#! /bin/bash
# invoke gnuplot to compare crop output from WEPS generated runs.

# invocation: cropstack [Col_num-1 Col_num-2 ... Colnum-# file-1] [Col_num-1 Col_num-2 ... Colnum-# file-2] ... [Col_num-1 Col_num-2 ... Colnum-# file-#]

# columns are stacked in the order they are entered, and a seperate graph is created for each separate file listing

# set up column and title correspondence
mincol=5
maxcol=42
coltitle[5]=`echo "5) Heat Unit Index"`
coltitle[6]=`echo "6) Standing Stem Mass (kg/m^2)"`
coltitle[7]=`echo "7) Standing Leaf Mass (kg/m^2)"`
coltitle[8]=`echo "8) Standing Store Mass (kg/m^2)"`
coltitle[9]=`echo "9) Flat Stem Mass (kg/m^2)"`
coltitle[10]=`echo "10) Flat Leaf Mass (kg/m^2)"`
coltitle[11]=`echo "11) Flat Store Mass (kg/m^2)"`
coltitle[12]=`echo "12) Root Store Mass (kg/m^2)"`
coltitle[13]=`echo "13) Root Fiber Mass (kg/m^2)"`
coltitle[14]=`echo "14) Below Ground Stem Mass (kg/m^2)"`
coltitle[15]=`echo "15) Total Stem Mass (kg/m^2)"`
coltitle[16]=`echo "16) Total Leaf Mass (kg/m^2)"`
coltitle[17]=`echo "17) Plant Height (meters)"`
coltitle[18]=`echo "18) Number of Stems"`
coltitle[19]=`echo "19) Whole field area based Leaf Area Index (traditional)"`
coltitle[20]=`echo "20) Effective Leaf Area Index"`
coltitle[21]=`echo "21) Root Depth (meters)"`
coltitle[22]=`echo "22) Reproductive Mass Grain Fraction"`
coltitle[23]=`echo "23) Temperature Stress Factor"`
coltitle[24]=`echo "24) Water Stress Factor"`
coltitle[25]=`echo "25) Frost Damage Factor"`
coltitle[26]=`echo "26) Fraction Loss of Live Leaf Mass (scenescence)"`
coltitle[27]=`echo "27) Fraction Loss of Total Leaf Mass (weathering)"`
coltitle[28]=`echo "28) Photosynthetically Active Radiation (MJ/m2)"`
coltitle[29]=`echo "29) Intercepted Photosynthetically Active Radiation (MJ/m2)"`
coltitle[30]=`echo "30) Increment in Potential Dry Matter (kg/plant)"`
coltitle[31]=`echo "31) Fibrous Root Partitioning Ratio"`
coltitle[32]=`echo "32) Stem Partitioning Ratio"`
coltitle[33]=`echo "33) Leaf Partitioning Ratio"`
coltitle[34]=`echo "34) Reproductive Partitioning Ratio"`
coltitle[35]=`echo "35) Stem Mass Fraction Allocated To Standing Stems (Rem. Goes Flat)"`
coltitle[36]=`echo "36) Plant canopy diameter (or reach)(m/plant)"`
coltitle[37]=`echo "37) Plant canopy coverage area (m^2/plant)"`
coltitle[38]=`echo "38) Plant canopy diameter fraction (plant diameter / max diameter)"`
coltitle[39]=`echo "39) Plant canopy coverage area fraction (m^2/m^2)"`
coltitle[40]=`echo "40) Heat Unit Delay factor (1-no delay, 0-full delay)"`
coltitle[41]=`echo "41) Stem area index (m^2/m^2)"`
coltitle[42]=`echo "42) Representative stem diameter (m)"`

# short column titles
shortcoltitle[5]=`echo "HUI"`
shortcoltitle[6]=`echo "S Stem"`
shortcoltitle[7]=`echo "S Leaf"`
shortcoltitle[8]=`echo "S Store"`
shortcoltitle[9]=`echo "F Stem"`
shortcoltitle[10]=`echo "F Leaf"`
shortcoltitle[11]=`echo "F Store"`
shortcoltitle[12]=`echo "R Store"`
shortcoltitle[13]=`echo "R Fiber"`
shortcoltitle[14]=`echo "BG Stem"`
shortcoltitle[15]=`echo "T Stem"`
shortcoltitle[16]=`echo "T Leaf"`
shortcoltitle[17]=`echo "Height"`
shortcoltitle[18]=`echo "# Stems"`
shortcoltitle[19]=`echo "LAI"`
shortcoltitle[20]=`echo "Eff LAI"`
shortcoltitle[21]=`echo "R Depth"`
shortcoltitle[22]=`echo "GRF"`
shortcoltitle[23]=`echo "T Stress"`
shortcoltitle[24]=`echo "W Stress"`
shortcoltitle[25]=`echo "F Damage"`
shortcoltitle[26]=`echo "Senes"`
shortcoltitle[27]=`echo "Weath"`
shortcoltitle[28]=`echo "PAR"`
shortcoltitle[29]=`echo "I PAR"`
shortcoltitle[30]=`echo "iDM"`
shortcoltitle[31]=`echo "Root P"`
shortcoltitle[32]=`echo "Stem P"`
shortcoltitle[33]=`echo "Leaf P"`
shortcoltitle[34]=`echo "Repr P"`
shortcoltitle[35]=`echo "Stand F"`
shortcoltitle[36]=`echo "Reach"`
shortcoltitle[37]=`echo "Coverage"`
shortcoltitle[38]=`echo "Reach R"`
shortcoltitle[39]=`echo "Coverage R"`
shortcoltitle[40]=`echo "HU Delay"`
shortcoltitle[41]=`echo "SAI"`
shortcoltitle[42]=`echo "Rep Stem D"`

# set up column groupings
tgroups=12
colgroupnum[5]=1
colgroupnum[6]=2
colgroupnum[7]=2
colgroupnum[8]=2
colgroupnum[9]=2
colgroupnum[10]=2
colgroupnum[11]=2
colgroupnum[12]=2
colgroupnum[13]=2
colgroupnum[14]=2
colgroupnum[15]=2
colgroupnum[16]=2
colgroupnum[17]=3
colgroupnum[18]=4
colgroupnum[19]=5
colgroupnum[20]=5
colgroupnum[21]=3
colgroupnum[22]=1
colgroupnum[23]=1
colgroupnum[24]=1
colgroupnum[25]=1
colgroupnum[26]=1
colgroupnum[27]=1
colgroupnum[28]=6
colgroupnum[29]=6
colgroupnum[30]=7
colgroupnum[31]=8
colgroupnum[32]=8
colgroupnum[33]=8
colgroupnum[34]=8
colgroupnum[35]=8
colgroupnum[36]=9
colgroupnum[37]=10
colgroupnum[38]=1
colgroupnum[39]=1
colgroupnum[40]=1
colgroupnum[41]=11
colgroupnum[42]=12

# group y axis labels
grouplabel[1]=`echo "Fraction (0-1)"`
grouplabel[2]=`echo "Mass (kg/m^2)"`
grouplabel[3]=`echo "meters"`
grouplabel[4]=`echo "count per m^2"`
grouplabel[5]=`echo "m^2 leaf per m^2"`
grouplabel[6]=`echo "Radiation (MJ/m^2)"`
grouplabel[7]=`echo "kg per plant"`
grouplabel[8]=`echo "Partitioning Ratio"`
grouplabel[9]=`echo "meters per plant"`
grouplabel[10]=`echo "m^2 per plant"`
grouplabel[11]=`echo "m^2 per m^2"`
grouplabel[12]=`echo "meters"`

# grab and count command arguments
let ncmdarg=0
for ncmd in $*
do
    let ncmdarg=ncmdarg+1
    cmdarg[ncmdarg]="$ncmd"
    # echo "Command argument $ncmdarg = ${cmdarg[ncmdarg]}"
done

# check command argument count, zero means none
if [[ ncmdarg -eq 0 ]]
then
    echo 'invocation: cropstack [Col_num-1 Col_num-2 ... Colnum-# file-1] [Col_num-1 Col_num-2 ... Colnum-# file-2] ... [Col_num-1 Col_num-2 ... Colnum-# file-#]'
    echo 'Valid Column Numbers are:'
    for num in $( seq $mincol $maxcol )
    do
        echo ${coltitle[num]}
    done
    exit
fi

# parse command arguments checking for numbers and when not a number checking for a valid file name
# initialize total number of columns parsed
tcols=0
# initialize total number of valid file names parsed (must assume one when column numbers preceed file names)
tfiles=1
# initialize column count for first file name
tcolfile[tfiles]=0
for ncmd in $( seq 1 $ncmdarg )
do
    # test if it is an integer number
    echo "${cmdarg[ncmd]}" | grep [^0-9] > /dev/null 2>&1
    if [ "$?" -eq "0" ]
    then
        # not a column number, check for file name
        if [ -e "${cmdarg[ncmd]}" ]
        then
            # valid file name, check for preceeding columns
            if [[ tcolfile[tfiles] -gt 0 ]]
            then
                # columns are listed in front of this name
                # back fill column file name and number and serial pairings
                for ncol in $( seq 1 ${tcolfile[tfiles]} )
                do
                    let index=(tcols-tcolfile[tfiles])+ncol
                    # write serial number
                    colfileser[index]=${ncol}
                    # write file name
                    filename[index]="${cmdarg[ncmd]}"
                done
                # add file name to unique file names list
                ufilename[tfiles]="${cmdarg[ncmd]}"
                # Increment file number counter
                let tfiles+=1
            fi

            # find number of index blocks in this file
            linecount=`wc -l < ${ufilename[tfiles-1]}`
            lineswithnumbers=`grep -c '\.' < ${ufilename[tfiles-1]}`
            let fileindex=(linecount-lineswithnumbers-1)/2
            #echo "fileindex = ${fileindex}"

            # check to use minimum of all files
            numindex=`echo "$fileindex $numindex" | stats min`
            #echo "numindex now equal to $numindex"
        else
            # not a valid file name, show error message and exit
            echo \'"${cmdarg[ncmd]}"\' is not valid file name.
            exit
        fi
    else
        # it is an integer number, check for valid column number
        if [[ ${cmdarg[ncmd]} -lt $mincol ]]
        then
            echo \'"${cmdarg[ncmd]}"\' is a Bad Column Number
            echo 'invocation: cropstack [Col_num-1 Col_num-2 ... Colnum-# file-1] [Col_num-1 Col_num-2 ... Colnum-# file-2] ... [Col_num-1 Col_num-2 ... Colnum-# file-#]'
            echo 'Valid Column Numbers are:'
            for num in $( seq $mincol $maxcol )
            do
                echo ${coltitle[num]}
            done
            exit
        elif [[ ${cmdarg[ncmd]} -gt $maxcol ]]
        then
            echo \'"${cmdarg[ncmd]}"\' is a Bad Column Number
            echo 'invocation: cropstack [Col_num-1 Col_num-2 ... Colnum-# file-1] [Col_num-1 Col_num-2 ... Colnum-# file-2] ... [Col_num-1 Col_num-2 ... Colnum-# file-#]'
            echo 'Valid Column Numbers are:'
            for num in $( seq $mincol $maxcol )
            do
                echo ${coltitle[num]}
            done
            exit
        fi

        # valid column number, add into column number array and increment indexes
        let tcols+=1
        let tcolfile[tfiles]+=1
        colnum[tcols]="${cmdarg[ncmd]}"
        # set column group number
        colgroup[tcols]=${colgroupnum[${colnum[tcols]}]}
        # set column file number
        colfilenum[tcols]=${tfiles}
    fi
done

# screen for terminating valid file name
if [ ! -e "${filename[tcols]}" ]
then
    echo "No terminating file name."
    echo 'invocation: cropstack [Col_num-1 Col_num-2 ... Colnum-# file-1] [Col_num-1 Col_num-2 ... Colnum-# file-2] ... [Col_num-1 Col_num-2 ... Colnum-# file-#]'
fi

# set tfiles to the correct count
let tfiles-=1

# echo the resulting arrays of column numbers and file names
# echo "The input command line results in the following columns and file names:"
# for num in $( seq 1 ${tcols} )
# do
#     echo "${colnum[num]}  ${colgroup[num]}  ${filename[num]}  ${colfilenum[num]}  ${colfileser[num]}"
# done
# exit

# set up graph to column group correspondence
# sort group list (result is zero reference array)
colgroupsort=(`echo ${colgroup[@]} | transpose | sort | transpose`)

# total number of column groups to be plotted
tgroups=1
# list of groups represented
groupnum[1]=${colgroupsort[0]}
let tindex=tcols-1
for num in $( seq 1 ${tindex} )
do
    let index=num-1
    if [[ ${colgroupsort[num]} -ne ${colgroupsort[index]} ]]
    then
        let tgroups+=1
        groupnum[tgroups]=${colgroupsort[num]}
    fi
done

# show groups
# echo "unique group numbers"
# echo ${groupnum[@]}
# exit

# Find the number of unique crops in each file
numcrops[1]=`cut -c 315-400 < ${ufilename[1]} | uniq | grep '[:print:]' | sort -u | wc -l`
#echo "${ufilename[1]} has ${numcrops[1]} unique crops"
for num in $( seq 2 ${tfiles} )
do
    numcrops[num]=`cut -c 315-400 < ${ufilename[num]} | uniq | grep '[:print:]' | sort -u | wc -l`
    #echo "${ufilename[num]} has ${numcrops[num]} unique crop(s)"
    if [[ numcrops[num] -ne numcrops[1] ]]
    then
        # for multiple file plots, the number of unique crops must be equal
        echo "Different number of unique crops for two files"
        echo "Check and try again"
    fi
done

# Find maximum values for each unique crop year
# all files have the same number of crop years
for idx in $( seq 1 ${numcrops[1]} )
do
    for num in $( seq 1 ${tfiles} )
    do
        # extract unique crop names in order
        cropname=`cut -c 315-400 < ${ufilename[num]} | uniq | grep '[:print:]' | linex ${idx} | sed 's/ $//'`
        echo "Crop name: ${cropname} :end"

        # Find maximum column value for x axis "day after planting" column 4 for just the lines containing the crop name
        cropmaxdap[idx]=`grep "${cropname}" < ${ufilename[num]} | dm "if x4>0 then x4 else SKIP" | stats max`
        echo "cropmaxdap: ${cropmaxdap[idx]}"
        # set maximum across all files
        afcropmaxdap[idx]=`echo "${cropmaxdap[idx]} ${afcropmaxdap[idx]}" | stats max`
        echo "afcropmaxdap: ${afcropmaxdap[idx]}"

        # find maximum for each stack for just the lines containing the crop name
        for idy in $(seq 1 $tcols)
        do
            if [[ colfilenum[idy] -eq ${num} ]]
            then
                # add column number to dm string
                if [[ colfileser[idy] -eq 1 ]]
                then
                    summedcol="x${colnum[idy]}"
                else
                    summedcol="${summedcol}+x${colnum[idy]}"
                fi
            fi
        done
        stackmaxval[idx]=`grep "${cropname}" < ${ufilename[num]} | dm "if x1>0 then ${summedcol} else SKIP" | stats max`
        echo "Stack ${summedcol} maximum is ${stackmaxval[idx]}"
        # set maximum across all files
        afstackmaxval[idx]=`echo "${stackmaxval[idx]} ${afstackmaxval[idx]}" | stats max`
        echo "afstackmaxval: ${afstackmaxval[idx]}"

    done
done

# find maximum column value for x axis "day after planting" column 4 for all input files
#for num in $( seq 1 ${tfiles} )
#do
#    # Check for maximum days after planting for one file
#    filemaxdap=`dm "if x4>0 then x4 else SKIP" < ${ufilename[num]} | stats max`
#    # Check for maximum days after planting for all file
#    allmaxdap=`echo "$filemaxdap $allmaxdap" | stats max`
#    echo "maximum day after planting now equal to $allmaxdap"
#done

# find maximum column value for each column and assign that to the maximum for the group
#for num in $( seq 1 $tcols )
#do
#    echo -n " Find maximum value: column ${colnum[num]} in ${filename[num]} : "
#
#    # find selected column maximum value for this file
#    filemaxval=`dm "if x${colnum[num]}>0 then x${colnum[num]} else SKIP" < ${filename[num]} | stats max`
#    echo "${filemaxval}"
#
#    # check for maximum for this column group for all files
#    groupmaxval[${colgroup[num]}]=`echo "$filemaxval ${groupmaxval[${colgroup[num]}]}" | stats max`
#    echo "groupmaxval(${colgroup[num]}) now equal to ${groupmaxval[${colgroup[num]}]}"
#done

# Find stack maximum value by summing all columns
#for idy in $( seq 1 $tfiles )
#do
#    for num in $(seq 1 $tcols)
#    do
#        if [[ colfilenum[num] -eq ${idy} ]]
#        then
#            # add column number to dm string
#            if [[ colfileser[num] -eq 1 ]]
#            then
#                summedcol="x${colnum[num]}"
#            else
#                summedcol="${summedcol}+x${colnum[num]}"
#            fi
#        fi
#    done
#    stackmaxval[idy]=`dm "if x1>0 then ${summedcol} else SKIP" < ${ufilename[idy]} | stats max`
#    echo "Stack ${summedcol} maximum is ${stackmaxval[idy]}"
#done

# rather than loop within gnuplot, create specific plot lines
# for each file so parameters can be added to the 
# titles of the graphs.

# create text for graph title, using file names
for num in $( seq 1 ${tfiles} )
do
    graphtitle[num]=`echo "${ufilename[num]}"`
done

# Set up plot sizes for multiple plots (ie. groups)
if [[ $tfiles -gt 1 ]]
then
    # plot sizes for each file
    psizebase=$( echo "scale=4; 0.9/${tfiles}" | bc -l )
    for num in $( seq 1 $tfiles )
    do
        # create coordinates
        # y size for plot (x is 1.0)
        if [[ $num -eq $tfiles ]]
        then
            # increase the size of the last plot (both title and axis)
            psize[num]=$( echo "scale=4; ${psizebase}+0.1" | bc -l )
            porigin[num]=0
        else
            # other plots have just title
            psize[num]=${psizebase}
            # place plots from the top down in the order specified
            porigin[num]=$( echo "scale=4; 0.1+($tfiles-$num)*${psizebase}" | bc -l )
        fi
    done
fi

# write single instance lines top plot file

#--- start pdf ---
echo "set terminal pdf" > temp.plt
echo "set output 'cropstack.pdf'" >> temp.plt
view_pause=0
#--- end pdf ---

#--- start emf ---
# create temporary directory for files if needed
#tempdir="htemp"
#mkdir -p ${tempdir}
## clear any files
#rm ${tempdir}/*.emf
#echo "set terminal emf monochrome dashed" > temp.plt
#view_pause=0
#echo "set line style 1 lt 1 lw 1" >> temp.plt
#echo "set line style 2 lt 2 lw 1" >> temp.plt
#echo "set line style 3 lt 3 lw 1" >> temp.plt
#echo "set line style 4 lt 4 lw 1" >> temp.plt
#echo "set line style 5 lt 5 lw 1" >> temp.plt
#echo "set line style 6 lt 1 lw 3" >> temp.plt
#echo "set line style 7 lt 2 lw 3" >> temp.plt
#echo "set line style 8 lt 3 lw 3" >> temp.plt
#echo "set line style 9 lt 4 lw 3" >> temp.plt
#echo "set line style 10 lt 5 lw 3" >> temp.plt
#echo "set line style 11 lt 1 lw 5" >> temp.plt
#--- end emf ---

#--- start screen ---
#view_pause=-1
#echo "" > temp.plt
#--- end screen ---

# set legend location
echo "set key left top" >> temp.plt

for year in $(seq $numindex)
do
    echo "crop year = ${year}"

#    # --- emf output files ---
#    echo "set output '${tempdir}/${year}.emf'" >> temp.plt

    # set the crop that is growing
    cropnumyr=$( echo "(${year} - 1) % ${numcrops[1]}" | bc )
    let cropnumyr++
    # echo "${cropnumyr}"

    # set so that graphs use same total days and maximum values for that crop
    echo "set xrange [0:${afcropmaxdap[cropnumyr]}]" >> temp.plt
    echo "set yrange [0:${afstackmaxval[cropnumyr]}]" >> temp.plt

    # set up single or multiple plot windows
    if [[ $tfiles -gt 1 ]]
    then
        echo "multiple plots"
        echo "set size 1.0, 1.0" >> temp.plt
        echo "set origin 0.0, 0.0" >> temp.plt
        echo "set multiplot" >> temp.plt
    fi

    # create plot commands for each file
    for idy in $( seq 1 $tfiles )
    do
        # create graph title line
        echo "set title 'Crop Yr ${year}, ${graphtitle[idy]}'" >> temp.plt

        # remove x axis from all but last graph
        if [[ $idy -lt $tfiles ]]
        then
            # remove x axis labels
            echo "set format x ''" >> temp.plt
            echo "set xlabel ''" >> temp.plt
        else
            # format x axis labels
            echo "set format x '% g'" >> temp.plt
            echo "set xlabel 'Days After Planting'" >> temp.plt
        fi

        # individual sizes for multiplots
        if [[ $tfiles -gt 1 ]]
        then
            # set plot size
            echo "set size 1.0, ${psize[idy]}" >> temp.plt
            echo "set origin 0.0, ${porigin[idy]}" >> temp.plt
        fi

        # create plot lines for each column in this file
        index=0
        for num in $(seq 1 $tcols)
        do
            if [[ colfilenum[num] -eq ${idy} ]]
            then
                for idx in $(seq 1 ${colfileser[num]})
                do
                    # set the index local to the file name
                    let locindex=(num-colfileser[num])+idx
                    if [[ idx -eq 1 ]]
                    then
                        # set axis labels
                        echo "set ylabel '${grouplabel[${colgroup[num]}]}'" >> temp.plt
                        # initialize column sums
                        summedcol="(\$${colnum[locindex]}"
                    else
                        # add all previous column numbers to list to be summed for plot
                        summedcol="${summedcol}+${colnum[locindex]}"
                    fi
                done
                summedcol="${summedcol})"
                summedcol=`echo $summedcol | sed 's/+/+\$/g'`
                let index+=1
                let yearm=year-1
                plotline[index]="'${filename[num]}' index ${yearm} using 4:${summedcol} with lines title '${shortcoltitle[${colnum[num]}]}', \\"
            fi
        done

        # add plot command to first plotline
        plotline[1]=`echo "${plotline[1]}" | sed -e 's/^.*/plot &/'`

        # strip last plotline of 3 extra characters
        plotline[index]=`echo "${plotline[index]}" | sed -e 's/...$//'`

        # write out plot lines to file
        for num in $(seq 1 $index)
        do
            echo ${plotline[num]} >> temp.plt
        done

    done

    # check multiple plots
    if [[ $tfiles -gt 1 ]]
    then
      # this command necessary to display all plots on some terminals
      echo "unset multiplot" >> temp.plt
    fi

    echo "pause ${view_pause}" >> temp.plt

done

gnuplot temp.plt

#rm temp.plt

exit