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+<article id="content">
+<header>
+<h1 class="title">Module <code>pymskt.mesh.anatomical.femur_cylinder</code></h1>
+</header>
+<section id="section-intro">
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">from scipy.optimize import least_squares
+from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
+import numpy as np
+from pymskt.statistics.pca import pca_svd
+class FitCylinderFemur:
+    def __init__(
+        self,
+        femur,
+        labels_name=&#39;labels&#39;,
+        labels=(12, 13, 14, 15),
+        z_resolution=50,
+        theta_resolution=50,
+        cylinder_percent_bone_width=0.9,
+#         copy_femur=True,
+        ftol=1e-4
+    ):
+        # not using the copy method becuase the femur is a pymskt object not vtk so it
+        # doesnt work with vtk_deep_copy - would need to create new femur object.
+#         if copy_femur is True:
+#             self.femur = mskt.mesh.utils.vtk_deep_copy(femur)
+#         else:
+#             self.femur = femur
+        self.femur = femur
+        self.labels_name = labels_name
+        if (type(labels) == int) or (type(labels) == float):
+            self.labels = [labels,]
+        else:
+            self.labels = labels
+        self.z_resolution = z_resolution
+        self.theta_resolution = theta_resolution
+        self.cylinder_percent_bone_width = cylinder_percent_bone_width
+        self.ftol = ftol
+        self.pts_articular_cylinder = None
+        self.inertial_matrix_artic_surf = None
+        self.inertial_aligned_pts_articular_cylinder = None
+        self._height = None
+        self._origin = None
+        self._vector = None
+        self._radius = None
+        self.bounds = None
+        self.params = None
+    def get_initial_parameters(self):
+        self.get_articular_surf_points()
+        self.guess_height()
+        self.guess_origin()
+        self.guess_vector()
+        self.guess_radius()
+    def get_articular_surf_points(self):
+        label_idx = vtk_to_numpy(self.femur.mesh.GetPointData().GetArray(self.labels_name))
+        cylinder_labels = label_idx == self.labels[0]
+        if len(self.labels) &gt; 1:
+            for idx in range(1, len(self.labels)):
+                cylinder_labels += (label_idx == self.labels[idx])
+        cylinder_labels = np.asarray(cylinder_labels, dtype=int)
+        cylinder_scalars = numpy_to_vtk(cylinder_labels)
+        cylinder_scalars.SetName(&#39;cylinder labels&#39;)
+        self.femur.mesh.GetPointData().AddArray(cylinder_scalars)
+        self.pts_articular_cylinder = self.femur.point_coords[cylinder_labels == 1, :]
+    def get_inertial_matrix_articular_surface(self):
+        self.inertial_matrix_artic_surf, _ = pca_svd(self.pts_articular_cylinder.T)
+        self.inv_inertial_matrix_artic_surf = np.linalg.inv(self.inertial_matrix_artic_surf)
+    def get_artic_pts_aligned_inertial_matrix(self):
+        if self.inertial_matrix_artic_surf is None:
+            self.get_inertial_matrix_articular_surface()
+        self.inertial_aligned_pts_articular_cylinder = self.inertial_matrix_artic_surf @ self.pts_articular_cylinder.T
+    def guess_height(self):
+        if self.inertial_aligned_pts_articular_cylinder is None:
+            self.get_artic_pts_aligned_inertial_matrix()
+        height_guess = self.inertial_aligned_pts_articular_cylinder[0,:].max() - self.inertial_aligned_pts_articular_cylinder[0,:].min()
+        self._height = self.cylinder_percent_bone_width * height_guess
+    def guess_origin(self):
+        if self.inertial_matrix_artic_surf is None:
+            self.get_inertial_matrix_articular_surface()
+        min_x = self.inertial_aligned_pts_articular_cylinder[0,:].min() # this is going to be fully medial or laterl
+        max_x = self.inertial_aligned_pts_articular_cylinder[0,:].max() # this is going to be fully medial or laterl (opposite above)
+        mean_y = self.inertial_aligned_pts_articular_cylinder[1,:].mean() # use this as the origin y
+        mean_z = self.inertial_aligned_pts_articular_cylinder[2,:].mean() # I think this is going to be too close to the articular surface... but maybe good enought start?
+        # Get points in roughly the center of the cylinder of the condyle on the medial &amp; lateral sides.
+        origin1 = np.asarray([[min_x, mean_y, mean_z],])
+        origin2 = np.asarray([[max_x, mean_y, mean_z],])
+        origin1 = self.inv_inertial_matrix_artic_surf @ origin1.T
+        origin1 = np.squeeze(origin1.T)
+        origin2 = self.inv_inertial_matrix_artic_surf @ origin2.T
+        origin2 = np.squeeze(origin2.T)
+        # Set the origin to a point just inside of the extreme on the min_x side (whether thats medial or lateral)
+        origin = (origin2 - origin1) * 0.05 + origin1
+        self._origin = origin
+    def guess_vector(self):
+        if self.inertial_matrix_artic_surf is None:
+            self.get_inertial_matrix_articular_surface()
+        vector = np.asarray([
+            self.inertial_matrix_artic_surf[0,0], # vector X
+            self.inertial_matrix_artic_surf[1,0], # vector Y
+            self.inertial_matrix_artic_surf[2,0], # vector Z
+        ], dtype=float)
+        if np.linalg.norm(vector) != 1:
+            vector = vector/np.linalg.norm(vector)
+        self._vector = vector
+    def guess_radius(self):
+        if self.inertial_aligned_pts_articular_cylinder is None:
+            self.get_artic_pts_aligned_inertial_matrix()
+        range_y = self.inertial_aligned_pts_articular_cylinder[1,:].max() - self.inertial_aligned_pts_articular_cylinder[1,:].min()
+        radius = range_y/2
+        self._radius = radius
+    @staticmethod
+    def get_unit_cylinder(z_resolution, theta_resolution):
+        theta = np.linspace(0, 2*np.pi, theta_resolution)
+        unit_cylinder = np.zeros((theta_resolution * z_resolution, 3))
+        unit_cylinder[:, 0] = np.tile(np.cos(theta), z_resolution)
+        unit_cylinder[:, 1] = np.tile(np.sin(theta), z_resolution)
+    #     for i in range(z_resolution):
+        unit_cylinder[:, 2] = np.repeat(np.linspace(0, 1, z_resolution), theta_resolution)
+        return unit_cylinder
+    def cylinder_function(self, origin, height, radius, vector, z_resolution=None, theta_resolution=None):
+        if z_resolution is None:
+            z_resolution = self.z_resolution
+        if theta_resolution is None:
+            theta_resolution = self.theta_resolution
+        # ensure vector is np array of floats.
+        vector = np.asarray(vector, dtype=float)
+        if np.linalg.norm(vector) != 1:
+            vector = vector/np.linalg.norm(vector)
+        # scale the size of the cylinder
+        unit_cylinder = FitCylinderFemur.get_unit_cylinder(z_resolution=z_resolution, theta_resolution=theta_resolution)
+        unit_cylinder[:, 0] = unit_cylinder[:, 0] * radius
+        unit_cylinder[:, 1] = unit_cylinder[:, 1] * radius
+        unit_cylinder[:, 2] = unit_cylinder[:, 2] * height
+        # Create rotation matrix to rotate cylinder axis
+        #make some vector not in the same direction as v
+        not_v = np.array([1, 0, 0])
+        if (vector == not_v).all():
+            not_v = np.array([0, 1, 0])
+        #make vector perpendicular to v
+        norm1 = np.cross(vector, not_v)
+        #normalize n1
+        norm1 /= np.linalg.norm(norm1)
+        #make unit vector perpendicular to v and n1
+        norm2 = np.cross(vector, norm1)
+        rot_matrix = np.zeros((3,3))
+        rot_matrix[:,0] = norm1
+        rot_matrix[:,1] = norm2
+        rot_matrix[:,2] = vector
+        # rotate the cylinder along the vector axis
+        unit_cylinder = rot_matrix @ unit_cylinder.T
+        unit_cylinder = unit_cylinder.T
+        unit_cylinder += origin
+        return unit_cylinder
+    @staticmethod
+    def residuals(points, cylinder):
+        &#34;&#34;&#34;
+        Find closest point on cylinder for each point. Calcualte
+        &#34;&#34;&#34;
+        diff = points[None, :, :] - cylinder[:, None, :]
+        diff = np.sqrt(np.sum(diff **2, axis=-1))
+        resids = diff.min(axis=0)
+        return resids
+    def get_func(self):
+        &#34;&#34;&#34;
+        Function to create the function that we want to minimize. The returned function
+        returns the residuals of the points vs the generated cylinder.
+        &#34;&#34;&#34;
+        def func(params):
+            cylinder = self.cylinder_function(
+                origin=[params[0], params[1], params[2]],
+                height=params[3],
+                radius=params[4],
+                vector=np.asarray([params[5],params[6],params[7]], dtype=float),
+                z_resolution=self.z_resolution,
+                theta_resolution=self.theta_resolution
+            )
+            resid = FitCylinderFemur.residuals(self.pts_articular_cylinder, cylinder)
+            return resid
+        return func
+    def get_bounds(self):
+        self.bounds = [
+            [
+                self.pts_articular_cylinder[:,0].min(),
+                self.pts_articular_cylinder[:,1].min(),
+                self.pts_articular_cylinder[:,2].min(),
+                self._height - self._height * 0.2,
+                self._radius - self._radius * 0.2,
+                -1,
+                -1,
+                -1
+            ],
+            [
+                self.pts_articular_cylinder[:,0].max(),
+                self.pts_articular_cylinder[:,1].max(),
+                self.pts_articular_cylinder[:,2].max(),
+                self._height + self._height * 0.2,
+                self._radius + self._radius * 0.2,
+,
+,
+            ]
+        ]
+    def get_params(self):
+        if (self._origin is None) or (self._height is None) or (self._radius is None) or (self._vector is None):
+            self.get_initial_parameters()
+        self.params = [
+            self._origin[0],
+            self._origin[1],
+            self._origin[2],
+            self._height,
+            self._radius,
+            self._vector[0],
+            self._vector[1],
+            self._vector[2]
+        ]
+    def fit(self):
+        if self.params is None:
+            self.get_params()
+        if self.bounds is None:
+            self.get_bounds()
+        func = self.get_func()
+        result = least_squares(
+            func,
+            self.params,
+            bounds=self.bounds,
+            ftol=self.ftol
+        )
+        self.optimization_success = result[&#39;success&#39;]
+        self.params = result[&#39;x&#39;]
+        self._origin = np.array([self.params[0], self.params[1], self.params[2]])
+        self._height = self.params[3]
+        self._radius = self.params[4]
+        self._vector = np.array([self.params[5], self.params[6], self.params[7]])
+        self._vector /= np.linalg.norm(self._vector)
+        if self.optimization_success is True:
+            print(&#39;Fitting cylinder to condyles completed successfully!&#39;)
+        else:
+            print(&#39;Fitting cylinder to condyles did not converge properly:\n&#39;, result)
+    @property
+    def height(self):
+        return self._height
+    @property
+    def radius(self):
+        return self._radius
+    @property
+    def origin(self):
+        return self._origin
+    @property
+    def vector(self):
+        return self._vector
+    @property
+    def cylinder(self):
+        return self.cylinder_function(
+            origin=self._origin,
+            height=self._height,
+            radius=self._radius,
+            vector=self._vector
+        )</code></pre>
+</details>
+</section>
+<section>
+</section>
+<section>
+</section>
+<section>
+</section>
+<section>
+<h2 class="section-title" id="header-classes">Classes</h2>
+<dl>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur"><code class="flex name class">
+<span>class <span class="ident">FitCylinderFemur</span></span>
+<span>(</span><span>femur, labels_name='labels', labels=(12, 13, 14, 15), z_resolution=50, theta_resolution=50, cylinder_percent_bone_width=0.9, ftol=0.0001)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">class FitCylinderFemur:
+    def __init__(
+        self,
+        femur,
+        labels_name=&#39;labels&#39;,
+        labels=(12, 13, 14, 15),
+        z_resolution=50,
+        theta_resolution=50,
+        cylinder_percent_bone_width=0.9,
+#         copy_femur=True,
+        ftol=1e-4
+    ):
+        # not using the copy method becuase the femur is a pymskt object not vtk so it
+        # doesnt work with vtk_deep_copy - would need to create new femur object.
+#         if copy_femur is True:
+#             self.femur = mskt.mesh.utils.vtk_deep_copy(femur)
+#         else:
+#             self.femur = femur
+        self.femur = femur
+        self.labels_name = labels_name
+        if (type(labels) == int) or (type(labels) == float):
+            self.labels = [labels,]
+        else:
+            self.labels = labels
+        self.z_resolution = z_resolution
+        self.theta_resolution = theta_resolution
+        self.cylinder_percent_bone_width = cylinder_percent_bone_width
+        self.ftol = ftol
+        self.pts_articular_cylinder = None
+        self.inertial_matrix_artic_surf = None
+        self.inertial_aligned_pts_articular_cylinder = None
+        self._height = None
+        self._origin = None
+        self._vector = None
+        self._radius = None
+        self.bounds = None
+        self.params = None
+    def get_initial_parameters(self):
+        self.get_articular_surf_points()
+        self.guess_height()
+        self.guess_origin()
+        self.guess_vector()
+        self.guess_radius()
+    def get_articular_surf_points(self):
+        label_idx = vtk_to_numpy(self.femur.mesh.GetPointData().GetArray(self.labels_name))
+        cylinder_labels = label_idx == self.labels[0]
+        if len(self.labels) &gt; 1:
+            for idx in range(1, len(self.labels)):
+                cylinder_labels += (label_idx == self.labels[idx])
+        cylinder_labels = np.asarray(cylinder_labels, dtype=int)
+        cylinder_scalars = numpy_to_vtk(cylinder_labels)
+        cylinder_scalars.SetName(&#39;cylinder labels&#39;)
+        self.femur.mesh.GetPointData().AddArray(cylinder_scalars)
+        self.pts_articular_cylinder = self.femur.point_coords[cylinder_labels == 1, :]
+    def get_inertial_matrix_articular_surface(self):
+        self.inertial_matrix_artic_surf, _ = pca_svd(self.pts_articular_cylinder.T)
+        self.inv_inertial_matrix_artic_surf = np.linalg.inv(self.inertial_matrix_artic_surf)
+    def get_artic_pts_aligned_inertial_matrix(self):
+        if self.inertial_matrix_artic_surf is None:
+            self.get_inertial_matrix_articular_surface()
+        self.inertial_aligned_pts_articular_cylinder = self.inertial_matrix_artic_surf @ self.pts_articular_cylinder.T
+    def guess_height(self):
+        if self.inertial_aligned_pts_articular_cylinder is None:
+            self.get_artic_pts_aligned_inertial_matrix()
+        height_guess = self.inertial_aligned_pts_articular_cylinder[0,:].max() - self.inertial_aligned_pts_articular_cylinder[0,:].min()
+        self._height = self.cylinder_percent_bone_width * height_guess
+    def guess_origin(self):
+        if self.inertial_matrix_artic_surf is None:
+            self.get_inertial_matrix_articular_surface()
+        min_x = self.inertial_aligned_pts_articular_cylinder[0,:].min() # this is going to be fully medial or laterl
+        max_x = self.inertial_aligned_pts_articular_cylinder[0,:].max() # this is going to be fully medial or laterl (opposite above)
+        mean_y = self.inertial_aligned_pts_articular_cylinder[1,:].mean() # use this as the origin y
+        mean_z = self.inertial_aligned_pts_articular_cylinder[2,:].mean() # I think this is going to be too close to the articular surface... but maybe good enought start?
+        # Get points in roughly the center of the cylinder of the condyle on the medial &amp; lateral sides.
+        origin1 = np.asarray([[min_x, mean_y, mean_z],])
+        origin2 = np.asarray([[max_x, mean_y, mean_z],])
+        origin1 = self.inv_inertial_matrix_artic_surf @ origin1.T
+        origin1 = np.squeeze(origin1.T)
+        origin2 = self.inv_inertial_matrix_artic_surf @ origin2.T
+        origin2 = np.squeeze(origin2.T)
+        # Set the origin to a point just inside of the extreme on the min_x side (whether thats medial or lateral)
+        origin = (origin2 - origin1) * 0.05 + origin1
+        self._origin = origin
+    def guess_vector(self):
+        if self.inertial_matrix_artic_surf is None:
+            self.get_inertial_matrix_articular_surface()
+        vector = np.asarray([
+            self.inertial_matrix_artic_surf[0,0], # vector X
+            self.inertial_matrix_artic_surf[1,0], # vector Y
+            self.inertial_matrix_artic_surf[2,0], # vector Z
+        ], dtype=float)
+        if np.linalg.norm(vector) != 1:
+            vector = vector/np.linalg.norm(vector)
+        self._vector = vector
+    def guess_radius(self):
+        if self.inertial_aligned_pts_articular_cylinder is None:
+            self.get_artic_pts_aligned_inertial_matrix()
+        range_y = self.inertial_aligned_pts_articular_cylinder[1,:].max() - self.inertial_aligned_pts_articular_cylinder[1,:].min()
+        radius = range_y/2
+        self._radius = radius
+    @staticmethod
+    def get_unit_cylinder(z_resolution, theta_resolution):
+        theta = np.linspace(0, 2*np.pi, theta_resolution)
+        unit_cylinder = np.zeros((theta_resolution * z_resolution, 3))
+        unit_cylinder[:, 0] = np.tile(np.cos(theta), z_resolution)
+        unit_cylinder[:, 1] = np.tile(np.sin(theta), z_resolution)
+    #     for i in range(z_resolution):
+        unit_cylinder[:, 2] = np.repeat(np.linspace(0, 1, z_resolution), theta_resolution)
+        return unit_cylinder
+    def cylinder_function(self, origin, height, radius, vector, z_resolution=None, theta_resolution=None):
+        if z_resolution is None:
+            z_resolution = self.z_resolution
+        if theta_resolution is None:
+            theta_resolution = self.theta_resolution
+        # ensure vector is np array of floats.
+        vector = np.asarray(vector, dtype=float)
+        if np.linalg.norm(vector) != 1:
+            vector = vector/np.linalg.norm(vector)
+        # scale the size of the cylinder
+        unit_cylinder = FitCylinderFemur.get_unit_cylinder(z_resolution=z_resolution, theta_resolution=theta_resolution)
+        unit_cylinder[:, 0] = unit_cylinder[:, 0] * radius
+        unit_cylinder[:, 1] = unit_cylinder[:, 1] * radius
+        unit_cylinder[:, 2] = unit_cylinder[:, 2] * height
+        # Create rotation matrix to rotate cylinder axis
+        #make some vector not in the same direction as v
+        not_v = np.array([1, 0, 0])
+        if (vector == not_v).all():
+            not_v = np.array([0, 1, 0])
+        #make vector perpendicular to v
+        norm1 = np.cross(vector, not_v)
+        #normalize n1
+        norm1 /= np.linalg.norm(norm1)
+        #make unit vector perpendicular to v and n1
+        norm2 = np.cross(vector, norm1)
+        rot_matrix = np.zeros((3,3))
+        rot_matrix[:,0] = norm1
+        rot_matrix[:,1] = norm2
+        rot_matrix[:,2] = vector
+        # rotate the cylinder along the vector axis
+        unit_cylinder = rot_matrix @ unit_cylinder.T
+        unit_cylinder = unit_cylinder.T
+        unit_cylinder += origin
+        return unit_cylinder
+    @staticmethod
+    def residuals(points, cylinder):
+        &#34;&#34;&#34;
+        Find closest point on cylinder for each point. Calcualte
+        &#34;&#34;&#34;
+        diff = points[None, :, :] - cylinder[:, None, :]
+        diff = np.sqrt(np.sum(diff **2, axis=-1))
+        resids = diff.min(axis=0)
+        return resids
+    def get_func(self):
+        &#34;&#34;&#34;
+        Function to create the function that we want to minimize. The returned function
+        returns the residuals of the points vs the generated cylinder.
+        &#34;&#34;&#34;
+        def func(params):
+            cylinder = self.cylinder_function(
+                origin=[params[0], params[1], params[2]],
+                height=params[3],
+                radius=params[4],
+                vector=np.asarray([params[5],params[6],params[7]], dtype=float),
+                z_resolution=self.z_resolution,
+                theta_resolution=self.theta_resolution
+            )
+            resid = FitCylinderFemur.residuals(self.pts_articular_cylinder, cylinder)
+            return resid
+        return func
+    def get_bounds(self):
+        self.bounds = [
+            [
+                self.pts_articular_cylinder[:,0].min(),
+                self.pts_articular_cylinder[:,1].min(),
+                self.pts_articular_cylinder[:,2].min(),
+                self._height - self._height * 0.2,
+                self._radius - self._radius * 0.2,
+                -1,
+                -1,
+                -1
+            ],
+            [
+                self.pts_articular_cylinder[:,0].max(),
+                self.pts_articular_cylinder[:,1].max(),
+                self.pts_articular_cylinder[:,2].max(),
+                self._height + self._height * 0.2,
+                self._radius + self._radius * 0.2,
+,
+,
+            ]
+        ]
+    def get_params(self):
+        if (self._origin is None) or (self._height is None) or (self._radius is None) or (self._vector is None):
+            self.get_initial_parameters()
+        self.params = [
+            self._origin[0],
+            self._origin[1],
+            self._origin[2],
+            self._height,
+            self._radius,
+            self._vector[0],
+            self._vector[1],
+            self._vector[2]
+        ]
+    def fit(self):
+        if self.params is None:
+            self.get_params()
+        if self.bounds is None:
+            self.get_bounds()
+        func = self.get_func()
+        result = least_squares(
+            func,
+            self.params,
+            bounds=self.bounds,
+            ftol=self.ftol
+        )
+        self.optimization_success = result[&#39;success&#39;]
+        self.params = result[&#39;x&#39;]
+        self._origin = np.array([self.params[0], self.params[1], self.params[2]])
+        self._height = self.params[3]
+        self._radius = self.params[4]
+        self._vector = np.array([self.params[5], self.params[6], self.params[7]])
+        self._vector /= np.linalg.norm(self._vector)
+        if self.optimization_success is True:
+            print(&#39;Fitting cylinder to condyles completed successfully!&#39;)
+        else:
+            print(&#39;Fitting cylinder to condyles did not converge properly:\n&#39;, result)
+    @property
+    def height(self):
+        return self._height
+    @property
+    def radius(self):
+        return self._radius
+    @property
+    def origin(self):
+        return self._origin
+    @property
+    def vector(self):
+        return self._vector
+    @property
+    def cylinder(self):
+        return self.cylinder_function(
+            origin=self._origin,
+            height=self._height,
+            radius=self._radius,
+            vector=self._vector
+        )</code></pre>
+</details>
+<h3>Static methods</h3>
+<dl>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_unit_cylinder"><code class="name flex">
+<span>def <span class="ident">get_unit_cylinder</span></span>(<span>z_resolution, theta_resolution)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@staticmethod
+def get_unit_cylinder(z_resolution, theta_resolution):
+    theta = np.linspace(0, 2*np.pi, theta_resolution)
+    unit_cylinder = np.zeros((theta_resolution * z_resolution, 3))
+    unit_cylinder[:, 0] = np.tile(np.cos(theta), z_resolution)
+    unit_cylinder[:, 1] = np.tile(np.sin(theta), z_resolution)
+#     for i in range(z_resolution):
+    unit_cylinder[:, 2] = np.repeat(np.linspace(0, 1, z_resolution), theta_resolution)
+    return unit_cylinder</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.residuals"><code class="name flex">
+<span>def <span class="ident">residuals</span></span>(<span>points, cylinder)</span>
+</code></dt>
+<dd>
+<div class="desc"><p>Find closest point on cylinder for each point. Calcualte</p></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@staticmethod
+def residuals(points, cylinder):
+    &#34;&#34;&#34;
+    Find closest point on cylinder for each point. Calcualte
+    &#34;&#34;&#34;
+    diff = points[None, :, :] - cylinder[:, None, :]
+    diff = np.sqrt(np.sum(diff **2, axis=-1))
+    resids = diff.min(axis=0)
+    return resids</code></pre>
+</details>
+</dd>
+</dl>
+<h3>Instance variables</h3>
+<dl>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.cylinder"><code class="name">var <span class="ident">cylinder</span></code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@property
+def cylinder(self):
+    return self.cylinder_function(
+        origin=self._origin,
+        height=self._height,
+        radius=self._radius,
+        vector=self._vector
+    )</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.height"><code class="name">var <span class="ident">height</span></code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@property
+def height(self):
+    return self._height</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.origin"><code class="name">var <span class="ident">origin</span></code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@property
+def origin(self):
+    return self._origin</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.radius"><code class="name">var <span class="ident">radius</span></code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@property
+def radius(self):
+    return self._radius</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.vector"><code class="name">var <span class="ident">vector</span></code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">@property
+def vector(self):
+    return self._vector</code></pre>
+</details>
+</dd>
+</dl>
+<h3>Methods</h3>
+<dl>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.cylinder_function"><code class="name flex">
+<span>def <span class="ident">cylinder_function</span></span>(<span>self, origin, height, radius, vector, z_resolution=None, theta_resolution=None)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def cylinder_function(self, origin, height, radius, vector, z_resolution=None, theta_resolution=None):
+    if z_resolution is None:
+        z_resolution = self.z_resolution
+    if theta_resolution is None:
+        theta_resolution = self.theta_resolution
+    # ensure vector is np array of floats.
+    vector = np.asarray(vector, dtype=float)
+    if np.linalg.norm(vector) != 1:
+        vector = vector/np.linalg.norm(vector)
+    # scale the size of the cylinder
+    unit_cylinder = FitCylinderFemur.get_unit_cylinder(z_resolution=z_resolution, theta_resolution=theta_resolution)
+    unit_cylinder[:, 0] = unit_cylinder[:, 0] * radius
+    unit_cylinder[:, 1] = unit_cylinder[:, 1] * radius
+    unit_cylinder[:, 2] = unit_cylinder[:, 2] * height
+    # Create rotation matrix to rotate cylinder axis
+    #make some vector not in the same direction as v
+    not_v = np.array([1, 0, 0])
+    if (vector == not_v).all():
+        not_v = np.array([0, 1, 0])
+    #make vector perpendicular to v
+    norm1 = np.cross(vector, not_v)
+    #normalize n1
+    norm1 /= np.linalg.norm(norm1)
+    #make unit vector perpendicular to v and n1
+    norm2 = np.cross(vector, norm1)
+    rot_matrix = np.zeros((3,3))
+    rot_matrix[:,0] = norm1
+    rot_matrix[:,1] = norm2
+    rot_matrix[:,2] = vector
+    # rotate the cylinder along the vector axis
+    unit_cylinder = rot_matrix @ unit_cylinder.T
+    unit_cylinder = unit_cylinder.T
+    unit_cylinder += origin
+    return unit_cylinder</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.fit"><code class="name flex">
+<span>def <span class="ident">fit</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def fit(self):
+    if self.params is None:
+        self.get_params()
+    if self.bounds is None:
+        self.get_bounds()
+    func = self.get_func()
+    result = least_squares(
+        func,
+        self.params,
+        bounds=self.bounds,
+        ftol=self.ftol
+    )
+    self.optimization_success = result[&#39;success&#39;]
+    self.params = result[&#39;x&#39;]
+    self._origin = np.array([self.params[0], self.params[1], self.params[2]])
+    self._height = self.params[3]
+    self._radius = self.params[4]
+    self._vector = np.array([self.params[5], self.params[6], self.params[7]])
+    self._vector /= np.linalg.norm(self._vector)
+    if self.optimization_success is True:
+        print(&#39;Fitting cylinder to condyles completed successfully!&#39;)
+    else:
+        print(&#39;Fitting cylinder to condyles did not converge properly:\n&#39;, result)</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_artic_pts_aligned_inertial_matrix"><code class="name flex">
+<span>def <span class="ident">get_artic_pts_aligned_inertial_matrix</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_artic_pts_aligned_inertial_matrix(self):
+    if self.inertial_matrix_artic_surf is None:
+        self.get_inertial_matrix_articular_surface()
+    self.inertial_aligned_pts_articular_cylinder = self.inertial_matrix_artic_surf @ self.pts_articular_cylinder.T</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_articular_surf_points"><code class="name flex">
+<span>def <span class="ident">get_articular_surf_points</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_articular_surf_points(self):
+    label_idx = vtk_to_numpy(self.femur.mesh.GetPointData().GetArray(self.labels_name))
+    cylinder_labels = label_idx == self.labels[0]
+    if len(self.labels) &gt; 1:
+        for idx in range(1, len(self.labels)):
+            cylinder_labels += (label_idx == self.labels[idx])
+    cylinder_labels = np.asarray(cylinder_labels, dtype=int)
+    cylinder_scalars = numpy_to_vtk(cylinder_labels)
+    cylinder_scalars.SetName(&#39;cylinder labels&#39;)
+    self.femur.mesh.GetPointData().AddArray(cylinder_scalars)
+    self.pts_articular_cylinder = self.femur.point_coords[cylinder_labels == 1, :]</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_bounds"><code class="name flex">
+<span>def <span class="ident">get_bounds</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_bounds(self):
+    self.bounds = [
+        [
+            self.pts_articular_cylinder[:,0].min(),
+            self.pts_articular_cylinder[:,1].min(),
+            self.pts_articular_cylinder[:,2].min(),
+            self._height - self._height * 0.2,
+            self._radius - self._radius * 0.2,
+            -1,
+            -1,
+            -1
+        ],
+        [
+            self.pts_articular_cylinder[:,0].max(),
+            self.pts_articular_cylinder[:,1].max(),
+            self.pts_articular_cylinder[:,2].max(),
+            self._height + self._height * 0.2,
+            self._radius + self._radius * 0.2,
+,
+,
+        ]
+    ]</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_func"><code class="name flex">
+<span>def <span class="ident">get_func</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"><p>Function to create the function that we want to minimize. The returned function
+returns the residuals of the points vs the generated cylinder.</p></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_func(self):
+    &#34;&#34;&#34;
+    Function to create the function that we want to minimize. The returned function
+    returns the residuals of the points vs the generated cylinder.
+    &#34;&#34;&#34;
+    def func(params):
+        cylinder = self.cylinder_function(
+            origin=[params[0], params[1], params[2]],
+            height=params[3],
+            radius=params[4],
+            vector=np.asarray([params[5],params[6],params[7]], dtype=float),
+            z_resolution=self.z_resolution,
+            theta_resolution=self.theta_resolution
+        )
+        resid = FitCylinderFemur.residuals(self.pts_articular_cylinder, cylinder)
+        return resid
+    return func</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_inertial_matrix_articular_surface"><code class="name flex">
+<span>def <span class="ident">get_inertial_matrix_articular_surface</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_inertial_matrix_articular_surface(self):
+    self.inertial_matrix_artic_surf, _ = pca_svd(self.pts_articular_cylinder.T)
+    self.inv_inertial_matrix_artic_surf = np.linalg.inv(self.inertial_matrix_artic_surf)</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_initial_parameters"><code class="name flex">
+<span>def <span class="ident">get_initial_parameters</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_initial_parameters(self):
+    self.get_articular_surf_points()
+    self.guess_height()
+    self.guess_origin()
+    self.guess_vector()
+    self.guess_radius()</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_params"><code class="name flex">
+<span>def <span class="ident">get_params</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_params(self):
+    if (self._origin is None) or (self._height is None) or (self._radius is None) or (self._vector is None):
+        self.get_initial_parameters()
+    self.params = [
+        self._origin[0],
+        self._origin[1],
+        self._origin[2],
+        self._height,
+        self._radius,
+        self._vector[0],
+        self._vector[1],
+        self._vector[2]
+    ]</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_height"><code class="name flex">
+<span>def <span class="ident">guess_height</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def guess_height(self):
+    if self.inertial_aligned_pts_articular_cylinder is None:
+        self.get_artic_pts_aligned_inertial_matrix()
+    height_guess = self.inertial_aligned_pts_articular_cylinder[0,:].max() - self.inertial_aligned_pts_articular_cylinder[0,:].min()
+    self._height = self.cylinder_percent_bone_width * height_guess</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_origin"><code class="name flex">
+<span>def <span class="ident">guess_origin</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def guess_origin(self):
+    if self.inertial_matrix_artic_surf is None:
+        self.get_inertial_matrix_articular_surface()
+    min_x = self.inertial_aligned_pts_articular_cylinder[0,:].min() # this is going to be fully medial or laterl
+    max_x = self.inertial_aligned_pts_articular_cylinder[0,:].max() # this is going to be fully medial or laterl (opposite above)
+    mean_y = self.inertial_aligned_pts_articular_cylinder[1,:].mean() # use this as the origin y
+    mean_z = self.inertial_aligned_pts_articular_cylinder[2,:].mean() # I think this is going to be too close to the articular surface... but maybe good enought start?
+    # Get points in roughly the center of the cylinder of the condyle on the medial &amp; lateral sides.
+    origin1 = np.asarray([[min_x, mean_y, mean_z],])
+    origin2 = np.asarray([[max_x, mean_y, mean_z],])
+    origin1 = self.inv_inertial_matrix_artic_surf @ origin1.T
+    origin1 = np.squeeze(origin1.T)
+    origin2 = self.inv_inertial_matrix_artic_surf @ origin2.T
+    origin2 = np.squeeze(origin2.T)
+    # Set the origin to a point just inside of the extreme on the min_x side (whether thats medial or lateral)
+    origin = (origin2 - origin1) * 0.05 + origin1
+    self._origin = origin</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_radius"><code class="name flex">
+<span>def <span class="ident">guess_radius</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def guess_radius(self):
+    if self.inertial_aligned_pts_articular_cylinder is None:
+        self.get_artic_pts_aligned_inertial_matrix()
+    range_y = self.inertial_aligned_pts_articular_cylinder[1,:].max() - self.inertial_aligned_pts_articular_cylinder[1,:].min()
+    radius = range_y/2
+    self._radius = radius</code></pre>
+</details>
+</dd>
+<dt id="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_vector"><code class="name flex">
+<span>def <span class="ident">guess_vector</span></span>(<span>self)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def guess_vector(self):
+    if self.inertial_matrix_artic_surf is None:
+        self.get_inertial_matrix_articular_surface()
+    vector = np.asarray([
+        self.inertial_matrix_artic_surf[0,0], # vector X
+        self.inertial_matrix_artic_surf[1,0], # vector Y
+        self.inertial_matrix_artic_surf[2,0], # vector Z
+    ], dtype=float)
+    if np.linalg.norm(vector) != 1:
+        vector = vector/np.linalg.norm(vector)
+    self._vector = vector</code></pre>
+</details>
+</dd>
+</dl>
+</dd>
+</dl>
+</section>
+</article>
+<nav id="sidebar">
+<h1>Index</h1>
+<div class="toc">
+<ul></ul>
+</div>
+<ul id="index">
+<li><h3>Super-module</h3>
+<ul>
+<li><code><a title="pymskt.mesh.anatomical" href="index.html">pymskt.mesh.anatomical</a></code></li>
+</ul>
+</li>
+<li><h3><a href="#header-classes">Classes</a></h3>
+<ul>
+<li>
+<h4><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur">FitCylinderFemur</a></code></h4>
+<ul class="">
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.cylinder" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.cylinder">cylinder</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.cylinder_function" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.cylinder_function">cylinder_function</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.fit" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.fit">fit</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_artic_pts_aligned_inertial_matrix" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_artic_pts_aligned_inertial_matrix">get_artic_pts_aligned_inertial_matrix</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_articular_surf_points" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_articular_surf_points">get_articular_surf_points</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_bounds" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_bounds">get_bounds</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_func" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_func">get_func</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_inertial_matrix_articular_surface" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_inertial_matrix_articular_surface">get_inertial_matrix_articular_surface</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_initial_parameters" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_initial_parameters">get_initial_parameters</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_params" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_params">get_params</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_unit_cylinder" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.get_unit_cylinder">get_unit_cylinder</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_height" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_height">guess_height</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_origin" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_origin">guess_origin</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_radius" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_radius">guess_radius</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_vector" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.guess_vector">guess_vector</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.height" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.height">height</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.origin" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.origin">origin</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.radius" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.radius">radius</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.residuals" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.residuals">residuals</a></code></li>
+<li><code><a title="pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.vector" href="#pymskt.mesh.anatomical.femur_cylinder.FitCylinderFemur.vector">vector</a></code></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</nav>
+</main>
+<footer id="footer">
+<p>Generated by <a href="https://pdoc3.github.io/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc</cite> 0.10.0</a>.</p>
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+</body>
+</html>