Chris follett

DataSet From DARWIN/AddRrsCorrection/README.md

@@ -0,0 +1,3 @@
+# Add RrsCorrection.jl will open the DARWIN Dataset from the oceanclustering repository (stored here in this folder ) and apply
+# the zenith angle correction to it
+

DataSet From DARWIN/AddRrsCorrection/RrsCorrection.jl

@@ -0,0 +1,10 @@
+using Plots, Distributions, NetCDF, NCDatasets, Interpolations
+
+filename="HalfDegree.nc"
+varnames=["Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555", "Rirr670"]
+for n in 1:length(varnames)
+    Rirr=ncread(filename, varnames[n])
+    tmp=Rirr/3
+    Rrs0=(0.52*tmp)./(1.0 .-1.7*tmp)
+    ncwrite(Rrs0,"HalfDegree.nc",varnames[n])
+end

DataSet From DARWIN/Main_MakeGridDarwin2.jl

@@ -3,10 +3,10 @@
 
 include("MakeGridDarwin2.jl")
 
-if ~isfile("MasterHalf.nc")
+#if ~isfile("MasterHalf.nc")
     MakeMasterHalf()
-end
-realnames=["Latitude","Longitude","Month","THETA", "SALT", "Chl", "Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555","Rirr670","MXLDEPTH","Bottom Depth", "Wind Speed", "TKE","PAR","Euphotic Depth"]
-for n in [.5 1 2 4]
-MakeDarwinGrid(n,realnames)
-end
+#end
+# realnames=["Latitude","Longitude","Month","THETA", "SALT", "Chl", "Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555","Rirr670","MXLDEPTH","Bottom Depth", "Wind Speed", "TKE","PAR","Euphotic Depth"]
+# for n in [.5 1 2 4]
+# MakeDarwinGrid(n,realnames)
+# end

DataSet From DARWIN/MakeGridDarwin2.jl

@@ -9,6 +9,8 @@ function MakeMasterHalf()
     #This is the starting folder for the Climatology
     #name="C:\\Users\\folle\\Dropbox (MIT)\\201805-CBIOMES-climatology\\interp"
     name="C:\\Users\\folle\\Documents\\CBIOMES\\interp"
+    #name="/nfs/cnhlab001/cnh/cbiomes/201805-CBIOMES-climatology/interp/"
+
     #This is the filename for the .5 degree monthly climatology
     filename="HalfDegree.nc"
     #These are the variable names which we would like on the grid
@@ -121,7 +123,10 @@ function MakeMasterHalf()
     OCCIbands=["Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555",
     "Rirr670"]
     #export OCCIbands
-    if ~isfile("InterpedWavebands.nc")
+    if isfile("InterpedWavebands3.nc")
+        rm("InterpedWavebands3.nc")
+    end
+    if ~isfile("InterpedWavebands3.nc")
         for n in 1:6
         nccreate("InterpedWavebands3.nc", OCCIbands[n],"Lon",collect(-179.75:.5:179.75),"Lat",collect(-89.75:.5:89.75),"Month",collect(1:12))
         ncwrite(wbcci[:,:,:,n],"InterpedWavebands3.nc", OCCIbands[n])
@@ -191,7 +196,7 @@ function MakeMasterHalf()
     if isfile("EuphoticDepth.nc")
          rm("EuphoticDepth.nc")
     end
-    nccreate("EuphoticDepth.nc", "Euphotic Depth","Lon",collect(.5:.5:360),"Lat",collect(-89.75:.5:89.75),"Month",collect(1:12))
+    nccreate("EuphoticDepth.nc", "Euphotic Depth","Lon",collect(-179.75:.5:179.75),"Lat",collect(-89.75:.5:89.75),"Month",collect(1:12))
     ncwrite(Eudepth,"EuphoticDepth.nc", "Euphotic Depth")
     #lon lat depth t
 
@@ -207,8 +212,8 @@ function MakeMasterHalf()
     #We have everything except PAR, Ekman pumping, Kd, and Euphotic Depth.
     vars=["THETA", "SALT", "Chl", "Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555",
     "Rirr670","MXLDEPTH","Bottom Depth", "EXFwspee", "GGL90TKE","PAR","Euphotic Depth"]
-    realnames=["THETA", "SALT", "Chl", "Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555",
-    "Rirr670","MXLDEPTH","Bottom Depth", "Wind Speed", "TKE","PAR","Euphotic Depth"]
+    realnames=["SST", "SALT", "Chl", "Rrs412", "Rrs443", "Rrs490", "Rrs510", "Rrs555",
+    "Rrs670","MLD","Bathymetry", "wind", "EKE","PAR","Euphotic Depth"]
     #export vars
     Tg=Array{Float64,4}(undef,720,360,12,length(vars))
     for n in [1 2 3]
@@ -255,7 +260,7 @@ function MakeDarwinGrid(deg,names)
     for n in 1:length(names)
         if sum(k.==names[n])>=1
             vartmp=ncread("MasterHalf.nc",names[n])
-            nccreate("DarwinGrid"*string(deg)*".nc", names[n],"Londim",collect(.5:deg:360),"Latdim",collect(-89.75:deg:89.75),"Monthdim",collect(1:12))
+            nccreate("DarwinGrid"*string(deg)*".nc", names[n],"Londim",collect(-179.75:deg:179.75),"Latdim",collect(-89.75:deg:89.75),"Monthdim",collect(1:12))
             #println(size(vartmp[1:Int(deg/.5):end,1:Int(deg/.5):end,:]))
             #println(size(vartmp))
             tmp=vartmp[1:Int(deg/.5):end,1:Int(deg/.5):end,:];
@@ -268,15 +273,15 @@ function MakeDarwinGrid(deg,names)
             ncwrite(tmp,"DarwinGrid"*string(deg)*".nc", names[n])
         end
         if sum(k.==names[n])==0
-            tmp=zeros(length(collect(.5:deg:360)), length(collect(-89.75:deg:89.75)),12)
+            tmp=zeros(length(collect(-179.75:deg:179.75)), length(collect(-89.75:deg:89.75)),12)
             if names[n]=="Latitude"
                 Lat=collect(-89.75:deg:89.75);
                 for m in 1:length(Lat)
                     #fill!(HalfDegree[:,n,:,1],Lat[n])
                     tmp2=fill(Lat[m],size(tmp[:,m,:]))
                     tmp[:,m,:]=tmp2
                 end
-                nccreate("DarwinGrid"*string(deg)*".nc", names[n],"Londim",collect(.5:deg:360),"Latdim",collect(-89.75:deg:89.75),"Monthdim",collect(1:12))
+                nccreate("DarwinGrid"*string(deg)*".nc", names[n],"Londim",collect(-179.75:deg:179.75),"Latdim",collect(-89.75:deg:89.75),"Monthdim",collect(1:12))
                 ncwrite(tmp,"DarwinGrid"*string(deg)*".nc", names[n])
                 sztmp=size(tmp)
             end

DataSet From DARWIN/README.md

@@ -14,19 +14,19 @@ This folder contains code written in Julia to generate gridded data for the foll
 - "Lat"             (degrees)
 - "Lon"             (degrees)
 - "Month"           (month)
-- "THETA"           (degrees C)
+- "SST"           (degrees C)
 - "SALT"            (psu)
 - "Chl"             (mg/l)
-- "Rirr412"         (irradiance reflectance for waveband at wavelength)
-- "Rirr443"         (irradiance reflectance for waveband at wavelength)
-- "Rirr490"         (irradiance reflectance for waveband at wavelength)
-- "Rirr510"         (irradiance reflectance for waveband at wavelength)
-- "Rirr555"         (irradiance reflectance for waveband at wavelength)
-- "Rirr670"         (irradiance reflectance for waveband at wavelength)
-- "MXLDEPTH"        (depth, meters)
-- "Bottom Depth"    (depth, meters)
-- "Wind Speed"      (m/s)
-- "TKE"             (m^2/s^2) is GGL90 sub-grid turbulent kinetic energy
+- "Rrs412"         (irradiance reflectance for waveband at wavelength)
+- "Rrs443"         (irradiance reflectance for waveband at wavelength)
+- "Rrs490"         (irradiance reflectance for waveband at wavelength)
+- "Rrs510"         (irradiance reflectance for waveband at wavelength)
+- "Rrs555"         (irradiance reflectance for waveband at wavelength)
+- "Rrs670"         (irradiance reflectance for waveband at wavelength)
+- "MLD"        (depth, meters)
+- "Bathymetry"    (depth, meters)
+- "wind"      (m/s)
+- "EKE"             (m^2/s^2) is GGL90 sub-grid turbulent kinetic energy
 - "PAR"             () 
 - "Euphotic Depth"  Depth (m) where light is 1% of the surface values
 

Try Jackson/JacksonModelRemote.jl

@@ -0,0 +1,92 @@
+#This script will attempt to apply the Jackson classifier to the DARWIN reflectance data
+
+using Plots, Distributions, NetCDF, NCDatasets, Interpolations
+
+
+##This is Gael's Code, taken from 05-OceanColourClassifiers.ipynb##
+
+function fcm(M,Sinv,Rrs)
+    f=Array{Any,1}(undef,length(M))
+    for ii=1:length(M)
+        X=vec(Rrs)-M[ii]
+        Z=transpose(X)*Sinv[ii]*X
+        f[ii]=ccdf(Chisq(6),Z)
+    end
+    f
+end
+
+function getJackson(file)
+    #Jackson et al 2017:
+    tmpM = ncread("J17.nc", "cluster_means")
+    tmpSinv = ncread("J17.nc", "inverse_covariance")
+    wv_cci=[412, 443, 490, 510, 555, 670]
+    M=Array{Any,1}(undef,14)
+    Sinv=Array{Any,1}(undef,14)
+    for ii=1:length(M)
+        M[ii]=vec(tmpM[ii,:])
+        Sinv[ii]=tmpSinv[1:6,1:6,ii]
+    end
+
+    J17=Dict("M" => M, "Sinv" => Sinv, "S" => inv.(Sinv))
+    #plot(wv_cci,M,w=3); xlabel!("nm"); ylabel!("Rrs")
+
+
+    ds = Dataset(file)
+
+    Rrs_412=ds["Rrs412"]
+    Rrs_443=ds["Rrs443"]
+    Rrs_490=ds["Rrs490"]
+    Rrs_510=ds["Rrs510"]
+    Rrs_555=ds["Rrs555"]
+    Rrs_670=ds["Rrs670"]
+
+    Rrs_412=Rrs_412[1:4:720,1:4:360,1:4:12]
+    Rrs_443=Rrs_443[1:4:720,1:4:360,1:4:12]
+    Rrs_490=Rrs_490[1:4:720,1:4:360,1:4:12]
+    Rrs_510=Rrs_510[1:4:720,1:4:360,1:4:12]
+    Rrs_555=Rrs_555[1:4:720,1:4:360,1:4:12]
+    Rrs_670=Rrs_670[1:4:720,1:4:360,1:4:12]
+
+    tmp=fill(false,size(Rrs_412))
+    for ii in eachindex(Rrs_412)
+        !ismissing(Rrs_412[ii]) ? tmp[ii]=!ismissing(Rrs_443[ii].*Rrs_490[ii].*Rrs_510[ii].*Rrs_555[ii].*Rrs_670[ii]) : nothing
+    end
+    ii=findall(tmp)
+    sz=size(Rrs_412)
+    #export ii, sz, Rrs_412, Rrs_443, Rrs_490, Rrs_510, Rrs_555, Rrs_670
+    mbrshp=Array{Float64,4}(undef,(sz[1],sz[2],sz[3],14));
+    for jj=1:length(ii); 
+        kk=ii[jj]
+        Rrs_tmp=[Rrs_412[kk] Rrs_443[kk] Rrs_490[kk] Rrs_510[kk] Rrs_555[kk] Rrs_670[kk]]
+        mbrshp[kk[1],kk[2],kk[3],:]=fcm(J17["M"],J17["Sinv"],Rrs_tmp)
+        println(kk)
+    end
+    return mbrshp
+end
+#path="https://rsg.pml.ac.uk/shared_files/brj/CBIOMES_ecoregions/ver_0_2_5"
+path="https://rsg.pml.ac.uk/shared_files/brj/CBIOMES_ecoregions/ver_0_2_5/"
+filegeo="gridded_geospatial_montly_clim_360_720_ver_0_2.nc"
+filedarwin="gridded_darwin_montly_clim_360_720_ver_0_2_2.nc"
+#run(`wget $path/$file`)
+if ~isfile(filegeo)
+    download(string(path, filegeo), filegeo)
+end
+if ~isfile(filedarwin)
+    download(string(path, filedarwin), filedarwin)
+end
+
+#varnames=["Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555", "Rirr670"]
+varnames=["Rrs412", "Rrs443", "Rrs490", "Rrs510", "Rrs555", "Rrs670"]
+
+for n in 1:length(varnames)
+    Rirr=ncread(filedarwin, varnames[n])
+    tmp=Rirr/3
+    Rrs0=(0.52*tmp)./(1.0 .-1.7*tmp)
+    ncwrite(Rrs0,filedarwin,varnames[n])
+    #renameVar(filedarwin,varnames[n],newnames[n])
+end
+
+DarwinMembers=getJackson(filedarwin)
+GeoMembers=getJackson(filegeo)
+export DarwinMembers
+export GeoMembers

Try Jackson/M09.jl

@@ -0,0 +1,63 @@
+
+#Moore et al 2009 mean vectors:
+M=Array{Any,1}(undef,8)
+M[1]=vec([0.0234 0.0192 0.0129 0.0075 0.0031 0.0002])
+M[2]=vec([0.0162 0.0141 0.0112 0.0073 0.0034 0.0002])
+M[3]=vec([0.0107 0.0098 0.0092 0.0070 0.0039 0.0003])
+M[4]=vec([0.0065 0.0064 0.0070 0.0064 0.0048 0.0006])
+M[5]=vec([0.0033 0.0034 0.0042 0.0042 0.0043 0.0009])
+M[6]=vec([0.0064 0.0074 0.0105 0.0116 0.0140 0.0041])
+M[7]=vec([0.0121 0.0140 0.0192 0.0204 0.0231 0.0084])
+M[8]=vec([0.0184 0.0230 0.0333 0.0359 0.0409 0.0137])
+
+#Moore et al 2009 covariance matrices:
+S=Array{Any,1}(undef,8)
+S[1]=[0.00000959 0.00000556 0.00000138 -0.00000034 -0.00000024 -0.00000003; 
+        0.00000556 0.00000493 0.00000193 0.00000060 0.00000023 0.00000001; 
+        0.00000138 0.00000193 0.00000282 0.00000223 0.00000119 0.00000007; 
+        -0.00000034 0.00000060 0.00000223 0.00000232 0.00000119 0.00000007; 
+        -0.00000024 0.00000023 0.00000119 0.00000119 0.00000071 0.00000005; 
+        -0.00000003 0.00000001 0.00000007 0.00000007 0.00000005 0.00000001]
+S[2]=[0.00000346 0.00000186 -0.00000011 -0.00000060 -0.00000062 -0.00000005; 
+        0.00000186 0.00000228 0.00000086 0.00000033 -0.00000007 0.00000003; 
+        -0.00000011 0.00000086 0.00000231 0.00000221 0.00000145 0.00000023; 
+        -0.00000060 0.00000033 0.00000221 0.00000266 0.00000191 0.00000034; 
+        -0.00000062 -0.00000007 0.00000145 0.00000191 0.00000175 0.00000041; 
+        -0.00000005 0.00000003 0.00000023 0.00000034 0.00000041 0.00000021]
+S[3]=[0.00000241 0.00000144 0.00000035 -0.00000031 -0.00000063 -0.00000006; 
+        0.00000144 0.00000138 0.00000076 0.00000015 -0.00000021 -0.00000001; 
+        0.00000035 0.00000076 0.00000161 0.00000156 0.00000121 0.00000016; 
+        -0.00000031 0.00000015 0.00000156 0.00000227 0.00000209 0.00000031; 
+        -0.00000063 -0.00000021 0.00000121 0.00000209 0.00000225 0.00000037; 
+        -0.00000006 -0.00000001 0.00000016 0.00000031 0.00000037 0.00000013]
+S[4]=[0.00000166 0.00000091 0.00000034 -0.00000009 -0.00000080 -0.00000025; 
+        0.00000091 0.00000097 0.00000071 0.00000025 -0.00000041 -0.00000015; 
+        0.00000034 0.00000071 0.00000118 0.00000103 0.00000072 0.00000003; 
+        -0.00000009 0.00000025 0.00000103 0.00000137 0.00000162 0.00000025; 
+        -0.00000080 -0.00000041 0.00000072 0.00000162 0.00000290 0.00000065; 
+        -0.00000025 -0.00000015 0.00000003 0.00000025 0.00000065 0.00000050]
+S[5]=[0.00000178 0.00000132 0.00000104 0.00000081 0.00000018 -0.00000014; 
+        0.00000132 0.00000127 0.00000121 0.00000099 0.00000034 -0.00000010; 
+        0.00000104 0.00000121 0.00000150 0.00000142 0.00000110 0.00000013; 
+        0.00000081 0.00000099 0.00000142 0.00000158 0.00000177 0.00000042; 
+        0.00000018 0.00000034 0.00000110 0.00000177 0.00000351 0.00000131; 
+        -0.00000014 -0.00000010 0.00000013 0.00000042 0.00000131 0.00000081]
+S[6]=[0.00000715 0.00000586 0.00000409 0.00000292 0.00000005 -0.00000075; 
+        0.00000586 0.00000589 0.00000520 0.00000398 0.00000027 -0.00000114; 
+        0.00000409 0.00000520 0.00000634 0.00000541 0.00000188 -0.00000097; 
+        0.00000292 0.00000398 0.00000541 0.00000528 0.00000392 0.00000070; 
+        0.00000005 0.00000027 0.00000188 0.00000392 0.00000995 0.00000657; 
+        -0.00000075 -0.00000114 -0.00000097 0.00000070 0.00000657 0.00000819]
+S[7]=[0.00002625 0.00001981 0.00001058 0.00000544 -0.00000654 -0.00001122; 
+        0.00001981 0.00001745 0.00001314 0.00000822 -0.00000431 -0.00001228; 
+        0.00001058 0.00001314 0.00001629 0.00001226 0.00000035 -0.00001311; 
+        0.00000544 0.00000822 0.00001226 0.00001170 0.00000742 -0.00000500; 
+        -0.00000654 -0.00000431 0.00000035 0.00000742 0.00002241 0.00001782; 
+        -0.00001122 -0.00001228 -0.00001311 -0.00000500 0.00001782 0.00003987]
+S[8]=[0.00001186 0.00001134 0.00001139 0.00000919 0.00000395 -0.00000186; 
+        0.00001134 0.00001484 0.00002034 0.00001907 0.00001531 0.00000087; 
+        0.00001139 0.00002034 0.00003467 0.00003546 0.00003555 0.00000708; 
+        0.00000919 0.00001907 0.00003546 0.00003907 0.00004604 0.00001733; 
+        0.00000395 0.00001531 0.00003555 0.00004604 0.00007306 0.00004953; 
+        -0.00000186 0.00000087 0.00000708 0.00001733 0.00004953 0.00006542];
+

Try Jackson/README.md

@@ -0,0 +1,7 @@
+# TryJackson
+
+This folder contains code that will download the half degree data grids for DARWIN and GEO and attempt to apply the OC-CCI water class algorithm to it.
+
+The important code is JacksonModelRemote.jl. In the current version, the Rirr to Rrs correction is applied to the DARWIN dataset still.
+
+

Try Jackson/tryJackson.jl

@@ -0,0 +1,85 @@
+#This script will attempt to apply the Jackson classifier to the DARWIN reflectance data
+
+using Plots, Distributions, NetCDF, NCDatasets, Interpolations
+
+
+##This is Gael's Code, taken from 05-OceanColourClassifiers.ipynb##
+
+function fcm(M,Sinv,Rrs)
+    f=Array{Any,1}(undef,length(M))
+    for ii=1:length(M)
+        X=vec(Rrs)-M[ii]
+        Z=transpose(X)*Sinv[ii]*X
+        f[ii]=ccdf(Chisq(6),Z)
+    end
+    f
+end
+
+#Jackson et al 2017:
+tmpM = ncread("J17.nc", "cluster_means")
+tmpSinv = ncread("J17.nc", "inverse_covariance")
+wv_cci=[412, 443, 490, 510, 555, 670]
+M=Array{Any,1}(undef,14)
+Sinv=Array{Any,1}(undef,14)
+for ii=1:length(M)
+    M[ii]=vec(tmpM[ii,:])
+    Sinv[ii]=tmpSinv[1:6,1:6,ii]
+end
+
+J17=Dict("M" => M, "Sinv" => Sinv, "S" => inv.(Sinv))
+plot(wv_cci,M,w=3); xlabel!("nm"); ylabel!("Rrs")
+
+#path="https://rsg.pml.ac.uk/shared_files/brj/CBIOMES_ecoregions/ver_0_2_5"
+path="https://https://rsg.pml.ac.uk/shared_files/brj/CBIOMES_ecoregions/ver_0_2_5/"
+file="gridded_geospatial_montly_clim_360_720_ver_0_2.nc"
+file="gridded_darwin_montly_clim_360_720_ver_0_2_2.nc"
+#run(`wget $path/$file`)
+download(string(path, file), file)
+#Using NCDatasets
+#Dataset(file)
+#fil="C:\Users\folle\Dropbox (MIT)\CBIOMES_TransitionZone\Chris Follett\StatsGroup\ocean_clustering\DataSet From DARWIN\AddRrsCorrection\HalfDegree.nc"
+#fil="C:\\Users\\folle\\Dropbox (MIT)\\CBIOMES_TransitionZone\\Chris Follett\\StatsGroup\\ocean_clustering\\DataSet From DARWIN\\AddRrsCorrection\\HalfDegree.nc"
+#dir0="../samples/"
+#fil="MasterHalf.nc"
+##
+varnames=["Rirr412", "Rirr443", "Rirr490", "Rirr510", "Rirr555", "Rirr670"]
+for n in 1:length(varnames)
+    Rirr=ncread(filename, varnames[n])
+    tmp=Rirr/3
+    Rrs0=(0.52*tmp)./(1.0 .-1.7*tmp)
+    ncwrite(Rrs0,"HalfDegree.nc",varnames[n])
+end
+##
+
+ds = Dataset(file)
+
+Rrs_412=ds["Rirr412"]
+Rrs_443=ds["Rirr443"]
+Rrs_490=ds["Rirr490"]
+Rrs_510=ds["Rirr510"]
+Rrs_555=ds["Rirr555"]
+Rrs_670=ds["Rirr670"]
+
+Rrs_412=Rrs_412[1:4:720,1:4:360,1:4:12]
+Rrs_443=Rrs_443[1:4:720,1:4:360,1:4:12]
+Rrs_490=Rrs_490[1:4:720,1:4:360,1:4:12]
+Rrs_510=Rrs_510[1:4:720,1:4:360,1:4:12]
+Rrs_555=Rrs_555[1:4:720,1:4:360,1:4:12]
+Rrs_670=Rrs_670[1:4:720,1:4:360,1:4:12]
+
+tmp=fill(false,size(Rrs_412))
+for ii in eachindex(Rrs_412)
+    !ismissing(Rrs_412[ii]) ? tmp[ii]=!ismissing(Rrs_443[ii].*Rrs_490[ii].*Rrs_510[ii].*Rrs_555[ii].*Rrs_670[ii]) : nothing
+end
+ii=findall(tmp)
+sz=size(Rrs_412)
+export ii, sz, Rrs_412, Rrs_443, Rrs_490, Rrs_510, Rrs_555, Rrs_670
+mbrshp=Array{Float64,4}(undef,(sz[1],sz[2],sz[3],14));
+for jj=1:length(ii); 
+    kk=ii[jj]
+    Rrs_tmp=[Rrs_412[kk] Rrs_443[kk] Rrs_490[kk] Rrs_510[kk] Rrs_555[kk] Rrs_670[kk]]
+    mbrshp[kk[1],kk[2],kk[3],:]=fcm(J17["M"],J17["Sinv"],Rrs_tmp)
+    println(kk)
+end
+export mbrshp
+heatmap(mbrshp[:,:,1,10])