RelateObjects: index out of bounds

[minh-doan]

Calculate child-parent distance?

• If set to anything other than "None", it throws error:

Error while processing RelateObjects: index 300 is out of bounds for axis 0 with size 171

[minh-doan]

Hmm.. could be pipeline specific (uploaded here). When tested with example pipeline PercentPositive, it didn't have error.

I saw this in rc5 and rc7 (Mac)

Images_Pipeline.zip

[bethac07]

I can reproduce on my machine; note that Minimum seems to run fine, but Centroid and Both give the error.

[0x00b1]

Verified. Here's the Sentry issue:

https://sentry.io/allen-goodman/cellprofiler/issues/361525693/

[mmasinas]

Hi, we are getting the same index error on the RelateObjects module. The pipeline properly processes some of the input image sets but for some cases, in encounters an IndexError.
File ".../src/CellProfiler/cellprofiler/modules/relateobjects.py", line 633, in get_parents_of
reverse_lookup[primary_parents_of_parent] = numpy.arange(1, len(primary_parents_of_parent) + 1)
IndexError: index 134 is out of bounds for axis 1 with size 134

We tried to do modify the line where reverse_lookup_len is computed (see line 628) into
reverse_lookup_len = max(numpy.max(primary_parents_of), len(primary_parents_of_parent)) + 1
and now the pipeline works for all the input image sets. However, we are not sure if this will cause any downside issues.

I am attaching the pipeline and the image set which runs into the error.
Plate1.zip