NEW: Solve the lamino-alignment problem

[carterbox]

Purpose

Provide a function for solving the lamino-alignment problem with ADMM.

Approach

Solve the laminography + alignment problem using the Laminography operators, Lanczos Interpolation operator, and Flow solver which wraps OpenCV's Farneback's method.

Also includes some changes to the ThreadPool and scatter/gather CUDA kernels which should be merged separately.

Pre-Merge Checklists

Submitter

• Write a helpfully descriptive pull request title.
• Organize changes into logically grouped commits with descriptive commit messages.
• Document all new functions.
• Write tests for new functions or explain why they are not needed.
• Build the documentation successfully
• Use yapf to format python code.

Reviewer

• Actually read all of the code.
• Run the new code yourself.
• Write a summary of the changes as you understand them.
• Thank the submitter.

[pep8speaks]

Hello @carterbox! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file src/tike/admm/pal.py:

Line 137:21: E131 continuation line unaligned for hanging indent
Line 141:21: E131 continuation line unaligned for hanging indent

• In the file src/tike/admm/subproblem/__init__.py:

Line 35:1: E402 module level import not at top of file
Line 36:1: E402 module level import not at top of file
Line 37:1: E402 module level import not at top of file

• In the file src/tike/admm/subproblem/align.py:

Line 45:5: E265 block comment should start with '# '

• In the file src/tike/align/align.py:

Line 35:1: E302 expected 2 blank lines, found 1

• In the file src/tike/align/solvers/cgrad.py:

Line 27:13: E122 continuation line missing indentation or outdented

• In the file src/tike/align/solvers/cross_correlation.py:

Line 52:81: E501 line too long (81 > 80 characters)

• In the file src/tike/operators/cupy/gradient.py:

Line 19:31: E201 whitespace after '['
Line 19:45: E201 whitespace after '['

• In the file src/tike/ptycho/ptycho.py:

Line 352:81: E501 line too long (95 > 80 characters)

• In the file tests/operators/test_gradient.py:

Line 32:24: E201 whitespace after '{'
Line 32:31: E202 whitespace before '}'

Comment last updated at 2021-07-27 16:34:15 UTC