I am doing Texture Segmentation in Images Using Gabor Filters. I have generated Feature images and now i want to cluster them using square clustering or K-means.
Since i am working in MATLAB, I am using the matlab defined functions.
The official documentation for K-means clustering states
idx = kmeans(X,k)
where,X= n by p data matrix and k is the number of clusters.
I want to know how to use this function for my dataset since i have n feature images which means i have n features for every pixel of the original image. So my question is how do I use my dataset in the above function.
Also, if no function exists please explain how can I implement it on my own.
I am referring this research paper( page 6 )
Gabor filters for texture Segmentation
Related
I have a dataset which I need to cluster and display in a way wherein elements in the same cluster should appear closer together. The dataset is based out of a research study, and has around 16 rows(entries) and about 50 features. I do agree that its not an ideal dataset to begin with, but unfortunately thats is the situation on hand.
Following is the approach I took:
I first applied KMeans on the dataset after normalizing it.
In parallel I also tried to use TSNE to map the data into 2 dimensions and plotted them on a scatterplot. From my understanding of TSNE, that technique should already be placing items in same clusters closer to each other. When I look at the scatterplot, however, the clusters are really all over the place.
The result of the scatterplot can be found here: https://imgur.com/ZPhPjHB
Is this because TSNE and KMeans intrinsically work differently? Should I just do TSNE and try to label the clusters (and if so, how?) or should I be using TSNE output to feed into KMeans somehow?
I am really new in this space and advice would be greatly appreciated!
Thanks in advance once again
Edit: The same overlap happens if I first use TSNE to reduce dimensions to 2 and then use those reduced dimensions to cluster using KMeans
There is a difference between TSNE and KMeans. TSNE is used for visualization mostly and it tries to project points on the 2D/3D space (from bigger spaces) in order to keep distances (if in the bigger space 2 points were far away TSNE will try to show it).
So TSNE is not a real clustering. And that's why results you got that strange scatter plot.
For TSNE sometimes you need to apply PCA before but that is needed if your number of features is big. Just to speed-up calculations.
As already advised, try to use hierarchical clustering or simply generate more rows.
Apply tSNE and fit k-means is one of the basic things you can start from.
I would say consider using different f-divergence.
Stochastic Neighbor Embedding under f-divergences https://arxiv.org/pdf/1811.01247.pdf
This paper tries five different f- divergence functions : KL, RKL, JS, CH (Chi-Square), HL (Hellinger).
The paper goes over which divergence emphasize what in terms of precision and recall.
First,Is it true to extract surf feature and use them in clustering? I want to cluster similar objects in images ?(each image contain one object)
If yes,how is it possible.
I extract features like this:
I = imread('cameraman.tif');
points = detectSURFFeatures(I);
[features, valid_points] = extractFeatures(I, points);
features is not a vector and is a matrix.Also number of points extracted by 'detectSURFFeatures' differ in different images.
how should features use?
First, you are detecting SURF features, not SIFT features (although they serve the same basic purpose). The reason you get multiple SURF features is that SURF is a local image feature, i.e. it describes only a small portion of the image. In general, multiple features will be detected in a single image. You probably want to find a way to combine these features into a single image descriptor before clustering.
A common method for combining these features is Bag-of-words.
Since it seems you are doing unsupervised learning, you will first need to learn a codebook. A popular method is to use k-means clustering on all the SURF features you extracted in all of your images.
Use these clusters to generate a k-dimensional image descriptor by creating a histogram of "codeword appearances" for each image. In this case there is one "codeword" per cluster. A codeword is said to "appear" each time a SURF feature belongs to its associated cluster.
The histogram of codewords will act as an image descriptor for each image. You can then apply clustering on the image descriptors to find similar images, I recommend either normalizing the image descriptors to have constant norm or using the cosine similarity metric (kmeans(X,k,'Distance','cosine') in MATLAB if you use k-means clustering).
That said, a solution which is likely to work better is to extract a deep feature using a convolutional neural network that was trained on a very large, diverse dataset (like ImageNet) then use those as image descriptors.
I have computed colour descriptors of a dataset of images and generated a 152×320 matrix (152 samples and 320 features). I would like to use PCA to reduce the dimensionality of my image descriptors space. I know that I could implement this using Matlab PCA built-in function but as I have just started learning about this concept I would like to implement the Matlab code without the built-in function so I can have a clear understanding how the function works. I tried to find how to do that online but all I could find is the either the general concept of PCA or the implementation of it with the built-in functions without explaining clearly how it works. Anyone could help me with a step by step instructions or a link that could explain a simple way on how to implement PCA for dimensionality reduction. The reason why I'm so confused is because there are so many uses for PCA and methods to implement it and the more I read about it the more confused I get.
PCA is basically taking the dominant eigen vectors of the data (Or better yet their projection of the dominant Eigen Vectors of the covariance matrix).
What you can do is use the SVD (Singular Value Decomposition).
To imitate MATLAB's pca() function here what you should do:
Center all features (Each column of your data should have zero mean).
Apply the svd() function on your data.
Use the V Matrix (Its columns) as your vectors to project your data on. Chose the number of columns to use according to the dimension of the data you'd like to have.
The projected data is now you new dimensionality reduction data.
I am working with a classification algorithm that requires the size of the feature vector of all samples in training and testing to be the same.
I am also to use the SIFT feature extractor. This is causing problems as the feature vector of every image is coming up as a different sized matrix. I know that SIFT detects variable keypoints in each image, but is there a way to ensure that the size of the SIFT features is consistent so that I do not get a dimension mismatch error.
I have tried rootSIFT as a workaround:
[~, features] = vl_sift(single(images{i}));
double_features = double(features);
root_it = sqrt( double_features/sum(double_features) ); %root-sift
feats{i} = root_it;
This gives me a consistent 128 x 1 vector for every image, but it is not working for me as the size of each vector is now very small and I am getting a lot of NaN in my classification result.
Is there any way to solve this?
Using SIFT there are 2 steps you need to perform in general.
Extract SIFT features. These points (first output argument of
size NPx2 (x,y) of your function) are scale invariant, and should in
theory be present in each different image of the same object. This
is not completely true. Often points are unique to each frame
(image). These points are described by 128 descriptors each (second
argument of your function).
Match points. Each time you compute features of a different image the amount of points computed is different! Lots of them should be the same point as in the previous image, but lots of them WON'T. You will have new points and old points may not be present any more. This is why you should perform a feature matching step, to link those points in different images. usually this is made by knn matching or RANSAC. You can Google how to perform this task and you'll have tons of examples.
After the second step, you should have a fixed amount of points for the whole set of images (considering they are images of the same object). The amount of points will be significantly smaller than in each single image (sometimes 30~ times less amount of points). Then do whatever you want with them!
Hint for matching: http://www.vlfeat.org/matlab/vl_ubcmatch.html
UPDATE:
You seem to be trying to train some kind of OCR. You would need to probably match SIFT features independently for each character.
How to use vl_ubcmatch:
[~, features1] = vl_sift(I1);
[~, features2] = vl_sift(I2);
matches=vl_ubcmatch(features1,features2)
You can apply a dense SIFT to the image. This way you have more control over from where you get the feature descriptors. I haven't used vlfeat, but looking at the documentation I see there's a function to extract dense SIFT features called vl_dsift. With vl_sift, I see there's a way to bypass the detector and extract the descriptors from points of your choice using the 'frames' option. Either way it seems you can get a fixed number of descriptors.
If you are using images of the same size, dense SIFT or the frames option is okay. There's a another approach you can take and it's called the bag-of-features model (similar to bag-of-words model) in which you cluster the features that you extracted from images to generate codewords and feed them into a classifier.
I am trying to develop a system for image classification. I am using following the article:
INDEPENDENT COMPONENT ANALYSIS (ICA) FOR TEXTURE CLASSIFICATION by Dr. Dia Abu Al Nadi and Ayman M. Mansour
In a paragraph it says:
Given the above texture images, the Independent Components are learned by the method outlined above.
The (8 x 8) ICA basis function for the above textures are shown in Figure 2. respectively. The dimension is reduced by PCA, resulting in a total of 40 functions. Note that independent components from different windows size are different.
The "method outlined above" is FastICA, the textures are taken from Brodatz album , each texture image has 640x640 pixels. My question is:
What the authors means with "The dimension is reduced by PCA, resulting in a total of 40 functions.", and how can I get that functions using matlab?
PCA (Principal Component Analysis) is a method for finding an orthogonal basis (think of a coordinate system) for a high-dimensional (data) space. The "axes" of the PCA basis are sorted by variance, i.e. along the first PCA "axis" your data has the largest variance, along the second "axis" the second largest variance, etc.
This is exploited for dimension reduction: Say you have 1000 dimensional data. Then you do a PCA, transform your data into the PCA basis and throw away all but the first 20 dimensions (just an example). If your data follows a certain statistical distribution, then chances are that the 20 PCA dimensions describe your data almost as well as the 64 original dimensions did. There are methods for finding the number of dimensions to use, but that is beyond scope here.
Computationally, PCA amounts to finding the Eigen-decomposition of your data's covariance matrix, in Matlab: [V,D] = eig(cov(MyData)).
Note that if you want to work with these concepts you should do some serious reading. A classic article on what you can do with PCA on image data is Turk and Pentland's Eigenfaces. It also gives some background in an understandable way.
PCA reduce the dimension of data,ICA extracts the components of the data of which dimension must <=
data dimension