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NEW: Solve the lamino-alignment problem #94

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NEW: Solve the lamino-alignment problem #94

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Commits on Jul 13, 2020

  1. NEW: Flow operator for CuPy

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Commits on Jul 14, 2020

  1. Merge branch 'flow' into cuda-lam

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  2. Merge branch 'flow'

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  3. BUG: Copy cupy.map_coordinates from future version

    @carterbox
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  4. TST: Skip Farneback on GPU

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  5. DOC: Add CuPy License to thier code section

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  6. Merge branch 'flow'

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  7. Merge branch 'cuda-lam'

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  8. REF: Use 'original' and 'unaligned' variable names

    @carterbox
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Commits on Jul 15, 2020

  1. NEW: Add solver for recovering distorted image

    @carterbox
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  2. BUG: Lamino angles must by converted to CuPy arrays

    @carterbox
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Commits on Jul 20, 2020

  1. API: Use average of complex and real farneback results

    @carterbox
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  2. API: Add normalization to align solver using rho

    @carterbox
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  3. REF: Use Lanzcos remapping instead of scipy.map_coordinates 

    Because map_coordinates is not implemented for higher orders in
CuPy.
    @carterbox
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  4. Merge branch 'flow'

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Commits on Jul 22, 2020

  1. NEW: Use CachedFFT for Laminography operator 

    In theory, this should improve runtimes for long-lived Lamino
operators.
    @carterbox
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  2. BUG: Rescale farneback input by unaligned instead of original

    @carterbox
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  3. REF: Lamino scatter gather kernel for any dimensions 

    Make the CUDA scatter gather kernels for the Lamino operator
work for any number of dimensions because we will reuse it for
the Tomo operator.
    @carterbox
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  4. NEW: Lamino alignment problem in admm module

    @carterbox
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Commits on Aug 7, 2020

  1. DEV: Save intermediate ADMM results and allow precomputing scales

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Commits on Aug 27, 2020

  1. Merge remote-tracking branch 'upstream/master' into catalyst 

    Conflicts:
	src/tike/operators/cupy/flow.py
	src/tike/operators/cupy/lamino.py
	src/tike/operators/numpy/flow.py
	src/tike/operators/numpy/lamino.py
	tests/test_align.py
    @carterbox
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  2. NEW: Allow specifying specific GPUs for ThreadPool

    @carterbox
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  3. BUG: Wrong indexing in CUDA kernel

    @carterbox
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  4. STUB: Change how lamino-alignment intermediates are saved

    @carterbox
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Commits on Sep 1, 2020

  1. Merge branch 'catalyst' of github.com:carterbox/tike into catalyst

    @carterbox
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Commits on Sep 2, 2020

  1. STUB: ptycho-lamino-alignment

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  2. Merge remote-tracking branch 'upstream/master' into catalyst

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  3. Merge branch 'catalyst' of github.com:carterbox/tike into catalyst

    @carterbox
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Commits on Sep 8, 2020

  1. ADMM that runs, but does it work?

    @carterbox
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  2. Loop through crop and rotate

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Commits on Sep 9, 2020

  1. ADMM working but diverges

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Commits on Sep 10, 2020

  1. API: better constants for rotation

    @carterbox
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  2. REF: Move lamino cost functions

    @carterbox
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  3. Two problems only (remove alignment)

    @carterbox
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Commits on Sep 16, 2020

  1. BUG: Change edge behavior to nearest for flow operator

    @carterbox
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Commits on Sep 19, 2020

  1. NEW: Implement correct adjoint Flow operator

    @carterbox
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Commits on Sep 21, 2020

  1. REF: Autoselect operator in align.reconstruct()

    @carterbox
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Commits on Sep 22, 2020

  1. admm ptycho-align-lamino with penalty updates

    @carterbox
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  2. TST: Add normalization test to operators tests 

    Because:
- We want to know not only if the adjoint operator is actually
  adjoint but also if it preserves the magnitude of the original
    @carterbox
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Commits on Sep 23, 2020

  1. Required regularization arguments.

    @carterbox
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  2. Merge branch 'sequential' of github.com:carterbox/tike into sequential

    @carterbox
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  3. NEW: Allow setting lamino accuracy from reconstruct

    @carterbox
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  4. NEW: Add gaussian kernel to interp.cu

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Commits on Sep 25, 2020

  1. NEW: Alignment operator composed of rotate and pad

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Commits on Oct 7, 2020

  1. NEW: Only recale ptycho when flux is off by more than 1 percent

    @carterbox
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  2. DEV: Before pad rotate as official operator

    @carterbox
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  3. MAI: Add tiff files to gitignore

    @carterbox
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  4. REF: Update Pad operator to pad symmetrically by default

    @carterbox
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  5. API: Remove padding from Shift operator

    @carterbox
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  6. NEW: Make some operators identity when params are None

    @carterbox
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  7. BUG: Push lamino params to GPU

    @carterbox
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  8. PATCH: Make some operators identity

    @carterbox
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  9. API: Have farneback solver return 'flow'

    @carterbox
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  10. STY: Whitespace

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  11. API: Use Alignment operator in alignment module

    @carterbox
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  12. DEV: Add helpful info to assert statement

    @carterbox
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  13. API: Replace kwargs with catch for num_iter

    @carterbox
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  14. API: Switch from 'wrap' to 'constant value' interpolation 

    Because:
- It provides better aligment when rotating the object doesn't
  a duplicate object to appear on the edge
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Commits on Oct 8, 2020

  1. BUG: cval was always set to zero in rotate

    @carterbox
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  2. DEV: Avoid atomicAdd() in interpolation kernel 

    Because:
- Maybe it runs faster to avoid atomic operations during gather

Not yet tested to see whether there are performance benefits.
The trade off is less parallelism because each element of the
interpolation kernel is now processed sequentially.
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Commits on Oct 9, 2020

  1. REF: Split admm into module

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Commits on Oct 23, 2020

  1. Merge branch 'flow-adjoint' into sequential 

    Conflicts:
	src/tike/operators/cupy/alignment.py
	src/tike/operators/cupy/flow.py
	src/tike/operators/cupy/interp.cu
	src/tike/operators/cupy/pad.py
	src/tike/operators/cupy/rotate.py
	tests/operators/test_pad.py
    @carterbox
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Commits on Jan 28, 2021

  1. Merge branch 'master' into catalyst

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Commits on Feb 4, 2021

  1. BUG: Use float32 for Farneback API

    @carterbox
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  2. NEW: Add Shift operator to Alignment composition

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Commits on Feb 5, 2021

  1. Merge branch 'parallel-lamino' into catalyst

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Commits on Feb 6, 2021

  1. API: Make laminography theta a parameter instead of constant 

    Because:
- This is required in order to divide the operator amongst
  multiple devices.
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Commits on Feb 8, 2021

  1. NEW: Add regularizer to cross_correlation

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Commits on Feb 10, 2021

  1. REF: Modularize admm subproblems into separate functions

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Commits on Feb 11, 2021

  1. BUG: Missing import in tike.admm.alignment

    @carterbox
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  2. REF: Save result before reconstruction admm.lamino

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  3. NEW: Add inverse operator to alignment module

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  4. NEW: Save ptycho result in admm.ptycho

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  5. NEW: Add rescale optional parameter to ptycho

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  6. BUG: inverse alignment operator

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  7. NEW: Smaller cross correlation weight

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  8. NEW: Set subproblem iters separate from cg_iter

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  9. BUG: Proper alignment in ptycho_lamino

    @carterbox
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  10. Merge remote-tracking branch 'upstream/master' into catalyst

    @carterbox
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  11. REF: Use same subproblems for each formulation

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Commits on Feb 12, 2021

  1. BUG: Mismatched indent

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  2. BUG: Changed parameter name

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  3. BUG: Missing imports

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  4. STY: Name all parameters

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  5. REF: Use MSE instead of L2-Norm in Lagrangian

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  6. DOC: Save angle instead of imag in lamino subproblem

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Commits on Feb 16, 2021

  1. Merge remote-tracking branch 'origin/rescale-lamino' into catalyst

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  2. NEW: Access early termination for ptycho subproblem

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  3. REF: Remove skimage dependency for center mass

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  4. REF: Ensure correct lagrangians again

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  5. REF: Update penalty params more often

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  6. BUG: Reenable u broadcase

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  7. NEW: Enable center of mass in alignment subproblem

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  8. REF: Only minmax when needed

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  9. REF: Put admm subproblem into own module

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Commits on Feb 23, 2021

  1. BUG: Don't convert scalars to arrays

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  2. NEW: Remove duplicate interpolation in Alignment operator

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Commits on Feb 25, 2021

  1. BUG: Start with shift as initial flow

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  2. DOC: Fix typo in penalty docstring

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  3. API: Change regularization scheme for cross_correlation

    @carterbox
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  4. BUG: Properly log strings in log_line

    @carterbox
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  5. NEW: Track winsize parameter

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Commits on Mar 9, 2021

  1. BUG: Avoid MPI buffer overflow

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  2. API: Use overwrite intermediate saves

    @carterbox
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Commits on Mar 12, 2021

  1. REF: Move alignment operator to left

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Commits on Mar 15, 2021

  1. REF: Solve inverse flow problem

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    carterbox committed Mar 15, 2021
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Commits on Mar 19, 2021

  1. NEW: Gradient operator for reg subproblem

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    carterbox committed Mar 19, 2021
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  2. NEW: Gradient operator for reg subproblem

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    carterbox committed Mar 19, 2021
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  3. REF: Move laminography cost/grad out of operators

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    carterbox committed Mar 19, 2021
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  4. NEW: Add functions for total variation regularization

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    carterbox committed Mar 19, 2021
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Commits on Mar 22, 2021

  1. NEW: Add regularization to lamino cost function

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    carterbox committed Mar 22, 2021
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  2. Merge branch 'total-variation' into catalyst 

    Conflicts:
	src/tike/align/solvers/cross_correlation.py
	src/tike/operators/cupy/alignment.py
	src/tike/operators/cupy/gradient.py
	src/tike/ptycho/ptycho.py
    @carterbox
    carterbox committed Mar 22, 2021
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Commits on Mar 23, 2021

  1. NEW: Change tomography linear approximation

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    carterbox committed Mar 23, 2021
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  2. BUG: New handling of K

    @carterbox
    carterbox committed Mar 23, 2021
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Commits on Mar 24, 2021

  1. STUB: Regularization subproblem

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    carterbox committed Mar 24, 2021
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Commits on Mar 26, 2021

  1. REF: Avoid astype() copies

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    carterbox committed Mar 26, 2021
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Commits on Mar 27, 2021

  1. REF: Reduce Lamino mem footprint

    @carterbox
    carterbox committed Mar 27, 2021
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Commits on Mar 29, 2021

  1. Merge remote-tracking branch 'origin/catalyst' into catalyst

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    carterbox committed Mar 29, 2021
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Commits on Mar 30, 2021

  1. Undo new tomography model

    @carterbox
    carterbox committed Mar 30, 2021
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  2. BUG: Fix lamino step length search

    @carterbox
    carterbox committed Mar 30, 2021
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  3. BUG: Add missing equals sign

    @carterbox
    carterbox committed Mar 30, 2021
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Commits on Jul 21, 2021

  1. DOC: Add more information to Lamino docstrings

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    carterbox committed Jul 21, 2021
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  2. Merge branch 'master' into catalyst

    @carterbox
    carterbox committed Jul 21, 2021
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Commits on Jul 23, 2021

  1. DOC: Use object instead of particle label

    @carterbox
    carterbox committed Jul 23, 2021
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  2. REF: Allow skipping ptycho subproblem in alignment lamino admm

    @carterbox
    carterbox committed Jul 23, 2021
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Commits on Jul 27, 2021

  1. BUG: Add error if padded shape is smaller than unpadded

    @carterbox
    carterbox committed Jul 27, 2021
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  2. DEV: Require 2x upsampling for lamino problem to mitigate noise

    @carterbox
    carterbox committed Jul 27, 2021
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