#' Extract Bit-Encoded Information and Create Weights Raster
#' 
#' @description 
#' This function applies \code{\link{bitAnd}} and \code{\link{bitShiftR}} 
#' from \strong{bitops} to convert bit-encoded information. It is also possible 
#' to convert this information to a scale from 0 to 1 in order to use it as 
#' weighting information in functions like \code{\link{whittaker.raster}} or 
#' \code{\link{smooth.spline.raster}}.
#' 
#' @param x \code{matrix}, vector or \code{Raster*} object.
#' @param X \code{Raster*} object.
#' @param bitShift \code{integer}. Bit starting point, see examples and 
#' \code{\link{detectBitInfo}}. 
#' @param bitMask \code{integer}. Bit mask size, see examples and 
#' \code{\link{detectBitInfo}}.
#' @param threshold \code{integer}. Threshold for valid quality.
#' @param filename \code{character} passed to \code{\link{writeRaster}}. If not 
#' specified, output is written to a temporary file.
#' @param decodeOnly \code{logical}. If \code{FALSE} (default), convert bits to 
#' weights from 0 (not used) to 1 (best quality). If \code{TRUE}, only extract 
#' selected bits and convert to decimal system.
#' @param keep If \code{NULL} (default), bits are only encoded, else an 
#' \code{integer} vector of values you want to keep (becomes \code{TRUE}), the 
#' rest becomes \code{NA}. See examples.
#' @param datatype \code{character}. Output datatype, see 
#' \code{\link{writeRaster}}.
#' @param ... Other arguments passed to \code{\link{writeRaster}}.     
#' 
#' @return 
#' A \code{Raster*} object.
#' 
#' @note 
#' \code{\link{makeWeights}} and \code{\link{extractBits}} are identical with 
#' the only difference that \code{\link{makeWeights}} does additionally convert 
#' the data into weighting information.
#' 
#' @seealso 
#' \code{\link{detectBitInfo}}.
#' 
#' @author 
#' Matteo Mattiuzzi
#' 
#' @examples 
#' \dontrun{
#' 
#' # example MOD13Q1 see https://lpdaac.usgs.gov/products/modis_products_table/mod13q1 
#' # enter in Layers
#' # See in TABLE 2: MOD13Q1 VI Quality
#' # column 1 (bit) row 2 VI usefulness 
#' bitShift = 2
#' bitMask = 15 # ('15' is the decimal of the binary '1111')  
#' # or try to use
#' detectBitInfo("MOD13Q1") # not all products are available!
#' viu <- detectBitInfo("MOD13Q1","VI usefulness") # not all products are available!
#' viu
#' 
#' # simulate bit info
#' bit <- round(runif(10*10,1,65536))
#' 
#' # extract from vector
#' makeWeights(bit,bitShift,bitMask,decodeOnly=TRUE)
#' # the same as
#' extractBits(bit,bitShift,bitMask)
#' 
#' # create a Raster object
#' VIqual <- raster(ncol=10,nrow=10)
#' VIqual[] <- bit
#' 
#' # extract from Raster object
#' a <- makeWeights(VIqual,bitShift,bitMask,decodeOnly=TRUE)
#' 
#' # linear conversion of 0 (0000) to 15 (1111) to 1 fo 0 
#' b <- makeWeights(VIqual,bitShift,bitMask,decodeOnly=FALSE)
#' 
#' threshold=6 # every thing < threshold becomes a weight = 0
#' c <- makeWeights(VIqual,bitShift,bitMask,threshold,decodeOnly=FALSE)
#' 
#' res <- round(cbind(a[],b[],c[]),2)
#' colnames(res) <- c("ORIG","Weight","WeightThreshold") 
#' res
#' 
#' #####
#' # water mask
#' tif = runGdal(product="MOD13A2",begin="2009001",end="2009001", extent=extent(c(-9,-3 ,54,58)),
#'               SDSstring="001",job="delme") # 6.4 MB
#' x <- raster(unlist(tif))
#' 
#' res1 <- maskWater(x)
#' plot(res1)
#' 
#' res2 <- maskWater(x,keep=1) # 1 = Land (nothing else)
#' x11()
#' plot(res2)
#' 
#' # Land (Nothing else but land) + Ocean coastlines and lake shorelines + shallow inland Water,
#' # the rest becomes NA
#' x11()
#' res3 <- maskWater(x,keep=c(1,2,3)) 
#' plot(res3)
#' 
#' ###############
#' 
#' # as on Linux you can read HDF4 directly you can also do:
#' if(.Platform$OS.type=="unix")
#' {
#'   x <- getHdf(HdfName="MOD13A2.A2009001.h17v03.005.2009020044109.hdf", wait=0) # 6.4 MB
#'   
#'   detectBitInfo(x) # just info
#'   getSds(x) # just info
#'   
#'   x <- getSds(x)$SDS4gdal[3] # you need 'VI Quality'
#'   x  <- raster(x) 
#'   # plot(x)
#'   # ex <- drawExtent()
#'   ex <- extent(c(-580779,-200911,5974929,6529959))
#'   x  <- crop(x,ex) # just for speed-up
#'   
#'   res1 <- maskWater(x)
#'   plot(res1)
#'   
#'   res2 <- maskWater(x,keep=1) # 1 = Land (Nothing else but land), the rest becomes NA
#'   x11()
#'   plot(res2)
#'   
#'   # Land (Nothing else but land) + Ocean coastlines and lake shorelines + shallow inland Water,
#'   # the rest becomes NA
#'   res3 <- maskWater(x,keep=c(1,2,3))
#'   x11()
#'   plot(res3)
#' }
#' }
#' 
#' @describeIn makeWeights Extract bit-encoded information from \code{Raster*} file
#' @aliases extractBits
#' @export extractBits
extractBits <- function(x, bitShift=2, bitMask=15, filename='',...)
{
    if (inherits(x,"Raster"))
    {
        out <- brick(x, values=FALSE)
        if(nlayers(out)==1)
        {
            out <- raster(x)
        }
    
        out <- writeStart(out, filename=filename,...)
        tr  <- blockSize(out)
    
        for (i in 1:tr$n) 
        {
            v  <- getValues(x, row=tr$row[i], nrows=tr$nrows[i])
            ve <- dim(v)

            v[v==0] <- NA    
            
            # decode bits
            v <- bitAnd(bitShiftR(v, bitShift ), bitMask)
            
            v[is.na(v)] <- bitMask
                        
            if (!is.null(ve))
            {
                v <- matrix(v,ncol=ve[2],nrow=ve[1],byrow=FALSE)
            } 
    
            out <- writeValues(out, v, tr$row[i])
        }
        out <- writeStop(out)
        return(out)
    } else
    {
        ve <- dim(x)
        
        x[x==0] <- NA

        # decode bits
        x <- bitAnd(bitShiftR(x, bitShift ), bitMask)

        x[is.na(x)] <- bitMask        

        if (!is.null(ve))
        {
            x <- matrix(x,ncol=ve[2],nrow=ve[1],byrow=FALSE)
        }
        return(x)
    }
}    


#' @export makeWeights
#' @name makeWeights
makeWeights <- function(x, bitShift=2, bitMask=15, threshold=NULL, filename='', decodeOnly=FALSE,...)
{
    if (inherits(x,"Raster"))
    {
        out <- brick(x, values=FALSE)
        if(nlayers(out)==1)
        {
            out <- raster(x)
        }
    
        out <- writeStart(out, filename=filename,...)
        tr  <- blockSize(out)
    
        for (i in 1:tr$n) 
        {
            v  <- getValues(x, row=tr$row[i], nrows=tr$nrows[i])
            ve <- dim(v)

            v[v==0] <- NA    
            
            # decode bits
            v <- bitAnd(bitShiftR(v, bitShift ), bitMask)
            
            v[is.na(v)] <- bitMask
                    
            if (!is.null(threshold))
            {
                v[v > threshold] <- bitMask
            }
           
            if (!decodeOnly)
            {
                # turn up side down and scale bits for weighting
                v <- ((-1) * (v - bitMask))/bitMask
                v[v > 1] <- 1
                v[v < 0] <- 0      
            }
    
            if (!is.null(ve))
            {
                v <- matrix(v,ncol=ve[2],nrow=ve[1],byrow=FALSE)
            } 
    
            out <- writeValues(out, v, tr$row[i])
        }
        out <- writeStop(out)
        return(out)
    } else
    {
        ve <- dim(x)
        
        x[x==0] <- NA

        # decode bits
        x <- bitAnd(bitShiftR(x, bitShift ), bitMask)

        x[is.na(x)] <- bitMask        

        if (!is.null(threshold))
        {
            x[x > threshold] <- bitMask
        }
       
        if (!decodeOnly)
        {
            # turn up side down and scale bits for weighting
            # theoretically best is 0 but the lowest value I have ever noticed is 1! So: (x-1)
            x <- ((-1) * (x - bitMask))/bitMask     
            x[x > 1] <- 1
            x[x < 0] <- 0
        }

        if (!is.null(ve))
        {
            x <- matrix(x,ncol=ve[2],nrow=ve[1],byrow=FALSE)
        }

        return(x)
    }
}    

### maskWater (experimental)
#' @describeIn makeWeights Masks water (additional information required)
#' @aliases maskWater
#' @export maskWater
maskWater <- function(X, bitShift=NULL, bitMask = NULL, keep = NULL, datatype="INT1U",...)
{
    if (!inherits(X,"Raster"))
    {
        stop("'maskWater' requires a raster* object")
    }
    
    if (is.null(bitShift) | is.null(bitMask))
    {
        cat("'bitShift', 'bitMask' not defined, trying to autodetect 'Land/Water Flag'!...\n")
        fname    <- basename(names(X)[1])        
        prodinfo <- strsplit(fname,"\\.")[[1]][1]

        bits     <- detectBitInfo(prodinfo, what='Land/Water Flag',warn=FALSE)
        bitShift <- bits$bitShift
        bitMask  <- bits$bitMask
        
        if(is.null(bits))
        {
            stop(paste("No 'Land/Water Flag' found, please set 'bitShift', 'bitMask' manualy. See: https://lpdaac.usgs.gov/products/modis_products_table/",tolower(prodinfo),sep=""))
        } else 
        {
            message("Ok 'Land/Water Flag' found!")
        }
    }
    
    result <- extractBits(X, bitShift = bitShift, bitMask = bitMask,...)

    if (!is.null(keep))
    {
        eval(parse(text=paste("result <- result %in% ", paste0("c(",paste(keep,collapse=","),")"))))  
        NAvalue(result) <- 0  
    }
return(result)
}