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Merge pull request #286 from sentinel-hub/fix/mago
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Fixed example link, wrong whitespace in script
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@jonasViehweger
jonasViehweger authored Nov 30, 2023
2 parents 8d575f0 + 6396fe7 commit 2850de0
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2 changes: 1 addition & 1 deletion sentinel-2/mago_water_quality_monitoring_tool/README.md
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Expand Up @@ -9,7 +9,7 @@ nav_exclude: true


## Evaluate and visualize
- [EO Browser](https://sentinelshare.page.link/Dk75)
- [EO Browser](https://sentinelshare.page.link/GUdK)

## General description of the script
MAGO Water Quality Monitoring tool is a code to estimate water quality parameters in lakes, reservoir or large ponds from Sentinel-2 images. The user can visualize water quality parameters (chlorophyll-a, cyanotoxins, turbidity...) on the EO Browser map and get the corresponding time series at selected points or areas.
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105 changes: 52 additions & 53 deletions sentinel-2/mago_water_quality_monitoring_tool/script.js
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@@ -1,121 +1,121 @@
//VERSION=3
// User must set these three values
var indexNumber = 0; // Necessary to choose the visualization option
var indexNumber = 0; // Necessary to choose the visualization option
var minValue = 0;
var maxValue = 30;

// Color Scale
//var scaleLimits = [0, 5, 10, 20, 30]; // Define the borders
var scaleLimits = [minValue, (maxValue + 3*minValue)/4, (maxValue + minValue)/2, (3*maxValue + minValue)/4, maxValue]
var scaleLimits = [minValue, (maxValue + 3 * minValue) / 4, (maxValue + minValue) / 2, (3 * maxValue + minValue) / 4, maxValue]
var s = 255; // Values range from 0 to 255 for every color channel
var colorScale = // Define the RGB colors for each border
[
[0/s, 0/s, 255/s], // Blue
[0/s, 255/s, 255/s], // Cyan
[0/s, 255/s, 0/s], // Green
[255/s, 255/s, 0/s], // Yellow
[255/s, 0/s, 0/s], // Red
[0 / s, 0 / s, 255 / s], // Blue
[0 / s, 255 / s, 255 / s], // Cyan
[0 / s, 255 / s, 0 / s], // Green
[255 / s, 255 / s, 0 / s], // Yellow
[255 / s, 0 / s, 0 / s], // Red
];

// For evalscript V3 you need to specify two functions
// setup() - where you specify inputs and outputs
// evaluatePixel() - which calculates the output values for each pixel
function setup() {
return {
input: ["B01", "B02", "B03", "B04", "B05", "B06", "B07", "B08", "SCL","dataMask"], // You need to add here all the bands you are going to use
input: ["B01", "B02", "B03", "B04", "B05", "B06", "B07", "B08", "SCL", "dataMask"], // You need to add here all the bands you are going to use
output: [
{ id:"default", bands: 3 },
{ id: "default", bands: 3 },
{ id: "index", bands: 1, sampleType: "FLOAT32" },
{ id: "eobrowserStats", bands: 2, sampleType: 'FLOAT32' },
{ id: "dataMask", bands: 1 }
]
]
};
}

function evaluatePixel(samples) {
let NDWI = index(samples.B03, samples.B08); // Calculate the Normalized Difference Water Index, used in visualization
let TrueColor = [samples.B04*2.5, samples.B03*2.5, samples.B02*2.5]; // Define true color composites multiplying each band by 2.5 to improve the appearance of images, used in visualization
let TrueColor = [samples.B04 * 2.5, samples.B03 * 2.5, samples.B02 * 2.5]; // Define true color composites multiplying each band by 2.5 to improve the appearance of images, used in visualization

// Visualization
// choose which one to use for visualization by setting indexNumber at the beginning of the code
// indexNumber = 0 | Chlorophyll a mg / m3 (Mishra 2012 – Based on NDCI)
let index0 = 14.039 + (86.11 * (samples.B05-samples.B04)/(samples.B05+samples.B04))+(194.325*Math.pow((samples.B05-samples.B04)/(samples.B05+samples.B04), 2));
// indexNumber = 0 | Chlorophyll a mg / m3 (Mishra 2012 – Based on NDCI)
let index0 = 14.039 + (86.11 * (samples.B05 - samples.B04) / (samples.B05 + samples.B04)) + (194.325 * Math.pow((samples.B05 - samples.B04) / (samples.B05 + samples.B04), 2));
let viz0 = colorBlend(index0, scaleLimits, colorScale);
// indexNumber = 1 | Chlorophyll a for high values > 5 mg / m3 (Soria-Perpinyà 2021)
let index1 = 19.866 * Math.pow(samples.B05/samples.B04, 2.3051); 
// indexNumber = 1 | Chlorophyll a for high values > 5 mg / m3 (Soria-Perpinyà 2021)
let index1 = 19.866 * Math.pow(samples.B05 / samples.B04, 2.3051);
let viz1 = colorBlend(index1, scaleLimits, colorScale);
  // indexNumber = 2 | Chlorophyll a low values < 5 mg / m3 (Soria-Perpinyà 2021) 
let index2 = Math.pow(10,-2.4792*Math.log10(Math.max(samples.B03,samples.B02)/samples.B03)-0.0389);
// indexNumber = 2 | Chlorophyll a low values < 5 mg / m3 (Soria-Perpinyà 2021)
let index2 = Math.pow(10, -2.4792 * Math.log10(Math.max(samples.B03, samples.B02) / samples.B03) - 0.0389);
let viz2 = colorBlend(index2, scaleLimits, colorScale);
  // indexNumber = 3 | Cyanobacteria (phycocyanin) cells/mL (Potes et al. 2018)
let index3 = 115530.31 * Math.pow((samples.B03 * samples.B04) / samples.B02, 2.38);         
// indexNumber = 3 | Cyanobacteria (phycocyanin) cells/mL (Potes et al. 2018)
let index3 = 115530.31 * Math.pow((samples.B03 * samples.B04) / samples.B02, 2.38);
let viz3 = colorBlend(index3, scaleLimits, colorScale);
// indexNumber = 4 | Cyanobacteria (Phycocyanin) mg/m3 (Soria-Perpinyà 2021)
let index4 = 21.554 * Math.pow((samples.B05/samples.B04), 3.47941);       
let viz4 = colorBlend(index4, scaleLimits, colorScale);
// indexNumber = 5 | Turbidity NTU (Zhan et al. 2022)
let index5 = 194.79 * (samples.B05*(samples.B05/samples.B02)) + 0.9061;
let viz5 = colorBlend(index5, scaleLimits, colorScale);
// indexNumber = 6 | CDOM ug/L (Soria-Perpinyà 2021)
let index6 = 2.4072 * (samples.B04/samples.B02) + 0.0709;
// indexNumber = 4 | Cyanobacteria (Phycocyanin) mg/m3 (Soria-Perpinyà 2021)
let index4 = 21.554 * Math.pow((samples.B05 / samples.B04), 3.47941);
let viz4 = colorBlend(index4, scaleLimits, colorScale);
// indexNumber = 5 | Turbidity NTU (Zhan et al. 2022)
let index5 = 194.79 * (samples.B05 * (samples.B05 / samples.B02)) + 0.9061;
let viz5 = colorBlend(index5, scaleLimits, colorScale);
// indexNumber = 6 | CDOM ug/L (Soria-Perpinyà 2021)
let index6 = 2.4072 * (samples.B04 / samples.B02) + 0.0709;
let viz6 = colorBlend(index6, scaleLimits, colorScale);
// indexNumber = 7 | Total Suspended Solids (TSS) mg/L (Soria-Perpinyà 2021)
let index7 = 14.464 * (samples.B07/samples.B02) + 16.336;
let viz7 = colorBlend(index7, scaleLimits, colorScale);
// indexNumber = 7 | Total Suspended Solids (TSS) mg/L (Soria-Perpinyà 2021)
let index7 = 14.464 * (samples.B07 / samples.B02) + 16.336;
let viz7 = colorBlend(index7, scaleLimits, colorScale);


let imgVals = null;
let val = NaN;
// We made a first filter by NDWI (Water Index)
if (NDWI < -0) { // If NDWI is lower than 0 is not water, so return true color
imgVals = [...TrueColor, samples.dataMask];
}else { // Evaluate indexNumber
switch (indexNumber) {
case 0: // indexNumber = 0
} else { // Evaluate indexNumber
switch (indexNumber) {
case 0: // indexNumber = 0
imgVals = [...viz0, samples.dataMask];
val = index0;
break;
    case 1: // indexNumber = 1
break;
case 1: // indexNumber = 1
imgVals = [...viz1, samples.dataMask];
val = index1;
break;
    case 2: // indexNumber = 2
break;
case 2: // indexNumber = 2
imgVals = [...viz2, samples.dataMask];
val = index2;
break;
    case 3: // indexNumber = 3
break;
case 3: // indexNumber = 3
imgVals = [...viz3, samples.dataMask];
val = index3;
break;
    case 4: // indexNumber = 4
case 4: // indexNumber = 4
imgVals = [...viz4, samples.dataMask];
val = index4;
break;
    case 5: // indexNumber = 5
break;
case 5: // indexNumber = 5
imgVals = [...viz5, samples.dataMask];
val = index5;
break;
    case 6: // indexNumber = 6
break;
case 6: // indexNumber = 6
imgVals = [...viz6, samples.dataMask];
val = index6;
break;
    case 7: // indexNumber = 7
case 7: // indexNumber = 7
imgVals = [...viz7, samples.dataMask];
val = index7;
break;
    default: // By default true color
default: // By default true color
imgVals = [...TrueColor, samples.dataMask];
}
}

  // The library for tiffs works well only if there is only one channel returned.
  // So we encode the "no data" as NaN here and ignore NaNs on frontend.
// The library for tiffs works well only if there is only one channel returned.
// So we encode the "no data" as NaN here and ignore NaNs on frontend.
const indexVal = samples.dataMask === 1 ? val : NaN;

return {
default: imgVals,
index: [indexVal],
eobrowserStats:[val,isCloud(samples.SCL)?1:0],
eobrowserStats: [val, isCloud(samples.SCL) ? 1 : 0],
dataMask: [samples.dataMask]
};
}
Expand Down Expand Up @@ -145,8 +145,7 @@ function isCloud(scl) {
} else if (scl == 2) {
// SC_DARK_FEATURE_SHADOW
return false;
} else{
} else {
return false;
}

}
}

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