So I have the code to import a stack of images, but I am getting an error: Subscripted assignment dimension mismatch.
myPath = 'E:\folder name\'; %'
fileNames = dir(fullfile(myPath, '*.tif'));
width = 1400;
height = 1050;
nbImages = length(fileNames);
C=uint8(zeros(width, height, nbImages));
for i=1:length(fileNames)
C(:,:,i)=imread(cat(2,'E:\folder name\',fileNames(i).name));
i
end
I understand that the error is originating from the for loop, but I don't know of any other way to fill in an empty matrix with images.
Your images must not be all the same size. You can handle this by using explicit assignment for the first two dimensions. This will zero-pad any images which are smaller than the rest.
im = imread(...);
C(1:size(im, 1), 1:size(im, 2), i) = im;
Also, there is a good chance that your images have multiple color channels (the third dimension), so you'll likely want to concatenate along the fourth dimension rather than the third.
C(:,:,:,i) = imread(...)
Obviously it all depends what you want to do with the images, but in general, if you want a "stack" of images (or a "stack" of anything, really), then it sounds like you should be collecting them as a cell array instead.
Also, the correct way to create safe filenames is using the fullfile command
e.g.
C = cell(1, length(nbImages));
for i = 1 : length (fileNames)
C{i} = imread (fullfile ('E:','folder name', fileNames(i).name));
end
If you really want to concatenate to a 3D matrix from your cell array, assuming you have checked this is possible, you can do this very easily using comma-separated-list generator syntax:
My3DMatrix = cat(3, C{:});
Related
I have data that change in size and want to display them in the same window. The command
void ImageResize( BasicImage im, Number num_dim, Number... )
seems like a potential fit, but the syntax is not clear at all.
Let's say I have 512x5 data set and now it needs to be 367x5.
The , Number...) indicates that this command takes a different number of parameters, all of them interpreted as number parameters. Commands which do this, usually use one of their other parameters to specify how many such parameters follow.
A typical example for this is also the SliceN command.
In this particular case, the command not only allows you to change the size of the dimensions in the image, but also the number of dimensions. It is a very useful command to f.e. change a 2D image into a 3D stack or the like.
The command ImageResize( BasicImage im, Number num_dim, Number... ) does several things:
It replaces im in-place, so the meta-data, display and window remains the same
It adjusts the dimension calibration when the dimension size is changed. Here, the assumption is, that the field-of-view before and
after the resize is the same. (The command can be used to easily scale
images as shown in the example below.)
All values of the image im are set to zero. ( If you need to keep the values, you need to act on an image clone!)
Example 1: Resizing image with bilinar interpolation
image before := GetFrontImage()
number sx, sy
before.GetSize(sx,sy)
number factor = 1.3
image after := before.ImageClone()
after.ImageResize( 2, factor*sx, factor*sy ) // Adjusts the empty container with meta-data
after = warp(before, icol/factor, irow/factor ) // interpolate data
after.ShowImage()
Example 2: Extend 2D image into 3D stack
number sx = 100
number sy = 100
image img := RealImage("2D",4,sx,sy)
img = iradius* Random()
img.ShowImage()
OKDialog("Now into a stack...")
number sz = 10
img.ImageResize(3,sx,sy,sz) // All values are zero now!
img = iradius * Random()
I need the size of the image as a variable.
Here is what I tried:
a = dir('C:\example\Desktop\imagefolder\*.png');
numberofImages = length(a);
%sizeofimage?
matrix = zeros(numberofImages, sizeofimage);
How can I get the size of my image?
Maybe this will help. It will give you the size of each of the images in your folder.
a = dir('C:\example\Desktop\imagefolder\*.png');
numberofImages = length(a);
for i=1:numberofImages
img = imread(a(i).name);
sizeofImage{i} = size(img)
end
You can then access the sizes of the images using this notation:
sizeofImage{1}
Which will return something like this for an image 400x400:
ans =
400 400 3
You require an array of numbers to go into zeros, and size already provides you with one. Simply horzcat that (or use square brackets) with the number of images and you're done:
matrix = zeros([numberofImages, size(image)]);
Although I strongly suggest you to stop working on your project and start taking a class in MATLAB, read a book on it or take the MathWorks own tutorial, as this is about as basic as MATLAB gets. Since MATrix LABoratory is about matrices, size is important.
I have the following code to import multiple images from one directory into a struct in Matlab, here is an example of the images.
myPath= 'E:\conduit_stl(smooth contour)\Collagen Contour Slices\'; %'
fileNames = dir(fullfile(myPath, '*.tif'));
C = cell(length(fileNames), 1);
for k = 1:length(fileNames)
filename = fileNames(k).name;
C{k} = imread(filename);
se = strel('disk', 2, 0);
C = imclose(C, se);
filled = imfill(C,'holes');
end
Though now I would like to perform a fill on all the images, later finding the centroids. However, when attempting this, an error stating: "Expected input number 1, I1 or BW1, to be one of these types: double, ... etc" I tried converting the images into double precision, though that just resulted in: "Conversion to double from cell is not possible."
This is most likely due to the structure type, the images are 'housed' in, but I have no idea concerning that.
Help on this would be greatly appreciated.
So to elaborate on my previous comments, here are a few things to change with your code:
C is not a structure but a cell array. The content of a cell array is access with {curly brackets}. If all your images are the same size, then it is more efficient to store them into a numeric array instead of a cell array. Since they seem to be logical images, your array would have 3 dimensions:
[height, width, numberofimages]
You could therefore start your code with:
myPath= 'E:\conduit_stl(smooth contour)\Collagen Contour Slices\'; %'
fileNames = dir(fullfile(myPath, '*.tif'));
%// if your images are of type uint8
C(height,width,length(fileNames)) = uint8(0);
C_filled = C; %// initialize new array to stored filled images
Also, since you are using the same structuring elements for your morphological operation on all the images, you can define it once outside the loop.
So your code could look like this:
se = strel('disk', 2, 0);
for k = 1:length(fileNames)
C(:,:,k) = imread(fileNames(k).name);
C_filled(:,:,k) = imfill(imclose(C(:,:,k), se),'holes');
end
I read the image with:
W=double(imread('rose32.bmp'));
Then:
imshow(W,[]);
or
imshow(W);
But the shown image seems to be inverted with respect to the original image. How can I solve this problem ? Is it a MATLAB problem?
The problem is probably caused by the formatting the the imagefile!
When you use imread what it returns depends of the formatting of the image in the image file. imread returns tree values [A,map,transparency] = imread(___), where A might be hxw-matrix or a hxwx3-matrix (h and w are short for height and width) of several different possible classes (eg. double or uint8).
In the case of the hxwx3-matrix the output-variable map will be empty, and you can show the image directly using imshow(A). This is called an RGB-image.
The other possibility (called an indexed image) is the hxw-matrix. In this case map is a colormap, and you can show the image by imshow(A,map).
You can easily convert between these two types of images by ind2rgb(A,map) and rgb2ind(A).
The other thing you need to be careful with is the class of the image.
If you have an rgb-image of class uint8, then the values of image will be integers between 0 and 255, whereas rgb-images of type double have values between 0 and 1. You should never convert an image to double-class by the double-function like you do; in stead use im2double.
So to solve your problem try the following code:
[img,map] = imread('rose32.bmp');
if ~isempty(map)
img = ind2rgb(img,map);
end
img = im2double(img);
Now imshow(img) should show the image correctly. Or you can simply use the following code:
[W,map] = imread('rose32.bmp');
imshow(W,map);
I tried the following program for reading multiple images(about 300 images). Now I want to store these images immediately after reading each to some location by some name as g1,g2,g3... Is it possible to do this in a loop?
Here is my attempt:
for i=1:5
m=imread(['C:\Users\shree\Desktop\1\im' num2str(i) '.jpg']);
figure,imshow(m);
end
I highly recommend that you store them in a cell array:
for k=1:5
image_path = ['C:\Users\shree\Desktop\1\im' num2str(i) '.jpg']; %// I have moved this to be on its own line as it will make debugging easier. You don't have to, but I think it's a good idea.
images_all{k} = imread(image_path);
end
By using eval to create variable names like g1, g2 etc you pollute your workspace with an unmanageable amount of variables. Plus if they are all in a cell array then it's really easy to apply the same function to each of them either in a loop or with cellfun.
For example if you want to convert them all to greyscale now:
images_grey = cellfun(#rgb2gray, images_all, 'UniformOutput', false);
You can simply save all them into one big matrix:
for i=1:5
images_all(:, :, :, i) = imread(['C:\Users\shree\Desktop\1\im' num2str(i) '.jpg'])
end
After this, all images will be stored in images_all (here assume that all images are colored images, i.e. 3 channels).
Try this -
for i=1:5
img =imread(['C:\Users\shree\Desktop\1\im' num2str(i) '.jpg']);
evalc(['g' num2str(i) '=img;']);
end
figure,imshow(g1);
figure,imshow(g2);
Another approach could be to use STRUCT and store those images as fields of a struct.
Storing as a 4D matrix is another efficient way as suggested by herohuyongtao.