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  1. Aug 14, 2023
  2. Jul 26, 2023
    • Arin Wongprommoon's avatar
    • Arin Wongprommoon's avatar
      feat(postproc): crosscorr has stationary option · 97ed1cbb
      Arin Wongprommoon authored
      WHY IS THIS CHANGE NEEDED?:
      - crosscorr process does not have stationary option and therefore will
        not perform calculations correctly if all signals are in-phase.
      
      HOW DOES THE CHANGE SOLVE THE PROBLEM?:
      - Additional 'stationary' parameter that tells the process to compute
        the mean over replicates AND time points.
      
      WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
      - crosscorr process not used anywhere else in aliby, so should not
        affect aliby.
      - crosscorr process used in multiple places in skeletons (particularly
        arin's projects).  this is an *additional* parameter, and the existing
        behaviour of crosscorr process is same as stationary=False, so i don't
        expect breaking changes.
      
      EVIDENCE THAT COMMIT WORKS:
      - new test to be run
      
      REFERENCES:
      - #72
      97ed1cbb
  3. Mar 17, 2023
  4. Feb 28, 2023
  5. Feb 27, 2023
  6. Jan 17, 2023
    • 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
  7. Jan 13, 2023
  8. Jan 12, 2023
  9. Jan 11, 2023
    • Arin Wongprommoon's avatar
      test(postproc): whether interpolate fills in existing values · 1492fd6e
      Arin Wongprommoon authored
      WHY IS THIS CHANGE NEEDED?:
      - need a simple test to see if gitlab visualises coverage
      
      HOW DOES THE CHANGE SOLVE THE PROBLEM?:
      - write a test for interpolate post-process; this test checks that
        interpolated values are as expected by leveraging a dummy signal that
        is a gradient.
      
      REFERENCES:
      - issue #46
      - merge request !8
      1492fd6e
  10. Jan 08, 2023
  11. Jan 05, 2023
  12. Jan 04, 2023
  13. Dec 21, 2022
  14. Sep 26, 2022
  15. Sep 24, 2022
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