Displaying differences for changeset
 
display as  

Rlibs/package.txt

@@ -1,3 +1,4 @@
+stringi
 raster
 rgdal
 sp

simulation/rlz_psql/common.inc

@@ -14,6 +14,7 @@ OMS3.sim {
            "dpd" "com.ficus.subset_tools.psql.tools.density.DiseasePopulationDensity"
            "c" "fullSim.runSim"
            "plot" "com.ficus.subset_tools.psql.utils.PlotMap"
+           "plotpeople" "com.ficus.subset_tools.psql.utils.PlotMap"
         }
         
         connect {
@@ -22,6 +23,7 @@ OMS3.sim {
             "subpop.Ycoord" "dpd.yCoord"
 
             "dpd.kdeResult"      "c.pop"
+            "dpd.kdeResult"      "plotpeople.vals"
 
             "c.printvar" "plot.vals"
             "c.i"        "plot.i"
@@ -33,6 +35,13 @@ OMS3.sim {
             "dpd.yMax" "plot.yMax"
             "dpd.rlz"  "plot.rlz"
             "dpd.cellSize"  "plot.cellSize"
+
+            "dpd.xMin" "plotpeople.xMin"
+            "dpd.xMax" "plotpeople.xMax"
+            "dpd.yMin" "plotpeople.yMin"
+            "dpd.yMax" "plotpeople.yMax"
+            "dpd.rlz"  "plotpeople.rlz"
+            "dpd.cellSize"  "plotpeople.cellSize"
         }
         
         parameter {
@@ -58,12 +67,19 @@ OMS3.sim {
             "dpd.cellSize" 200
             "dpd.bandwidth" 1
 
+
             "plot.epsg"  "32651"
 
             "c.maxTime" 365
-          
+
             "plot.path" "output/Disease"
             "plot.name" "Disease"
+
+            "plotpeople.i" 0
+            "plotpeople.maxTime" 1
+            "plotpeople.epsg"  "32651"
+            "plotpeople.path" "output/Disease/PopulationCount/"
+            "plotpeople.name" "PopulationCount"
         }
     }
 }

src/engr/csu/median.R

@@ -1,5 +1,6 @@
 #!/usr/bin/env Rscript
 
+suppressMessages(library(stringi))
 suppressMessages(library(raster))
 suppressMessages(library(rgdal))
 suppressMessages(library(sp))
@@ -15,49 +16,57 @@ prefix
 # @Execute
 exec <- function() {
 
-    dir <- paste(path,prefix,sep="/")
+    dirlist <- list.dirs(paste(path,prefix,sep="/"))
+    dirlist <- dirlist[which(stri_detect_fixed(dirlist,"_allRealizations"))]
 
-    dirName <- basename(dir)
-    dirPathQO <- paste(dir,"_quickOverview/",sep="/")
-    dirPathZO <- paste(dir,"_zOthers/",sep="/")
-    fileList <- list.files(paste(dir,"_allRealizations",sep="/"),pattern="*.tif")
+    numberOfCores <- detectCores()
+    cl <- makeCluster(numberOfCores, type="FORK")
+    registerDoParallel(cl)
 
-    list <- c()
-    for (file in fileList) {
-        tmpRaster <- raster(paste(dir,"_allRealizations",file,sep="/"))
-        list <- c(list, tmpRaster)
-    }
+    foreach(completeDir=dirlist, .packages=c('raster','rgdal')) %dopar% {
+        dir <- dirname(completeDir)
+        dirName <- basename(dir)
+        dirPathQO <- paste(dir,"_quickOverview/",sep="/")
+        dirPathZO <- paste(dir,"_zOthers/",sep="/")
+        fileList <- list.files(paste(dir,"_allRealizations",sep="/"),pattern="*.tif")
 
-    mapBrick <- brick(list)
-    rm(list, fileList)
+        list <- c()
+        for (file in fileList) {
+            tmpRaster <- raster(paste(dir,"_allRealizations",file,sep="/"))
+            list <- c(list, tmpRaster)
+        }
 
-    outNameQO <- paste(dirPathQO,dirName,sep="")
-    if (!dir.exists(dirPathQO)) {
-        dir.create(dirPathQO, recursive=T)
-    }
-    outNameZO <- paste(dirPathZO,dirName,sep="")
-    if (!dir.exists(dirPathZO)) {
-        dir.create(dirPathZO, recursive=T)
-    }
+        mapBrick <- brick(list)
+        rm(list, fileList)
 
-    r_median <- calc(mapBrick, function(x){summary(x)[3]})
-    writeRaster(r_median,paste(outNameQO,"_median",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_mean <- calc(mapBrick, function(x){summary(x)[4]})
-    writeRaster(r_mean,paste(outNameQO,"_mean",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_min <- calc(mapBrick, function(x){summary(x)[1]})
-    writeRaster(r_min,paste(outNameQO,"_min",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_max <- calc(mapBrick, function(x){summary(x)[6]})
-    writeRaster(r_max,paste(outNameQO,"_max",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_1q <- calc(mapBrick, function(x){summary(x)[2]})
-    writeRaster(r_1q,paste(outNameQO,"_1q",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_3q <- calc(mapBrick, function(x){summary(x)[5]})
-    writeRaster(r_3q,paste(outNameQO,"_3q",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-
-    r_sd <- calc(mapBrick, function(x){sd(x, na.rm=T)})
-    writeRaster(r_sd,paste(outNameZO,"_std",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_iqr <- calc(mapBrick, function(x){IQR(x, na.rm=T)})
-    writeRaster(r_iqr,paste(outNameZO,"_iqr",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
-    r_range <- calc(mapBrick, function(x){summary(x)[6] - summary(x)[1]})
-    writeRaster(r_range,paste(outNameZO,"_range",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        outNameQO <- paste(dirPathQO,dirName,sep="")
+        if (!dir.exists(dirPathQO)) {
+            dir.create(dirPathQO, recursive=T)
+        }
+        outNameZO <- paste(dirPathZO,dirName,sep="")
+        if (!dir.exists(dirPathZO)) {
+            dir.create(dirPathZO, recursive=T)
+        }
+
+        r_median <- calc(mapBrick, function(x){summary(x)[3]})
+        writeRaster(r_median,paste(outNameQO,"_median",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_mean <- calc(mapBrick, function(x){summary(x)[4]})
+        writeRaster(r_mean,paste(outNameQO,"_mean",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_min <- calc(mapBrick, function(x){summary(x)[1]})
+        writeRaster(r_min,paste(outNameQO,"_min",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_max <- calc(mapBrick, function(x){summary(x)[6]})
+        writeRaster(r_max,paste(outNameQO,"_max",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_1q <- calc(mapBrick, function(x){summary(x)[2]})
+        writeRaster(r_1q,paste(outNameQO,"_1q",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_3q <- calc(mapBrick, function(x){summary(x)[5]})
+        writeRaster(r_3q,paste(outNameQO,"_3q",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+
+        r_sd <- calc(mapBrick, function(x){sd(x, na.rm=T)})
+        writeRaster(r_sd,paste(outNameZO,"_std",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_iqr <- calc(mapBrick, function(x){IQR(x, na.rm=T)})
+        writeRaster(r_iqr,paste(outNameZO,"_iqr",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+        r_range <- calc(mapBrick, function(x){summary(x)[6] - summary(x)[1]})
+        writeRaster(r_range,paste(outNameZO,"_range",sep=""),format="GTiff",NAflag=-9999.0,overwrite=T)
+    }
 
 }