Wednesday, March 19, 2014

QGIS Tutorial Links

With the release of QGIS 2.0 (and greater), this open source project has become a serious contender for a full-blown GIS solution that covers nearly all of the necessary features found in ArcGIS but at a reasonable price (free!). I’ve started to use QGIS in all of my projects and am very pleased by its features and performance. Like all complex software, there is a learning curve but if one knows ArcGIS already most of it is fairly self-explanatory. I’ve started to assemble some tutorials that I can point students towards. Here’s the list I have to date:
I will add more to this list as I come across useful resources for learning QGIS.

Monday, November 25, 2013

Archaeology Blog Carnival

From now until the April 2014, I am going to be participating in the Archaeology Blog Carnival - “Blogging Archaeology”. From what I can tell, this is a bit of a meta- enterprise in which we write about the process/practice of writing about archaeology. Ill be interested to see how the questions evolve for I fear the degree of meta-ness may produce a bit of self-indulgence and navel gazing. I suppose, however, that the “carnival" provides a forum for folks who are blogging out there in the blogosphere to share some perspectives on their writing habits. We shall see. We even get a twitter hash to use: #blogarch.

The question for November is: Why blogging? – Why did you start a blog?

I began blogging mostly as an experiment and to see what all the hoopla about “blogs” was about. I certainly did not start writing to broadcast a specific message or to report on anything in a consistent fashion (as a review of evobeach.com will show you). From what I had read, the blog medium seemed to be a great way for sharing information and  as an academic, sharing has direct value. It is clearly beneficial to us to share information in as many media forms as possible as measures of academic success center around how many people share the ideas that one has originated (via citation analysis, for example). Of course, sharing is not the only property of value for ideas: they also have to accomplish something. If academics were all about sharing, science (at least) would be an enterprise that encourages Kardashianism rather than the generation of knowledge. While I know that in some areas of the anthropological realms sharing may be the only value held (I’m looking at you faux French philosophers), I choose to believe that knowledge ultimately trumps sharing by itself. Mendel clearly had the latter down but knew nothing about marketing, not that it mattered in the long run. The best situation occurs, of course, when both sharing and knowledge can be merged. The Mars missions, perhaps, are good examples of how the work of scientists can find its way into everyone daily informational lives. Of course, the value of the sharing can be maximized when the sharing occurs between professionals/academics since those individuals not only appreciate what we each are doing but have the opportunity to put shared knowledge into practice. But the value of sharing also goes to those who are just interested or simply wonder where tax dollars go.  

The blog world is just the tip of the iceberg in terms of new ways of communication. Give the rapidity of change in the way in which we share information, it behooves all professionals to become familiar with new media forms, if only to ensure that one's message has the best change of being heard. It remains fairly clear that dead-tree media still retains a core value in the academic world, but the degree of centrality is slipping rapidly as electronic media becomes a larger part of one’s research base (and the holdouts retire). Blogging is a way of exploring digital means of sharing with low cost and low overhead. 

Blogging also gives one a way of sharing ideas that ordinarily do not qualify as material for the standard range of professional publications.  Beyond just the yammering and sharing of groovy photos and whatnot, one can discuss technical details that are difficult to share in traditional academic media. For example, I just wrote about my work on building a multispectral camera based on Raspberry Pi (http://www.evobeach.com/2013/10/nir-raspberry-pi-camera.html). How one goes about building and tinkering with such a camera is not ordinarily material that is going to get a journal editor (at least in archaeology) particularly excited. Yet the technology (being inexpensive and opening doors to entirely new ways of studying the archaeological record) can be transformational. So blogging becomes a way of sharing this kind of information. 

In addition to being a platform for discussing technical details and geeky stuff, blogging is also an interactive platform. Individuals can respond to posts or pose public questions to authors that would otherwise be impossible. This interaction can lead to debates, clarifications, or collaborations — all of which mirrors the real kind of interaction that goes on within the closed doors academia but at a dramatically faster pace and with enormously expanded inclusiveness. No longer are some hand-picked crew the only ones allows to write critiques about an article (e.g., the Current Anthropology CA Treatment): everyone can get engaged with academic dialog (for better or worse). Given that the interaction is public (and not some private email chain) and  the publications are nearly instantaneous, the blogosphere opens new doors for enhancing information that exist in other formats (such as dead trees).  For example, I recently responded to a critic about our moai transport work and answered questions that were posed. I like to think that blogging such interaction enhances the value of the publications and contributes to make the ideas clearer.  



Sunday, November 17, 2013

Response to Comment

 

A Sophist wrote a comment in response to the blog entry Diamond attempts to defend myths of Easter Island: Lipo and Hunt respond :

My questions remain: 1. Were there Palm trees on Easter Island when the first Europeans visited? And if not, then H+L are arguing this was rats and not humans cutting the trees down? 2. If Palm Trees are unable to be made into canoes, how did the people make ocean going canoes? In there were no canoes, how did Dolphin get into the diet? I guess I am missing the problem. This seems to be a lesson in how isolated political leaders who do not feel the pain of their actions (cutting down the forest for whatever bloody reason: fuel, canoes, to move statues, etc) can lead their society to the brink of destruction. 

The questions themselves point to common but false assumptions often made about Easter Island prehistory and they are worthing examining. 

Question #1:  Palm Trees.  I’m not sure how the two different parts to the question are related (i.e., whether there were palm trees at contact in 1722 and whether rats “cut down” the trees). For the first question: no one knows exactly whether there living examples of palm trees on the island in AD 1722 when Roggeveen first arrived nor later in the 1770s when the Spanish and English arrived.  The overall impression we get from these early written accounts is that the island was largely devoid of trees though there are also mentions of “palms” in some of the descriptions.  The pollen and macro  botanical record is equally unclear given the relatively poor dating of the island as a whole and relatively few dates of palm nuts in particular. A major effort to date events on the island (with modern understanding of the need to link past events with dated events) would go a long way to resolve this issue (among many others). 

One difficulty in resolving pre- versus post- contact differences in the island’s landscape and ecology is the fact that point at which researchers arrived on the island to make systematic descriptions is more than 250 years after initial contact and decades after the island was turned into a sheep ranch. Certainly, the presence of 60,000 sheep and associated ranching activities likely resulted in the final termination of many plants that may have been present in small numbers in late prehistory.  So the timing of the final termination of the palm is still a bit unclear.

The second part of the question seems to assume that we (Hunt and Lipo) argued that it was “rats… cutting the trees down.” The statement is absurd to begin with and of course we have never argued this. What we have argued is that arrival of rats with humans on to the island brought immediate and substantial changes to the ecology of the island. The introduction of rats is really the introduction of the first teeth on the island and their presence (as is well documented in many environments) will impact native vegetation especially that which has coevolved dispersal mechanisms with birds. The impact of rat is a fact and indisputable given the evidence that exists of rat gnawing seeds. But did they “cause” the trees to go extinct (as this question implies we say)?

The answer is, of course, no. The rats did not cause the palm forest to go extinct for several reasons. First, things don’t “cause” other things to happen except in common sense (see Sellars 1963: Science, perception and reality).  Second, while rat predation on palm nuts has been an ignored factor in the vegetation changes that are commensurate with human arrivals, rats were not the sole factor.  We *do* know that rat predation on seeds can make massive changes in vegetation and even extinction even when humans are not present.  As Hunt has discussed, the elimination of Pritchardia palm in the Ewa Plain clearly predates the actual arrival of humans (see Hunt, T., 2007. Journal of Archaeological Science 34 (2007) 485-502; Athens, J.S., Tuggle, H.D., Ward, J.V., Welch, D.J., 2002. Avifaunal extinc- tions, vegetation change, and Polynesian impacts in prehistoric Hawai’i. Archaeology in Oceania 37, 57-78.p. 73).

On Easter Island with its tiny size (about 6x10miles), however, there was never a point at which rats were separate from humans. It takes about an afternoon to walk from one side of Rapa Nui to the other: human and rat impacts will be effectively simultaneous across the the entire island.  We know that the people arriving on Easter Island were slash-and-burn cultivationists — a strategy we side widespread across the Pacific (and indeed around the world). Their lives depended on transforming the environment to one that was capable of supporting human life through the growth of Polyensian domesticated plants. Thus, humans burned the forest down right from the get-go.  The combination of human burning for land clearance with rat predation on palm nuts would mean that the forest have a difficult time to grow back on its own.  Recent excavations by a Belgian team up at Vaitea (I believe: I heard about this second hand) show that in prehistory there were attempts to grow these palm trees. This is not at all surprising: the trees were certainly disappearing given activities of slash-and-burn and rat predation and this would be something that prehistoric people noticed (contra the assumptions inherent in claims by Diamond). 

What gets confused as a claim that we (Hunt and Lipo) argued that rats “caused” palm tree extinction are some comments that Hunt made in his paper in American Scientist that:

 

The evidence from elsewhere in the Pacific makes it hard to believe that rats would not have caused rapid and widespread environmental degradation. But there is still the question of how much of an effect rats had relative to the changes caused by humans, who cut down trees for a number of uses and practiced slash-and-burn agriculture. I believe that there is substantial evidence that it was rats, more so than humans, that led to deforestation.

and in his 2007 JAS article where he says:

 

In this review I have examined ar- chaeological, palaeo-environmental, and contemporary eco- logical evidence to suggest that the Pacific rat may have played a major role in Rapa Nui’s ecological catastrophe. The fact that rats alone are capable of widespread forest de- struction compels us to evaluate their contribution to the trans- formation of Rapa Nui, as well as in other island ecosystems. While I argue that the role of rats has often been underesti- mated, direct human actions of felling and use of fire likely have played a significant role as well. Additional research will be essential to disentangle the contributing factors. The environmental catastrophe of Rapa Nui is likely a complex history, one that has been masked by speculations about the in- tentions of people cutting down the last tree. Indeed, the ‘‘last tree’’ may simply have died. Rats may have simply eaten the last seeds. Perhaps the lessons of Rapa Nui tell of the effects of invasive species, invasional meltdowns, and the synergy of ef- fects that ensue as people and their portmanteau biota reach evolutionary isolates in the remote islands of the Pacific. 

But what is clear in the context of these quotes is that what Hunt is arguing (as we both do later on) is that the loss of the forest is the outcome of a number of factors among which rats is one. It is certainly possible to argue that rats could have caused the extinction of the palm trees, but in the case of Rapa Nui it also seems clears that the rat predation was occurring simultaneously with human burning and clearing of the palm forest. Empirically, this is undebatable  as we have rat gnawed seeds that are found contemporaneously with burned palm. 

It is also silly to argue that the presence of non-gnawed seeds somehow “disproves” the role of rat predation. Some nuts probably didn’t get eaten especially if the tree was burned before the rats were able to consume them.  Even a small impact to seed production for these trees is likely to have caused changes in the life history structure of the forest whereby there become fewer and fewer young trees. Rats do not have to eat every single palm nut for the forest to go into major decline or even extinction. Clearly the r-selected strategy of palm trees embodied by nut production is a testament to the fact that the palm is evolutionarily successful by maximizing the number of offspring due to the fact on average some of the nuts will grow into new trees, not all.  The novel introduction of toothed predators likely only had to have a small effect to have upset the balance between forest regeneration and failure. Of course, this is topic that clearly needs more research. 

Question #2:  Canoes and Dolphins: In the second part of his/her question, A Sophist writes: "2. If Palm Trees are unable to be made into canoes, how did the people make ocean going canoes?”  I guess the assumption here is that the presence of dolphin remains at Anakena must somehow have required large ocean going canoes. It also refers to the fact that we argue that palm trees are not useful for constructing canoes, at least not the sailing/voyaging canoes used by Polynesians. To disentangle this question, let’s start by saying that it is likely that whatever canoes brought people to Easter Island were likely around for some period after their arrival. We don’t know this specifically since we have no evidence but the faunal record seems to record more deep water/pelagic fish in the early assemblages than later. The acquisition of these fish would have required canoes and early on there would have been the original canoes to use.  It also seems that at some point these canoes rot away, are lost, or used to sail elsewhere as the faunal remains show significantly less pelagic fish. From that point on the emphasis of the population was nearly entirely on terrestrial resources (though some small % of fish from the limited nearshore reef seemed to supplement the diet). The palm trees appear to have been lost over 4 centuries were not used in canoe manufacturing even though they were present.  This is almost certainly because palm trees are not good raw material for canoes: they are flexible grasses filled with mush. 

The presence of dolphin remains at Anakena is certainly interesting but it doesnt seems to contradict our overall understanding of the archaeological record.  The remains are few in number and were never a major source of food. Ethnographically we know that dolphin come into the Anakena bay and were sometime hunted there. The bay is shallow. Traditional means of hunting dolphin often involved trapping them in shallow water by driving them toward shore with rocks knocked underwater (see http://www.youtube.com/watch?v=QP3FbrF5YyM if you stomach it). Deep water canoes were not necessary for hunting dolphin. 

Final Comment:  The final comment by A Sophist is a bit puzzling: "This seems to be a lesson in how isolated political leaders who do not feel the pain of their actions (cutting down the forest for whatever bloody reason: fuel, canoes, to move statues, etc) can lead their society to the brink of destruction. “ It is not clear at all what “this” refers to or who the “isolated political leaders” are or what “brink of destruction” means. Inherent in here is the idea that somehow the forest was a vital resource upon which people depended. The fact is that there is no evidence that palm trees ever played a central role in the subsistence or settlement activity of people of the island. As sweet potato farmers, the clearance of trees (like all farmers) resulted in more land available for growing crops. The burning of the forest resulted in temporarily increased nutrients in the soil. The fact that rat predation (not to mention the slow growth and reproduction of the tree itself) meant that the forest never regrew was not a catastrophe. Alternative (laborious yet, but indeed clever) means of enriching the soil through rock mulch as well as intensely tended gardens (manavai) were able to keep the soils growing food. The trees simply were not a vital resource to the prehistoric population.

Monday, October 28, 2013

NIR Raspberry Pi Camera

I am excited to read that one can now buy a near-infrared Raspberry Pi camera. The regular one  can be modified to measure NIR light but the process is futzy and error prone. I destroyed 2 cameras trying to get the damn thing apart. This new camera has the NIR filter removed so one is set to go right from the start.  Adafruit has them in stock (as of this morning but I’m fairly certain they will sell out quickly). 

http://www.adafruit.com/products/1567

My efforts to build the RPi multispectral camera are now made much simpler: http://www.evobeach.com/2013/09/a-raspberry-pi-based-multispectral.html 

Friday, October 18, 2013

Remote Sensing with UAVs and eCognition

PLoS published an interesting new article about the use of UAVs to track invasive weeds in maize fields using UAV imagery and remote sensing techniques. This is a good example of an article that uses remote sensing and UAVs in an analytic sense and not just "camera in the air." While elevated camera angles are cool, they do not really take advantage of the technology nor offer much in the way of actual research. This article points to how this kind of work can be done (and will be a good article to use for our REU program). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0077151

Monday, October 14, 2013

Giant Human Sized Salamanders

Every couple of years when we lived in Wisconsin, the woods around us would be invaded by different kinds of newts and salamanders. Although I never did figure out what caused these events, I assume that those waves of critters were related to population booms or some conditions that resulted in 1000s of them running across the driveway and into our garage. I would have loved, however, to see a plague of these guys: http://www.wired.com/wiredscience/2013/10/absurd-creature-6-foot-salamander/?utm_source=tumblr&utm_medium=socialmedia&utm_campaign=tumblrclickthru#slideid-285261

Thursday, September 19, 2013

A Raspberry Pi based multispectral camera

 

I have been working on constructing a new version of the DIY multispectral camera that I began last year.  The first version was based on a paper by Shaw et al a group at Montana State University. Their MS camera made use of solid-state DVR boards with a 1MP black and white cameras. A X-bee based radio relay triggered all the cameras to take photos on 4 separate SD cards. Each of the cameras has a filter to create Red, NIR, Green and Blue bands. Put together and one can get 4-band multispectral image with good control over the contents of each of the bands (due to the pass/cut filters that select a range of wavelengths of interest for each camera). 
 
Last year, I replicated what they were doing but found that the firmware on the DVR cards (http://www.electronics123.net/amazon/datasheet/dvr8100.pdf) left a lot to be desired. The software interface on the cards is clunky and randomly stopped working. With the control software entirely in the firmware there wasn't much I could do to fix things or troubleshoot.  
 
With the release of the Raspberry Pi camera, I figured this might offer a cheaper and more robust solution. The RPi camera is also 5MP which offers better resolution. With separate Raspberry Pis controlling each camera, I can then potentially add more sophisticated processing (on the fly), have some sanity checks, and generally make the whole thing more robust.  Potentially I can create NDVIs on the fly so that the analysis part is complete by the time the images are downloaded. The demonstration that the IR filter can be removed clinched the decision for me and I dove into building a new RPi based version. 
 
For this I have 4 Raspberry Pis driving 4 separate CMOS cameras. Separate controllers are needed for two reasons: (1) the PI only has one port for driving a camera. (2) In an aerial setting one needs to take the photos all at the same time -- not in sequence since the camera is moving.  Ultimately, I will add the filters to restrict the light to each of the cameras.  The camera run a python script that listens to a GPIO port for a triggering announcement. A fifth Pi runs as a master. It has a GPS and a real time clock on board to track its location and time.  When sufficient distance from the previous photos has passed, the master pi triggers the other cameras with the GPIO. The master then ftps the images back to a central location and (when the script is done), these are assembled into a single multispectral image using GDAL libraries (aligned and so on). A UBEC provides the power to the whole thing so that it can be run off of the balancing plug of a LiPo battery (assuming its installed in some sort of UAV/plane/copter). 
 
As of last night, It is all assembled (see photo) and I'm working on the software part of the project.  Ive got the master program working with the gps and so on and the basic triggering scripts for the individual cameras. Using GPIO on the Pi is pretty sweet though having to run the scripts as sudo is a bit wonky IMHO. Ultimately the individual pis will boot in headless fashion and begin running their scripts. Ive got the master pi now functioning as a wireless access device so that the other pis can connect to it. I still have to work on getting the transfers going. That will requiring making sure that the script can find the right images that go together. One way to do that might to have the slave pis ftp to the master using a number scheme to make it clear what goes with what. That is work yet to be done...