CellProfiler/CellProfiler — Issue #46: JIRA [IMG-1555] RunImageJ"failed to load pipeline"
Author: thouis
Created: 2011-11-23 20:49:40+00:00
State: open
Labels: current

Error loading this pipeline with SVN 11602, at the RunImageJ module:
https://imageweb.broadinstitute.org/imaging/analysis/2007_05_14_Mitochondria_AnneCataldo/McPhie/Pipelines/PIPE_2011_10_14_1st_AND_2nd.cp
This will load on my Windows VM. Tubeness_2.0.jar is installed in the respective ImageJ preferences directories.
Here's the stacktrace:
***********
INFO:PipelineStatistics:Pipeline saved with CellProfiler SVN revision 11488
Pipeline saved with CellProfiler SVN revision 11488
ERROR:root:Failed to load pipeline
Traceback (most recent call last):
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/pipeline.py", line 760, in loadtxt
module_name, from_matlab)
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/cpmodule.py", line 191, in set_settings_from_values
v.value = value
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/settings.py", line 119, in __internal_set_value
self.set_value(value)
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/settings.py", line 199, in set_value
raise NotImplementedError("The count should be inferred, not set - actual: %d, set: %d"%(len(self.__sequence), count))
NotImplementedError: The count should be inferred, not set - actual: 0, set: 4
Failed to load pipeline
Traceback (most recent call last):
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/pipeline.py", line 760, in loadtxt
module_name, from_matlab)
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/cpmodule.py", line 191, in set_settings_from_values
v.value = value
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/settings.py", line 119, in __internal_set_value
self.set_value(value)
File"/Users/dlogan/svn/CellProfiler/trunk/CellProfiler/cellprofiler/settings.py", line 199, in set_value
raise NotImplementedError("The count should be inferred, not set - actual: %d, set: %d"%(len(self.__sequence), count))
NotImplementedError: The count should be inferred, not set - actual: 0, set: 4

Original reporter: dlogan
Jira link: https://jira.broadinstitute.org/browse/IMG-1555
Fix version: Current
Assignee: leek

**Comment from leek on Wed, 19 Oct 2011 13:57:17 -0400:**
Unfortunately the interprocess bridge that was done for the Mac is incomplete and doesn't support the parameters. This should be resolved when we have ImageJ 2.0 support because we will be able to run ImageJ 2.0 headless on the Mac.