Opening flex files

Hi,

The new version of CP does not open flex files anymore. It returns an error message which I attach here. Can you please help?
Thank you,
Marc

Traceback (most recent call last):
File “/cc/release_10953/CellProfiler/cellprofiler/pipeline.py”, line 1238, in prepare_run
File “/cc/release_10953/CellProfiler/cellprofiler/modules/loadimages.py”, line 1396, in prepare_run
File “/cc/release_10953/CellProfiler/cellprofiler/modules/loadimages.py”, line 1821, in prepare_run_of_flex
File “/cc/release_10953/CellProfiler/cellprofiler/utilities/jutil.py”, line 439, in method
File “/cc/release_10953/CellProfiler/cellprofiler/utilities/jutil.py”, line 377, in call
JavaException: Index: 0, Size: 0

Hi Marc,

Could you post the .flex file which causes the error message?

Thanks!
-Mark

Hi Mark,

sorry for answering so late. flex files are very big so it will not do as attachement. Please download it from the following link
idisk-srv1.mpi-cbg.de/~bickle/001001000.flex

I’ve tried with several standard OPERA files and always had the same problem.
Thanks
Marc

Hi Marc,

It appears that the latest Bio-Formats reader now breaks on this format. We are looking into an updated reader that is compatible with our file systems, and will post here when we find a solution.

Regards,
-Mark

Hi Mark,

thank you, looking forward to the patch.

Hi Mark,

I was wondering whether you found a solution for the flex files. Currently I’m running two versions of CP due to that problem and it would be nice to make a clean transition. Hope you come up with a solution.
Thank you,
Marc

Hi Marc,

We have recently incorporated the latest version of BioFormats in our source code; hopefully this will fix your problem. If so, the fix will be included in the next release, but if you’re daring, you can try it out with our latest public build from source code here.

The trunk build is not as heavily vetted as our releases, so you should take that into account; please note the caveats mentioned on the page linked.

Regards,
-Mark

Hi Mark,

I finally got round installing the trunk version. All works fine with flex, OPERETTA tif and cellomis c01. Thank you.
bye,
Marc

Hi,

the new version is not able to open flex files again. The version works fine for BDPathway images and Arrayscan images though.
Thanks,
Marc

Traceback (most recent call last):
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.6/cellprofiler/pipeline.py”, line 1238, in prepare_run
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.6/cellprofiler/modules/loadimages.py”, line 1397, in prepare_run
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.6/cellprofiler/modules/loadimages.py”, line 1822, in prepare_run_of_flex
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.6/cellprofiler/utilities/jutil.py”, line 439, in method
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.6/cellprofiler/utilities/jutil.py”, line 377, in call
JavaException: Index: 0, Size: 0

Hi Marc,

The release only incorporates a few minor bug fixes described in the release notes (also please see the News section on cellprofiler.org/), and not the various bug fixes that have been included in the trunk build thus far. Until we do a major release, please continue using the trunk build the maintain the functionality you need.

Regards,
-Mark