I have a data file containing n coordinate positions at t time steps of c number of figures which I would like to create an animation of in a gif file using gnuplot.
The data file is setup giving the n coordinate positions of all c figures at each time step, as
x1,1 y1,1
x1,2 y1,2
.
.
.
x1,n y1,n
x2,1 y2,1
.
.
.
xc,n yc,n
At each time step, I want to plot all n positions of my c figures in my gif animation.
The following code isn't exactly working.
set terminal gif animate
set output "output.gif"
do for [i=1:time_final] {
do for [j=1:c] {
plot "file.dat" every 1::(i-1)*(j-1)*n::i*j*n-1 u 1:2 w filledcurves
}}
set output
I apologize for the newbie-ness of this question.
I think that the every statement needs a small adjustment. Each of your "time steps" contains in total c*n records. Point numbers in Gnuplot in the context of every keyword are 0-based. This means that time-step i (assuming that the first one has i=1 as in your do loop) begins at point (i-1)*c*n. In order to move to "figure" j (assuming again that the first one within each time step has j=1), we need to add an offset of (j-1)*n. Now, since each "figure" has n points, the offset of the last point within each figure is n-1. In total:
do for [i=1:time_final] {
stepOffset = (i-1)*c*n
do for [j=1:c] {
firstPoint = stepOffset + (j-1)*n
lastPoint = firstPoint + (n-1)
plot "file.dat" every ::firstPoint::lastPoint u 1:2 w filledcurves
}}
In case you would want to merge the c "figures" into one plot, you could do:
do for [i=1:2] {
stepOffset = (i-1)*c*n
plot for [j=1:c] "file.dat" every ::(stepOffset + (j-1)*n)::(stepOffset + (j-1)*n + (n-1)) u 1:2 w filledcurves
}
By the way, since your data file has only two columns, the w filledcurves style seems to be misplaced here, if you want to fill the area between the curve and for example x-axis, w filledcurves x1 should work...
Related
The goal is to find coordinates in a figure with an unknown shape. What IS known is a list of coordinates of the boundary of that figure, for example:
boundary = [(0,0),(1,0),(2,0),(3,0),(3,1),(3,2),(3,3),(2,3),(2,2),(1,2),(1,3),(0,3),(0,2),(0,1]
which would look something like this:
Square with a gab
This is a very basic example and i'd like to do it with very larg lists of very different kinds of figures.
The question is how to get a random coordinate that lies within the figure WITHOUT hardcoding the anything about the shape of the figure, because this will be unknown at the beginning? Is there a way to know for certain or is making an estimate the best option? How would I implement an estimate like that?
Here is tentative answer. You sample numbers in two steps.
Before, do preparation work - split your figure into simple elementary objects. In your case you split it into rectangles, often people triangulate and split it into triangles.
So you have number N of simple objects, each with area of Ai and total area A = Sum(Ai).
First sampling step - select which rectangle you pick point from.
In some pseudocode
r = randomU01(); // random value in [0...1) range
for(i in N) {
r = r - A_i/A;
if (r <= 0) {
k = i;
break;
}
}
So you picked up one rectangle with index k, and then just sample point uniformly in that rectangle
x = A_k.dim.x * randomU01();
y = A_k.dim.y * randomU01();
return (x + A_k.lower_left_corner.x, y + A_k.lower_left_corner.y);
And that is it. Very similar technique for triangulated figure.
Rectangle selection could be optimized by doing binary search or even more complicated alias method
UPDATE
If your boundary is generic, then the only good way to go is to triangulate your polygon using any good library out there (f.e. Triangle), then select one of the triangles based on area (step 1), then sample uniformly point in the triangle using two random U01 numbers r1 and r2,
P = (1 - sqrt(r1)) * A + (sqrt(r1)*(1 - r2)) * B + (r2*sqrt(r1)) * C
i.e., in pseudocode
r1 = randomU01();
s1 = sqrt(r1);
r2 = randomU01();
x = (1.0-s1)*A.x + s1*(1.0-r2)*B.x + r2*s1*C.x;
y = (1.0-s1)*A.y + s1*(1.0-r2)*B.y + r2*s1*C.y;
return (x,y);
I want to know how to make a Gnuplot 2d animation using the gnuplot matrix non uniform format, with the first column being the time, the first row being the x axis ticks and the first number of the first row being the number of columns after the first one, an example of such a matrix is given by, imagine we have 2 time iterations and 2 space points. If the index goes from 0 to 1 then,such matrix would be like this
2 x[0] x[1]
t[0] f(0,0) f(0,1)
t[1] f(1,0) f(1,1)
How to make a 2d animation in gnuplot for f(t,x) for each time iteration?
Thanks
it probably might be easier if your data looked the following way:
2x2 t[0] t[1]
x[0] f(0,0) f(0,1)
x[1] f(1,0) f(1,1)
If your data already exists with columns x[..] and rows t[..] there is probably also a way to do it, but probably a bit more complicated.
The following example will create some dummy data (writes it also into a file) and will plot it into an animated GIF. In gnuplot, also check help gif for more information. Change the code to your needs.
### create some animated graph
reset session
set term gif size 300,300 animate delay 10 loop 0 optimize
set output "Animate.gif"
# create some dummy data
m = 50
n = 50
set print $Data
temp = sprintf("%gx%g\t",m,n)
do for [j=1:n] {
temp = temp.sprintf("t[%g]",j)
if (j<n) {temp = temp."\t"}
}
print temp
do for [i=1:m] {
temp = ""
do for [j=1:n] {
temp = temp.sprintf("%g", sin(2*pi*j/real(n)+2*pi*i/real(m)))
if (j<n) {temp = temp."\t"}
}
temp = sprintf("x[%g]\t",i).temp
print temp
}
set print "Animate.dat"
print $Data
set print
# dummy data finished
FILE = "Animate.dat"
stats FILE u 0 nooutput
set yrange[-1:1]
set xtics 10
set grid xtics, ytics
do for [i=2:STATS_columns] {
plot FILE u 0:i w lp lt 7 lc rgb "red" title columnhead(i)
}
set output
### end code
I have a matrix named figmat from which I obtain the following pcolor plot (Matlab-Version R 2016b).
Basically I only want to extract the bottom red high intensity line from this plot.
I thought of doing it in some way of extracting the maximum values from the matrix and creating some sort of mask on the main matrix. But I'm not understanding a possible way to achieve this. Can it be accomplished with the help of any edge/image detection algorithms?
I was trying something like this with the following code to create a mask
A=max(figmat);
figmat(figmat~=A)=0;
imagesc(figmat);
But this gives only the boundary of maximum values. I also need the entire red color band.
Okay, I assume that the red line is linear and its values can uniquely be separated from the rest of the picture. Let's generate some test data...
[x,y] = meshgrid(-5:.2:5, -5:.2:5);
n = size(x,1)*size(x,2);
z = -0.2*(y-(0.2*x+1)).^2 + 5 + randn(size(x))*0.1;
figure
surf(x,y,z);
This script generates a surface function. Its set of maximum values (x,y) can be described by a linear function y = 0.2*x+1. I added a bit of noise to it to make it a bit more realistic.
We now select all points where z is smaller than, let's say, 95 % of the maximum value. Therefore find can be used. Later, we want to use one-dimensional data, so we reshape everything.
thresh = min(min(z)) + (max(max(z))-min(min(z)))*0.95;
mask = reshape(z > thresh,1,n);
idx = find(mask>0);
xvec = reshape(x,1,n);
yvec = reshape(y,1,n);
xvec and yvec now contain the coordinates of all values > thresh.
The last step is to do some linear polynomial over all points.
pp = polyfit(xvec(idx),yvec(idx),1)
pp =
0.1946 1.0134
Obviously these are roughly the coefficients of y = 0.2*x+1 as it should be.
I do not know, if this also works with your data, since I made some assumptions. The threshold level must be chosen carefully. Maybe some preprocessing must be done to dynamically detect this level if you really want to process your images automatically. There might also be a simpler way to do it... but for me this one was straight forward without the need of any toolboxes.
By assuming:
There is only one band to extract.
It always has the maximum values.
It is linear.
I can adopt my previous answer to this case as well, with few minor changes:
First, we get the distribution of the values in the matrix and look for a population in the top values, that can be distinguished from the smaller values. This is done by finding the maximum value x(i) on the histogram that:
Is a local maximum (its bin is higher than that of x(i+1) and x(i-1))
Has more values above it than within it (the sum of the height of bins x(i+1) to x(end) < the height of bin x):
This is how it is done:
[h,x] = histcounts(figmat); % get the distribution of intesities
d = diff(fliplr(h)); % The diffrence in bin height from large x to small x
band_min_ind = find(cumsum(d)>size(figmat,2) & d<0, 1); % 1st bin that fit the conditions
flp_val = fliplr(x); % the value of x from large to small
band_min = flp_val(band_min_ind); % the value of x that fit the conditions
Now we continue as before. Mask all the unwanted values, interpolate the linear line:
mA = figmat>band_min; % mask all values below the top value mode
[y1,x1] = find(mA,1); % find the first nonzero row
[y2,x2] = find(mA,1,'last'); % find the last nonzero row
m = (y1-y2)/(x1-x2); % the line slope
n = y1-m*x1; % the intercept
f_line = #(x) m.*x+n; % the line function
And if we plot it we can see the red line where the band for detection was:
Next, we can make this line thicker for a better representation of this line:
thick = max(sum(mA)); % mode thickness of the line
tmp = (1:thick)-ceil(thick/2); % helper vector for expanding
rows = bsxfun(#plus,tmp.',floor(f_line(1:size(A,2)))); % all the rows for each column
rows(rows<1) = 1; % make sure to not get out of range
rows(rows>size(A,1)) = size(A,1); % make sure to not get out of range
inds = sub2ind(size(A),rows,repmat(1:size(A,2),thick,1)); % convert to linear indecies
mA(inds) = true; % add the interpolation to the mask
result = figmat.*mA; % apply the mask on figmat
Finally, we can plot that result after masking, excluding the unwanted areas:
imagesc(result(any(result,2),:))
I have a simple pcolor plot in Matlab (Version R 2016b) which I have uploaded as shown in the image below. I need to get only the blue sloped line which extends from the middle of the leftmost corner to the rightmost corner without hard-coding the matrix values.
For instance: One can see that the desired slope line has values somewhere approximately between 20 to 45 from the pcolor plot. (From a rough guess just by looking at the graph)
I'm applying the following code on the matrix named Slant which contains the plotted values.
load('Slant.mat');
Slant(Slant<20|Slant>50)=0;
pcolor(Slant); colormap(jet); shading interp; colorbar;
As one can see I hard-coded the values which I don't want to. Is there any method of detecting certain matrix values while making the rest equal to zero?
I used an other small algorithm of taking half the maximum value from the matrix and setting it to zero. But this doesn't work for other images.
[maxvalue, row] = max(Slant);
max_m=max(maxvalue);
Slant(Slant>max_m/2)=0;
pcolor(Slant); colormap(jet); shading interp; colorbar;
Here is another suggestion:
Remove all the background.
Assuming this "line" results in a Bimodal distribution of the data (after removing the zeros), find the lower mode.
Assuming the values of the line are always lower than the background, apply a logic mask that set to zeros all values above the minimum + 2nd_mode, as demonstrated in the figure below (in red circle):
Here is how it works:
A = Slant(any(Slant,2),:); % save in A only the nonzero data
Now we have A that looks like this:
[y,x] = findpeaks(histcounts(A)); % find all the mode in the histogram of A
sorted_x = sortrows([x.' y.'],-2); % sort them by their hight in decendet order
mA = A<min(A(:))+sorted_x(2,1); % mask all values above the second mode
result = A.*mA; % apply the mask on A
And we get the result:
The resulted line has some holes within it, so you might want to interpolate the whole line from the result. This can be done with simple math on the indices:
[y1,x1] = find(mA,1); % find the first nonzero row
[y2,x2] = find(mA,1,'last'); % find the last nonzero row
m = (y1-y2)/(x1-x2); % the line slope
n = y1-m*x1; % the intercept
f_line = #(x) m.*x+n; % the line function
So we get a line function f_line like this (in red below):
Now we want to make this line thicker, like the line in the data, so we take the mode of the thickness (by counting the values in each column, you might want to take max instead), and 'expand' the line by half of this factor to both sides:
thick = mode(sum(mA)); % mode thickness of the line
tmp = (1:thick)-ceil(thick/2); % helper vector for expanding
rows = bsxfun(#plus,tmp.',floor(f_line(1:size(A,2)))); % all the rows for each coloumn
rows(rows<1) = 1; % make sure to not get out of range
rows(rows>size(A,1)) = size(A,1); % make sure to not get out of range
inds = sub2ind(size(A),rows,repmat(1:size(A,2),thick,1)); % convert to linear indecies
mA(inds) = 1; % add the interpolation to the mask
result = A.*mA; % apply the mask on A
And now result looks like this:
Idea: Use the Hough transform:
First of all it is best to create a new matrix with only the rows and columns we are interested in.
In order to apply matlab's built in hough we have to create a binary image: As the line always has lower values than the rest, we could e.g. determine the lowest quartile of the brightnesses present in the picture (using quantile, and set these to white, everything else to black.
Then to find the line, we can use hough directly on that BW image.
I'd like to know exactly how this line of code works
corners = (m==n)&(n>threshold);
It's in a piece of code I'm using and I want to understand it. Basically, m and n are both equal-sized images, and "threshold" is a decimal value.
To understand the context, a segment of the code is below.
% compute the m cornerness measure
m = (ix2s.*iy2s - ixys.^2) - 0.04*(ix2s+iy2s).^2;
% perform non-maximal suppression using ordfilt2
n = ordfilt2(m, radius^2, ones([radius radius]));
% display corner spots
corners = (m==n)&(n>threshold);
% superimpose corners
Q = corners+im;
Q(Q>1) = 1;
C = repmat(im,[1 1 3]);
C(:,:,1) = Q;
If I understand correctly, n is the max of m ("cornerness measure") for the vicinity, so the line means - "if m is the local maximum and large enough(larger than threshold), then this is probably a corner", it could have arguably been more readable as:
corners = (m==n)&(m>threshold);
You should read more about Harris corner detector. Taken from Wikipedia:
This line is implementation of the function mentioned above. It is used to detect corners.