How can I take a group of picture files and divide each picture into bins?

I have 45 frames that I need to divide into bins and plot the average intensity over time. How can I do this?

[Image Analyst]

Define "bins" - I don't think you're talking about histogram bins because it's not necessary to calculate those just to get the mean intensity of the entire image. For that, see my Answer below.

Do you mean "blocks" or "tiles" as if you divide the image up into some number of non-overlapping blocks or tiles, like quadrants or something like that?

[Jenna]

yes. I mean blocks or tiles of the image.

Answer 1

[Iain]

If you have all of your frames within a single matrix:

eg. if you have: colour(x,y,rgb,frame)

mean_of_each_frame = mean(mean(mean(colour,3),2),1);

if memory serves, mean_of_each_frame will be a 1x1x1x45 vector which you can reshape or squeeze as needed.

[Iain]

Apologies, I just reread your question.

You need a way of identifying your bins, either as defined areas, or as the result of a logical comparison and labelling (bwlabel or bwlabeln), if these change from frame to frame, you will need to loop through the whole set of frames, and calculate the mean for each "bin".

It is also possible to use those results to create an array of "NaN", where the data is invalid and 1, where the data is valid, and elementwise multiply and take the means as my answer.

Pseudocode:

for each frame

   for each bin_number
    averages(frame_no,bin_no) = mean(frame(labelled == bin_number));
   end
end

Answer 2

[Image Analyst]

Answer my comment first. But if you want to get the mean intensity as a function of frame, I posted code for that here: http://www.mathworks.com/matlabcentral/answers/59194#answer_71636

Answer 3

[Image Analyst]

Here's a demo on splitting an image into non-overlapping blocks or tiles.

% Demo to divide an image up into blocks (non-overlapping tiles).
% The first way to divide an image up into blocks is by using mat2cell().
% In this demo, I demonstrate that with a color image.
% Another way to split the image up into blocks is to use indexing.
% In this demo, I demonstrate that method with a grayscale image.

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
workspace;  % Make sure the workspace panel is showing.
fontSize = 20;

% Read in a standard MATLAB color demo image.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
baseFileName = 'peppers.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
if ~exist(fullFileName, 'file')
  % Didn't find it there.  Check the search path for it.
  fullFileName = baseFileName; % No path this time.
  if ~exist(fullFileName, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
% Read the image from disk.
rgbImage = imread(fullFileName);

% Test code if you want to try it with a gray scale image.
% Uncomment line below if you want to see how it works with a gray scale image.
% rgbImage = rgb2gray(rgbImage);

% Display image full screen.
imshow(rgbImage);
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
drawnow;
% Get the dimensions of the image.  numberOfColorBands should be = 3.
[rows columns numberOfColorBands] = size(rgbImage)

%==========================================================================
% The first way to divide an image up into blocks is by using mat2cell().
blockSizeR = 150; % Rows in block.
blockSizeC = 100; % Columns in block.

% Figure out the size of each block in rows. 
% Most will be blockSizeR but there may be a remainder amount of less than that.
wholeBlockRows = floor(rows / blockSizeR);
blockVectorR = [blockSizeR * ones(1, wholeBlockRows), rem(rows, blockSizeR)];
% Figure out the size of each block in columns. 
wholeBlockCols = floor(columns / blockSizeC);
blockVectorC = [blockSizeC * ones(1, wholeBlockCols), rem(columns, blockSizeC)];

% Create the cell array, ca.  
% Each cell (except for the remainder cells at the end of the image)
% in the array contains a blockSizeR by blockSizeC by 3 color array.
% This line is where the image is actually divided up into blocks.
if numberOfColorBands > 1
  % It's a color image.
  ca = mat2cell(rgbImage, blockVectorR, blockVectorC, numberOfColorBands);
else
  ca = mat2cell(rgbImage, blockVectorR, blockVectorC);
end

% Now display all the blocks.
plotIndex = 1;
numPlotsR = size(ca, 1);
numPlotsC = size(ca, 2);
for r = 1 : numPlotsR
  for c = 1 : numPlotsC
    fprintf('plotindex = %d,   c=%d, r=%d\n', plotIndex, c, r);
    % Specify the location for display of the image.
    subplot(numPlotsR, numPlotsC, plotIndex);
    % Extract the numerical array out of the cell
    % just for tutorial purposes.
    rgbBlock = ca{r,c};
    imshow(rgbBlock); % Could call imshow(ca{r,c}) if you wanted to.
    [rowsB columnsB numberOfColorBandsB] = size(rgbBlock);
    % Make the caption the block number.
    caption = sprintf('Block #%d of %d\n%d rows by %d columns', ...
      plotIndex, numPlotsR*numPlotsC, rowsB, columnsB);
    title(caption);
    drawnow;
    % Increment the subplot to the next location.
    plotIndex = plotIndex + 1;
  end
end

% Display the original image in the upper left.
subplot(4, 6, 1);
imshow(rgbImage);
title('Original Image');

% Inform user of next stage where we process a gray scale image.
promptMessage = sprintf('Now I will do the same for a gray scale image.');
titleBarCaption = 'Continue?';
button = questdlg(promptMessage, titleBarCaption, 'OK', 'Cancel', 'OK');
if strcmpi(button, 'Cancel')
  return;
end

%==============================================================================
% Another way to split the image up into blocks is to use indexing.
% Read in a standard MATLAB gray scale demo image.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
baseFileName = 'cameraman.tif';
fullFileName = fullfile(folder, baseFileName);
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
if ~exist(fullFileName, 'file')
  % Didn't find it there.  Check the search path for it.
  fullFileName = baseFileName; % No path this time.
  if ~exist(fullFileName, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
grayImage = imread(fullFileName);
% Get the dimensions of the image.  numberOfColorBands should be = 1.
[rows columns numberOfColorBands] = size(grayImage);
% Display the original gray scale image.
figure;
subplot(2, 2, 1);
imshow(grayImage, []);
title('Original Grayscale Image', 'FontSize', fontSize);
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);

% Divide the image up into 4 blocks.
% Let's assume we know the block size and that all blocks will be the same size.
blockSizeR = 128; % Rows in block.
blockSizeC = 128; % Columns in block.
% Figure out the size of each block. 
wholeBlockRows = floor(rows / blockSizeR);
wholeBlockCols = floor(columns / blockSizeC);
% Preallocate a 3D image
image3d = zeros(wholeBlockRows, wholeBlockCols, 3);
% Now scan though, getting each block and putting it as a slice of a 3D array.
sliceNumber = 1;
for row = 1 : blockSizeR : rows
  for col = 1 : blockSizeC : columns
    % Let's be a little explicit here in our variables
    % to make it easier to see what's going on.
    % Determine starting and ending rows.
    row1 = row;
    row2 = row1 + blockSizeR - 1;
    row2 = min(rows, row2); % Don't let it go outside the image.
    % Determine starting and ending columns.
    col1 = col;
    col2 = col1 + blockSizeC - 1;
    col2 = min(columns, col2); % Don't let it go outside the image.
    % Extract out the block into a single subimage.
    oneBlock = grayImage(row1:row2, col1:col2);
    % Specify the location for display of the image.
    subplot(2, 2, sliceNumber);
    imshow(oneBlock);
    % Make the caption the block number.
    caption = sprintf('Block #%d of 4', sliceNumber);
    title(caption, 'FontSize', fontSize);
    drawnow;
    % Assign this slice to the image we just extracted.
    if (row2-row1+1) == blockSizeR && (col2-col1+1) == blockSizeC
      % Then the block size is the tile size, 
      % so add a slice to our 3D image stack.
      image3D(:, :, sliceNumber) = oneBlock;
    else
      newTileSize = [(row2-row1+1), (col2-col1+1)];
      warningMessage = sprintf('Warning: this block size of %d rows and %d columns\ndoes not match the preset block size of %d rows and %d columns.\nIt will not be added to the 3D image stack.',...
        newTileSize(1), newTileSize(2), blockSizeR, blockSizeC);
      uiwait(warndlg(warningMessage));
    end
    sliceNumber = sliceNumber + 1;
  end
end
% Now image3D is a 3D image where each slice, 
% or plane, is one quadrant of the original 2D image.

msgbox('Done with demo!  Check out the two figures.');