Skip to main content

list manipulation - Slope and frequency of line-like structure in image


I have the following image:


enter image description here


A linear structure of parallel bright stripes is seen going from the lower left to the upper right edge of the image.


I want to determine the mean slope and frequency of these stripes.



To measure the slope, I tried the following code.


ed = 22;
edgeImg = EdgeDetect[img, ed];
lines = ImageLines[edgeImg];

The first 20 lines are:


HighlightImage[img, {Red, Thickness[0.01], Line /@ lines[[1 ;; 20]]}] 

enter image description here


The mean slope is then:



Mean@Table[(lines[[i, 2, 2]] - lines[[i, 1, 2]]) /
(lines[[i, 2, 1]] - lines[[i, 1, 1]]),
{i, 1, 20}]

How would you determine the slope and what do you propose to measure the stripe frequency?



Answer



Here's an extremely simple way to do this: First, load the image and calculate gradients:


img = Import["https://i.stack.imgur.com/f4iZt.png"];
pixels = ImageData[img][[All, All, 1]];


sigma = 10; (* roughly the with of a line *)
gradient =
GaussianFilter[pixels, sigma, {0, 1}] +
I GaussianFilter[pixels, sigma, {1, 0}];

I've stored the gradients as complex numbers, with the gradient in x-direction as real and gradient in y direction as imaginary part. So Abs[gradient] is the gradient strength at each pixel, and Arg[gradient] is the gradient direction.


Now, if I sum up all the gradients in the image, the gradients above and below each line will cancel each other, as they point in opposite directions. But if I sum up all the gradients squared, angles are doubled, so gradients pointing in opposite directions will add up:


sumSquaredGradient = Total[gradient^2, ∞];

So I get the mean gradient direction (weighted by the gradient strength) over the whole image as:



angle = Arg[Sqrt[sumSquaredGradient]]

That's it. Three lines of code. The rest is just display to verify the result:


{w, h} = ImageDimensions[img];
Show[
ImageAdjust[GaussianFilter[img, sigma]],
Graphics[
{
Red,
Table[

Line[{{0, y}, {w, w*Cot[angle] + y}}],
{y, 0, h, 20}]
}]]

enter image description here


As I said, this is probably one of the simplest things you can do. The sigma parameter basically selects the gradient scale you're looking at. For fine-tuning, you can try preprocessing the image (e.g. ImageAdjust[RidgeFilter[img, 10]] looks good), or you can re-weight the gradients, either iteratively, based on direction (to reduce the influence of "outlier" angles) or source image brightness.


Fun fact: If the orientation is not constant over the whole image, you can also use this to get the average orientation in a neighborhood, by using a large smoothing filter instead of a sum overall pixels.


To illustrate this, I'll add a circular disturbance to the data:


pixels = ImageData[img][[All, All, 1]];
pixels[[;; 200, ;; 200]] +=

0.5 GaussianFilter[DiskMatrix[50, 200], 30];

...calculate the gradient as above...


sigma = 10;
gradient =
GaussianFilter[pixels, sigma, {0, 1}] +
I GaussianFilter[pixels, sigma, {1, 0}];

then find a smoothed orientation for a 50-pixel neighborhood around each pixel.


smoothedOrientation = Sqrt[GaussianFilter[gradient^2, 50]];


Visualization:


stream = ListStreamPlot[
Reverse[ReIm[I*Conjugate@smoothedOrientation]]\[Transpose],
AspectRatio -> h/w, StreamStyle -> Red];
Show[Image[Rescale@pixels], stream]

enter image description here


ADD: how you find with your code the stripe frequency?


You could obviously use a Fourier transform for that, but it's probably even simpler to just rotate the image so the stripes are vertically aligned and take the mean over all rows:



rotate = ImageRotate[img, angle];
columnMean = Mean[ImageData[rotate][[All, All, 1]]];

Which looks like this:


ListLinePlot[columnMean, 
Epilog -> {Red, Point[FindPeaks[columnMean]]}]

enter image description here


And then take the differences between the peak positions:


Differences[FindPeaks[columnMean][[All, 1]]]



{37, 31, 36, 35, 42, 31, 38, 40, 35, 41, 43, 36, 33, 42, 37, 39, 30, 37, 34, 31, 29, 29}



Which is centered around 36 pixels.


Comments

Popular posts from this blog

plotting - Filling between two spheres in SphericalPlot3D

Manipulate[ SphericalPlot3D[{1, 2 - n}, {θ, 0, Pi}, {ϕ, 0, 1.5 Pi}, Mesh -> None, PlotPoints -> 15, PlotRange -> {-2.2, 2.2}], {n, 0, 1}] I cant' seem to be able to make a filling between two spheres. I've already tried the obvious Filling -> {1 -> {2}} but Mathematica doesn't seem to like that option. Is there any easy way around this or ... Answer There is no built-in filling in SphericalPlot3D . One option is to use ParametricPlot3D to draw the surfaces between the two shells: Manipulate[ Show[SphericalPlot3D[{1, 2 - n}, {θ, 0, Pi}, {ϕ, 0, 1.5 Pi}, PlotPoints -> 15, PlotRange -> {-2.2, 2.2}], ParametricPlot3D[{ r {Sin[t] Cos[1.5 Pi], Sin[t] Sin[1.5 Pi], Cos[t]}, r {Sin[t] Cos[0 Pi], Sin[t] Sin[0 Pi], Cos[t]}}, {r, 1, 2 - n}, {t, 0, Pi}, PlotStyle -> Yellow, Mesh -> {2, 15}]], {n, 0, 1}]

plotting - Plot 4D data with color as 4th dimension

I have a list of 4D data (x position, y position, amplitude, wavelength). I want to plot x, y, and amplitude on a 3D plot and have the color of the points correspond to the wavelength. I have seen many examples using functions to define color but my wavelength cannot be expressed by an analytic function. Is there a simple way to do this? Answer Here a another possible way to visualize 4D data: data = Flatten[Table[{x, y, x^2 + y^2, Sin[x - y]}, {x, -Pi, Pi,Pi/10}, {y,-Pi,Pi, Pi/10}], 1]; You can use the function Point along with VertexColors . Now the points are places using the first three elements and the color is determined by the fourth. In this case I used Hue, but you can use whatever you prefer. Graphics3D[ Point[data[[All, 1 ;; 3]], VertexColors -> Hue /@ data[[All, 4]]], Axes -> True, BoxRatios -> {1, 1, 1/GoldenRatio}]

plotting - Mathematica: 3D plot based on combined 2D graphs

I have several sigmoidal fits to 3 different datasets, with mean fit predictions plus the 95% confidence limits (not symmetrical around the mean) and the actual data. I would now like to show these different 2D plots projected in 3D as in but then using proper perspective. In the link here they give some solutions to combine the plots using isometric perspective, but I would like to use proper 3 point perspective. Any thoughts? Also any way to show the mean points per time point for each series plus or minus the standard error on the mean would be cool too, either using points+vertical bars, or using spheres plus tubes. Below are some test data and the fit function I am using. Note that I am working on a logit(proportion) scale and that the final vertical scale is Log10(percentage). (* some test data *) data = Table[Null, {i, 4}]; data[[1]] = {{1, -5.8}, {2, -5.4}, {3, -0.8}, {4, -0.2}, {5, 4.6}, {1, -6.4}, {2, -5.6}, {3, -0.7}, {4, 0.04}, {5, 1.0}, {1, -6.8}, {2, -4.7}, {3, -1.