I have run into a very peculiar problem. It might seem silly to a lot of you. But I am in dire need of a way out. I am analyzing sets of high-speed images with MATLAB. The image of interest (https://www.dropbox.com/s/h4h26y3mvpao8m6/sample.png?dl=0) is an average of 3000 images (background subtracted). As shown in the picture, I am reading the pixel intensities/values along columns. As this is a laser beam, the shape or beam profile away from the wall has the shape of a Gaussian distribution. As I approach to the wall (the brightest part at the right of the image) because of some effect the shape is turning into one like a log-normal distribution. In this spreadsheet (https://www.dropbox.com/s/yeim06a5cq3iqg8/sample.xlsx?dl=0) I have pasted the raw intensities as I read thru from point A to point B. The column D has the raw intensities and the column E has the values achieved with a 'sgolay' fit of the column D values. If I plot these it pretty much has the shape of a lognormal distribution. I can get the mu and sigma with the 'lognfit' or 'fitdist' functions. Now the question is what is the equation [expressed as a function of pixel location (x) or the pixel intensity (y)] of the fitted 'lognormal curve' that could be used to recreate the fitted curve? Your help is highly appreciated.
The lognfit extracts the mu and the sigma of the lognormal distribution. The mu is the mean of logarithmic values and sigma the standard deviation of logarithmic values. You can refer to https://en.wikipedia.org/wiki/Log-normal_distribution for the shape of the function given mu and sigma.
With logrnd(mu,sigma) you can generate samples from the same distribution:
https://it.mathworks.com/help/stats/lognrnd.html?searchHighlight=lognrnd&s_tid=srchtitle_lognrnd_1
Related
I want to evaluate the grid quality where all coordinates differ in the real case.
Signal is of a ECG signal where average life-time is 75 years.
My task is to evaluate its age at the moment of measurement, which is an inverse problem.
I think 2D approximation of the 3D case is hard (done here by Abo-Zahhad) with with 3-leads (2 on chest and one at left leg - MIT-BIT arrhythmia database):
where f is a piecewise continuous function in R^2, \epsilon is the error matrix and A is a 2D matrix.
Now, I evaluate the average grid distance in x-axis (time) and average grid distance in y-axis (energy).
I think this can be done by Matlab's Image Analysis toolbox.
However, I am not sure how complete the toolbox's approaches are.
I think a transform approach must be used in the setting of uneven and noncontinuous grids. One approach is exact linear time euclidean distance transforms of grid line sampled shapes by Joakim Lindblad et all.
The method presents a distance transform (DT) which assigns to each image point its smallest distance to a selected subset of image points.
This kind of approach is often a basis of algorithms for many methods in image analysis.
I tested unsuccessfully the case with bwdist (Distance transform of binary image) with chessboard (returns empty square matrix), cityblock, euclidean and quasi-euclidean where the last three options return full matrix.
Another pseudocode
% https://stackoverflow.com/a/29956008/54964
%// retrieve picture
imgRGB = imread('dummy.png');
%// detect lines
imgHSV = rgb2hsv(imgRGB);
BW = (imgHSV(:,:,3) < 1);
BW = imclose(imclose(BW, strel('line',40,0)), strel('line',10,90));
%// clear those masked pixels by setting them to background white color
imgRGB2 = imgRGB;
imgRGB2(repmat(BW,[1 1 3])) = 255;
%// show extracted signal
imshow(imgRGB2)
where I think the approach will not work here because the grids are not necessarily continuous and not necessary ideal.
pdist based on the Lumbreras' answer
In the real examples, all coordinates differ such that pdist hamming and jaccard are always 1 with real data.
The options euclidean, cytoblock, minkowski, chebychev, mahalanobis, cosine, correlation, and spearman offer some descriptions of the data.
However, these options make me now little sense in such full matrices.
I want to estimate how long the signal can live.
Sources
J. Müller, and S. Siltanen. Linear and nonlinear inverse problems with practical applications.
EIT with the D-bar method: discontinuous heart-and-lungs phantom. http://wiki.helsinki.fi/display/mathstatHenkilokunta/EIT+with+the+D-bar+method%3A+discontinuous+heart-and-lungs+phantom Visited 29-Feb 2016.
There is a function in Matlab defined as pdist which computes the pairwisedistance between all row elements in a matrix and enables you to choose the type of distance you want to use (Euclidean, cityblock, correlation). Are you after something like this? Not sure I understood your question!
cheers!
Simply, do not do it in the post-processing. Those artifacts of the body can be about about raster images, about the viewer and/or ... Do quality assurance in the signal generation/processing step.
It is much easier to evaluate the original signal than its views.
I have to distributions p and q I have no knowledge about their mean and variance I want to fit a normal distribution curve to the histograms I have and get the mean and variance of the fitting
when I use
histfit(p);
histfit(q);
I get the results in the figure:
when I use
[f,x]=hist[p];
[mu,sigma]=normfit(p)
pdf=normpdf(x,mu,sigma);
figure;
hold on
bar(x,f);
plot(x,pdf);
I get the results in the figure where I don't see the fitting at all:
Eventually I would like to present graphically histfit,
,but also obtain the true standard deviation and mean of the fitting for further use.
help anyone?
What histfit does is plotting a pdf normalized to the scale of the histogram. A scaling factor of numel(p).*mean(diff(x)) is applied to match the curve with the histogram. It scales the area under the pdf to the area the histogram covers.
I have an RGB image and I am trying to calculate its Gaussian derivative.
Image is a greyscale image and the Gaussian window is 5x5,st is the standard deviation
This is the code i am using in order to find a 2D Gaussian derivative,in Matlab:
N=2
[X,Y]=meshgrid(-N:N,-N:N)
G=exp(-(x.^2+y.^2)/(2*st^2))/(2*pi*st)
G_x = -x.*G/(st^2);
G_x_s = G_x/sum(G_x(:));
G_y = -y.*G/(st^2);
G_y_s = G_y/sum(G_y(:));
where st is the standard deviation i am using. Before I proceed to the convolution of the Image using G_x_s and G_y_s, i have the following problem. When I use a standard deviation that is an even number(2,4,6,8) the program works and gives results as expected. But when i use an odd number for standard deviation (3 or 5) then the G_y_s value becomes Inf because sum(G_y(:))=0. I do not understand that behavior and I was wondering if there is some problem with the code or if in the above formula the standard deviation can only be an even number. Any help will be greatly appreciated.
Thank you.
Your program doesn't work at all. The results you find when using an even number is just because of some numerical errors.
Your G will be a matrix symmetrical to the center. x and y are both point symmetrical to the center. So the multiplication (G times x or y) will result in a matrix with a sum of zero. So a division by that sum is a division by zero. Everything else you observe is because of some roundoff errors. Here, I see a sum og G_xof about 1.3e-17.
I think your error is in the multiplication x.*G and y.*G. I can not figure out why you would do that.
I assume you want to do edge detection rigth? You can use fspecialto create several edge filters. Laplace of gaussian for instance. You could also create two gaussian filters with different standard deviations and subtract them from another to get an edge filter.
this is my problem:
I have the next data "A", which looks like:
As you can see, I have drawn with red circles the apparently peaks, the most defined are 2 and 7, I say that they are defined because its standard deviation is low in comparison with the other peaks (especially the second one).
What I need is a way (anyway) to get the values and the standard deviation of n peaks in a numeric array.
I have tried with "clusters", but I got no good results:
First of all, I used "kmeans" MATLAB function, and I realize that this algorithm doesn't group peaks as I need. As you can see in the picture above, in the red circle, that cluster has at less 3 or 4 peaks. And kmeans need that you set the number of clusters, and I need to identify it automatically.
I hope that anyone can give me some ideas, or a way to get better results, thanks.
Pd: I leave the data "A" in the next link.
https://drive.google.com/file/d/0B4WGV21GqSL5a2EyQ2l0SHZURzA/edit?usp=sharing
The problem is that your axes have very different meaning.
K-means optimizes variance. But variance in X is something entirely different than variance in Y, isn't it? Furthermore, each of these methods will split your data in both X and Y, whereas I assume you want the data to be partitioned on the X axis only.
I suggest the following: consider the Y axis to be a weight, and X axis to be a position.
Then perform weighted density estimation, and look for low density to separate your clusters.
I can't help you with MATLAB. I don't use it.
Mathematically, what you want to do is place a Gaussian at each point, with area Y and center X. Then find minima and maxima on the sum of these Gaussians. See Wikipedia, Kernel Density Estimation for details; except that you want to use the Y axis as weights. You could maybe also use 1/Y as standard deviation, if you don't want to use weights.
I know that I can fit a histogram with a gamma distribution in this way:
histfit(data,bins-number,'gamma');figure(gcf);
And I know too that I can normalize a histogram with histnorm. But how can I create a normalized gamma distribution with its histogram?
Any idea or suggestion? Thanks for any help!
EDIT:
In response to BruceWarrior's comment below, histfit will normalize the data for you... just replace x with your data. If you want to know how to normalize a histogram yourself such that it is a probability density, see my answer to that very question. Note that the accepted answer will not give you a probability density (i.e., the area under the curve will not be 1).
You can use the gamrnd function to generate random variables with a Gamma distribution for a given shape parameter a and scale parameter b. You can then call histfit on this data to fit the Gamma distribution to the normalized histogram. Here's an example:
x=gamrnd(1,2,1000,1);
histfit(x,50,'gamma')
a=1,b=2
a=2, b=2