Green snow algae classification

Description: This script uses Sentinel-2 level-2A imagery and applies filtering, masking and classification algorithms to identify green snow algae across Antarctica.

//SUMMER FILTER
var summer17 =ee.Filter.date('2017-12-01','2018-03-01');
var summer18 =ee.Filter.date('2018-12-01','2019-03-01');
var summer19 =ee.Filter.date('2019-12-01','2020-03-01');
var summer20 =ee.Filter.date('2020-12-01','2021-03-01');
var summer21 =ee.Filter.date('2021-12-01','2022-03-01');
var summerAll = ee.Filter.or(summer17, summer18, summer19, summer20, summer21); //combined summer filter

//S2_L2 Image Search and Filter
var S2 = S2L2.filter(summerAll).filterBounds(coastline).filterMetadata('CLOUDY_PIXEL_PERCENTAGE', 'less_than', 20);

//CLIP BY BUFFERED LAND MASK
var clip = function(image) {
    return image.clip(seamask3);
};
var clipped = S2.map(clip);

//MASK BY ELEVATION
var elemsk = function(image) {
  var lt100 = image.where((REMA.select('elevation').lte(0).or(REMA.select('elevation').gte(500))), 0);
  return image.updateMask(lt100);
};
var ele_masked = clipped.map(elemsk);

//SEA ICE REMOVAL
var min = S2.reduce(ee.Reducer.min());
var seaicemsk = function(image) {
  var SCL_min = image.where((min.select('SCL_min').eq(6)).or(min.select('SCL_min').eq(2)),0);
  return image.updateMask(SCL_min);
};
var water_masked = ele_masked.map(seaicemsk);

//MASK BY BAND FUNCTIONS
var mask = function(image) {
  var mask_fun = image.where((image.select('B2').lte(10)).or((image.select('B2')).gt(5500)).or(image.select('SCL').neq(11)).or((image.select('B2')).gte(image.select('B5'))).or((image.select('B2')).gt(image.select('B3'))).or(image.select('B11').gt(1500)).or((image.select('B2').lte(3000)).and(image.select('B8').lte(2500))).or((image.select('B8')).lt(image.select('B8A'))).or((image.select('B4')).gt(image.select('B5'))), 0);
  return image.updateMask(mask_fun);
  };
var masked = water_masked.map(mask);

//I68
var processing = function(image) {
  var i68 = ((((((((image.select('B3')).multiply(50)).add((image.select('B5')).multiply(89))).divide(139)).subtract(image.select('B4'))).divide((((image.select('B3')).multiply(50)).add ((image.select('B5')).multiply(89))).divide(139))).multiply(293006)).add(5579.7)).rename('i68').uint32();
  return image.addBands(i68);
  };
var processed = masked.map(processing);

//celden filter
var filter = function(image) {
  var i68filter = image.where(((image.select('i68')).lte(15000)),0);
  return image.updateMask(i68filter);
  };
var i68pix = processed.map(filter);
var max = i68pix.reduce(ee.Reducer.max());
var celden = max.select('i68_max').gt(15000);

var algae = max.select('i68_max').rename('celden');

//Average filter

var celdenMask = algae.gt(20000);
var avFilt = celdenMask
    .reduceNeighborhood({
    reducer: ee.Reducer.min(),
    kernel: ee.Kernel.circle(7),
  })
   .reproject({
      crs: 'EPSG:4326',
      scale: 50
    });

var algaemasked = algae.updateMask(avFilt);

//Map.addLayer(algaemasked);