//Access in the Google Earth Engine code editor: https://code.earthengine.google.com/?accept_repo=users/tatiana/SeteSetembro

//////////////////////////////
//                          //
//  VISUALISATION SCRIPT    //
//                          //
//////////////////////////////

///////////////////////////////////////////////////
//ENTER IMPORT AND EXPORT VARIABLES

//Enter these 4 variables
var Clear = false;                                  //Is the image clear (true) or cloudy (false)?
var datatake = '20190123';                         //Enter datatake as in classified images name
var dateFrom = '2019-01-23';                       //ENTER IMAGE DATES
var dateTo = '2019-01-24';                         //ENTER IMAGE DATES

//Automatic variables
var ClassifClouds = datatake+'_classifiedClouds';
var ClassifForest = datatake+'_classifiedForest';
var nameExp = datatake;                       


///////////////////////////////////////////////////
//Study zone
//Polygone around the study zone
var studySite = ee.Geometry.Polygon(
  [[[-61.4417, -10.7464],
    [-61.4383, -11.2584],
    [-60.8973, -11.2551],
    [-60.9098, -10.7198]]]);

//Center on study zone
Map.centerObject(studySite,11);

//Polygone of the SSIL
//Source: "WCMC/WDPA/current/polygons").filterMetadata('NAME','equals','Sete de Setembro')
var protectedArea = ee.FeatureCollection([ee.Geometry.Polygon(
  [[[-61.430890367207255,-10.751891444900613],
[-61.42519163574619,-11.11447884042015], 
[-61.37005491417673,-11.114298205538441],
[-61.31491808398053,-11.114117608447993],
[-61.31458365364846,-11.249759040437475],
[-61.23209698577483,-11.249121383106058],
[-61.149610266132704,-11.248483719229005], 
[-61.09324164199908,-11.175238503746515],
[-61.036873050995155,-11.101993360397458],
[-60.98050448006274,-11.028748124678014],
[-60.92413582759241,-10.955502938986513],
[-60.92913000110267,-10.738589998072223],
[-60.99185011285132,-10.740252698436697],
[-61.05457014507297,-10.741915331211235],
[-61.11729013718773,-10.743578015404607],
[-61.180010217902435,-10.745240724477434],
[-61.24273024957612,-10.746903404731825],
[-61.30545027262106,-10.748566097570336],
[-61.368170327808194,-10.750228766894775],
[-61.430890367207255,-10.751891444900613]]])]);

// New empty image (bytes) in which the SSIL polygone will be painted
var empty = ee.Image().byte();
var seteSetembro = empty.paint({
  featureCollection: protectedArea,
  width: 1.5
});

//Bitmap of the indigenous land + mask
var borderBM = ee.Image('users/tatiana/Masks/BorderBM');

//Bitmap of the rivers + mask
var waterBM = ee.Image('users/tatiana/Masks/WaterBM');
var waterBMMask = waterBM.updateMask(waterBM);
var waterBMMaskDisp = waterBM.updateMask(waterBM.not());


///////////////////// IF CLOUDY IMAGE //////////////////////
if (Clear === false) {
    print('The image is cloudy.');


///////////////////////////////////////////
//LOAD ALL IMAGES AND CLIP ON STUDY SITE
//Clip function
var clipStudySite = function(image){
  return image.clip(studySite)};

//Clouds classification
var imgClouds = ee.Image('users/tatiana/'+ClassifClouds);
var imgClouds = clipStudySite(imgClouds);

//Forest classification
var imgForest = ee.Image('users/tatiana/'+ClassifForest)
var imgForest = clipStudySite(imgForest);

//Original image
var imgS2 = ee.ImageCollection('COPERNICUS/S2')
  .filterDate(dateFrom,dateTo) 
  .filterBounds(studySite);
  
//Cloud percentage
print('Images in image collection (must be 4):',imgS2.size());
var meanClouds = imgS2.aggregate_mean('CLOUDY_PIXEL_PERCENTAGE');
print('Mean cloud cover percentage: ',meanClouds);

//Make the image collection to a single image and clip it
var imgS2 = imgS2
  .map(clipStudySite)
  .mean();


///////////////////////////////////////////////////
//GENERATING BITMAPS FOR CLOUDS, SHADOW, VEGETATION
//Where 1 = yes / 0 = other
//Please note that the prediction map for the forest ist already a bitmap with 1 = not vegetation

//Vegetation bitmap function
var addBMVegetation = function(image) {
  var imagePred = image.select('notVegetationBM').not().rename('vegetationBM');
  return image.addBands(imagePred);
};

//Clouds bitmap function
var addBMClouds = function(image) {
  var imagePred = image.select('predictions');
  var BitMapValues = imagePred.gt(4).and(imagePred.lt(7)).rename('cloudsBM');
  return image.addBands(BitMapValues);
};

//Shadows and water bitmap function
var addMBShW = function(image) {
  var imagePred = image.select('predictions');
  var BitMapValues = imagePred.expression(
    'water + shadow', {
      'water': imagePred.gt(3).and(imagePred.lt(5)),
      'shadow': imagePred.gt(6)
}).rename('shadowBM');
  return image.addBands(BitMapValues);
};

var imgForest = addBMVegetation(imgForest);
var imgClouds = addBMClouds(imgClouds);
var imgClouds = addMBShW(imgClouds);


///////////////////////////////////////////////////
//GENERATING ALL MASKS
//Clouds mask function
var maskClouds = function(image) {
  var imagePred = image.select('cloudsBM');
  var BitMask = imagePred.updateMask(imagePred).rename('cloudsMask');
  return image.addBands(BitMask);
};

//Shadows and water mask function
var maskShW = function(image) {
  var imagePred = image.select('shadowBM');
  var BitMask = imagePred.updateMask(imagePred).rename('shadowMask');
  return image.addBands(BitMask);
};

//Vegetation mask function (+ masked clouds and shadow)
var maskVegetation = function(image) {
  var imagePred = image.select('vegetationBM');
  var maskClouds = imgClouds.select('cloudsBM').not();
  var maskShadow = imgClouds.select('shadowBM').not();
  var mask = imagePred.and(maskClouds).and(maskShadow).and(waterBMMask);
  var BitMask = imagePred.updateMask(mask).rename('vegetationMask');
  return image.addBands(BitMask);
};

//Not Vegetation mask function (+ masked clouds and shadow)
var maskNotVegetation = function(image) {
  var imagePred = image.select('notVegetationBM');
  var maskClouds = imgClouds.select('cloudsBM').not();
  var maskShadow = imgClouds.select('shadowBM').not();
  var mask = imagePred.and(maskClouds).and(maskShadow).and(waterBMMask);
  var BitMask = imagePred.updateMask(mask).rename('notVegetationMask');
  return image.addBands(BitMask);
};

//Add the masks
var imgClouds = maskClouds(imgClouds);
var imgClouds = maskShW(imgClouds);
var imgForest = maskVegetation(imgForest);
var imgForest = maskNotVegetation(imgForest);

///////////////////////////////////////////////////
//DISPLAY PARAMETERS
//True colors
var visTrueColors = {              
  bands: ['B4','B3','B2'],
  min: 200,
  max: 6200,
  gamma: 1.8
};

//Clouds
var visClouds = {              
  bands: ['cloudsMask'],
  palette: 'ffffff'
};

//Shadows
var visShadow = {              
  bands: ['shadowMask'],
  palette: '876f9d'
};

//Vegetation
var visVeg = {              
  bands: ['vegetationMask'],
  palette: '89d4a4'
};

//Bare
var visNotVeg = {              
  bands: ['notVegetationMask'],
  palette: 'e46346'
};


///////////////////////////////////////////////////
//LOAD MAPS
Map.addLayer(imgS2, visTrueColors, 'True Colors', true);
Map.addLayer(imgForest,visVeg,'Vegetation', true);
Map.addLayer(imgForest,visNotVeg,'Not vegetation', true);
Map.addLayer(imgClouds, visShadow, 'Shadows',true);
Map.addLayer(waterBMMaskDisp, {palette: '5a7cba'}, 'Water',true);
Map.addLayer(imgClouds, visClouds, 'Clouds', true);
Map.addLayer(seteSetembro, {palette: '525252'}, 'Sete de Setembro',true);


///////////////////////////////////////////////////
//PREPARE IMAGES FOR EXPORT
//Prepare export for visualisation
var cloudsBM = imgClouds.select('cloudsBM').multiply(5)
var shadowBM = imgClouds.select('shadowBM').subtract(waterBM.not()).eq(1).multiply(4)
var ForestBM = imgForest.select('vegetationBM').subtract(waterBM.not()).subtract(cloudsBM).subtract(shadowBM).eq(1);
var NotForestBM = imgForest.select('notVegetationBM').subtract(waterBM.not()).subtract(cloudsBM).subtract(shadowBM).eq(1).multiply(2);
var RiverBM = waterBM.not().subtract(cloudsBM).eq(1).multiply(3)
var AllBM = ForestBM.add(NotForestBM).add(RiverBM).add(cloudsBM).add(shadowBM).rename('all').byte();

//Visualisation parameters for the export
var visExport1 = {              
  bands: ['all'],
  palette: ['89d4a4','e46346','5a7cba','876f9d','ffffff'],
  min: 1,
  max: 5,
};

Map.addLayer(AllBM, visExport1, 'Export image 1',false);

//Prepare export for data storage
var ForestBMS = imgForest.select('vegetationBM').subtract(waterBM.not()).subtract(borderBM.not()).subtract(cloudsBM).subtract(shadowBM).eq(1);
var NotForestBMS = imgForest.select('notVegetationBM').subtract(waterBM.not()).subtract(borderBM.not()).subtract(cloudsBM).subtract(shadowBM).eq(1).multiply(2);
var AllBMS = ForestBMS.add(NotForestBMS).rename('all').byte();

//Visualisation parameters for the export
var visExport2 = {              
  bands: ['all'],
  palette: ['ffffff','89d4a4','e46346'],
  min: 0,
  max: 2,
};

Map.addLayer(AllBMS, visExport2, 'Export image 2',false);


///////////////////////////////////////////
//EXPORT IMAGES

//Current date and time
var datetime = new Date(); 
var datetime =  datetime.getFullYear() + ""
                + ("0" + (datetime.getMonth() + 1)).slice(-2) + ""
                + ("0" + datetime.getDate()).slice(-2) + "_"  
                + ("0" + datetime.getHours()).slice(-2) + ""
                + ("0" + datetime.getMinutes()).slice(-2);
                
//Export
Export.image.toDrive({
  image: AllBM,
  description: nameExp+'_ExportVis_'+datetime,
  folder: 'GEEexportVIS',
  scale: 30,
  region: studySite,
  fileFormat: 'GeoTIFF'});
  
Export.image.toDrive({
  image: AllBMS,
  description: nameExp+'_ExportSt_'+datetime,
  folder: 'GEEexportST',
  scale: 30,
  region: studySite,
  fileFormat: 'GeoTIFF'});
  
Export.image.toAsset({
  image: AllBMS,
  description: nameExp+'_classifiedStorage',
  scale: 30,
  region: studySite});


///////////////////// IF THE IMAGE IS CLEAR //////////////////////
} else {
    print('The image is clouds-free.')
    
    
///////////////////////////////////////////
//LOAD ALL IMAGES AND CLIP ON STUDY SITE
//Clip function
var clipStudySite = function(image){
  return image.clip(studySite)};

//Forest classification
var imgForest = ee.Image('users/tatiana/'+ClassifForest)
var imgForest = clipStudySite(imgForest);

//Original image
var imgS2 = ee.ImageCollection('COPERNICUS/S2')
  .filterDate(dateFrom,dateTo) 
  .filterBounds(studySite);
  
//Cloud percentage
print('Images in image collection (must be 4):',imgS2.size());
var meanClouds = imgS2.aggregate_mean('CLOUDY_PIXEL_PERCENTAGE');
print('Mean cloud cover percentage: ',meanClouds);

//Make the image collection to a single image and clip it
var imgS2 = imgS2
  .map(clipStudySite)
  .mean();


///////////////////////////////////////////////////
//GENERATING BITMAPS FOR VEGETATION
//Where 1 = yes / 0 = other
//Please note that the prediction map for the forest ist already a bitmap with 1 = not vegetation

//Vegetation bitmap function
var addBMVegetation = function(image) {
  var imagePred = image.select('notVegetationBM').not().rename('vegetationBM');
  return image.addBands(imagePred);
};
var imgForest = addBMVegetation(imgForest);


///////////////////////////////////////////////////
//GENERATING ALL MASKS

//Vegetation mask function (+ masked clouds and shadow)
var maskVegetation = function(image) {
  var imagePred = image.select('vegetationBM');
  var mask = imagePred.and(waterBMMask);
  var BitMask = imagePred.updateMask(mask).rename('vegetationMask');
  return image.addBands(BitMask);
};

//Not Vegetation mask function (+ masked clouds and shadow)
var maskNotVegetation = function(image) {
  var imagePred = image.select('notVegetationBM');
  var mask = imagePred.and(waterBMMask);
  var BitMask = imagePred.updateMask(mask).rename('notVegetationMask');
  return image.addBands(BitMask);
};

//Add the masks
var imgForest = maskVegetation(imgForest);
var imgForest = maskNotVegetation(imgForest);

///////////////////////////////////////////////////
//Display parameters
//true colors
var visTrueColors = {              
  bands: ['B4','B3','B2'],
  min: 200,
  max: 6200,
  gamma: 1.8
};

//Vegetation
var visVeg = {              
  bands: ['vegetationMask'],
  palette: '89d4a4'
};

//Bare
var visNotVeg = {              
  bands: ['notVegetationMask'],
  palette: 'e46346'
};


///////////////////////////////////////////////////
//LOAD MAPS
Map.addLayer(imgS2, visTrueColors, 'True Colors', true);
Map.addLayer(waterBMMaskDisp, {palette: '5a7cba'}, 'Water', true);
Map.addLayer(imgForest,visVeg,'Vegetation', true);
Map.addLayer(imgForest,visNotVeg,'Not vegetation', true);
Map.addLayer(seteSetembro, {palette: '525252'}, 'Sete de Setembro', true);


///////////////////////////////////////////////////
//PREPARE IMAGES FOR EXPORT
//Export for visualisation
var ForestBM = imgForest.select('vegetationBM').subtract(waterBM.not()).eq(1);
var NotForestBM = imgForest.select('notVegetationBM').subtract(waterBM.not()).eq(1).multiply(2);
var RiverBM = waterBM.not().multiply(3)
var AllBM = ForestBM.add(NotForestBM).add(RiverBM).rename('all').byte();

//Visualisation parameters for the export
var visExport1 = {              
  bands: ['all'],
  palette: ['89d4a4','e46346','5a7cba'],
  min: 1,
  max: 3,
};

Map.addLayer(AllBM, visExport1, 'Export image 1',false);

//Export for data storage
var ForestBMS = imgForest.select('vegetationBM').subtract(waterBM.not()).subtract(borderBM.not()).eq(1);
var NotForestBMS = imgForest.select('notVegetationBM').subtract(waterBM.not()).subtract(borderBM.not()).eq(1).multiply(2);
var AllBMS = ForestBMS.add(NotForestBMS).rename('all').byte();

//Visualisation parameters for the export
var visExport2 = {              
  bands: ['all'],
  palette: ['ffffff','89d4a4','e46346'],
  min: 0,
  max: 2,
};

Map.addLayer(AllBMS, visExport2, 'Export image 2',false);


///////////////////////////////////////////
//EXPORT IMAGES

//Current date and time
var datetime = new Date(); 
var datetime =  datetime.getFullYear() + ""
                + ("0" + (datetime.getMonth() + 1)).slice(-2) + ""
                + ("0" + datetime.getDate()).slice(-2) + "_"  
                + ("0" + datetime.getHours()).slice(-2) + ""
                + ("0" + datetime.getMinutes()).slice(-2);
                
//Export
Export.image.toDrive({
  image: AllBM,
  description: nameExp+'_ExportVis_'+datetime,
  folder: 'GEEexportVIS',
  scale: 30,
  region: studySite,
  fileFormat: 'GeoTIFF'});
  
Export.image.toDrive({
  image: AllBMS,
  description: nameExp+'_ExportSt_'+datetime,
  folder: 'GEEexportST',
  scale: 30,
  region: studySite,
  fileFormat: 'GeoTIFF'});
  
Export.image.toAsset({
  image: AllBMS,
  description: nameExp+'_classifiedStorage',
  scale: 30,
  region: studySite});

}