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Swain Lab / aliby / aliby-mirror
205 commits behind the upstream repository.

Arin Wongprommoon
authored
WHY IS THIS CHANGE NEEDED?: - using dev_testimage.py in skeletons: when dummy tiler is created and tiler.initialise_traps() is invoked, segment_traps() (still) raises 'No valid 'tiling regions found' HOW DOES THE CHANGE SOLVE THE PROBLEM?: - in tiler.initialise_traps(), initial_image was defined based on self.ref_channel and self.ref_z; however, if ref_z was not 0, then initial_image would be a zero array. - this was because ImageDummy.pad_array() put the input image at the 0 position and pads with zeros regardless of the value of ref_z. - so i wanted the output of ImageDummy.get_data_lazy() to be defined in such a way that the (ref_z)th slice in the z-direction is the input image. - therefore, i added a new argument to Image.Dummy.pad_array() so that ref_z can be used to achieve the above. WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?: - tech debt: no (easy) way to deal with ref_channel because it's a string. workaround is to keep the ref_channel the first channel in the dummy tiler, and assume that throughout. EVIDENCE THAT COMMIT WORKS: - modified test_image.py works - skeletons: dummy tiler can be defined and dummy_tiler._run_tp(0) runs without errors
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agora | ||
aliby | ||
extraction | ||
parsers | ||
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