Issue with image accumulation in memory though successive images are loaded in the same variable ( already alocated memory ?)

Hi everyone !

I have binary files of staked images. One image is ( 2048, 2048, 'uint16'), so that the full file is ( 2048, 2048, imageNumber, 'uint16').

I made a GUI to naviguate one file wihtout opening it full, but one by one image using fseek and fread, and then select one of this image.

However, each time a new image is loaded the used memory increases, although the image is loaded to the same variable and so I thought to the same allocated memory.

This memory is not released when the GUI is closed, or even the workspace cleared. It is only released when matlab is terminated.

Here is my source code:

function selectedReference = PEEMstartOnTheFlyAnalysis_test(fileBaseName)
    % Open data file.
    IDfile = fopen(fileBaseName, 'r');
    % Open meta file to get the total number of layer.
    IDfile_meta = fopen(fileBaseName+'_meta', 'r');
    layers = fread(IDfile_meta, Inf, 'uint64');
    layerNumber = size(layers, 1);
    fprintf("%u layers in file.\n", layerNumber);
    
    % Write header for log file.
    system( 'top -n 1 | awk ''/RES/ {print( $7 "\t" $11 "\t" $12 "\t" $13)}'' > mem.log' );
    writeMemLogEntry( 'Before opening first image.' );
    % Create figure and display first figure for reference selection.
    refID = 1;
    figShownIm = figure; 
    shownIm = imagesc( loadOneBinPEEMimgAt( IDfile, refID) ); 
    colormap gray; axis image; axis off;
    writeMemLogEntry( 'First image loaded.' );
    % Handles for GUI checkout function.
    setappdata(figShownIm,'layerNumber',layerNumber);
    setappdata(figShownIm,'imID',refID);
    setappdata(figShownIm,'IDfile',IDfile);
    setappdata(figShownIm,'shownIm',shownIm);
    % GUI
    shownImID = uicontrol('Style', 'text',...
        'String', sprintf('Current image: %u / %u', refID, layerNumber),...
        'Units', 'normalized',...
        'Position', [0.33 0.05 .15 .03]);
    setappdata(figShownIm,'shownImID',shownImID);
    prevIm = uicontrol('String', '<-',...
        'Callback', @loadNewImg,...
        'Units','normalized',...
        'Position',[0.17 0 .15 .04]);
    nextIm = uicontrol('String', '->',...
        'Callback', @loadNewImg,...
        'Units','normalized',...
        'Position',[0.34 0 .15 .04]);
    selectRef = uicontrol('String', 'Select as reference',...
        'Callback', 'uiresume()',...
        'Units','normalized',...
        'Position',[0.51 0 .15 .04]);
    % Wait until the user select an image as reference.
    uiwait();

    fclose(IDfile);
    fclose(IDfile_meta);
    % Return selected reference image.
    selectedReference = shownIm.CData;
    close(figShownIm);
    writeMemLogEntry( 'Image figure closed.' );
end

function loadNewImg(hObject, eventData, handles)
    layerNumber = getappdata(hObject.Parent,'layerNumber');
    imID = getappdata(hObject.Parent,'imID');
    IDfile = getappdata(hObject.Parent,'IDfile');
    shownIm = getappdata(hObject.Parent,'shownIm');
    shownImID = getappdata(hObject.Parent,'shownImID');

    switch(hObject.String)
        case '<-'
          diffID = -1;
        case '->'
          diffID = 1;
    end
    % Keep imID inside the existing layers.
    if( (imID+diffID)<=0 || (imID+diffID)>layerNumber )
        diffID=0;
    end

    % Update display
    shownImID.String = sprintf('Current image: %u / %u', imID+diffID, layerNumber);
    setappdata(hObject.Parent,'imID',imID+diffID);
    % Load new image
    shownIm.CData = loadOneBinPEEMimgAt( IDfile, imID+diffID);
    % Write use of memory in log file.
    writeMemLogEntry( shownImID.String );
end

function writeMemLogEntry( comment )
    system( [ 'top -o RES -n 1 | awk ''/MATLAB/ {print( $7 "\t" $11 "\t" $12 "\t" $13 "\t' comment '")}'' >> mem.log' ] );
end

The source of the loading function:

function img = loadOneBinPEEMimgAt( IDfile, refID)
% loadOneBinPEEMimgAt Load one PEEM image from a binary file at a specific position.
%   Load the 'refID'th image in a file previously opened with fopen at 'IDfile'.
% Inputs:
%   IDfile : ID of the source file provided by fopen.
%   refID  : position of the image to be loaded within the file.
%
% Outputs:
%   img    : Loaded image.

    % Here we assume image to be 2048*2048 uint16.
    % fseek function places pointer on a (u)int8 basing,
    % so one image is a 2048*2048*2 block.
    fseek( IDfile, 2048*2048*2*(refID-1), 'bof'); % 'bof' stands for begining of file.
    img = fread( IDfile, [2048 2048], 'uint16');
end

The code output the memory usage in log file (as it can be seen in the code), here is this log file:

RES	%MEM	TIME+	COMMAND
779628	2.4	0:11.32	MATLAB	Before opening first image.
949800	2.9	0:15.31	MATLAB	First image loaded.
1.0g	3.3	0:17.95	MATLAB	Current image: 2 / 500
1.1g	3.5	0:18.67	MATLAB	Current image: 3 / 500
1.1g	3.6	0:18.85	MATLAB	Current image: 4 / 500
1.2g	3.8	0:20.79	MATLAB	Current image: 5 / 500
1.2g	3.9	0:21.16	MATLAB	Current image: 4 / 500
1.2g	3.9	0:21.39	MATLAB	Current image: 3 / 500
1.3g	4.2	0:21.84	MATLAB	Current image: 2 / 500
1.3g	4.2	0:22.18	MATLAB	Image figure closed.

Do you have any suggestions to avoid this data accumulation or to release the memory?

Thanks a lot for your help!

Answer 1

[Cedric Bareille]

This was an opengl rendering issue. Using software rendering allows to avoid accumulating data in the memory.

opengl('save','software')

Answer 2

[BC]

Does resetting the axes after a figure is displayed help? I had this issue with imshow(), at least, after each figure was displayed the memory usage increased every time.

cla reset

[Cedric Bareille]

Thanks a lot for your help !

Your solution did not work ^^' but you put me on the right track.

If I load the image into a simple array instead of a graphic object memory remain stable.

So it was really related to the graphic object. However by doing a loop like that:

while(refID<20)
    shownIm.CData = loadOneBinPEEMimgAt( IDfile, refID);
    refID = refID+1;
end

The memory was also remaining stable, despite using the graphic object...

However the graphic object did not have time to update. By adding a pause:

while(refID<20)
    shownIm.CData = loadOneBinPEEMimgAt( IDfile, refID);
    refID = refID+1;
    pause(1);
end

we get back the memory trouble... this was clearly a graphic issue.

Everything gets solve by using software rendering:

opengl('save','software')

I guess I have a trouble of compatibility with my graphic card... still the workaround works fine.

[BC]

Glad you got to the bottom of it, thanks for sharing your solution!

[Image Analyst]

Rather than pause(1) use drawnow.