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cpmorphology shape broadcast error #324

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dlogan opened this Issue May 9, 2012 · 1 comment

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dlogan commented May 9, 2012

Error doing grayscale erosion in Morph open operation:


Traceback (most recent call last):
File "C:\Trunk\CellProfiler.git\trunk\cellprofiler\gui\pipelinecontroller.py", line 1019, in do_step
module.run(workspace)
File "C:\Trunk\CellProfiler.git\trunk\cellprofiler\modules\morph.py", line 543, in run
function.custom_repeats.value)
File "C:\Trunk\CellProfiler.git\trunk\cellprofiler\modules\morph.py", line 701, in run_function
footprint=strel)
File "C:\Trunk\CellProfiler.git\trunk\cellprofiler\cpmath\cpmorphology.py", line 2501, in opening
eroded_image = grey_erosion(image, radius, mask, footprint)
File "C:\Trunk\CellProfiler.git\trunk\cellprofiler\cpmath\cpmorphology.py", line 2336, in grey_erosion
big_image[iradius:-iradius,iradius:-iradius] = image
ValueError: operands could not be broadcast together with shapes (721,1024,13) (721,1024,3)


INPUT:
\iodine\imaging_analysis\People\David\Forum\interlaced

PIPELINE:

\iodine\imaging_analysis\People\David\Forum\interlaced\interlaced_test_pipeline.cp

@ghost ghost assigned LeeKamentsky May 9, 2012

@LeeKamentsky

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LeeKamentsky commented May 9, 2012

The image was color with all 3 channels being the same. I made Morph do a gentle color -> gray (warns user if it's color, but converts to gray anyway, and from there, possibly it converts to binary for things like skeletonize).

The work-around for the user is to do the color to gray explicitly in the pipeline.

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