[ome-devel] Problem extracting videos of a lif project larger than 4GB

[David Gault (Staff)]

Hi,

Looking at the sample code provided I believe the cause of the issue is likely the line
writer.saveBytes(0, reader.openBytes(image));

which should be using the image index as below:
writer.saveBytes(image, reader.openBytes(image));

I would also recommend removing the setup and teardown of the reader and writer from within the loop, I have modified the sample code you provided to show how this might look at https://github.com/dgault/bio-formats-examples/blob/MailingListConvertExample/src/main/java/ReadWriteExample.java.


With Thanks,
David Gault


On 19 Apr 2018, at 17:16, dalsim at eresmas.com<mailto:dalsim at eresmas.com> wrote:

Hi,

 I am developing a tool in Java using loci-tools.jar 5.8.1. Here you can see an extract of the code: https://shrib.com/#RjFIQ2X6UyqkAvv-eyCl
The idea of the code is to extract the videos from the .lif project, which only have black and white 16bit videos. I extract all the tiffs from all the videos and then I join them with ffmpeg. So at the end, if a video has 300 frames, I will have 300 tiffs images, 1 image per frame. If the .lif project is <4GB everything works. If the .lif project, for example, is 10 or 17 GB, the extraction runs but the images are wrong. Here you can see an example: http://i68.tinypic.com/63ujgw.png On your left, frame 1 series 0. On your rigth, frame 2 series 0. Time between images is 40ms so I suspect the tiny white particle on top of frame 1 is the same as the one down in frame 2. Videos inside both cases (4GB and 10GB) weight around 600 MB. If I remove the last videos of the 10 or 17 GB .lif project so I save it in a new .lif project that weitgths less than 4 GB, the conversion is done without problems. Btw, ffmpeg is giving me an error of "Error in tiff header" with those "wrong images" but I can open them with ImageJ and the result is what you saw in the previous images.

What is the problem here?


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