Extract line shaped objects - matlab

I'm working on images with overlapping line shapes (left plot). Ultimately I want to segment single objects. I'm working with a Hough transform to achieve this and it works well in finding lines of (significantly) different orientation - e.g. represented by the two maxima in the hough space below (middle plot).
the green and yellow lines (left plot) and crosses (right plot) stem from an approach to do something with the thickness of the line. I couldn't figure out how to extract a broad line though, so I didn't follow up.
I'm aware of the ambiguity of assigning the "overlapping pixels". I will address that later.
Since I don't know, how many line objects one connected region may contain, my idea is to iteratively extract the object corresponding to the hough line with the highest activation (here painted in blue), i.e. remove the line shaped object from the image, so that the next iteration will find only the other line.
But how do I detect, which pixels belong to the line shaped object?
The function hough_bin_pixels(img, theta, rho, P) (from here - shown in the right plot) gives pixels corresponding to the particular line. But that obviously is too thin of a line to represent the object.
Is there a way to segment/detect the whole object that is orientied along the strongest houghline?

The key is knowing that thick lines in the original image translate to wider peaks on the Hough Transform. This image shows the peaks of a thin and a thick line.
You can use any strategy you like to group all the pixels/accumulator bins of each peak together. I would recommend using multithresh and imquantize to convert it to a BW image, and then bwlabel to label the connected components. You could also use any number of other clustering/segmentation strategies. The only potentially tricky part is figuring out the appropriate thresholding levels. If you can't get anything suitable for your application, err on the side of including too much because you can always get rid of erroneous pixels later.
Here are the peaks of the Hough Transform after thresholding (left) and labeling (right)
Once you have the peak regions, you can find out which pixels in the original image contributed to each accumulator bin using hough_bin_pixels. Then, for each peak region, combine the results of hough_bin_pixels for every bin that is part of the region.
Here is the code I threw together to create the sample images. I'm just getting back into matlab after not using it for a while, so please forgive the sloppy code.
% Create an image
image = zeros(100,100);
for i = 10:90
image(100-i,i)=1;
end;
image(10:90, 30:35) = 1;
figure, imshow(image); % Fig. 1 -- Original Image
% Hough Transform
[H, theta_vals, rho_vals] = hough(image);
figure, imshow(mat2gray(H)); % Fig. 2 -- Hough Transform
% Thresholding
thresh = multithresh(H,4);
q_image = imquantize(H, thresh);
q_image(q_image < 4) = 0;
q_image(q_image > 0) = 1;
figure, imshow(q_image) % Fig. 3 -- Thresholded Peaks
% Label connected components
L = bwlabel(q_image);
figure, imshow(label2rgb(L, prism)) % Fig. 4 -- Labeled peaks
% Reconstruct the lines
[r, c] = find(L(:,:)==1);
segmented_im = hough_bin_pixels(image, theta_vals, rho_vals, [r(1) c(1)]);
for i = 1:size(r(:))
seg_part = hough_bin_pixels(image, theta_vals, rho_vals, [r(i) c(i)]);
segmented_im(seg_part==1) = 1;
end
region1 = segmented_im;
[r, c] = find(L(:,:)==2);
segmented_im = hough_bin_pixels(image, theta_vals, rho_vals, [r(1) c(1)]);
for i = 1:size(r(:))
seg_part = hough_bin_pixels(image, theta_vals, rho_vals, [r(i) c(i)]);
segmented_im(seg_part==1) = 1;
end
region2 = segmented_im;
figure, imshow([region1 ones(100, 1) region2]) % Fig. 5 -- Segmented lines
% Overlay and display
out = cat(3, image, region1, region2);
figure, imshow(out); % Fig. 6 -- For fun, both regions overlaid on original image

Related

Smooth out a single sharp corner in a function in Matlab

So I want to smooth out Sharkfin signal at the point where it goes down and at the point where it goes up. As shown in the figure below, the Sharkfin waveform has sharp fall and rise at time 2 sec and 4 seconds:
Any idea on how to round of that area so that it is smooth in that section so that it looks something like this:
There are two separate things here - how do you detect a sharp transition, and how do you filter it.
Let's take these in turn.
A sharp transition is characterized by a large curvature - we can easily detect this by taking the diff of the input curve. Using the second parameter = 2 takes diff twice and results in something "like" the second derivative - but it's offset by one. So when we find points where the diff(sharkfin,2) is large, we need to offset by 1 to get the corner points.
Next, the smoothing itself. There are many techniques - I show a simple convolution with a box function. Doing this twice gives a smoothed version of the input. By picking the original "far from the discontinuity" and the filtered version "close to the discontinuity" we get exactly what you were asking for. If you wanted, you could "blend" the points - using a weighted version of filtered and unfiltered depending on how close you were to the corner points. I didn't show that explicitly but it should be easy to see how to expand the code I already wrote:
% generate a "shark fin" function:
fin = exp(-linspace(0,4,60));
shark = [fin (1-fin+fin(end))];
shark = repmat(shark, [1 3]);
D2 = diff(shark, 2);
roundMe = find(abs(D2)>0.1*max(D2))+1; % offset by 1 because second derivative
figure;
subplot(3,1,1)
plot(shark); title 'shark plot'
hold on;
plot(roundMe, shark(roundMe),'r*')
legend('input','corners found')
% take N points on either side of the sharp corners:
N = 3;
% boxplot filtered version of the curve
boxFilt = ones(1, 2*N+1)/(2*N+1);
smoothShark1 = convn(shark, boxFilt, 'same'); % box plot
% second filter - smoother
smoothShark2 = convn(smoothShark1, boxFilt, 'same');
% plot the filtered results:
subplot(3,1,2)
plot(shark)
hold on
plot(smoothShark1);
hold on
plot(smoothShark2);
xlim([114 126])
ylim([0.8,1.1])
legend('original','box','box x2')
title 'smoothed everywhere'
% Now apply filtering only to points near the discontinuity
smoothMe = zeros(size(shark));
smoothMe(roundMe)=1;
smoothMe = convn(smoothMe, boxFilt, 'same');
smoothMe(smoothMe>0)=1; % this finds N points on either side of the corner
subplot(3,1,3)
plot(shark)
finalPlot=shark;
hold on
smoothIndx = find(smoothMe);
finalPlot(smoothIndx)=smoothShark2(smoothIndx);
plot(finalPlot,'g')
plot(smoothIndx, finalPlot(smoothIndx), 'r*')
xlim([114 126])
ylim([0.8,1.1])
legend('original','smoothed','changed')
title 'smoothed only near discontinuity'
Output:

Count circle objects in an image using matlab

How to count circle objects in a bright image using MATLAB?
The input image is:
imfindcircles function can't find any circle in this image.
Based on well known image processing techniques, you can write your own processing tool:
img = imread('Mlj6r.jpg'); % read the image
imgGray = rgb2gray(img); % convert to grayscale
sigma = 1;
imgGray = imgaussfilt(imgGray, sigma); % filter the image (we will take derivatives, which are sensitive to noise)
imshow(imgGray) % show the image
[gx, gy] = gradient(double(imgGray)); % take the first derivative
[gxx, gxy] = gradient(gx); % take the second derivatives
[gxy, gyy] = gradient(gy); % take the second derivatives
k = 0.04; %0.04-0.15 (see wikipedia)
blob = (gxx.*gyy - gxy.*gxy - k*(gxx + gyy).^2); % Harris corner detector (high second derivatives in two perpendicular directions)
blob = blob .* (gxx < 0 & gyy < 0); % select the top of the corner (i.e. positive second derivative)
figure
imshow(blob) % show the blobs
blobThresshold = 1;
circles = imregionalmax(blob) & blob > blobThresshold; % find local maxima and apply a thresshold
figure
imshow(imgGray) % show the original image
hold on
[X, Y] = find(circles); % find the position of the circles
plot(Y, X, 'w.'); % plot the circle positions on top of the original figure
nCircles = length(X)
This code counts 2710 circles, which is probably a slight (but not so bad) overestimation.
The following figure shows the original image with the circle positions indicated as white dots. Some wrong detections are made at the border of the object. You can try to make some adjustments to the constants sigma, k and blobThresshold to obtain better results. In particular, higher k may be beneficial. See wikipedia, for more information about the Harris corner detector.

Matlab: Matrix manipulation: Change values of pixels around center pixel in binary matrix

I have another problem today:
I have a binary matrix t, in which 1 represents a river channel, 0 represents flood plane and surrounding mountains:
t = Alog>10;
figure
imshow(t)
axis xy
For further calculations, I would like to expand the area of the riverchannel a few pixels in each direction. Generally speaking, I want to have a wider channel displayed in the image, to include a larger region in a later hydraulic model.
Here is my attempt, which does work in certain regions, but in areas where the river runs diagonal to the x-y axis, it does not widen the channel. There seems to be a flow in approaching this, which I cannot quite grasp.
[q,o] = find(t == 1);
qq = zeros(length(q),11);
oo = zeros(length(o),11);
% add +-5 pixel to result
for z=1:length(q)
qq(z,:) = q(z)-5:1:q(z)+5;
oo(z,:) = o(z)-5:1:o(z)+5;
end
% create column vectors
qq = qq(:);
oo = oo(:);
cords = [oo qq]; % [x y]
% remove duplicates
cords = unique(cords,'rows');
% get limits of image
[limy limx] = size(t);
% restrict to x-limits
cords = cords(cords(:,1)>=1,:);
cords = cords(cords(:,1)<=limx,:);
% restrict to y-limits
cords = cords(cords(:,2)>=1,:);
cords = cords(cords(:,2)<=limy,:);
% test image
l = zeros(size(img));
l(sub2ind(size(l), cords(:,2)',cords(:,1)')) = 1;
figure
imshow(l)
axis xy
This is the image I get:
It does widen the channel in some areas, but generally there seems to be a flaw with my approach. When I use the same approach on a diagonal line of pixels, it will not widen the line at all, because it will just create more pairs of [1 1; 2 2; 3 3; etc].
Is there a better approach to this or even something from the realm of image processing?
A blur filter with a set diameter should be working somewhat similar, but I could not find anything helpful...
PS: I wasn't allowed to add the images, although I already have 10 rep, so here are the direct links:
http://imageshack.us/a/img14/3122/channelthin.jpg
http://imageshack.us/a/img819/1787/channelthick.jpg
If you have the image processing toolbox, you should use the imdilate function. This performs the morphological dilation operation. Try the following code:
SE = strel('square',3);
channelThick = imdilate(channelThin,SE);
where SE is a 3x3 square structuring element used to dilate the image stored in channelThin. This will expand the regions in channelThin by one pixel in every direction. To expand more, use a larger structuring element, or multiple iterations.
You may apply morphological operations from image processing. Morphological dilation can be used in your example.
From the image processing toolbox, you can use bwmorth command BW2 = bwmorph(BW,'dilate') or imdilate command IM2 = imdilate(IM,SE).
Where IM is your image and SE is the structuring element. You can set SE = ones(3); to dilate the binary image by "one pixel" - but it can be changed depending on your application. Or you can dilate the image several times with the same structuring element if needed.

remove the holes in an image by average values of surrounding pixels

can any one please help me in filling these black holes by values taken from neighboring non-zero pixels.
thanks
One nice way to do this is to is to solve the linear heat equation. What you do is fix the "temperature" (intensity) of the pixels in the good area and let the heat flow into the bad pixels. A passable, but somewhat slow, was to do this is repeatedly average the image then set the good pixels back to their original value with newImage(~badPixels) = myData(~badPixels);.
I do the following steps:
Find the bad pixels where the image is zero, then dilate to be sure we get everything
Apply a big blur to get us started faster
Average the image, then set the good pixels back to their original
Repeat step 3
Display
You could repeat averaging until the image stops changing, and you could use a smaller averaging kernel for higher precision---but this gives good results:
The code is as follows:
numIterations = 30;
avgPrecisionSize = 16; % smaller is better, but takes longer
% Read in the image grayscale:
originalImage = double(rgb2gray(imread('c:\temp\testimage.jpg')));
% get the bad pixels where = 0 and dilate to make sure they get everything:
badPixels = (originalImage == 0);
badPixels = imdilate(badPixels, ones(12));
%# Create a big gaussian and an averaging kernel to use:
G = fspecial('gaussian',[1 1]*100,50);
H = fspecial('average', [1,1]*avgPrecisionSize);
%# User a big filter to get started:
newImage = imfilter(originalImage,G,'same');
newImage(~badPixels) = originalImage(~badPixels);
% Now average to
for count = 1:numIterations
newImage = imfilter(newImage, H, 'same');
newImage(~badPixels) = originalImage(~badPixels);
end
%% Plot the results
figure(123);
clf;
% Display the mask:
subplot(1,2,1);
imagesc(badPixels);
axis image
title('Region Of the Bad Pixels');
% Display the result:
subplot(1,2,2);
imagesc(newImage);
axis image
set(gca,'clim', [0 255])
title('Infilled Image');
colormap gray
But you can get a similar solution using roifill from the image processing toolbox like so:
newImage2 = roifill(originalImage, badPixels);
figure(44);
clf;
imagesc(newImage2);
colormap gray
notice I'm using the same badPixels defined from before.
There is a file on Matlab file exchange, - inpaint_nans that does exactly what you want. The author explains why and in which cases it is better than Delaunay triangulation.
To fill one black area, do the following:
1) Identify a sub-region containing the black area, the smaller the better. The best case is just the boundary points of the black hole.
2) Create a Delaunay triangulation of the non-black points in inside the sub-region by:
tri = DelaunayTri(x,y); %# x, y (column vectors) are coordinates of the non-black points.
3) Determine the black points in which Delaunay triangle by:
[t, bc] = pointLocation(tri, [x_b, y_b]); %# x_b, y_b (column vectors) are coordinates of the black points
tri = tri(t,:);
4) Interpolate:
v_b = sum(v(tri).*bc,2); %# v contains the pixel values at the non-black points, and v_b are the interpolated values at the black points.

matlab: how to plot multidimensional array

Let's say I have 9 MxN black and white images that are in some way related to one another (i.e. time lapse of some event). What is a way that I can display all of these images on one surface plot?
Assume the MxN matrices only contain 0's and 1's. Assume the images simply contain white lines on a black background (i.e. pixel value == 1 if that pixel is part of a line, 0 otherwise). Assume images are ordered in such a way as to suggest movement progression of line(s) in subsequent images. I want to be able to see a "side-view" (or volumetric representation) of these images which will show the surface that a particular line "carves out" in its movement across the images.
Coding is done in MATLAB. I have looked at plot (but it only does 2D plots) and surf, which does 3D plots but doesn't work for my MxNx9 matrix of images. I have also tried to experiment with contourslice, but not sure what parameters to pass it.
Thanks!
Mariya
Are these images black and white with simple features on a "blank" field, or greyscale, with more dense information?
I can see a couple of approaches.
You can use movie() to display a sequence of images as an animation.
For a static view of sparse, simple data, you could plot each image as a separate layer in a single figure, giving each layer a different color for the foreground, and using AlphaData to make the background transparent so all the steps in the sequenc show through. The gradient of colors corresponds to position in the image sequence. Here's an example.
function plotImageSequence
% Made-up test data
nLayers = 9;
x = zeros(100,100,nLayers);
for i = 1:nLayers
x(20+(3*i),:,i) = 1;
end
% Plot each image as a "layer", indicated by color
figure;
hold on;
for i = 1:nLayers
layerData = x(:,:,i);
alphaMask = layerData == 1;
layerData(logical(layerData)) = i; % So each layer gets its own color
image('CData',layerData,...
'AlphaData',alphaMask,...
'CDataMapping','scaled');
end
hold off
Directly showing the path of movement a "line" carves out is hard with raster data, because Matlab won't know which "moved" pixels in two subsequent images are associated with each other. Don't suppose you have underlying vector data for the geometric features in the images? Plot3() might allow you to show their movement, with time as the z axis. Or you could use the regular plot() and some manual fiddling to plot the paths of all the control points or vertexes in the geometric features.
EDIT: Here's a variation that uses patch() to draw each pixel as a little polygon floating in space at the Z level of its index in the image sequence. I think this will look more like the "surface" style plots you are asking for. You could fiddle with the FaceAlpha property to make dense plots more legible.
function plotImageSequencePatch
% Made-up test data
nLayers = 6;
sz = [50 50];
img = zeros(sz(1),sz(2),nLayers);
for i = 1:nLayers
img(20+(3*i),:,i) = 1;
end
% Plot each image as a "layer", indicated by color
% With each "pixel" as a separate patch
figure;
set(gca, 'XLim', [0 sz(1)]);
set(gca, 'YLim', [0 sz(2)]);
hold on;
for i = 1:nLayers
layerData = img(:,:,i);
[x,y] = find(layerData); % X,Y of all pixels
% Reshape in to patch outline
x = x';
y = y';
patch_x = [x; x+1; x+1; x];
patch_y = [y; y; y+1; y+1];
patch_z = repmat(i, size(patch_x));
patch(patch_x, patch_y, patch_z, i);
end
hold off