The ball starts moving!

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Earlier this week we had a programmers meeting to decide the direction for the app such as the mechanics and architecture. While we initially will hold off on the graphic designs for the app there is still much to be done!

I’ve started researching the process states within Android and how the app will interact with the hardware of the Nexus. So far the developer webpage has been most beneficial in understanding the way that processes work by default and how to tweak that to individual needs. I also found a very valuable system service called prostats that allows you to see how RAM is being allocated and gives you to the tools to analyze it for specific features.

Thermal Camera and the Internet Issue

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We finally have our hands on the Fluke thermal imaging camera! It is very exciting because we can start to test out our theories and protocols to figure out something that will work.  I have read the manual which was semi helpful because I found that it measures infrared energy radiated based on two factors: the surface temperature of the object and the emissivity of the surface. This camera is not used normally for living things but it should work based on how it detects energy however focusing in on the small birds might be difficult in getting an exact temperature reading. After charging it up we turned it on and are definitely able to detect humans so the next step is to look at some squirrels and then bird of similar size and temperature to the birds we will be looking at.


The other issue I have started to work on is the internet problem at Skalanes. Basically I need to find the point at which a balloon would need to be elevated in order to be in direct line of sight of the ferry station. In order to do this I am going to first find the elevation of Skalanes, The antena at the ferry station and the mountains in between using the information we have, google earth and ArcGIS.


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After finishing finalizing the new data model after staring at the iterations we’ve had since 2013,I started making a “master table” this week.It has all the data from all the different iterations,and they aren’t groomed to look the same or follow the same model,but they’re all getting put in one place,so that it’s easy to find all the data we do have once I start grooming it.

This next week,I plan to do exactly that.I plan on putting all the data,in their newly organized format according to our model,into the database,so that  it’s all consistent and in one place.I have a feeling this will be messy and take a while,but I now know what the format is and where the data is,so I’m hopeful of traversing it better.

Building, Bluetooth, and Boards

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These week I focused primarily on what I need to start actually building the for-field-use soil moisture/temperature sensor platform, as well as selecting a bluetooth shield for communicating with our field science app, and picking a board to actually build the platform on.

I tracked down circuit schematics for the Infrared temperature sensor. So far I think it will work for our purposes, and at around ~$3 a unit I see no reason not to try it out.

Screen Shot 2015-10-05 at 2.42.31 PM

We already have several moisture (and temp – a useful calibration for the IR measurements) sensing platforms laying around so I will probably cannibalize one of those for it’s sensor. I just need to figure out which one…

Screen Shot 2015-10-05 at 2.43.00 PM

My next order of business is selecting the best bluetooth shield for this project. I’m looking at Bluetooth LE (low energy) because we don’t want it to die in the field. The LightBlue Bean that Kristin found for the Ambiance platform looks promising – it has extra functionality built in that might not be necessary for bench-top applications but could be useful out in the field. Even though the ambiance platform will have a LightBlue Bean sending back temperature and accelerometer data, it might be nice to have this data associated with a sensor value on the ground as well. Also the onboard battery is very nice. I’ve been looking at other shields but I think I need a second set of more knowledgeable eyes to discern which ones might work best for bench applications.

Up until now we have primarily used the Arduino Yun for field sensors because of it’s wifi capabilities, which are handy for in-field debugging. Now that we are moving towards bluetooth, this is no longer necessary. I was thinking about using the Arduino UNO. This seems to be the flagship board from Arduino, and is advertised as being the best for beginners (which I am). I also know we have lots of them around already, which will make it easier to get started right away.

Field Day Application :)

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We’ve begun work on the new $FieldScience Android application! This application is yet to be named, but what do people think of the name FieldDay? I think it’s snappy. 🙂 I created a shell in Android Studio and pushed the code to our Gitlab repo. All of the developers have been able to checkout the code locally to their machines. The old application has been archived and made read-only in Gitlab.

The current developers of the application — Nic, Charlie, and myself — met last week to discuss the details of the application. During the meeting we discussed the basic outline of what we want the application to do. There will be ‘skins’ for each sensor, and all of those will interact with a basic communications library that is built to interact with all of the sensors that we have. There are many things that the old application — Seshat — did well and we discussed those and the pieces of code we want to keep — camera option on sensor skins, writing to csv, sending to database. Android applications have very particular states and processes that they go through. Through some research, we have figured out that they way our old application handled those could have been part of the problem with it crashing a lot. There is still more research to be done in that area, because we don’t fully understand it but we are getting closer.

We are not going to focus on the aesthetics of the application right now, but we did decide that we liked the front/main screen of the old app and will keep it. I’ve added that to the new application with a few enhancements. I made the skins circles and made the colors stand out more. You can see the difference and changes below (Seshat is on the left, new application on the right). Prettier, don’t you think? 

Seshat Main ScreenNew App Main Screen


A few weeks in, lots to do

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Unfortunately, we haven’t been keeping an overall summary each week, but that’s going to change now, from this week on.

In our meeting on September 28th, members came with a lot of progress and new information. Charlie and I had received an email from Oli (our contact at Skalanes in Iceland) with answers for our questions about specific projects. Oli is very interested in the Bird Nest Site Survey and the Sustainable energy project to power the ranch. He sent a link and information for the nearest weather station to Skalanes in Iceland to retrieve averages for different types of weather (wind, solar, etc.). We are giving this project thought as we progress, but no members are focusing on it as their one project right now.

Erin and Ben are the two members focusing on the Bird Nest Site Survey. Erin has been in contact with Bernard, a Scottish student that we met last time in Iceland, who has given her lot of information on all different types of birds in Skalanes. Erin is trying to research the exact nesting times for all of the birds at Skalanes, and which birds will be nesting when we go next summer. A question that needs to be answered is: what birds do we care about surveying? Only the endangered ones? Erin and Ben have also acquired the thermal camera and will begin testing it out. Oli noted that he is very into using a drone for the surveying, so as to avoid trampling through the bird’s nesting areas.

Oli also told us that the Archaeological Site projects will have to be on the back burner for now, because their license with the site has expired. We are going to ask him if we can do something that won’t involve actually being in the sites or digging up the sites to identify more sites. We’ve considered and research Archaeology Site Survey Techniques (Geophysical Surveying) and some of the options are Ground Penetrating Radar, Magnetometers, Electrical Resistance and Conductivity).

While at Skalanes last summer, we noticed that the internet was extremely slow and unreliable. Oli noted in his last message that the internet has gotten even worse. Nic mentioned using a balloon for internet. This may work. Google has been doing this for a little while, trying to give ‘Loon for All,’ where they are trying to give internet to areas that do not have it, under a project called Project Loon (Project Loon).

The soil platform/s is almost ready for prototype. Tara has decided that using the old soil platform in a better built casing, and Bluetooth is the option for the in-the-field platform. There are also three other platforms that are being researched that will be considered and used ‘on-the-bench’. They are the organic matter content, pH, and Munsell color. The organic matter content sensor is almost ready for prototype. Tara has come up with an idea that uses lasers and photoreceptors. A tube of soil will be placed in a stand, a laser will start at one end (top or bottom) and scan the the tube with a photoreceptor collecting light values on the other side of the tube. Organic matter in soil floats, so once the photoreceptor has a light value much lower than and previous value, then the organic matter has started. The photoreceptor should record that value until the organic matter has stopped, meaning the value is high again (a lot of light is going through). Tara has found some information on using Arduino with pH and will most likely follow those people’s tutorials. More information and research is still to be done about the Munsell color sensor.

The Field Science Android application is finally in the position to be worked on.Gitlab is all setup with our old repositories and we have all been able to pull from them. Our old code, Seshat, has been archived and is not allowed to be edited. This will force us to begin work on a new project, which Kristin has already created the shell for and pushed to the Gitlab repository. Nic, Kristin, and Charlie will decide a time to meet to discuss where to begin on the application, and what code to save from the old app.

The Ambiance platform has gotten some thought as well. We are no longer going to use Yoctopuce devices. They are more expensive than something like Arduino, do not work well with Bluetooth (which is something we desperately desire) and we have all agreed having similar types of sensors for each platform would be nice. More research is being done about which board and sensors to use.

Eamon has been able to extract the rows and columns from all of our CSV files and import them into a postgres database. He has been working with Flask for the Data Visualization project. There has been some debate on what is the correct language to use — php vs. javascript. Which one scales better? Eamon is waiting on more information from us about what exactly we want it to do. Some characteristics that we already know we want the data viz to have are: the ability to easily use it the night after sampling, and make sure we covered all the spots in the area that we wanted to cover, start out simple connect it to our project first, uses a static data model that we all decide on. Next week, the Data Viz will be the focus of our meeting after we briefly discuss the progress of the other projects.

Deeksha has been doing some work on the data model. She’s looked at our old data dictionary file and all of the CSVs from our different trips (Iceland 2013, Iceland 2014, and Nicaragua 2014) which are in wildly different formats and has figured out the exact data model with used for each of those trips and the differences between those models. She is using a database modeling tool to map out what we want the database to look like — primary keys, different tables, etc. and will then put them into postgres to have them all in the same place and format.

LightBlue Bean for Ambiance <3

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After our meeting last Monday, we have decided to step away from Yoctopuce devices for any platform, but specifically the ambiance platform. Although, the Yoctopuce devices are nice, and have the ‘plug and play’ option, they are expensive and complex (in terms of debugging) compared to other options.

We are moving to Arduino-like design for the Ambiance platform. After some research, I found a device called the LightBlue Bean (see below). The LightBlue Bean is a very small device that is configured entirely through Bluetooth Low Energy. You can even upload code on the go with an Android or IPhone application, which is exactly what we need. The Bean has the same chipset as an Arduino, and even has a built in Temperature sensor. A key characteristic of the LightBlue Bean is the on-board battery. In the past, we’ve struggled with our sensor platforms drawing too much energy from our Nexii. We would have to pack extra charged battery packs, which would take up space in the limited space we have for our day. When you’re climbing a volcano or a glacier, it’s ideal to carry the least amount of weight as possible.

We’ve ordered about 4 of the LightBlue Beans and they should get here sometime this week. Once they arrive, we’ll play with them and attach sensors to see how well they work. Can’t wait to play with them!

Week of 20 September 2015

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Kristin and I wrote a long email to Oli @ Skalanes with a bunch of answers and questions for him, his reply arrived this morning. Spoke with Tara about soil sampling protocols and parameters, Erin about infrared imaging for the nest sites and scaling aerial imagery, and Deeksha and Eamon about data models and data conversion. We also talked about where all the various older sets are that need to be harvested and brought into the central data store on the field science machine.

Skalanes Nesting Birds

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After receiving Bernard Lundie’s information, I was able to make headway in nesting birds. He sent me a complete document that lists the birds he know that have nested around Skalanes including waterfowl, grouse, waders and passerines. Eider (waterfowl) and Arctic Terns seemed to be most common in terms of nesting. There is an extensive list, so know narrowing down a specific research question involving the survey of nesting birds will be key, because there are so many species. Do we look just more extensively at nesting arctic terns or do we just survey nest totals in the area, disregarding species. I also spoke with Earlham’s ornithologist, Wendy Tori and she sent me several papers on arctic terns. We talked a little bit about methods but she has never done anything quite like this. The final challenge this week has been getting the thermo camera. Still an issue that might take some more time.

Joys of Reconciliation

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I’ve mainly spent time working on identifying the specific differences in the formats of data we’ve used for the last two years.There are some differences between Iceland 2014 data and Nicaragua 2015 data,and even more significant differences between Iceland 2013 data and the rest of what we’ve collected.To be able to start putting together the pieces of what we have and effectively cleaning them up,we need to locate and tag everything we can find,which is what I’ve been upto.

I now have a master table of sorts of Iceland 2014 data and Nicaragua 2015 data,so I know what/where we need to add/modify so as to have a consistent pattern in our data.

I’ve been working on what additional functionalities we want our data model to accommodate before we go back,and how to fit in the pieces of whatever we do have into the data model we decide is best this year.


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