Merge pull request #6 from reedmaxwell/Expanded_Ouptuts

Merging in extended outputs branch

Examples/EcoSLIM_ReadBin_fxn.R

@@ -0,0 +1,66 @@
+#function to read EcoSLIM binary file OUTPUTS
+# Inputs -
+# filename - name of .bin file to reads
+# filetype = 'exited' or 'restart'
+# nind = The number of indicators specified in the EcloSLIM driver file
+
+ES_read <- function(filename, type = "exited", nind=0){
+if(nind>0){
+  ind_names=c(paste("IndAge", 1:nind, sep=""), paste("IndLen", 1:nind, sep=""))
+}
+  if(type == "restart"){
+    to.read = file(filename,"rb")
+    npart=readBin(to.read, integer(), endian="little",size=4,n=1)
+    pid=readBin(to.read, integer(), endian="little",size=4,n=1)
+    print(npart)
+    print(pid)
+
+    n.col=17+nind*2
+
+    #NOTE: These are written out transposed from the exited particles file see below
+    data = matrix(0,ncol=n.col,nrow=npart,byrow=F)
+    for (i in 1:n.col) {
+      data[,i] = readBin(to.read, double(), endian="little",size=8,n=npart)
+    }
+    close(to.read)
+    data[1,]
+    particle_restart <- data.frame(data)
+    #X, Y, Z, Age, Saturated_Age, Mass, Source, Status, Particle_Concentration, Exit_Status, ParticleID,
+    #InitialX, InitialY, InitialZ, InsertTime, Path_Length, Saturated_Path_Length
+    col.names=c("X","Y","Z","age","sat_age","mass","source","status", "conc","exit_status",
+              "ID","init_X","init_Y","init_Z","ins_time","path_len","spath_len")
+    if(nind>0){col.names=c(col.names,ind_names)}
+    colnames(particle_restart) <- col.names
+
+
+    return(particle_restart)
+
+  } else if(type == "exited"){
+    #lines = file.info(filename)$size
+    n.col=16+nind*2
+    lines = (file.info(filename)$size/8)/(n.col)
+
+    data = matrix(0,ncol=n.col,nrow=lines,byrow=F)
+    to.read = file(filename,"rb")
+    for (i in 1:lines) {
+      data[i,1:n.col] = readBin(to.read, single(), endian="little",size=8,n=n.col)
+    }
+    readBin(to.read, double(), endian="little",size=8,n=n.col)
+    close(to.read)
+    #1 = Time #2 = X #3 = Y  #4 = Z #5 = age #6 = mass #7 = source #8 = out(1), ET(2)
+
+    exited_particles <- data.frame(data)
+    # Time, X, Y, Z, Age, Saturated_Age, Mass, Source, Exit_Status, ParticleID,
+    #InitialX, InitialY, InitialZ, InsertTime, Path_Length, Saturated_Path_Length
+    col.names= c("Time","X","Y","Z","age","sat_age","mass","source","out_as","ID","init_X",
+                                    "init_Y","init_Z","ins_time","path_len","spath_len")
+
+    if(nind>0){col.names=c(col.names,ind_names)}
+    colnames( exited_particles) <- col.names
+
+    return(exited_particles)
+
+  } else {
+    print("error")
+  }
+}