Fix Orientations IO (#293)

* Fix Orientations IO

* Allow different primitive matrices

* Remove duplicate methods

* Update src/gemdat/rotations.py

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>

* Fix plot test

* Remove .set_transform

* Fix docstrings

* Use functions instead of classes for transforms

* Avoid expensive np sqrt

* Code cleanup

* Return Orientation from transforms

* Refactor Orientations

* Update tests

* Fix line endings

* Update hooks

---------

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
Co-authored-by: Stef Smeets <s.smeets@esciencecenter.nl>

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ exclude: |
   \.vol
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
@@ -23,7 +23,7 @@ repos:
     hooks:
       - id: nbcheckorder
   - repo: https://github.com/google/yapf
-    rev: v0.40.1
+    rev: v0.40.2
     hooks:
       - id: yapf
         additional_dependencies:
@@ -34,17 +34,17 @@ repos:
     hooks:
       - id: docformatter
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.5
+    rev: v0.3.5
     hooks:
       - id: ruff
         args: [--fix]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.0
+    rev: v1.9.0
     hooks:
       - id: mypy
         additional_dependencies: [matplotlib, MDAnalysis, numpy, pymatgen, rich, scikit-image, scipy]
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.8.5
     hooks:
       - id: nbqa-yapf
         additional_dependencies: [toml, yapf]

src/gemdat/plots/matplotlib/_rotations.py

@@ -5,47 +5,44 @@
 from scipy.optimize import curve_fit
 from scipy.stats import skewnorm
 
-from gemdat.rotations import Orientations, calculate_spherical_areas, mean_squared_angular_displacement
+from gemdat.rotations import (
+    Orientations,
+    calculate_spherical_areas,
+    mean_squared_angular_displacement,
+)
 from gemdat.utils import cartesian_to_spherical
 
 
 def rectilinear_plot(*,
                      orientations: Orientations,
                      shape: tuple[int, int] = (90, 360),
-                     symmetrize: bool = True,
-                     normalize: bool = True) -> plt.Figure:
-    """Plot a rectilinear projection of a spherical function.
+                     normalize_histo: bool = True) -> plt.Figure:
+    """Plot a rectilinear projection of a spherical function. This function
+    uses the transformed trajectory.
 
     Parameters
     ----------
     orientations : Orientations
         The unit vector trajectories
-    symmetrize : bool, optional
-        If True, use the symmetrized trajectory
     shape : tuple
         The shape of the spherical sector in which the trajectory is plotted
-    normalize : bool, optional
+    normalize_histo : bool, optional
         If True, normalize the histogram by the area of the bins, by default True
 
     Returns
     -------
     fig : matplotlib.figure.Figure
         Output figure
     """
-
-    if symmetrize:
-        trajectory = orientations.get_symmetric_trajectory()
-    else:
-        trajectory = orientations.get_conventional_coordinates()
     # Convert the trajectory to spherical coordinates
-    trajectory = cartesian_to_spherical(trajectory, degrees=True)
+    trajectory = cartesian_to_spherical(orientations.vectors, degrees=True)
 
     az = trajectory[:, :, 0].flatten()
     el = trajectory[:, :, 1].flatten()
 
     hist, xedges, yedges = np.histogram2d(el, az, shape)
 
-    if normalize:
+    if normalize_histo:
         # Normalize by the area of the bins
         areas = calculate_spherical_areas(shape)
         hist = np.divide(hist, areas)
@@ -80,16 +77,13 @@ def rectilinear_plot(*,
 
 def bond_length_distribution(*,
                              orientations: Orientations,
-                             symmetrize: bool = True,
                              bins: int = 1000) -> plt.Figure:
     """Plot the bond length probability distribution.
 
     Parameters
     ----------
     orientations : Orientations
         The unit vector trajectories
-    symmetrize : bool, optional
-        If True, use the symmetrized trajectory
     bins : int, optional
         The number of bins, by default 1000
 
@@ -99,12 +93,8 @@ def bond_length_distribution(*,
         Output figure
     """
 
-    if symmetrize:
-        trajectory = orientations.get_symmetric_trajectory()
-    else:
-        trajectory = orientations.get_conventional_coordinates()
     # Convert the trajectory to spherical coordinates
-    trajectory = cartesian_to_spherical(trajectory, degrees=True)
+    trajectory = cartesian_to_spherical(orientations.vectors, degrees=True)
 
     fig, ax = plt.subplots()
 
@@ -163,7 +153,7 @@ def unit_vector_autocorrelation(
     """
 
     # The trajectory is expected to have shape (n_times, n_particles, n_coordinates)
-    trajectory = orientations.get_unit_vectors_trajectory()
+    trajectory = orientations.vectors
 
     ac = mean_squared_angular_displacement(trajectory)
     ac_std = ac.std(axis=0)