plot_general.sh

expName=$1
maxIter=$2
outputtype=$3
write_model_cuts=$4
use_max_radius=$5
yerrorbars=$6
gt_map_mode=$7

# if [ -n $8 ]
# then
	# resultsdir=../../../results/
# else
	# resultsdir=results
# fi

#
# Do the plots.
#

# Set title and output type 
title=${expName}
font=/usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf
fontsize=9
width=1200
height=800
if [ "${outputtype}" == "ps" ]
then
    outputFile=${expName}_results.ps
    gnustr="set term postscript enhanced color eps font 'Helvetiva,10'"
    gnustr="${gnustr}; set output '${outputFile}'"
elif [ "${outputtype}" == "svg" ]
then
    outputFile=${expName}_results.svg
    gnustr="set term svg enhanced font '${font},${fontsize}' size ${width}, ${height}"
    gnustr="${gnustr}; set output '${outputFile}'"
else  
    outputFile=${expName}_results.png
    gnustr="set terminal png font '${font},${fontsize}' size ${width}, ${height}"
    gnustr="${gnustr}; set output '${outputFile}'"
    # gnustr="${gnustr}; set output '| display png:-'"
fi
gnustr="${gnustr}; set multiplot layout 2, 3 title '${title} results'"


# Incremental FSC curves
title="Incremental FSC plots"
xlabel="Resolution"
ylabel=""
str="set title '${title}'"
str="${str}; set xlabel '${xlabel}'"
str="${str}; set ylabel '${ylabel}'"
str="${str}; set yrange [0:1.05]"
str="${str}; set xrange [*:*]"
str="${str}; plot "
let itersn=maxIter-1
doIterations=$(seq 2 1 ${itersn})
for k in ${doIterations}
do 
	let n=k+1
	str="${str} '${expName}_fsc_`printf %02d $k`_`printf %02d $n`.txt' with lines "
	if [ "$k" == "$itersn" ]; then 
		str=${str}
	else
		str="${str} , "; 
	fi
done
gnustr="${gnustr}; ${str}"

# FSC curves
title="FSC curves"
xlabel="Resolution"
ylabel=""
str="set title '${title}'"
str="${str}; set xlabel '${xlabel}'"
str="${str}; set ylabel '${ylabel}'"
str="${str}; set yrange [0:1.05]"
str="${str}; set xrange [0:.15]"
str="${str}; plot "
doIterations=$(seq 2 1 ${maxIter})
lw=2
for k in ${doIterations}
do 
    int=$(( 255-255*${k}/${maxIter} ))
    hexx=`printf %02X $int`
    # lw=$(( 3*$k/15 ))
    # if [ "$gt_map_mode" == "1" ]
    # then
        # rgb="#FF${hexx}${hexx}"
        # str="${str} '${expName}_CSP_`printf %02d $k`_gt_fsc.txt' using 1:2 with lines lw $lw lc rgbcolor '$rgb' "
        # if [ "$k" == "$maxIter" ]; then 
            # str="${str} ti \"CSP vs. GT\", "; 
        # else
            # str="${str} ti \"\", "; 
        # fi
    # fi
    rgb="#FF${hexx}${hexx}"
    str="${str} '${expName}_CSP_`printf %02d $k`_fsc.txt' with lines lw $lw "
    if [ "$k" == "$maxIter" ]; then 
		str=${str}
		#str="${str} ti \"CSP\" "; 
    else
		#str="${str} ti \"\", "; 
		str="${str} , "; 
    fi
	#let lw=lw+1
done
str="${str}; set yrange [*:*]"
str="${str}; set xrange [*:*]"
gnustr="${gnustr}; ${str}"

# FSC curves
if [ "$gt_map_mode" == "1" ]
then    
    title="FSC curves to GT" 	
    xlabel="Resolution"
    ylabel=""
    str="set title '${title}'"
    str="${str}; set xlabel '${xlabel}'"
    str="${str}; set ylabel '${ylabel}'"
    str="${str}; set yrange [0:1.05]"
    str="${str}; set xrange [0:.15]"
    str="${str}; plot "
    doIterations=$(seq 2 1 ${maxIter})
    # doIterations="2 ${maxIter}"
    # for k in ${doIterations}
    # do 
        # int=$(( 255-255*${k}/${maxIter} ))
        # hexx=`printf %02X $int`
        # lw=$(( 3*$k/15 ))
        # rgb="#${hexx}FF${hexx}"
        # str="${str} '${expName}_USP_`printf %02d $k`_gt_fsc.txt' using 1:2 with lines lw $lw lc rgbcolor '$rgb' "
        # if [ "$k" == "$maxIter" ]; then 
            # str="${str} ti \"USP vs. GT\", "; 
        # else
            # str="${str} ti \"\", "; 
        # fi
    # done
    for k in ${doIterations}
    do 
        int=$(( 255-255*${k}/${maxIter} ))
        hexx=`printf %02X $int`
        #lw=$(( 3*$k/15 ))
        rgb="#FF${hexx}${hexx}"
        str="${str} '${expName}_CSP_`printf %02d $k`_gt_fsc.txt' with lines lw $lw "
        if [ "$k" == "$maxIter" ]; then 
			str=${str}
            #str="${str} ti \"CSP vs. GT\" "; 
        else
            #str="${str} ti \"\", "; 
			str="${str} , "; 
        fi
    done
#    str="${str}; set yrange [*:*]"
    gnustr="${gnustr}; ${str}"
fi

# Global PR
file=${expName}_DATA_PR
# sed -i 1d ${file} # remove first line
title="Mean Phase Residual per Iteration"
xlabel=Iterations
ylabel="Mean Phase Residual"
str="set title '${title}'"
str="${str}; set xlabel '${xlabel}'"
str="${str}; set ylabel '${ylabel}'"
str="${str}; set style data linespoints"
str="${str}; set xrange [*:*]; set yrange [*:*]";
if [ "$yerrorbars" == "0" ]; then
    #str="${str}; plot '${file}' using 1:2 pt 5 ti \"CSP\", '${file}' using 1:5 pt 5 ti \"USP\""
    str="${str}; plot '${file}' using 1:2 pt 5 ti \"CSP\""
else
    str="${str}; plot '${file}' using 1:2:3:4 with yerrorbars pt 5 ti \"CSP\", '${file}' using 1:5:6:7 with yerrorbars pt 5 ti \"USP\""
fi
gnustr="${gnustr}; ${str}"

# Global DPR
file=${expName}_DATA_DPR
# sed -i 1d ${file} # remove first line
title="Mean Differential Phase Residual"
xlabel=Iterations
ylabel="Mean Differential Phase Residual per Iteration"
str="set title '${title}'"
str="${str}; set xlabel '${xlabel}'"
str="${str}; set ylabel '${ylabel}'"
str="${str}; set style data linespoints"
str="${str}; plot '${file}' using 1:2 pt 5 lc rgb \"green\" ti \"CSP\" "
#str="${str} '${file}' using 1:3 pt 5 ti \"USP\""
gnustr="${gnustr}; ${str}"

output=${expName}_DATA.txt
str="set xrange [*:*]; set yrange [*:*]; set xlabel 'Iterations'; set ylabel 'Resolution'; plot"
str="${str} '${output}' using 1:2 with linespoints ti \"Internal FSC\","
str="${str} '${output}' using 1:3 with linespoints ti \"FSC to GT\","
str="${str} '${output}' using 1:4 with linespoints ti \"RMEASURE\""
gnustr="${gnustr}; ${str}"

# # Frobenius of Transformation Matrices
# title="Frobenius of Difference in Transformation Matrices"
# xlabel="Particle Projection Index"
# ylabel=""
# str="set title '${title}'"
# # str="${str}; set logscale y"
# str="${str}; set xlabel '${xlabel}'"
# str="${str}; set ylabel '${ylabel}'"
# str="${str}; set style data points"
# # str="${str}; set key title 'CSP iter'"
# str="${str}; plot "
# doIterations="2 ${maxIter}"
# index=1
# for k in ${doIterations}
# do 
    # titer=`printf %02d $k`
    # file1=${expName}_DATA_FROB_${titer}
    # file2=${expName}_DATA_FROB_SORT_${titer}
# #    str="${str} '${file1}' using 1:2 pt 4 ps .5 lt ${index} ti \"CSP ${k}\", "
# #    str="${str} '${file2}' using 1:2 with lines lc ${index} lw 2 ti \"\", "
    # str="${str} '${file2}' using 1:2 with lines lc ${index} lw 2 ti \"CSP ${k}\", "
    # index=$(( index + 1 ))
# #    str="${str} '${file1}' using 1:3 pt 2 ps .5 lt ${index} ti \"USP ${k}\", "
# #    str="${str} '${file2}' using 1:3 with lines lc ${index} lw 2 ti \"\" "
    # str="${str} '${file2}' using 1:3 with lines lc ${index} lw 2 ti \"USP ${k}\" "
    # if [ "${k}" -lt "${maxIter}" ]; then str="${str}, "; fi
    # index=$(( index + 1 ))
# done
# gnustr="${gnustr}; ${str}"

# # Plot angles differences
# if [ "$use_max_radius" == "1" ]; then
    # max_radius=`cat .max_radius`
# else
    # max_radius=1
# fi
# xtics=`echo  "0.5 * $max_radius" | bc -l`
# yposition=`echo  "0.9 * $max_radius" | bc -l`
# max_radius=`echo  "1.1 * $max_radius" | bc -l`
# title="Angles difference"
# str="set title '${title}'"
# str="${str}; set key title ''"
# str="${str}; unset border"
# str="${str}; unset logscale y"
# str="${str}; set angles degrees"
# str="${str}; set grid polar 15"
# str="${str}; set polar"
# str="${str}; set size square"
# str="${str}; set style data points"
# str="${str}; set xtics ${xtics} norotate"
# str="${str}; unset ytics"
# str="${str}; set format x \"%2.0te%L\""
# str="${str}; set yrange [-${max_radius}:${max_radius}]"
# str="${str}; set xrange [-${max_radius}:${max_radius}]"
# str="${str}; set label 'radius=sin(theta) vs. angle=phi' at -${max_radius},-${yposition}"
# str="${str}; plot "
# # doIterations=$(seq 2 1 ${maxIter})
# doIterations="2 ${maxIter}"
# for k in ${doIterations}
# do 
    # titer=`printf %02d $k`
    # file=${expName}_DATA_POLARANGDIF_${titer}
    # str="${str} '${file}' using 4:3 pt 4 ps .7 ti \"CSP iter $k\", "
    # str="${str} '${file}' using 7:6 pt 4 ps .7 ti \"USP iter $k\""
    # if [ "${k}" -lt "$maxIter" ]; then str="${str}, "; fi
# done
# gnustr="${gnustr}; ${str}"

# Run gnuplot
command=`echo "${gnustr}" | gnuplot`
# echo ${gnustr}
echo $command 

size=`header ${expName}_CSP_02.mrc | grep sections | awk '{print $9}'`
midsection=`echo $size/2 | bc`

halfsection=`echo $size/2-64 | bc`

# Obtain the axial, sagital and coronal cuts for all the final density
# map. Then concatenate them in one image.
if [ "$write_model_cuts" == "1" ]
then 
    tput civis
    for XSP in CSP
    do
        doIterations=$(seq 2 1 ${maxIter})
        for k in ${doIterations}
        do
            iter=`printf %02d $k`
            model=${expName}_${XSP}_${iter}.mrc
            modellpf=${expName}_${XSP}_${iter}_lpf.mrc
			# proc3d $model $modellpf apix=1.4 lp=10
            echo -ne "Generating model cuts for ${model}\r"
            axial=${expName}_${XSP}_${iter}_axial
            coronal=${expName}_${XSP}_${iter}_coronal
            sagital=${expName}_${XSP}_${iter}_sagital
            
            newstack ${model} ${axial}.mrc -secs $midsection -scale 0,255 -mode 0 > /dev/null
            mrc2tif ${axial}.mrc ${axial}.tif > /dev/null
            convert -normalize -crop 128x128+${halfsection}+${halfsection} ${axial}.tif ${axial}.png
            
            rotatevol -input ${model} -output ${sagital}.mrc -angles 0,90,0 > /dev/null
            newstack ${sagital}.mrc ${sagital}.mrc -secs ${midsection} -scale 0,255 -mode 0 > /dev/null
            mrc2tif ${sagital}.mrc ${sagital}.tif > /dev/null
            convert -normalize -rotate 90 -crop 128x128+${halfsection}+${halfsection} -negate ${sagital}.tif ${sagital}.png
            convert -negate ${sagital}.png ${sagital}.png
            
            rotatevol -input ${model} -output ${coronal}.mrc -angles 0,90,90 > /dev/null
            newstack ${coronal}.mrc ${coronal}.mrc -secs ${midsection} -scale 0,255 -mode 0 > /dev/null
            mrc2tif ${coronal}.mrc ${coronal}.tif > /dev/null
            convert -normalize -rotate 90 -crop 128x128+${halfsection}+${halfsection} -negate ${coronal}.tif ${coronal}.png
            convert -negate ${coronal}.png ${coronal}.png
            
            rm -f *.mrc~ $modellpf
            montage -tile 3x -geometry 256x256 ${expName}_${XSP}_${iter}_{axial,coronal,sagital}.png ${XSP}_${iter}.png
        done
        montage -tile 1x -geometry 768x256 ${XSP}_*.png ${XSP}.png
        rm -f ${XSP}_*.png *_{axial,coronal,sagital}.*
    done
    montage -tile 2x1 -geometry 768x$(( 256 * ( maxIter - 1 ) )) CSP.png CSP.png ${expName}_model_cuts.png
    rm -f CSP.png USP.png
    echo ""
    tput cnorm
fi

# Move the results to the results folder
#mv ${outputFile} ${resultsdir}
echo "Results plotted in ${outputFile}"

# # Show the results
# if [ "${outputtype}" == "ps" ]
# then
    # evince ${outputFile} &
# else  
    # display ${outputFile} &
# fi