Write a notebook that simulates cryoEM images with the linear simulator

[ninamiolane]

What?

• [ ] Write a tutorial notebook on the use of the simSPI/linear_simulator module.
• [ ] Add corresponding unit-tests.
• [ ] Use pre-commit (see README) to make sure that your code follows style guidelines.

Why?

The linear simulator is a differentiable simulator of cryo-EM images that implements the so-called "weak-phase approximation" of the cryo-EM image formation model.

This simulator is a key piece for deep generative models. Being able to explain its use is fundamental for simSPI, which makes this task a high-priority task.

Where?

• The notebook should go in the notebooks folder with the title micrographs.ipynb.
• The test of the notebook should go in a new file test_notebooks.py in the tests folder, inspired by this file.

How?

Get an mrc file representing a 3D volume density map that can be input to the linear simulator, such as:

• e2map.mrc

Get inspiration on how to write your notebook, look at:

• other notebooks, e.g. here.
• the test files for the sub-modules defining the linear_simulator, such as the test_noise module, the test_shift module, etc.
• notebook sim_tutorial.ipynb using some modules from the linear_simulator.