Problem with CellProfiler integration

Hello,

I've got a cellprofiler pipeline that working on cellprofiler but not working on knime.

I've got this error in console  :

WARN CellProfilerInstance Finished group

WARN CellProfilerInstance

WARN CellProfilerInstance Traceback (most recent call last):

WARN CellProfilerInstance File "cellprofiler\knime_bridge.pyc", line 143, in run

WARN CellProfilerInstance File "cellprofiler\knime_bridge.pyc", line 427, in run_group_request

WARN CellProfilerInstance File "cellprofiler\measurements.pyc", line 369, in __getitem__

WARN CellProfilerInstance File "cellprofiler\measurements.pyc", line 959, in get_measurement

WARN CellProfilerInstance File "cellprofiler\utilities\hdf5_dict.pyc", line 373, in __getitem__

WARN CellProfilerInstance File "cellprofiler\utilities\hdf5_dict.pyc", line 377, in __getitem__

WARN CellProfilerInstance AssertionError

ERROR CellProfiler Pipeline Executor Execute failed: ("RuntimeException"):

 

In attachment you can find images, pipeline cp in test.zip

Somebody can help me ?

Hi Cedunia,

thanks for the report. I will take a look as soon as possible. One question which just came to my mind: Which CellProfiler version are you using locally?

Have a nicer weekend,

Christian

Hi Cedunia,

I was able to reproduce the problem and filed a bug-report for the CellProfiler guys: https://github.com/CellProfiler/knime-bridge/issues/6. I will let you know as soon as there is a fix available.

Sorry for the hassle,

Christian

Hi Cedunia,

the bug has been fixed on CellProfiler side! See: https://github.com/CellProfiler/knime-bridge/issues/6#event-302128928 (Thanks Lee!!).

You can use the trunk build of CellProfiler to get your workflow running.

Hope this helps,

 

Christian