Harmful Algal Blooms – Part 6: Finally, a Project

This semester, I’ve been working with Dr. Kenton Ross, the national science advisor at NASA DEVELOP, to understand the spectral properties of Alexandrium monilatum. I am using aspects of this work as my term project for GIS 295 and GIS 255.

In Harmful Algal Blooms – Part 5: Trouble in Data Land, I discussed the challenge of completing a mapping project when the data has lost its geospatial reference.  However, we were able to obtain approximate locations for each hyperspectral scene by estimating pixel size and lining up the time field in the hyperspectral data  with the time field in the the flight path data set. You can see the scene center lines in black on the image below.

Scene Center lines

The water in this map looks unusual. NDVI is a band ratio index used to indicate vegetation. I used ((Landsat 8 band 5 – band 4)/ (band 5+band 4)) to mask out the land  in ArcGIS. I then clipped out the unmasked water and used false color imagery (bands 6, 5 and 4) to enhance different features of the water.  The water on the right side looks thick and yellow because it is very turbid.

Once I knew where each scene was located, I analyzed each hyperspectral image individually. This is York scene 5.

20150817_YK5

The first thing I noticed was that any detail was hard to see. That’s because one side is in shadow. So, I clipped out the black edges and the bright, overly illuminated right side of the image. I also reduced my number of bands from 283 to 13 carefully selected bands in order to reduce noise and maximize the spectral signal. The resulting image is in the slide below.

Slide7

The deep red swirl is the algal bloom.

I used bands 146 (710 nm), 128 (665 nm) and 85 (559 nm) to create a NIR, red, green false color composite to highlight areas with high chlorophyll.  That’s the second image in the slide.

High chlorophyll should appear red in these images, but the areas of intense blooms appeared bright yellow-green. This is because there is also a red pigment in the blooms that gives them their color.

The third image is estimated chlorophyll. I used the  ratio of band 146 (710 nm) over band 128 (665 nm) as a proxy for chlorophyll-a. Red and yellow indicate high chlorophyll, while dark blue indicates low chlorophyll. You can see that despite the red color, the algal bloom has plenty of chlorophyll.

What about the third image? I used ENVI to run an unsupervised classification. This means that ENVI sorted the pixels in the image into five groups according to their spectral properties. I then used class statistics to obtain the spectral signature of each group. That’s the big image on the left of the slide.

I repeated this procedure on seven images from the York River, four images from the James River, and one image from Mobjack Bay. The signatures in the York River were distinctive enough that we believe we are on the right track to find the spectral signature of Alexandrium monolatum.

For my GIS 295 class project, I created an web app which shows the imagery and spectral signatures at each scene. If you are a member of Northern Virginia Community College GIS group, you can access the app here. Everyone else will have to wait until we are ready to make the app public.

References:

Moses, Wesley J.; Gitelson, Anatoly; Perk, Richard L.; Gurlin, Daniela; Rundquist, Donald C.; Leavitt, Bryan C.; Barrow, Tadd M.; and Brakhage, Paul, “Estimation of chlorophyll-a concentration in turbid productive waters using airborne hyperspectral data” (2012). Papers in Natural Resources. Paper 313. http://digitalcommons.unl.edu/natrespapers/313

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Tobler, Steno and Geologic Maps

Waldo Tobler is a geographer at my alma mater, UC Santa Barbara. He is known for Tobler’s Law or the “first law of geography” which states “Everything is related to everything else, but near things are more related to each other than distant things.”

My classmate Sunil Bharuchi recently published a discussion of Tobler’s Law on his blog, GIS 295 Web GIS. He included this image, which explains spatial auto correlation.

Spatial autocorrelation measures how well a set of spatial features and their values are clustered together in space. A spatial feature is a point, line or polygon that identifies the geographic location of a real world object; this object could be a building, a forest, a rock unit or a lake.

According to Tobler’s law, spatial features will be clustered next to more similar spatial features – this is illustrated in the first image above. But, is this always true? Sunil’s post got me thinking.

Here is a geologic map of Yosemite National Park. Which of the images above does it look like?

Map of Yosemite National Park.svg
Map of Yosemite National Park” by General_geologic_map_of_Yosemite_area.png: en:United States Geological Survey derivative work: Grandiose – This file was derived from  General geologic map of Yosemite area.png: . Licensed under CC BY-SA 3.0 via Commons.

I’ve spent years looking at geologic maps, so I told Sunil “image three looks more like geology.” But, does that mean Tobler is wrong?

Not at all.

Nicolas Steno (Niels Stensen, 1638-1686) was a Danish scientist and bishop who made important contributions to the fields of anatomy, paleontology, crystallography and geology. Steno’s principles of statigraphy explain the formation of sedimentary rock and are still used by geologists to determine the history of a rock unit. There are three principles:

  1. The Principle of Superposition: When sediments are deposited, the sediment that is deposited first is at the bottom while sediment that is deposited later is at the top. Therefore, the lower sediments are older.
  2. The Principle of Original Horizontality: Sediment is originally deposited in horizontal layers.
  3. The Principle of Original Continuity: Sediment is deposited in continuous sheets that only stop when they meet an obstacle or taper off because of distance from the source.

Doesn’t the Principle of Original Horizontality sound a lot like Tobler’s Law? Then why don’t geological maps look like the first picture on Sunil’s image?

First of all, sedimentary rock isn’t the only type of rock on Earth.Steno’s principles do not apply to igneous and metamorphic rock.

Second, the Earth is an active planet. Plate tectonics causes sedimentary layers to bend, break and even overturn. Igneous rocks intrude into existing rock from below the Earth’s surface or erupt from above. These processes mean that geologic units are often very complex and the resulting spatial patterns reflect that complexity.

Yosemite USA.JPG
Yosemite USA” by GuyFrancisOwn work. Licensed under CC BY-SA 3.0 via Commons.

James Hutton (1726-1997) was a Scottish physician and geologist who is known as the founder of modern geology. He was the first to suggest that the Earth is continually being formed and that based on the rates of geologic processes, the Earth must be much,much older than the accepted estimate of a few thousand years. He is also known for the Law of Cross-cutting Relationships.

Law of Cross-cutting Relationships: If a fault or other body of rock cuts through another body of rock, then that intrusion must be younger in age than the rock that it cuts or displaces.

It is this Law of Cross-cutting Relationships that helps us interpret geological units and create geological maps.

Can you figure out the temporal relationships in this cross section?

geology
From Earth: Portrait of a Planet, 4th Edition (2011) by Stephen Marshak.

So, how does Tobler’s Law fit in? It depends on scale. If you are standing on an outcrop of sandstone, chances are good that the rock surrounding you will also be sandstone – especially if you are in the tectonically quieter center of a continent. But, If you are mapping Yosemite park using one kilometer pixels, you will find a lot more variation in neighboring areas.

 

200 Years of Geological Mapping

This is a geologic map of Britain. It is a screen shot of the British Geologic Survey’s “Geology of Britain” viewer.

Brit1

I chose to show bedrock and surface geology because that’s what William Smith showed when he produced the first geologic map of Britain two hundred years ago in 1815.

Unlike many of the English men who made great scientific contributions, William Smith was not nobility – or even well off. He was the son of a farmer. As a young man, he became an apprentice to a surveyor. He eventually went to work for the Somersetshire Coal Canal Company.

While working in the mines, Smith noticed that individual layers of rock on the sides of the pit were  always arranged in the same recognizable relative order. He also noticed that some layers were identifiable by the fossils they contained, and that these fossils were also always in a predictable order.  He was inspired to see if the relationship between the layers of rock or strata, their positions and the fossils they contain was consistent throughout Britain.

As William Smith studied the rocks of England, he drew cross-sections showing relationships and maps showing location. Eventually his work evolved into the first national geologic map. It measured 6 feet by 8.5 feet and showed the rocks of Britain at the a scale of 5 miles per inch.

Smith’s map isn’t so different from the BGS map created using GPS units and satellite data.

627px-Geological_map_Britain_William_Smith_1815
By William Smith (1769-1839) {Public Domain], via Wikimedia Commons

Two hundred years ago, one man created a map by walking through Britain. Since then, geologic maps have been created for every part of the Earth. Thanks to William Smith, mapping is an intergal part of the training of every geologist.

As a geology student, I learned to map in the field by carefully measuring and plotting geologic contacts, folds and faults on a topographic base map.  It wasn’t always easy to distinguish between the greyish-brown of one unit and the brownish-grey of another or determine my location based on map contours. Yet, I eventually learned to make a map that could be interpreted to tell the geologic history of a small area. William Smith didn’t have a topographic base map. How did he do it?

Smith’s map is more than the distribution of rocks. It is a first edition volume of Britain’s geologic history. Since 1815, that volume has been edited and revised hundreds of times, but William Smith is remembered and honored as the original author.

You learn more about William Smith and his maps  and play with an interactive William Smith mapping app here.

Edited some typos (12/7/15)

 

New York: Why the Height of a Skyscraper Depends on Location

Take a look at the New York City skyline. It’s unique and recognizable because of its skyscrapers. New York City is home to some of the tallest buildings in the world.

Suppose you are interested the height of skyscrapers in New York City. You could make a list of building heights, like this list from Wikipedia.

  1. The Freedom Tower, One World Trade Center (1,776 ft.)
  2. 423 Park Avenue (1,400 ft.)
  3. Empire State Building (1,250 ft.)
  4. Bank of America Tower (1,200 ft.)
  5. Chrysler Building (1,046 ft.)
  6. The New York Times Building (1,046 ft.)
  7. One57 (1,005 ft.)
  8. Four World Trade Center (978 ft.)
  9. 70 Pine Street (952 ft.)
  10. The Trump Building, 4o Wall Street (927 ft.)

This list tells me that the Empire State Building is the third tallest building in the City. It tells me that Freedom Tower is about 750 feet taller than the Chrysler Building. But, what does that look like?

I’d get a better idea of what this means with a bar graph. Or. I could use an image like this (also from Wikipedia):

NYCbyPinHt_update
r

This gives me a much better idea of how building heights compare. But, this information is still limited.

What if I want to know where these buildings are? What if I care about their locations? I will need a map.

I used the Building Footprints shapefile from NY OpenData to create this map of buildings with a roof height over 500 feet tall in NYC. Only 177 out of 1,082,433 buildings in NYC are over 500 feet tall. Those buildings are indicated in red.

 

TallBuildings1

The most interesting thing about this map is that all these very tall buildings are clumped in two locations: Midtown and the Financial District. You can see these clumps in this photograph:

NYCangle2

Here’s a closer look:TallBuilding2.What is going on? Did New York City specifically zone these locations to have tall buildings? Is this meant to preserve the skyline? Or, is it intended to show the importance of the Financial District?

The answers can also be found in a map. The location of New York’s skyscrapers is all about geology. As you can see in my hideously ugly geological map (colors courtesy of USGS’s New York Geological Map downloaded as a shapefile), the island of Manhattan has a different type of surface rock than the surrounding area. This bedrock is a metamorphic rock called the Manhattan schist (in pale lavender).

NYCGeo1

The Manhattan schist formed more than 400 million years ago when a volcanic island arc (similar to today’s Japan) crashed into the eastern side of the continent of Laurentia forming a huge mountain range known as the Taconic Orogeny. The high temperatures and pressures associated with mountain building caused the clay minerals in the mud that accumulated of the coast of Laurentia to transform to more resistant minerals such as biotite, muscovite and quartz.

manhattan schist
Manhattan Schist

Throughout most of Manhattan, this erosion-resistant bedrock is covered with large amounts of unconsolidated sediments. But,  this exceptionally hard rock lies very close to the surface in Downtown and Midtown Manhattan. Because this rock is so strong, it makes the perfect foundation for a skyscraper.

What about other cities? There are only two structures over 500 feet tall in Washington DC: the Hughes Memorial radio tower (761 ft) and the Washington Monument (555 ft). Why doesn’t Washington DC have tall skyscrapers?

While there are some strong metamorphic rocks in Northwest DC, most of DC is built on much softer sedimentary rocks. These rocks cannot support a skyscraper.

So, maps can help us understand where things are, but they can also help us understand why they are where they are. In New York, the height of a building depends on location and location depends on geology.

(Many of the other tallest buildings in the U.S. are located in Chicago. Chicago is weird. You can learn more about the challenges of building skyscrapers in a swamp here. )

This post was inspired by Episode 1 of Making North America on PBS.

 

 

 

 

On Shaky Ground Part 1: Earthquakes in Virginia

It’s been just over four years since a 5.8 magnitude earthquake in the Central Virginia Seismic Zone damaged the Washington Monument. That was a significant earthquake for our area.

Last Sunday (9/27/15) the Central Virginia Seismic Zone experienced another earthquake.  The magnitude 2.0 quake was one of hundreds of small earthquakes that have occurred in the area over the past four years. And, InsideNova feels the need to report every single one.

So, is Virginia really a seismically active area? I placed esri’s USA Earthquake Risk map on top of a topographic base map. The map shows potential ground shaking intensity from earthquakes, an estimate of the amount of damage an earthquake is likely to cause in an area.  I set the scale so the highest risk in shown in dark red while the lowest risk appears as dark blue. I added the past week’s worth of earthquakes (from esri Disater Response) to the map. You can see the our 2.0 quake in Central Virginia.

Seismic zones

Moost of Virginia falls in the medium blue range indicating a very low risk of damage from earthquakes. Our recent earthquake is small compared to the many of the other earthquakes that occurred in the U.S. last week.

It’s not surprising that the West Coast of the United States is covered in red and orange. The California, Oregon, and Washington coasts are active margins. This means that the edge of the continent coincides with the edges of one or more tectonic plates (in this case: North American, Juan de Fuca, Pacific). Geologic activity such as earthquakes and volcanoes generally occurs at the edges of tectonic plates.

The East Coast is a passive margin. The eastern edge of the North American tectonic plate is far out in the Atlantic ocean. So, geologic activity on the East Coast and most of the U.S. is relatively rare as indicated by the blue coloring.

Behind California is an area known as the Basin Range province. This is the remnant of an ancient rift zone. In the early Miocene (about 17 ma), the North American continent began to stretch and thin. But, before the continent could rift into two tectonic plates, seismic activity stopped. This left a network of faults which still responds to the stresses from activity on the West Coast. The New Madrid fault zone which underlies Alabama, Arkansas, Illinois, Indiana, Kansas, Kentucky, Mississippi, Missouri, Oklahoma, Tennessee and Texas is another example of an ancient rift zone.

But, not all rift zones are ancient. The red area in Northern New York and New Hampshire indicates activity from the St. Lawrence rift system, an active rift zone that runs along the St. Lawrence River. Perhaps one day, North America will split and a new Canadian plate will form.

If you are looking carefully you might notice that there are medium blue areas in the middle of continents far from any plate boundaries that have recently experienced larger earthquakes. Is that rifting? Does that mean we should worry?

No, it’s not rifting, but we may have reasons to worry. The cluster of earthquakes in Oklahoma includes several with a magnitude between 2.0 and 3.0. These small earthquakes have been linked to fracking rather than seismic activity. The 3.2 earthquake near Stamford, NY may also be caused by human activity. It is likely the result of water pressure from the Gilboa Dam.

Like Oklahoma and New York, Virginia has networks of ancient faults that can be reactivated by human activity. However, seismologists believe that most of our earthquakes are simply the result of old faults moving because of sea floor spreading in the Atlantic Ocean.

You can view my map here.

Where Will I Put the Bottled Water?

When we were in class on Wednesday night, Hurricane Joaquin seemed to be headed straight for Virginia. I’m pretty well prepared, but I donated last year’s bottled water stash in the spring. So, on Thursday morning, I stopped at Target to stock up on bottled water which is now sitting in the hallway because I don’t have space for it.

The latest forecasts show that I didn’t really need to rush and buy water; Joaquin isn’t likely to reach the East Coast. But, thoughts of hurricanes inspired a map.

hurricanes

I mapped esri’s active hurricanes and recent hurricanes as well as hurricane tracks from historic hurricanes (in blue, from Maps.com) on top of a base map. Hurricane Joaquin’s path is shown in black, while the yellow dots represent the tracks of recent hurricanes. As you can see, we might be safe from Hurricane Joaquin, but (historically speaking) it’s only a matter of time until a hurricane does hit Virginia.

You can see the ArcGIS Online map here.

I think I’ll keep the water.