LAI predictor added

Prosail

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+// A sensor invariant Atmospheric Correction (SIAC) GEE version
+// v1 -- 2019-05-06
+// Author: Fengn Yin, UCL
+// Email: ucfafy@ucl.ac.uk
+// Github: https://github.com/MarcYin/SIAC
+// DOI: https://eartharxiv.org/ps957/
+// LICENSE: GNU GENERAL PUBLIC LICENSE V3
+
+var get_2D = function(image, nb, ny){
+  var array   = ee.List(image.reduceRegion(ee.Reducer.toList(), image.geometry()).get('b1'))
+  var sub_len = array.size().divide(nb)
+  var i;
+  var j;
+  var list_2d = []
+  for (j = 0; j < nb; j++){
+    var start = sub_len.multiply(j)
+    var end   = sub_len.multiply(j).add(ny)
+    var sub = array.slice(start, end)
+    list_2d.push(sub)
+  }
+  return ee.List(list_2d).reverse()
+}
+
+var get_3D = function(image, nb, nx, ny){
+  var array   = ee.List(image.reduceRegion(ee.Reducer.toList(), image.geometry()).get('b1'))
+  var sub_len = array.size().divide(nb)
+  var i;
+  var j;
+  var ret = []
+  for (j = 0; j < nb; j++){
+    var list_2d = []
+    for (i = 0; i < nx; i++) {
+      var start = sub_len.multiply(j).add(i*ny)
+      var end   = sub_len.multiply(j).add((i+1)*ny)
+      var sub = array.slice(start, end)
+      list_2d.push(sub)
+    }
+    ret.push(list_2d)
+  }
+  return ee.List(ret).reverse()
+}
+
+var parse_out = function(image){
+  var dict = ee.Dictionary(image.reduceRegion(ee.Reducer.toList(), image.geometry()))
+  var ret  = ee.List([dict.get('b1')])
+  return ret
+}
+
+var Prosail_H1_offset  = get_2D(ee.Image('users/marcyinfeng/Prosail_H1_offset'),  1, 256).get(0)
+var Prosail_H2_offset  = get_2D(ee.Image('users/marcyinfeng/Prosail_H2_offset'),  1, 256).get(0)
+var Prosail_Out_offset = parse_out(ee.Image('users/marcyinfeng/Prosail_Out_offset'))
+
+
+var Prosail_H1_scale  = get_3D(ee.Image('users/marcyinfeng/Prosail_H1_scale'),  1,  10, 256).get(0)
+var Prosail_H2_scale  = get_3D(ee.Image('users/marcyinfeng/Prosail_H2_scale'),  1, 256, 256).get(0)
+var Prosail_Out_scale = get_3D(ee.Image('users/marcyinfeng/Prosail_Out_scale'), 1, 256, 1).get(0)
+
+// print(Prosail_H1_scale)
+// print(Prosail_H2_scale)
+
+// print(Prosail_H1_offset)
+// print(Prosail_H2_offset)
+
+// print(Prosail_Out_offset)
+// print(Prosail_Out_scale)
+
+exports.Prosail_H1_scale  = Prosail_H1_scale
+exports.Prosail_H2_scale  = Prosail_H2_scale
+exports.Prosail_Out_scale = Prosail_Out_scale
+exports.Prosail_H1_offset  =  Prosail_H1_offset
+exports.Prosail_H2_offset  =  Prosail_H2_offset
+exports.Prosail_Out_offset = Prosail_Out_offset

S2_Toa2Lai

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+// A sensor invariant Atmospheric Correction (SIAC) GEE version
+// v1 -- 2019-05-06
+// Author: Fengn Yin, UCL
+// Email: ucfafy@ucl.ac.uk
+// Github: https://github.com/MarcYin/SIAC
+// DOI: https://eartharxiv.org/ps957/
+// LICENSE: GNU GENERAL PUBLIC LICENSE V3
+var tnn = require('users/marcyinfeng/SIAC:Two_NN')
+var prosail = require('users/marcyinfeng/Toa2Lai:Prosail')
+var siac_processor = require('users/marcyinfeng/SIAC:AC_processor')
+
+var inv_prosail = function(image){
+  image     = ee.Image(image)
+  var geom  = image.geometry()
+  var image_date = image.date()
+  var projection = image.select('B2').projection()
+  var crs = projection.crs()
+  var boa = siac_processor.get_boa(image)
+  var saa  = ee.Image.constant(ee.Number(image.get('MEAN_SOLAR_AZIMUTH_ANGLE'))).rename('saa')
+  var sza  = ee.Image.constant(ee.Number(image.get('MEAN_SOLAR_ZENITH_ANGLE' ))).rename('sza')
+  var vaa  = ee.Image.constant(ee.Number(image.get('MEAN_INCIDENCE_AZIMUTH_ANGLE_B2'))).rename('vaa')
+  var vza  = ee.Image.constant(ee.Number(image.get('MEAN_INCIDENCE_ZENITH_ANGLE_B2' ))).rename('vza')
+  var raa  = vaa.subtract(saa)
+  var deg2rad = ee.Number(Math.PI).divide(ee.Number(180.0))
+  var cos_sza = (sza.multiply(deg2rad)).cos()
+  var cos_vza = (vza.multiply(deg2rad)).cos()
+  var cos_raa = (raa.multiply(deg2rad)).cos()
+  var name     = ['B1', 'B2', 'B3', 'B4', 'B5', 'B6', 'B7', 'B8', 'B8A',  'B11', 'B12']
+  var new_name = ['B01', 'B02', 'B03', 'B04', 'B05', 'B06', 'B07', 'B08', 'B8A',  'B11', 'B12']
+  var prosail_bands = ['B02', 'B03', 'B04', 'B05', 'B06', 'B07', 'B8A']
+  var prosail_inputs = ee.Image.cat([boa.select(name, new_name).select(prosail_bands), 
+                                     cos_sza, cos_vza, cos_raa])
+
+  var H1_scale = prosail.Prosail_H1_scale
+  var H2_scale = prosail.Prosail_H2_scale
+  var Out_scale = prosail.Prosail_Out_scale
+
+  var H1_offset = prosail.Prosail_H1_offset
+  var H2_offset = prosail.Prosail_H2_offset
+  var Out_offset = prosail.Prosail_Out_offset
+
+  var arrayImage1D = prosail_inputs.toArray()
+  var arrayImage2D = arrayImage1D.toArray(1);
+  var imageAxis = 0;
+  var bandAxis  = 1;
+  var arrayLength = arrayImage2D.arrayLength(imageAxis);
+  arrayImage2D    = arrayImage2D
+  var h1  = arrayImage2D.arrayTranspose().matrixMultiply(ee.Image(ee.Array(H1_scale))).add(ee.Image(ee.Array(H1_offset)).toArray(1).arrayTranspose())
+  var in1 = h1.max(0)
+  var h2  = in1.matrixMultiply(ee.Image(ee.Array(H2_scale))).add(ee.Image(ee.Array(H2_offset)).toArray(1).arrayTranspose())
+  var in2 = h2.max(0)
+  var oup = in2.matrixMultiply(ee.Image(ee.Array(Out_scale)).toArray(1))
+  var out = oup.add(ee.Image(ee.Array(Out_offset.get(0))).toArray(1).arrayTranspose())
+               .arrayProject([1])
+               //.arrayFlatten([['lai'], ['Cab'], ['Cbrown'], ['Ala'], ['N']])
+               .arrayFlatten([['Lai']])
+  var Lai    = out.select('Lai'   ).log().multiply(-2)
+  // Map.addLayer(Lai, {min:0, max:8})
+  // Map.addLayer(image.divide(10000), {bands:['B4', 'B3', 'B2'], min:0, max:0.2}, 'TOA')
+  // Map.addLayer(prosail_inputs)
+  var fname = ee.String(image.get('PRODUCT_ID')).getInfo() 
+  Export.image.toDrive({
+              image: Lai.multiply(100).toInt(),
+              description: fname + '_lai',
+              scale: 10,
+              fileFormat: 'GeoTIFF',
+              folder:'S2_SUR',
+              region: geom,
+              maxPixels: 1e13
+            })
+}
+
+// var s2_file = '20190303T184259_20190303T184825_T10SGF'
+// var s2_file = '20180115T030049_20180115T030132_T50SND'
+// var image = ee.ImageCollection('COPERNICUS/S2').filterMetadata('system:index', 'equals', s2_file)
+//                       .first()
+// var id = 'S2B_MSIL1C_20190513T030549_N0207_R075_T50SLG_20190513T054821'
+// var image = ee.ImageCollection('COPERNICUS/S2').filterMetadata('PRODUCT_ID', 'equals', id)
+//                       .first()
+
+// // var s2_file = '20190122T034049_20190122T034312_T47PPR'
+// // var image = ee.ImageCollection('COPERNICUS/S2').filterMetadata('system:index', 'equals', s2_file)
+// //                       .first()
+
+// print(image)
+// inv_prosail(image)
+// Map.centerObject(image)
+
+exports.inv_prosail = inv_prosail