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How to Use the Zoo Notebook

  • ⚠️ Ensure you have downloaded data from Google Earth Engine before running Zoo models
  • ⚠️ Zoo notebook runs one region of interest (ROI) at a time

Run Start Up Cell

zoo_run_cell

Step 1: Select a Model

  • Select the Model input you would like to use (RGB, MNDWI, or NDWI)
  • The NDWI and MNDWI will be automatically created using avalible RGB imagery

zoo_step1

Basic Model Settings

  • By default the global segformer model is selected

Advanced Model Settings (Experienced Users Only)

  • Otsu Threshold (off by default)

zoo_otsu

  • Time Test Augmentation (off by default)

zoo_time_test

Step 2: Select Settings

  • Select the settings you would like for your current session
  • Make sure to click the save settings button to ensure your settings have been applied (Can check in the view settings tab)
  • For more information on these settings see the Extract Shorelines Settings Guide

zoo_step2

Step 3: Upload Files

  • Upload a GeoJSON file that contains either transects or shorelines
  • If both the transects and shorelines are within the same ‘config_gdf.geojson’ file, you will need to upload the same file for the reference shoreline and the transects
  • If no file is provided, CoastSeg will attempt to load an available file for you
    • If no transects or shorelines are available within the region of interest, an error will occur

zoo_step3

Example of uploading transect GeoJSON file

zoo_step3_add_transects

Step 4: Extract Shorelines with Model

1: Session Name - Enter a name for your session. A new folder will be created with this name in the ‘sessions’ directory

2: Select Images - Select the RGB directory from your region of interest (roi) with downloaded imagery from the ‘data’ directory

3: Run Model

zoo_step4

Example of Step 4 set up

Red arrow showing the RGB folder to be selected containing the images for shoreline extraction. Green arrow showing the final step to extract shorelines.

zoo_step4_details

Example of a running session in progress

  • ⚠️ Zoo workflow takes longer on average to complete than the CoastSat workflow.
    • This is because the zoo workflow loads a more advanced model that takes longer to process all the imagery in a session.
    • In the screeshot below you can see the progress bar, called "Applying Model", updates as the zoo model finishes running on each image. (note the warnings are normal)

zoo_step4_run_model zoo_step4_run_model_pt2

Step 5: Tidal Correction

  • Ensure the tide model has been downloaded to CoastSeg/tide_model for tidal correction to work
  • Follow the guide to download the tide model
  • Ensure shorelines have been extracted prior to tidal correction. Not all imagery will contain suitable shorelines and result in tide correction being not possible

Step 1: Section a Session - Select a session from the ‘sessions’ directory that contains extracted shorelines

Step 2: Run Tidal Correction - Runs the tide model and saves tidally corrected CSV files in the selected sessions directory

Select between the FES 2014 or FES 2022 model before clicking correct tides.

  • Tidal correction will take a few minutes to run because the tide model is large, several GB

zoo_step5