we could not walk on the ice and the shore-based deployment was complicated by the shallow waters. Nevertheless, she again proved to be liquid-worthy, and spent some time swimming in the shallow waters with some fish.

Bubbles heading under the ice. Photo by E. Lynne Harden

Bubbles operations. Photo by E. Lynne Harden

Bubbles was built by Ken Mankoff and E. Lynne Harden.

WISSARD Introduction

A video (and written) news segment on part of my PhD project:

It is Wet

These are most enjoyable and relaxing if played in HD full screen. Inspiration for BUBBLES. More on that later.

YAGEL – Multiple Balloons on Mars

I’m releasing Yet Another Google Earth Layer, this one featuring some more KML tricks and hacks pushing Google Earth to do things that Google does not officially support: multiple placemark description balloons visible at once.

Download: Mariner Mars 1971 (MM71) Ultraviolet Spectrometer (UVS) Data in Google Earth. This is a work in progress as part of a Planetary Data Restoration Project at the Laboratory for Atmospheric and Space Physics and as such the data is not finalized and is subject to change.

The data comes from the Ultraviolet Spectrometer on the Mariner Mars 1971 spacecraft, and had previously been processed for the Albatross software tool back in 2002. Neither Google Earth nor its predecessor KeyHole, nor even KML, existed back in 2002, and the data needs to be accessible in a more modern and accessible visualization tool (Google Earth) in order to remain useful.

The footprints are where the instrument was looking. In each of these regions a spectral range from 2107 to 3497 Ångströms was sampled, and the spectra are visible in both the hacked multi-balloon display, and in the more detailed official Google Earth balloon visible by clicking on the footprint. Each footprint is colored, both in the map view and in the sidebar, by the response at 3049 Å, which is roughly where the ozone signal is. For more information on the data and science see the references listed at the end of this post.

Previously I implemented vertical data “curtains” in KML, useful for oceanographic transects, seismic lines, spacecraft looking down through the atmosphere in profile (as opposed to a 2D surface image), or any other vertical data. Along with vertical data (solved) and subsurface data (no known work-around), another major limitation of Google Earth is that only one description balloon is allowed to be visible at a time. However, Google Earth does support multiple placemarks (by default yellow pushpins in Google Earth, or red pins in Google Maps). The hack to get multiple balloons visible at once is to make custom icons that look like balloons and then use them in place of the default icons. If this technique is used it is advised to implement various other KML features to make the balloons only appear in certain views and therefore avoid overwhelming the viewer. I’ve used both the TimeStamp and the Level of Detail features to limit when the icons appear.

@article{barth1974atmosphere,
  title={{The atmosphere of Mars}},
  author={Barth, C.A.},
  journal={Annual Review of Earth and Planetary Sciences},
  volume={2},
  number={1},
  pages={333--367},
  year={1974},
  publisher={Annual Reviews}
}

@article{barth1971mariner,
  title={{Mariner 6 and 7 ultraviolet spectrometer
                   experiment: Upper atmosphere data}},
  author={Barth, CA and Hord, CW and Pearce, JB and
                 Kelly, KK and Anderson, GP and Stewart, AI},
  journal={J. geophys. Res},
  volume={76},
  year={1971}
}

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.