[ome-users] Error on max intensity for large volumes

[Josh Moore]

On Jun 12, 2013, at 1:07 PM, ingvar wrote:

> Dear OMERO,

Hi Ingvar,

> On an EM volume that contains more than 2^31 data points, I get an error when attempting to do "Max Intensity" in the OMERO.web image viewer.  The error message in OMEROweb.log and OMEROweb_request.log indicate that the cause is an overflow in an integer index in Java.  Assuming that the index points into a Java array, then there may be a bigger problem, as Java arrays in the standard Oracle implementation is limited to MAX_INTEGER - 8 (or some other small offset depending on who you believe).
> 
> There are several possible solutions here:
> direct memory management (http://www.omsn.de/blog/big-arrays-in-java)
> use a 3rd party library such as fastutil (http://fastutil.di.unimi.it)
> rewrite the code, I do not think the whole data array has to be in memory for max intensity

It's unlikely we'd try any of the more advanced workarounds in the short-term, but certainly loading sections of the data should work.


> Steps to reproduce:
> Fetch the file ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-2362/map/emd_2362.map.gz (2.6 GB)
> Upload into OMERO
> In OMERO.web's image viewer select "Max Intensity"

Thanks for the steps and the data. I'll download and try to reproduce.


> I am on a pretty old version, 4.3.3, if I remember correctly, so if this has been addressed since then, I guess this is the incentive for me to upgrade.

Let's hope so!

> Kind Regards,
> Ingvar Lagerstedt

Cheers,
~Josh