Movefile and wtifc error

Hi everyone,

I am using a script to crop images at certain ROIs for further processing. During this I have had an issue and could not figure out what it may be. I tried the other solutions in the community but did not solve it. Any help would be highly appreciated.

Initially I received an error for wtifc which returned to:

TIFF library error - 'TIFFOpenW:  C:\Users\A\Croppeddata\crop_X_1.tif: Cannot open.'
Error in writetif (line 110) wtifc(data, map, filename, writemode, colorspace, required_tags);

So I tried to instead try to move the problematic files that cause this issue with this:

 Settings.num_planes(tryp_ind)  = size(im1,3) ;
        num_planes = Settings.num_planes(tryp_ind) ;
        for kk = 1:File.num_t  % for all the timepoints of the given position
                    ii = jj+kk -1 ;
                    im2 = TIFFStack(File.Name(ii).CropX) ;
                    im22 = uint16(im2( :,:, indk0_delta_2_all : indkf_delta_2_all)) ;

                    mkdir([File.pathname, filesep, 'trash']) ;
                    [ ~, ~, filename,] = fileparts(File.Name(ii).CropX) ;
                    movefile(File.Name(ii).CropX, [File.pathname, filesep, 'trash', filesep, filename, '.tif'], "f" ) ;
               
    
                    imwrite( im22(:,:,1),  File.Name(ii).CropX, 'compression', 'none') ; 
                    for m=2: size(im22,3)
                        imwrite( im22(:,:,m),  File.Name(ii).CropX, 'WriteMode', 'append', 'compression', 'none') ;
                    end

But then this returned to:

                    Error using movefile
Cannot read from source: C:\Users\A\Croppeddata\crop_X_1.tif.

Error in cell_cropper_ (Line 755)
                    movefile(File.Name(ii).CropX, [File.pathname, filesep, 'trash', filesep, filename, '.tif'], "f" ) ;
                    

Answer 1

[Walter Roberson]

                    [ ~, ~, filename,] = fileparts(File.Name(ii).CropX) ;

The third output from fileparts() is the file extension, not the file name.

[ibrahim halilullah]

Hi, thanks for the response I changed it to below but still getting the error for movefile.

[ ~, filename, ~, ] = fileparts(File.Name(ii).CropX) ;

[Walter Roberson]

I recommend that you learn how to use fullfile to build file names.

I notice that you are using Windows. It appears you are using https://www.mathworks.com/matlabcentral/fileexchange/32025-dylanmuir-tiffstack

I speculate that TIFFstack is opening the file, and that movefile() is potentially complaining because it is being asked to move a file that is already in use. But I do not know what the expected behaviour would be on Windows in such a case (I know what would happen on Linux or MacOS)