To-Do List

[ItoErika]

I. Data and database!!!

Questions for Joe Paradiso, Brian Meyton and Gershon Dublon:

1. Can we store DTS, weather, image and soil moisture data on the MIT servers?

   Yes, we can and this is desirable for everyone. a. What permissions are required to do this? All we need is a login credential which we will be given when needed. b. What agreements/ protocols/ standards are in place for data sharing, security, handling, formatting and access? An ongoing working group has formed called the Living Observatory Data Sharing/ Data Management Plan/ Group. This group will work through procedures, protocols and handling of all data. c. How are provisional data handled? Erika proposed a gatekeeper function for some one or some people, such that data could be passed through when calibrated/ QA/QC checked, etc. There would likely be someplace to flag provisional data, and finalized public-ready data could be stored in a related but separate place. d. How should we handle DTS data (every 25cm along a ~1,000m length at three depths)? TBD with data protocols, but likely these should remain as vectors.

2. Is there a size limit to the amount of data we can upload and store?  Yes, the server that pushes data out to the visualization from the nodes has limited capacity. It could take point-sensor data, and possibly some processed DTS vectors, but not all of the raw DTS data, nor the photos from the webcam – these can be stored in a separate MIT repository with more capacity.

3. Can the modem/ logger listed above communicate with your server at MIT?

   • My graduate student Erika Ito will be joining us, and has worked with API's this past year.  Yes, hopefully that can be made to happen. What is still missing here is a user interface. I’m still not sure where this interface lives, and how the modem will talk to it, but this will be resolved through the Living Observatory Data Management Plan in time. Glorianna has indicated interest in hiring someone to code the interface.  Christine should recommend the SCE programmer to Glorianna.

4. Can our logger be outfitted with a base station to communicate with your remote loggers, allowing us to place some at Tidmarsh West?
    Brian Mayton has a base station that will be incorporated into our long-term station at Tidmarsh West. Any locations within line-of-sight should be fair game for nodes to be installed. See later points for additional information.

II. Data, Maps, Analyses and Calculations

A. From Soil Moisture Probe measurements

• [x] Check and re-do Luke’s calculations (Excel)

• [x] Check and re-do Autocorrelation calculations and plots (Matlab) at multiple scales

• [ ] Try Wavelets on these data

• [ ] was there a rain event between West and East data collection?

• [ ] Check local weather, confirm data collection dates

• [x] Compile and map Atlantic White Cedar data (convert mV to θ)

• [x] Compile and map GSM sites at East (convert mV to θ) Mapping these Data in Matlab:

• [x] Get Routines from Christine

• [x] Get Sample Files from Christine

• [x] Get GIS coordinates from GIS unit

• [x] Make sure they are compatible with google earth (W is negative)

• [ ] Make a change map from 2014 to now?

• Thinking Big: Possible Paper from the GSM 2014 to GSM 2017 data and two transects, hummocks vs. not, to describe value in these restoration techniques???

B. DTS Hydro Data from ditch (Ecohydrology Class)

• [ ] First look at a few data files in Excel – we can talk through what’s there and what it means. Maybe we need to have a few DTS 101 sessions?

• [ ] Try processing the data in MATLAB/ R Objectives:

  1. Make a vector of distances
  2. Make a vector of times (you may note the difference between DTS, computer, and local time and probably want to convert these to local time – hopefully in the notes!)
  3. Make a matrix of temperatures (vs. time and distance)
  4. Plot something!
  5. Ultimately… we’re looking for evidence of inflows from cool groundwater. Groundwater T here should be around 10-11 degC and have a very low variance.

  Tools:

  1. First, you’ll need to make a benchmarking spreadsheet that includes an index value (either a row or column position; if you have a row vector for distances, then the index integer will identify in which row you will find a given distance), a distance, meter marks, and notes (here, you’ll gather from the data and notebooks where key things occur along the cable: connect to the DTS, leave barn, enter and exit baths ---which one? corresponding to which external probe and hobo logger? ---, enter stream, in calibration coils, crossing a key landscape feature… etc.) – I’ll send you an example.  Christine send file
  2. We can do more advanced calibration later….
  3. You have an m-file (Matlab program file) that should generate the vectors and matrix (along with the PT100 = platinum thermocouple 100-ohm temperature sensor data) variables and will save them together into a *.mat file. There should be explanatory information in the header that can be accessed in the directory with the file by typing

     help Process_Silixa at the prompt.

  4. The DTS workshop in December 2017 did a good calibration of these data using the single-ended calibration tool. Use this version for plots and further analysis.  Did we see the class’s notes for benchmarking these data or just mine? They may augment some of the meter mark locations and specifics. • Thinking Big: What else can we measure with the SW-GW Interactions class this Spring to augment this data set?
• water levels, isotopes, discharge, • SUMMER DTS run in ditches will take advantage of cold groundwater on the bottom due to buoyancy. Let’s try to coordinate this with drone thermal imagery.

C. Detailed Site Map Make, track, add to… a single, good map [GIS? Illustrator?] containing:

• [x] Best LiDAR base
• [x] Optional ditches and waterways
• [x] UMass Piezometers
• [x] Town of Plymouth piezometers
• [x] Soil DTS cable(s)
• [x] (temporary) installation of cable in water/ ditch
• [x] Chris Neil’s vegetation plots
• [x] soil cores
• [x] isotope samples
• [ ] Rob Vincent’s data? (GHG’s and vegetation – repeat these?)

D. Hydrologic Data

• [ ] Get Town of Plymouth PZ data
• [ ] Compile WL measurements (manual)
• [x] Get nearby baro data
• [ ] Get PZ pressure WL data
• [ ] AT TIDMARSH! Take manual measurements of WL and download!]
• [ ] Get flow data from Jim Limbrunner James.Limbrunner@tufts.edu (Christine has this!)
• [ ] Get flow data from Casey Kennedy (is there any?) (Christine has this if it exists) • Thinking Big: (repeat from above…) What else can we measure with the SW-GW Interactions class this Spring to augment this data set? We could try for a winter DTS run in the main ditch (always cool to look at)… or??? It would be great to have a semester long project or projects that are semi student-run…

E. Soil DTS Data

• [ ] VERY careful Benchmarking of the location, meter marks, distances, and indices of all three cables – use known points with identifiable features to cross-check notes.
• [ ] Christine to send installation notes
• [ ] Robust calibration of all data sets and validation of temperatures with independent external logger data (Hobos and PT100’s)  We have good calibration baths that are distinct from the cable temperatures and each other for some times, we do not for many other times. We need to index when are the “good calibration” times and when are not. Likely we can apply a calibration based on those times and extend it through the other times.  We need to build and install a resistance-heater in one of the baths!!!
• [ ] Careful processing notes: what are you doing with what, file names and locations, observations as you go, questions etc. • THE SCIENCE: What do we see under the ground? What are the times/ scales of interest for these observations? Where are data reliable? Unreliable/why? What can we quantify? Can we get passive soil moisture? Data Assimilation? Can we key to Luke’s surface measurements? Are each representative? More brainstorming needed here…  If you want to go the Data Assimilation route, we can get in touch with Susan Steele-Dunne at TU Delft and/or Dara at MIT.

F. Soil Cores (Hyprop/ LOI)

• [x] Repair Hyprop  Christine complain again to METER group (was Decagon) ☐ Christine to send back to METER (when RMA and label arrive)
• [ ] Continue to analyze remaining samples with Hyprop to get good hydraulic properties for Tidmarsh geologic materials
• [ ] Review curve-fitting and interpretation from Hyprop post-processing software (need to install this somewhere). We need to make sure that the input parameters are correct (dry weights etc.) and that curve selection and other inputs make sense, as well as curve-fits, start/stop points and data weighting for optimal results.
• [ ] Conduct LOI on finished samples
• [ ] Contact Todd Caldwell for figuring out how to correctly estimate the moisture and moisture curves in Peat samples using the Hyprop
• [ ] We have 2 samples from 1 location at Tidmarsh West. It would be good to collect cores from at least 9 more sites. These should be analyzed with the Hyprop and LOI.  No, scratch that – we’ll use the ~12 full-depth sites and 71 total sites (plus the addition ~10 at new reference site: Farm Stand Bog) from vegetation monitoring for these locations.

G. VEGETATION MONITORING (Soil Cores, Soil Chemistry, LOI, θ):

• [x] Collect volumetric soil moisture cores at the same plots where vegetation will be monitored; this will be a really great spatial survey of moisture that can be repeated post-restoration and correlated. Weigh samples the same day of collection for wet weight, then dry and weigh again for dry weight to get gravimetric water content.
• [x] Take synchronous probe measurements. If we could do 0-6”, 6-12” and 12-18” depths, these will be similar to both the cable depths and the pre-restoration samples at East from 2014.  Took core samples at 0-5cm, 5-10cm, 10-20cm and 20-30cm depths.
• [x] Chemical analysis from all surface samples and with depth at 12 sites, 2/bog.
• [ ] Chemical analysis from all surface samples and with depth at 12 sites, 2/bog in Marco Keiluweit’s lab: pH for all samples???
• [ ] LOI from all samples.
• [ ] Textural analysis from all samples.
• [ ] Repeat everything post-restoration.

H. LiDAR Data ☐ Christine emailed Forrest Bowlick with GIS student project description: • Map the Bog with Ground-based LiDAR: Create a clean, detailed, DEM Map from ground-based LiDAR data for the "pre-restoration" condition at a fallow cranberry (bog) farm in Plymouth, MA, and a "post-restoration" DEM from the sister site where restoration actions have already occurred. Spatial analysis options could include statistical analysis of topographical variability between restored and control sites, and/or comparison between data from two different LiDAR units • Data are available, but note that both will require learning the RealWorks software package to stitch images together (for restored vs. control), AND another software system to compare between two units' data (for this option).

Steps:

• [ ] Stitch together images from Tidmarsh East
• [ ] Get Colin Leason’s data from Tidmarsh East, stitch
• [ ] Compare data between them: how are they different? similar? why? operating principles? better for different things? designed for different things?
• [ ] Stitch together images from Tidmarsh West
• [ ] Make a nice DEM map, pointcloud and contoured surface
• [ ] Share with MIT Media Lab
• [ ] Compare topography at West vs. East: how much microtopography is there? Using a baseline near the old cranberry may surface, how much land is above vs. below that level at East? Calculate metrics: roughness, boundary layer thickness, etc. on both areas

Learn RealWorks: are the Trimble Lab computers updated?  Ask Alex Schreyer what is the status of those licenses?  Perpetual and available, coordinate installation with Alex Schreyer Install on (my) machine?  Done and licensed. Or in GIS Lab?  No but YES installed on server that Drone class students have access to in addition to point-cloud processing software (AgiSoft) and DroneDeploy

Other:

• Possible Difference map between State LiDAR and Ours? (this would be what we changed during cable installation)
• Chickley River images

I. Isotope Samples and Surface Water Chemistry Samples

• [ ] What is the distribution of Springs at Tidmarsh West? How do these relate to the location and depth of peat? What kinds of Springs are they? What is their source and path length? • How do these compare to the data from piezometer waters? • What is the difference between PEAT waters and SAND waters??? • Get new data from Marsha

J. Surface Geophysics

• [ ] Can Surface Geophysics (GPR from USDA) tell us the depth to, thickness of, and extent of the underlying clay? (Bug Bill Clement) • Kamini Singha would love to participate! Let’s call her! Maybe she’ll come to Plymouth or Erika can go to Colorado!

K. Notes for Restoration • Lessons from Isotopes? • Lessons from Surface Geophysics? • Paul Wetzel would like to set up some of the restoration actions in a deliberate way across Chris Neill’s vegetation plots such that we can directly monitor the changes in vegetation induced by (a) the placing of a log/ large wood, (b) the presence of hummocks, (c) the presence of surficial peat, (d) the presence of hollows, etc. – this will have to be coordinated with restoration maps/ plans.

III. Fieldwork To Do List

A. Piezometers

• Water levels

IV. Lab work To Do List

A. Hyprop

•

[cehatch]

Does this format track changes and history?

[cehatch]

Also, is this version your edited version from the previous one?

[ItoErika]

@cehatch This is the same version as the first version you gave me (only difference is I tried to break it down in check box form to make it more readable).

Issues do not keep a history of changes like scripts do in GitHub repositories, but the comment section is a good way to track any changes relevant to filed issues.

I also emailed you with a more detailed explanation!

[ItoErika]

@cehatch GitHub is actulaly about to roll out an update to include edit histories for issues! [https://help.github.com/articles/tracking-changes-in-a-comment/]