I have 500 files to plot and I want to do this automatically. I have the gnuplot script that does the plotting with the file name hard coded. I would like to have a loop that calls gnuplot every iteration with a different file name, but it does not seem that gnuplot support command line arguments.
Is there an easy way? I also installed the gnuplot-python package in case I can do it via a python script.However, I couldn't find the api so it's a bit difficult to figure out.
Thank you!
You can transform your gnuplot script to a shell script by prepending the lines
#!/bin/sh
gnuplot << EOF
appending the line
EOF
and substituting every $ by \$. Then, you can substitute every occurence of the filename by $1 and call the shell script with the filename as parameter.
Regarding the $'s in Sven Marnach's solution (the lines between EOF are called a "here script" in shell parlance): in my experience, one uses shell variables as usual, but $s that are meant for gnuplot itself must be escaped.
Here is an example:
for distrib in "uniform" "correlated" "clustered"
do
gnuplot << EOF
# gnuplot preamble omitted for brevity
set output "../plots/$distrib-$eps-$points.pdf"
set title "$distrib distribution, eps = $eps, #points = $points"
plot "../plots/dat/$distrib-$eps-$points.dat" using 1:(\$2/$points) title "exact NN"
EOF
done
Note the backslash escaping the dollar so that gnuplot sees it.
A simple way is to generate 500 gnuplot scripts like so:
for filename in list_of_files:
outfile = open(filename + '-script', 'w')
outfile.write(script_text % (filename,))
where script_text is the text of your gnuplot script with the filename replaced with a %s.
I've done this some times. But don't use EOF, because you cannot write on bash inside the << EOF and EOF tags. Depending on the names of the files you can do it in diferent ways.
a) If the filenames are loopable (sort of 1.dat 2.dat 3.dat, etc.)
#!/bin/bash
for((i=0;i<1;i++)) do
echo "plot '-' u 1:2"
for((j=1;j<=3;j++)) do
cat $i.dat
echo "e"
done
done | gnuplot -persist
The first loop is a kind of buffer to feed it all to gnuplot.
b) If the filenames aren't loopable (such as ñlasjkd.dat ajñljd.mov añlsjkd.gif) you first need to move them to a new folder. Then do
#!/bin/bash
ffiles=$(ls | xargs) # a list of the folder's files
# Use the list to pipe all the data to gnuplot using cat
for((i=0;i<1;i++)) do
echo "plot '-' u 1:2 w lp";
cat $ffiles;
echo "e";
done | gnuplot -persist
c) If you want some more, that is: to keep the information of the separated files just on one file... but maintaning the datasheets alive use "index" of gnuplot (if gnuplot reads two black lines guesses that is another datasheet)
#!/bin/bash
ffiles=$(ls|xargs)
ls $ffiles > ffiles.list # A file with the folder's files
while read line
do
cat $line;
echo -e; echo -e;
done < ffiles.list > alldata.dat
# ^-feeding ffiles.list to the while loop
# and writing the file alldata.dat
now you can go to gnuplot and acces to one datasheet
plot 'alldata.dat' index 1 u 1:2
and you will see the first file appearing on the list "ffiles.list". If you whant to see more than one, say 4
plot 'alldata.dat' index 1:4 u 1:2
tricky but easy.
Unless I'm misunderstanding your question, there's an easier way.
In the gnuplot script, replace all occurrences of your filename with $0.
Then in bash, loop over your plot files (let's say they are .txt files in $plotsDir) and call gnuplot:
for f in "$plotsDir/*.txt"; do
echo "call '$f'" | gnuplot
done
Here is one way to do this. Your gnuplot input file, say plot.gp, contains a line
plot "data"
or something like that. Save the lines before this line in plot1.gp and the lines after this line in plot2.gp. Now call gnuplot as
gnuplot plot1.gp -e `plot "data"` plot2.gp
which facilitates passing the name of data on the command line.
I create a file named test.txt containing plot [0:20] x;
I run gnuplot test.txt and I see that gnuplot has indeed read contents of my file, so it does support arguments at runtime.
Different methods of solving this problem are also covered in How to pass command line argument to gnuplot? :
-e-c or call with ARG0 like variables (gnuplot >= 5)call with $0 like variables (gnuplot <= 4.6.6)system()