Open Microscopy Environment

Hi All,

The program for which we develop our OMERO Matlab client is FLIMfit.
To store service files in OMERO (like IRFs, etc.), we use "annotation file" option.
It works well for text IRF files, but for small B&H *sdt's there were difficulties.

Here is the code retrieving the bytes:

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        originalFile = ann.getFile();       
        rawFileStore = session.createRawFileStore();
        rawFileStore.setFileId(originalFile.getId().getValue());       
        byteArr  = rawFileStore.read(0,originalFile.getSize().getValue());
        rawFileStore.close();


Here is how these bytes are saved on disk (bytes are "str" variable):
Then, the saved file becomes useful for loading to program.

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            full_temp_file_name = [tempdir fname];
            fid = fopen(full_temp_file_name,'w');   
            %
            if strcmp('sdt',fname(numel(fname)-2:numel(fname)))
                fwrite(fid,typecast(str,'uint16'),'uint16');
            else               
                fwrite(fid,str,'*uint8');
            end
            %
            fclose(fid);


Other words, if it is "sdt" file, bytes are written after casting them to 'uint16' - that was found by trials and errors. Reasons are unknown, but "sdt" files are saved to disk correctly this way.

The next challenge is to work with Excel "xlsx" annotation files, as our program loads Plate metadata in this format. Both methods shown above failed to write the "xlsx" file to disk correctly, - the saved file has the same size as original but Excel can't open it. It is also binary-different from the original.

If one uses "Download" option in "Insight" - the file is saved to disk correctly, Excel opens it.

I wonder if anyone has any thoughts about why it behaves like this, and how to resolve it.
I use Omero Matlab Toolbox 4.4.6, but problem with "sdt" was there for some time, for previous versions.

Best regards,
Y.

Hi Yuriy,

Can you try casting your byte array to 'int8' instead of 'uint8' and let me know if this solves your problem?

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fwrite(fid, byteArr, 'int8');


Sebastien

Hi Sebastien,

Yes it worked.

I will check if switching to "int8" solves it in other places.

Many thanks,
Y.

Hi Yuriy,

glad to hear it worked.
Fyi, we opened a Pull Request with a new OMERO.matlab function to download the content of a file annotation using OMERO.matlab (https://github.com/openmicroscopy/openm ... y/pull/976).

Sebastien