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    • Arin Wongprommoon's avatar
      fix!(aliby): incorporate ref_z in creating dummy image object · 1a762d7e
      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
      1a762d7e
    • Arin Wongprommoon's avatar
      fix!(aliby): initialise traps based on dummy image · 353a452c
      Arin Wongprommoon authored
      WHY IS THIS CHANGE NEEDED?:
      - when tiler.initialise_traps() is invoked, "No valid tiling regions
        found" is raised from traps.segment_traps() (aliby.tile.traps).
      
      HOW DOES THE CHANGE SOLVE THE PROBLEM?:
      - the image called by segment_traps() was a blank image.
      - this was because tiler.initialise_traps() uses the first timepoint to
        define the initial image (line 400 in tiler.py).
      - the first timepoint was a blank image because ImageDummy.pad_array()
        added zero arrays BEFORE the input array.
      - so fixed it by reversing the behaviour of ImageDummy.pad_array()
      - and modified the test_image test to reflect this change.
      
      WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
      - none known -- only potential effect is the test, which was modified
      
      EVIDENCE THAT COMMIT WORKS:
      - test_image passed
      353a452c
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