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eroullit/csv2gnuplot.sh

Created October 25, 2011 11:13
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CSV -> GNUplot conversion script
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csv2gnuplot.sh
#!/bin/bash
#
# This transforms a CSV file into a gnuplot file.
# use option '-h' to display a help screen for all options.
#
# FracPete
# the usage of this script
function usage()
{
echo
echo "usage: ${0##*/} [-i <file>] [-o <file>] [-g <file>] [-G <file>]"
echo " [-O <file>] [-d <delim>] [-t] [-x] [-a] [-l] [-T]"
echo " [-W <width> -H <height>]] [-F <x11|png|ps>]"
echo " [-b <files>] [-e]"
echo " [-h]"
echo
echo "Transforms a given CSV file into a gnuplot input file. It can also"
echo "produce a gnuplot script for plotting the data, as well as batch"
echo "processing of several files with automatic output generation."
echo
echo " -h this help"
echo " -i <file>"
echo " the CSV file to use as input"
echo " -o <file>"
echo " the gnuplot output file, output to stdout if not provided"
echo " -g <file>"
echo " generates a gnuplot script with this name to display the data"
echo " it assumes that the first column is the index for the x-axis."
echo " In combination with '-b' this parameter is only used to indicate"
echo " that a script is wanted, the filename itself is ignored."
echo " -G <file>"
echo " a file containing gnuplot options, comments etc. to be added "
echo " before the plots"
echo " -O <file>"
echo " generates a script that outputs the plot in the format specified"
echo " with '-F' in a file with the given name, instead of displaying "
echo " it in a window"
echo " -d <delim>"
echo " the delimiter that separates the columns, default: $DELIMITER"
echo " -t transposes the matrix first"
echo " -x adds a column for the x-axis (numbers starting from 1)"
echo " -a generates the average of the columns"
echo " -l adds 'with lines' to the gnuplot script"
echo " -T adds a number as title to the gnuplot script"
echo " -F <x11|png|ps>"
echo " the format of the output, default: $FORMAT"
echo " -W <width>"
echo " the width of the output (if '-F png'), default: $WIDTH"
echo " -H <height>"
echo " the height of the output (if '-F png'), default: $HEIGHT"
echo " -b <files>"
echo " processes the given files in batch mode, i.e. '-i' and '-o' are"
echo " not necessary. the files get new extensions automatically."
echo " Note: use \" if you're using wildcards like '*'"
echo " -e generates the desired output files directly, i.e. in creates a"
echo " temp. gnuplot file and runs this (in combination with '-b',"
echo " otherwise '-g' must be given). "
echo " Works only if format is ps or png ('-F')."
echo
}
# variables
INPUT=""
OUTPUT=""
OUTPUT_PLOT=""
GNUPLOT=""
GNUPLOT_OPTIONS=""
HAS_OUTPUT="no"
HAS_GNUPLOT="no"
DELIMITER=","
TRANSPOSE="no"
XAXIS="no"
AVERAGE="no"
LINES="no"
TITLE="no"
FORMAT="x11"
WIDTH="800"
HEIGHT="600"
BATCH_FILES=""
BATCH_OPTIONS=""
EXECUTE="no"
# interprete parameters
while getopts ":hi:o:g:d:txalTF:W:H:O:b:eG:" flag
do
case $flag in
i) INPUT=$OPTARG
;;
o) OUTPUT=$OPTARG
HAS_OUTPUT="yes"
;;
g) GNUPLOT=$OPTARG
HAS_GNUPLOT="yes"
;;
G) GNUPLOT_OPTIONS=$OPTARG
BATCH_OPTIONS="$BATCH_OPTIONS -$flag $OPTARG"
;;
d) DELIMITER=$OPTARG
;;
t) TRANSPOSE="yes"
BATCH_OPTIONS="$BATCH_OPTIONS -$flag"
;;
x) XAXIS="yes"
BATCH_OPTIONS="$BATCH_OPTIONS -$flag"
;;
a) AVERAGE="yes"
BATCH_OPTIONS="$BATCH_OPTIONS -$flag"
;;
l) LINES="yes"
BATCH_OPTIONS="$BATCH_OPTIONS -$flag"
;;
T) TITLE="yes"
BATCH_OPTIONS="$BATCH_OPTIONS -$flag"
;;
O) OUTPUT_PLOT=$OPTARG
;;
W) WIDTH=$OPTARG
BATCH_OPTIONS="$BATCH_OPTIONS -$flag $OPTARG"
;;
H) HEIGHT=$OPTARG
BATCH_OPTIONS="$BATCH_OPTIONS -$flag $OPTARG"
;;
F) FORMAT=$OPTARG
BATCH_OPTIONS="$BATCH_OPTIONS -$flag $OPTARG"
;;
b) BATCH_FILES=$OPTARG
;;
e) EXECUTE="yes"
BATCH_OPTIONS="$BATCH_OPTIONS -$flag"
;;
h) usage
exit 0
;;
*) echo
echo "Unknown option: '-$OPTARG'"
echo
usage
exit 1
;;
esac
done
# valid combinations of parameters?
if [ ! "$BATCH_FILES" = "" ] && [ "$EXECUTE" = "yes" ] && [ "$FORMAT" = "x11" ]
then
echo
echo "ERROR: a format other than '$FORMAT' must be specified if '-b' and"
echo " '-e' are specified, e.g. 'ps'."
echo
usage
exit 2
fi
# batch-mode?
if [ ! "$BATCH_FILES" = "" ]
then
for i in $BATCH_FILES
do
echo "$i..."
# build options
OPTIONS=$BATCH_OPTIONS
OPTIONS="$OPTIONS -i $i"
OPTIONS="$OPTIONS -o $i.dat"
if [ "$HAS_GNUPLOT" = "yes" ]
then
OPTIONS="$OPTIONS -g $i.scr"
fi
if [ "$FORMAT" = "png" ]
then
OPTIONS="$OPTIONS -O $i.png"
fi
if [ "$FORMAT" = "ps" ]
then
OPTIONS="$OPTIONS -O $i.ps"
fi
# run script
$0 $OPTIONS
done
exit 0
fi
# test files
if [ ! "$INPUT" = "" ] && [ ! -f "$INPUT" ]
then
INPUT=""
fi
if [ ! "$GNUPLOT_OPTIONS" = "" ] && [ ! -f "$GNUPLOT_OPTIONS" ]
then
echo "Warning: '$GNUPLOT_OPTIONS' not found - ignored!"
GNUPLOT_OPTIONS=""
fi
if [ "$HAS_OUTPUT" = "no" ]
then
OUTPUT=$INPUT".tmp"
fi
# everything provided?
if [ "$INPUT" = "" ] || [ "$DELIMITER" = "" ]
then
echo
echo "ERROR: not all parameters provided or incorrect!"
echo
usage
exit 1
fi
if [ "$EXECUTE" = "yes" ] && [ "$HAS_GNUPLOT" = "no" ]
then
echo
echo "ERROR: '-g' must be specified with option '-e'!"
echo
usage
exit 3
fi
if [ "$OUTPUT_PLOT" = "" ] && [ ! "$FORMAT" = "x11" ]
then
echo "Warning: output file for format '$FORMAT' not specified, falling back to 'x11'"
FORMAT="x11"
fi
# some variables
TMPFILE=$OUTPUT".tmp"
# init
cp $INPUT $OUTPUT
# change modifier into " "
if [ ! "$DELIMITER" = " " ]
then
cat $OUTPUT | sed s/$DELIMITER/" "/g > $TMPFILE
cp $TMPFILE $OUTPUT
fi
# transpose matrix?
if [ "$TRANSPOSE" = "yes" ]
then
cat $OUTPUT | exec awk '
NR == 1 {
n = NF
for (i = 1; i <= NF; i++)
row[i] = $i
next
}
{
if (NF > n)
n = NF
for (i = 1; i <= NF; i++)
row[i] = row[i] " " $i
}
END {
for (i = 1; i <= n; i++)
print row[i]
}' > $TMPFILE
cp $TMPFILE $OUTPUT
fi
# average columns?
if [ "$AVERAGE" = "yes" ]
then
COLCOUNT=`head -n1 $OUTPUT | wc -w | sed s/" "*//g`
ROWCOUNT=`cat $OUTPUT | wc -l | sed s/" "*//g`
rm -f $TMPFILE
for ((i = 1; i <= $COLCOUNT; i++))
do
COL=`cat $OUTPUT | cut -f$i -d" "`
# average
TMP="("`echo $COL | sed s/" "/+/g`")/$ROWCOUNT"
if [ $i -gt 1 ]
then
echo -n " " >> $TMPFILE
fi
TMP=`echo "scale=4; $TMP" | bc -l`
echo -n $TMP >> $TMPFILE
# stddev
echo -n " " >> $TMPFILE
TMP="sqrt(($ROWCOUNT * ("`echo $COL | sed s/" "/"^2+"/g | sed s/$/"^2"/g`") - ("`echo $COL | sed s/" "/"+"/g`")^2) / ($ROWCOUNT * ($ROWCOUNT - 1)))"
TMP=`echo "scale=4; $TMP" | bc -l`
echo -n $TMP >> $TMPFILE
done
echo >> $TMPFILE
cp $TMPFILE $OUTPUT
fi
# add x-axis?
if [ "$XAXIS" = "yes" ]
then
cat $OUTPUT | grep -n "." | sed s/":"/" "/g > $TMPFILE
cp $TMPFILE $OUTPUT
fi
# gnuplot script?
if [ "$HAS_GNUPLOT" = "yes" ]
then
# data columns
COUNT=`head -n1 $OUTPUT | wc -w | sed s/" "*//g`
# build output/format statement
TERM="set terminal X11"
OUT="set output"
if [ "$FORMAT" = "png" ]
then
TERM="set terminal png size $WIDTH,$HEIGHT"
OUT="set output \"$OUTPUT_PLOT\""
fi
if [ "$FORMAT" = "ps" ]
then
TERM="set terminal postscript"
OUT="set output \"$OUTPUT_PLOT\""
fi
# build "with" statement
TMP=""
WITH=""
if [ "$LINES" = "yes" ]
then
TMP=$TMP" lines"
fi
if [ "$TITLE" = "yes" ]
then
TMP=$TMP" title #"
fi
if [ ! "$TMP" = "" ]
then
WITH=" with"$TMP
fi
# init
echo "# gnuplot script for '$OUTPUT'" > $GNUPLOT
if [ ! "$GNUPLOT_OPTIONS" = "" ]
then
cat $GNUPLOT_OPTIONS >> $GNUPLOT
fi
# the plots
echo "plot \"$OUTPUT\" using 1:2 `echo $WITH | sed s/"#"/"\'1\'"/g`" >> $GNUPLOT
for ((i = 2; i < $COUNT; i++))
do
echo "replot \"$OUTPUT\" using 1:$((i+1)) `echo $WITH | sed s/"#"/"\'$i\'"/g`" >> $GNUPLOT
done
echo >> $GNUPLOT
# only pause if displayed in window
if [ "$FORMAT" = "x11" ]
then
echo "pause -1" >> $GNUPLOT
else
echo "$TERM" >> $GNUPLOT
echo "$OUT" >> $GNUPLOT
echo "replot" >> $GNUPLOT
fi
# run gnuplot
if [ "$EXECUTE" = "yes" ]
then
if [ "$FORMAT" = "x11" ]
then
echo "Press <Return> to close window..."
fi
gnuplot "$GNUPLOT"
fi
fi
# clean up
rm -f $TMPFILE
if [ "$HAS_OUTPUT" = "no" ]
then
cat $OUTPUT
rm -f $OUTPUT
fi
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