CellProfiler/CellProfiler — Issue #278: MeasureImageQuality: Error on post_run for HDF5 version
Author: braymp
Created: 2012-01-24 19:16:48+00:00
State: open

Running the following batch (http://imagingweb.broadinstitute.org/batchprofiler/cgi-bin/CellProfiler2.0/CellProfiler/BatchProfiler/ViewBatch.py?batch_id=3494), I get the following error:
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ERROR:root:Failed to complete post_run processing for module MeasureImageQuality.
Traceback (most recent call last):
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/2012_01_23_16_42_03/cellprofiler/pipeline.py", line 1525, in post_run
module.post_run(workspace)
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/2012_01_23_16_42_03/cellprofiler/modules/measureimagequality.py", line 723, in post_run
statistics += self.calculate_experiment_threshold(image_group, workspace)
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/2012_01_23_16_42_03/cellprofiler/modules/measureimagequality.py", line 1052, in calculate_experiment_threshold
threshold_group.threshold_feature_name(image_name))
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/2012_01_23_16_42_03/cellprofiler/measurements.py", line 576, in get_all_measurements
self.get_image_numbers())
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/2012_01_23_16_42_03/cellprofiler/measurements.py", line 549, in get_measurement
vals = self.hdf5_dict[object_name, feature_name, image_set_number]
File "/imaging/analysis/CPClusterSingle/CellProfiler-2.0/2012_01_23_16_42_03/cellprofiler/utilities/hdf5_dict.py", line 184, in __getitem__
assert feature_exists
AssertionError
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What makes this error confusing is that I cannot replicate this error using the same pipeline and running CP on unix with the same CPCluster version 2012_01_23_16_42_03 (nor with the pre-Git 11675)

I can however, run it on the cluster with a pre-HDF5 version (I am doing so now, batch #3495)

Pipeline: \\iodine\imaging_analysis\2008_01_24_Hepatotoxicity_GolubLab_DavidThomas\2012_01_23_Expanded60CmpdSet\Pipelines\2012_01_23_IllumCorr.cp
Batch file: \\iodine\imaging_analysis\2008_01_24_Hepatotoxicity_GolubLab_DavidThomas\2012_01_23_Expanded60CmpdSet\Output\batch_data.h5