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Study of seasonal meadow ecohydrology in Sagehen Creek Basin.

R 0.07% Python 0.10% MATLAB 0.02% Jupyter Notebook 94.22% HTML 5.59% Shell 0.01%
groundwater vegetation phenology

sagehen_meadows's Introduction

Directory Description

scripts

phenopix

scripts for phenopix data processing of phenocam imagery in meadows (in R + python)

groundwater

scripts for groundwater data processing of manual and logger measurements in meadows (in matlab, so far)

data

field_observations

field-collected data for four meadows in Sagehen Creek basin, includes:

  • groundwater measurement (manual and loggers)
  • mapped hydrologic delineations (e.g. springs, channels)
  • soil observations at new wells
  • phenology descriptions through 2018-2019 growing season. The "raw" data include unprocessed field observations as a starting-point and archive.

instrumentation

files in this folder contain geospatial data related to field instruments such as wells, stream gages, weather-related devices

phenocam

files in this folder include OUTPUT from phenopix processing.

please note:

  • files do NOT include the actual phenocam images, the INPUT for phenopix processing.
  • For now (will need to be moved by mid-July 2024), the phenocam images (and status sheet) live on Jen's UCB Google Drive in /GoogleDrive/PhD/Manuscripts/2018_ISEECI Sagehen GW Pheno/Analysis/Data/Phenology/phenocam/
  • The phenocam images require a large amount of storage.

transects_geophysical

files in this folder contain data related to subsurface geophysical imaging of meadow transects.

remote

(not yet populated) satellite and aerial imagery of meadows in Sagehen Creek basin

sagehen_meadows's People

Contributors

jnatali avatar

Stargazers

Allison Zau avatar

Watchers

 avatar Brian Kallay avatar

sagehen_meadows's Issues

Rename wells

Rename wells based on field observations of HGMZ + PFT

  • Rename EEF-XA1N to EWR-XA1N; "aside gravel bar in willows" noted on 07/05/2021
  • Consider renaming EFF-XA2N to EFR, note that it's clearly riparian and pines within 2 meters on 07/05/2021
  • Address more comments on renaming wells on 07/05/2021

Generate vegetation phenology time series from camera images

Phenocam Vegetation Time Series

Goal: Develop and analyse phenology curve data sets based on time-lapse imagery from field-mounted cameras, known as “phenocams”. In Sagehen basin, 6 phenocams were deployed in 2018, 8 in 2019, 10 in 2021 and 2024.

Deliverables:

  • Develop phenology time series curves using Phenopix R library for each phenocam site and plant functional type at Sagehen.
  • Develop and document an averaging process for determining daily "greenness" index values (time period, images/day, handling abnormalities in images).
  • Establish Regions of Interest (ROI) to process phenology time series curves for each plant functional type per phenocam site. Will need to collaborate with Jen, she can delineate the regions of interest as you're ready for them.
  • Plot, validate and compare phenology time series. Calculate metrics and statistics across plant functional types, meadow sites and possibly hydrogeomorphic, climatic or other factors.
  • Collaborate with Jen to co-write and co-submit a poster abstract for AGU24 annual meeting in December, Wash DC. Abstracts are due July 31.
  • In Fall 2024, help to develop and review the results and discussion for the poster.

Phenopix Considerations

  • Adjust brightness via calibration card or reference object
  • Understand other potential indices to track over time (GCC, ExG, VIGreen)
  • Literature review with focus on use of phenology curves to compare plant functional types across sites and years, especially in meadows or other wetlands.

2018 Phenocam Sites

sageeast-1
sageeast-2
sagekiln-1
sagekiln-2
sageup-1
sageup-2 (missing files)
sagelo-1 (wrong datestamp on files after 08/25)
sagelo-2

Phenocam image files

Located on Google Drive: https://drive.google.com/drive/folders/10P6tmRPVmY4LC_h-BAYol38xEKynZKWt?usp=drive_link

field validate groundwater well data

Need to measure top-to-ground and well-depth on wells listed in:
data / field / groundwater / Wells_with_Missing_Data.xlsx

then update file and recalc water levels in:
data / field / groundwater / Groundwater_Manual_WaterLevel

welltop measurements from 2021 in this sheet

validate gw well data from plots

Validate 2018, 2019 and 2021 data from plots

  • EER-1 in 2021, How handle additional PM reading on same day?
  • EFF-XA2N, Odd low reading in early-Mid October 2019
  • EWT-1, no early readings (prior to mid-July) in 2021
  • EEF-1, odd low reading around 06/01/2019, no readings in 2021
  • EHT-XC6S, only two readings in 2018, none 2019, 2021
  • EFR-XB3S, B2S sporadic readings esp 2018 + 2021
  • LHT-1 odd high then low readings in Fall 2019
  • LWT-1 odd high reading in Oct 2021, why earlier recovery than LET, LHT?
  • KHT-XE4S, why gap in 2021 data, is it no water? how signify?
  • KHT-XE5S, why no early/late 2021 readings?
  • KHT-XE6S, why no early 202 readings?
  • KFF-XE8S, why no late 2019 readings? why gap in 2021 readings?
  • KWT-1, why no late 2021 readings?
  • KEF-1, why 100 cm drop for KEF-1 in Nov 2018?
  • KHF-1, weird early 2021 pattern, why few mid-2019 readings, why late 2018 start (probably b/c new well)
  • KWR-1, why late start in 2021?
  • KER-XD5N, why no 2018 readings?
  • KHR-XD1N, no readings in 2018

Generally:

  • Wells with no water need different plotting style, esp in 2018-19
  • KHF-XD4S
  • EHT-XA5S

No or oddly few readings in 2021 only

  • EWF-XA2S, Only one 2021 reading (Nov)
  • EWF-XA3S, Only one 2021 reading (Nov)
  • KHT-XD6N, no readings in 2021
  • EFR-XB1S, no readings in 2021
  • EET-1, oddly few readings in 2021
  • EEF-1,
  • EHR-XB1N, B2N, B3N, B4N expected readings in 2021, but none
  • EHT-XC6S
  • KER-1
  • KFR-XE1S
  • KFR-XE2S
  • KFF-XD6S
  • KHT-XD3S
  • KWF-1
  • EHT-XA5S

No reading on any dates, any years for:

  • EFF-XA1N
  • EHT-XC5S
  • EET-2 (need a prefix?), one reading in 2021
  • EFT-XB6S
  • EET-XB4S
  • KHR-XD1S
  • KHR-1
  • KHF-XE7S

field GPS control points for B transects

Need to capture high-resolution GPS control points for B transects.
Need to lookup points captured in 2018 survey (not in csv annotations, need to go back to field book), but likely hit the weather station and a sunk rebar at the eastern edge of the meadow, under a large pine to the left of the path.

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