gnuplot.log

Jerri Hopefully everybody here is using linux and has an installed version of gnuplot on his harddrive. Jerri gnuplot is also available for windows and most of the things we will discuss today will also be possible with windows. So just try it. Jerri I will only give you a small outline about creating simple plots with gnuplot. Jerri From there on try to learn more yourself. The gnuplot help-system is rather good and will give you also a lot of examples. Jerri Now, everybody ready? sundance yupppppppp ticallion :) Jerri Fine. So lets start Jerri Later on we will need some data for a very interesting application of gnuplot. Jerri To gather this data please download the following script from -!- maestro [mathias@adsl-97-199-zh1.tiscali.ch] has joined #gnuplot Angus_Young yep :) Jerri http://jerri.hopto.org/gather_load.sh.txt Jerri Rename to gather_load.sh desaster 404 -!- nox5000 [~nox5000@200.84.181.151] has quit ["gtkBitchX-1.0c19 -- just do it."] ticallion howto instead of hopto tarzeau forbidden ticallion oops, sorry Jerri Damn. One moment please. Jerri OK. Jerri http://jerri.hopto.org/gnuplot/gather_load.sh.txt Jerri Sorry -!- nox5000 [~nox5000@200.84.181.151] has joined #gnuplot Jerri All of the following files will be found there. Jerri Hello nox5000 nox5000 :) Jerri Later on we will need some data for a very interesting application of gnuplot. Jerri To gather this data please download the following script from Jerri http://jerri.hopto.org/gnuplot/gather_load.sh.txt Jerri Rename to gather_load.sh Jerri Take a look into it. It just gets the current date and the current load and output them. Jerri Now in one window lets start this script and save the output to load.data Jerri sh gather_load.sh | tee load.data -!- decaf [~mehmed@abn198-126.izmir-ports.kablonet.net.tr] has quit [Read error: 60 (Operation timed out)] Jerri Please do so now. I how you see a lot of number appearing. Jerri how=hope Jerri Now let this run while we start with the course. Jerri lets start with our first plot. Jerri - Plot a graph Jerri Start gnuplot in an xterm. You will see a prompt like "gnuplot> ". Now enter Jerri plot sin(x) Jerri Congratulations. You created a plot of the sinus-function in a new x-window. gnuplot normally plots graph with x running through a range and plotting the result of a function on x. Jerri Hopefully everybody sees this. If something goes wrong please say so! Jerri in our plot x-axis goes from -10 to 10. y-axis goes from -1 to 1. Jerri If you don't specify the ranges for the axis' gnuplot tries to plot the whole graph into the window. Jerri Lets change the xrangee to see one period of the sinus Jerri set xrange [0:6.282] Jerri replot Jerri replot plots the functions you last specified with the plot command. Jerri Everything ok till now? ticallion Jerri: great here Jerri If you need help with one of the commands for gnuplot or a summary of commands, use the help command. Try for example Jerri help replot Jerri or do a "help help" to get information about the help system. Jerri To get out of help just enter return till you again see the gnuplot-prompt. Jerri Now if you want to compare the sinus and the cosinus you would plot both graphs in on window. Lets do it Jerri plot sin(x), cos(x) Jerri You now see two plots in one window. Angus_Young so x is in radians? Jerri Angus: Yes. sin and cos are the normal c-functions, which get x in radians. Jerri - Change some properties of the plot Jerri If you want to get some numbers out of this plot it would be nice to have a grid. Just enter Jerri set grid Jerri replot Jerri and your plot is better to read. Jerri gnuplot normally magically gets the correct number of gridlines. Jerri If you want more or less tics (gridlines) on the axis' you use xtics or ytics. Jerri Lets for example put the gridlines on the yaxis on pi and pi/2. Jerri set xtics 3.141/2 Jerri As you can see everywhere you can enter a number, you also can enter a term. Jerri For more information about tics do help xtics. Do so also with other settings or commands I may bring up. But not now. nox5000 set xtics 3.141/2 Jerri Save this for later reading... :) nox5000 oops sorry Jerri :) Jerri Now to nice up the plot how about some headline and titles for the axis'. Jerri set title "My first plot" Jerri set xlabel "x" Jerri set ylabel "f(x)" Jerri replot Jerri I hope you all see a nice plot now. Jerri Output the plot for further use Jerri We will now take this nice plot and output it to a file. Jerri gnuplot knows a lot of filetypes. To see them do Jerri help terminal Jerri Do this now! Jerri At the bottom of this helppage you see the filetypes, your gnuplot can output. Jerri Please check if your gnuplot-version can output png Jerri Normally it can. If not, please tell me now! oktay this is not like Excel at all.. lol -!- A_Young [~joepublic@203.134.130.12] has quit [Read error: 110 (Connection timed out)] Jerri It isn't! :-) But you will see later you have great opportunties with this tool. Jerri To output the active plot to a png file please enter the following commands Jerri set terminal png Jerri set output "myfirstplot.png" Jerri replot Jerri Now nothing was output to the X-window. Jerri Open up another terminal and check if there is a new file in the directory you started gnuplot from. There should be a new file "myfirstplot.png". Jerri Use for example display from the image magick kit to display that graph. Jerri You might see, that the output to the png doesn't look exactly like the x-window-output. This is normal. gnuplot optimizes the output for the given terminal. Jerri If you want to continue using gnuplot after changing the terminal to a file enter: Jerri set terminal X11 Jerri The your output goes again to the xwindow. Jerri The = Then Jerri Everybody saw this picture? Jerri It should look like this one ticallion Jerri: uhuh Angus_Young hmm the file is 0 bytes Jerri http://jerri.hopto.org/gnuplot/myfirstplot-auto.png tarzeau Angus_Young: same here Jerri Oh... Jerri Mhm. Angus_Young damn this debian ;) oktay You might not have the PNG libraries on your systems Jerri You didn't restart gnuplot, did you? desaster it worked here fine (debian woody) Angus_Young no didn't restart it .. the x11 window still displays the graph and so on nox5000 yes it worked oktay Angus_Young~: debian? ticallion worked here also Angus_Young hmm .. walkd and here Jerri Mhm. Maybe you forget to set the terminal. Any warnings? Jerri set terminal png Jerri set output "myfirstplot.png" Jerri replot Jerri Please try again. tarzeau worked now Jerri Angus? maxy debian, and it worked for me... Angus_Young still 0 bytes maxy most likely you forgot replot...? Angus_Young i have libpng runtimes installed Angus_Young no i did the replot desaster perhaps try postscript? Jerri Three command lines. nox5000 im also using woody ;) tarzeau i've got sid/i386 here Angus_Young hmm .. even tried deleting it .. i will try postscript Jerri desaster: We will do postscript later on. Maybe Angus just ignore for now and we will go on. oktay tarzeau~: do you have png devel packages installed ? oktay maybe that's what Angus_Young needs tarzeau oktay: no you need -dev packages only for compiling/developing things tarzeau oktay: no that's not it oktay ok Angus_Young mm the .ps file is also 0 bytes tarzeau Angus_Young: df -h ? enough space? tarzeau Angus_Young: i've had permission denied where i wanted to plot... Jerri This is strange. You seem to have a problem with your system. Angus_Young bizarre .. i can't see the reason Angus_Young ah Angus_Young "This document may describe drivers that are not available to you because they Angus_Young were not installed" Angus_Young maybe there is another gnuplot package ofr output drivers? Jerri Lets take a look later on and just go on with the course. Saving the plot is not that necessary for this course. Angus_Young anyway, continue with the lesson if you like .. i'll try to figure it out and watch at the same time ;) Jerri Fine. Jerri Using gnuplot as a filter Jerri gnuplot is able to read the commands also from stdin. Jerri So you could have entered all of the commands line by line into a file and pipe that file to gnuplot. Jerri Please quit from gnuplot now with the command quit. Jerri Download the following file from Jerri http://jerri.hopto.org/gnuplot/myfirstplot.plot Jerri take a look inside and pipe it to gnuplot. Jerri cat myfirstplot.plot | gnuplot Jerri It will create the file myfirstplot-auto.png and then exit. Jerri Angus: Sorry, but for you it will create a zero sized file. Jerri Nevertheless: You would get this output Jerri http://jerri.hopto.org/gnuplot/myfirstplot-auto.png Jerri You can also load that file at the gnuplot prompt with tarzeau you can also have a file executable with this in the first line: #!/usr/bin/gnuplot Jerri load "myfirstplot.plot" Jerri It will do the same as piping it in. Jerri You can use the save command to save all of your current settings and the last plot command to a file. Take a look at "help save" to get further informations. Angus_Young heh yay the file contains data this time :) Jerri btw: Just for the curious. gnuplot also can plot 3d-surfaces. oktay Jerri~: these are allwhile inside the gnuplot shell right? Jerri Cool :-) tarzeau Jerri: surfaces too? tarzeau Jerri: not just wires? Jerri load "mz..." yes. nox5000 :) Jerri Both tarzeau. But not very nice. Jerri Just as an example, restart gnuplot Jerri And then do Jerri splot sin(x)*cos(y) Jerri (for further information do "help splot") Jerri If you want to get a hiddenline plot, add Jerri set hidden3d Jerri replot -!- decaf [~mehmedk@adsluser-2562.adsl.ttnet.net.tr] has joined #gnuplot Jerri But we would have to set a lot more settings to get a really nice picture. Please use the help system to get further information. Jerri Scientific Use Jerri This might get a little bit complicated. So ask if you have questions. Jerri gnuplot was specifically build to output data to a graph and put that into your work. Jerri We will now use some data, plot that into a graph, fit a function to the data and output all of it to a postscript-file. Jerri First please load the datafile we will use from the following url tarzeau try splot sin(x/5)*cos(y/6) Jerri http://jerri.hopto.org/gnuplot/scientific.data Jerri and take a look at it. Consider we did an experiment and saved the data for Jerri x and y and the errors we think we did during measurement in both directions, meaning: Jerri x y dx dy Jerri We will now get some information about this data and some specific parameters. Jerri (btw: I created this data using a small perl-script. So it's not really scientific data.. :-) Jerri - Plotting data Jerri First restart gnuplot and let us plot just the position of the points in the dataset: Jerri plot 'scientific.data' Jerri gnuplot reads the data from the file and uses the first two rows to create the plot. Jerri Does everybody see this plot now? Angus_Young :) Jerri we can be even more specific and tell gnuplot to use the first and the second row to plot the graph via Jerri plot 'scientific.data' using 1:2 Jerri you can see this seems to be a gaussian curve based around 4. Lets connect the dots ticallion Jerri: just tried out succesfully tab-completion on the filename, very cool Jerri plot 'scientific.data' using 1:2 with lines Jerri Yeah. Gnuplot normally uses the readline-library and does nearly the same as the bash-shell. Angus_Young ticallion: which version do you have? did you need a special setting for tab completion? Jerri Please be aware, that the order of the options to plot are important. The following won't work ticallion Angus_Young: nope Angus_Young doh ticallion Angus_Young: 3.7.2 Jerri Angus: It has to be compiled with readline-library. Jerri Please be aware, that the order of the options to plot are important. The following won't work Jerri plot 'scientific.data' with lines using 1:2 Jerri Errors Jerri Now lets use that extra data in the 3rd and 4th row to output some errorbars Jerri plot 'scientific.data' using 1:2:3:4 with xyerrorbars Jerri If you just want to see the yerrorbars try Jerri plot 'scientific.data' using 1:2:4 with yerrorbars Jerri Taking a look on the data we can assume that we here have some sort of gaussian data. So we might be interested in the sharpness, position and altitude of the peak. Jerri So lets try to put a gaussian curve through this data. We begin by defining the function. Enter the following at the gnuplot prompt: Jerri gauss(x)=altitude/exp((sharpness*(x-position))**2) Jerri We can guess the parameters using the plot. So enter: -!- decaf [~mehmedk@adsluser-2562.adsl.ttnet.net.tr] has left #gnuplot [] Jerri altitude=4.1 position=6.9 Jerri sharpness=1.5 Jerri This are three lines! Jerri Now plot data and our guessed curve. Jerri plot 'scientific.data' using 1:2:4 with yerrorbars, gauss(x) Jerri You should see now the datapoints and a curve going through them. Jerri More or less. Jerri Lets redefine our guesses: Jerri altitude=4.2 Jerri position=6.7 Jerri sharpness=1.0 Jerri and replot Jerri replot Jerri This is better, but not good enough. We now could readjust and replot time after time and check if we already got the correct parameters. Jerri Better yet: Let the computer do the work. gnuplot is able to fit curves to given data and present you with the necessary parameters. Jerri Fitting Jerri As we already defined the curve and also gave some good guessed parameter to begin with just start the fit-routine Jerri fit gauss(x) 'scientific.data' using 1:2:4 via altitude, position, sharpness Jerri This tells gnuplot to fit the curve to the data by variing the given parameters. Jerri After some iterations you get the "Final set of parameters" for your parameters and some Standard Error. Jerri The fit-Routine already set the parameters to the optimal values, so now just replot data and curve. Jerri replot Jerri And voila. Perfect fit. :) Jerri Did it work for everybody? ticallion nice! Angus_Young voila! Jerri For further information about fit take a look at "help fit". Jerri If you consider using the fitting-routine from gnuplot for scientific work you even should take a look at some books which describe the fitting algorithmus gnuplot uses: nonlinear least-squares (NLLS) Marquardt-Levenberg algorithm. Jerri Without that knowledge you don't really know what the errors mean you are presented by gnuplot. Jerri Furthermore the fitting-routine doesn't work with all functions equally good. Sometimes the algorithm doesn't converge. Jerri Output the graph for your work Jerri Now lets create a graph which presents our results and helps understanding your work... :) Jerri First we don't want to see the reader which file we used for this data, but which data he sees on our graph: Jerri plot 'scientific.data' using 1:2:4 title 'measured data' with yerrorbars, gauss(x) title 'guessed curve' Jerri Now lets show where the peak exactly is. We will draw an arrow showing the peak of the measured data. Jerri set arrow 1 from position,2 to position,gauss(position) Jerri replot Jerri Here we define an arrow with the number 1 pointing from position,2 to the peak of the curve. Lets write "Peak" at the beginning of the arrow: Jerri set label 1 "Peak" at position,2-0.1 center Jerri replot Jerri Now lets draw some lines showing the border of the gauss-peak by defining two arrows without head. Jerri set arrow 2 from position-1/sharpness, graph 0 to position-1/sharpness, graph 1 nohead Jerri set arrow 3 from position+1/sharpness, graph 0 to position+1/sharpness, graph 1 nohead Jerri replot Jerri The first number in the arrow definition is sort of a name for the arrow. You can edit the endings of the arrow by using the same id in a new set command. Jerri Another thing: You can refer to a point on the graph with several different coordinate-systems. For the two arrows above I used graph-coordinates, which start at 0,0 on the left,lower corner and go to 1,1 in the right, upper corner. Jerri More info about coordinate-systems for arrow and label can be found using Jerri help coordinates Jerri Now set a title for this graph Jerri set title "My scientific graph" Jerri and output this graph to a postscript file Jerri set terminal postscript color Jerri set output "scientific.ps" Jerri replot Jerri Us gv (or another postscript-view) or just pipe the postscript-file to a postscript printer and admire your wonderful scientific graph. -!- walkd [~walkd@host81-132-91-174.in-addr.btopenworld.com] has left #gnuplot [] Jerri Hopefully everybody could follow and see this graph on his display. Jerri Now lets leave the scientific use and go on to some geek use of gnuplot. :) Jerri Not so scientific Use Jerri Output data over time (with simple script, e.g. load average) Jerri Do you remember the script we started at the beginning. Now we will take a look at this data. Jerri Don't stop the script. Just go to the directory you started this script in. Jerri If you take a look at the data, this time x is a date. So gnuplot has to interpret the first two rows as a date and a time. Jerri Lets tell gnuplot to interpret the time correctly. Restart gnuplot in the directory you started the script where the datafile lies. Jerri Now enter Jerri set xdata time Jerri set timefmt "%Y.%m.%d %H:%M:%S" Jerri This tells gnuplot that your x-coordinate is of timeformat and how it looks like. Jerri Now plot the data Jerri plot 'load.data' using 1:3 title "Load Avg" with lines tarzeau could i also use unix time (date +%s) ? Jerri Note that we used 1:3. This is necessary as gnuplot will interpret the 1st and 2nd row as a date and time. But our load is in the third row. Jerri tarzeau: Sure, but you wouldn't get nice labels on the axis. ticallion Jerri: very nice Jerri Try and see. Jerri Again: Using gnuplot as filter Jerri Now lets use gnuplot to create a onthefly graph of the current load on the system. Jerri Download the following gnuplot-File. Jerri http://jerri.hopto.org/gnuplot/show_load.plot Jerri It contains the same commands as we just did, with a size-setting and png as output-terminal. Jerri Note that we didn't give gnuplot a filename with output. This tells gnuplot to output the graph to stdout. Now at an normal bash-prompt do the following Jerri cat show_load.plot | gnuplot | display - Jerri Hopefully you all have image magick installed. Jerri We just created an onthefly-picture with gnuplot which wasn't saved to disk. Jerri To save this png to disk just do Jerri cat show_load.plot | gnuplot > myload.png Jerri Using other commands in a gnuplot-script Jerri Just for your information: Jerri You can do things like Jerri plot "<cat scientific.data" using 1:2 with lines Jerri Meaning gnuplot starts a command to output the lines and takes these lines to get the data for the graph. Jerri Even s.th. like this is possible Jerri plot "<echo 'select data1,data2 from table' | mysql data | head +2" using 1:2 with lines Jerri Don't try it, it's just an example. Jerri which means you can create a plot with data from a database on the fly. Jerri Do "help plot special-filenames" to get more information. Jerri We come near the end now. One last thing to show you: Jerri Output as graph for e.g. website Jerri Consider this an exercise for the reader. Download Jerri http://jerri.hopto.org/gnuplot/show_load.cgi.txt Jerri and take a look at the script. It shows you in principle how you can create graphs on the fly to show on a webpage. Rename from show_load.cgi.txt to show_load.cgi. Jerri Well. I hope you did get a small insight into using gnuplot. Now use the really good help system from gnuplot and go further. tarzeau one moment Jerri Questions: tarzeau there's bezier curves i found out lately and colors and multiple curves! -!- sundance [~Dervish@ist00510.ultranet.com.tr] has quit ["Client Exiting"] Jerri Well. Ask. tarzeau see http://apt-get.mine.nu/woody-o-meter/ for those interested tarzeau Jerri: i have the datafiles just one number each line, how could i add dates to the plots? tarzeau the data is filled once daily, i would like a date for each day back to when i started oktay Jerri~: Thanks. This was a pretty good introduction to gnuplot. ticallion Jerri: question... ticallion lemme backtrack a bit, there was no difference between "plot 'scientific.data' using 1:2" and "plot 'scientific.data'" tarzeau can i have comments in datafiles? Jerri tarzeau: Show me the data. I don't understand. ticallion Jerri: at the beginning of the tutorial tarzeau Jerri: i have at the same url base.dat std.dat and total.dat Jerri ticallion: Yes. Normally gnuplot uses 1 and 2. But you can have a file with several rows and then can define to plot 1 and 4 with Jerri using 1:4 ticallion Jerri: understood Jerri tarzeau: Which url? Jerri ticallion: So you can output all of your data to one file and do several different plots from it. tarzeau Jerri: http://apt-get.mine.nu/woody-o-meter/ ticallion Jerri: i get it :) Angus_Young thanks jerri - it made learning a complex tool very easy :) nox5000 :) Jerri I hope I was of some help. Thanks too -!- oktay [~foo@ool-4353c8e6.dyn.optonline.net] has quit ["Lost terminal"] Angus_Young something i would never have tried in fact on my own .. i would probably try to write a custom perl script for each case instead of learnign a useful tool Jerri :) Who doesn't ticallion Jerri: very nice, gnuplot used to scare me, needed to use it at one point for plotting tc qdisc usage... gave up on it, I'm ready to give it another go, am sure it'll go smoothly with some "help bla" in gnuplot ticallion :))) ticallion tarzeau: when will the blog be online?! tarzeau ticallion: soon after these questions Angus_Young tarzeau: did you restart gnuplot before it wrote the output file before? i think that is what fixed it for me .. perhaps there is a small bug that it won't write output files the first time it runs ticallion tarzeau: very nice, thank u for advertizing this :) tarzeau Jerri: thank you! that .cgi and |display - were nice tricks i've never used that way Jerri tarzeau: How often do you get the data. I think you have to change the routine which creates the data to do something like my gather_load.sh script. tarzeau Jerri: every morning (daily) tarzeau i would've liked thicker curves/lines but that doesn't seem to work with png but fine with postscript output Jerri Mhm. You have to change your script to get it. Can't help there now. tarzeau Jerri: ok now that i know how :) Jerri tarzeau: Yeah. Unfortunatelly gnuplot has some drawbacks. But most of the time its a great tool. tarzeau plot "your.dat" smooth bezier with lines tarzeau Jerri: you probably know smooth bezier , don't you? Jerri tarzeau: Sure. But it's not one of the nicest things in gnuplot. Jerri It doesn't really work with a lot of datapoints. -!- michael [michael@bakker.li] has left #gnuplot [] Jerri Its rather slow and hides peaks really good. Jerri So I only use it sometimes. Angus_Young bezier is not a scientific way of fitting data .. it's just a way of making nice curves that look pretty :) tarzeau i've never claimed something else :) Jerri Angus: Right. Thats what I wanted to say... :) Jerri So, any more questions regarding gnuplot? ticallion Jerri: none, ur coverage was very easy to swallow :) tarzeau it was very fresh, not too slow, not too fast, not boring either! thank you Jerri Well. So I thank you all very much for participating and wish you a good evening (or night, or what ever... :-) Angus_Young is the windows version good? i am just curious .. maybe some day i would be trapped at work and need to make a graph or something ;) nox5000 jajajaja :) Angus_Young ta night :) Jerri Angus: It works like the linux gnuplot version.. Angus_Young good :) nox5000 bye... :) Generated by irclog2html.pl 2.1 by Jeff Waugh - find it at freshmeat.net!