#Correct 1st column-------------------------------------------------------------------------------------------------

library (raster)

path<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate"

#Get h09v04 tiles:

h09v04_infiles <- list.files(path=path, pattern="*.h09v04.005.ClearDay.img$")

for (i in 1: length(h09v04_infiles)){

  h09v04_infiles[i]<- paste (path,"/",h09v04_infiles[i],sep="")

}

h09v04_infiles

#raster(h09v04_infiles[311])[1200,1]

#raster(h09v04_infiles[311])[1200,2]

rastfunction<- function (h09v04_infiles){

    r<-raster(h09v04_infiles)

    val<-raster(h09v04_infiles)[,2]

    r[,1]<-val

    name1<-sub("_Extracts/ByDate","_Extracts/ByDate/BadPixelsCorrected_Tiles",h09v04_infiles)

    name<-sub(".ClearDay.img",".ClearDay_corrected.img",name1)

    writeRaster(r,filename=name,format="HFA")

}

for (i in 1:length (h09v04_infiles)){

  rastfunction(h09v04_infiles[i])

}

#Correct last row, overwrite corrected files-------------------------------------------------------------------------------------------

path1<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles"

#Get h09v04 tiles:

newh09v04_infiles <- list.files(path=path1, pattern="*.h09v04.005.ClearDay_corrected.img$")

for (i in 1: length(newh09v04_infiles)){

  newh09v04_infiles[i]<- paste (path1,"/",newh09v04_infiles[i],sep="")

}

newh09v04_infiles

#raster(h09v04_infiles[311])[1200,1]

#raster(h09v04_infiles[311])[1200,2]

newrastfunction<- function (newh09v04_infiles){

    r<-raster(newh09v04_infiles)

    val<-raster(newh09v04_infiles)[1199,]

    r[1200,]<-val

    writeRaster(r,filename=newh09v04_infiles,format="HFA",overwrite=TRUE)

}

for (i in 1:length (newh09v04_infiles)){

  newrastfunction(newh09v04_infiles[i])

}