added ndci and ndre and cloudless mosaic, eobrowserstats (#317)

* added ndci and ndre and cloudless mosaic, eobrowserstats fixed bad cloud filter in ndvi and added 3 new scripts * changed input bands names to new names * samples to sample for simple mosaicking * samples to sample for simple mosaicking * samples to sample for simple mosaicking * avoid divison by zero, threshold on ndci, updated fcc and true color * resolved comments from Jonas * use index() for ndwi * Added links, formatting --------- Co-authored-by: Jonas Viehweger <[email protected]>
sentinel-hub · Jun 12, 2024 · 9090f77 · 9090f77
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diff --git a/planet_scope/cloudless_mosaic/README.md b/planet_scope/cloudless_mosaic/README.md
@@ -0,0 +1,18 @@
+---
+title: Cloudless Mosaic, PlanetScope
+parent: PlanetScope
+grand_parent: Planet
+layout: script
+permalink: /planet_scope/cloudless_mosaic/
+nav_exclude: true
+scripts:
+    - [Visualization, script.js]
+---
+
+## General description
+
+The cloudless mosaic script composites together observations across a time range, which is set as 7 days in this script. Pixels which are not clear in the Useable Data Mask (UDM) are removed. There are two options for functions to select which scene to get the pixel from, `getLastObservation` and `getMedian`. `getLastObservation` will put the most recent non cloudy pixel on top. `getMedian` will remove outliers due to shadows or cloud haze that may have been missed by the UDM algorithm.
+
+Below is an example of several PlanetScope scenes being composited across an area that spans several strips and contains gaps when viewed per day. The script returns a continuous image without gaps.
+
+![Cloudless mosaic](fig/fig1.png)
diff --git a/planet_scope/cloudless_mosaic/fig/fig1.png b/planet_scope/cloudless_mosaic/fig/fig1.png
diff --git a/planet_scope/cloudless_mosaic/script.js b/planet_scope/cloudless_mosaic/script.js
@@ -0,0 +1,77 @@
+//VERSION=3
+//Cloudless Mosaic with PlanetScope
+
+function setup() {
+    return {
+        input: ["red", "green", "blue", "dataMask", "clear"],
+        output: { bands: 4 },
+        mosaicking: "ORBIT",
+    };
+}
+
+function preProcessScenes(collections) {
+    collections.scenes.orbits = collections.scenes.orbits.filter(function (
+        orbit
+    ) {
+        var orbitDateFrom = new Date(orbit.dateFrom);
+        const nAggregationDays = 7;
+        return (
+            orbitDateFrom.getTime() >=
+            collections.to.getTime() - nAggregationDays * 24 * 3600 * 1000
+        );
+    });
+    return collections;
+}
+
+function getLastObservation(arr) {
+    for (let i = arr.length - 1; i >= 0; i--) {
+        if (arr[i] !== 0) {
+            // optional check if you are sure all invalid observations are filtered out
+            return arr[i];
+        }
+    }
+    return 0;
+}
+
+function getMedian(sortedValues) {
+    var index = Math.floor(sortedValues.length / 2);
+    return sortedValues[index];
+}
+
+function evaluatePixel(samples, scenes) {
+    var reds = [];
+    var greens = [];
+    var blues = []; //empty arrays for reds greens and blues
+    var a = 0; //incrementer
+
+    for (var i = 0; i < samples.length; i++) {
+        //for each sample
+        var sample = samples[i]; //get current sample
+        var clear = sample.dataMask && sample.clear; //0 for clouds OR datamask, 1 for neither
+
+        if (clear === 1) {
+            //if not clouds nor datamask
+            reds[a] = sample.red; //assign values for that sample to the channel arrays
+            blues[a] = sample.blue;
+            greens[a] = sample.green;
+            a = a + 1; //increment a to represent that at this specific pixel, a value was detected
+        }
+    }
+
+    var rValue;
+    var gValue;
+    var bValue;
+
+    if (a > 0) {
+        rValue = getMedian(reds); // or call getLastObservation - which is less guaranteed to remove hazy images
+        gValue = getMedian(greens);
+        bValue = getMedian(blues);
+        transparency = 1;
+    } else {
+        rValue = 1;
+        gValue = 1;
+        bValue = 1;
+        transparency = 0;
+    }
+    return [rValue / 3000, gValue / 3000, bValue / 3000, transparency];
+}
diff --git a/planet_scope/false_color/script.js b/planet_scope/false_color/script.js
@@ -2,12 +2,17 @@
 //False Color
 
 function setup() {
-  return {
-    input: ["nir", "green", "blue"],
-    output: { bands: 3 }
-  };
+    return {
+        input: ["nir", "green", "blue", "dataMask"],
+        output: { bands: 4 },
+    };
 }
 
 function evaluatePixel(sample) {
-  return [sample.nir / 3000, sample.green / 3000, sample.blue / 3000];
-}
+    return [
+        sample.nir / 3000,
+        sample.green / 3000,
+        sample.blue / 3000,
+        sample.dataMask,
+    ];
+}
diff --git a/planet_scope/ndci/README.md b/planet_scope/ndci/README.md
@@ -0,0 +1,29 @@
+---
+title: Normalized difference chlorophyll index, PlanetScope
+parent: PlanetScope
+grand_parent: Planet
+layout: script
+permalink: /planet_scope/ndci/
+nav_exclude: true
+scripts:
+    - [Visualization, script.js]
+    - [EO Browser, eob.js]
+---
+
+## General description
+
+The normalized difference chlorophyll index, abbreviated NDCI, is defined as   
+
+$$NDCI := \mathtt{Index}(rededge,red) = \frac{rededge-red}{rededge+red}$$  
+
+This is an example script which can be used with EO Browser and is configured to return statistics in a format which can be used with the statistical info chart.  For more information, see <a href = "https://www.sentinel-hub.com/faq/how-configure-your-layers-statistical-info-eo-browser/"> How Can I Configure My Layers For Statistical Information In EO Browser?</a>
+
+## Representative image
+
+NDCI over Lake Elsinore in California.
+
+<img src="fig/fig1.png" height="300">
+
+
+## References
+Sachidananda Mishra, Deepak R. Mishra (2012) Normalized difference chlorophyll index: A novel model for remote estimation of chlorophyll-a concentration in turbid productive waters, Remote Sensing of Environment, 117:394-406, DOI: [10.1016/j.rse.2011.10.016](https://doi.org/10.1016/j.rse.2011.10.016)
diff --git a/planet_scope/ndci/eob.js b/planet_scope/ndci/eob.js
@@ -0,0 +1,56 @@
+//VERSION=3
+//PlanetScope NDCI EO Browser
+
+function setup() {
+    return {
+        input: [
+            {
+                bands: ["red", "rededge", "green", "blue", "dataMask", "clear"],
+            },
+        ],
+        output: [
+            { id: "default", bands: 4 },
+            { id: "index", bands: 1, sampleType: "FLOAT32" },
+            { id: "eobrowserStats", bands: 2, sampleType: "FLOAT32" },
+            { id: "dataMask", bands: 1 },
+        ],
+    };
+}
+
+function evaluatePixel(sample) {
+    let ndci = index(sample.rededge, sample.red);
+    const clear = sample.dataMask && sample.clear;
+
+    let ndci_colored = colorBlend(
+        ndci,
+        [0.0, 0.2, 0.4, 0.6, 0.8, 1.0],
+        [
+            [0, 0, 1], // Blue
+            [0, 0, 1], // Blue
+            [0, 1, 0], // Green
+            [0, 0.8, 0], // Yellow-green
+            [0, 0.6, 0], // Darker green
+            [0, 0.4, 0], // Even darker green
+        ]
+    );
+
+    // Normalize true color bands
+    let true_color = [
+        sample.red / 3000,
+        sample.green / 3000,
+        sample.blue / 3000,
+    ];
+
+    // Threshold value for switching between true color and ndci_map
+    let threshold = 0.3;
+
+    // Conditional logic to select either true_color or ndci_map
+    let ndci_colored_masked = ndci < threshold ? true_color : ndci_colored;
+
+    return {
+        default: [...ndci_colored_masked, clear],
+        index: [ndci],
+        eobrowserStats: [ndci, !clear],
+        dataMask: [sample.dataMask],
+    };
+}
diff --git a/planet_scope/ndci/fig/fig1.png b/planet_scope/ndci/fig/fig1.png
diff --git a/planet_scope/ndci/script.js b/planet_scope/ndci/script.js
@@ -0,0 +1,12 @@
+//PlanetScope NDCI
+let ndci = index(rededge, red);
+
+return colorBlend(
+    ndci,
+    [0.0, 0.5, 1.0],
+    [
+        [1, 0, 0],
+        [1, 1, 0],
+        [0.1, 0.31, 0],
+    ]
+);
diff --git a/planet_scope/ndre/README.md b/planet_scope/ndre/README.md
@@ -0,0 +1,28 @@
+---
+title: Normalized difference red edge index, PlanetScope
+parent: PlanetScope
+grand_parent: Planet
+layout: script
+permalink: /planet_scope/ndre/
+nav_exclude: true
+scripts:
+    - [Visualization, script.js]
+    - [EO Browser, eob.js]
+---
+
+## General description
+
+The normalized difference red edge index, abbreviated NDRE, is defined as   
+
+$$NDRE := \mathtt{Index}(nir,rededge) = \frac{nir-rededge}{nir+rededge}$$  
+
+This is an example script which can be used with EO Browser and is configured to return statistics in a format which can be used with the statistical info chart.  For more information, see <a href = "https://www.sentinel-hub.com/faq/how-configure-your-layers-statistical-info-eo-browser/"> How Can I Configure My Layers For Statistical Information In EO Browser?</a>
+
+## Description of representative images
+
+NDRE of agriculture fields in California. 
+
+<img src="fig/fig1.png" height="300">
+
+## References
+ [1] Wikipedia, [Normalized Difference Vegetation Index](https://en.wikipedia.org/wiki/Normalized_Difference_Red_Edge_Index).
diff --git a/planet_scope/ndre/eob.js b/planet_scope/ndre/eob.js
@@ -0,0 +1,40 @@
+//VERSION=3
+//PlanetScope NDRE EO Browser
+
+function setup() {
+    return {
+        input: [
+            {
+                bands: ["nir", "rededge", "dataMask", "clear"],
+            },
+        ],
+        output: [
+            { id: "default", bands: 4 },
+            { id: "index", bands: 1, sampleType: "FLOAT32" },
+            { id: "eobrowserStats", bands: 2, sampleType: "FLOAT32" },
+            { id: "dataMask", bands: 1 },
+        ],
+    };
+}
+
+function evaluatePixel(sample) {
+    let ndre = index(sample.nir, sample.rededge);
+    const clear = sample.dataMask && sample.clear;
+
+    let ndre_colored = colorBlend(
+        ndre,
+        [0.0, 0.5, 1.0],
+        [
+            [1, 0, 0],
+            [1, 1, 0],
+            [0.1, 0.31, 0],
+        ]
+    );
+
+    return {
+        default: [...ndre_colored, clear],
+        index: [ndre],
+        eobrowserStats: [ndre, !clear],
+        dataMask: [sample.dataMask],
+    };
+}
diff --git a/planet_scope/ndre/fig/fig1.png b/planet_scope/ndre/fig/fig1.png
diff --git a/planet_scope/ndre/script.js b/planet_scope/ndre/script.js
@@ -0,0 +1,12 @@
+//PlanetScope NDRE
+let ndre = index(nir, rededge);
+
+return colorBlend(
+    ndre,
+    [0.0, 0.5, 1.0],
+    [
+        [1, 0, 0],
+        [1, 1, 0],
+        [0.1, 0.31, 0],
+    ]
+);
diff --git a/planet_scope/ndvi/README.md b/planet_scope/ndvi/README.md
@@ -26,11 +26,11 @@ $$NDVI := \mathtt{Index}(nir,red) = \frac{nir-red}{nir+red}.$$
 
 This is an example script which can be used with EO Browser and is configured to return statistics in a format which can be used with the statistical info chart.  For more information, see <a href = "https://www.sentinel-hub.com/faq/how-configure-your-layers-statistical-info-eo-browser/"> How Can I Configure My Layers For Statistical Information In EO Browser?</a>
 
-## Description of representative images
+## Representative images
 
 NDVI of agriculture fields in Iowa. 
 
-![NDVI of agriculture fields in Iowa](fig/fig1.png)
+<img src="fig/fig1.png" height="300">
 
 ## References
  [1] Wikipedia, [Normalized Difference Vegetation Index](https://en.wikipedia.org/wiki/Normalized_Difference_Vegetation_Index). Accessed on October 4th 2017.
diff --git a/planet_scope/ndvi/eob.js b/planet_scope/ndvi/eob.js
@@ -1,41 +1,40 @@
 //VERSION=3
-//NDVI
+//PlanetScope NDVI EO Browser
 
 function setup() {
-  return {
-    input: [{
-      bands: [
-        "red",
-        "nir",
-        "dataMask",
-        "clear"
-      ]
-    }],
-    output: [
-      { id: "default", bands: 4 },
-      { id: "index", bands: 1, sampleType: "FLOAT32" },
-      { id: "eobrowserStats", bands: 2, sampleType: "FLOAT32" },
-      { id: "dataMask", bands: 1 },
-    ]
-  }
+    return {
+        input: [
+            {
+                bands: ["red", "nir", "dataMask", "clear"],
+            },
+        ],
+        output: [
+            { id: "default", bands: 4 },
+            { id: "index", bands: 1, sampleType: "FLOAT32" },
+            { id: "eobrowserStats", bands: 2, sampleType: "FLOAT32" },
+            { id: "dataMask", bands: 1 },
+        ],
+    };
 }
 
-function evaluatePixel(samples) {
-  let ndvi = (samples.nir - samples.red) / (samples.nir + samples.red);
-  const indexVal = samples.dataMask === 1 ? ndvi : NaN;
-  const clear = samples.dataMask * samples.clear;
+function evaluatePixel(sample) {
+    let ndvi = index(sample.nir, sample.red);
+    const clear = sample.dataMask && sample.clear;
 
-  let id_default = colorBlend(ndvi, [0.0, 0.5, 1.0],
-    [
-      [1, 0, 0, clear],
-      [1, 1, 0, clear],
-      [0.1, 0.31, 0, clear],
-    ])
+    let ndvi_colored = colorBlend(
+        ndvi,
+        [0.0, 0.5, 1.0],
+        [
+            [1, 0, 0],
+            [1, 1, 0],
+            [0.1, 0.31, 0],
+        ]
+    );
 
-  return {
-    default: id_default,
-    index: [indexVal],
-    eobrowserStats: [indexVal, samples.clear],
-    dataMask: [samples.dataMask],
-  };
+    return {
+        default: [...ndvi_colored, clear],
+        index: [ndvi],
+        eobrowserStats: [ndvi, +!clear],
+        dataMask: [sample.dataMask],
+    };
 }