Implement io tools to manipulate cryo-EM density maps

[ninamiolane]

What?

• Create a module density_maps.py in the folder ioSPI that provides code to manipulate data structures of density maps. (see Section "How?" below).
• Add a file test_density_maps.py with corresponding unit-tests in the tests folder.
• Create a tutorial density_maps.ipynb in the folder ioSPI/notebooks/ that showcases the use of density_maps.py
• Use pre-commit (see README) to make sure that your code follows style guidelines.

Why?

Density maps are 3D maps that represent the electrostatic potential of the atomic structures we are interested in. Knowing how to manipulate the main data structure that contain them is primordial for any cryo-EM analysis.

Where?

The module density_maps.py should be created in the folder ioSPI/ioSPI

The test file test_density_maps.py should be created in the folder ioSPI/tests.

The tutorial notebook should be created in the folder ioSPI/notebooks/.

How?

• List the file formats that traditionally hold 3D density maps: mrc, ...others? (Note: Only include .h5 format if a common convention exists about h5 in the cryo-EM communities).
• Write functions converting this files into np.arrays.
  • Note: Use API (i.e. naming conventions of functions and inputs) from the functions currently existing in ioSPI.
  • You can take inspiration from these lines of code.
• Provide a way of visualizing the 3D maps.

[artajmir3]

I'm thinking about this.