Mergeoutputfiles does not work

Hi,

The mergeoutputfiles does not work for either the Mac 10997 or 11488 verions. It works well with the Windows version. I analyze a screen on a cluster which splits the images in many jobs. As I cannot write to a database directly from the cluster, I attempted merging but this does not work. Essentially the windows opens and all the dialogs work, but it does not respond to the settings, meaning the boxes for the merged file stays empty and the same is true for the selected mat files, even though everything was clicked on.
Thanks,
Marc

Hi Marc,
We have confirmed this behavior on our end, and I’ve filed a bug report. We’ll repost here when we have a fix.
-Mark

The fix is available from our trunk builds here. Please let us know if it doesn’t work or other problems arise.
-Mark

Hi Mark,

me again. I tried the merge output file in the new version and it fails again. I guess the modification that went into the trunk version did not go into the new version.
Cheers,
Marc

That’s correct; see my response to one of your related posts here.
-Mark

Hi Mark,

so I did as you asked, but the trunk version also threw an exception (still the Mac version). Could you please check? Thanks,
Marc

Traceback (most recent call last):
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/gui/cpframe.py”, line 301, in on_data_tool
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/gui/cpframe.py”, line 656, in __on_data_tool
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/modules/mergeoutputfiles.py”, line 161, in run_as_data_tool
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/modules/mergeoutputfiles.py”, line 351, in merge_files
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/measurements.py”, line 472, in add_measurement
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/utilities/hdf5_dict.py”, line 262, in setitem
File “/Applications/CellProfilerTrunk.app/Contents/Resources/lib/python2.6/cellprofiler/utilities/hdf5_dict.py”, line 49, in new_setitem
File “build/bdist.macosx-10.3-fat/egg/h5py/_hl/dataset.py”, line 404, in setitem
File “h5d.pyx”, line 218, in h5py.h5d.DatasetID.write (h5py/h5d.c:2689)
File “_proxy.pyx”, line 141, in h5py._proxy.dset_rw (h5py/_proxy.c:1616)
File “_proxy.pyx”, line 248, in h5py._proxy.needs_bkg_buffer (h5py/_proxy.c:2289)
KeyError: conversion function not found (Datatype: Object not found)

Hi Mark,

I just found out that it works for two files, but not for more than that. Already with three files it fails. Maybe that helps?
Marc

I think this may be something specific in the data files. Can you post the three of them that fail?

Hi,

I have deleted the file since then and redid the analysis. I did manage to merge the files using a PC version, so I doubt it was dependent on the mat files. I have just tried merging another three files with the Mac Trunk version and this has worked, so I’m to sure what’s going on. If encounter the problem again, I’ll post again together with the mat files.
Thank you,
Marc