SQLite DB for Data.

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On Saturday, Charlie and I discussed the notion of persistent data for the Field Day android application. Previously, we would stream all of our data to a CSV — even empty lines or entries that are missing data in some spots, and this would cause data to be in a bunch of different data models.

I recently read a chapter on SQLite databases in Android and it seems really powerful. We’ve decided that we are going to use a SQLite database instead of just writing to a CSV file. With this, we could create primary keys and easily pick out all the lines that have empty fields for one column or another. Using a SQLite database will also be useful for our plans to implement an ‘On-Bench’ and ‘In-Field’ option for the soil platform. There are some sensor data that you wouldn’t take in the field and would need to do later that day — like pH or organic content. Using a SQLite database, we’ll be able to simply ask for the sample ID from earlier that day and update it with the pH and Organic Content. Our data will be less messy and we’ll have less random lines of data floating around.

Saw a Squirrel

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This week I dedicated most of my time to helping Erin with figuring out how to use and implement the thermal camera as well as with setting up a plan with the balloon use. In terms of the thermal imagery, we were able to verify that at ~15m you could spot a squirrel on the camera screen though the actual heat reading appeared fairly inaccurate. Squirrels, like most mammals have a body temperature around 37 degrees C – the the camera however only picked up a heat signature of 20 degrees C. Weather would have been a factor in degreasing the body temperature, but this means that we can’t get an accurate reading to be able to tell differences in species so we will be heavily relying on post processing to determine animals. This leads into the second worry that the current camera cannot give a live feed or any form of video. This means that we need to either look into a different thermal tech or gutting and reworking the current camera we have.

From ‘Blink’ to BLE

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This week I am getting acquainted with Arduino. I started with this basic guide – ‘install software, plug in board, make it do a thing with a sketch in Arduino. I played around with some other sketches and basic searches. When I had success with that I moved on to  connecting the BLE shield to the arduino uno and getting it to work. I followed these simple instructions to setting up the RedBear Labs libraries and getting the shield to talk to the stock android tablet available through the app store.

Screenshot_2015-11-02-15-27-37Screen Shot 2015-11-02 at 3.41.57 PM

Next I will be trying to get the IR light sensor to work with the BLE shield. I will need to decide sampling frequency as well as how to transport data packets to ‘Field Day’.

 

 

 

 

Week of November 1, 2015

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I accomplished very little last week on this project (homecoming, dedication) other than planting some fundraising seeds with some potential donors over the weekend. Over the next week I plan to:

  1. Begin the conversation about if, and if so how, the field science project can become a regular Wilderness Program offering.
  2. Process Oli’s most recent message and prepare a reply.
  3. Develop initial materials for A/D to use with potential donors; meet with SallyS and AvisS.
  4. Work on Field Day.

Squirrels and the Internet

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This week Nic and I spent time brainstorming and testing the thermal camera. We were able to see squirrels from approximately 15 meters away. Squirrels have a body temperature of about 36-38 degrees C and the arctic terns have a body temperature of just over 40 degrees C. The terns are a little bit smaller but being able to detect the squirrels is a great indication of what our success with the camera could look like. We are still trying to figure out the best way to test aerially. We could use water bottles with water, heated to the correct temperature. Right now however, we need to figure out if this is going to be the best technology to use, because the set-up might prove to be a little difficult. First we would need to mount the camera with Sugru (not very difficult).  However figuring out how to make the camera take the photo or live feed a stream might be difficult. It looks like right now our options are either to try and open the camera and wire something into it that could stream the feed (not sure if this is possible), or we can start looking at other technology. One option that Ben and I discussed early on in the year is Flir One Thermal Vision. However the website for the technology is very poor so finding information has proved difficult, however it is basically an attachment to a smartphone that displays thermal image.

Latitude and longitude for the the yellow point on the map below for the internet:

65°17’39.06″N

13°54’30.42″W

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Cleaning Up

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I’ve continued working on my master table.I’ve been doing two things to the data,cleaning up the format it’s in,and substituting dummy values for those records where we don’t have values.I’ve also been doing a reasonableness check with the data by comparing our calendars and where the calendars said we were to the data we have.This has let me know what data we can safely get rid of,like the couple of testing streams we have from around hostels.

I’m almost done with cleaning up and should be able to just put all of my nice clean data (all in one format!!) into the fieldscience db.

Android Architecture

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Nic, Charlie and I have been struggling with finding a time to meet so we can talk about the Field Day android application. We were able to briefly talk about it on Saturday morning, and decided some things about the architecture of the application.

Currently, the main screen of our application shows all 8 “skins” (Earth, Ambiance, Gas, Water, Settings, About, Notepad, and Protocols). We’ve decided that we want the main screen to have just 4 skins (Settings, ‘Take a Sample’, ‘Lab Notebook’, and About). The Take and Sample and Lab Notebook skins, once clicked, will open up into a variety of options underneath. All of the types of sample skins from before (Earth, Ambiance, Gas, and Water) will now move underneath ‘Take a Sample’ skin. Under ‘Lab Notebook’ we are going to move Protocols, Notepad, Checklist and whatever else we decide.

Having a separate page for just sampling will make using fragments a lot easier. I’ve started on making icons for the new skins we decided on, and will implement those in the code as soon as they are ready.

Hopefully today we will be able to talk and get more work done in the meeting.

BLE shield and laser diodes have arrived! New options for fertility spectrophotometry.

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BLE Shield

The Makershed BLE shield I ordered arrived this week! My plan right now is to use this shield on the temperature/moisture sensor designed for use in the field. The field sensor will look a lot like soil platforms we have used in the past with the addition of an IR sensor for measuring temperature of the soil. I have ordered a small IR sensor that I am expecting to arrive soon. To test it’s accuracy I will use a fluke IR thermometer as a benchmark.

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I am pretty new to Arduino development so I have been reading up on how to interface a BLE shield with an android application. I downloaded the BLE libraries for Arduino. Now I am trying to think about how my sensor will interface with Field day. I want a reading to come up on the screen as it is taken so that the user can confirm data is being recorded in the app.

The next thing to consider is the casing for the platform. I think the 3D printed ‘flask’ idea from the first Iceland trips is pretty solid and I would like to do something like that again. I would also like to case the outside of a plastic case with rubber to make the flask more impact resistant if it is dropped.

Laser Diode

The laser diodes arrived this week. I will begin prototyping the optical density sensing rig this week in lego.

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Spectrophotometry

There are some interesting commercial solutions for near IR component analysis. One is the Scio – a kick starter project that has now gone into production. The Scio goes into the near IR range and comes with a developer SDK that would allow us to test it on soil and interpret the spectral results based on known soil composition and Mike Deibel’s more advanced IR sensors. There is another option called Tellspec but it seems much more closed-source.

Imaging from the Top of Campus

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We did lots more testing with the Fluke Thermal imaging camera. We tested various objects and different distances in the building, including down the Stanley hall which proved even more difficult (most likely because the lighting makes the hall warmer and we were just detecting our cell phones). From the roof of Dennis we played around with manual settings and tried detecting different things (mostly other people). It works well! The battery also lasted the whole time we were up there. Next we can look at something that is the same size and temperature as the birds we will be looking at. One idea is to microwave water in bottle to the temperature we want because that can be consistently replicated and we can know what the temperature should be. Another idea is to use the camera to look at some squirrels on campus which might be good for testing small, moving objects.

Oli emailed Charlie back with answers to our questions from earlier. The two species that we will be surveying are the Arctic Terns and the Eiders (waterfowl). I sent Bernard an email asking him if we should also put energy into surveying the Limosa limosa which is vulnerable to loss of breeding sites. In the email I sent I also asked if he thought there were any other species that might be worth surveying. The Eider is a larger duck-like bird that is fairly common in Iceland and used for down. Apparently they are all around Skalanes. I have read some papers on them, but I need some more information about where exactly in Skalanes. Are they near domesticated? Because if they are using human shelters or are in some other way larger affected by human activity, then a survey will be hard if we are trying to get an accurate survey on their natural breeding grounds.

Weeks of 18 and 25 October 2015

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Lots of little pieces over the past two weeks:

  1. After breaking my Android development environment in Nicaragua last December I finally have a working setup again. I can build and run hello world on my Nexus7 and HTC One!
  2. Started a conversation with Sally Southwick in Alumni/Development about NSF and foundation support for this project. Developed a preliminary budget (see GDrive folder) to be refined as we learn more.
  3. Started a conversation with Jay Roberts and GLI about developing a wilderness like program in Iceland. There is a lot of enthusiasm for this idea. The next step is for us to discuss this, and if we think it’s practical/interesting to do we would develop a proposal to the GLI for funding the development over the coming year.
  4. Oli replied to our last message, I will start working on a reply from us.

Things I’d like to do this coming week:

  1. Develop and distribute a signed APK of hello world that someone else downloads and runs using Android Studio.
  2. Nudge Sally Southwick, this is not a typical project and obtaining funding, especially from the NSF, will require a certain amount of effort and finesse.
  3. If the wilderness bit sounds like a good idea develop a proposal for funding the development of it for the GLI.
  4. Work with folks on the sub-terrain survey ideas.
  5. Work with folks on the ballon terrain survey ideas.
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