Sentinel Cloud-free Collection Google Earth Engine Code Editor

Question

I am trying to create and map an image collection (not image or mosaic if that is even possible), where QA60 defines the Cloud-mask. I have written the code below - however, it seems the Jan2016 images do not correspond the cloud mask, even though the pixel inspector shows the same image time stamp for all layers. Hence, "NoCLouds" layer contains many pixels with clouds and has many other without masked. Maybe my mask is wrong?

var Jan2016 = ee.ImageCollection('COPERNICUS/S2')
      .filterBounds(NSW)
      .filterDate('2016-01-01', '2016-01-30');

var trueColor = {bands: ['B4', 'B3', 'B2'], min: 0, max: 3000};
var falseColor= {bands: ['B8', 'B3', 'B4'], min: 0, max: 3000};
//Define the CLoud layer (here: QA60 is MSI2's quality mask)
var Clouds = {bands: ['QA60']};

//Add the cloud mask as layer; PROBLEM: SEEMS QA60 is taken from different images every time..
//Clouds is just a band, do i need to specify the threshold?
Map.addLayer(Jan2016, Clouds, "CloudsJan16");

// Mask clouds
var noclouds = Jan2016.map(function(img) {
              var mask = 
img.select(['QA60']).neq(11); 
//.neq(xx) doesn't seem to make a difference
                   return img.updateMask(mask);

});

//Add the layer/imagery to the map with variable, display type, and name  
Map.addLayer(noclouds, trueColor, "NoClouds");
Map.addLayer(Jan2016, falseColor, "Jan2016false");

Answer 1

Here is an example of cloud masking for Sentinel-2:

var s2 = ee.ImageCollection("COPERNICUS/S2");
var pt = ee.Geometry.Point([-122.41653442382812, 37.77180027337861]);

var cloudyImage = ee.Image('COPERNICUS/S2/20151207T190417_20151207T221905_T10SEG');
Map.centerObject(cloudyImage, 10);
Map.addLayer(cloudyImage, {bands: ['B4', 'B3', 'B2'], max: 2000}, 'cloudy image');

// Bits 10 and 11 are clouds and cirrus, respectively.
var cloudBitMask = ee.Number(2).pow(10).int();
var cirrusBitMask = ee.Number(2).pow(11).int();

var qa = cloudyImage.select('QA60');

Map.addLayer(qa.bitwiseAnd(cloudBitMask).neq(0), {}, 'clouds');
Map.addLayer(qa.bitwiseAnd(cirrusBitMask).neq(0), {}, 'cirrus');

function maskS2clouds(image) {
  var qa = image.select('QA60');
  // Both flags should be set to zero, indicating clear conditions.
  var mask = qa.bitwiseAnd(cloudBitMask).eq(0).and(
             qa.bitwiseAnd(cirrusBitMask).eq(0));
  return image.updateMask(mask);
}

var cloudMasked = s2.filterBounds(pt).map(maskS2clouds);

var median = cloudMasked.median();
Map.addLayer(median, {bands: ['B4', 'B3', 'B2'], max: 2000}, 'median');

Answer 2

Here is a comprehensive tutorial on how to mask clouds and their shadows over an entire Sentinel-2 image collection: https://developers.google.com/earth-engine/tutorials/community/sentinel-2-s2cloudless

It uses the Sentinel-2 Cloud Probability image collection to mask clouds (rather than the QA60 band), which is a separate but compatible dataset.

The tutorial is in Python, but I've re-written it for those interested in a JavaScript version: https://code.earthengine.google.com/f0fa2a9ae2f478b89f9f8ba8aab644a5

There's a minor addition to the JS version: for those wanting to use the Top Of Atmosphere (TOA) instead of surface reflectance, it won't work because line 53 requires the SCL (Scene CLassification map) to remove water pixels when detecting cloud shadows, and SCL is absent from the TOA dataset. Instead, use line 54 which thresholds NDWI to identify water pixels.