I am having problem un using load command.

I am having this problem is using load command. Anyone who can help me please?

% Extract 10 cell features for each image in 'imageInfo'
clear
tic

% nucleus area in real size
mpp_40 = 0.2525; % 40X
realMin = 80*mpp_40^2;
realMax = 1100*mpp_40^2;
realPSize = 2000*mpp_40;


% Load openslide library
openslide_load_library();

strc = load('C:/image-mRNA-prognostic-model-master/imageAndClinicalInfo/imageInfo.mat');
imInfo = strc.imageInfo;
dirData = 'C:/image-mRNA-prognostic-model-master/bin.png';

% process each image
nFile = size(imInfo, 1);
for i = 1:nFile
    t1 = tic;
    file = imInfo.file{i};
    parts = regexp(file, '/', 'split');
    filename = parts{2}(1:end-4);
    
    % test if the image is already processed
    if exist(['extractCellFeas_cellLevel/', filename, '.mat'], 'file');        
        fprintf('image %d/%d already processed\n', i, nFile);
        continue;
    end
    
    slidePtr = openslide_open([dirData, file]);
    mpp = imInfo.mppX(i);
    width = imInfo.width(i);
    height = imInfo.height(i);
    ps = round(realPSize/mpp);
    
    %% select patches using thumnail
    % Get thumbnail
    thumnail = openslide_read_associated_image(slidePtr, 'thumbnail');
    thumnail = thumnail(:, :, 2:4);
    [ht, wt, ~] = size(thumnail);
    ratio = width/wt;
    
    % patch size in thumbnail
    pst = round(ps/ratio);

    % select patches of interest in thumbnail image
    [X, Y] = meshgrid(1:pst:wt-pst+1, 1:pst:ht-pst+1);
    xy = [X(:), Y(:)];
    d1 = size(xy, 1);
    indOk = zeros(d1, 1);
    for j = 1:d1
        r = xy(j, 2);
        c = xy(j, 1);
        rows = r:r+pst-1;
        cols = c:c+pst-1;
        tile = thumnail(rows, cols, :);
        tMean = mean(tile, 3);
        if sum(tMean(:)>210) < pst*pst/2
            indOk(j) = 1;
        end
    end
    xy = xy(indOk==1, :)-1; % move upper-left point to (0, 0)
    xy = round(xy*ratio);
    
    % remvoe coordinates exceeding width or height
    indOk = xy(:, 1)<=width-ps & xy(:, 2)<=height-ps;
    xy = xy(indOk, :);
    
    %% extract cell features for each tile
    d1xy = size(xy, 1);
    cellFeas = cell(d1xy, 1);
    for ixy = 1:d1xy
        x = xy(ixy, 1);
        y = xy(ixy, 2);
        tile = openslide_read_region(slidePtr, x, y, ps, ps, 0);
        tile = tile(:, :, 2:4);
        areaMin = round(realMin/mpp^2);
        bw = hmt(tile, areaMin);

        statsR = regionprops('table', bw, tile(:, :, 1), 'area', 'MeanIntensity',...
            'MajorAxisLength', 'MinorAxisLength', 'centroid');
        statsR.Area = statsR.Area*mpp^2;
        statsR.MajorAxisLength = statsR.MajorAxisLength*mpp;
        statsR.MinorAxisLength = statsR.MinorAxisLength*mpp;
        
        indOk = statsR.Area <= realMax;
        statsR = statsR(indOk, :);
        if size(statsR, 1) < 80
            continue;
        end
        
        statsG = regionprops('table', bw, tile(:, :, 2), 'MeanIntensity');
        statsB = regionprops('table', bw, tile(:, :, 3), 'MeanIntensity');
        
        statsG = statsG(indOk, :);
        statsB = statsB(indOk, :);

        feas1_7 = [statsR.Area, statsR.MajorAxisLength, statsR.MinorAxisLength,...
            statsR.MajorAxisLength ./ statsR.MinorAxisLength,...
            statsR.MeanIntensity, statsG.MeanIntensity, statsB.MeanIntensity];


        % last 3 features derived from Delaunay graph
        centroids = statsR.Centroid;
        feas8_10 = zeros(size(statsR, 1), 3);
        DT = delaunayTriangulation(double(centroids));
        E = edges(DT);
        for k = 1:size(centroids, 1)
            edgesCell = E(sum(E==k, 2)~=0, :);
            dist = zeros(size(edgesCell, 1), 1);
            for m = 1:numel(dist)
                p1 = centroids(edgesCell(m, 1), :);
                p2 = centroids(edgesCell(m, 2), :);
                dist(m) = norm(p1-p2);
            end
            feas8_10(k, :) = [mean(dist), max(dist), min(dist)];
        end

        cellFeas{ixy, 1} = [feas1_7, feas8_10*mpp];        
    end
        
    cellFeas(cellfun(@isempty, cellFeas)) = []; % remove empty elements
    save(['extractCellFeas_cellLevel', '/', filename, '.mat'], 'cellFeas');
    fprintf('image %d/%d processed, time %f\n', i, nFile, toc(t1));
end


toc

% Close whole-slide image, note that the slidePtr must be removed manually
openslide_close(slidePtr)
clear slidePtr

% Unload library
openslide_unload_library

[Ashish Azad]

Hi Muhammad,

Could you be please more specific where exactly you are getting error, and also paste the error here.

[Walter Roberson]

dirData = 'C:/image-mRNA-prognostic-model-master/bin.png';

That already includes a file extension. Is bin.png truly a directory name or is it a file name?

    file = imInfo.file{i};
    parts = regexp(file, '/', 'split');
    filename = parts{2}(1:end-4);

You can be sure that filename will not have any / in it, but file probably does have / in it (otherwise you would not split it)

        slidePtr = openslide_open([dirData, file]);

Is file certain to start with a / ? Because dirData does not end in a / . Is file intended to be within a directory named bin.png ? Use fullfile()

[Image Analyst]

And, you forgot to attach ''C:/image-mRNA-prognostic-model-master/imageAndClinicalInfo/imageInfo.mat"

[Muhammad Adeel Ahsan Awan]

Actually, this is the whole simulation. I don't how should i ask this question. I need to run this simulation and test it for more files. This is a ready made simulation but i am stuck at some errors. Can anyone guide me how should i ask this question here and you guys can help me in sorting out this issue

[Steven Lord]

What does "this problem" mean?

• Do you receive warning and/or error messages? If so the full and exact text of those messages (all the text displayed in orange and/or red in the Command Window) may be useful in determining what's going on and how to avoid the warning and/or error.
• Does it do something different than what you expected? If so, what did it do and what did you expect it to do?
• Did MATLAB crash? If so please send the crash log file (with a description of what you were running or doing in MATLAB when the crash occured) to Technical Support using the telephone icon in the upper-right corner of this page so we can investigate.

[Muhammad Adeel Ahsan Awan]

Actually, i sent the crash report but they said you are using third part product so contact them. This is a whole simulation and i have to run many m-files in it. The basic purpose of this simulation is to extract the image feautures and corrleate witht the existing data.

[Muhammad Adeel Ahsan Awan]

The third part product is Open Slide Library i guess.

[Walter Roberson]

Move the

strc = load('C:/image-mRNA-prognostic-model-master/imageAndClinicalInfo/imageInfo.mat');

To before the

openslide_load_library();

If you still have a problem with the load() crashing MATLAB then you can construct an example that does not use openslide library at all, and Mathworks will pay attention to that.

[Muhammad Adeel Ahsan Awan]

Hey Walter i somewhat knows why my MATLAB is crashing. The file command is unable to read the info in file imageInfo.mat.

Because i ran little chunks of program, every things works good but there shows an error at line 23. I ran this command in command window and i got the error mentioned below.

imInfo.file{i}

Error:

Array indices must be positive integers or logical values.

[Muhammad Adeel Ahsan Awan]

I will have to modify the data in imageInfo file to be filed. but, i don't know how to.

[Walter Roberson]

If you run in chunks then you probably did not execute the for i so probably i has its default value of sqrt(-1)

[Muhammad Adeel Ahsan Awan]

Ohh i got it. But, the way you mentioned earlier, it is not working even that way.

[Walter Roberson]

Could you confirm that if you do nothing other than run

strc = load('C:/image-mRNA-prognostic-model-master/imageAndClinicalInfo/imageInfo.mat');

at the command line, that MATLAB crashes?

[Muhammad Adeel Ahsan Awan]

no it gets loaded sorry i was doing "i" mistake, the code crashes at this line now i checked and i am sure. Line 33

slidePtr = openslide_open([dirData, file]);

[Walter Roberson]

You have not responded to my concerns in https://www.mathworks.com/matlabcentral/answers/551932-i-am-having-problem-un-using-load-command#comment_908500

Answer 1

[Muhammad Adeel Ahsan Awan]

I did there was a mistake. I changed it. and the code is working fine uptill this part.

% Extract 10 cell features for each image in 'imageInfo'
clear
tic

% nucleus area in real size
mpp_40 = 0.2525; % 40X
realMin = 80*mpp_40^2;
realMax = 1100*mpp_40^2;
realPSize = 2000*mpp_40;


% Load openslide library
%openslide_load_library();

strc = load('imageAndClinicalInfo/imageInfo.mat');
imInfo = strc.imageInfo;
dirData = 'imageAndClinicalInfo/images/';

% process each image
nFile = size(imInfo, 1);
for i = 1:nFile
    t1 = tic;
    file = imInfo.file{i};
    parts = regexp(file, '/', 'split');
    filename = parts{2}(1:end-4);

    % test if the image is already processed
    if exist(['extractCellFeas_cellLevel/', filename, '.mat'], 'file');        
        fprintf('image %d/%d already processed\n', i, nFile);
        continue;
    end

Is there any way that i can attach simulation or provide you th link of Github ?