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CellProfiler / centrosome

An open source image processing library
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Index error in circular_average_filter #92

Closed bethac07 closed 5 years ago

bethac07 commented 5 years ago

See also https://github.com/CellProfiler/CellProfiler/issues/3686#issuecomment-442080325

Traceback (most recent call last):
  File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/gui/pipelinecontroller.py", line 2889, in do_step
    self.__pipeline.run_module(module, workspace)
  File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/pipeline.py", line 2031, in run_module
    module.run(workspace)
  File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/modules/smooth.py", line 212, in run
    output_pixels = circular_average_filter(pixel_data, object_size / 2 + 1, image.mask)
  File "/usr/local/lib/python2.7/site-packages/centrosome/filter.py", line 756, in circular_average_filter
    sgrid[crad,crad] = np.minimum(np.pi*radius**2,np.pi/2)
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices