Time for a cup of Java

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Week 2 began with copying and reading trough the old files for the $FIELDSCIENCE program. Once on my local machine I was able to load the program and begin to sift my way through the app’s source code. One challenge that I was made aware of is that the original code was written using Eclipse IDE and the current supported system is Android Studio IDE. Luckily, the book (The Big Nerd Ranch Guide to Android Programming) that I chose to learn from is written entirely for Eclipse IDE and I will be translating the learner’s programs to ones working within Android Studio (to quote Charlie “sometimes its like drinking from a fire hydrant”). With this being the case, I should have a firm grasp on the differences between the two IDE’s.

My time this week was spent learning through google searches and reading/attempting the programs within the book. Progress is going well and I am feeling fairly comfortable using Android Studio and the basics of java with the help of a cheatsheet for syntax. My goal in the next week is to have a firmer grasp on the program we already have and the direction/updates that we plan to make in the future.

In any case, all this talk of java really makes me crave coffee.

Did I mention Android Studio?

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This past week I’ve been working more on Android development for the $FIELDSCIENCE application that we develop.

I mentioned in my last post that we’ve moved from Eclipse IDE to Android Studio IDE, and that involves migrating projects. The migration from Eclipse to Android Studio is not as straight-forward as Google sets it out to be. Android Studio uses a different build process (gradle). The project architecture is set-up differently, and different files are created during the build process.

I finally think that our Android application is in the form that Android Studio needs, with an updated YoctoLib library! This code has been pushed to git on hopper and can be checked out from any machine, with authentication. I’m working on a ‘to-do’ document of getting the code and importing it into Android studio.

Preliminary research

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I was kindly reminded today by Tara to post some of my research so far.

My plan so far, to use a non-contact thermometer to better identify nesting sites, has been primarily based on a paper summarizing the use of thermal cameras to identify nesting sites. Using a Thermographic Imager to Find Nests of Grassland Birds by Edward W. Galligan, George S. Bakken and Steven L. Lima appeared in Wildlife Society Bulletin in Fall, 2003.

This paper, in summary, finds that thermal cameras cannot discern nests from any considerable distance, and found that they were useful in tandem with rope-dragging as a way of confirming nesting sites after potential nests had been previously identified. This is useful for my approach in Iceland, where years of rope-dragging will hopefully mean potential sites have been identified can we can then focus on that data rather than mapping massive swaths of terrain with painstaking detail. My primary ambition is to improve on the technique described in the paper by causing reducing nest disturbances caused by rope dragging.




Testing Sensor Possibilities

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Beginning this week, I plan to first test the sensitivity and capabilities of a non-contact thermometer. If this is successful, I will start looking for a potential thermopile to use in an array in order to detect heat more quickly. This array will probably covering a 360 degrees view, though much of the configuration depends on the results of our testing with the non-contact thermometer and studies into cost and effectiveness.

Possible variables include:
At what range are these thermometers accurate and fast? Should we be scanning for heat from a UAV or the ground? If we decide to scan from the air (UAV), should we use a quadrocopter or build a RC plane? What angle should we be scanning at? Should there be redundancy or overlap in the thermopiles? Should the sensor array be moving? How fast could it be scanning?

There are many other considerations, but I hope that my testing this week will reveal answers to some of my questions. Hopefully by the end of this week I will have a general idea of how the sensor array will be designed.

Progress Report for Sept 13-19

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Hi! This is my first blog post for the EC Field Science blog detailing my progress working on a survey of birds in Iceland. Be sure to check out my partner Erin’s blog.

During last week we focused on formulating a list of tasks with a few basic set of attributes, which I hope will help prioritize my work into a more manageable longer term structure.

Primary questions we have decided to first pursue include:

What are the properties of the birds we are studying?
How is thermal data digitally captured? Of the various methods, what are the uses and limitations of each?
One of our (Erin and my) first experiments will be attempting to detect animals (squirrels?) on campus with a non-contact thermometer. This might not be ideal, and I’ll have to double check that this is a reasonable method after learning more about the birds we are studying.

Database design tools

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I spent this past week learning about what options exist as far as small scale database diagram tools exist.
I found a lot of tools that are standalone desktop applications,but once I decided that we needed a design tool that was a browser based application,the search was narrowed down quite a bit.I think being able to collaboratively look at the current designs lends itself to the kind of work we’re trying to do,so this is the final list of what I’ve narrowed the search down to:

  1. https://dbdiffo.com/
  2. http://www.vertabelo.com/
  3. https://diagrams.seaquail.net/

I’m partial to using Vertabelo at this point,having played around with it for a while.I really like the interface and it’s pretty intuitive.It’s also free as long as the project is small,and we definitely come under what Vertabelo identifies as such.


Jumping headfirst into Android Dev

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This first week has been all about learning the environment in which I’ll be working in, mainly Android Studio. Having done some minor iOS dev in the past the concepts are not foreign to me and instead of being completely fresh its going to be an exercise in how to apply knowledge to a new syntax.

Much of my time has been spent getting to know how android apps functions, both behind the scenes (the code) as well as how to use the device (completed apps and such). I began viewing forums, guides, and videos to better my understanding of the mechanics and the tools available to me. Following that I started where every self respecting programmer starts, with a simple “hello world” program.

Once I felt I had a basic understanding of who things worked I started to wade my way through github in search of interesting code to read. I am a tinkerer at heart and learn new code through working my way through existing code to get a feel for whats what.

DIY Christmas light pH probe

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I have been weighing the options of testing soil in the field vs. on the bench for parameters of interest. The parameters I am focusing on are soil ph, temperature, moisture, fertility, conductivity and organic content. Of these seven, only temperature and moisture must be collected in the field. I believe that the others can be more accurately determined in a bench-top environment. I am developing my hardware designs accordingly. The next steps for me are to track down materials to build this ph probe and figure out how to interface it with an arduino board and relay information back to the field science android app through bluetooth. I am also planning to have a conversation with Mike Deibel this week about using optical measurements for organic content and fertility tests (and possibly munsell color tests). I also have a back-burner interest in geophysical surveying techniques for archeological dig sights that is still very much in the research stage.

“Science in a Box” Soil Platform

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My current project is to develop a functional and consistent set of sensors and protocols to collect information about important soil parameters such as pH, fertility, conductivity, temperature, organic content, and moisture. In Iceland and Nicaragua, the approach was to construct a unified soil sensor platform using Arduino and Yoctopuce technology that takes readings in the field.



Screen Shot 2015-09-17 at 10.24.48 AMScreen Shot 2015-09-17 at 10.25.38 AM

The potential benefits of this approach are that every parameter of interest is collected in the field and immediately saved in .csv format on a nexus device. The downside is that it is not particularly easy (or in some cases, possible) to test every parameter in harsh environments accurately or without causing damage to the sensors.

With this in mind, I am planning to take a sightly different approach: a sensor for use in the field that measures parameters that must be collected in situ (such as temperature and moisture), supplemented by benchwork preformed in the evening to collect other relevant soil parameters. The evening benchwork would also have hardware and software components. For example LED/photometer sensors could be used to measure organic content and other optical sensors could be used to make observations about the color of the soil and its composition.

The next steps for me are:

  1. Learn more about the chemistry of soil fertility and ph and find a way to test them cheaply without using standard kits.
  2. Consider the hardware element. Look for cheap sensors that are compatible with Arduino boards and begin preliminary designs. I will probably build the temp/moisture sensor first since it most closely follows the paradigm of sensors that have already been developed as a part of this research.


How to Bird Survey

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My focus of this week has been on researching the best techniques for a bird nesting survey. Through many papers the way I think will work best with what we want to achieve is to use thermography to map nesting locations. This has been done in grassland birds as well as several others and there is likely enough literature to find the best and most successful techniques. The issue we are running into is what to use for the thermo-camera, because they are very expensive. We are not a large research institution so we will not be able to spend what they would. We also would need to especially test the cheaper options to see if they can actually detect relatively small birds. The other factor will be how to detect how far away the bird is and whether we will mount an aerial camera or from the ground. Looking into range finders will be key. Both options have major complications involved that we need to research further.

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