- Aug 14, 2023
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pswain authored
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- Jul 26, 2023
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Arin Wongprommoon authored
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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
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- Mar 17, 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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- Feb 28, 2023
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Alán Muñoz authored
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- Feb 27, 2023
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Alán Muñoz authored
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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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- Jan 13, 2023
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - test dummy tiler, see if it crashes REFERENCES: - issue #53
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56786 because AttributeError: 'function' object has no attribute 'shape' REFERENCES: - issue #53
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56781 failed REFERENCES: - issue #53
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56767 failed because ValueError: The truth value of a Array is ambiguous. HOW DOES THE CHANGE SOLVE THE PROBLEM?: - use numpy.array_equal() to compare arrays instead REFERENCES: - issue #53
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56762 failed because TypeError: compute() takes 1 positional argument but 2 were given HOW DOES THE CHANGE SOLVE THE PROBLEM?: - corrected a stupid typo: compute() is a function that takes no arguments that gives out an array, and i want to index that array REFERENCES: - issue #53
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Arin Wongprommoon authored
WHY IS THIS CHANGE NEEDED?: - https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56757 failed because TypeError raised: 'int' object is not iterable HOW DOES THE CHANGE SOLVE THE PROBLEM?: - @pytest.mark.parametrize() takes an iterable, e.g. a list -- I forgot about it. fixed it by putting the values in a list. REFERENCES: - issue #53
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Arin Wongprommoon authored
EVIDENCE THAT COMMIT WORKS: - issue #53 REFERENCES:
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- Jan 12, 2023
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dadjavon authored
Relates to #52
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- Jan 11, 2023
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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
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- Jan 08, 2023
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Alán Muñoz authored
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Alán Muñoz authored
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- Jan 05, 2023
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Alán Muñoz authored
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- Jan 04, 2023
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Alán Muñoz authored
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- Dec 21, 2022
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Alán Muñoz authored
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Alán Muñoz authored
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- Sep 26, 2022
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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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- Sep 24, 2022
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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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- Sep 22, 2022
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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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