How to apply a Cloud Mask in a collection?

Question

I am trying to apply a mask cloud in a SAVI collection (LANDSAT) to get a chart with time variations between pixels.

var region = table3

    Map.addLayer(table3)

    var col = ee.ImageCollection('LANDSAT/LE7_SR')
        .filterDate('2004-01-01', '2011-12-31')
        .filterBounds(table3)
        .filter(ee.Filter.eq('WRS_PATH', 1))
        .filter(ee.Filter.eq('WRS_ROW', 72));

        print(col)

    // Mask clouds
    var col_noclouds = col.map(function(img) {
                       var mask = 
    img.select(['cfmask']).neq(4).neq(1).neq(2).neq(3)
                       return img.updateMask(mask)
                       })

    // Median image
    var medians = ee.Image(col_noclouds.median())

    var clipper = medians.clip(table3)


    // A function to compute Soil Adjusted Vegetation Index.
    var SAVI = function(image) {
      return clipper.expression(
          '(1 + L) * float(nir - red)/ (nir + red + L)',
          {
            'nir': image.select('B5'),
            'red': image.select('B4'),
            'L': 0.5
          }).set('system:time_start', image.get('system:time_start'));
    };

    // Shared visualization parameters.
    var vis = {
      min: 0,
      max: 1,
      palette: [
          'FFFFFF', 'CE7E45', 'DF923D', 'F1B555', 'FCD163', '99B718',
          '74A901', '66A000', '529400', '3E8601', '207401', '056201',
          '004C00', '023B01', '012E01', '011D01', '011301'
      ]
    };


    var image = ee.ImageCollection(col) 
       .map(SAVI);

    print(image)

    Map.addLayer(image,vis);


    var TS5 = Chart.image.seriesByRegion(image, region,  
    ee.Reducer.mean(),'constant', 500, 'system:time_start').setOptions({
              title: 'NDVI Long-Term Time Series',
              vAxis: {title: 'constant'},
    });
    print(TS5);

I can make the chart for "image" (collection with SAVI function) but I do not know how to insert the cloud mask.

Any recommendation?

Answer 1

The problem is in the creation of the cloud mask. Use:

var mask = image.select(['cfmask']).neq((2,4))

instead:

var mask = image.select(['cfmask']).neq(4).neq(1).neq(2).neq(3)

Value 2 and 4 are for cloud shadows and clouds in cfmask.

With a reproducible example:

var col = ee.ImageCollection('LANDSAT/LE7_SR')
    .filterDate('2004-01-01', '2011-12-31')
    .filter(ee.Filter.eq('WRS_PATH', 1))
    .filter(ee.Filter.eq('WRS_ROW', 72));

// Mask clouds
var col_noclouds = col.map(function(img) {
  var mask = img.select(['cfmask']).neq(4).neq(1).neq(2).neq(3);
      return img.updateMask(mask);
});

// A function to compute Soil Adjusted Vegetation Index.
var SAVI = function(image) {
  var img = image.expression(
      '(1 + L) * float(nir - red)/ (nir + red + L)',
      {
        'nir': image.select('B5'),
        'red': image.select('B4'),
        'L': 0.5
      }).set('system:time_start', image.get('system:time_start'));
  var mask = image.select(['cfmask']).neq((2,4));
  return img.updateMask(mask);
};

// Shared visualization parameters.
var vis = {
  min: 0,
  max: 1,
  palette: [
      'FFFFFF', 'CE7E45', 'DF923D', 'F1B555', 'FCD163', '99B718',
      '74A901', '66A000', '529400', '3E8601', '207401', '056201',
      '004C00', '023B01', '012E01', '011D01', '011301'
  ]
};


var image = ee.ImageCollection(col).map(SAVI);

Map.addLayer(ee.Image(image.first()),vis);

By the way, cfmsk is not used anymore. Change to pixel_qa_band