Refactor and re-implement virtual fitting (OpenwaterHealth#147)

Major changes:
- The input volume is now just given as a numpy array with an affine,
  not an xarray thing. This is more like how a user would actually
  have a volume after reading it from disk.
- Many operations are now vectorized rather than relying on a python loop.
  There is still a python loop over the virtual fit search grid points,
  but there is no inner python loop over the plane-fitting points.
- We work in RAS rather than LPS, since typically when you load a nifti
  file into memory it will come in with an affine that maps into RAS.
  We can always add a conversion layer later if we want to add flexibility
  with how the volume and target are provided. (The transducer transforms
  that are returned however still map into LPS space, since all openlifu
  transducer transforms have been working this way.) This is just keeping
  things simpler for the initial approach.
- The algorithm has been written in an imperative functional style rather than using
  a dataclass. This is easier to read and iterate on at first, and while
  some object oriented approach probably makes sense eventually, it is
  hard to get it exactly right without first having a fully working
  algorithm in place to see how it fits in with the rest of the
  application.
- The virtual_fit module has been moved to the top level, so no more vf
  package to go through first. We can move it into its own vf package if
  we add tons of new independent files, but to start with we should
 organize things more simply.
- (internal change) yaw and pitch are internally converted to spherical
  coordinates $\theta$ and $\phi$ to make it easier to work in that
  coordinate system. Also $\theta$ and $\phi$ were swapped from the minor
  previously existing usage, to match the physics convention. The relation
  is that pitch is $\phi$ and yaw is $90-\theta$. The $90-\theta$ is there
  to allow us to use a more standard version of spherical coordinates
  (where previously we had a confusing swap of sines with cosines from the
  standard approach).

Author: ebrahimebrahim

src/openlifu/__init__.py

@@ -34,7 +34,7 @@
     seg_methods,
 )
 from openlifu.sim import SimSetup
-from openlifu.vf import VirtualFit
+from openlifu.virtual_fit import virtual_fit
 from openlifu.xdc import Transducer
 
 from ._version import version as __version__
@@ -44,7 +44,6 @@
     "Transducer",
     "Protocol",
     "Solution",
-    "VirtualFit",
     "Material",
     "SegmentationMethod",
     "seg_methods",
@@ -65,6 +64,7 @@
     "SimSetup",
     "Database",
     "User",
+    "virtual_fit",
     "LIFUInterface",
     "__version__",
 ]