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##############################################################################################
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#
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# CreateImageDiffPlots
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# 
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# R script generates collection of nine plots that display the distributions of  populations of 
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# three elevation pixel pairs in proximity to the border between ASTER and STRM data in mosaic 
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# images# under development for the Environment and Organisms project.
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# 
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#
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# Inputs: 
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#   1) Comma Separated Value (CSV) table containing randomly-sampled elevation value pairs,
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#      extracted from ASTER/CGIAR mosaic and CDEM images, created by the R script: makeImagePairTable.r
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#      Note: At present, be sure that this file has been sorted by column 1 (ColumnID) in Excel
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#      before using in this program. 
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#      NOTE: This filename is set in the body of the script.
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#
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#   2) sampling factor: integer (range=1 to number of recors in input table. Determines
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#      the size of randomly-selected sampe of total table record 'triplets' (north, border,
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#      and south) rows of each column sample) to be displayed in the plots: 
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#           sampling factor = 1  : plot every table record
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#                             10 : plot a random sample containing 1/10th of records
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#                            100 : plot random sample containing 1/100th of records.
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#   3) JpgPlotFileFlag: Set to TRUE to have *individual* plots written to JPG files.
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#
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# To run:
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#
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#  1) place this file and the input file "tableForMark4000_5_8_SortColID.csv" in folder
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#  2) start R
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#  3) > source("CreateImageDiffPlotsOverlayNewPlots.r")
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#  4) > CreateImageDiffPlots(sampling factor, JpegFlag)
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#     < press <cr> key to view plots sequentially
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#  
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# TODO: add symbol legend to each plot.
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# Author: Rick Reeves, NCEAS
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# May 14, 2011
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# May 17, 2011: This version generates 'delta scatterplots' specified by Mark and Jim.
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# May 18, 2011: If JpgPlotFlag set, write individual plot files to JPG files.
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##############################################################################################
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CreateImageDiffPlots <- function(plotSampFact = 1,JpgPlotFileFlag = TRUE)
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{
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# Check plotSampleFact range
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   if (plotSampFact < 1)
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      plotSampFact = 1
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# Read input table that was sorted OFFLINE in Excel on the first column (ColumnID)
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   pointTable <-read.csv("pixelPairs36000_5_8_TS.csv")
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# Table created by randomly sampling from two superimposed 
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# image: 
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#  1) DOM mosaic image comprised of ASTER and SRTM components.
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#  2) 'Baseline' Canadian DEM (CDEM) image.
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# 
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# The input table contains three rows for each randomly-selected
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# pixel pair from both images. Each row contains two pixel pairs,
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# the first pair drawn from the image mosaic, the second pair
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# drawn from the CDEM image: 
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#   First pair: North pixel, South pixel (ASTER/SRTM mosaic)
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#   Second pair: North pixel, South pixel (CDEM)
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#
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#  The first row of each 'triplet' contains pixel pairs North of border,
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#  The second row contains pixel pairs spanning  border,
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#  The third row contains pixel pairs South of border,
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#
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# This script generates a series of plots that display
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# differences between:
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#    1) The mosaic and CDEM images
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#    2) Image pixels on and away from the ASTER / SRTM boundary.
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# 
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   northRowIndexes = seq(from=1, to=(nrow(pointTable) - 3),by=3)
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   borderRowIndexes = seq(from=2, to=(nrow(pointTable) - 1),by=3)   
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   southRowIndexes = seq(from=3, to=(nrow(pointTable)),by=3)
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#
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# calculate and append the difference between elevations
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# and CDEM
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# these lines create the inputs for differnce image plots for each of three
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# pixel pair subsets: North of border (All Aster), border (combo Aster/Srtm),
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#                     South of border (all Srtm)
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# 
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# First, add the 'difference columns' to the entire table
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#
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   pointTable <-cbind(pointTable,(pointTable$elevNorth - pointTable$elevSouth))
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   pointTable <-cbind(pointTable,(pointTable$cdemNorth - pointTable$cdemSouth))
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   pointTable <-cbind(pointTable,(pointTable$elevNorth - pointTable$cdemNorth))
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   pointTable <-cbind(pointTable,(pointTable$elevSouth - pointTable$cdemSouth))
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#   
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   colnames(pointTable)[6] <- "diffMosaicNorthSouth"
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   colnames(pointTable)[7] <- "diffCDEMNorthSouth"
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   colnames(pointTable)[8] <- "diffNorthMosaicCDEM"
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   colnames(pointTable)[9] <- "diffSouthMosaicCDEM"   
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# add a placeholder for the 'boundary' value, across each table
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#  pointTable <-cbind(pointTable,(-1))
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#  colnames(pointTable)[10] <- "deltaAcrossBorder"
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# Difference between Mosaic (ASTER or CGIAR or border) 
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# and CDEM elevation as pertentage of the mosaic elevation
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   pointTable <-cbind(pointTable,(pointTable$diffNorthMosaicCDEM/pointTable$elevNorth * 100)) 
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   pointTable <-cbind(pointTable,(pointTable$diffSouthMosaicCDEM/pointTable$elevSouth * 100)) 
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   colnames(pointTable)[10] <- "magDiffMosaicCDEMNorthPct"
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   colnames(pointTable)[11] <- "magDiffMosaicCDEMSouthPct"   
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# For the plots, subdivide the table into three segments: 
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#     rows north of border
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#     rows crossing border
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#     rows south of border
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   northRowTblAll = pointTable[northRowIndexes,]
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   borderRowTblAll = pointTable[borderRowIndexes,]
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   southRowTblAll = pointTable[southRowIndexes,]
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   subset <- 1:nrow(northRowTblAll)
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   randSub <- sample(subset,as.integer(length(subset) / plotSampFact)) 
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   northRowTbl <- northRowTblAll[randSub,]
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   borderRowTbl <- borderRowTblAll[randSub,]
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   southRowTbl <- southRowTblAll[randSub,]   
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message("hit key to create each plot...")
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browser()
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# Three plotting characters used
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   plotCh1 <- 17 # 'north' (aster) points
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   plotCh2 <- 18 # 'border' (aster+srtm) points 
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   plotCh3 <- 20 # 'south' (srtm) points
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# NEW: Three plots: The difference between Mosaic and CDEM for pixels along
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# each of three border edges: North (ASTER), Border, South (SRTM)
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# for now, north, border, south have separate plots
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# We need to tailor the plot 'triplet' X and Y axes to the dynamic ranges of all three data sets.
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# Create values for the three 'delta across pixel boundaries' plots: 
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#  1) Y-Axis: columnIDs 
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#  2) Y-Axis: CDEM elevations
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#  3) Y-Axis: 
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   deltaBoundaryASTER <- northRowTbl$diffNorthMosaicCDEM - northRowTbl$diffSouthMosaicCDEM
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   deltaBoundaryBorder <- borderRowTbl$diffNorthMosaicCDEM - borderRowTbl$diffSouthMosaicCDEM  
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   deltaBoundarySRTM <- southRowTbl$diffNorthMosaicCDEM - southRowTbl$diffSouthMosaicCDEM   
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   normDeltaBoundaryASTER <-  (deltaBoundaryASTER / northRowTbl$cdemNorth * 100)
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   normDeltaBoundaryBorder <- (deltaBoundaryBorder / borderRowTbl$cdemNorth * 100)  
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   normDeltaBoundarySRTM <-   (deltaBoundarySRTM / southRowTbl$cdemNorth * 100)
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   par(mfrow=c(3,1)) # Create a set of three column multi-plots
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   commonXAxis <- c(0,max(pointTable$ColumnID))   
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   commonYAxis <- range(c(deltaBoundarySRTM,deltaBoundaryBorder,deltaBoundaryASTER),na.rm=TRUE)   
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(deltaBoundaryASTER,na.rm=TRUE),sd(deltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,deltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Row Boundary Delta: ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(deltaBoundaryBorder,na.rm=TRUE),sd(deltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,deltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Row Boundary Delta: Border",sub="E-W Col",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(deltaBoundarySRTM,na.rm=TRUE),sd(deltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,deltaBoundarySRTM,main="Boundary Delta: SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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message("ColumnID-X-Axis is done")
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browser()
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#dev.new()
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#   par(mfrow=c(3,1)) # Create a three column multi-plot pointTable$diffNorthMosaicCDEM/pointTable$elevNorth * 100))
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   commonXAxis <- c(0,max(pointTable$cdemNorth))   
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   commonYAxis <- range(c(deltaBoundarySRTM,deltaBoundaryBorder,deltaBoundaryASTER),na.rm=TRUE)   
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(deltaBoundaryASTER,na.rm=TRUE),sd(deltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,deltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Boundary Delta (CDEM Elev): ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(deltaBoundaryBorder,na.rm=TRUE),sd(deltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,deltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Boundary Delta (CDEM Elev): Border",sub="vs Elev",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(deltaBoundarySRTM,na.rm=TRUE),sd(deltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,deltaBoundarySRTM,main="Boundary Delta (CDEM Elev): SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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message("ColumnID-CDEM Elevation done")
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browser()
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   commonXAxis <- c(0,max(pointTable$cdemNorth))   
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   commonYAxis <- range(c(normDeltaBoundarySRTM,normDeltaBoundaryBorder,normDeltaBoundaryASTER),na.rm=TRUE)   
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(normDeltaBoundaryASTER,na.rm=TRUE),sd(normDeltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,normDeltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta (CDEM Elev): ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(normDeltaBoundaryBorder,na.rm=TRUE),sd(normDeltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,normDeltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta (CDEM Elev): Border",sub="vs Elev",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(normDeltaBoundarySRTM,na.rm=TRUE),sd(normDeltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,normDeltaBoundarySRTM,main="Norm Bdry Delta (CDEM Elev): SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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message("NORMALIZED ColumnID-CDEM Elevation done")
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browser()
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   commonXAxis <- c(0,max(pointTable$ColumnID))   
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   commonYAxis <- range(c(normDeltaBoundarySRTM,normDeltaBoundaryBorder,normDeltaBoundaryASTER),na.rm=TRUE)   
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(normDeltaBoundaryASTER,na.rm=TRUE),sd(normDeltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,normDeltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta: ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(normDeltaBoundaryBorder,na.rm=TRUE),sd(normDeltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,normDeltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta: Border",sub="E-W Col",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(normDeltaBoundarySRTM,na.rm=TRUE),sd(normDeltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,normDeltaBoundarySRTM,main="Norm Bdry Delta: SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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message("NORMALIZED ColumnID-X-Axis is done...")
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# if 'plot flag' is set, send the plots to a JPG file. 
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if (JpgPlotFileFlag)
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{
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  message("creating JPG plot files...")
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  browser()
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jpeg(file="RowBoundaryDeltaColIDXAxisASTER.jpg")
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(deltaBoundaryASTER,na.rm=TRUE),sd(deltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,deltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Row Boundary Delta: ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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dev.off()
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jpeg(file="RowBoundaryDeltaColIDXAxisBORDER.jpg")   
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(deltaBoundaryBorder,na.rm=TRUE),sd(deltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,deltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Row Boundary Delta: Border",sub="E-W Col",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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dev.off()
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jpeg(file="RowBoundaryDeltaColIDXAxisSRTM.jpg")   
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(deltaBoundarySRTM,na.rm=TRUE),sd(deltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,deltaBoundarySRTM,main="Row Boundary Delta: SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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message("ColumnID-X-Axis plots are  done")
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#dev.new()
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   commonXAxis <- c(0,max(pointTable$cdemNorth))   
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   commonYAxis <- range(c(deltaBoundarySRTM,deltaBoundaryBorder,deltaBoundaryASTER),na.rm=TRUE)   
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jpeg(file="RowBoundaryDeltaCDEMElevXAxisASTER.jpg")
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(deltaBoundaryASTER,na.rm=TRUE),sd(deltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,deltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Boundary Delta (CDEM Elev): ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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dev.off()
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jpeg(file="RowBoundaryDeltaCDEMElevXAxisBORDER.jpg")
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(deltaBoundaryBorder,na.rm=TRUE),sd(deltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,deltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Boundary Delta (CDEM Elev): Border",sub="vs Elev",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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dev.off()
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jpeg(file="RowBoundaryDeltaCDEMElevXAxisCDEM.jpg")
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(deltaBoundarySRTM,na.rm=TRUE),sd(deltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,deltaBoundarySRTM,main="Boundary Delta (CDEM Elev): SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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dev.off()
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message("ColumnID-CDEM Elevation Plots are done")
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#browser()
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   commonXAxis <- c(0,max(pointTable$cdemNorth))   
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   commonYAxis <- range(c(normDeltaBoundarySRTM,normDeltaBoundaryBorder,normDeltaBoundaryASTER),na.rm=TRUE)   
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jpeg(file="NormRowBoundaryDeltaColIDXAxisASTER.jpg")
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(normDeltaBoundaryASTER,na.rm=TRUE),sd(normDeltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,normDeltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta (CDEM Elev): ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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dev.off()
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jpeg(file="NormRowBoundaryDeltaColIDXAxisBORDER.jpg")
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(normDeltaBoundaryBorder,na.rm=TRUE),sd(normDeltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,normDeltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta (CDEM Elev): Border",sub="vs Elev",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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dev.off()
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jpeg(file="NormRowBoundaryDeltaColIDXAxisSRTM.jpg")
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(normDeltaBoundarySRTM,na.rm=TRUE),sd(normDeltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$cdemNorth,normDeltaBoundarySRTM,main="Norm Bdry Delta (CDEM Elev): SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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dev.off()
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message("NORMALIZED ColumnID-CDEM Elevation Plots are done")
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browser()
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   commonXAxis <- c(0,max(pointTable$ColumnID))   
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   commonYAxis <- range(c(normDeltaBoundarySRTM,normDeltaBoundaryBorder,normDeltaBoundaryASTER),na.rm=TRUE)   
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jpeg(file="NormRowBoundaryDeltaCDEMElevXAxisASTER.jpg")   
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   xAxisLbl <- sprintf("M/SD: ASTER: %.2f / %.2f",mean(normDeltaBoundaryASTER,na.rm=TRUE),sd(normDeltaBoundaryASTER,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,normDeltaBoundaryASTER,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta: ASTER",xlab=xAxisLbl,col="red",pch=plotCh1)
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dev.off()
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jpeg(file="NormRowBoundaryDeltaCDEMElevXAxisBORDER.jpg")
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   xAxisLbl <- sprintf("M/SD: BORDER: %.2f / %.2f",mean(normDeltaBoundaryBorder,na.rm=TRUE),sd(normDeltaBoundaryBorder,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,normDeltaBoundaryBorder,xlim=commonXAxis, ylim=commonYAxis,main="Norm Bdry Delta: Border",sub="E-W Col",xlab=xAxisLbl,col="darkgreen",pch=plotCh2)
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dev.off()
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jpeg(file="NormRowBoundaryDeltaCDEMElevXAxisSRTM.jpg")
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   xAxisLbl <- sprintf("M/SD: SRTM: %.2f / %.2f",mean(normDeltaBoundarySRTM,na.rm=TRUE),sd(normDeltaBoundarySRTM,na.rm=TRUE))
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   plot(northRowTbl$ColumnID,normDeltaBoundarySRTM,main="Norm Bdry Delta: SRTM",xlim=commonXAxis, ylim=commonYAxis,xlab=xAxisLbl,col="blue",pch=plotCh3)
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dev.off()   
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message("NORMALIZED ColumnID-X-Axis Plot files have been created..")
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}
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message("...All plots created - hit key to delete them...")
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browser()
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graphics.off()
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} 
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