This codebook.txt file was generated on 20180802 by Samuel T Swanson, MS ------------------- GENERAL INFORMATION ------------------- 1. Title Experiments on the Hydraulics and Swimming Responses of Juvenile Chinook Salmon Encountering a Floating Guidance Structure - Experimental Dataset 2. Author Information Principal Investigator Contact Information Name: Samuel T Swanson, MS Institution: OSU Water Resources Graduate Program Address: 116 Gilmore Hall, Corvallis, OR 97331 Email: swanssam@lifetime.oregonstate.edu Associate or Co-investigator Contact Information Name: Desiree D Tullos, PhD, PE Institution: OSU Dept of Biological and Ecological Engineering Address: 116 Gilmore Hall, Corvallis, OR 97331 Email: Associate or Co-investigator Contact Information Name: Richard A Goodwin Institution: Environmental Laboratory, US Army Engineer Research and Development Center Address: Portland, OR 97208 Email: andy.goodwin@usace.army.mil 3. Date of data collection: June - August 2017 4. Geographic location of data collection: Oregon Hatchery Research Center, Alsea, OR 5. Information about funding sources that supported the collection of the data: This project was financially supported by the PADI Foundation, a generous donation from the Edward S Allen Ag Engineering Student of 1941 Endowment Fund, and OSU’s Department of Biological and Ecological Engineering. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Creative Commons Attribution 4.0 (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/ 2. Links to publications that cite or use the data: N/A Swanson, S. T. (2018). Experiments on the Hydraulics and Swimming Responses of Juvenile Chinook Salmon Encountering a Floating Guidance Structure. Master's thesis. Oregon State University, Corvallis, OR, USA. http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/8g84mr91q 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: N/A 5. Was data derived from another source? No 6. Recommended citation for the data: Swanson, S. T. (2018). Experimental data for Experiments on the Hydraulics and Swimming Responses of Juvenile Chinook Salmon Encountering a Floating Guidance Structure [Data set]. Oregon State University. https://doi.org/10.7267/H989R8272 7. DOI 10.7267/h989r8272 8. Citeable URL http://ir.library.oregonstate.edu/concern/datasets/h989r8272 --------------------- DATA & FILE OVERVIEW --------------------- These files contain all the relevant information for the Sam Swanson's 2018 Masters thesis, "Experiments on the Hydraulics and Swimming Responses of Juvenile Chinook Salmon Encountering a Floating Guidance Structure", excluding the raw video files used in VidSync. Those files are located on an external hard drive called LACIE SHARE, number AR25U32, under file name "Swanson", in the Rivers lab at Oregon State University. Please contact Desiree Tullos (desiree.tullos@oregonstate.edu) for the raw videos. 1. File List A. Filename: Calibration Short description: These files are for calibrating and reducing distortion of the VidSync videos. File names match the location of the camera pairs in the channel. B. Filename: Experiment photos Short description: This folder contains photos of the experimental channel. C. Filename: Fish tagging Short description: Fish were tagged over the course of three days. This folder contains photos of each fish, along with their length, weight, and tag number and color in a "master" spreadsheet. D. Filename: Hydraulics Short description: This folder contains both raw and finalized hydraulic data. "Final hydraulic data (meshes)" contains dense meshes with interpolated hydraulic measurements from the nearest 10 neighbors. "Final hydraulic data (points)" contain the locations and hydraulic measurements where measurements were physically taken in the channel, before interpolation. Photos and other spreadsheets contain information that identified the location of every measurement. E. Filename: Trials - Grouping Short description: These spreadsheets contain information regarding the individual fish that comprised every trial, as well as the time of day, water temperature, and duration of each trial. F. Filename: Trials - VidSync output Short description: These folders contain the VidSync output (in arbitrary and real-world coordinates, in units of meters) created by Mr. Swanson. Observations are only of the first encounter of each fish with the guidance structure. The location of behavior changes, as identified by the single break point analysis tool in 'smoove', are given. "VidSync checklist.csv" contains qualitative information on every trial, including proportion halted vs passed, the proportion of fish seen in every trial, and the tag number of every fish in the trial. 2. Additional related data collected that was not included in the current data package: The raw video files used to produce the files contained in "Trials - VidSync output" are not included in this dataset due to their size (1 TB). Those files are located on an external hard drive called LACIE SHARE, number AR25U32, under file name "Swanson", in the Rivers lab at Oregon State University. Please contact Desiree Tullos (desiree.tullos@oregonstate.edu) for the raw videos. 3. Are there multiple versions of the dataset? As of July 2018, no. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See Swanson et al. for a description of methods used in the collection and processing of these data. 3. Instrument- or software-specific information needed to interpret the data: Several file types are specific to VidSync software, including .xml ("Calibration") and .vsd ("Trials - VidSync"). Furthermore, WinADV (publicly available and free at https://www.usbr.gov/tsc/techreferences/computer%20software/software/winadv/index.html) is required to open files containing hydraulic data measured by ADVs (.ADV, .sdr, and .sds in "Hydraulics/.../Raw SonData"). 4. Calibration information: Calibration of distances using VidSync were conducted using the videos in "Calibration/Calibration and distortion videos" and are given as .xml files in the Calibration file. The file type .xml is the output of calibration using calibration videos, and can be used directly in VidSync. Reducing distortion is also possible using the same videos and subsequent .xml files in the same location; however, distortion reduction was not found to be useful in the analysis for Swanson 2018. 5. Environmental/experimental conditions: Trial time, water temperature, group number, and tags of each fish in every trial are given by day in "Trials - Grouping". 6. People involved with sample collection, processing, analysis and/or submission: The authors would like to thank the Graduate Committee (Dr. Carl Schreck and Dr. Tyler Radniecki), the Oregon Hatchery Research Center (Dr. David Noakes, Joseph O’Neill, Jennifer Krajcik and Alex Powell) for the use of their facilities, the Hinsdale Wave Research Lab (Dr. Daniel Cox and Tim Maddux) for loaning their ADVs, the Surrogate Project (Dr. Carl Schreck, Dr. Karen Cogliati, and Rob Chitwood) for the fish, and Cara Walter for technical help. In addition, Anna Wagner, Nicole Feiten, Christina Welch, Trevor Grandy, Eileen Gale Swanson, Todd Swanson, Matt Swanson, Ploypenmas S. Boyd, and Dolores E. P. Shelton volunteered their time to tag fish, measure hydraulics, run behavior trials, and provide company at the OHRC – thank you. -------------------------------------------- DATA-SPECIFIC INFORMATION FOR: "Calibration" -------------------------------------------- 1. SUB-FOLDER: Calibration and distortion videos These folders contain .mp4 formatted videos necessary to calibrate and control for distortion using the VidSync manual instructions (http://www.vidsync.org/User+Guide). Videos for both the left and right cameras in the upstream and downstream camera pairs are included. 2. SUB-FOLDER: Calibration and distortion files This folder contains the result of the above calibration and distortion. File names describe the camera (left or right), location (upstream, downstream, or middle camera pair), and type (calibration or distortion) of each file. -------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: "Experiment photos" -------------------------------------------------- These photos illustrate the experimental setup. File names describe the image. --------------------------------------------- DATA-SPECIFIC INFORMATION FOR: "Fish tagging" --------------------------------------------- 1. SUB-FOLDER: Fish photos Photos were taken over 3 days of every tagged fish that show tag color, date of tagging, and fish length. The accompanying "Master spreadsheet.csv" compiles all of this information, as well as fish weight. "Master_Tested.csv" includes only the fish that were used in the experimental trials for Swanson 2018. The variables measured in both spreadsheets are: Date: date of tagging, in format yyyymmdd TagColor: description of tag color. Possible colors are W - white; B - blue; G - green; O - orange; P - pink. TagAdj: full identification number, formatted color (W, B, G, O, or P) and number, between 3 and 6 digits. Weight (g): weight of fish upon tagging, in grams TailForkLength (cm): tail fork length of fish upon tagging, in centimeters Picture: was a picture taken? y - yes; n - no. Notes: any other details relevant to tagging. ------------------------------------------- DATA-SPECIFIC INFORMATION FOR: "Hydraulics" ------------------------------------------- 1. SUB-FOLDER: __ degree These folders, one for each guide wall angle, contain raw (unprocessed) hydraulic data from ADV measurements ("__ degree/Raw SonData"). The location at which each of these measurements is visually shown in the .jpg image within each folder. The "__ degree workbook.csv" file contains detailed information regarding the location of each measurement. The "__ degree coordinates.csv" file describes the location of each measurement, with accompanying file name in a spreadsheet. Finally, the "__ degree coordinates measurements.csv" file contains the location of hydraulic measurements, the file name associated with the measurement, and hydraulic data associated with that point (filtered and summarized by WinADV and given in units of cm or cm/s unless otherwise noted). Variables: long: longitudinal distance of measurement (upstream-downstream) in the channel lat: latitudinal distance of measurement across the channel (left bank-right bank) Z: height of measurement above channel bottom All other variables (except TKE) are outputs of WinADV from raw SonData. 2. SUB-FOLDER: Final hydraulic data (points) The locations of each measurement in "__ degree coordinates measurements" are converted from an arbitrary coordinate system to that measure using a total station to produce three .csv files, one for each guide wall angle. Variables (all in m or m/s unless otherwise noted): X: latitudinal position (left bank-right bank) of measurement Y: longitudinal position (upstream-downstream) of measurement Z: elevation of measurement k: arbitrary identifier of cross-section Avg V_: one-directional velocity, in m/s, in X, Y, or Z direction Mag V-Avg: magnitude of velocity, averaged Avg Vmag: average velocity magnitude RMS[V_prime]: root mean square of velocity in one direction Water Speed: identical to Mag V-Avg TKE Gradient: derived from meshes in CloudCompare (cloudcompare.org) Velocity Gradient: derived from meshes in CloudCompare 3. SUB-FOLDER: Final hydraulic data (meshes) Point measurements from "Final hydraulic data (points)" are interpolated to a high-density mesh for each guide wall angle. Variables (all in m or m/s unless otherwise noted): Water Speed: identical to Mag V-Avg TKE Gradient: derived from meshes in CloudCompare (cloudcompare.org) Velocity Gradient: derived from meshes in CloudCompare -------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: "Trials - Grouping" -------------------------------------------------- These spreadsheets contain information regarding the individual fish (identified by tag number) that comprised every trial, as well as the time of day, water temperature, and duration of each trial. -------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: "Trials - VidSync output" -------------------------------------------------------- Within each "__ degree" folder, several sub-folders exist. "VidSync checklist.csv" contains qualitative information regarding each trial, including water temperature, fish ID, and the count and fraction of halting behavior. 1. SUB-FOLDER: Behavior changes from R This .csv file contains the most likely single behavioral change point, identified by the smoov package in R, of every fish trajectory with enough data points to analyze. 2. SUB-FOLDER: OBS___degree This folder contains fish observations untransformed from VidSync output. "Time" is in seconds. X, Y, and Z coordinates are in meters. 3. SUB-FOLDER: Pick Points __ This folder contains the transformation matrix used to transform OBS___degree .csv files to CL_degree .csv files. The .csv file that accompanies it is the output of a VidSync selection that picked objects with known locations from observational videos. 3. SUB-FOLDER: CL___degree This folder contains fish observations transformed from an arbitrary VidSync coordinate system to the coordinate system used by the total station, using the transformation matrix in the corresponding "Pick Points __" file. 4. SUB-FOLDER: Colors_CL___degree These .csv files contain individual fish trajectories, pulled from "CL___degree" files (which contain 5 fish's trajectories). Each color is indicated in the file name. 5. SUB-FOLDER: VSDs This folder contains the files necessary to output the .csv files given in "OBS___degree". These files can be opened in VidSync with the accompanying video files.