Cytomine-core
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cytomine
Files upload but don't deploy - maximum file size limit / ndpi file reading issue?
I'm adding ndpi images to the docker setup and whenever I try with a file larger than 5gb they upload but fail to deploy. Nothing is shouting out in the logs but maybe you can help?
I'm emailing the reporting tar to [email protected] with a link to this issue - thanks in advance for your help
Hello,
Regarding your logs, the uploads reached the server but Cytomine was not able to identify the format.
I assume that it is related to this OpenSlide limitation https://github.com/openslide/openslide/issues/174
You are right, thanks so much for the link - looks like it's fixed in that openslide pull - any idea how I can get that into cytomine?
On Wed, 1 Apr 2020, 17:48 geektortoise, [email protected] wrote:
Hello,
Regarding your logs, the uploads reached the server but Cytomine was not able to identify the format.
I assume that it is related to this OpenSlide limitation openslide/openslide#174 https://github.com/openslide/openslide/issues/174
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Hello,
A first test could be to compile custom Docker images to integrate this OpenSlide version.
OpenSlide is active in two components :
- ims for the image metadata fetching
- iipCyto for the tiling.
The Dockerfile for the iipCyto is here :
https://github.com/cytomine/Dockerfiles/blob/master/iipCyto/Dockerfile#L26
You can change the line by
RUN cd /tmp && git clone https://github.com/ntrahearn/openslide && cd /tmp/openslide && autoreconf -i && ./configure && make && make install
And the same modification for ims
https://github.com/cytomine/Dockerfiles/blob/master/ims/Dockerfile#L41
recompile your Docker images with the docker build -t command (as shown in the Dockerfiles README), restart your Cytomine and it would be ready for a test.
I'm not able to currently make the tests because I don't have one of the concerned image in my test set.
Have a nice day
Hello, @AndyBlake
Did you succeed with this operation ?
Have a nice day
Hiya Sorry for the delay in replying - Even though the hotfix looked like it should have worked when I tried it with some recompiled binaries it still doesn't seem to handle the larger files. When I have fixed this I'll be sure to update this with how I managed to integrate this into the system - thanks for your help and guidance. Kind regards Andy