This readme.txt file was generated on 20220707 by Daniel Furuta Recommended citation for the data: ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data and analysis code for "Capturing High Resolution Plant Movement in the Field" 2. Author Information Principal Investigator Contact Information Name: Deborah Heuschele Institution: USDA Agricultural Research Service Address: 1991 Upper Buford Circle, St. Paul, MN, 55108 Email: Jo.Heuschele@usda.gov ORCID: 0000-0002-8157-8458 Associate or Co-investigator Contact Information Name: Daniel Furuta Institution: UMN Bioproducts and Biosystems Engineering Address: 1390 Eckles Ave, St. Paul MN 55108 Email: furut011@umn.edu ORCID: 0000-0002-9603-9262 Associate or Co-investigator Contact Information Name: Kevin Smith Institution: UMN Agronomy and Plant Genetics Address: 1991 Upper Buford Circle, St. Paul, MN 55108 Email: smith376@umn.edu ORCID: 0000-0001-8253-3326 Associate or Co-investigator Contact Information Name: Peter Marchetto Institution: Sensing, LLC. Address: Roseville, MN 55113 Email: petmar@sensinginc.com ORCID: 0000-0002-7302-0905 3. Date published or finalized for release: 2022 4. Date of data collection (single date, range, approximate date) 2019-2020 5. Geographic location of data collection (where was data collected?): UMN Twin Cities crop research plots 6. Information about funding sources that supported the collection of the data: This research was funded by the MNDRIVE Robotics Sensing and Advanced Manufacturing initiative, Minnesota Department of Agriculture Grant No. 122130, and the University of Minnesota Rapid Agricultural Response Fund Grant No. AES00RR234. 7. Overview of the data (abstract): This is the dataset and analysis code used for the paper D J Heuschele, D Furuta, K P Smith, P Marchetto, Capturing High Resolution Plant Movement in the Field, Integrative and Comparative Biology, 2022;, icac075, https://doi.org/10.1093/icb/icac075 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Public domain 2. Links to publications that cite or use the data: https://doi.org/10.1093/icb/icac075 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Folder: analysis_code Short description: Python scripts used for the paper. 1. File: check_csvs.py Short description: A script to remove corrupted entries from the raw data, and to split the raw files into multiple smaller files of manageable size. 2. File: find_baseline.py Short description: A script to estimate daily gyroscope baselines over the course of data collection, which can then be used to correct for sensor drift. 3. File: motion_analysis.py Short description: The main script for analyzing our dataset, using the outputs generated by the above scripts to estimate plant motion parameters relative to wind over the course of the season. 4. Folder: visualization Short description: A collection of six python scripts used to generate figures for the paper. All scripts have short descriptions in comments at the start of the files. These scripts are written to account for particularities of our collected dataset, but can be used as inspiring or guidance for visualizing other data collected with the same system. 5. File: script_usage.txt A file giving brief notes on library versions and the order of script usage. B. Folder: cleaned_data Short description: Data used in the paper. There are two folders, one for 2019 data and one for 2020 data. Each contains folders for motion data, wind data, and a key, which are further described below. C. Folder: sensing_system_firmware Short description: Firmware used for the IMU systems, written in the Arduino language for Adafruit Adalogger M0 microcontrollers. For further details, please see the paper. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See paper 2. Methods for processing the data: See paper and README file in the cleaned_data folder 3. Instrument- or software-specific information needed to interpret the data: See paper and appropriate README files 4. Standards and calibration information, if appropriate: See paper 5. Environmental/experimental conditions: See paper 6. Describe any quality-assurance procedures performed on the data: See paper 7. People involved with sample collection, processing, analysis and/or submission: Daniel Furuta, Deborah Heuschele, Dimitri von Ruckert, Marcos de Souza, Stijn Vandycke ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: wind data ----------------------------------------- General note: The project deployed several anemometer stacks, as described in the paper. Each csv file corresponds to one numbered anemometer stack. Some consecutive numbers are missing, corresponding to units which malfunctioned in the field or were destroyed by weather events. 1. Number of variables: Four 2. Number of cases/rows: Varies by file 3. Variable List A. Name: datetime Description: Date and time for the entry. B. Name: anemometer Description: Anemometer unit in the stack, as described in the paper C. Name: speed Description: Wind speed in m/s. D. Name: dir Description: Wind direction, given as one of 16 divisions of the circle. E. Name: battery Description: Battery voltage, recorded primarily as a diagnostic variable for system health. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: motion data ----------------------------------------- 1. Number of variables: 15 2. Number of cases/rows: Varies by file 3. Variable List A. Name: system_ms Description: System time, recorded as ms elapsed since power-on. B. Name: gx, gy, gz Description: Gyroscope readings in the x, y, and z axes, in degrees/second. C. Name: ax, ay, az Description: Accelerometer readings in the x, y, and z axes, recorded as multiples of gravitational acceleration (g). D. Name: mx, my, mz Description: Magnetometer readings in the x, y, and z axes, in Gauss. E. Name: gps_time, gps_date Description: Time and date from GPS. 0 values indicate that satellite lock has failed. F. Name: lat, long Description: Latitude and longitude from GPS. G. Name: bat_voltage Description: Battery voltage, recorded primarily as a diagnostic variable for system health. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: key.csv ----------------------------------------- General note: This file is used to associate motion data files, the originating sensing unit, and the anemometer we used with that data for our analysis. Note that most sensing units have multiple data files, due to power resets in the field or the need to split the raw data into manageable file sizes for processing. 1. Number of variables: Three 2. Number of cases/rows: 83 for 2020 data and 285 for 2019 data. 3. Variable List A. Name: imu Description: The originating sensor unit for the data file. B. Name: motion Description: The filename of the corresponding data file. C. Name: wind Description: The filename of the corresponding anemometer file used for our analysis.