when I try to average a folder of jpeg matlab images, all that I get is a blank image. I've gone over my code a million times, and I don't know where I'm
going wrong. (also I know I hard coded some of the numbers but that just because I wanted it to take a specific folder and I've double checked those a million times, they're right.)
%takes all the images in a folder and averages their values
%opens folder
function avg_image = average_images()
folder_name = uigetdir;
folder_directory = dir(folder_name);
filename = folder_directory(3).name;
len = length(folder_directory);
org_image = imread(filename);
sum_image = org_image;
%adds files together
for i = 4:len
filename = folder_directory(i).name;
org_image = imread(filename);
sum_image = sum_image + org_image;
end
%calculates average
avg_image = sum_image/(len-2);
%saves average as a fits file and displays it
imwrite(avg_image, 'averagefile.jpg');
read_image = imread('averagefile.jpg');
imshow(read_image)
end
The problem with your code is that you are reading in the JPGs as uint8 (default) and then doing math with the images as matrices of uint8's (0-255 integers). As you read in org_image, above and inside the for loop, cast the result as a double:org_image = double(imread(filename)). After you're done with the averaging, you need to cast it back, avg_image = uint8(sum_image/(len-2)).
When you do math with uint8's, divisions are messy since decimals are truncated. 4 divided by 8 when both are doubles gives you 0.5. When both are integers, you get 0.
Related
I'm reading in 3d arrays, subtracting all of them from one of them, and trying to save the results as the same type of arrays. They are all equal sizes to each other, 1888x3520x6.
Here is the piece of code that I have:
[FileName,PathName,FilterIndex] = uigetfile('*.x3d*','MultiSelect','on');
numfiles = size(FileName,2);
FileName{1}
entirefile1 =fullfile(PathName,FileName{1})
Im1 = x3dread(entirefile1);
for j = 2:numfiles
FileName{j}
entirefile2 =fullfile(PathName,FileName{j})
Im2 = x3dread(entirefile2);
J = num2str(j);
strcat('ImDelta', J);
ImDelta = imsubtract(Im1, Im2);
end
I see that I'm creating a character sring by using strcat. But I'm not making it into a new file name. Only one file is resulting at the end of the loop.
(x3dread function is similar to "load" for working with images, only it is specifically written to handle the type of the 3dimention files that I have.)
Any help is appreciated. I'm just a beginner.
I've been given a task to create image filtering function for 3x3 matrices, and its outcome must be equal to conv2's. I have written this function, but it filters image incorrectly:
function [ image ] = Func134( img,matrix )
image=img;
len=length(img)
for i=2:1:len-1
for j=2:1:len-1
value=0;
for g=-1:1:1
for l=-1:1:1
value=value+img(i+g,j+l)*matrix(g+2,l+2);
end
end
image(i,j)=value;
end
end
i=1:1:length
image(i,1)=image(i,2)
image(i,len)=image(i,len-1)
image(1,i)=image(2,i)
image(len,i)=image(len-1,i)
end
Filtration matrix is [3,10,3;0,0,0;-3,-10,-3]
Please help to figure out what is wrong with my code.
Some sample results I get between conv2 and my code are seen below.
First off, this line doesn't make sense:
i=1:1:length;
I think you meant to use len instead of length as the ending index:
i=1:1:len;
Now referring to your code, it is correct, but what you are doing is correlation not convolution. In 2D convolution, you have to perform a 180 degree rotation of the kernel / mask and then do the weighted sum. As such, if you want to achieve the same results using conv2, you must pre-rotate the mask before calling it.
mask = [3,10,3;0,0,0;-3,-10,-3]
mask_flip = mask(end:-1:1,end:-1:1);
out = conv2(img, mask, 'same');
mask_flip contains the 180 degree rotated kernel. We use the 'same' flag to ensure that the output size of the result is the same size as the input. However, when using conv2, we are assuming that the borders of the image are zero-padded. Your code simply copies the border pixels of the original image into the resulting image. This is known as replicating behaviour but that is not what conv2 does natively. conv2 assumes that the border pixels are zero-padded as I mentioned before, so what I would suggest you do is create two additional images, one being the output image that has 2 more rows and 2 more columns and another being the input image that is the same size as the output image but you place the input image inside this matrix. Next, perform the filtering on this new image, place the resulting filtered pixels in the output image then crop this result. I've decided to create a new padded input image in order to keep most of your code intact.
I would also recommend that you abolish the use of length here. Use size instead to determine the image dimensions. Something like this will work:
function [ image ] = Func134( img,matrix )
[rows,cols] = size(img); %// Change
%// New - Create a padded matrix that is the same class as the input
new_img = zeros(rows+2,cols+2);
new_img = cast(new_img, class(img));
%// New - Place original image in padded result
new_img(2:end-1,2:end-1) = img;
%// Also create new output image the same size as the padded result
image = zeros(size(new_img));
image = cast(image, class(img));
for i=2:1:rows+1 %// Change
for j=2:1:cols+1 %// Change
value=0;
for g=-1:1:1
for l=-1:1:1
value=value+new_img(i+g,j+l)*matrix(g+2,l+2); %// Change
end
end
image(i,j)=value;
end
end
%// Change
%// Crop the image and remove the extra border pixels
image = image(2:end-1,2:end-1);
end
To compare, I've generated this random matrix:
>> rng(123);
>> A = rand(10,10)
A =
0.6965 0.3432 0.6344 0.0921 0.6240 0.1206 0.6693 0.0957 0.3188 0.7050
0.2861 0.7290 0.8494 0.4337 0.1156 0.8263 0.5859 0.8853 0.6920 0.9954
0.2269 0.4386 0.7245 0.4309 0.3173 0.6031 0.6249 0.6272 0.5544 0.3559
0.5513 0.0597 0.6110 0.4937 0.4148 0.5451 0.6747 0.7234 0.3890 0.7625
0.7195 0.3980 0.7224 0.4258 0.8663 0.3428 0.8423 0.0161 0.9251 0.5932
0.4231 0.7380 0.3230 0.3123 0.2505 0.3041 0.0832 0.5944 0.8417 0.6917
0.9808 0.1825 0.3618 0.4264 0.4830 0.4170 0.7637 0.5568 0.3574 0.1511
0.6848 0.1755 0.2283 0.8934 0.9856 0.6813 0.2437 0.1590 0.0436 0.3989
0.4809 0.5316 0.2937 0.9442 0.5195 0.8755 0.1942 0.1531 0.3048 0.2409
0.3921 0.5318 0.6310 0.5018 0.6129 0.5104 0.5725 0.6955 0.3982 0.3435
Now running with what we talked about above:
mask = [3,10,3;0,0,0;-3,-10,-3];
mask_flip = mask(end:-1:1,end:-1:1);
B = Func134(A,mask);
C = conv2(A, mask_flip,'same');
We get the following for your function and the output of conv2:
>> B
B =
-5.0485 -10.6972 -11.9826 -7.2322 -4.9363 -10.3681 -10.9944 -12.6870 -12.5618 -12.0295
4.4100 0.1847 -2.2030 -2.7377 0.6031 -3.7711 -2.5978 -5.8890 -2.9036 2.7836
-0.6436 6.6134 4.2122 -0.7822 -2.3282 1.6488 0.4420 2.2619 4.2144 3.2372
-4.8046 -1.0665 0.1568 -1.5907 -4.6943 0.3036 0.4399 4.3466 -2.5859 -3.4849
-0.7529 -5.5344 1.3900 3.1715 2.9108 4.6771 7.0247 1.7062 -3.9277 -0.6497
-1.9663 2.4536 4.2516 2.2266 3.6084 0.6432 -1.0581 -3.4674 5.3815 6.1237
-0.9296 5.1244 0.8912 -7.7325 -10.2260 -6.4585 -1.4298 6.2675 10.1657 5.3225
3.9511 -1.7869 -1.9199 -5.0832 -3.2932 -2.9853 5.5304 5.9034 1.4683 -0.7394
1.8580 -3.8938 -3.9216 3.8254 5.4139 1.8404 -4.3850 -7.4159 -4.9894 -0.5096
6.4040 7.6395 7.3643 11.8812 10.6537 10.8957 5.0278 3.0277 4.2295 3.3229
>> C
C =
-5.0485 -10.6972 -11.9826 -7.2322 -4.9363 -10.3681 -10.9944 -12.6870 -12.5618 -12.0295
4.4100 0.1847 -2.2030 -2.7377 0.6031 -3.7711 -2.5978 -5.8890 -2.9036 2.7836
-0.6436 6.6134 4.2122 -0.7822 -2.3282 1.6488 0.4420 2.2619 4.2144 3.2372
-4.8046 -1.0665 0.1568 -1.5907 -4.6943 0.3036 0.4399 4.3466 -2.5859 -3.4849
-0.7529 -5.5344 1.3900 3.1715 2.9108 4.6771 7.0247 1.7062 -3.9277 -0.6497
-1.9663 2.4536 4.2516 2.2266 3.6084 0.6432 -1.0581 -3.4674 5.3815 6.1237
-0.9296 5.1244 0.8912 -7.7325 -10.2260 -6.4585 -1.4298 6.2675 10.1657 5.3225
3.9511 -1.7869 -1.9199 -5.0832 -3.2932 -2.9853 5.5304 5.9034 1.4683 -0.7394
1.8580 -3.8938 -3.9216 3.8254 5.4139 1.8404 -4.3850 -7.4159 -4.9894 -0.5096
6.4040 7.6395 7.3643 11.8812 10.6537 10.8957 5.0278 3.0277 4.2295 3.3229
I am trying to save a montage of many (~500, 2MB each) images using MATLAB function imwrite, however I keep getting this error:
Error using imwrite>validateSizes (line 632)
Images must contain fewer than 2^32 - 1 bytes of data.
Error in imwrite (line 463)
validateSizes(data);
here is the code I am working with:
close all
clear all
clc
tic
file = 'ImageRegistrations.txt';
info = importdata(file);
ImageNames = info.textdata(:,1);
xoffset = info.data(:,1);
yoffset = info.data(:,2);
for i = 1:length(ImageNames);
ImageNames{i,1} = imread(ImageNames{i,1});
ImageNames{i,1} = flipud(ImageNames{i,1});
end
ImageNames = flipud(ImageNames);
for i=1:length(ImageNames)
diffx(i) = xoffset(length(ImageNames),1) - xoffset(i,1);
end
diffx = (diffx)';
diffx = flipud(diffx);
for j=1:length(ImageNames)
diffy(j) = yoffset(length(ImageNames),1) - yoffset(j,1);
end
diffy = (diffy)';
diffy = flipud(diffy);
matrix = zeros(max(diffy)+abs(min(diffy))+(2*1004),max(diffx)+abs(min(diffx))+(2*1002));
%matrix(1:size(ImageNames{1,1},1),1:size(ImageNames{1,1},2)) = ImageNames{1,1};
for q=1:length(ImageNames)
matrix((diffy(q)+abs(min(diffy))+1):(diffy(q)+abs(min(diffy))+size(ImageNames{q,1},1)),(diffx(q)+abs(min(diffx))+1):((diffx(q)+abs(min(diffx))+size(ImageNames{q,1},2)))) = ImageNames{q,1};
end
graymatrix = mat2gray(matrix);
graymatrix = flipud(graymatrix);
figure(2)
imshow(graymatrix)
imwrite(graymatrix, 'montage.tif')
toc
I use imwrite because it perserves the final montage in a full resolution file, whereas if I simply click save on the figure file it saves it as a low resolution file.
thanks!
Error does what it says on the tin, really. There is some sort of inbuilt limitation to input variable size in imwrite, and you're going over it.
Note that most images are stored as uint8 but I would guess that you end up with doubles as a result of your processing. That increases the memory usage.
It may be, therefore, that casting to another type would help. Try using im2uint8 (presuming your variable graymatrix is double, scaled between 0 and 1), before calling imwrite.
I am attempting to write a function that stack up series of images into image stack and converting it into a gdf file. I don't really know much about GDF files, so please help me out.
X=[];
for i=1:10
if numel(num2str(i))==1
X{i}=imread(strcat('0000',num2str(i),'.tif'));
elseif numel(num2str(i))==2
X{i}=imread(strcat('000',num2str(i),'.tif'));
end
end
myImage=cat(3,X{1:10});
s=write_gdf('stack.gdf',myImage);
Above is to read my images labeled 00001 to 00010, all in grayscale. Everything is fine except in the last line
s=write_gdf('stack.gdf',myImage);
as when I run it, I receive an error:
Data type uint8 not supported
Any help on what this means? Should I convert it to some other colour format?
Thank you in advance!
I would write the code rather like this (I do not have write_gdf function so I can not properly test the code):
NumberOfFiles = 10;
X={}; % preallocate CELL array
for n=1:NumberOfFiles % do not use "i" as your varable because it is imaginary unit in MatLab
FileName = sprintf('%05d.tif',n);
img = imread(FileName); % load image
X{i} = double(img); % and convert to desired format
end
myImage = cat(3,X{1:NumberOfFiles});
s = write_gdf('stack.gdf',myImage);
Keep in mind that
double(img); % and convert to desired format
will not change data range. Your image even in double format will have data range from 0 to 255 if it was in uint8 format on disk. If you need to normalize your data to 0..1 range you should do
X{i} = double(img)/255;
or in more unversal form
X{i} = double(img) / intmax(class(img));
I have a load of data in 100 .sdf files (labelled 0000.sdf to 0099.sdf), each of which contain a still image, and I'm trying to produce a .gif from these images.
The code I use to plot the figure are (in the same directory as the sdf files):
q = GetDataSDF('0000.sdf');
imagesc(q.data');
I've attempted to write a for loop that would plot the figure and then save it with the same filename as the sdf file but to no avail, using:
for a = 1:100
q=GetDataSDF('0000.sdf');
fh = imagesc(q.dist_fn.x_px.Left.data');
frm = getframe( fh );
% save as png image
saveas(fh, 'current_frame_%02d.jpg');
end
EDIT: I received the following errors when trying to run this code:
Error using hg.image/get
The name 'Units' is not an accessible property for an instance of class 'image'.
Error in getframe>Local_getRectanglesOfInterest (line 138)
if ~strcmpi(get(h, 'Units'), 'Pixels')
Error in getframe (line 56)
[offsetRect, absoluteRect, figPos, figOuterPos] = ...
Error in loop_code (line 4)
frm = getframe( fh );
How do I save these files using a for loop, and how do I then use those files to produce a movie?
The reason for the error is that you pass an image handle to getframe, but this function excpects a figure handle.
Another problem is that you always load the same file, and that you saveas will not work for gifs. (For saving figures as static images, maybe print is the better option?)
I tried to modify my own gif-writing loop so that it works with your data. I'll try to be extra explicit in the comments, since you seem to be starting out. Remember, you can always use help name_of_command to display a short Matlab help.
% Define a variable that holds the frames per second your "movie" should have
gif_fps = 24;
% Define string variable that holds the filename of your movie
video_filename = 'video.gif';
% Create figure 1, store the handle in a variable, you'll need it later
fh = figure(1);
for a = 0:99
% Prepare file name so that you loop over the data
q = GetDataSDF(['00' num2str(a,'%02d') 'sdf']);
% Plot image
imagesc(q.dist_fn.x_px.Left.data');
% Force Matlab to actually do the plot (it sometimes gets lazy in loops)
drawnow;
% Take a "screenshot" of the figure fh
frame = getframe(fh);
% Turn screenshot into image
im = frame2im(frame);
% Turn image into indexed image (the gif format needs this)
[imind,cm] = rgb2ind(im,256);
% If first loop iteration: Create the file, else append to it
if a == 0;
imwrite(imind,cm,video_filename,'gif', 'Loopcount',inf);
else
imwrite(imind,cm,video_filename,'gif','WriteMode','append','DelayTime',1/gif_fps);
end
end
One more note: When the size of the data is the same for each plot, it makes sense to only use the plot(or in this case, imagesc) command once, and in later loop iterations replace it with a set(ah,'Ydata',new_y_data) (or in this case set(ah,'CData',q.dist_fn.x_px.Left.data'), where ah is a handle of the plot axes (not the plot figure!). This is orders of magnitude faster than creating a whole new plot in each loop iteration. The downside is that the scaling (here, the color-scaling) will be the same for each plot. But in every case that I have worked on so far, that was actually desirable.