GEE Sentinel 2 cloud mask with QA60

Question

I'm running a script on GEE to download EVI images from a certain time period and place, and also the cloud masks from each image calculated from the QA60 band with the following function. But the mask I always export gives me all 1s, even when it's cloudy. Why could this be?

function maskS2clouds(image) {
  // Seleccionar la banda 'QA60' de la imagen.
  var qa = image.select('QA60');

  // Los bits 10 y 11 representan las nubes y el cirrus, respectivamente.
  var cloudBitMask = 1 << 10;
  var cirrusBitMask = 1 << 11;

  // Crear una máscara donde 1 indica nubes y 0 indica condiciones despejadas.
  var mask = qa.bitwiseAnd(cloudBitMask).or(qa.bitwiseAnd(cirrusBitMask)).not();

  // Convertir la máscara a un formato uint8.
  var maskBand = mask.toUint8();

  // Renombrar la banda de la máscara.
  maskBand = maskBand.rename('cloudMask');

  // Devolver la imagen con la banda de la máscara añadida y la misma información de fecha.
  return image.addBands(maskBand).set('system:time_start', image.get('system:time_start'));
}

var colMask = col.map(maskS2clouds)
                .select('cloudMask');
                  

function exportmask(collection, folder, scale, region, crs) {
  var list = collection.toList(collection.size());
  var n = list.size().getInfo();
  for (var i = 0; i < n; i++) {
    var image = ee.Image(list.get(i));
    var id = campo + '_' + ee.Date(image.date().format('YYYY-MM-dd')).format('YYYYMMdd').getInfo() + '_mask';
    Export.image.toDrive({
      image: image.toUint8(),
      description: id,
      folder: folder,
      scale: scale,
      region: region,
      crs: 'EPSG:32720'
    });
  }
}

// Exportar todas las imágenes de la colección colEVI a Google Drive
exportmask(colMask, 'EVI_exports', 10, geometry);

Answer 1

I don't think anything is wrong with your code. It's QA60 that is really lousy. It's working bad enough that I wonder if something isn't wrong with the ingestion.

Clouds are detected in this image: ee.Image('COPERNICUS/S2_HARMONIZED/20171003T100009_20171003T100257_T32TQM'), but not this ee.Image('COPERNICUS/S2_HARMONIZED/20230505T100029_20230505T100612_T32TQM').

https://code.earthengine.google.com/addd0b59ea196bba514b49a8072d403b

You might want to consider using COPERNICUS/S2_CLOUD_PROBABILITY for cloud masking instead. It's slower but a lot better.

var geometry = Map.getBounds(true)
var cloudThreshold = 30 // Tweak to be more or less aggressive in the cloud masking

var filter = ee.Filter.and(
  ee.Filter.bounds(geometry),
  ee.Filter.date('2023-01-01', '2023-06-01')
)

var col = ee.ImageCollection(
    ee.Join.saveFirst('cloudProbability').apply({
        primary: ee.ImageCollection('COPERNICUS/S2_SR_HARMONIZED')
          .filter(filter)
          .filter(ee.Filter.lt('CLOUDY_PIXEL_PERCENTAGE', 75)), // Filter out really cloudy scenes up-front
        secondary: ee.ImageCollection('COPERNICUS/S2_CLOUD_PROBABILITY')
          .filter(filter),
        condition: ee.Filter.equals({leftField: 'system:index', rightField: 'system:index'})
    })
).map(maskClouds)

Map.addLayer(col.mosaic(), {bands: 'B4,B3,B2', max: 3000, gamma: 1.5})


function maskClouds(image) {
  var cloudFree = ee.Image(image.get('cloudProbability')).lt(cloudThreshold)
  return image.updateMask(cloudFree)
}

Answer 2

Thank you for your response. The curious thing is that I have downloaded the QA60 band from the Sentinel's page for a scene with clouds and the QA60 pixels mark it, but when I run it in GEE it doesn't work.