Implement Shift in Image Space (Translation)

[ninamiolane]

What?

• Implement the shift operation of the cryo-EM image formation model in image space, which is a translation operation.
• Add details about the structure of the config input to the docstrings of the simSPI/linear_simulator/shift_utils.py module.
• Add corresponding unit-tests.
• Use pre-commit (see README) to make sure that your code follows style guidelines.

Why?

Cryo-EM image formation model has different characteristics depending on whether it is formulated in image space (real space) or Fourier space (reciprocal space).

The community needs to be able to experiment with both formulations of the image formation model.

Where?

• The Shift class is located in the simSPI/linear_simulator/shift_utils.py module.
• The unit-tests are here.

How?

• Rename the shift_utils.py module into shift.py and make sure the unit-tests and notebooks run.
• Allow the config input to the Shift class to have a space key, where the value will be either image or fourier.
• Rename current forward method into a private _forward_fourier method.
• Create a _forward_image method, with the projection operation in fourier space.
• Create a forward method that calls either _forward_image or _forward_fourier depending on the value in the self.config attribute.

Details on the cryo-EM image formation models can be found in Donnat et al 2022.

[ninamiolane]

@gggg is working on this.