- Jan 31, 2023
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Arin Wongprommoon authored
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- Jan 24, 2023
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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- Jan 23, 2023
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
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Alán Muñoz authored
fix: debug post-merge requests 10, 11 See merge request !12
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Arin Wongprommoon authored
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - a case in which x and y dimensions are unequal is better at revealing dimension storage/conversion issues HOW DOES THE CHANGE SOLVE THE PROBLEM?: - tile existing image to size x = 1800, y = 1200 WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?: - filenames have changed EVIDENCE THAT COMMIT WORKS: - doesn't seem to break existing tests, specifically test_image.py and test_tiler.py
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - TypeError raised when Tiler.dummy object was instantiated ('method' object is not iterable) HOW DOES THE CHANGE SOLVE THE PROBLEM?: - dummy_omero_metadata was a tuple of dicts, changed it to a dict. this also makes available the .update() method of a dict. and is also consistent with the datatype it should be in the return statement. EVIDENCE THAT COMMIT WORKS: - Tiler.dummy object can be instantiated from a parametes dict without errors
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Alán Muñoz authored
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Arin Wongprommoon authored
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Alán Muñoz authored
- Change the order to match tczyx where appropriate - Make name and dimorder properties for Imagedummy
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Arin Wongprommoon authored
REFERENCES: - issue #62
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Alán Muñoz authored
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Alán Muñoz authored
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- Jan 18, 2023
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Alán Muñoz authored
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- Jan 17, 2023
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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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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
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