I have an 3D matrix 512*512*100. I want to apply fftshift on each page of it using the GPU. What I am doing right now is:
G = rand(512,512,100, 'gpuArray');
for i=1:100
G(:,:,i) = fftshift(G(:,:,i));
end
Is there a faster way to apply fftshift without doing it in a loop? For example, fft2 can be applied directly to an 3D array performing the operation on each page separately. However, fftshift does not work like that. Furthermore, fftshift is not supported by pageFun.
fftshift has an optional second input argument that selects along which dimension to apply the shift. Unfortunately, it is not possible to provide two dimensions, so fftshift(G,[1,2]) will not work. You'll have to call fftshift twice:
G = fftshift(fftshift(G,1),2);
Hopefully this is faster than calling it 100 times for a single page.
Related
I am trying trying to graph the polynomial fit of a 2D dataset in Matlab.
This is what I tried:
rawTable = readtable('Test_data.xlsx','Sheet','Sheet1');
x = rawTable.A;
y = rawTable.B;
figure(1)
scatter(x,y)
c = polyfit(x,y,2);
y_fitted = polyval(c,x);
hold on
plot(x,y_fitted,'r','LineWidth',2)
rawTable.A and rawTable.A are randomly generated numbers. (i.e. the x dataset cannot be represented in the following form : x=0:0.1:100)
The result:
second-order polynomial
But the result I expect looks like this (generated in Excel):
enter image description here
How can I graph the second-order polynomial fit in MATLAB?
I sense some confusion regarding what the output of each of those Matlab function mean. So I'll clarify. And I think we need some details as well. So expect some verbosity. A quick answer, however, is available at the end.
c = polyfit(x,y,2) gives the coefficient vectors of the polynomial fit. You can get the fit information such as error estimate following the documentation.
Name this polynomial as P. P in Matlab is actually the function P=#(x)c(1)*x.^2+c(2)*x+c(3).
Suppose you have a single point X, then polyval(c,X) outputs the value of P(X). And if x is a vector, polyval(c,x) is a vector corresponding to [P(x(1)), P(x(2)),...].
Now that does not represent what the fit is. Just as a quick hack to see something visually, you can try plot(sort(x),polyval(c,sort(x)),'r','LineWidth',2), ie. you can first sort your data and try plotting on those x-values.
However, it is only a hack because a) your data set may be so irregularly spaced that the spline doesn't represent function or b) evaluating on the whole of your data set is unnecessary and inefficient.
The robust and 'standard' way to plot a 2D function of known analytical form in Matlab is as follows:
Define some evenly-spaced x-values over the interval you want to plot the function. For example, x=1:0.1:10. For example, x=linspace(0,1,100).
Evaluate the function on these x-values
Put the above two components into plot(). plot() can either plot the function as sampled points, or connect the points with automatic spline, which is the default.
(For step 1, quadrature is ambiguous but specific enough of a term to describe this process if you wish to communicate with a single word.)
So, instead of using the x in your original data set, you should do something like:
t=linspace(min(x),max(x),100);
plot(t,polyval(c,t),'r','LineWidth',2)
Can someone explain to me the correlation function corr2 in MATLAB? I know that it is for 2D comparing similarities of objects, but in the equation I have doubts what it is A and B (probably matrices for comparison), and also Amn and Bmn.
I'm not sure how MATLAB executes this function, because I have found in several cases that the correlation is not executed for the entire image (matrix) but instead it divides the image into blocks and then compares blocks of one picture with blocks of another picture.
In MATLAB's documentation, the corr2 equation is not put as referral point to the way the equation itself is calculated, like in other functions in MATLAB's documentation, such as referring to what book it is taken from and where it is explained.
The correlation coefficient is a number representing the similarity between 2 images in relation with their respective pixel intensity.
As you pointed out this function is used to calculate this coefficient:
Here A and B are the images you are comparing, whereas the subscript indices m and n refer to the pixel location in the image. Basically what Matab does is to compute, for every pixel location in both images, the difference between the intensity value at that pixel and the mean intensity of the whole image, denoted as a letter with a straightline over it.
As Kostya pointed out, typing edit corr2 in the command window will show you the code used by Matlab to compute the correlation coefficient. The formula is basically this:
a = a - mean2(a);
b = b - mean2(b);
r = sum(sum(a.*b))/sqrt(sum(sum(a.*a))*sum(sum(b.*b)));
where:
a is the input image and b is the image you wish to compare to a.
If we break down the formula, we see that a - mean2(a) and b-mean2(b) are the elements in the numerator of the above equation. mean2(a) is equivalent to mean(mean(a)) or mean(a(:)), that is the mean intensity of the whole image. This is only calculated once.
The 3rd line of code calculates the coefficient. Here sum(sum(a.*b)) calculates the double-sum present in the formula element-wise, that is considering each pixel location separately. Be aware that using sum(a) calculates the sum in every column individually, hence in order to get a single value you need to apply sum twice.
That's pretty much the same happening in the denominator, however calculations are performed on a-mean2(a)^2 and b-mean2(b)^2. You can see this a some kind of normalization process in which you consider the pixel intensity difference among each individual image.
As for your last comment, you can break down an image into small blocks and calculate the correlation coefficient on them; that might save some time for very large images but since everything is vectorized the calculation is quite fast. It might be useful in distributed processing I guess. Of course the correlation coefficient between 2 blocks of images is not necessarily identical to that of the whole image.
For the sake of curiosity you can look at this paper which highlights some caveats in using the correlation coefficient for image comparison.
Hope that makes things a bit clearer!
First I describe the physics, it is in a axisymmetric space, one sound source was placed at the original point, one sensor was placed on the axis under the source. Giving the source wave form, I try to get the sensor's waveform. all materiel parameter were known, for instance, sound speed, density.
I write the Matlab script to calculate it, by solving the sound propagation equation I can get
one function, say, A(w,k), w is frequency and k is wavenumber, this is so called frequency-wavenumber field. My matlab code like this,
discrete w and k, get a A array. first use FFT to k, get space and frequency information
then, FFT to w, get space and time information, that is the waveform at different point.
the fake code
for i_w=...
w=...
for i_k=...
k=...
M=A(w,k)
end
wave_space_freq=ifft(M)
end % here can specify the only point of the sensor
wave_space_freq=ifft(wave_space_freq)
My question is do I need to make conjugation and flip when I use IFFT,like ifft(M,0,fliplr(conj(M))) . because I saw some-others use them, but I don't understand why?
If you want a strictly real-valued result waveform (not complex with significant imaginary components), then the input to an IFFT has to be conjugate symmetric, such as:
ifft(dc_term,M,0,fliplr(conj(M))).
Let's say For each pixel, the gradient ∇g= [∂f/∂x, ∂f/∂y]. Then the first derivative should be measured by two operators like 1/2[1,0,1;0,0,0;-1,0,-1] & 1/2[-1,0,1;0,0,0;-1,0,-1]
then:
[i,j]=gradient(im);
filt1=[1,0,1;0,0,0;-1,0,-1];
filt2=[-1,0,1;0,0,0;-1,0,-1];
ii=(1./2).*(conv2(filt1,i));
jj=(1./2).*(conv2(filt2,j));
G_x=conv2(ii,im);
G_y=conv2(jj,im);
Is it correct or I should first multiply 1/2 to the operators, and then convolve them?
since associativity (with scalars) is a quality of convolutions the order of the multiplication should not play any rolle.
On the other hand your filters don't seem to me like they perform a differentiation. The classical filter for the discrete differentiation would be a Sobel that looks something like this:
[1,0,-1
2,0,-2
1,0,-1]
and
[1,2,1
0,0,0
-1,-2,-1]
For the purposes of optimizing the computation, it helps to apply the scaling of 1/2 directly to the filter kernels
filt1 = filt1/2;
Otherwise, if done afterward, N^2 additional multiplications have to be done to the NxN image pixels, instead of just 9 multiplications to a 3x3 kernel.
Beyond that, I agree with McMa. Your computations don't look anything like a differentiation. In fact, you already apply gradient() in the very first line, so I don't understand what more you need.
I'd be inclined to use the imgradient and imgradientxy functions in MATLAB. If you want directional gradients, use imgradientxy and if you want gradient magnitude and direction components, use imgradient.
You can choose to have derivatives computed using Sobel,Prewitt or Roberts gradient kernels or using central or intermediate differences.
Here's an example:
[Gx,Gy] = imgradientxy(im,'Sobel');
Instead if you want to continue using conv2, you can get gradient kernels using the fspecial function.
kernelx = fspecial('sobel');
kernely = kernelx';
I have a dataset Sig of size 65536 x 192 in Matlab. If I want to take the one-dimensional fft along the second dimension, I could either do a for loop:
%pre-allocate ect..
for i=1:65536
F(i,:) = fft(Sig(i,:));
end
or I could specify the dimension and do it without the for loop:
F = fft(Sig,[],2);
which is about 20 times faster for my dataset.
I have looked for something similar for the discrete wavelet transform (dwt), but been unable to find it. So I was wondering if anyone knows a way to do dwt across a specified dimension in Matlab? Or do I have to use for loops?
In your loop FFT example, it seems you operate on lines. Matlab use a Column-major order. It may explain the difference of performance. Is the performance the same if you operate on columns ?
If this is the right explanation, you could use dwt in a loop.
A solution if you really need performance is to do your own MEX calling a C discrete wavelet transform library the way you want.
I presume you're using the function from the Wavelet Toolbox: http://www.mathworks.co.uk/help/toolbox/wavelet/ref/dwt.html
The documentation doesn't seem to describe acting on an array, so it's probably not supported. If it does allow you to input an array, then it will operate on the first non-singleton dimension or it will ignore the shape and treat it as a vector.