API: Add leading dimension to object for multi-slice

[carterbox]

Purpose

Adds a leading dimension to the reconstructed object in preparation for multi-slice objects.

Approach

• Refactor the Pytcho Operator and related Operators to accept a 3-dimensional psi array, where the first dimension is a placeholder singleton dimension for future multi-slice operations.
• Remove unused adjoint methods which will make implementing multi-slice more difficult
• Add a ZeroPropagation Operator as a placeholder for the between-slice Operator.
• Add a SingleSlice Operator as a placeholder for a MultiSlice Operator.

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.
• Click 'details' on the readthedocs check to view the updated docs.
• Write tests for new functions or explain why they are not needed.
• Address any complaints from pep8speaks.

Reviewer

• Actually read all of the code.
• Run the new code yourself; the included tests should make this easy.
• 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/operators/cupy/ptycho.py:

Line 51:81: E501 line too long (81 > 80 characters)

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

Line 162:81: E501 line too long (85 > 80 characters)

Comment last updated at 2024-05-28 17:44:57 UTC

[a4894z]

a few random comments:

1. In convolution.py, it looks like we just have a name change of the class (e.g. Convolution --> ConvolutionFFT)?

2. In tests/ptycho/io.py, it still seems like it should be average instead of sum for plotting phase and magnitude of sample...this is also closer to what fold_slice does for the final 2D sample projection for sinogram creation

3. The new unit tests for the stuff changed look OK, I haven't run them since I'm not sure about the bigger context of what they're testing.

4. Fresnel Spect Prop has been removed from this; will be reintroduced in subsequent pull request.

5. Introduced a SingleSlice instance of Multislice class in order to make this whole TIKE single slice --> TIKE multislice upgrade process easier to follow.