I generated a .dat file with 100 matrix 15x15, now I want to create a gif which shows the evolution from the first to the last matrix. They are all matrix with 1 or -1, so if I want to represent the inicial matrix I can copy and paste it in another file and I put this in gnuplot:
plot 'firstmatrix.dat' matrix with image
It represents the 1, -1 matrix with yellow and black.
To create the gif I'm trying to do this in gnuplot:
set terminal gif animate delay 20
set output 'evolution.gif'
set xrange [0:15]
set yrange [0:15]
N=15
nframes=5
do for [i=1:int(nframes)] {
plot 'evolution.dat' every ::(i-1)*N+1::i*N matrix with image
}
I intend to read from the first line of the file to the 15th line, then from the 16th to the 30th and so on.
I put only 5 frames to see better the result, and I obtain that the gif shows the first matrix in the first frame and nothing more, only white frames.
The error message is four times this one:
warning: Skipping data file with no valid points
So the data for the first frame, the first matrix, is well processed but not the rest. So here is my problem, I don't know why it process good the first one and no more.
Thanks in advance.
It shows only the first matrix in the first frame
You've been pretty close. But it took me also some iterations and testing...
Apparently, slicing a block of rows from a matrix requires every :::rowFirst::rowLast (mind the 3 colons at the beginning). And then gnuplot apparently takes the row index of the whole matrix as y-coordinate. Since you want to have it "on top of each other" you need the modulo operator % (check help operators binary). It might have been a bit easier if your matrices were separated by one or two empty lines.
Code:
### animated matrix data
reset session
### create some random data
set print $Data
do for [n=1:20] {
do for [y=1:15] {
Line = ''
do for [x=1:15] {
Line=Line.sprintf("% 3g",int(rand(0)*2)*2-1)
}
print Line
}
}
set print
set terminal gif animate delay 30
set output "tbMatrixAnimated.gif"
unset key
N=15
do for [i=1:20] {
plot $Data u 1:(int($2)%N):3 matrix every :::N*(i-1)::N*i-1 with image
}
set output
### end of code
Result: (only 20 matrices)
Related
I am trying to plot a set of 3D trajectories in a single plot in Julia. By 3-D trajectories I mean: different sets of 3-D coordinates over time. These trajectories are stored in a multidimensional array called positions, where the dimensions respectively correspond to the Trajectory ID, X-Y-Z coordinate and Time. For example, positions[75,2,1:100] refers to the Y (2nd) coordinate of the 75th Trajectory, across the first 100 timesteps of the trajectory.
I am trying to figure out why the following code doesn't work:
using Plots
plotlyjs()
time_indices = 1:100
ax= scatter3d(positions[1,1,time_indices],positions[1,2,time_indices],positions[1,3,time_indices],label="Trajectory 1 for times 1 to 100")
for n in 2:size(positions,1)
scatter3d!(ax, positions[n,1,time_indices], positions[n,2,time_indices],positions[n,3,time_indices],label="Trajectory $n for times 1 to 100")
end
When I run that code, I don't see anything in the Plots window (I'm using Atom), although I don't get any errors / it appears to run successfully. Any thoughts on what I'm doing wrong? Should I use a different backend? It doesn't work on either gr() or plotlyjs() (those are the only ones I know of, based on tutorials I've completed).
Follow up question: once I can successfully plot such 3-D trajectories in a single static plot, I am wondering how you would go about animating them over time (using #gif or #animate macros, presumably)? I am asking this here, because I wasn't able to understand the documentation / tutorial on 3D animations, unfortunately. Googling / other sources have also not helped :(
It looks like you're just missing a display(ax) at the end, after the loop.
Edit: to animate, try
anim = #animate for n in 1:size(positions,1)
scatter3d(positions[n,1,time_indices], positions[n,2,time_indices],positions[n,3,time_indices],label="Trajectory $n for times 1 to 100")
end
gif(anim, "some_file_name.gif", fps=15)
(or if you want the prior trajectories to show up as well in later frames of the gif, then replace the scatter3d with scatter3d!)
I can't test the above without having your positions, but here is another example that I have just tested on Julia 1.5.0beta with Plots and the GR backend:
using Plots; gr();
anim = #animate for i=1:100
plot(sin.(range(0,i/10*pi,length=1000)), label="", ylims=(-1,1))
end
gif(anim, "anim_fps15.gif", fps=15)
How to do the second bit (the animation - see details in comments on the accepted answer):
gr()
anim = #animate for t in time_indices
all_positions_t = positions[:,:,t] # positions of all trajectories at time t
scatter3d(all_positions_t[:,1], all_positions_t[:,2],all_positions_t[:,3],label="")
end
gif(anim, "some_file_name.gif", fps=15)
This question already has an answer here:
How to create an array according to row and column number [duplicate]
(1 answer)
Closed 5 years ago.
The problem is the following: I have a .txt file containing 3 columns of numbers. The first 2 columns are the coordinate x,y of the points. The third columnn (z vector) is made of numbers that express the luminosity of each point. (The .txt files have been generated by a software that is used to study the pictures of a combustion process). Each vector (x,y,z) is made of 316920 elements (all integer numbers). Now: is there a way to create from these 3 vectors an image in matlab relating the luminosity value to the coordiantes of the point?
Thanks for your time!
consider a file image.txt contains y x and intensity values separated line. like this.
1 1 0
1 2 12
1 3 10
....
....
255 255 0
open the text file using fopen function
fid = fopen(image.txt,'r');
im=[];
and read a string-line of characters by fgetl function, convert string-line into vector using sscanf and put intensity value into y and x coordinates of a image matrix, im.
tline=fgetl(fid) ;
rd=sscanf(tline,'%d');
im(rd(1),rd(2))=rd(3);
The same process is iterated up-to end of file.
at last close file-handle fid
I am going to assume that the three columns in your text file are comma separated( The code will need to be a bit different if they are not comma separated) . Since you said all numbers are integers, I am going to assume that you have all the data needed to fill a 2D grid using your x and y coloumns is present. I am not assuming that it is in a ordered form. With these assumptions the code will look like
data = csvread(filename)
for i=1:length(data)
matrix(data(i,2)+1,data(i,1)+1)=data(i,3) // +1 is added since there maybe a index starting from 0 and matlab needs them to start from 1
end
image(matrix)
For other delimiters use
data = dlmread(filename,delimiter)
I have a matrix of data, which is an output of automatic music transcription program. I want to plot it using gnuplot, assigning appropriate labels. Here's my dropbox with some data, where Intensity.dat is actual data, example.stn is a column of string values, some of which are to be displayed on y axis and example.all is just a result of paste example.stn Intensity.dat > example.all Script:
reset
set title "Intensity detection"
set palette negative grayscale
set cbrange [0.01:1]
set xlabel "Time [s]"
set ylabel "Musical note"
set terminal qt font "Verdana,16"
set logscale cb
xincr=0.04644
yincr=1
plot 'example.all' u (($1+0.5)*xincr):($2*yincr):3 matrix with image
produces
plot produced by script 1. Everything's OK, now just tic labels...
After I change the last line to plot 'example.all' u (($1+0.5)*xincr):($2*yincr):3 matrix rowheaders with image, the y-axis becomes too densly populated (It's plot2.jpg from my dropbox, link on top. Sorry guys, I'm new and it doesn't allow me to post more than 2 links).
What I want is a way to present only the labels I want (or hide others, whatever), not all at a time (because it looks unreadable). I'd also like to be able to quickly change them to the others when I need to do so. Supposingly, I want to display every 12th label, but still keep entire matrix with all rows plotted. Or every 12th starting from 2nd label AND every 12th starting from 6th. I've already tried many ways but I'm stuck. Functions like :ytics() or :yticlabels() can't make it, at least for me. And yes, I need this Verdana 16, and removing labels completely is out of question.
I'll be extra grateful if the method applies also for x-axis, as I have an analogical problem with x-axis in other plot, but I generally appreciate any help.
You can separate plotting the image from plotting the ytics like this:
condition(n) = (ceil(n)%12-2 == 0) || (ceil(n)%12-6 == 0)
plot 'Intensity.dat' u (($1+0.5)*xincr):($2*yincr):3 matrix with image ,\
'example.stn' u (NaN):0:ytic(condition($0) ? strcol(1) : "") notitle
The function condition checks whether the label should be plotted or not. I have used ceil to convert from a real number to an integer which is required by the modulo operator (%). The condition function is called with the linenumber $0. The NaN while plotting 'example.stn' avoids plotting data points while keeping the chance for setting the labels. If the condition is met (12th label starting from 2nd or 12th starting from 6th), we use the actual label, else an empty string is used.
I have a data file of two column, ten row ‘blocks’, with two lines of whitespace between each block. Each frame of the animation I want the ten points in the successive block to be plotted, until the end of the data file.
I've searched for how to do this for ages but can't appropriate any of the examples I've found to my case as I don't understand the syntax and can't find an explanation of it anywhere.
How would the example here or here be extended to blocks of x rows?
E.g., in the second example, pasted below for easy reference
n=10 # n present here the number of blocks in your file
plot "output.dat" using 1:2 every :::i::i
i=i+1
if i<n reread
What do the number of colons in every :::i::i mean? Is that three data lines, then two whitespace lines? (Appropriating assuming that doesn't work.)
(If this question seems too obvious, I assure you it is due to my lack of knowledge, not my lack of effort in researching. I would very gladly accept being pointed towards the place in the documentation where this is covered.)
This is not an answer regarding the syntax of every, but a way to achieve this animated plot that is scalable for future users in my position.
A datablock, or block, is x consecutive lines of data, separated by exactly two lines of whitespace.
The plot command option index can be used to access each of these blocks.
For example, plot "datafile.dat" using 1:2 index 1 would plot only the points in the first dataset (block of data).
A loop can be used to animate your data. The stats command can be used to find the number of datasets/blocks in your file, to use in the loop.
set terminal x11
stats 'bdata.txt' nooutput
set xrange [0:10]
set yrange [0:10]
do for [a = 1: int(STATS_blocks - 1)] {
plot "bdata.txt" using 1:2 index a
pause 0.1
}
I'm trying to make an "animated" plot a lot of data (the position of 1000 particles) from a big text file with a script like:
set terminal wxt size 1000,600
k=999999
N = 999
do for [i=0:k]{
plot for [j=0:N-1] "pos.txt" using 2*j+1:2*j+2 every ::2*i+1::2*i+1 ls 1 pt 7 ps 2 notitle
In the file, every line has the coordinates X and Y at a certain time of the points I want to plot. I'm using every to plot all the data in each row once and then move on to the next row.
The output is something like this (1000 particles moving)
However the plotting is way too slow and I don't know what I can do to make it plot faster. It plots a row once every 5 or more seconds. The file weights some MBs. Should I change the terminal? Or the way I store the data? I think there might be a problem when gnuplot loads a big file.
Some particles dissappear in the simulation so I also get the error line 14: warning: Skipping data file with no valid points when the index j (well 2j+1) goes over the number of particles but I tried making it so that it reads the number of particles each time and it's even slower. Many thanks.
I suspect gnuplot is reading the whole file every time you plot, as opposite to read up to the line in question, then next line, then next, etc. One possible strategy is to separate your particles trajectory into different files, but specially it could help to remove the plot for by simply a plot plus a block selection with every, where instead of selecting the column for the particle you have your particles positions for the same time step in the same block.
Now your data looks something like this:
x1 y1 x2 y2 x3 y3 # Time step 1
x1 y1 x2 y2 x3 y3 # Time step 2
And gnuplot needs to read the file once for every time step and particle. If you structure the file as follows (note one blank line between blocks):
# Time step 1
x1 y1
x2 y2
x3 y3
# Time step 2
x1 y1
x2 y2
x3 y3
Then you don't need the plot for, instead just select the corresponding block with all the particles by inserting one extra semicolon in every:
set terminal wxt size 1000,600
k=999999
#N = 999 you don't need this anymore!
do for [i=0:k] {
plot "pos.txt" every :::i::i
}
The code above reads the file for every time step, rather than every time step and particle, and plots all the particles at once.
If performance is very critical, you may consider using a completely different data format. Although changing the format of the ASCII file gives a huge improvement, it scales badly, because gnuplot must always scan from the beginning of the data file in order to determine the position where to start at. I did some testing, and to plot the first 1000 frames it took me 60s, whereas the points 9000 to 10000 took 600s to plot.
You would need a data format which allows you to seek at any data set in constant time. In my thesis I saved all my experimental data (huge data sets) with hdf5, and then you can use the external utility h5totxt to extract the desired data set. Here, the position of the requested data set can be calculated without scanning the whole file, and the access time is independent of the frame number.
For testing I used the following python script to generate a test data file points.h5:
from numpy import random
import h5py
P = random.normal(size=(10000,1000,2))
f = h5py.File('points.h5', 'w')
f.create_dataset('points', data=P)
The gnuplot script for plotting is
set terminal wxt size 1000,600
k=9999
do for [i=0:9999]{
plot sprintf("< h5totxt -s ' ' -x %d points.h5", i) using 1:2 ls 1 pt 7 ps 2 title sprintf("%d", i)
}
Now, plotting of 1000 frames takes 40s, no matter which frames you take (0-1000 or 9000-10000).