read and store data from struct file during each iteration in the for loop

Hi,

I have a for loop as shown. During each iteration the will store entire output in the struct file named Measurements. (file attached here)

From this struct file file, I need to read and store only 'Centroid', 'Eccentricity', 'EquivDiameter' in the sepearte array.

for i = 1:1:1000
    
    % some operation
    Measurements = some operation
    
end

Answer 1

[Star Strider]

I am not certain what result you want.

Try this —

% load('matlab')
% whos('-file', 'matlab')
% 
% Measurements

fields = {'Centroid', 'Eccentricity', 'EquivDiameter'};

files = dir('*.mat');
NrFiles = numel(files);

for k = 1:NrFiles
    LD = load(files(k).name);
    MeasTable = struct2table(LD.Measurements);
    VN = MeasTable.Properties.VariableNames;
    ColNrs = find(ismember(VN,fields));    
    ForFile = MeasTable(:,ColNrs);
    writetable(ForFile,sprintf('NewTable%04d.txt',k))
end

readtable('NewTable0001.txt')

ans = 8x4 table
    Centroid_1    Centroid_2    Eccentricity    EquivDiameter
    __________    __________    ____________    _____________

       268.6         397.8        0.76509          2.5231    
       333.8         643.5        0.33229          9.4407    
      339.86        403.57        0.54188          13.303    
      355.02        557.21        0.66171          34.761    
      355.85         445.2        0.47857          34.943    
      356.29        744.16        0.35417          35.396    
      353.46        806.41        0.25141          26.511    
      360.73        838.97        0.44367          28.702    

If all the .mat files have the same internal structure, then ‘MeasTable’ also will, and some of the lines in the loop can be defined prior to it.

.

[Turbulence Analysis]

Thanks!

Actually this code is a part of image processing. I am processing 5000 images in the for loop. For each image in the for loop, the below command will generate Measurements struct file. From that file I need to store only 'Centroid', 'Eccentricity', 'EquivDiameter' in the seperate array, lets say 'A'. Then the data will append in the array 'A' for sequence of images in the for loop.

By doing this I may reach the memory limit, however I am running this in the HPC, so that shouldn't be a problem

for i =1:1:500
    %% do image processing
    Measurements = regionprops(mask, 'all');
end

[Turbulence Analysis]

And forgot to mention, teh size of the Measurements struct file will different during each iteration..

[Star Strider]

My pleasure!

The variable column sizes can vary so long as within each file they are all the same sizes. If the structures are in different orders, esch table derived from them will be different in each iteration, and that could cause problems with my code as currently written. However it would be straightforward to have all the table arrays be saved in the same column orientation, regardlkess of their initial orientation. (I need to know if that is an issue.)

The table arrays can be vertically concatenated to produce one table as the final result, if that is what you want.

However, I’m still not sure what you want as the result. Saving the arrays as a single table is certainly possible.

[Turbulence Analysis]

Thanks again!

Now, I am saving the struct file gnerated during each for loop iteration in the cell array C3.

Then I modifed your code as follows, however I a couldn't concatenate to get one table.

The overall idea is to create one table which stores all the results generated duirng each for loop iteration

fields = {'Centroid', 'Eccentricity', 'EquivDiameter'};
% files = dir('*.mat');
% NrFiles = numel(files);
for k = 1:3
    LD = (c3{1,k});
    MeasTable = struct2table(LD);
    VN = MeasTable.Properties.VariableNames;
    ColNrs = find(ismember(VN,fields));    
    ForFile = MeasTable(:,ColNrs);
    writetable(ForFile,sprintf('NewTable%04d.txt',k));
end

[Turbulence Analysis]

Actually, the above operation saves three new tables NewTable0001.txt; NewTable0002.txt; NewTable0003.txt, how to combine them to a single table?

[Star Strider]

As always, my pleasure!

To get one table (assuming all the variables are the same in each ‘ForFile’ table) create a column-oriented collection of them using:

ForFile{k,:} = MeasTable(:,ColNrs);

and then concatenate that at the end —

load('matlab')                                              % Information (Delete Later)
whos('-file', 'matlab')                                     % Information (Delete Later)

  Name      Size             Bytes  Class    Attributes

  c3        1x3             446028  cell               

fields = {'Centroid', 'Eccentricity', 'EquivDiameter'};
% files = dir('*.mat');
% NrFiles = numel(files);
for k = 1:3
    LD = c3{k};
    MeasTable = struct2table(LD);
    VN = MeasTable.Properties.VariableNames;
    ColNrs = find(ismember(VN,fields));    
    ForFile{k,:} = MeasTable(:,ColNrs);
end
ForFile{:}                                                  % Information (Delete Later)

ans = 5x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    348.91     699.7      0.81707          47.014    
    345.18    899.77      0.40595          29.468    
    352.85    455.82      0.51376          35.414    
    347.92    547.24      0.52267          25.805    
    360.68    659.78      0.43788          8.7404    

ans = 5x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

     348.8     702.4      0.82225           46.96    
    345.02    903.09      0.44569          29.403    
    352.75    458.27      0.56003          35.252    
    347.88    550.03       0.5379          25.904    
    360.95    663.25       0.4336          8.7404    

ans = 6x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    348.75    705.11      0.82348          46.906    
    345.03    906.35       0.4668          29.316    
    352.64    460.75      0.58144          35.234    
    351.56    346.11      0.54136          31.855    
    347.92    552.75      0.54632          25.953    
       361     666.5      0.43593          8.7404    

Combined = vertcat(ForFile{:})

Combined = 16x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    348.91     699.7      0.81707          47.014    
    345.18    899.77      0.40595          29.468    
    352.85    455.82      0.51376          35.414    
    347.92    547.24      0.52267          25.805    
    360.68    659.78      0.43788          8.7404    
     348.8     702.4      0.82225           46.96    
    345.02    903.09      0.44569          29.403    
    352.75    458.27      0.56003          35.252    
    347.88    550.03       0.5379          25.904    
    360.95    663.25       0.4336          8.7404    
    348.75    705.11      0.82348          46.906    
    345.03    906.35       0.4668          29.316    
    352.64    460.75      0.58144          35.234    
    351.56    346.11      0.54136          31.855    
    347.92    552.75      0.54632          25.953    
       361     666.5      0.43593          8.7404    

writetable(Combined,'Combined.txt');
Check = readtable('Combined.txt')                           % Check Result

Check = 16x4 table
    Centroid_1    Centroid_2    Eccentricity    EquivDiameter
    __________    __________    ____________    _____________

      348.91         699.7        0.81707          47.014    
      345.18        899.77        0.40595          29.468    
      352.85        455.82        0.51376          35.414    
      347.92        547.24        0.52267          25.805    
      360.68        659.78        0.43788          8.7404    
       348.8         702.4        0.82225           46.96    
      345.02        903.09        0.44569          29.403    
      352.75        458.27        0.56003          35.252    
      347.88        550.03         0.5379          25.904    
      360.95        663.25         0.4336          8.7404    
      348.75        705.11        0.82348          46.906    
      345.03        906.35         0.4668          29.316    
      352.64        460.75        0.58144          35.234    
      351.56        346.11        0.54136          31.855    
      347.92        552.75        0.54632          25.953    
         361         666.5        0.43593          8.7404    

I needed to understand what ‘c3’ is and how to work with it in order to check my code to be sure it works correctly with it. (It does.)

It is easier (and probably more efficient) to concatenate the ‘ForFile’ tables at the end rather than concatenate them in the loop.

You can sefely delete the lines I commented, since they are for my information only in order for me to understand your new .mat file and to work with its contents.

This was interesting!

.

[Turbulence Analysis]

Thanks again!

It's doing it's job!

[Star Strider]

As always, my pleasure!

Thank you!

[Turbulence Analysis]

Hi,

In the 'c3' file some struct files has a size of 1x1, I am getting the below error whenever it reads those file

Error using struct2table
Input structure is a scalar, but its fields have different numbers of rows. If
you intended to create a table with one row, set 'AsArray' to true. 

code

for k = 1:1
    LD = c3{k};
    MeasTable = struct2table(LD);
    VN = MeasTable.Properties.VariableNames;
    ColNrs = find(ismember(VN,fields));    
    ForFile{k,:} = MeasTable(:,ColNrs);
end

[Star Strider]

I have never gotten that error before.

Adding a conditional test using structfun could work. The problem is that if the three desired variables have different numbers of rows, it would be necessary to either pad the missing rows with NaN or truncate the longer rows to the lengths of the shorter rows. Since only the three desired variables actually ‘count’, using structfun to determine if they are all the same row lengths could be appropriate.

The error suggests using AsArray, however after reading the documentation on it, it would likely not work the way it needs to here, and an alternative would have to be designed.

I need that particular structure (and if possible some others that throw the same error to see if there is any common problem amongst them) in order to design a work-around.

Meanwhile, in the event that the three desired variables have different numbers of rows, would you want to expand the shorter ones filling the empty rows with NaN, or truncate the longer ones? The table will not work if they have different numbers of rows.

[Turbulence Analysis]

for e.g. in the attached c3, it works well from k = 1 to 243, however it throws error at k = 244 as it is 1x1

[Star Strider]

That one errant structure managed to defeat what I considered a reasonably efficient approach to this. The problem is that structures do not index as other array types do, so I had to revert to a different approach. I am not sure if it is more efficient than my original approach, however it appear to work correctly and reads and processes all 245 elements of ‘c3’ without problems. (I specifically checked the last four to see if they were processed correctly. They appear to have been. You can delete that line.)

My revised code —

load('matlab')                                              % Information (Delete Later)
whos('-file', 'matlab')                                     % Information (Delete Later)

  Name      Size                Bytes  Class    Attributes

  c3        1x245            20809949  cell               

fields = {'Centroid', 'Eccentricity', 'EquivDiameter'};
% files = dir('*.mat');
% NrFiles = numel(files);
for k = 1:numel(c3)
    LD = c3{k};
    select = {LD.Centroid; LD.Eccentricity; LD.EquivDiameter};
    MeasTable = cell2table(select.', 'VariableNames',fields);
    VN = MeasTable.Properties.VariableNames;
    ColNrs = find(ismember(VN,fields));    
    ForFile{k,:} = MeasTable(:,ColNrs);
end

fprintf('\nRead and collected %d elements of ‘c3’\n', k)

Read and collected 245 elements of ‘c3’

ForFile{end-4:end}                                          % Information (Delete Later)

ans = 2x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    344.01    986.29      0.93342          39.153    
    345.73    870.05      0.72502          28.322    

ans = 2x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    343.98    989.42       0.9338          39.413    
    345.66    873.01      0.69685          28.028    

ans = 2x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    343.98    992.56      0.93325          39.606    
     345.6    876.28      0.68287            28.3    

ans = 1x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    345.42    879.79      0.61662          28.412    

ans = 1x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    345.49    883.11      0.52828           28.3     

Combined = vertcat(ForFile{:})

Combined = 1157x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    345.92    846.33      0.51444          27.915    
    345.02    1008.9      0.36766          26.318    
    345.78    875.08      0.47321          23.963    
    346.06    927.47      0.50862          26.845    
     345.5    753.92      0.65757          26.535    
    344.29     778.5      0.10048           8.444    
    345.83    850.03      0.50788          27.663    
    345.52    756.75      0.58771          26.678    
    345.79    878.01      0.46224          23.963    
    346.13    930.74       0.5168          26.798    
    344.25       782      0.34512          8.5191    
    345.89    853.75      0.47479          27.315    
    345.52    759.75      0.54122          26.726    
    345.75    881.11      0.41682          23.857    
    346.08    934.06      0.52776          26.916    
    344.07    785.51      0.20784          8.3683    

writetable(Combined,'Combined.txt');
Check = readtable('Combined.txt')                           % Check Result

Check = 1157x4 table
    Centroid_1    Centroid_2    Eccentricity    EquivDiameter
    __________    __________    ____________    _____________

      345.92        846.33        0.51444          27.915    
      345.02        1008.9        0.36766          26.318    
      345.78        875.08        0.47321          23.963    
      346.06        927.47        0.50862          26.845    
       345.5        753.92        0.65757          26.535    
      344.29         778.5        0.10048           8.444    
      345.83        850.03        0.50788          27.663    
      345.52        756.75        0.58771          26.678    
      345.79        878.01        0.46224          23.963    
      346.13        930.74         0.5168          26.798    
      344.25           782        0.34512          8.5191    
      345.89        853.75        0.47479          27.315    
      345.52        759.75        0.54122          26.726    
      345.75        881.11        0.41682          23.857    
      346.08        934.06        0.52776          26.916    
      344.07        785.51        0.20784          8.3683    

My apololgies for the delay. I had major computer problems last night with something Micro$oft did that really screwed up my computer. It took a bit over four hours, several uninstalls/reinstalls of some of the apps I need (and whose installations Micro$oft screwed up) and at least 20 warm reboots to get it back to the way I want it. I absolutely hate Windows. It used to be a decent operating system. Now, it’s just unstable crap and loaded with bloatware.

.

[Turbulence Analysis]

No worries at all. Thank you very much for your kind support despite the problem you had with your computer.

I undertand the pain with the Microsoft. I had the similar issue last week, all of sudden it stopped working and end with blue screen error. I somehow rectified it. Yeah,these days, particularly working with Windows 11 is a real pain. Too many auto updates and some apps always need frequent restart for proper fucntioning.

[Star Strider]

As always, my pleasure!

Thank you for understanding my predicament.

[Turbulence Analysis]

Hello again,

In the attached c3 file some columns got 0x1 struct files.

First I need to know idx of those columns and delete those columns from the c3 file before creating table.

Could you please help. I can create a seperate thred if you prefer!

[Star Strider]

We just need to test for empty cells and not consider those.

Added that. The rest of my previous code is unchanged.

My revised code —

load('matlab')                                              % Information (Delete Later)
whos('-file', 'matlab')                                     % Information (Delete Later)

  Name      Size               Bytes  Class    Attributes

  c3        1x100            2409977  cell               

fields = {'Centroid', 'Eccentricity', 'EquivDiameter'};
% files = dir('*.mat');
% NrFiles = numel(files);
for k = 1:numel(c3)
    LD = c3{k};
    SzLD = size(LD)                                         % Information (Delete Later)
    if ~isempty(LD)
        select = {LD.Centroid; LD.Eccentricity; LD.EquivDiameter};
        MeasTable = cell2table(select.', 'VariableNames',fields);
        VN = MeasTable.Properties.VariableNames;
        ColNrs = find(ismember(VN,fields));    
        ForFile{k,:} = MeasTable(:,ColNrs);
    end
end

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SzLD = 1x2

2 1

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SzLD = 1x2

2 1

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SzLD = 1x2

1 1

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SzLD = 1x2

1 1

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1 1

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1 1

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SzLD = 1x2

2 1

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2 1

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2 1

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1 1

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1 1

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1 1

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1 1

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SzLD = 1x2

0 1

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0 1

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0 1

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0 1

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0 1

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fprintf('\nRead and collected %d elements of ‘c3’\n', k)

Read and collected 100 elements of ‘c3’

% ForFile{end-4:end}                                          % Information (Delete Later)

Combined = vertcat(ForFile{:})

Combined = 152x3 table
        Centroid        Eccentricity    EquivDiameter
    ________________    ____________    _____________

    324.19    869.78      0.54943          25.382    
     323.5    956.85      0.53722          23.534    
    323.37    988.12      0.59806           23.48    
    324.09    915.21      0.69311          7.7358    
    324.22    1018.5       0.2681          8.3683    
     324.5     874.3      0.58058          25.054    
     323.6    961.95        0.225          23.723    
    323.33    992.42      0.61297           23.75    
    323.96    920.67      0.49505          7.8987    
    324.56    878.72      0.55415          24.437    
    323.66    967.22       0.4225          23.857    
    323.42    996.59      0.63476           23.99    
    324.07    925.53      0.49865          8.5191    
    324.44     882.9      0.44595          24.541    
    323.76    987.07      0.93823          34.281    
    323.82    929.93      0.46072          7.5694    

writetable(Combined,'Combined.txt');
Check = readtable('Combined.txt')                           % Check Result

Check = 152x4 table
    Centroid_1    Centroid_2    Eccentricity    EquivDiameter
    __________    __________    ____________    _____________

      324.19        869.78        0.54943          25.382    
       323.5        956.85        0.53722          23.534    
      323.37        988.12        0.59806           23.48    
      324.09        915.21        0.69311          7.7358    
      324.22        1018.5         0.2681          8.3683    
       324.5         874.3        0.58058          25.054    
       323.6        961.95          0.225          23.723    
      323.33        992.42        0.61297           23.75    
      323.96        920.67        0.49505          7.8987    
      324.56        878.72        0.55415          24.437    
      323.66        967.22         0.4225          23.857    
      323.42        996.59        0.63476           23.99    
      324.07        925.53        0.49865          8.5191    
      324.44         882.9        0.44595          24.541    
      323.76        987.07        0.93823          34.281    
      323.82        929.93        0.46072          7.5694    

.

[Turbulence Analysis]

Perfect! Thanks very much.

Just crusious to know how to extract only the indices of the column of c3 which got 0 x 1 struct similar to one we do for removing NaN in normal arrays

index_nan = find(isnan(A);

[Star Strider]

I did not look closely, however I do not beleive there is anything at all in the empty structures. The fields are all there, however there is nothing in any of them. There is a difference between ‘empty’ (generally although not always denoted by empty square brackets []) and ‘missing’ or NaN values. They are two different conditions, with NaN values being just that — not a number or not a time (NaT) and therefore not ‘empty’ — and empty elements that are only allowed in structures and cell arrays, and not in others, such as numeric arrays or table arrays. The ‘empty’ and NaN/NaT conditions are not equivalent.

[Turbulence Analysis]

Okay, Thanks a lot for the details!

[Star Strider]

As always, my pleasure!