Sample Volume and SCIO

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On Saturday Charlie and I talked about what the maximum number of samples we could reasonably process in the evening with bench-top sensors would be. We decided that 20 would be the upper limit. In the evening we will be collecting pH, conductivity, munsell color, fertility and organic content data. The most time-intensive test is organic content, which requires the sample to settle in water for up to 30 minutes so that the organic content can rise to the top. It will be very important for us to test the bench-top sensors with a large volume of samples before we take it into the field.

This week, the SCIO was ordered. I have been looking through the developer blog to see if anyone has used the SCIO for applications like ours. So far I have found that there is an interest but most people don’t have access to higher-caliber IR spectroscopy technology for calibration. However, we are fortunate enough to be working right down the hall from Mike Deibel. Mike has offered to let us use his Fluke portable FTIR to calibrate the SCIO. The developer SDK workflow has three steps, using the SCIO itself, the ‘development model’ web app, and the mobile developer package. The developer web app offers control of the algorithms and statistical methods that the SCIO uses to determine the composition of a sample. Using the spectra generated by the FTIR I think we can definitely ‘teach’ the SCIO to recognize the chemical signatures of different nutrients. The mobile app SDK is open and will ultimately allow Field Day to communicate with the SCIO.

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.

12 October 2015

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In this weeks meeting Charlie started things off with laying out what questions we still had for Oli such as dates for the trip, in what location, and where would we be staying. We also discussed the logistics of the Xsede conference and the likely-hood of needing to fly directly from Iceland to Miami. On a side note, the idea of a Wilderness type program at Earlham was brought up. Our next topic was brought up by Erin, that we might have some issues with the balloon idea but that running the balloon off of a telephone pole might be the better option. Ben detailed what he had found regarding the thermal camera and that will start on a way to map the data and logistics of using it. Nic annotated a page on android dev explaining how processes work and when to use them, as well as possible implementations of old Sheshat code into the FieldDay app. Deeksha went over requirements for the SIGCSE poster. Kristin has been working with the LightBlueBean, figuring out the interface enough to get a test up and running and has been working with Charlie and Nic with the design and implementation of FieldDay app. Tara has been doing work with the sensors and has been working with Mike Deibel on soil fertility and found we might be bale to build an equivalent to a near IR spectroscopy. The Munsel colour test is definitely viable for use with visible light. Eamon started doing work with the front end and getting google maps to geolocate points and the Drop menus are finished and easily useable.

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.

Screen Shot 2015-10-26 at 4.07.56 PM

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.

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