Tomography Module

[cedriclim1]

What does this PR do?

Tutorial notebooks to be written in https://github.com/electronmicroscopy/quantem-tutorials/tree/tomography_tutorials, reorganizing conventional_tomography.py and implementation of AutoSerialize needed, do not review yet - 1/30
Tutorials ready; still have some cleanup to do 2/02
Implementation of conventional (simutlaneous iterative reconstruction technique (SIRT) and filtered back projection (FBP)) and machine-learning enabled (implicit neural representations) tomographic reconstruction methods.

The code implements the overall design patterns of diffractive_imaging i.e, usage of core/ml classes, and reconstruction loop design. Hopefully everything is still able to be easily extended to different types of tomography experiments.

Since this a big PR, I'll provide a brief description of the relevant .py files in tomography.

• tomography.py: Top-level file that contains the reconstruction loop and instantiation of the Tomography object through .from_models.
• tomography_lite.py: Similar to ptychography_lite.py, this file abstracts the object, model, optimizer, and scheduler initialization to simply loading the tomographic dataset and perform an immediate reconstruction.
• tomography_base.py: Base class that inherits from AutoSerialize, RNGMixin, and DDPMixin (new) with the appropriate properties that is needed for every reconstruction.
• tomography_opt.py: Contains all the necessary optimizer parameters for reconstructions i.e, object and pose.
• object_models.py: Contains the classes for both pixelated and INR reconstructions. Can directly pretrain the volume from conventional methods.
• dataset_models.py: Contains pixelated and INR datasets with their respective .forward and .__getitem__ calls.
• logger_tomography.py: Contains the logger for tomography reconstructions.
• utils.py: Various functions for helping process tilt series datasets and also has the tools for performing voxelwise AD reconstructions.

There are also some added functionalities to core/ml that was implemented for helping initialization of distributed computing on HPC platforms (NERSC). The updates included briefly described here:

• core/ml/ddp.py: Initializes all the necessary parameters needed for doing distirbuted computing (defining world size, global rank, and local rank). Also contains helper functions for setting up model parallelization using DistributedDataParalleland setting up DataLoader distributed sampling using DistributedSampler
• core/ml/inr.py: Added Winner initialization to SIREN neural networks.
• core/ml/loss_functions.py: Added custom loss functions as nn.Module's.
• core/ml/profiling.py: Context manager for profiling code using NVIDIA Nsight.

What should the PR reviewer do?

The main points to check for this PR would be:

• Ensure that all example scripts and notebooks are easily run using local or HPC clusters.
• Check all changes in core/ml priority to loss_functions.py if we want to turn loss functions into nn.Module's.
• object_models.py and dataset_models.py follow the same design patterns and does not contain any redundant code that might be inherited from base classes.
• Check the reconstruction loop in tomography.py and check if loss calculations are being performed correctly, i.e stepping the scheduler/optimizer at the correct places.

Please make note of any design patterns that were not followed or potential bugs.

@arthurmccray will notify you when examples are ready to be tested.

[cedriclim1]

@arthurmccray Please look at commit bfc6e06. There are some functions that I had to do pyright ignores. For example: get_tv_loss is an abstract method in the class ObjectBase. However, ObjectPixelated and ObjectINR both have different implementations of get_tv_loss, so the base method would have **kwargs which gave linting errors with the overloaded methods with different keyword args.

[cedriclim1]

@arthurmccray I think I addressed your 3 comments. Please look at the tutorials again, as they have been updated in addition to some minor changes in the files here due to issues in the tutorials.