probe options and object options now include relevant Fresnel spectrum propagation multislice parameters and are used in the fwd and adj operators

[a4894z]

Purpose

Previously the multislice class and resulting forward and adjoint operators didn't use the specified parameters (e.g. probe wavelength, probe field of view (FOV), and multislice propagation distance), and instead always used the defaults.

Now, these parameters are explicitly passed into the multislice class.

Also, I now use the same propagator that fold_slice uses, not the one without phase prefactors and with the square root taylor expansion.

Approach

The probe wavelength and probe field of view (FOV) are now part of probe_options and multislice propagation distance is part of object options.

These parameters are then used in the multislice class for a composite operator which uses fresnel spectrum propagation of the type fold_slice uses.

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 @a4894z! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

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

Line 41:50: E201 whitespace after '('
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Line 123:81: E501 line too long (99 > 80 characters)
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• In the file src/tike/operators/cupy/multislice.py:

Line 43:17: E251 unexpected spaces around keyword / parameter equals
Line 43:19: E251 unexpected spaces around keyword / parameter equals
Line 59:1: W293 blank line contains whitespace

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

Line 104:1: W293 blank line contains whitespace

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

Line 76:1: W293 blank line contains whitespace
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Line 93:81: E501 line too long (81 > 80 characters)
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• In the file src/tike/ptycho/probe.py:

Line 76:58: W291 trailing whitespace
Line 80:54: E201 whitespace after '('
Line 80:69: E202 whitespace before ')'
Line 82:65: W291 trailing whitespace

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

Line 355:81: E501 line too long (102 > 80 characters)

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

Line 42:29: E251 unexpected spaces around keyword / parameter equals
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[carterbox]

Looks like you have replaced pixel_size with probe_FOV in all cases, so you can completely remove it from the API.

[carterbox]

You probably don't need to explicitly pass all of these variables down the stack because keyword arguments are implicitly passed to the component classes using **kwargs.

[carterbox]

Use caution when handling unit sizes in the resample functions. I think this might not be correct because when you resample the grid, the real unit sizes of one pixel will change.