Satellite Imagery and HAB in 3D

Final Design and Notes

Download Raster Imagery from Copernicus Browser

1. Navigate to the Copernicus Browser Website
2. Create an account and log in, or continue as anonymous.
3. In the top-right corner, use the Go to Place search box to zoom to your desired location. You can type something like City, STATE but since this app is based in the EU, the results might not look like you expect. For example, typing Toledo, OH will result in the first dropdown option being Toledo, United States of America. If you click on this first result, it will be the correct Toledo, even though you don't see the state name.
4. In the left side menu under CONFIGURATIONS, click the dropdown and select Ocean and Water Bodies.
5. In the left side menu under DATA COLLECTIONS, stay with the default Sentinel 2 and select Sentinel-2 L2A. Note: I'm not sure what the practical difference is between L2A and L1C.
6. At the top left of the side menu, click on the YYYY-MM-DD and use the resulting date picker to go to the date of interest.
   1. After selecting the initial date, you can use the arrows next to YYYY-MM-DD to quickly move to the next or previous date with acceptable cloud coverage.
   2. You can change the acceptable cloud coverage, but the default 30% works.
   3. This value decides which days to ignore. Cloudy days make for bad satellite imagery.
7. After you've selected all the previous configuration options, you can zoom in further to the area of interest.
8. In the left menu under LAYERS select Ulyssys Water Quality Viewer which can be used to colorize the satellite imagery for Water Quality.
   1. This custom script colorizes based on Total Suspended Solids (TSS) and Chlorophyll (CHL) to get an aggregate view of water quality.
   2. After selecting the layer, you can modify its parameters by clicking on the </> button which opens an in-browser code editor.
   3. Here, you can turn off TSS to get a Chlorophyll only view by changing the tssIndex: 'default', line to instead be tssIndex: null,.
   4. Still in the code editor, scroll down to the bottom of the PARAMS section (around line 17) and change the line background: 'default', to background: [255, 255, 255],. This sets the "background", or land pixels to render as pure white instead of rendering the actual satellite view.
      1. This is useful for trimming land and getting a TIFF of water only.
9. When exporting the layer to a GeoTIFF file, you can either export your current view, or you can define a viewbox using a square or draw a polygon.
10. On the far right side of the map, select the fourth from the bottom icon showing an image with a download arrow.
    1. Change the tab to Analytical
    2. Change the Image format to TIFF (32-bit float)
    3. Change the Image resolution to HIGH
    4. Leave everything else default, scroll down, and click Download

Trim Raster GeoTIFF File with QGIS

We can trim certain parts of a GeoTIFF using QGIS. Before this step, however, you should first download from the browser. Also, make sure that the content you want to trim (i.e. land pixels or background layer in the water quality example) are rendered as a single solid color, white for simplicity.

1. Open QGIS
2. Select Layer > Add Layer > Add Raster Layer and navigate to your downloaded TIFF.
3. Right click the newly added layer and select Properties.
4. Go to the Transparency tab.
5. In Custom Transparency Options section, click the green plus (+) sign.
6. Click on the newly created row and change the Red, Green, and Blue values to each be 255.
7. Leave the Percent Transparent at the default 100 and click Apply/OK. Note: You can add the OpenStreetMap layer beneath the raster to verify that the white pixels have disappeared.
8. Right click the layer and select Export > Save as.
9. For Output mode select the second radio Rendered image.
10. Fill in the filename and path, then click OK.

At this point, you will have a trimmed TIFF raster file. You can upload this to Cesium Ion and use it in any of our Cesium-enabled React apps.

Satellite Imagery in ESRI

I found this ESRI video which discusses some of the data sources available.

At 36:45 they show how to bring in GeoTIFF Data from "local files", however it's "Local Files - via hosted TIle Service"

NOTE: There was an image here, but it got corrupted and is causing errors, so I just removed the image complete. The subtext was "esri geotiff local files via tile service"

They also allow "External Online Source - via Cloud Optimized GeoTIFF (COG)" as shown in this screenshot:

This external online source is probably what we want. We should be able to load the tif file from the SWA's static content directory.

Satellite Imagery in Cesium

https://cesium.com/learn/3d-tiling/ion-tile-imagery/

HAB's

I couldn't find anything for Harsha Lake, but Erie has more promising results:

NOAA Coastal Science HABs Site

Cyanobacteria Algal Bloom from Satellite in Western Lake Erie Basin

Current Lake Erie Sentinel-3 a and b Composited Satellite Imagery from the Ocean and Land Color Imager (OLCI) as of 2024-11-02 showing bloom location and extent

All of these that I've found are the "latest" available data, not necessarily historical or unique events.

I will still grab one of the geotiffs to render.

HAB Event on Lake Erie

Lake Erie Blooms - August 2024

Copernicus Browser Findings

I was able to find a rough approximation of the August 2024 HAB from the previous section in the Copernicus Browser:

This was found in Sentinel 3 from the dropdown, then Sentinel-3 OLCI L1B with Enhanced Natural Color layer selected.

The Sentinel-3 OLCI L2 Water collection of data has some more interesting layers to play with, but they're color ramp overlays of the radiation data from the satellite's sensors, as opposed to a realistic view from the sky.

We could probably use the OLCI L2 Water collection for some good visualization of HAB. They include some interesting layer options:

We might be able to make the land transparent using this information:

Transparent Tif Images with GDAL and QGIS

Ask Community for Help Exporting

I am using Ulyssys Water Quality Viewer script in Copernicus Browser to visualize water quality from satellite data. I want to export the resulting images as geotiff for use in a 3D data viewer (Cesium). I can do this well enough. However, I would like to trim off the non-water pixels. I've tried modifying the opacity for non-water pixels, but that just makes the base satellite imagery show up. Is there a way to export the geotiff with non-water pixels completely transparent, effectively trimming so only the water is exported? I've found a stack exchange post that I think is describing how to do what I want from QGIS and with GDAL, but I'm curious if it can be done at the time of image export.

Ulyssys Water Quality Viewer

The script aims to dynamically visualise the chlorophyll and sediment conditions of water bodies, which are primary indicators of water quality. The chlorophyll content ranges in colors from dark blue (low chlorophyll content) through green to red (high chlorophyll content). Sediment concentrations are colored brown; opaque brown indicates high sediment content.

This is a potentially interesting view.

More details on the UWQV

Issues Rendering Tiles in Copernicus Browser

Sometimes, the tiles won't load properly and I simply can't see the data. This seems to happen mainly in the Sentinel-2 data, however I also think Sentinel-2 might have better resolution than Sentinel-3.