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[Gnuplot-info] 回?: 回?: 回?: 回?: system command in gnuplot
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From: <qin...@st...> - 2020-12-30 16:41:37
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I added the command system("chmod +x myscript.sh ") in gnuplot script.
It indeed makes myscript.sh become executable.
But the variable passing (index of loop k) is still not successful. And I have another worry that $1 in awk command means the first column of data file.
The gnuplot script is
system("chmod +x myscript.sh ")
system("bash -c ./myscript.sh ".sprintf("%.1f", k))
plot for [k= 1: 20: 1] "< bash ./myscript.sh" u 1:2
the myscript.sh is
paste <(cat Q_byE_i*.txt) <(cat Q_byM_i*.txt)|awk -v vtime=$1 ' {if($1==vtime*1.0) { e[$3] += $4; m[$3] += $9}} END { for ( i in e) { print i , e[i], m[i], vtime}}' h is
For your convenience to test. I share some data file with you through the OneDrive link as follow.
https://stkyotouac-my.sharepoint.com/:u:/g/personal/qin_zhihao_87m_st_kyoto-u_ac_jp/EbyAJ0_82mlMu_4bnTYK0m4B2fl1Yw7UIPju3tOVsQq_9Q?e=VJcgTW
****************************************************
秦志豪
京都大学大学院 エネルギー科学研究科
エネルギー基礎科学専攻 プラズマ・核融合基礎学分野
岸本研究室
E-mail : qin...@st...
****************************************************
?件人: Andrew Rasmussen<mailto:an...@gm...>
?送??: 2020年12月30日 22:51
收件人: qin...@st...<mailto:qin...@st...>
抄送: gnu...@li...<mailto:gnu...@li...>
主?: Re: 回?: 回?: 回?: [Gnuplot-info] system command in gnuplot
Without testing (I might have time later), there are two things that look like they need to be fixed:
1. in order for "./myscript.sh" not to have the 'Permission denied' error, it needs to be executable. You can do this on the command line with> chmod +x myscript.sh
2. When a bash script takes command line arguments, they have the names $1, $2, etc. So, you might have to change $k to $1.
Andy
On Wed, Dec 30, 2020 at 2:29 AM qin...@st...<mailto:qin...@st...> <qin...@st...<mailto:qin...@st...>> wrote:
Thanks for your answer.
But there are some other problems.
When I do
>system("bash -c ./myscript.sh ".sprintf("%.1f", k))
An error appears : nan: ./myscript.sh: : Permission denied
I modified the command as system("/bin/bash combine.sh ".sprintf("%.1f", k))
The script is executed. However, not only passing the variable k, the whole script is executed.
What I want is that executing the
plot for [k= 1: 20: 1] "< bash ./myscript.sh" u 1:2
the index of loop k can be paased into the script as a variable (the red parameter as follow).
The code in the script is
paste <(cat Q_byE_i*.txt) <(cat Q_byM_i*.txt)|awk -v vtime=$k ' {if($1==vtime*1.0) { e[$3] += $4; m[$3] += $9}} END { for ( i in e) { print i , e[i], m[i], vtime}}'
For your convenience to test, I send you some data files。
****************************************************
秦志豪
京都大学大学院 エネルギー科学研究科
エネルギー基礎科学専攻 プラズマ・核融合基礎学分野
岸本研究室
E-mail : qin...@st...<mailto:qin...@st...>
****************************************************
?件人: Andrew Rasmussen<mailto:an...@gm...>
?送??: 2020年12月30日 5:32
收件人: qin...@st...<mailto:qin...@st...>
抄送: gnu...@li...<mailto:gnu...@li...>
主?: Re: 回?: 回?: [Gnuplot-info] system command in gnuplot
You can definitely pass arguments to a bash script. In the script, you use the arguments as variables $1, $2, etc. (Reference example: https://www.golinuxcloud.com/beginners-guide-to-use-script-arguments-in-bash-with-examples/).
It will take some fiddling to construct the command in gnuplot, but if the variables are var1 and var2 for example, you can do it like this:
> system("bash -c ./myscript.sh ".var1." ".var2)
The '.' concatenates the string variables. If var1 or var2 is a number like 16.0 instead of a string "16.0", you might have to do something like the below with sprintf to get it to turn into a string correctly:
> system("bash -c ./myscript.sh ".var1." ".sprintf("%.1f", var2))
Andy
On Tue, Dec 29, 2020 at 12:48 AM qin...@st...<mailto:qin...@st...> <qin...@st...<mailto:qin...@st...>> wrote:
Dear Andy
As your advice, we can reduce syntax / escape errors by put the paste / awk script in a separate file ("myscript.sh").
Then call it from inside gnuplot as plot "< bash ./myscript.sh"
But if the data file name (Q_byE_i*.txt) is a string variable and “16.0” of “if($1==16.0” in awk part is also a variable,
How can I pass these variables from gnuplot into myscript.sh.
Because I'm not very familiar with linux, my questions might be very basic or stupid.
please forgive me.
****************************************************
秦志豪
京都大学大学院 エネルギー科学研究科
エネルギー基礎科学専攻 プラズマ・核融合基礎学分野
岸本研究室
E-mail : qin...@st...<mailto:qin...@st...>
****************************************************
?件人: Andrew Rasmussen<mailto:an...@gm...>
?送??: 2020年12月29日 1:13
收件人: qin...@st...<mailto:qin...@st...>
抄送: gnu...@li...<mailto:gnu...@li...>
主?: Re: 回?: [Gnuplot-info] system command in gnuplot
Yes, you should be able to make a similar modification, something like:
plot "< bash -c 'paste <(cat Q_byE_i*.txt) <(cat Q_byM_i*.txt)|awk \'{if($1==16.0) { e[$3] += $4 }}END { for ( i in e) { print i , e[i]}}\''"
I can't test it out, so you might have to escape some additional characters (* etc.).
When you are using a command that is this complicated, a way to simplify things and reduce syntax / escape errors is to put the paste / awk script in a separate file ("myscript.sh") and call that script from inside gnuplot:
plot "< bash ./myscript.sh"
Andy
On Mon, Dec 28, 2020 at 9:31 AM qin...@st...<mailto:qin...@st...> <qin...@st...<mailto:qin...@st...>> wrote:
Dear Andy
Thank you very much.
It worked. But I have another question.
In fact, I tried to merge some data files, then plot a graph.
The code is
plot "< paste <(cat Q_byE_i*.txt) <(cat Q_byM_i*.txt)|awk '{if($1==16.0) { e[$3] += $4 }}END { for ( i in e) { print i , e[i]}}'" u 1:2
The latter part of code about ‘awk’, I think there is no problem. Could I modify the code as the system("bash -c 'paste <(ls Q*) <(ls F*)'")?
Qin
****************************************************
秦志豪
京都大学大学院 エネルギー科学研究科
エネルギー基礎科学専攻 プラズマ・核融合基礎学分野
岸本研究室
E-mail : qin...@st...<mailto:qin...@st...>
****************************************************
?件人: Andrew Rasmussen<mailto:an...@gm...>
?送??: 2020年12月28日 23:57
收件人: qin...@st...<mailto:qin...@st...>
抄送: gnu...@li...<mailto:gnu...@li...>
主?: Re: [Gnuplot-info] system command in gnuplot
Hello,
Your error comes from the fact that gnuplot is running the system command using the sh shell instead of bash (or whatever your usual shell is). You can get the command to be interpreted by bash like this:
system("bash -c 'paste <(ls Q*) <(ls F*)'")
Andy
On Mon, Dec 28, 2020 at 4:11 AM qin...@st...<mailto:qin...@st...> <qin...@st...<mailto:qin...@st...>> wrote:
Hello
Now I am using gnuplot (Version 5.2 patchlevel 6) on a Linux system.
The information of operating system as follow
Linux version 4.4.162-94.72-default (geeko@buildhost) (gcc version 4.8.5 (SUSE Linux) )
LSB Version: n/a
Distributor ID: SUSE
Description: SUSE Linux Enterprise Server 12 SP3
Release: 12.3
Codename: n/a
My question:
I am trying to launch a system command in gnuplot like
Terminal type is now 'qt'
gnuplot> system(" paste <(ls Q*) <(ls F*)")
show me the error message as
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: ` paste <(ls Q*) <(ls F*)'
But if I exit the gnuplot and run the command, it can work.
qin@csc1:~/qin /txt> paste <(ls Q*) <(ls F*)
any help would be much appreciated
have a nice day
****************************************************
秦志豪
京都大学大学院 エネルギー科学研究科
エネルギー基礎科学専攻 プラズマ・核融合基礎学分野
岸本研究室
E-mail : qin...@st...<mailto:qin...@st...>
****************************************************
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