If I have a datafile that is simply
x y
0 0
1 1
2 2
3 3
4 4
for example, where each line is a new timestep, how can I create an animation of this with gnuplot?
The desired animation in this case would be a point moving one unit in the positive x direction and one unit in the positive y direction each timestep.
I've only read examples of how to do this when each timestep is in a new 'datablock'. In this case, the datafile would look like
x y
0 0
1 1
2 2
3 3
4 4
which seems silly and would mean that I cannot easily use that same datafile to plot x vs y in most programs.
I've noticed an utter dearth of gnuplot examples or syntax explanations online. Am I missing some good resources?
First determine what the desired range is on x and y. You will keep this range for the entire animation.
set xrange [ xmin : xmax ]
set yrange [ ymin : ymax ]
do for [n=1:*] {
plot 'data' using 1:2 every 1::n::n with points
pause 1
}
This will plot one point every second until it runs off the end of the file. After the last line of your file you will just get an error message every second until you kill it.
Both the user manual and worked demos are on-line at gnuplot.info. They should also somewhere in the installed gnuplot package although exactly where they end up probably depends on your OS configuration.
Related
I want to plot results in gnuplot that all lie on a circle. For each value I have the corresponding x-y coordinates and a corresponding ID number (so 4 columns in total), but in an unsorted order. The rows are to be sorted in such a way that the direction of rotation is from -x => -y => +x => +y and end again at -x. So the center of the circle is at 0. How to implement this with "sort" (or alternatively with "awk"?) command (using Linux)?
At Theozh's suggestion, I will formulate my problem a little more precisely.
Imagine the dial of a clock with small dots as minute symbols. The position of the minute points can be determined by polar coordinates or by Cartesian coordinates. My file contains the Cartesian coordinates with an associated value (result). The file contains 60 lines with x - y coordinates and the result in the third column. Depending on the quadrant, the signs of x and y change, of course. Unfortunately, the lines are NOT sorted in such a way that they correspond to the sense of circulation. So the line for the point "minute 30" is not in line 30, but e.g. in line 17. The task is to sort the lines by the coordinates so that they appear in the order from 1 to 60. In the diagram, the x-axis would then simply be defined from 1 to 60 and the y-axis would then contain the results (from the 3rd column)
My unsorted file (coordinates for a unit circle, result values simplified for a better overview)
And this is what I want to have (8 rows (every 45°) sorted counterclockwise):
The angle can be calculated directly from the x/y coordinates using the atan2() function.
You do not say exactly what it is that you want to plot. If it is simply the points themselves (one point per line in the file), then this can be done easily inside gnuplot. I show the output from gnuplot 5.5. In earlier versions, and depending on exactly what you want to plot, it might require additional commands to sort the data in a separate step and then plot the sorted data. If you clarify what exactly is supposed to go into the plot, I will modify the example accordingly.
Example using 100 points with random x and y coordinates:
set print $RANDOM
do for [i=1:100] { print rand(0)-0.5, rand(0)-0.5 }
unset print
set xrange [-1:1]
set yrange [-1:1]
set angle degrees
set cbrange [-180:180]; set cblabel "Angle"
set style data linespoints
plot $RANDOM using 1:2:(atan2($2,$1)):(atan2($2,$1)) smooth zsort lc palette
Updated answer
Revised to show a plot of the sample data as given
$DATA << EOD
X Y Result
-0.707 -0.707 222
-0.707 0.707 888
0.707 -0.707 444
-1 0 111
1 0 555
0.707 0.707 666
0 1 777
0 -1 333
EOD
set datafile columnheader # allow for the line of labels
unset key
# atan2() returns a number between -pi and pi; convert this to 0 -> 1
# You could make it run from 0->60 if you know in advance
# there will be 60 evenly spaced points
xcoord(a) = (a + pi) / (2 * pi)
plot $DATA using (xcoord(atan2($2,$1))):3:(atan2($2,$1)) smooth zsort with points
And actually, if you don't care what order the points are drawn in, only where they end up, the command is even simpler because there is no need to sort!
plot $DATA using (xcoord(atan2($2,$1))):3 with points
A datafile contains three columns with the first and second representing the x & y position of a circle at a time (in seconds) given by the third column. For example, the first two lines in "data.txt" give the position of two circles at time=0, followed by two blank lines then the position of the two circles at time=0.1 sec and so forth. The first few lines of data.txt are:
0 0 0
-1 -1 0
1 1.0 0.1
-1 -0.5 0.1
1.2 1.25 0.2
-0.5 -0.25 0.2
...
The Gnuplot code producing a series of frames (a movie) with the position of the two circles in time is:
set terminal gif size 1200,1200 animate delay 500
set output "movie.gif"
stats "data.txt" u 1:2 name "A"
set style circle radius graph 0.025; set style fill solid
set xrange [A_min_x*1.1:A_max_x*1.1]
set yrange [A_min_y*1.1:A_max_y*1.1]
do for [i=0:A_blocks-2] {
plot "data.txt" index i u 1:2 w circle
}
I'm trying to add a label or textbox of the form "Time=?" to each frame where the question mark is replaced by the number from the third column. Any suggestions on how to do it?
This answer requires the current version of gnuplot (5.4)
Assuming that all the column 3 entries in a given data block are the same, it should be sufficient to say
plot "data.txt" index i u 1:(FOO=strcol(3),column(2)) w circle title sprintf("Time = %s",FOO)
This updates the value of FOO for each line used. The title uses whatever the final update was for that plot. If you must specifically choose the column 3 value from a particular line within the block, or calculate something like an average, that's a harder problem. In that case please clarify.
Edit:
The reason this requires 5.4 is that earlier versions evaluated the title before reading the data for that plot. Version 5.4 evaluates the title after reading the data.
The first (not too obvious) solution which comes to my mind: plot your data in a loop and assign the value of the 3rd column to a variable, e.g. t. Use keyenty to print the legend with your time re-using the variable t. In order to avoid a symbol in the legend use plotting style with points and a point with pointsize 0.
Code:
### animation with time label
reset session
$Data <<EOD
0 0 0
-1 -1 0
1 1.0 0.1
-1 -0.5 0.1
1.2 1.25 0.2
-0.5 -0.25 0.2
EOD
set terminal gif size 400,400 animate delay 100
set output "SO70474478.gif"
stats $Data u 1:2 name "A" nooutput
set style circle radius graph 0.025; set style fill solid
set xrange [A_min_x*1.1:A_max_x*1.1]
set yrange [A_min_y*1.1:A_max_y*1.1]
set key top left
do for [i=0:A_blocks-1] {
plot $Data index i u 1:(t=$3,$2) w circle notitle, \
keyentry w points ps 0 ti sprintf("Time: %.1f",t)
}
set output
### end of code
Result:
After having read this question, I wanted to use this code to save my picture as to particular size.
I_c(:,:) = cropped_matrix(i,:,:);
set(I_c, 'PaperUnits', 'inches');
x_width = 7.25;
y_width = 9.125;
set(I_c, 'PaperPosition', [0 0 x_width y_width]);
imshow(I_c);
saveas(I_c,'fig1.pdf');
I_c represents a 2D matrix (about 40x40) of uint8's.
However, I get the error:
Error using set Invalid handle
This makes me believe that I can only use this code with figures and not matrices which contain matrices. How would I go about this?
I have looked at the API for print, as suggested as the first answer of the aforementioned linked question, but it also suggests using set and 'PaperUnits'.
Note: This question also looks at this problem but suggests the same solution.
Notes About Crowley's Answer
So I just tried the code that you have given with your answer. The .jpg being produced is the one shown below. How would I get rid of all the extra white area through code?
How would I change the colourmap of the figure being produced, to greyscale when I just use image(ImData)?
And here is how the actual figure appears:
Here is the code that I have put in:
im = image(I_c);
set(gcf,'units','inches','position',[1 2 5 5]);
set(gca,'ydir','normal','units','centimeters','position',[0 0 0.5 0.5].*get(gcf,'position')) ;
filename = strcat('slice',int2str(i),'_','bead',int2str(j),'.jpg');
saveas(im,filename);
Suppose we have matrix I_c containing values and x and y the coordinates so value I_c(ii,jj) corresponds to x(ii) and y(jj) coordinates.
Then:
ImMin=min(min(I_c)); % Find the minimum value in I_c
ImData=I_c-ImMin; % Ensure non-zero values
ImMax=max(max(ImData)); % Find maximum value in ImData
ImData=ImData./ImMax; % Ensure ImData do NOT exceed 1
image(x,y,ImData*[1 1 1]) % plot the image in greyscale
set(gcf,'units','inches','position',[1 2 5 5]) % set active figure properties
set(gca,'ydir','normal','units','inches','position',[0 0 1 1].*get(gcf,'position')) % set active axes properties
export_fig(gcf,'figure-I_c','-png','-nocrop')
'ydir','normal' parameter change default (1,1) point being in top-left corner to "normal" position in bottom-left corner.
[0 0 1 1].*get(gcf,'position) will read active figure position (here [1 2 5 5]) and after element-by-element multiplication the [0 0 5 5] is passed to the position which causes that axes fit the image.
export_fig function will create figure-I_c.png image as it is shown in Matlab figure, if -nocrop is omitted the possible white space in the edges is cropped out. This function is available from MathWorks' File Exchange.
My question about how to automate placing labels at the edge of a plot for data points that exceed the range of plot. This would be done for points that are outliers that, if plotted, skew the scale of the plot such that the plot is no longer useful, but still need to be noted.
For example, let's say I've got a data file called 'mydata.dat' that looks like this:
1 2
3 3
7 4
8 6
50 8
If I plot the data using
set yrange [0:10]
set xrange [0:10]
plot 'mydata.dat' w lp pt 1
then the last point (50,8) will not be plotted. To acknowledge, however, that there is a point outside the plotted range, a label and point would be placed at the edge (i.e., at 10,8) of the plot using
set label "" at 10,8 point pt 1
set label "50" at 9.75,8 right
Is there a way to automate this process? A way to have GNUplot read the entire data file and set points and labels at the edge of the plot?
To plot all point which are outside of the specified range, you'll need a second plot command using the labels plotting style.
In the using statement you can then check for the point being outside the range. If it is, you place a point with a corresponding label, otherwise you skip the point (using 1/0 as value):
set xrange [0:10]
set yrange [0:10]
set linetype 1 pt 7
plot 'mydata.dat' w lp lt 1, \
'' using ($1 > 10 ? 10 : 1/0):2:(sprintf('%d', $1)) with labels right offset -2,-0.25 point lt 1 notitle
Here, I check only for the x-value being larger than the specified maximum x-value. Maybe you need to adapt it in order to catch also outliers in y-direction or those smaller than 0.
After quite a bit of tweaking to an existing GNU plot, I managed to get the following:
reset
# png
set terminal png size 350,262 enhanced font 'Verdana,10'
# color definitions
set style line 1 lc rgb '#0060ad' lt 1 lw 2 pt 7 ps 2 # --- blue
unset key
set border 0
unset tics
# set view 342,0
set xrange [-300:300]
set yrange [-300:300]
n=0
do for [ii=1:99] {
n=n+1
set output sprintf('png/spiral%03.0f.png',n)
plot '1_1910.txt' every ::1::ii w l ls 1, \
'2_1910.txt' every ::1::ii w l ls 1
}
do for [ii=1:99] {
n=n+1
set output sprintf('png/spiral1%03.0f.png',n)
plot '1_1920.txt' every ::1::ii w l ls 1, \
'2_1920.txt' every ::1::ii w l ls 1
}
The idea is to create a set of PNG files, and then concatenate them all with animation.
I concatenate them all together using
convert -delay 2 -loop 0 png/*.png animation.gif
I want to make more tweaks:
I don't want to keep the line that follows the whole plot (even though animated). Instead, I want a "bullet point" (maybe the size of 5-10 pixels) with text moving next to it for each frame for each data point in the plot.
I want a text at the bottom right for the first set of frames (in the first 1:99 loop) and a different text replacing it, again in the bottom right corner (in the next 1:99 loop).
My code is based on this:
http://www.gnuplotting.org/animation-iv-trajectory/
but I can't figure out why his code has a "trail" that disappears, and why he has also a bullet point and I don't. As I said, I also want text that moves with the bullet point (same text for each data file).
I think you can do it with loops like this:
n = 0
do for [ii=0:60] {
n=n+1
set output sprintf('png/spiral%03.0f.png',n)
plot 'data.dat' every ::ii::ii w p ls 1, \
'data.dat' using 1:2:("foo") every ::ii::ii w labels offset 2
}
set label 1 "hyde" at 275,-275
do for [ii=60:0:-1] {
n=n+1
set output sprintf('png/spiral%03.0f.png',n)
plot 'data.dat' every ::ii::ii w p ls 1, \
'data.dat' using 1:2:("foo") every ::ii::ii w labels offset 2
}
Here is the result:
You can play with the offset coordinates to position the label text "foo" where you want.
To change the size of the point, change the value of ps in the line style command at the beginning of your script.
I am not sure what the purpose of the two different files is (1_1910.txt and 2_1920.txt), so I used the same file in my example. You may need to add to the plot command if you are plotting two different things at once.
As for your other questions, I think looking closely at the code in the example should give you an idea of what is going on. In the example, the range every ::1::ii plots points from 1 to ii, giving a line; the range every ::ii::ii plots just one point. Note that the abbreviations w l and w p in the example expand to with lines and with points, respectively.
In the example the line disappears due to the action of the second loop, which runs in reverse (for [ii=99:1:-1]). If you are copying that example, make sure also that your indices run over the correct values (you may have a number other than 99 of data points). Also note that indices in gnuplot start at 0, so if the first line of your data file contains data (not a header) you want to start your loop at ii=0 instead of ii=1.
I am having nearly the same problem here. I found a really nice hack! Instead of making multiple png's and then merge them, you just use set multiplot and then unset multiplot inside ONE loop. Being specific I used it this way:
do for [i=0:k]
{
set multiplot
plot function1
plot function2
unset multiplot
}
But unfortunately this won't work unless the data set you have is synchronized!, but yet can be solve this using if-statement!. Good Luck