Is there a way to copy plots in NetLogo? I need a relatively large number of plots in the interface tab that have similar code. Creating and adjusting these plots will take time. Is it possible to copy the plots in the interface tab?
Is there a way to copy plots in NetLogo?
Not from within the graphical interface, but you can copy plots and pens by opening your model's nlogo file in a normal text editor. Here are the docs for the format, and here is the section on plot widgets in particular. Here is an example plot as defined in the Wolf Sheep Predation model.
You can just copy/paste an existing plot widget in this way, or even the PENS, each is on their own line. I recommend being very careful if you do this - making sure you maintain blank spaces between widgets, the escape slashes \" for double-quotes in code, and the exact format of the PLOT sections. I'd take regular back-ups of your file and test your changes frequently as you work in case an edit goes wrong.
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I'm working on generating some figures for a paper from a simulink model, and would prefer to use minimal work to produce them so I'm trying to configure a simulink scope to output the figures I want on its own. The problem is, while I can get colors and such all arranged well, I can't seem to figure out how to modify the spacing between the graphs in a scope showing multiple signals. What I have now looks like the below:
Notice how the two plots have different vertical scales (probably a consequence of having the time scale only on the bottom one), and that there's a large gap of unused space between the plots. This is a concern when trying to publish in a journal, since page space is at a premium and we need to make the information as dense as possible.
So, how can I tweak these margins and formatting? I've tried looking at all the settings I can find, but none seem to affect these parameters.
I need some to produce some publication-quality figures. I first export the figures from matlab in .svg format, and then I do some post-processing in inkscape. I am no problem with figures generated using plot or scatter, but when I export figures generated using surf (in view(2)), I run into problems. If I use plot or scatter, I am able to ungroup and process various parts like the title, axes, scattered points, lines, etc. in inkscape. For surf, however, matlab just exports one single figures with all various parts grouped into one single unit. I can't separate individual part, and when I zoom very close I can actually see the bitmap resolution for the axes and titles (if I use plot, the titles and axes have 'infinite' resolution when I zoom very close). I am fine with the surface plot having finite resolution, but I need to at least be able to process the axes and titles (which I currently cannot do). What should I do so that I can 'separate' the title and axes from the main plot, just like figures generated from plot and scatter?
I stumbled across this question, since I encountered the same problem.
As mentioned by #vindarmagnus, it is possible to use tikz and get rather nice results. However, tikz experiences problems with large data sets in my experience as present when using surf etc..
Solution, that worked for me:
Change the renderer to painters and the exported .svg file will retain its vectorgraphic properties when opened e.g. in inkscape:
figure('Renderer','Painters');
I used to use Inkscape for my scientific publications as well, but I found that a lot of the time you can get better results with pgfplots in latex, together with the matlab2tikz matlabscript. There’s a ton of resources about this online, but here’s how my workflow would look adopted to your surf situation. I have macOSX with latex, matlab and matlab2tikz installed. Will work with little to no modifications on linux.
In Matlab:
surf(peaks(25))
matlab2tikz('plot.tikz’)
Then I have the following bash-script (just a script in the same folder as the image, which is executed by mere double-click). (Needs to be chmod-ed as an executable for that).
#!/bin/bash
cd ~/Desktop
rm *.eps
cat > plot.tex << EOF
\documentclass{standalone}
\usepackage{pgfplots}
\pgfplotsset{max space between ticks=50}
\pgfplotsset{scaled ticks = false}
\pgfplotsset{compat=1.6}
\pgfplotsset{xticklabel style={/pgf/number format/fixed}}
\pgfplotsset{yticklabel style={/pgf/number format/fixed}}
\begin{document}
\input{plot.tikz}
\end{document}
EOF
pdflatex plot.tex
pdf2ps plot.pdf
ps2eps plot.ps
Note that the row cd ~/Desktop above should be changed as to reflect which folder the script is supposed to be run from (a bit crappy, but needed since Finder doesn’t properly pass along the folder from a program is executed, afaik).
This yields high-quality images in eps or pdf or what you like, with a ton of settings for axes and ticks etc. And it all uses native latex fonts.
Edit:
Recently I’ve begun to use patch() in matlab and then export it to tikz in the same manner as above, with great results. That’s another suggestion!
You can use also:
set(gcf,'Renderer','Painters')
How to copy (to clipboard) only significant part of a plot in Matlab? Without that large gray margins Matlab loves so much?
Is it possible to populate clipboard from Matlab command line?
As far as programmatically populating the system clipboard with image data captured from a Matlab figure goes, you might try Yair Altman's, ScreenCatpture utility on the Matlab File Exchange:
screencapture('handle',gca,'target','clipboard');
It has a lot of options and will allow you to specify a region or an entire figure. It does require Java, i.e., it won't run in '-nojvm' mode. You can read more about it at Yair's Undocumented Matlab site.
Also, you can change the current figure's background color to white before copying it via:
set(gcf,'Color','w');
In the figure window, choose "edit" -> "Copy Figure".
It's equal to Ctrl+C on text, etc., but takes only the main part of the figure. So if you go to word, say, and press Ctrl+V, or RIght Click -> Paste, you will get only the main part of figure, without the gray margins you hate so much...
A figure file is saved. When several lines are intersected, I want to make one of the line visible. How should I modify the different layer of the lines without re-plotting the figure?
Use uistack (see doc). For example, after:
figure
hold on
hblue=plot([1 2],[3 4],'b','LineWidth',5);
hred=plot([1 2],[4 3],'r','LineWidth',5);
the red line is on top (and the blue line would not be seen if the the red line covered it). Then, if you use uistack(hblue,'top'), the blue line is brought to the top. Other options to reorder plots, instead of top, are up, down, and bottom. You can optionally specify the number of steps up or down (e.g. uistack(h,'up',2) to move a handle two layers up - though no need in my simple example).
If, as you say, the 'figure file is saved', and you don't have the handles for the plots, (hblue and hred in my example), after loading the plot, you can get the handles using get(gca,'children').
If I understood you correctly, try to use hold on before plotting...
Below is the user interface I have created to simulate LDPC coding and decoding
The code sequence is decoded iteratively by passing values between the left and right nodes through the connections.
The first thing it would be good to add in order to improve visualization is to add arrows to the connections in the direction of passing values. The alternative is to draw a bigger arrow at the top of the connection showing the direction.
Another thing I would like to do is displaying the current mathematical operation below the connection (in this example c * H'). What I don't know how to do is displaying special characters and mathematical symbols and other kinds of text such as subscript and superscript in the figure (for example sum sign and subscript "T" instead of sign ="'" to indicate transposed matrix).
I would be very thankful if anyone could point to any useful resources for the questions above or show the solution.
Thank you.
To add arrows, you can either use the built-in QUIVER, or, for more options, ARROW from the file exchange. Both of these have to be plotted into axes, so if you want a big arrow on the top, you have to create an additional set of axes above the main axes.
As far as I know, you cannot use TeX or LaTeX symbols in text uicontrols. However, you can use them in axes labels. Thus, I suggest that you add an XLabel to the axes, for example
xlabel('\sigma c*H_T')
or (note the $-signs required for LaTeX)
xlabel('$\sum c*H_T$','interpreter','latex')
EDIT
I hadn't mentioned the use of text (as suggested by #gnovice and #YYC) because I thought it wasn't possible to place text outside of the axes. It turns out that I was wrong. text(0.5,-0.2,'\Sigma etc.') should work fine as well. I guess the only advantage of using 'xlabel' would be that you can easily add and position the axes label during GUI creation.
In regards to the 1st question, annotation (http://www.mathworks.com/access/helpdesk/help/techdoc/ref/annotation.html) might be an alternative solution.
In regards to the 2nd question, try text property in Matlab Help.
Search "Character Sequence" for the special characters; search "Specifying Subscript and Superscript Characters" for the subscript and superscript.
For drawing the arrow, I would go Jonas' suggestion arrow.m by Erik Johnson on the MathWorks File Exchange. It's the easiest way I've found to create arrows in figures.
For creating text with symbols, you can use the function TEXT. It lets you place text at a given point in an axes, and you can use the 'tex' (default) or 'latex' options for the 'Interpreter' property to get access to different symbols. For example, this places the text you want at the point (0,0) using 'latex' as the interpreter:
hText = text(0,0,'$\sum c*H_T$','Interpreter','latex');
The variable hText is a handle to the text object created, which you can then use with the SET command to change the properties of the object (string, position, etc.).