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Double double, aberrations, bugs, and trouble #539

Merged
merged 71 commits into from
Oct 22, 2023
Merged

Double double, aberrations, bugs, and trouble #539

merged 71 commits into from
Oct 22, 2023

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gvarnavi
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@gvarnavi gvarnavi commented Oct 20, 2023 •
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Latest phase_contrast changes to be included in upcoming release pretty please!

This includes the following bugfixes and new features:

  • General ptycho:
    • Fixed preprocessing casting bug affecting uint datasets!
  • Multislice ptycho:
    • Depth-sectioning visualization
    • 0th and 1st order isotropic TV denoising
  • Mixedstate + Multislice ptycho:
    • Added initial support, not very thoroughly tested
  • DPC:
    • Fixed NaN bug when some DPs entirely empty
    • Added complex CoM plotting
  • Overlap tomography:
    • Switched to orientation matrices notation
    • (Still need to do this for overlap magnetic tomography)
  • General visualization:
    • Switched to linearly-perceptive complex colormap
    • Added support for boosting chroma for sharper zero-crossing contrast
  • Parallax:
    • Added KDE upsampling support
    • Added Thon rings fitting
    • Added aberration fitting directly on measured BF shifts

smribet and others added 30 commits August 3, 2023 17:32
@smribet
start for depth profile
6db566e
@gvarnavi
adding real-space kde upsampling
4eb461d
@smribet
Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast
0176914
@smribet
more depth profile
8c61a5b
@smribet
saving error
22d1bb4
@smribet
small name changes
5f919bd
@smribet
single slice tv denoise
68b31a7
@smribet
multislice tv denoise... will test more before adding to other classe…
5acdd58 
…s...
@gvarnavi
minor tv bugfix
aac2d12
@smribet
improvements for depth plotting
da85db0
@smribet
tv fixes
a582212
@smribet
everyone gets TV denoising
eaa3699
@smribet
subpixel alignment phase correct, part 1
cc36490
@smribet
removing print statement
41f319d
@smribet
parallax plotting fix
95beba5
@gvarnavi
generalizing overlap tomo to orientation matrices
c25e242
@gvarnavi
Merge branch 'phase_contrast' of github.com:py4dstem/py4DSTEM into ph…
a7b55aa 
…ase_contrast
@gvarnavi
black formatting
31b5525
@gvarnavi
flake8 6.1.0 found some more issues
d4363f4
@gvarnavi
adding mixed-state multi-slice ptycho class
e60071a
@smribet
small reset bug
807ac15
@gvarnavi
fixed NaN bug
8b35dbb
@gvarnavi
Merge branch 'phase_contrast' of github.com:py4dstem/py4DSTEM into ph…
9f24d5c 
…ase_contrast
@gvarnavi
changed complex plotting
6cb62f1
@gvarnavi
updated complex plotting phase calls
ad79416
@gvarnavi
adding complex CoM plotting and various dpc plotting bugs
356a3a1
@smribet
parallax descan correct
2bc9da9
@gvarnavi
complex plotting improvements, formatting
3a99d5a
@smribet
change to fitted intensities
d4099ea
@smribet
Merge remote-tracking branch 'origin/phase_contrast' into phase_contrast
8c6be92
@gvarnavi
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Attaching notebook to test latest parallax features:
parallax_aberrations_testing.zip

@gvarnavi gvarnavi mentioned this pull request Oct 20, 2023
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smribet
smribet approved these changes Oct 22, 2023
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Good stuff, thanks @gvarnavi!

@smribet smribet merged commit 6416804 into dev Oct 22, 2023
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@gvarnavi gvarnavi mentioned this pull request Oct 22, 2023
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@gvarnavi @smribet @cophus