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

ingvar ingvar at ebi.ac.uk
Wed Jun 12 12:07:00 BST 2013


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

Steps to reproduce:
Fetch the file 
(2.6 GB)
Upload into OMERO
In OMERO.web's image viewer select "Max Intensity"

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.

Kind Regards,
Ingvar Lagerstedt

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