[GIS] Creating Sentinel-2 cloud free, cloud-shadow free composite or scene on Google Earth Engine (GEE)

cloud covergoogle-earth-enginesentinel-2

Using this code, I am able to get a cloud-free composite, but it still includes shadows in my image.

var collection = ee.ImageCollection("COPERNICUS/S2")
  .filterBounds(ee.Geometry.Rectangle(-85.14404296875, 46.9502622421856, 
  -71.87255859375, 41.60722821271717));
var S2_cloud = collection.min();

How do I create a Sentinel-2 cloud free, cloud-shadow free composite or scene on Earth Engine (GEE)?

Best Answer

As far as I know, Sentinel 2 has no computed cloud-shadow mask, so I ommit that part. But for the rest, I think you should at least mask out clouds, and filter a little.

I've made public a repo I have to perform this: users/fitoprincipe/geetools

First the core:

var computeQAbits = function(image, start, end, newName) {
    var pattern = 0;

    for (var i=start; i<=end; i++) {
        pattern += Math.pow(2, i);
    }

    return image.select([0], [newName]).bitwiseAnd(pattern).rightShift(start);
};

var sentinel2 = function(image) {

  var cloud_mask = image.select("QA60");
  var opaque = computeQAbits(cloud_mask, 10, 10, "opaque");
  var cirrus = computeQAbits(cloud_mask, 11, 11, "cirrus");
  var mask = opaque.or(cirrus);

  return image.updateMask(mask.not());
}

You can use the function sentinel2 in a map function.

to your question:

Using min(), which may not be the best approach to generate a composite, (but that's another story so I am not diggin on it), this would be a complete 'solution':

var s2mask = require('users/fitoprincipe/geetools:cloud_masks').sentinel2;

var AOI = ee.Geometry.Rectangle(-85.14404296875, 46.9502622421856, 
  -71.87255859375, 41.60722821271717);

var collection = ee.ImageCollection("COPERNICUS/S2")
  .filterBounds(AOI)
  .filterMetadata('CLOUDY_PIXEL_PERCENTAGE', 'less_than', 70)
  .map(s2mask());

var image = ee.Image(collection.min());
Map.addLayer(image, {bands:['B8', 'B12', 'B4'], min:0, max:3000});
Map.centerObject(AOI);

Use the right parameters and always check metadata

You're trying to filter with BQA band and in SR product, there is no BQA band, there is pixel_qa band instead. Also, bits used are different (3 and 5). Finally, if you are trying to create a cloud-free composite, first sort by cloud cover.

var point = /* color: #98ff00 */ee.Geometry.Point([35.83946228027344, -3.5380934964711126]);

//load images for composite
var sr14= ee.ImageCollection('LANDSAT/LC08/C01/T1_SR')
.filterBounds(point)
.filterDate('2014-01-01','2014-03-01').sort('CLOUD_COVER',false);

// Temporally composite the images with a maximum value function.
var visParams = {bands: ['B4', 'B3', 'B2'], min:0,max: 1000};
Map.setCenter(35.8244, -3.5799);
Map.addLayer(sr14, visParams, 'max value composite');

var getQABits = function(image, start, end, newName) {
    // Compute the bits we need to extract.
    var pattern = 0;
    for (var i = start; i <= end; i++) {
       pattern += Math.pow(2, i);
    }
    // Return a single band image of the extracted QA bits, giving the band
    // a new name.
    return image.select([0], [newName])
                  .bitwiseAnd(pattern)
                  .rightShift(start);
};

// A function to mask out cloudy pixels.
var cloud_shadows = function(image) {
  // Select the QA band.
  var QA = image.select(['pixel_qa']);
  // Get the internal_cloud_algorithm_flag bit.
  return getQABits(QA, 3,3, 'cloud_shadows').eq(0);
  // Return an image masking out cloudy areas.
};

// A function to mask out cloudy pixels.
var clouds = function(image) {
  // Select the QA band.
  var QA = image.select(['pixel_qa']);
  // Get the internal_cloud_algorithm_flag bit.
  return getQABits(QA, 5,5, 'Cloud').eq(0);
  // Return an image masking out cloudy areas.
};

var maskClouds = function(image) {
  var cs = cloud_shadows(image);
  var c = clouds(image);
  image = image.updateMask(cs);
  return image.updateMask(c);
};

var composite_free = sr14.map(maskClouds);

Map.addLayer(composite_free,visParams, 'composite collection without clouds');

Link: https://code.earthengine.google.com/6a9d2bce417076d1f1b677e775584690

Google Earth Engine – Masking Out Shadows in Sentinel Images Using GEE

There has been an approach to do this using a decision tree: Ready-to-Use Methods for the Detection of Clouds, Cirrus, Snow, Shadow, Water and Clear Sky Pixels in Sentinel-2 MSI Images.

I have adapted the code to EE, and make it open source in geetools, both for the Python API and for the JavaScript API

var cld = require('users/fitoprincipe/geetools:cloud_masks')
var image = ee.Image('COPERNICUS/S2/20151123T142942_20170221T180430_T19GCN')

Map.centerObject(image)

var mask_shadow = cld.hollstein_S2(['shadow'])(image)

Map.addLayer(mask_shadow, {bands:['B8', 'B11','B4'], min:0, max:5000})

Best Answer

First the core:

to your question:

Related Solutions

Google Earth Engine – Cloud Masking for Landsat 8 on Google Earth Engine

Use the right parameters and always check metadata

Google Earth Engine – Masking Out Shadows in Sentinel Images Using GEE

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