The file size after conversion using version 0.11.0 is doubled

[nwango7]

It's me again. I recently noticed that the solution to issue #283 was updated to version 0.11.0, so I tried the new version again. I found that the size of the ome.tiff files generated by running raw2ometiff on the zarr files generated with the then-current version (0.11.0-SNAPSHOT) and the 0.11.0 version was significantly different. Opening the two images with qupath didn't seem to make any difference. I'm curious what caused the file size to increase so much?

[melissalinkert]

@nwango7, can you please include here the full bioformats2raw and raw2ometiff commands that were used to convert in both cases?

[nwango7]

Of course, my usage is very simple. I downloaded the .zip file, unzipped it, and then cd to the bin directory.

For 0.11.0-SNAPSHOT:
cd bioformats2raw-0.11.0-SNAPSHOT/bin/

~/bioformats2raw-0.11.0-SNAPSHOT/bin$ ./bioformats2raw "/home/project/data/data_mihc_mrxs/2401582-38.mrxs" /home/project/data/data_mihc_zarr/2401582-38_11_SNAPSHOT --series 0

cd raw2ometiff-0.8.0/bin/

~/raw2ometiff-0.8.0/bin$ ./raw2ometiff "/home/project/data/data_mihc_zarr/2401582-38_11_SNAPSHOT/" /home/project/data/data_mihc_ome_tiff/2401582-38_11_SNAPSHOT.ome.tiff

For 0.11.0:
cd bioformats2raw-0.11.0/bin/

~/bioformats2raw-0.11.0/bin$ ./bioformats2raw "/home/project/data/data_mihc_mrxs/2401582-38.mrxs" /home/project/data/data_mihc_zarr/2401582-38_11 --series 0

cd raw2ometiff-0.8.0/bin/

~/raw2ometiff-0.8.0/bin$ ./raw2ometiff "/home/project/data/data_mihc_zarr/2401582-38_11/" /home/project/data/data_mihc_ome_tiff/2401582-38_11.ome.tiff

[nwango7]

I figured out what was going on. I already had a file called 2401582-38_11.ome.tiff, and then I regenerated a file with the same name. It didn't overwrite the old file, but continued writing after it, causing the file to be twice as large. I used 0.11.0 to regenerate the file with the new name, and it was the same size as before. I apologize for not investigating the issue thoroughly. Perhaps the minor issue of continued writing can be fixed.

[melissalinkert]

Thanks, @nwango7, that makes sense. Moving this to the raw2ometiff repository then, as that's where we would need to fix.