I have an image that I want to divide in three parts and find the centroid of the parts separately and display them on original image, I used blkproc for dividing the image in [1 3] grids, but can't display the centroids. Here is the code I wrote,
i=imread('F:\line3.jpg');
i2=rgb2gray(i);
bw=im2bw(i2);
imshow(bw)
fun=#(x) regionprops(x,'centroid');
b=blkproc(bw,[1 3],fun);
But I can't get to display the centroids, as well as get their values. Any help will be much appreciated.
You can just use the plot command to plot over the top of the image.
Whatever you [X,Y] centroid coordinates are, say cx(1:3) and cy(1:3)
numCentroids is the number of centroids you are plotting.
hold on;
for ii = 1:length(numCentroids)
plot(cx(ii),cy(ii),'Marker','s','MarkerSize',10,'MarkerFaceColor','r','MarkerEdgeColor','k')
end
If you wanted to write more elegant code, you could run the plot command once across all your centroids and then make the line style type invisible. The answer I supplied should work though.
Here's an example image with made up centroids.
Strong recommendation - use blockproc instead of blkproc. It is better designed and easier to use.
Now, first of all, the second input to blockproc is the blocksize and not the grid size. So if you want to divide your image into [1 3] grid, which I understand as a single row of three blocks, then you should set your blocksize as:
blocksize = [size(i,1) ceil(size(i,2)/3)];
The second thing is to turn off the 'TrimBorder' parameter in blockproc. The code would look something like:
fun=#(x) regionprops(x,'centroid');
blocksize = [size(i,1) ceil(size(i,2)/3)];
b=blockproc(bw,blocksize,fun,'TrimBorder',false);
One minor thing - I would recommend not using the variable name 'i'. By default it represents the imaginary number i = sqrt(-1); in Matlab.
Related
I am working with particle tracking in images in MATLAB and using regionprops function. On the provided resource there is an example with circles:
stats = regionprops('table',bw,'Centroid',...
'MajorAxisLength','MinorAxisLength')
centers = stats.Centroid;
diameters = mean([stats.MajorAxisLength stats.MinorAxisLength],2);
radii = diameters/2;
In my Matlab R2014b, the line centers = stats.Centroid; produces undesired result: my stats.Centroid structure has 20 elements (each element is two numbers - the coordinates of the center of the region). However, after the following command, my variable center is only 1x2 matrix, instead of desired 20x2.
Screenshot attached.
I tried to go around this with different methods. The only solution I found is to do:
t=zeros(20,2);
for i=1:20
t(i,:)=stats(i).Centroid;
end
However, as we all know loops are slow in MATLAB. Is there another method that takes advantage of MATLAB matrix operations?
Doing stats.Centroid would in fact give you a comma-separated list of centroids, so MATLAB would only give you the first centre of that matrix if you did centers = stats.Centroid. What you must do is encapsulate the centres in an array (i.e. [stats.Centroid]), then reshape when you're done.
Something like this should work for you:
centers = reshape([stats.Centroid], 2, []).';
What this will do is read in the centroids as a 1 x 2*M array where M is the total number of blobs and because MATLAB does reshaping in column-major format, you should make sure that specify the total number of rows to be 2 and let MATLAB figure out how many columns there are after by itself. You would then transpose the result when you're done to complete what you want.
Minor Note
If you look at the regionprops documentation page in their Tips section - http://www.mathworks.com/help/images/ref/regionprops.html#buorh6l-1, you will see that they surround stats.Area, which is the area of each blob with [] brackets to ensure that the comma-separated list of values is encapsulated in an array. This is not an accident and there is a purpose of having those there and I've basically told you what that was.
All of this is done in Matlab. I have a 2D RGB image, with some depth data for key vertexes. That is, I have three vectors (m x 1): X, Y, Z. Together, [X(i), Y(i)] specifies the point in the image with depth Z(i).
The crux of my problem is this:
I would like to plot the image "warped" with the depth information. But, each time I keep calling functions like 'mesh(X,Y,Z,RGBImage)' and 'surf', I get weird errors like "Z need to be matrix not vector". Also, I haven't even been able to implement the 'warp' function, as I am not sure how to translate my data into a usable format.
Any help would be really appreciated.
EDIT: I finally got it to work the way I would like. The only thing that needed to be changed, that was not answered, was to include the line
s = surf(Xmat,Ymat,Zmat, T1, 'edgecolor', 'none', 'FaceColor', ...
'texturemap');
Where
T1 = rgb2gray(OrignialRGBImage);. Much thanks!
I don't have access to MATLAB right now, so I am giving the outline of the solution.
First, create two matrices using meshgrid: [Xmat,Ymat] = meshgrid(1:imgCols,1:imgRows);. Now, you can find every row of [X,Y] at [Xmat(i,j),Ymat(i,j)] for some (i,j). In the next step, create Zmat such that Zmat(i,j) is the correct depth value for [Ymat(i,j),Xmat(i,j)]. You should be able to do this as follows:
Zmat = zeros(imgRows,imgCols);
for i=1:size(X,1)
Zmat(Y(i),X(i))=Z(i);
end
Now you can do surf with Xmat,Ymat,Zmat as follows. Then overlay image as texture.
s = surf(Xmat,Ymat,Zmat);
set(s, 'faceColor', 'texture','edgecolor', 'none','cdata', subimage); %not tested,
%see if it works
Overlaying part taken from here.
If the above part doesn't work, then you can overlay Zmat in the heatmap style, see this question.
I am currently doing some seismic modelling and processing in MATLAB, and would like to come up with an easy way of muting parts of various datasets. If I plot the frequency-wavenumber spectrum of some of my data, for instance, I obtain the following result:
Now, say that I want to mute some of the data present here. I could of course attempt to run through the entire matrix represented here and specify a threshold value where everything above said value should be set equal to zero, but this will be very difficult and time-consuming when I later will work with more complicated fk-spectra. I recently learned that MATLAB has an inbuilt function called impoly which allows me to interactively draw a polygon in plots. So say I, for instance, draw the following polygon in my plot with the impoly-function:
Is there anything I can do now to set all points within this polygon equal to zero? After defining the polygon as illustrated above I haven't found out how to proceed in order to mute the information contained in the polygon, so if anybody can give me some help here, then i would greatly appreciate it!
Yes, you can use the createMask function that's part of the impoly interface once you delineate the polygon in your figure. Once you use create this mask, you can use the mask to index into your data and set the right regions to zero.
Here's a quick example using the pout.tif image in MATLAB:
im = imread('pout.tif');
figure; imshow(im);
h = impoly;
I get this figure and I draw a polygon inside this image:
Now, use the createMask function with the handle to the impoly call to create a binary mask that encapsulates this polygon:
mask = createMask(h);
I get this mask:
imshow(mask);
You can then use this mask to index into your data and set the right regions to 0. First make a copy of the original data then set the data accordingly.
im_zero = im;
im_zero(mask) = 0;
I now get this:
imshow(im_zero);
Note that this only applies to single channel (2D) data. If you want to apply this to multi-channel (3D) data, then perhaps a multiplication channel-wise with the opposite of the mask may be prudent.
Something like this:
im_zero = bsxfun(#times, im, cast(~mask, class(im)));
The above code takes the opposite of the polygon mask, converts it into the same class as the original input im, then performs an element-wise multiplication of this mask with each channel of the input separately. The result will zero each spatial location that's defined in the mask over all channels.
I have a simple question but is very interesting. As you know, Kmeans can be give different result after each running due to randomly initial cluster center. However, assume I know that cluster 1 has smaller mean value than cluster 2, cluster 2 has smaller mean value than cluster 3 and so on. I want to make a algorithm to implement that cluster has small mean value, then it will be assigned to small cluster index.
This is my Matlab code. If you are have more sort or more clear way. Please suggest to me
%% K-mean
num_cluster=2;
nrows = size(Img_original,1);
ncols = size(Img_original,2);
I_1D = reshape(Img_original,nrows*ncols,1);
[cluster_idx mu]=kmeans(double(I_1D),num_cluster,'distance','sqEuclidean','Replicates',3);
cluster_label = reshape(cluster_idx,nrows,ncols);
%% Sort based on mu
[mu_sort id_sort]=sort(mu);
idx=cell(1,num_cluster)
%% Save index of order if mu
for i=1:num_cluster
idx{i}=find(cluster_label==id_sort(i));
end
%% Sort cluster label based on mu
for i=1:num_cluster
cluster_label(idx{i})=i;
end
It's unclear to me as to why you'd want to relabel the clusters based on the ordering of each centroid. You can simply use the labelling vector that is output from k-means to reference which cluster / centroid each point belongs to.
Nevertheless, the initial idea that you had to sort the centroids is a good one. The last part of your code seems rather inefficient because you're looping over each label and doing the reassignment. One thing I could perhaps suggest is to have a lookup table where the input is the original label and the output is the reordered labels based on the sorted centroids.
If you want to pursue this route, you can use a containers.Map where the keys are the labels given from the sort order that is output from sort, and the values are the reordered labels... namely, a vector that goes from 1 up to as many classes you have. You need to do this because the second output of sort tells you where each value in the original array would appear in the sorted result, so you must use this ordering to properly perform the relabelling. In addition, I would use the sortrows function in MATLAB, not raw sort. With how you're doing it, you are sorting each column / variable independently and that will give the wrong centroids. This will work for grayscale images where you only have one feature to consider, namely the grayscale, but if you go beyond grayscale and perhaps go into RGB or whatever colour space you desire, using raw sort will give you incorrect results. You need to consider each row as a single point, then sort the rows jointly.
Given your code, you'd do something like this:
%% K-mean
num_cluster=2;
nrows = size(Img_original,1);
ncols = size(Img_original,2);
I_1D = reshape(Img_original,nrows*ncols,1);
[cluster_idx mu]=kmeans(double(I_1D),num_cluster,'distance','sqEuclidean','Replicates',3);
%% Sort based on mu
[mu_sort id_sort]=sortrows(mu);
%// New - Create lookup
lookup = containers.Map(id_sort, 1:size(mu_sort,1));
%// Relabel the vector
cluster_idx_sort = lookup.values(num2cell(cluster_idx));
cluster_idx_sort = [cluster_idx_sort{:}];
%// Reshape back to original image dimensions
cluster_label = reshape(cluster_idx_sort,nrows,ncols);
This should hopefully give you some speedup in your code.
To double check, I tried this on the cameraman.tif image, that's part of the image processing toolbox. Running the code gives me these cluster centres:
>> mu
mu =
153.3484
23.7291
Once I sort the clusters in ascending order, this is what I get for the ordering and for the centroids:
>> mu_sort
mu_sort =
23.7291
153.3484
>> id_sort
id_sort =
2
1
So that works as we expected... now if we display the original cluster label map before sorting on the centroids with:
cluster_label = reshape(cluster_idx, nrows, ncols);
imshow(cluster_label,[]);
... we get this image:
Now, if we run through the sorting logic and display the centroids:
imshow(cluster_label, []);
... we get this image:
This works as I expected. Because the centroids flipped, so should the colouring.
I finally solved my problem here with lennon310.
I have a picture of thousands of thin peaks in Time-Frequency picture.
I cannot see all the same time in one picture.
Depending on the physical width of my time window, some windows appear and some come visible.
Pictures of my data which I plot by imagesc
All pictures are from the same data points T, F, B.
How can you plot all peaks at once in a picture in Matlab?
You need to resize the image using resampling to prevent the aliasing effect (that craigim described as unavoidable).
For example, the MATLAB imresize function can perform anti-aliasing. Don't use the "nearest" resize method, that's what you have now.
Extension to #BenVoigt's answer
My try
B = abs(B);
F1 = filter2(B,T); % you need a different filter kernel because resolution is lower
T = filter2(B,F);
F = F1;
image1 = imagesc(B);
display1 = imresize(image1, [600 600], 'bilinear');
imshow(T*t, F*fs, display1);
where are some problems.
I get again picture where the resolution is not enough
2nd Extension to BenVoigt's answer
My suggestion for one kernel filter is with convolution of relative random error
data(find(data ~= 0)) = sin(pi .* data(find(data ~= 0))) ./ (pi*data(find(data ~= 0)));
data(find(data == 0)) = 1; % removing lastly the discontinuity
data1 = data + 0.0000001 * mean(abs(data(:))) * randn(size(data));
data = conv(data, data1);
Is this what BenVoigt means by the kernel filter for distribution?
This gives results like
where the resolution is still a problem.
The central peaks tend to multiply easily if I resize the window.
I had old code active in the above picture but it did not change the result.
The above code is still not enough for the kernel filter of the display.
Probably, some filter functions has to be applied to the time and frequency axis separately still, something like:
F1 = filter2(B,T); % you need a different kernel filter because resolution is lower
T = filter2(B,F);
F = F1;
These filters mess up the values on the both axis.
I need to understand them better to fix this.
But first to understand if they are the right way to go.
The figure has be resized still.
The size of the data was 5001x1 double and those of F and T 13635x1 double.
So I think I should resize lastly after setting axis, labels and title by
imresize(image, [13635 13635], 'bilinear');
since the distirbution is bilinear.
3rd Extension to BenVoigt's answer
I plot the picture now by
imagesc([0 numel(T)], [0 numel(F)], B);
I have a big aliasing problem in my pictures.
Probably, something like this should be to manipulate the Time-Frequency Representation
T = filter2(B,t); % you need a different filter kernel because resolution is lower
F = filter2(B,fs);
4th extension to BenVoigt's answer and comment
I remove the filters and addition of random relative errors.
I set the size of T,F,B, and run
imagesc([0 numel(T)], [0 numel(F)], B, [0 numel(B)])
I get still with significant aliasing but different picture
This isn't being flippant, but I think the only way is to get a wider monitor with a higher pixel density. MATLAB and your video card can only show so many pixels on the screen, and must decide which to show and which to leave out. The data is still there, it just isn't getting displayed. Since you have a lot of very narrow lines, some of them are going to get skipped when decisions are made as to which pixels to light up. Changing the time window size changes which lines get aliased away and which ones get lucky enough to show up on the screen.
My suggestions are, in no particular order: convolute your lines with a Gaussian along the time axis to broaden them, thus increasing the likelihood that part of the peak will appear on the screen. Print them out on a 600 dpi printer and see if they appear. Make several plots, each zooming in on a separate time window.
3rd Extension to BenVoigt's answer
My attempt to tell imagesc how big to make the image, instead of letting to use the monitor size, so it won't away data.
imagesc(T*t, F*fs, B, [50 50]);
% imagesc(T*t, F*fs, B');
% This must be last
imresize(image, 'bilinear', [64 30],);
I am not sure where I should specify the amount of pixels in x-axis and y-axis, either in the command imagesc or imresize.
What is the correct way of resizing the image here?