Merge the latest Spateo alignment in Yifan's branch into the main.

[YifanLu2000]

Summary

This pull request introduces significant improvements and new features to the alignment part of the Spateo. The alignment code has been completely rewritten to provide faster performance and greater flexibility.

Key Changes

1. Alignment Code Rewritten:

   • The alignment part of the code has been fully rewritten, resulting in a faster and more scalable implementation, flexible and unified Interface, and clearer code implementation logic.
   • The new implementation leverages a backend file that integrates both NumPy and PyTorch backends, eliminating the need for the POT package.

2. Mesh Correction Method:

   • A new mesh correction method has been added. This method utilizes mesh information to improve 3D reconstruction accuracy.

3. Plotting Functions:

   • New plotting functions have been added to improve data visualization and analysis.

4. Parameter Updates:

   • Some function parameters have been updated for greater flexibility:
     • The parameters layer and use_rep in the old spateo.align.morpho_align function have been replaced with rep_layer and rep_field.
   • The old morpho_align_sparse function has been deleted and its functionality has been integrated into spateo.align.morpho_align.

Instructions for Merging

• Parameter Adjustments: Be aware of the changes to function parameters. Update any scripts or downstream code that relies on the old parameter names (e.g., layer, use_rep) to use the new names (e.g., rep_layer, rep_field).
• Backward Compatibility: Review any legacy code for compatibility with the new structure, especially where morpho_align_sparse was previously used.