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RelateObjects: index out of bounds #3329

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minh-doan opened this issue Oct 3, 2017 · 4 comments
Open

RelateObjects: index out of bounds #3329

minh-doan opened this issue Oct 3, 2017 · 4 comments
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@minh-doan
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@minh-doan minh-doan commented Oct 3, 2017

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

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@minh-doan minh-doan commented Oct 3, 2017

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

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@bethac07 bethac07 commented Oct 3, 2017

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

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@0x00b1 0x00b1 commented Oct 3, 2017

@mmasinas

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@mmasinas mmasinas commented Oct 5, 2017

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

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