nlinfit appears better than fitgmdist for fitting normal mixture - matlab

I have a vector of data consisting of about 2 million samples that I suspect is a mixture of two gaussian's. I try to fit the data, Data, to a mixture using matlab's fitgmdist.
From histogram:
% histogram counts of X with 1000 bins.
[Yhist, x] = histcounts(Data, 1000, 'normalization', 'pdf');
x = (x(1:end-1) + x(2:end))/2;
Using fitgmdist:
% Increase no. of iterations. default is 100.
opts.MaxIter = 300;
% Ensure that it does all iterations.
opts.TolFun = 0;
GMModel = fitgmdist(Data, 2, 'Options', opts, 'Start', 'plus');
wts = GMModel.ComponentProportion;
mu = GMModel.mu;
sig = sqrt(squeeze(GMModel.Sigma));
Ygmfit = wts(1)*normpdf(x(:), mu(1), sig(1)) + wts(2)*normpdf(x(:), mu(2), sig(2));
Mixture results with fitgmdist:
wts = [0.6780, 0.322], mu = [-7.6444, -9.7831], sig = [0.8243, 0.5947]
Next I try using nlinfit:
% Define the callback function for nlinfit.
function y = nmmix(a, x)
a(1:2) = a(1:2)/sum(a);
y = a(1)*normpdf(x(:), a(3), a(5)) + a(2)*normpdf(x(:), a(4), a(6));
end
init_wts = [0.66, 1-0.66];
init_mu = [-7.7, -9.75];
init_sig = [0.5, 0.5];
a = nlinfit(x(:), Yhist(:), #nmmix, [init_wts, init_mu, init_sig]);
wts = a(1:2)/sum(a(1:2));
mu = a(3:4);
sig = a(5:6);
Ynlinfit = wts(1)*normpdf(x(:), mu(1), sig(1)) + wts(2)*normpdf(x(:), mu(2), sig(2));
Mixture results with nlinfit:
wts = [0.6349, 0.3651], mu = [-7.6305, -9.6991], sig = [0.6773, 0.6031]
% Plot to compare the results
figure;
hold on
plot(x(:), Yhist, 'b');
plot(x(:), Ygmfit, 'k');
plot(x(:), Ynlinfit, 'r');
It seems to be that the non-linear fit (red curve) is intuitively a better approximation to the histogram (blue curve) than "fitgmdist" (black curve).
The results are similar even if I use a finer histogram, say with 100,000 bins.
What can be the source of this discrepancy?
Added later: Of course one would not expect the results to be the same, but I would expect that the visual quality of the two fits would be comparable.

Related

Transform a hyperbolic Poincare disk to the band model

I want to transform a hyperbolic Poincaré disk with image textures (examples in https://www.flickr.com/photos/gbachelier/albums/72157676467905456) to the Bulatov band model and found in https://www.slideshare.net/chamb3rlain/a-poor-mans-hyperbolic-square-mapping (slide 25) the function based on the inverse hyperbolic tan that should do this: f(z) = 2*pi*atanh(z). But inserting it in a meshgrid based framework for image warping with complex valued functions I got nothing like the expected band structure.
So how could the mapping to the band model be made?
wh_out = num2cell([1000,2000]); [w_o,h_o] = wh_out{:};
[h_i, w_i, d] = size(img);
% GENERATE OUTPUT-GRID AND NORMALIZE [-1 1]
[xo1,yo1] = meshgrid(1:w_o,1:h_o);
xo1 = (xo1/w_o)*2 - 1;
yo1 = (yo1/h_o)*2 - 1;
% WARP OUTPUT-GRID WITH f(z) AND SEPARATE REAL AND IMAGINARY PARTS
fxiy = 2 * pi * atanh(deg2rad(xo1+1i*y_o1)));
xo1=real(fxiy);
yo1=imag(fxiy);
% NORMALIZE OUTPUT-GRID [0 1]
xo1 = (xo1+1)/2;
yo1 = (yo1+1)/2;
% GENERATE INPUT-GRID AND NORMALIZE [0 1]
[xi,yi] = meshgrid(linspace(0,w_i+1,w_i),linspace(0,h_i+1,h_i));
xi = xi / w_i;
yi = yi / h_i;
% INTERPOLATION OF OUTPUT-IMAGE
img = double(img);
img_out = zeros(h_o,w_o,d);
for k = 1:d; img_out(:,:,k) = uint8(interp2(xi, yi, img(:,:,k), xo1, yo1, interpol_meth)); end
After all I found in "Peichang Ouyang, Kwokwai Chung: Beautiful Math, Part 3: Hyperbolic Aesthetic Patterns Based on Conformal Mappings". DOI: 10.1109/MCG.2014.23 the mapping fz = (exp(0.5*pi.*z)-1)./(exp(0.5*pi.*z)+1) that generates a periodic band segment img_seg from a hyperbolic disc that can simply be transformed to a band with img_band = repmat(img_seg, 1, n).

Quantify sharpness using frequencies [duplicate]

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I was wondering if there is a way to determine if an image is blurry or not by analyzing the image data.
Another very simple way to estimate the sharpness of an image is to use a Laplace (or LoG) filter and simply pick the maximum value. Using a robust measure like a 99.9% quantile is probably better if you expect noise (i.e. picking the Nth-highest contrast instead of the highest contrast.) If you expect varying image brightness, you should also include a preprocessing step to normalize image brightness/contrast (e.g. histogram equalization).
I've implemented Simon's suggestion and this one in Mathematica, and tried it on a few test images:
The first test blurs the test images using a Gaussian filter with a varying kernel size, then calculates the FFT of the blurred image and takes the average of the 90% highest frequencies:
testFft[img_] := Table[
(
blurred = GaussianFilter[img, r];
fft = Fourier[ImageData[blurred]];
{w, h} = Dimensions[fft];
windowSize = Round[w/2.1];
Mean[Flatten[(Abs[
fft[[w/2 - windowSize ;; w/2 + windowSize,
h/2 - windowSize ;; h/2 + windowSize]]])]]
), {r, 0, 10, 0.5}]
Result in a logarithmic plot:
The 5 lines represent the 5 test images, the X axis represents the Gaussian filter radius. The graphs are decreasing, so the FFT is a good measure for sharpness.
This is the code for the "highest LoG" blurriness estimator: It simply applies an LoG filter and returns the brightest pixel in the filter result:
testLaplacian[img_] := Table[
(
blurred = GaussianFilter[img, r];
Max[Flatten[ImageData[LaplacianGaussianFilter[blurred, 1]]]];
), {r, 0, 10, 0.5}]
Result in a logarithmic plot:
The spread for the un-blurred images is a little better here (2.5 vs 3.3), mainly because this method only uses the strongest contrast in the image, while the FFT is essentially a mean over the whole image. The functions are also decreasing faster, so it might be easier to set a "blurry" threshold.
Yes, it is. Compute the Fast Fourier Transform and analyse the result. The Fourier transform tells you which frequencies are present in the image. If there is a low amount of high frequencies, then the image is blurry.
Defining the terms 'low' and 'high' is up to you.
Edit:
As stated in the comments, if you want a single float representing the blurryness of a given image, you have to work out a suitable metric.
nikie's answer provide such a metric. Convolve the image with a Laplacian kernel:
1
1 -4 1
1
And use a robust maximum metric on the output to get a number which you can use for thresholding. Try to avoid smoothing too much the images before computing the Laplacian, because you will only find out that a smoothed image is indeed blurry :-).
During some work with an auto-focus lens, I came across this very useful set of algorithms for detecting image focus. It's implemented in MATLAB, but most of the functions are quite easy to port to OpenCV with filter2D.
It's basically a survey implementation of many focus measurement algorithms. If you want to read the original papers, references to the authors of the algorithms are provided in the code. The 2012 paper by Pertuz, et al. Analysis of focus measure operators for shape from focus (SFF) gives a great review of all of these measure as well as their performance (both in terms of speed and accuracy as applied to SFF).
EDIT: Added MATLAB code just in case the link dies.
function FM = fmeasure(Image, Measure, ROI)
%This function measures the relative degree of focus of
%an image. It may be invoked as:
%
% FM = fmeasure(Image, Method, ROI)
%
%Where
% Image, is a grayscale image and FM is the computed
% focus value.
% Method, is the focus measure algorithm as a string.
% see 'operators.txt' for a list of focus
% measure methods.
% ROI, Image ROI as a rectangle [xo yo width heigth].
% if an empty argument is passed, the whole
% image is processed.
%
% Said Pertuz
% Abr/2010
if ~isempty(ROI)
Image = imcrop(Image, ROI);
end
WSize = 15; % Size of local window (only some operators)
switch upper(Measure)
case 'ACMO' % Absolute Central Moment (Shirvaikar2004)
if ~isinteger(Image), Image = im2uint8(Image);
end
FM = AcMomentum(Image);
case 'BREN' % Brenner's (Santos97)
[M N] = size(Image);
DH = Image;
DV = Image;
DH(1:M-2,:) = diff(Image,2,1);
DV(:,1:N-2) = diff(Image,2,2);
FM = max(DH, DV);
FM = FM.^2;
FM = mean2(FM);
case 'CONT' % Image contrast (Nanda2001)
ImContrast = inline('sum(abs(x(:)-x(5)))');
FM = nlfilter(Image, [3 3], ImContrast);
FM = mean2(FM);
case 'CURV' % Image Curvature (Helmli2001)
if ~isinteger(Image), Image = im2uint8(Image);
end
M1 = [-1 0 1;-1 0 1;-1 0 1];
M2 = [1 0 1;1 0 1;1 0 1];
P0 = imfilter(Image, M1, 'replicate', 'conv')/6;
P1 = imfilter(Image, M1', 'replicate', 'conv')/6;
P2 = 3*imfilter(Image, M2, 'replicate', 'conv')/10 ...
-imfilter(Image, M2', 'replicate', 'conv')/5;
P3 = -imfilter(Image, M2, 'replicate', 'conv')/5 ...
+3*imfilter(Image, M2, 'replicate', 'conv')/10;
FM = abs(P0) + abs(P1) + abs(P2) + abs(P3);
FM = mean2(FM);
case 'DCTE' % DCT energy ratio (Shen2006)
FM = nlfilter(Image, [8 8], #DctRatio);
FM = mean2(FM);
case 'DCTR' % DCT reduced energy ratio (Lee2009)
FM = nlfilter(Image, [8 8], #ReRatio);
FM = mean2(FM);
case 'GDER' % Gaussian derivative (Geusebroek2000)
N = floor(WSize/2);
sig = N/2.5;
[x,y] = meshgrid(-N:N, -N:N);
G = exp(-(x.^2+y.^2)/(2*sig^2))/(2*pi*sig);
Gx = -x.*G/(sig^2);Gx = Gx/sum(Gx(:));
Gy = -y.*G/(sig^2);Gy = Gy/sum(Gy(:));
Rx = imfilter(double(Image), Gx, 'conv', 'replicate');
Ry = imfilter(double(Image), Gy, 'conv', 'replicate');
FM = Rx.^2+Ry.^2;
FM = mean2(FM);
case 'GLVA' % Graylevel variance (Krotkov86)
FM = std2(Image);
case 'GLLV' %Graylevel local variance (Pech2000)
LVar = stdfilt(Image, ones(WSize,WSize)).^2;
FM = std2(LVar)^2;
case 'GLVN' % Normalized GLV (Santos97)
FM = std2(Image)^2/mean2(Image);
case 'GRAE' % Energy of gradient (Subbarao92a)
Ix = Image;
Iy = Image;
Iy(1:end-1,:) = diff(Image, 1, 1);
Ix(:,1:end-1) = diff(Image, 1, 2);
FM = Ix.^2 + Iy.^2;
FM = mean2(FM);
case 'GRAT' % Thresholded gradient (Snatos97)
Th = 0; %Threshold
Ix = Image;
Iy = Image;
Iy(1:end-1,:) = diff(Image, 1, 1);
Ix(:,1:end-1) = diff(Image, 1, 2);
FM = max(abs(Ix), abs(Iy));
FM(FM<Th)=0;
FM = sum(FM(:))/sum(sum(FM~=0));
case 'GRAS' % Squared gradient (Eskicioglu95)
Ix = diff(Image, 1, 2);
FM = Ix.^2;
FM = mean2(FM);
case 'HELM' %Helmli's mean method (Helmli2001)
MEANF = fspecial('average',[WSize WSize]);
U = imfilter(Image, MEANF, 'replicate');
R1 = U./Image;
R1(Image==0)=1;
index = (U>Image);
FM = 1./R1;
FM(index) = R1(index);
FM = mean2(FM);
case 'HISE' % Histogram entropy (Krotkov86)
FM = entropy(Image);
case 'HISR' % Histogram range (Firestone91)
FM = max(Image(:))-min(Image(:));
case 'LAPE' % Energy of laplacian (Subbarao92a)
LAP = fspecial('laplacian');
FM = imfilter(Image, LAP, 'replicate', 'conv');
FM = mean2(FM.^2);
case 'LAPM' % Modified Laplacian (Nayar89)
M = [-1 2 -1];
Lx = imfilter(Image, M, 'replicate', 'conv');
Ly = imfilter(Image, M', 'replicate', 'conv');
FM = abs(Lx) + abs(Ly);
FM = mean2(FM);
case 'LAPV' % Variance of laplacian (Pech2000)
LAP = fspecial('laplacian');
ILAP = imfilter(Image, LAP, 'replicate', 'conv');
FM = std2(ILAP)^2;
case 'LAPD' % Diagonal laplacian (Thelen2009)
M1 = [-1 2 -1];
M2 = [0 0 -1;0 2 0;-1 0 0]/sqrt(2);
M3 = [-1 0 0;0 2 0;0 0 -1]/sqrt(2);
F1 = imfilter(Image, M1, 'replicate', 'conv');
F2 = imfilter(Image, M2, 'replicate', 'conv');
F3 = imfilter(Image, M3, 'replicate', 'conv');
F4 = imfilter(Image, M1', 'replicate', 'conv');
FM = abs(F1) + abs(F2) + abs(F3) + abs(F4);
FM = mean2(FM);
case 'SFIL' %Steerable filters (Minhas2009)
% Angles = [0 45 90 135 180 225 270 315];
N = floor(WSize/2);
sig = N/2.5;
[x,y] = meshgrid(-N:N, -N:N);
G = exp(-(x.^2+y.^2)/(2*sig^2))/(2*pi*sig);
Gx = -x.*G/(sig^2);Gx = Gx/sum(Gx(:));
Gy = -y.*G/(sig^2);Gy = Gy/sum(Gy(:));
R(:,:,1) = imfilter(double(Image), Gx, 'conv', 'replicate');
R(:,:,2) = imfilter(double(Image), Gy, 'conv', 'replicate');
R(:,:,3) = cosd(45)*R(:,:,1)+sind(45)*R(:,:,2);
R(:,:,4) = cosd(135)*R(:,:,1)+sind(135)*R(:,:,2);
R(:,:,5) = cosd(180)*R(:,:,1)+sind(180)*R(:,:,2);
R(:,:,6) = cosd(225)*R(:,:,1)+sind(225)*R(:,:,2);
R(:,:,7) = cosd(270)*R(:,:,1)+sind(270)*R(:,:,2);
R(:,:,7) = cosd(315)*R(:,:,1)+sind(315)*R(:,:,2);
FM = max(R,[],3);
FM = mean2(FM);
case 'SFRQ' % Spatial frequency (Eskicioglu95)
Ix = Image;
Iy = Image;
Ix(:,1:end-1) = diff(Image, 1, 2);
Iy(1:end-1,:) = diff(Image, 1, 1);
FM = mean2(sqrt(double(Iy.^2+Ix.^2)));
case 'TENG'% Tenengrad (Krotkov86)
Sx = fspecial('sobel');
Gx = imfilter(double(Image), Sx, 'replicate', 'conv');
Gy = imfilter(double(Image), Sx', 'replicate', 'conv');
FM = Gx.^2 + Gy.^2;
FM = mean2(FM);
case 'TENV' % Tenengrad variance (Pech2000)
Sx = fspecial('sobel');
Gx = imfilter(double(Image), Sx, 'replicate', 'conv');
Gy = imfilter(double(Image), Sx', 'replicate', 'conv');
G = Gx.^2 + Gy.^2;
FM = std2(G)^2;
case 'VOLA' % Vollath's correlation (Santos97)
Image = double(Image);
I1 = Image; I1(1:end-1,:) = Image(2:end,:);
I2 = Image; I2(1:end-2,:) = Image(3:end,:);
Image = Image.*(I1-I2);
FM = mean2(Image);
case 'WAVS' %Sum of Wavelet coeffs (Yang2003)
[C,S] = wavedec2(Image, 1, 'db6');
H = wrcoef2('h', C, S, 'db6', 1);
V = wrcoef2('v', C, S, 'db6', 1);
D = wrcoef2('d', C, S, 'db6', 1);
FM = abs(H) + abs(V) + abs(D);
FM = mean2(FM);
case 'WAVV' %Variance of Wav...(Yang2003)
[C,S] = wavedec2(Image, 1, 'db6');
H = abs(wrcoef2('h', C, S, 'db6', 1));
V = abs(wrcoef2('v', C, S, 'db6', 1));
D = abs(wrcoef2('d', C, S, 'db6', 1));
FM = std2(H)^2+std2(V)+std2(D);
case 'WAVR'
[C,S] = wavedec2(Image, 3, 'db6');
H = abs(wrcoef2('h', C, S, 'db6', 1));
V = abs(wrcoef2('v', C, S, 'db6', 1));
D = abs(wrcoef2('d', C, S, 'db6', 1));
A1 = abs(wrcoef2('a', C, S, 'db6', 1));
A2 = abs(wrcoef2('a', C, S, 'db6', 2));
A3 = abs(wrcoef2('a', C, S, 'db6', 3));
A = A1 + A2 + A3;
WH = H.^2 + V.^2 + D.^2;
WH = mean2(WH);
WL = mean2(A);
FM = WH/WL;
otherwise
error('Unknown measure %s',upper(Measure))
end
end
%************************************************************************
function fm = AcMomentum(Image)
[M N] = size(Image);
Hist = imhist(Image)/(M*N);
Hist = abs((0:255)-255*mean2(Image))'.*Hist;
fm = sum(Hist);
end
%******************************************************************
function fm = DctRatio(M)
MT = dct2(M).^2;
fm = (sum(MT(:))-MT(1,1))/MT(1,1);
end
%************************************************************************
function fm = ReRatio(M)
M = dct2(M);
fm = (M(1,2)^2+M(1,3)^2+M(2,1)^2+M(2,2)^2+M(3,1)^2)/(M(1,1)^2);
end
%******************************************************************
A few examples of OpenCV versions:
// OpenCV port of 'LAPM' algorithm (Nayar89)
double modifiedLaplacian(const cv::Mat& src)
{
cv::Mat M = (Mat_<double>(3, 1) << -1, 2, -1);
cv::Mat G = cv::getGaussianKernel(3, -1, CV_64F);
cv::Mat Lx;
cv::sepFilter2D(src, Lx, CV_64F, M, G);
cv::Mat Ly;
cv::sepFilter2D(src, Ly, CV_64F, G, M);
cv::Mat FM = cv::abs(Lx) + cv::abs(Ly);
double focusMeasure = cv::mean(FM).val[0];
return focusMeasure;
}
// OpenCV port of 'LAPV' algorithm (Pech2000)
double varianceOfLaplacian(const cv::Mat& src)
{
cv::Mat lap;
cv::Laplacian(src, lap, CV_64F);
cv::Scalar mu, sigma;
cv::meanStdDev(lap, mu, sigma);
double focusMeasure = sigma.val[0]*sigma.val[0];
return focusMeasure;
}
// OpenCV port of 'TENG' algorithm (Krotkov86)
double tenengrad(const cv::Mat& src, int ksize)
{
cv::Mat Gx, Gy;
cv::Sobel(src, Gx, CV_64F, 1, 0, ksize);
cv::Sobel(src, Gy, CV_64F, 0, 1, ksize);
cv::Mat FM = Gx.mul(Gx) + Gy.mul(Gy);
double focusMeasure = cv::mean(FM).val[0];
return focusMeasure;
}
// OpenCV port of 'GLVN' algorithm (Santos97)
double normalizedGraylevelVariance(const cv::Mat& src)
{
cv::Scalar mu, sigma;
cv::meanStdDev(src, mu, sigma);
double focusMeasure = (sigma.val[0]*sigma.val[0]) / mu.val[0];
return focusMeasure;
}
No guarantees on whether or not these measures are the best choice for your problem, but if you track down the papers associated with these measures, they may give you more insight. Hope you find the code useful! I know I did.
Building off of Nike's answer. Its straightforward to implement the laplacian based method with opencv:
short GetSharpness(char* data, unsigned int width, unsigned int height)
{
// assumes that your image is already in planner yuv or 8 bit greyscale
IplImage* in = cvCreateImage(cvSize(width,height),IPL_DEPTH_8U,1);
IplImage* out = cvCreateImage(cvSize(width,height),IPL_DEPTH_16S,1);
memcpy(in->imageData,data,width*height);
// aperture size of 1 corresponds to the correct matrix
cvLaplace(in, out, 1);
short maxLap = -32767;
short* imgData = (short*)out->imageData;
for(int i =0;i<(out->imageSize/2);i++)
{
if(imgData[i] > maxLap) maxLap = imgData[i];
}
cvReleaseImage(&in);
cvReleaseImage(&out);
return maxLap;
}
Will return a short indicating the maximum sharpness detected, which based on my tests on real world samples, is a pretty good indicator of if a camera is in focus or not. Not surprisingly, normal values are scene dependent but much less so than the FFT method which has to high of a false positive rate to be useful in my application.
I came up with a totally different solution.
I needed to analyse video still frames to find the sharpest one in every (X) frames. This way, I would detect motion blur and/or out of focus images.
I ended up using Canny Edge detection and I got VERY VERY good results with almost every kind of video (with nikie's method, I had problems with digitalized VHS videos and heavy interlaced videos).
I optimized the performance by setting a region of interest (ROI) on the original image.
Using EmguCV :
//Convert image using Canny
using (Image<Gray, byte> imgCanny = imgOrig.Canny(225, 175))
{
//Count the number of pixel representing an edge
int nCountCanny = imgCanny.CountNonzero()[0];
//Compute a sharpness grade:
//< 1.5 = blurred, in movement
//de 1.5 à 6 = acceptable
//> 6 =stable, sharp
double dSharpness = (nCountCanny * 1000.0 / (imgCanny.Cols * imgCanny.Rows));
}
Thanks nikie for that great Laplace suggestion.
OpenCV docs pointed me in the same direction:
using python, cv2 (opencv 2.4.10), and numpy...
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
numpy.max(cv2.convertScaleAbs(cv2.Laplacian(gray, 3)))
result is between 0-255. I found anything over 200ish is very in focus, and by 100, it's noticeably blurry. the max never really gets much under 20 even if it's completely blurred.
One way which I'm currently using measures the spread of edges in the image. Look for this paper:
#ARTICLE{Marziliano04perceptualblur,
author = {Pina Marziliano and Frederic Dufaux and Stefan Winkler and Touradj Ebrahimi},
title = {Perceptual blur and ringing metrics: Application to JPEG2000,” Signal Process},
journal = {Image Commun},
year = {2004},
pages = {163--172} }
It's usually behind a paywall but I've seen some free copies around. Basically, they locate vertical edges in an image, and then measure how wide those edges are. Averaging the width gives the final blur estimation result for the image. Wider edges correspond to blurry images, and vice versa.
This problem belongs to the field of no-reference image quality estimation. If you look it up on Google Scholar, you'll get plenty of useful references.
EDIT
Here's a plot of the blur estimates obtained for the 5 images in nikie's post. Higher values correspond to greater blur. I used a fixed-size 11x11 Gaussian filter and varied the standard deviation (using imagemagick's convert command to obtain the blurred images).
If you compare images of different sizes, don't forget to normalize by the image width, since larger images will have wider edges.
Finally, a significant problem is distinguishing between artistic blur and undesired blur (caused by focus miss, compression, relative motion of the subject to the camera), but that is beyond simple approaches like this one. For an example of artistic blur, have a look at the Lenna image: Lenna's reflection in the mirror is blurry, but her face is perfectly in focus. This contributes to a higher blur estimate for the Lenna image.
Answers above elucidated many things, but I think it is useful to make a conceptual distinction.
What if you take a perfectly on-focus picture of a blurred image?
The blurring detection problem is only well posed when you have a reference. If you need to design, e.g., an auto-focus system, you compare a sequence of images taken with different degrees of blurring, or smoothing, and you try to find the point of minimum blurring within this set. I other words you need to cross reference the various images using one of the techniques illustrated above (basically--with various possible levels of refinement in the approach--looking for the one image with the highest high-frequency content).
I tried solution based on Laplacian filter from this post. It didn't help me. So, I tried the solution from this post and it was good for my case (but is slow):
import cv2
image = cv2.imread("test.jpeg")
height, width = image.shape[:2]
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
def px(x, y):
return int(gray[y, x])
sum = 0
for x in range(width-1):
for y in range(height):
sum += abs(px(x, y) - px(x+1, y))
Less blurred image has maximum sum value!
You can also tune speed and accuracy by changing step, e.g.
this part
for x in range(width - 1):
you can replace with this one
for x in range(0, width - 1, 10):
Matlab code of two methods that have been published in highly regarded journals (IEEE Transactions on Image Processing) are available here: https://ivulab.asu.edu/software
check the CPBDM and JNBM algorithms. If you check the code it's not very hard to be ported and incidentally it is based on the Marzialiano's method as basic feature.
i implemented it use fft in matlab and check histogram of the fft compute mean and std but also fit function can be done
fa = abs(fftshift(fft(sharp_img)));
fb = abs(fftshift(fft(blured_img)));
f1=20*log10(0.001+fa);
f2=20*log10(0.001+fb);
figure,imagesc(f1);title('org')
figure,imagesc(f2);title('blur')
figure,hist(f1(:),100);title('org')
figure,hist(f2(:),100);title('blur')
mf1=mean(f1(:));
mf2=mean(f2(:));
mfd1=median(f1(:));
mfd2=median(f2(:));
sf1=std(f1(:));
sf2=std(f2(:));
That's what I do in Opencv to detect focus quality in a region:
Mat grad;
int scale = 1;
int delta = 0;
int ddepth = CV_8U;
Mat grad_x, grad_y;
Mat abs_grad_x, abs_grad_y;
/// Gradient X
Sobel(matFromSensor, grad_x, ddepth, 1, 0, 3, scale, delta, BORDER_DEFAULT);
/// Gradient Y
Sobel(matFromSensor, grad_y, ddepth, 0, 1, 3, scale, delta, BORDER_DEFAULT);
convertScaleAbs(grad_x, abs_grad_x);
convertScaleAbs(grad_y, abs_grad_y);
addWeighted(abs_grad_x, 0.5, abs_grad_y, 0.5, 0, grad);
cv::Scalar mu, sigma;
cv::meanStdDev(grad, /* mean */ mu, /*stdev*/ sigma);
focusMeasure = mu.val[0] * mu.val[0];

How to extend the line of 2 PolyFit from either side to intersect and get a combined fit line

I am trying to get combined fit line made from two linear polyfit from either side (should intersect), here is the picture of fit lines:
I am trying to make the two fit (blue) lines intersect and produce a combined fit line as shown in the picture below:
Note that the crest can happen anywhere so I cannot assume to be in the center.
Here is the code that creates the first plot:
xdatPart1 = R;
zdatPart1 = z;
n = 3000;
ln = length(R);
[sX,In] = sort(R,1);
sZ = z(In);
xdatP1 = sX(1:n,1);
zdatP1 = sZ(1:n,1);
n2 = ln - 3000;
xdatP2 = sX(n2:ln,1);
zdatP2 = sZ(n2:ln,1);
pp1 = polyfit(xdatP1,zdatP1,1);
pp2 = polyfit(xdatP2,zdatP2,1);
ff1 = polyval(pp1,xdatP1);
ff2 = polyval(pp2,xdatP2);
xDat = [xdatPart1];
zDat = [zdatPart1];
axes(handles.axes2);
cla(handles.axes2);
plot(xdatPart1,zdatPart1,'.r');
hold on
plot(xdatP1,ff1,'.b');
plot(xdatP2,ff2,'.b');
xlabel(['R ',units]);
ylabel(['Z ', units]);
grid on
hold off
Below's a rough implementation with no curve fitting toolbox. Although the code should be self-explanatory, here's an outline of the algorithm:
We generate some data.
We estimate the intersection point by smoothing the data and finding the location of the maximum value.
We fit a line to each side of the estimated intersection point.
We compute the intersection of the fitted lines using the fitted equations.
We use mkpp to construct a function handle to an "evaluateable" piecewise polynomial.
The output, ppfunc, is a function handle of 1 variable, that you can use just like any regular function.
Now, this solution is not optimal in any sense (such as MMSE, LSQ, etc.) but as you will see in the comparison with the result from MATLAB's toolbox, it's not that bad!
function ppfunc = q40160257
%% Define the ground truth:
center_x = 6 + randn(1);
center_y = 78.15 + 0.01 * randn(1);
% Define a couple of points for the left section
leftmost_x = 0;
leftmost_y = 78.015 + 0.01 * randn(1);
% Define a couple of points for the right section
rightmost_x = 14.8;
rightmost_y = 78.02 + 0.01 * randn(1);
% Find the line equations:
m1 = (center_y-leftmost_y)/(center_x-leftmost_x);
n1 = getN(leftmost_x,leftmost_y,m1);
m2 = (rightmost_y-center_y)/(rightmost_x-center_x);
n2 = getN(rightmost_x,rightmost_y,m2);
% Print the ground truth:
fprintf(1,'The line equations are: {y1=%f*x+%f} , {y2=%f*x+%f}\n',m1,n1,m2,n2)
%% Generate some data:
NOISE_MAGNITUDE = 0.002;
N_POINTS_PER_SIDE = 1000;
x1 = linspace(leftmost_x,center_x,N_POINTS_PER_SIDE);
y1 = m1*x1+n1+NOISE_MAGNITUDE*randn(1,numel(x1));
x2 = linspace(center_x,rightmost_x,N_POINTS_PER_SIDE);
y2 = m2*x2+n2+NOISE_MAGNITUDE*randn(1,numel(x2));
X = [x1 x2(2:end)]; Y = [y1 y2(2:end)];
%% See what we have:
figure(); plot(X,Y,'.r'); hold on;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Estimating the intersection point:
MOVING_AVERAGE_PERIOD = 10; % Play around with this value.
smoothed_data = conv(Y, ones(1,MOVING_AVERAGE_PERIOD)/MOVING_AVERAGE_PERIOD, 'same');
plot(X, smoothed_data, '-b'); ylim([floor(leftmost_y*10) ceil(center_y*10)]/10);
[~,centerInd] = max(smoothed_data);
fprintf(1,'The real intersection is at index %d, the estimated is at %d.\n',...
N_POINTS_PER_SIDE, centerInd);
%% Fitting a polynomial to each side:
p1 = polyfit(X(1:centerInd),Y(1:centerInd),1);
p2 = polyfit(X(centerInd+1:end),Y(centerInd+1:end),1);
[x_int,y_int] = getLineIntersection(p1,p2);
plot(x_int,y_int,'sg');
pp = mkpp([X(1) x_int X(end)],[p1; (p2 + [0 x_int*p2(1)])]);
ppfunc = #(x)ppval(pp,x);
plot(X, ppfunc(X),'-k','LineWidth',3)
legend('Original data', 'Smoothed data', 'Computed intersection',...
'Final piecewise-linear fit');
grid on; grid minor;
%% Comparison with the curve-fitting toolbox:
if license('test','Curve_Fitting_Toolbox')
ft = fittype( '(x<=-(n2-n1)/(m2-m1))*(m1*x+n1)+(x>-(n2-n1)/(m2-m1))*(m2*x+n2)',...
'independent', 'x', 'dependent', 'y' );
opts = fitoptions( 'Method', 'NonlinearLeastSquares' );
% Parameter order: m1, m2, n1, n2:
opts.StartPoint = [0.02 -0.02 78 78];
fitresult = fit( X(:), Y(:), ft, opts);
% Comparison with what we did above:
fprintf(1,[...
'Our solution:\n'...
'\tm1 = %-12f\n\tm2 = %-12f\n\tn1 = %-12f\n\tn2 = %-12f\n'...
'Curve Fitting Toolbox'' solution:\n'...
'\tm1 = %-12f\n\tm2 = %-12f\n\tn1 = %-12f\n\tn2 = %-12f\n'],...
m1,m2,n1,n2,fitresult.m1,fitresult.m2,fitresult.n1,fitresult.n2);
end
%% Helper functions:
function n = getN(x0,y0,m)
% y = m*x+n => n = y0-m*x0;
n = y0-m*x0;
function [x_int,y_int] = getLineIntersection(p1,p2)
% m1*x+n1 = m2*x+n2 => x = -(n2-n1)/(m2-m1)
x_int = -(p2(2)-p1(2))/(p2(1)-p1(1));
y_int = p1(1)*x_int+p1(2);
The result (sample run):
Our solution:
m1 = 0.022982
m2 = -0.011863
n1 = 78.012992
n2 = 78.208973
Curve Fitting Toolbox' solution:
m1 = 0.022974
m2 = -0.011882
n1 = 78.013022
n2 = 78.209127
Zoomed in around the intersection:

How to create 64 Gabor features at each scale and orientation in the spatial and frequency domain

Normally, a Gabor filter, as its name suggests, is used to filter an image and extract everything that it is oriented in the same direction of the filtering.
In this question, you can see more efficient code than written in this Link
Assume 16 scales of Filters at 4 orientations, so we get 64 gabor filters.
scales=[7:2:37], 7x7 to 37x37 in steps of two pixels, so we have 7x7, 9x9, 11x11, 13x13, 15x15, 17x17, 19x19, 21x21, 23x23, 25x25, 27x27, 29x29, 31x31, 33x33, 35x35 and 37x37.
directions=[0, pi/4, pi/2, 3pi/4].
The equation of Gabor filter in the spatial domain is:
The equation of Gabor filter in the frequency domain is:
In the spatial domain:
function [fSiz,filters,c1OL,numSimpleFilters] = init_gabor(rot, RF_siz)
image=imread('xxx.jpg');
image_gray=rgb2gray(image);
image_gray=imresize(image_gray, [100 100]);
image_double=double(image_gray);
rot = [0 45 90 135]; % we have four orientations
RF_siz = [7:2:37]; %we get 16 scales (7x7 to 37x37 in steps of two pixels)
minFS = 7; % the minimum receptive field
maxFS = 37; % the maximum receptive field
sigma = 0.0036*RF_siz.^2 + 0.35*RF_siz + 0.18; %define the equation of effective width
lambda = sigma/0.8; % it the equation of wavelength (lambda)
G = 0.3; % spatial aspect ratio: 0.23 < gamma < 0.92
numFilterSizes = length(RF_siz); % we get 16
numSimpleFilters = length(rot); % we get 4
numFilters = numFilterSizes*numSimpleFilters; % we get 16x4 = 64 filters
fSiz = zeros(numFilters,1); % It is a vector of size numFilters where each cell contains the size of the filter (7,7,7,7,9,9,9,9,11,11,11,11,......,37,37,37,37)
filters = zeros(max(RF_siz)^2,numFilters); % Matrix of Gabor filters of size %max_fSiz x num_filters, where max_fSiz is the length of the largest filter and num_filters the total number of filters. Column j of filters matrix contains a n_jxn_j filter (reshaped as a column vector and padded with zeros).
for k = 1:numFilterSizes
for r = 1:numSimpleFilters
theta = rot(r)*pi/180; % so we get 0, pi/4, pi/2, 3pi/4
filtSize = RF_siz(k);
center = ceil(filtSize/2);
filtSizeL = center-1;
filtSizeR = filtSize-filtSizeL-1;
sigmaq = sigma(k)^2;
for i = -filtSizeL:filtSizeR
for j = -filtSizeL:filtSizeR
if ( sqrt(i^2+j^2)>filtSize/2 )
E = 0;
else
x = i*cos(theta) - j*sin(theta);
y = i*sin(theta) + j*cos(theta);
E = exp(-(x^2+G^2*y^2)/(2*sigmaq))*cos(2*pi*x/lambda(k));
end
f(j+center,i+center) = E;
end
end
f = f - mean(mean(f));
f = f ./ sqrt(sum(sum(f.^2)));
p = numSimpleFilters*(k-1) + r;
filters(1:filtSize^2,p)=reshape(f,filtSize^2,1);
fSiz(p)=filtSize;
end
end
% Rebuild all filters (of all sizes)
nFilts = length(fSiz);
for i = 1:nFilts
sqfilter{i} = reshape(filters(1:(fSiz(i)^2),i),fSiz(i),fSiz(i));
%if you will use conv2 to convolve an image with this gabor, so you should also add the equation below. But if you will use imfilter instead of conv2, so do not add the equation below.
sqfilter{i} = sqfilter{i}(end:-1:1,end:-1:1); %flip in order to use conv2 instead of imfilter (%bug_fix 6/28/2007);
convv=imfilter(image_double, sqfilter{i}, 'same', 'conv');
figure;
imagesc(convv);
colormap(gray);
end
phi = ij*pi/4; % ij = 0, 1, 2, 3
theta = 3;
sigma = 0.65*theta;
filterSize = 7; % 7:2:37
G = zeros(filterSize);
for i=(0:filterSize-1)/filterSize
for j=(0:filterSize-1)/filterSize
xprime= j*cos(phi);
yprime= i*sin(phi);
K = exp(2*pi*theta*sqrt(-1)*(xprime+ yprime));
G(round((i+1)*filterSize),round((j+1)*filterSize)) =...
exp(-(i^2+j^2)/(sigma^2))*K;
end
end
As of R2015b release of the Image Processing Toolbox, you can create a Gabor filter bank using the gabor function in the image processing toolbox, and you can apply it to an image using imgaborfilt.
In the frequency domain:
sigma_u=1/2*pi*sigmaq;
sigma_v=1/2*pi*sigmaq;
u0=2*pi*cos(theta)*lambda(k);
v0=2*pi*sin(theta)*lambda(k);
for u = -filtSizeL:filtSizeR
for v = -filtSizeL:filtSizeR
if ( sqrt(u^2+v^2)>filtSize/2 )
E = 0;
else
v_theta = u*cos(theta) - v*sin(theta);
u_theta = u*sin(theta) + v*cos(theta);
E=(1/2*pi*sigma_u*sigma_v)*((exp((-1/2)*(((u_theta-u0)^2/sigma_u^2))+((v_theta-v0)^2/sigma_v^2))) + (exp((-1/2)*(((u_theta+u0)^2/sigma_u^2))+((v_theta+v0)^2/sigma_v^2))));
end
f(v+center,u+center) = E;
end
end

MATLAB: One Step Ahead Neural Network Timeseries Forecast

Intro: I'm using MATLAB's Neural Network Toolbox in an attempt to forecast time series one step into the future. Currently I'm just trying to forecast a simple sinusoidal function, but hopefully I will be able to move on to something a bit more complex after I obtain satisfactory results.
Problem: Everything seems to work fine, however the predicted forecast tends to be lagged by one period. Neural network forecasting isn't much use if it just outputs the series delayed by one unit of time, right?
Code:
t = -50:0.2:100;
noise = rand(1,length(t));
y = sin(t)+1/2*sin(t+pi/3);
split = floor(0.9*length(t));
forperiod = length(t)-split;
numinputs = 5;
forecasted = [];
msg = '';
for j = 1:forperiod
fprintf(repmat('\b',1,numel(msg)));
msg = sprintf('forecasting iteration %g/%g...\n',j,forperiod);
fprintf('%s',msg);
estdata = y(1:split+j-1);
estdatalen = size(estdata,2);
signal = estdata;
last = signal(end);
[signal,low,high] = preprocess(signal'); % pre-process
signal = signal';
inputs = signal(rowshiftmat(length(signal),numinputs));
targets = signal(numinputs+1:end);
%% NARNET METHOD
feedbackDelays = 1:4;
hiddenLayerSize = 10;
net = narnet(feedbackDelays,[hiddenLayerSize hiddenLayerSize]);
net.inputs{1}.processFcns = {'removeconstantrows','mapminmax'};
signalcells = mat2cell(signal,[1],ones(1,length(signal)));
[inputs,inputStates,layerStates,targets] = preparets(net,{},{},signalcells);
net.trainParam.showWindow = false;
net.trainparam.showCommandLine = false;
net.trainFcn = 'trainlm'; % Levenberg-Marquardt
net.performFcn = 'mse'; % Mean squared error
[net,tr] = train(net,inputs,targets,inputStates,layerStates);
next = net(inputs(end),inputStates,layerStates);
next = postprocess(next{1}, low, high); % post-process
next = (next+1)*last;
forecasted = [forecasted next];
end
figure(1);
plot(1:forperiod, forecasted, 'b', 1:forperiod, y(end-forperiod+1:end), 'r');
grid on;
Note:
The function 'preprocess' simply converts the data into logged % differences and 'postprocess' converts the logged % differences back for plotting. (Check EDIT for preprocess and postprocess code)
Results:
BLUE: Forecasted Values
RED: Actual Values
Can anyone tell me what I'm doing wrong here? Or perhaps recommend another method to achieve the desired results (lagless prediction of sinusoidal function, and eventually more chaotic timeseries)? Your help is very much appreciated.
EDIT:
It's been a few days now and I hope everyone has enjoyed their weekend. Since no solutions have emerged I've decided to post the code for the helper functions 'postprocess.m', 'preprocess.m', and their helper function 'normalize.m'. Maybe this will help get the ball rollin.
postprocess.m:
function data = postprocess(x, low, high)
% denormalize
logdata = (x+1)/2*(high-low)+low;
% inverse log data
sign = logdata./abs(logdata);
data = sign.*(exp(abs(logdata))-1);
end
preprocess.m:
function [y, low, high] = preprocess(x)
% differencing
diffs = diff(x);
% calc % changes
chngs = diffs./x(1:end-1,:);
% log data
sign = chngs./abs(chngs);
logdata = sign.*log(abs(chngs)+1);
% normalize logrets
high = max(max(logdata));
low = min(min(logdata));
y=[];
for i = 1:size(logdata,2)
y = [y normalize(logdata(:,i), -1, 1)];
end
end
normalize.m:
function Y = normalize(X,low,high)
%NORMALIZE Linear normalization of X between low and high values.
if length(X) <= 1
error('Length of X input vector must be greater than 1.');
end
mi = min(X);
ma = max(X);
Y = (X-mi)/(ma-mi)*(high-low)+low;
end
I didn't check you code, but made a similar test to predict sin() with NN. The result seems reasonable, without a lag. I think, your bug is somewhere in synchronization of predicted values with actual values.
Here is the code:
%% init & params
t = (-50 : 0.2 : 100)';
y = sin(t) + 0.5 * sin(t + pi / 3);
sigma = 0.2;
n_lags = 12;
hidden_layer_size = 15;
%% create net
net = fitnet(hidden_layer_size);
%% train
noise = sigma * randn(size(t));
y_train = y + noise;
out = circshift(y_train, -1);
out(end) = nan;
in = lagged_input(y_train, n_lags);
net = train(net, in', out');
%% test
noise = sigma * randn(size(t)); % new noise
y_test = y + noise;
in_test = lagged_input(y_test, n_lags);
out_test = net(in_test')';
y_test_predicted = circshift(out_test, 1); % sync with actual value
y_test_predicted(1) = nan;
%% plot
figure,
plot(t, [y, y_test, y_test_predicted], 'linewidth', 2);
grid minor; legend('orig', 'noised', 'predicted')
and the lagged_input() function:
function in = lagged_input(in, n_lags)
for k = 2 : n_lags
in = cat(2, in, circshift(in(:, end), 1));
in(1, k) = nan;
end
end