Breaking news…

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For two weeks I’ve been trying to figure-out how to add the Iceland playlist Kristin created to my Spotify profile. Yesterday, Kristin explicitly shared it with me and that worked, phew. I was afraid we were going to have to cancel the whole project.

On more mundane fronts I’ve been working with Erin on the GIS and maps, with Kristin on Field Day, with Deeksha on the data model/data, with Tara on the NIR and tube turning rigs and Mothur, and with Nic on LiDAR, the UAS, and imagery. All of these are coming along well, we have lots to do but we are steadily moving along together. Go Team.

For Field Day Friday we made a simple lunch of pasta with pesto and then took a short walk around campus collecting data with Field Day/ambiance platform and the Yoctos. The streaming and sample data has been uploaded from the Nexus to Postgres, next week Craig is going to visualize it and start doing verification and validation on it. This is the first time we have had the luxury of working with an “independent lab” on this aspect, in the past developers did this (about as well as you would expect them to).

I setup IceBook (13″ MacBook Air) for Erin to install QGIS on. Slowly we will be migrating all of our software stack (database, analysis tools, visualization, time synchronization, etc) from hopper and other machines to IceBook. Just before we leave on the 22nd we’ll move our Git repository over and viola, we’ll have everything with us. We’ve done this twice before in Iceland and once in Nicaragua and it works really well, being self-contained helps a lot when Internet access is spotty.

Next week will probably look a lot like this past one. On Tuesday morning NIc, Erin and I are going to talk to Patrick about GIS and archeological surveying at Skalanes.

Building Device Housing and Bench Tools

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Each device I am prototyping for bench or field work needs some kind of housing so that it can serve its purpose and/or stay operational in wet or dirty situations. There are three  I am focusing on now:

  1. Bench top flacon tube spinner. Originally inspired by this device that costs $100+, the bench spinner is necessary for measuring accurate pH of soil. Charlie and I have come up with a device that can spin up to 10 falcon tubes at a time and will be made from PVC pipe, epoxy, and potentially a lego  motor.
    Screen Shot 2016-03-23 at 10.49.19 AM
  2. Field sensor case. Modeled off of the 3D printed ‘flask’ design previously used in Iceland. The case will be larger to house a BLE shield and will have a hole with some kind of cover to protect the IR temp sensor (working with BLE). Right now I am trying to figure out if the soil moisture/temp probe (not working right now, may be toast) and the conductivity probe (working) really need to be out in the field or if the same data can be gathered on the bench. Once everything is working and in some kind of preliminary housing I can test that.IMG_1558
  3. NIR TI Nano housing. We have just purchased two quartz crystal coverslips that transmit NIR radiation. I want to build one of these into the housing for the nano so that the internal optics as well as the micro controller are protected. The coverslip is about the size and thickness of a quarter. It is important that it is completely flush with the Nano optics and that it can be lowered completely onto the sample so that the distance between the optics and the sample is not only minimized but uniform. Until the quartz slips arrive I have stalled testing and calibration of the nano to protect it.

 

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Two other things that are temporarily on the back burner but are still important:

  1. The CO2 probe. If it works, this probe would allow us to measure CO2 respiration as a proxy for microbial biomass. Charlie had the excellent idea of attaching the probe to one end of a long PVC pipe full of soil, to increase our sample size and not disturb the microbes by digging up and mixing their soil habitat.
  2. The RGB Munsell color sensor. I have started experimenting with colors the RGB reads and have so far been a little disappointed by it’s accuracy. I will work on compensating for ambient light and optimizing the reading in one color space before using a linear transformation to convert those values to Munsell space.

Two final ideas are on the lowest priority in the ‘if I have time before we leave’ category. They are:

  1. Bench-top light-transmission organic content. A fancy name for shining light through a tube and measuring the thickness of an organic content band. This would be cool because it’s automated but it is easy to do visually and might even be more accurate, so it’s not a high priority.
  2. RGB pH strip measurements. This one is also easy to do by sight, it isn’t difficult to match the color of a pH strip to a key. However, once the Munsell color platform works, adding this functionality is simply a matter of writing the software, because the hardware setup is the same. For that reason it is more likely to be completed then the OC reader, which is somewhat design intensive.

Lab Notebook on Field Day

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This week, I’ve done a lot of work on Field Day. It doesn’t seem like much but that’s because I kept getting caught up in tiny errors during coding. The biggest thing that I’ve added to Field Day is part of the Lab Notebook activity. We decided this week that integrating Google Drive is less important than being able to open local files. We decided this because we will not always have internet access in Iceland and that’s essential for Drive if we want to update our files. The Google Drive API for Android also has limited options. The Android API only allows the application to access files that were created by the application itself. Since most of our files are PDFs and the Android API doesn’t allow uploading, we decided to move away from that for now. There’s a Java Client Library for Google Drive which has many more capabilities that we will probably use when we go back to Google Drive.

I’ve begun working on the local documents viewer and have successfully downloading files and displayed the pdfs. There’s now an option to download files where the user provides the URL of the server where the files are and the path to the directory with all of the files in it. The code relies on the directory having indexing enabled. Field Day goes out and queries the directory and returns a list of files and folders. The user is asked to select which files to download. If a folder is selected Field Day goes out and queries that folder, etc. until the user hits ‘Download.’ The files are downloaded and stored on the external storage (the SD card) keeping the directory structure that Field Day saw in the remote directory. A list of files of is displayed on the screen to the user. Upon clicking a file, the file is displayed. Currently it works for only PDFs and JPEGs which are handled as Bitmaps. Text files are not. If a folder is clicked then the folder is opened and the files and/or folders in that folder are displayed.

Iceland Land Survey and the Glaciers

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Early last week I found the National Land Survey of Iceland’s ArcGIS map viewer. This proved to be a very useful tool. This allowed me to make individual topographic maps of all of the places that we will be going. The tool allows the user to add there own lines which allowed me to create a scale. I highly recommend playing with the tool (link below)! I printed the maps in color on 8X11 paper and they are next to the computer in Hopper. The next step is just to laminate them and make sure we have all the places we need. The following is an example however I did this for the five different glaciers- Sólheimajökull (smaller glacier); Skaftafellsjökull, Kviárjökull, Svínafellsjökull and Fjallsjökull (big glacier). I also did this for Þingvellir, Heimay, Grímsey and Klauster, all of which are areas we will be visiting for either science or studies purposes. Klauster and Þingvellir have two maps of different scales in order to better capture the information we will need.

Land Survey of Iceland Arc Map in English

Land Survey of Iceland topo map of Skalanes with scale.
Land Survey of Iceland topographic map of Skálanes with scale.

 

I worked on many other small projects this week. One of these was getting in touch with TREK Iceland. This was a group who took the Iceland group on the glacier and to the river bank last time. I have been in tough with them over email and they will be taking us to the glaciers and to the river bank to get soil samples on June 28th and 29th. I have also been in contact with the map store in Iceland that I mentioned in my last post. Another small thing was researching glacier sampling a little more. I created a document in the glacier folder of links to informational papers and website to help us better understand the glaciers and how best to go about sampling them.

NIR Reflectance

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This past week I mostly worked on NIR, the field platform, and a little on the CO2 sensor.

I converted the collected absorbance data from the TI Nano to reflectance, which is better documented for organic content. I reran standards that are a mix of sandy soil with very little organic carbon and compost, which is very high in organic carbon. These are the results:

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For reference, this is a figure from Shuo Li et al. [1]

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I would really like if the nice peak between 1300-1400 was our organics peak, but I suspect we actually want to focus on the scraggly region out by 1700. My plan is to focus in on this region and increase the sampling rate of the device. The trend here is very promising.

The field platform prototype is coming along. I have incorporated the BLE and Field Day-friendly formatting, but I am getting readings that don’t make sense. This week I will focus more on hardware debugging.

The RGB platform is my next order of business. I am going to start with Munsell color. That will give me a good jumping off point for less crucial things like pH and NPK strip analysis.

[1] OrganicCarbonTibet

The low point of my day…

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As near as I can tell from a quick look at the data collected by Field Day and Grace (our prototype ambiance platform) and the Yocto altimeter (based on the same MPL3115A2 chip that we use) this was the low point of my day yesterday at about 201m:

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I started Field Day and the Yocto around Portland, Indiana and then drove home and walked down to the creek where this picture was taken. The highest point in Indiana is about half-way between Portland and where we live in Boston. The creek bed is the limestone floor of the ocean that covered this part of the US about 350mya. Neither device was calibrated, and we won’t know for sure how the track looks until Craig maps the data, but things are looking good.

 

In other news Nic has collected data from the LiDAR in the lab as it moved slowly over an object on the floor. We’re collecting theta, distance tuples at set intervals (1cm) along the track, I think we can visualize these as stacked wind roses as a first-order approach to “seeing” what it found. Matplotlib to the rescue!

Tests of light detection and ranging

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Charlie and I had a conversation at the beginning of the week about if the LiDAR module we are using is the “right” one for our purposes. The bottom line is that we don’t exactly know and so I set out to answer that question.

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I built a controlled slider that gives us nearly 20cm of movement that we have control over when taking LiDAR measurements. My first test was to place a pencil on the ground and take 1minute of scans at each centimetre. The hope was to be able to pick out the pencil given “perfect” circumstances. After collecting the scan data, which consisted of only the distance in mm and the theta (degree angle at which the scan was take), I then artificially created a Y value corresponding to the 20cm of data taken.

After I got the data into a pleasing form I began to try and visualise it. This proved to be a tad bit difficult and I still don’t have it quite right yet but I was able to see something;

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I am fairly certain that the object towards the top of that screenshot is one of the legs on the tripod that the beam picked up. I am not entirely sure though and will continue to do tests until something is conclusive.

Sending data back and forth

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As you remember, last week I finished the new data model implementation within Field Day and downloading remote database data. Field Day writes sensor database to the local database respecting the new model — populating fieldday_streaming, fieldday_reading, and fieldday_spot.

The big hurdle that still needed to be hopped over was sending those newly populated tables back to the remote database. This week I got over that big hurdle. The user can now upload the local tables to the remote tables. Field Day gets all of the rows in the tables I mentioned above, starting with fieldday_spot because the other two have foreign keys that reference the spot table. Moving the rows from the reading and streaming table is simple, but moving the spot table has different characteristics. If people are pushing to the database at the same time, we have to make sure that we are only inserting one of each ‘trip, site, sector, and spot’ which make up the primary key in the database. Field Day takes the ‘tripID, siteID, sectorID, and spotID’ of each row in the local database and queries the remote database asking for the count where a line has those four columns that equal the values in the local table. If the count comes back zero, then Field Day inserts the row. Each tables updating is wrapped up in a transaction, so if something goes wrong Field Day rolls back the transaction and sets the database to it’s previous state. Once the inserting has successfully finished, the database in the local table is copied to external storage in an /archive directory and the tables are dropped and created again so they are empty.

I moved ‘Take a Sample’ on the main screen to ‘Sampling’ and created a new option under that menu for ‘Database Actions.’ The downloading from remote database activity was previously under the Settings option, but since the application is basically doing the same thing in each, I merged them in to one activity. There are three buttons for the user to choose from (which you can see in the picture below) — setup local database, upload tables, clear local database. Upon the press of any of the buttons, the user is asked to confirm.  When the user selects clear local database, just like after the user upload the tables, the local database is copies and wiped.

A couple other small things that I’ve worked on this week are integrating the Google Drive Android API and fixing small things with the sensor sampling activity. As for the Google Drive API, I’ve gotten Field Day to the point where it asks for permission to access Google Drive, but doesn’t do anything after that. To my knowledge, this API only allows the app to interact with files that were created by the application itself. I’m not 100% sure of that so I’m still working on it. Small things that are fixed are the user is notified if they haven’t set up their local database with a remote database, which means they can’t write anything to the local database. When a Spot number is put in the spot edit text on the sampling activity, Field Day checks to make sure that spotID doesn’t already exist in the local database if it does, then it doesn’t write to the database.

 

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Our first Field Day Friday

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Tara, Kristin, Nic and I took Field Day, Grace (the prototype ambiance platform), and a Yoctopuce altimeter for their first field test today. We biked down to the Starr-Gannett building in the gorge, walked around where they are setting-up for the Richmond Shakespeare Festival, and then had a nice picnic and returned to campus. Craig Earley is working on mapping the first data sets from Field Day/Ambiance, all we have to show for our effort is this great selfie…

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Data Progress

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This past week, the new data model was implemented after some K,C and I talked about it for the past few weeks. We now have multiple tables in the model, with a table for basically every data point. I have been looking at Iceland 2014 data to figure out what data we can move over into this new model. I’ve learned that there isn’t very much data we’d like to move over from Iceland 2014, although almost all the Nicaragua data is good to move over (in the fall, once we’re back from the Iceland scrum.) The distance function came in really handy here, and made me really glad that we finally all have the old data in a single, easily searchable place. We’re not moving the data over into the new model, but it’s easy to query it where it is now (something that hasn’t been possible for a while)

 

So for now, we are keeping all the Iceland 2014 and Nicaragua data in the old model on Postgres, and focusing on this years’ data, and getting that working in time.

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