7yl4r

# analysis of west_of_canal and east_of_canal

import pandas as pd
import matplotlib.pyplot as plt
from pathlib import Path

# --- CONFIG ---
INDEX = "NDMoI"

files = {

7yl4r

import pandas as pd
import matplotlib.pyplot as plt
from pathlib import Path

# --- CONFIG ---
INDEX = "NDMoI"
AOI = "mangrove_recovery_RB"
# AOI = "mangrove_recovery_JB"
# AOI = "mangrove_death_JB"
# AOI = "mangrove_death_RB"

7yl4r

/**
  MANGROVE CLASSIFICATION SCRIPT 
  For Placencia 2025 USING SENTINEL 2
  2025/06/09
  Claudia Baron-Aguilar
  
Previous steps.
  1. Selection of best image (Using Image selection code)
  2. selection of positive and negative goriud-truth points 
      (Creating List of coordinates code with anotehr code)

7yl4r

This linux (ubuntu) machine is used to segement images from a planktoScope for submission to EcoTaxa.

To do this:

0. Planktoscope must be on and connected (via wifi)
1. Open a terminal on the desktop (ctrl+alt+t)
2. Type ./copyPlanktoScopeImages.sh and press enter

• this will prompt for the PlanktoScope password.
  • NOTE: nothing will show while typing the password.
• NOTE: use "tab completion" to make this easier

7yl4r

Contributor : Mehraz Hossain Rumman (he/him)
Organization : IOOS
Project Title : PyOBIS for stakeholders
Mentor : Tylar Wayne Cole Murray, PhD. (ey/em|he/him)
GSoC Project Page: https://summerofcode.withgoogle.com/programs/2025/projects/Af6KBBl2

---

7yl4r

var image = ee.Image('...Image Asset Path Here...')
var sunglintRegions = geometry;  // this is a geometry of sunglinted areas

// Select the bands
var NIR = image.select('b8');  // NIR

var minNIR = NIR.reduceRegion({
  reducer: ee.Reducer.min(),
  geometry: NIR.geometry(),
  scale: 4,

7yl4r

2025-07-16 13:33:47.371 | INFO     | planktoscope.mqtt:on_message:150 - segmenter_client: segmenter/segment 0 b'{"action":"segment","path":["/home/pi/data/img/sfer_mbon_ws16130_ws_200um_20160510_real","/home/pi/data/img/sfer_mbon_ws16207_ws_200um_20160726"],"settings":{"force":false,"recursive":true,"ecotaxa":true,"keep":true,"process_id":1}}'
2025-07-16 13:33:47.371 | DEBUG    | planktoscope.mqtt:on_message:154 - command is segment
2025-07-16 13:33:47.371 | DEBUG    | planktoscope.mqtt:on_message:157 - args are {'action': 'segment', 'path': ['/home/pi/data/img/sfer_mbon_ws16130_ws_200um_20160510_real', '/home/pi/data/img/sfer_mbon_ws16207_ws_200um_20160726'], 'settings': {'force': False, 'recursive': True, 'ecotaxa': True, 'keep': True, 'process_id': 1}}
2025-07-16 13:33:47.371 | DEBUG    | planktoscope.mqtt:on_message:159 - msg is {'topic': 'segmenter/segment', 'payload': {'action': 'segment', 'path': ['/home/pi/data/img/sfer_mbon_ws16130_ws_200um_20160510_real', '/home/pi/data/img/sfer_mbon_ws16207_ws_200u

7yl4r

    original.analyte.name == "Ammonium"                                    ~ "Ammonium",

    original.analyte.name == "Ammonia__N_"                                 ~ "Ammonia",

    original.analyte.name == "Chlorophyll_a"                               ~ "Chlorophyll_a",
    original.analyte.name == "Chlorophyll_a-_uncorrected"                  ~ "Chlorophyll_a",
    original.analyte.name == "Chlorophyll_a__uncorrected_for_pheophytin"   ~ "Chlorophyll_a"
    original.analyte.name == "Chlorophyll_a__free_of_pheophytin"           ~ "Chlorophyll_a",
    original.analyte.name == "Chlorophyll_a-_corrected"                    ~ "Chlorophyll_a",
    original.analyte.name == "Chlorophyll_a__corrected_for_pheophytin"     ~ "Chlorophyll_a",

7yl4r

graph TD

subgraph st_andrew_assets_folder
    roi_hab1(seagrass)
    roi_hab2(sand)
    roi_hab3(etc...)
end

7yl4r

import re

def canonical_station_name(station_name):
    station_aliases = {
        "1": ["1"],
        "2": ["2"],
        "3": ["3"],
        "4": ["4"],
        "5": ["5"],
        "5.5": ["5.5"],