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Forked from Swain Lab / aliby / aliby-mirror
205 commits behind the upstream repository.
Arin Wongprommoon's avatar
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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