1 |
7526fb1c
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Jim Regetz
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library (raster)
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path<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles"
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#Find monthly means for h09v04 tiles:
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h09v04_inFiles <- list.files(path=path, pattern="*.h09v04.005.ClearDay_corrected.img$")
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for (i in 1: length(h09v04_inFiles)){
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h09v04_inFiles[i]<- paste (path,"/",h09v04_inFiles[i],sep="")
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}
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h09v04_inFiles
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#Separate out monthly groupings
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Jan_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.1\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.1\\.9",h09v04_inFiles[i]) !=0)){
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Jan_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Jan_h09v04<-Jan_h09v04[!is.na(Jan_h09v04)]
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Jan_h09v04
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#Create rasters stack, calc means, scale
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Jan_h09v04_stack<- stack(Jan_h09v04) #checked nlayers(), 310: correct
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Jan_h09v04_mn<- mean(Jan_h09v04_stack, na.rm=TRUE)
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Jan_h09v04_mnScaled<- Jan_h09v04_mn*0.0005
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#Write results to new file
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Out_Jan<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Jan_h09v04_AVG_Scaled.img"
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writeRaster (Jan_h09v04_mnScaled, filename=Out_Jan,format="HFA",overwrite=TRUE)
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Feb_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.2\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.2\\.9",h09v04_inFiles[i]) !=0)){
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Feb_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Feb_h09v04<-Feb_h09v04[!is.na(Feb_h09v04)]
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Feb_h09v04
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Feb_h09v04_stack<- stack(Feb_h09v04)
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nlayers(Feb_h09v04_stack)
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Feb_h09v04_mn<- mean(Feb_h09v04_stack, na.rm=TRUE)
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Feb_h09v04_mnScaled<- Feb_h09v04_mn*0.0005
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Out_Feb<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Feb_h09v04_AVG_Scaled.img"
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writeRaster (Feb_h09v04_mnScaled, filename=Out_Feb,format="HFA",overwrite=TRUE)
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Mar_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.3\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.3\\.9",h09v04_inFiles[i]) !=0)){
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Mar_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Mar_h09v04<-Mar_h09v04[!is.na(Mar_h09v04)]
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Mar_h09v04
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Mar_h09v04_stack<- stack(Mar_h09v04)
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nlayers(Mar_h09v04_stack)
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Mar_h09v04_mn<- mean(Mar_h09v04_stack, na.rm=TRUE)
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Mar_h09v04_mnScaled<- Mar_h09v04_mn*0.0005
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Out_Mar<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Mar_h09v04_AVG_Scaled.img"
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writeRaster (Mar_h09v04_mnScaled, filename=Out_Mar,format="HFA",overwrite=TRUE)
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Apr_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.4\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.4\\.9",h09v04_inFiles[i]) !=0)){
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Apr_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Apr_h09v04<-Apr_h09v04[!is.na(Apr_h09v04)]
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Apr_h09v04
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Apr_h09v04_stack<- stack(Apr_h09v04)
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nlayers(Apr_h09v04_stack)
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Apr_h09v04_mn<- mean(Apr_h09v04_stack, na.rm=TRUE)
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Apr_h09v04_mnScaled<- Apr_h09v04_mn*0.0005
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Out_Apr<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Apr_h09v04_AVG_Scaled.img"
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writeRaster (Apr_h09v04_mnScaled, filename=Out_Apr,format="HFA",overwrite=TRUE)
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May_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.5\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.5\\.9",h09v04_inFiles[i]) !=0)){
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May_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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May_h09v04<-May_h09v04[!is.na(May_h09v04)]
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May_h09v04
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May_h09v04_stack<- stack(May_h09v04)
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nlayers(May_h09v04_stack)
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May_h09v04_mn<- mean(May_h09v04_stack, na.rm=TRUE)
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May_h09v04_mnScaled<- May_h09v04_mn*0.0005
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Out_May<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/May_h09v04_AVG_Scaled.img"
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writeRaster (May_h09v04_mnScaled, filename=Out_May,format="HFA",overwrite=TRUE)
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Jun_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.6\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.6\\.9",h09v04_inFiles[i]) !=0)){
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Jun_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Jun_h09v04<-Jun_h09v04[!is.na(Jun_h09v04)]
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Jun_h09v04
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Jun_h09v04_stack<- stack(Jun_h09v04)
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nlayers(Jun_h09v04_stack)
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Jun_h09v04_mn<- mean(Jun_h09v04_stack, na.rm=TRUE)
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Jun_h09v04_mnScaled<- Jun_h09v04_mn*0.0005
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Out_Jun<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Jun_h09v04_AVG_Scaled.img"
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writeRaster (Jun_h09v04_mnScaled, filename=Out_Jun,format="HFA",overwrite=TRUE)
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Jul_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.7\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.7\\.9",h09v04_inFiles[i]) !=0)){
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Jul_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Jul_h09v04<-Jul_h09v04[!is.na(Jul_h09v04)]
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Jul_h09v04
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Jul_h09v04_stack<- stack(Jul_h09v04)
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nlayers(Jul_h09v04_stack)
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Jul_h09v04_mn<- mean(Jul_h09v04_stack, na.rm=TRUE)
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Jul_h09v04_mnScaled<- Jul_h09v04_mn*0.0005
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Out_Jul<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Jul_h09v04_AVG_Scaled.img"
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writeRaster (Jul_h09v04_mnScaled, filename=Out_Jul,format="HFA",overwrite=TRUE)
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Aug_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.8\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.4",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.8\\.9",h09v04_inFiles[i]) !=0)){
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Aug_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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Aug_h09v04<-Aug_h09v04[!is.na(Aug_h09v04)]
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Aug_h09v04
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Aug_h09v04_stack<- stack(Aug_h09v04)
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nlayers(Aug_h09v04_stack)
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Aug_h09v04_mn<- mean(Aug_h09v04_stack, na.rm=TRUE)
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Aug_h09v04_mnScaled<- Aug_h09v04_mn*0.0005
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Out_Aug<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Aug_h09v04_AVG_Scaled.img"
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writeRaster (Aug_h09v04_mnScaled, filename=Out_Aug,format="HFA",overwrite=TRUE)
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Sep_h09v04<- c(1:length (h09v04_inFiles))*NA
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.9\\.1",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.2",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.3",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.4",h09v04_inFiles[i]) !=0)||
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220 |
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length(grep("\\.9\\.5",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.6",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.7",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.8",h09v04_inFiles[i]) !=0)||
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length(grep("\\.9\\.9",h09v04_inFiles[i]) !=0)){
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Sep_h09v04[i]<- h09v04_inFiles[i]
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}
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}
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228 |
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Sep_h09v04<-Sep_h09v04[!is.na(Sep_h09v04)]
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Sep_h09v04
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230 |
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Sep_h09v04_stack<- stack(Sep_h09v04)
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nlayers(Sep_h09v04_stack)
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Sep_h09v04_mn<- mean(Sep_h09v04_stack, na.rm=TRUE)
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234 |
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Sep_h09v04_mnScaled<- Sep_h09v04_mn*0.0005
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235 |
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236 |
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Out_Sep<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Sep_h09v04_AVG_Scaled.img"
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writeRaster (Sep_h09v04_mnScaled, filename=Out_Sep,format="HFA",overwrite=TRUE)
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238 |
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239 |
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Oct_h09v04<- c(1:length (h09v04_inFiles))*NA
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240 |
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for (i in 1: length(h09v04_inFiles)){
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if (length(grep("\\.10\\.1",h09v04_inFiles[i]) !=0)||
|
242 |
|
|
length(grep("\\.10\\.2",h09v04_inFiles[i]) !=0)||
|
243 |
|
|
length(grep("\\.10\\.3",h09v04_inFiles[i]) !=0)||
|
244 |
|
|
length(grep("\\.10\\.4",h09v04_inFiles[i]) !=0)||
|
245 |
|
|
length(grep("\\.10\\.5",h09v04_inFiles[i]) !=0)||
|
246 |
|
|
length(grep("\\.10\\.6",h09v04_inFiles[i]) !=0)||
|
247 |
|
|
length(grep("\\.10\\.7",h09v04_inFiles[i]) !=0)||
|
248 |
|
|
length(grep("\\.10\\.8",h09v04_inFiles[i]) !=0)||
|
249 |
|
|
length(grep("\\.10\\.9",h09v04_inFiles[i]) !=0)){
|
250 |
|
|
Oct_h09v04[i]<- h09v04_inFiles[i]
|
251 |
|
|
}
|
252 |
|
|
}
|
253 |
|
|
Oct_h09v04<-Oct_h09v04[!is.na(Oct_h09v04)]
|
254 |
|
|
Oct_h09v04
|
255 |
|
|
|
256 |
|
|
Oct_h09v04_stack<- stack(Oct_h09v04)
|
257 |
|
|
nlayers(Oct_h09v04_stack)
|
258 |
|
|
Oct_h09v04_mn<- mean(Oct_h09v04_stack, na.rm=TRUE)
|
259 |
|
|
Oct_h09v04_mnScaled<- Oct_h09v04_mn*0.0005
|
260 |
|
|
|
261 |
|
|
Out_Oct<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Oct_h09v04_AVG_Scaled.img"
|
262 |
|
|
writeRaster (Oct_h09v04_mnScaled, filename=Out_Oct,format="HFA",overwrite=TRUE)
|
263 |
|
|
|
264 |
|
|
Nov_h09v04<- c(1:length (h09v04_inFiles))*NA
|
265 |
|
|
for (i in 1: length(h09v04_inFiles)){
|
266 |
|
|
if (length(grep("\\.11\\.1",h09v04_inFiles[i]) !=0)||
|
267 |
|
|
length(grep("\\.11\\.2",h09v04_inFiles[i]) !=0)||
|
268 |
|
|
length(grep("\\.11\\.3",h09v04_inFiles[i]) !=0)||
|
269 |
|
|
length(grep("\\.11\\.4",h09v04_inFiles[i]) !=0)||
|
270 |
|
|
length(grep("\\.11\\.5",h09v04_inFiles[i]) !=0)||
|
271 |
|
|
length(grep("\\.11\\.6",h09v04_inFiles[i]) !=0)||
|
272 |
|
|
length(grep("\\.11\\.7",h09v04_inFiles[i]) !=0)||
|
273 |
|
|
length(grep("\\.11\\.8",h09v04_inFiles[i]) !=0)||
|
274 |
|
|
length(grep("\\.11\\.9",h09v04_inFiles[i]) !=0)){
|
275 |
|
|
Nov_h09v04[i]<- h09v04_inFiles[i]
|
276 |
|
|
}
|
277 |
|
|
}
|
278 |
|
|
Nov_h09v04<-Nov_h09v04[!is.na(Nov_h09v04)]
|
279 |
|
|
Nov_h09v04
|
280 |
|
|
|
281 |
|
|
Nov_h09v04_stack<- stack(Nov_h09v04)
|
282 |
|
|
nlayers(Nov_h09v04_stack)
|
283 |
|
|
Nov_h09v04_mn<- mean(Nov_h09v04_stack, na.rm=TRUE)
|
284 |
|
|
Nov_h09v04_mnScaled<- Nov_h09v04_mn*0.0005
|
285 |
|
|
|
286 |
|
|
Out_Nov<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Nov_h09v04_AVG_Scaled.img"
|
287 |
|
|
writeRaster (Nov_h09v04_mnScaled, filename=Out_Nov,format="HFA",overwrite=TRUE)
|
288 |
|
|
|
289 |
|
|
Dec_h09v04<- c(1:length (h09v04_inFiles))*NA
|
290 |
|
|
for (i in 1: length(h09v04_inFiles)){
|
291 |
|
|
if (length(grep("\\.12\\.1",h09v04_inFiles[i]) !=0)||
|
292 |
|
|
length(grep("\\.12\\.2",h09v04_inFiles[i]) !=0)||
|
293 |
|
|
length(grep("\\.12\\.3",h09v04_inFiles[i]) !=0)||
|
294 |
|
|
length(grep("\\.12\\.4",h09v04_inFiles[i]) !=0)||
|
295 |
|
|
length(grep("\\.12\\.5",h09v04_inFiles[i]) !=0)||
|
296 |
|
|
length(grep("\\.12\\.6",h09v04_inFiles[i]) !=0)||
|
297 |
|
|
length(grep("\\.12\\.7",h09v04_inFiles[i]) !=0)||
|
298 |
|
|
length(grep("\\.12\\.8",h09v04_inFiles[i]) !=0)||
|
299 |
|
|
length(grep("\\.12\\.9",h09v04_inFiles[i]) !=0)){
|
300 |
|
|
Dec_h09v04[i]<- h09v04_inFiles[i]
|
301 |
|
|
}
|
302 |
|
|
}
|
303 |
|
|
Dec_h09v04<-Dec_h09v04[!is.na(Dec_h09v04)]
|
304 |
|
|
Dec_h09v04
|
305 |
|
|
|
306 |
|
|
Dec_h09v04_stack<- stack(Dec_h09v04)
|
307 |
|
|
nlayers(Dec_h09v04_stack)
|
308 |
|
|
Dec_h09v04_mn<- mean(Dec_h09v04_stack, na.rm=TRUE)
|
309 |
|
|
Dec_h09v04_mnScaled<- Dec_h09v04_mn*0.0005
|
310 |
|
|
|
311 |
|
|
Out_Dec<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/Dec_h09v04_AVG_Scaled.img"
|
312 |
|
|
writeRaster (Dec_h09v04_mnScaled, filename=Out_Dec,format="HFA",overwrite=TRUE)
|