From 8b3b7777115f31f6db2fe82bdc1b423f3181eec6 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 17 Jul 2024 17:03:52 +0100
Subject: [PATCH] chore: move "make_cell_upright" to plotting utils

This functionality is not specific to the vispy plotter.
---
 pyneuroml/plot/PlotMorphologyVispy.py | 61 +--------------------------
 pyneuroml/utils/__init__.py           | 59 ++++++++++++++++++++++++++
 2 files changed, 60 insertions(+), 60 deletions(-)

diff --git a/pyneuroml/plot/PlotMorphologyVispy.py b/pyneuroml/plot/PlotMorphologyVispy.py
index 34c7e4add..6c57484f0 100644
--- a/pyneuroml/plot/PlotMorphologyVispy.py
+++ b/pyneuroml/plot/PlotMorphologyVispy.py
@@ -22,7 +22,7 @@
 from scipy.spatial.transform import Rotation
 
 from pyneuroml.pynml import read_neuroml2_file
-from pyneuroml.utils import extract_position_info, rotate_cell, translate_cell_to_coords
+from pyneuroml.utils import extract_position_info, make_cell_upright
 from pyneuroml.utils.plot import (
     DEFAULTS,
     get_cell_bound_box,
@@ -782,65 +782,6 @@ def plot_interactive_3D(
             app.run()
 
 
-def make_cell_upright(
-    cell: Cell = None,
-    inplace: bool = False,
-) -> Cell:
-    """Use cell's PCA to make it upright
-
-    .. versionadded:: 1.2.13
-
-    :param cell: cell object to translate
-    :type cell: neuroml.Cell
-    :param inplace: toggle whether the cell object should be modified inplace
-        or a copy created (creates and returns a copy by default)
-    :type inplace: bool
-    :returns: new neuroml.Cell object
-    :rtype: neuroml.Cell
-    """
-
-    # Get all segments' distal points
-    segment_points = []
-    segments_all = cell.morphology.segments
-    for segment in segments_all:
-        segment_points.append([segment.distal.x, segment.distal.y, segment.distal.z])
-
-    coords = numpy.array(segment_points)
-    from sklearn.decomposition import PCA
-
-    # Get the PCA components
-    pca = PCA()
-    pca.fit(coords)
-
-    # Get the principal component axes
-    principal_axes = pca.components_
-    # Get the first principal component axis
-    first_pca = principal_axes[0]
-    # y angle needed to eliminate z component
-    y_angle = math.atan(first_pca[2] / first_pca[0])
-    rotation_y = numpy.array(
-        [
-            [math.cos(y_angle), 0, math.sin(y_angle)],
-            [0, 1, 0],
-            [-math.sin(y_angle), 0, math.cos(y_angle)],
-        ]
-    )
-    rotated_pca = numpy.dot(rotation_y, first_pca)
-
-    # z angle needed to eliminate x component
-    z_angle = -math.atan(rotated_pca[0] / rotated_pca[1])
-
-    if z_angle < 0:
-        z_angle += numpy.pi
-
-    logger.debug("Making cell upright for visualization")
-    cell = translate_cell_to_coords(cell, inplace=inplace, dest=[0, 0, 0])
-    cell = rotate_cell(
-        cell, 0, y_angle, z_angle, "yzx", relative_to_soma=False, inplace=inplace
-    )
-    return cell
-
-
 def plot_3D_cell_morphology(
     offset: typing.List[float] = [0, 0, 0],
     cell: Optional[Cell] = None,
diff --git a/pyneuroml/utils/__init__.py b/pyneuroml/utils/__init__.py
index 18957c136..56de6228b 100644
--- a/pyneuroml/utils/__init__.py
+++ b/pyneuroml/utils/__init__.py
@@ -546,6 +546,65 @@ def translate_cell_to_coords(
     return newcell
 
 
+def make_cell_upright(
+    cell: neuroml.Cell = None,
+    inplace: bool = False,
+) -> neuroml.Cell:
+    """Use cell's PCA to make it upright
+
+    .. versionadded:: 1.2.13
+
+    :param cell: cell object to translate
+    :type cell: neuroml.Cell
+    :param inplace: toggle whether the cell object should be modified inplace
+        or a copy created (creates and returns a copy by default)
+    :type inplace: bool
+    :returns: new neuroml.Cell object
+    :rtype: neuroml.Cell
+    """
+
+    # Get all segments' distal points
+    segment_points = []
+    segments_all = cell.morphology.segments
+    for segment in segments_all:
+        segment_points.append([segment.distal.x, segment.distal.y, segment.distal.z])
+
+    coords = numpy.array(segment_points)
+    from sklearn.decomposition import PCA
+
+    # Get the PCA components
+    pca = PCA()
+    pca.fit(coords)
+
+    # Get the principal component axes
+    principal_axes = pca.components_
+    # Get the first principal component axis
+    first_pca = principal_axes[0]
+    # y angle needed to eliminate z component
+    y_angle = math.atan(first_pca[2] / first_pca[0])
+    rotation_y = numpy.array(
+        [
+            [math.cos(y_angle), 0, math.sin(y_angle)],
+            [0, 1, 0],
+            [-math.sin(y_angle), 0, math.cos(y_angle)],
+        ]
+    )
+    rotated_pca = numpy.dot(rotation_y, first_pca)
+
+    # z angle needed to eliminate x component
+    z_angle = -math.atan(rotated_pca[0] / rotated_pca[1])
+
+    if z_angle < 0:
+        z_angle += numpy.pi
+
+    logger.debug("Making cell upright for visualization")
+    cell = translate_cell_to_coords(cell, inplace=inplace, dest=[0, 0, 0])
+    cell = rotate_cell(
+        cell, 0, y_angle, z_angle, "yzx", relative_to_soma=False, inplace=inplace
+    )
+    return cell
+
+
 def get_pyneuroml_tempdir(rootdir: str = ".", prefix: str = "pyneuroml"):
     """Generate a pyneuroml directory name that can be used for various
     purposes.