geometry: Points and coordinate systems¶
 place  position and orientation of objects
 vector  operations on 3vectors
 bounds  bounds of objects in a scene
 Miscellaneous Routines  geometric calculations
place: Coordinate systems¶
A coordinate system is represented by a Place object which defines an origin and three axes specified relative to another coordinate system. A Place can specify the position and orientation of a model in a scene, defining the local coordinate system of the model relative to the global coordinate system of the scene. A Place can also represent the position and orientation of a camera within a scene. A Place can also be thought of as a coordinate transformation mapping Place coordinates to the other coordinate system. The transform consists of a linear part (often a rotation, but more generally a 3 by 3 matrix) followed by a shift along the 3 axes. Place objects use 64bit coordinates for axes and origin.
A point or vector is a onedimensional numpy array of 3 floating point values. Multiple points or vectors are represented as twodimensional numpy arrays of size N by 3. Points and vectors can have 32bit or 64bit floating point coordinates.

class
Place
(matrix=None, axes=None, origin=None)¶ Bases:
object
The Place class gives the origin and axes vectors for a model in the global coordinate system. A Place is often thought of as a coordinate transformation from local to global coordinates.
The axes can be specified as a sequence of three axis vectors. The origin can be specified as a point. Or both axes and origin can be specified as a 3 by 4 array where the first 3 columns are the axes and the last column is the origin.
The axes do not need to be orthogonal, for instance a crystallographic density map may use skewed axes, and the axis vectors need not be of unit length. The axes and origin are represented as 64bit floating point values.

apply_without_translation
(v)¶ Experimental API . Transform a vector. This applies the linear part of the transform without the shift. If the linear part is a rotation, then tangent and normal vectors are rotated.

axes
()¶ Experimental API . Return the coordinate system axes.

axis_center_angle_shift
()¶ Experimental API . Parameterize the transform as a rotation about a point around an axis and shift along that axis. Return the rotation axis, a point on the axis, rotation angle (in degrees), and shift distance parallel to the axis. This assumes the transformation linear part is a rotation.

description
()¶ Experimental API . Return a text description of the transformation including the 3 by 4 matrix, and the decomposition as a rotation about a point through an axis and shift along that axis.

determinant
()¶ Experimental API . Return the determinant of the linear part of the transformation.

interpolate
(tf, center, frac)¶ Experimental API . Interpolate from this transform to the specified one by a specified fraction. A fraction of 0 gives this transform while a fraction 1 gives transform tf. The interpolation is done by finding the transform mapping to tf, treating it as a rotation about the specified center point followed by a shift, then perform the specified fraction of the full rotation, and specified fraction of the shift. When the interpolated places are thought of as coordinate systems positions, the center point is in local coordinates.

inverse
()¶ Experimental API . Return the inverse transform.

is_identity
(tolerance=1e06)¶ Experimental API . Is the transform the identity transformation? Tests if each of the 3 by 4 matrix elements is within the specified tolerance of the identity transform.

matrix
= None¶ Experimental API . 3 by 4 numpy array, first 3 columns are axes, last column is origin.

move
(xyz)¶ Experimental API . Apply transform to an array of points, modifying the points in place.

moved
(xyz)¶ Experimental API . Returned transformed array of points. Makes a copy of points if place is not identity.

opengl_matrix
()¶ Experimental API . Return a numpy 4x4 array which is the transformation matrix in OpenGL order (columns major).

origin
()¶ Experimental API . Return the transformation shift vector, or equivalently the coordinate system origin.

rotation_angle
()¶ Experimental API . Return the rotation angle of the transform, or equivalently the rotation of the coordinate axes from the global axes. The return values is in radians from 0 to pi. The rotation is about the unique axis that takes the local to global coordinates. This assumes the transform is a rotation, or equivalently that the coordinate axes are orthonormal and right handed.

rotation_axis_and_angle
()¶ Experimental API . Return the rotation axis and angle (degrees) of the transform.

same
(p, angle_tolerance=0, shift_tolerance=0)¶ Experimental API . Is this transform the same as the given one to within a rotation angle tolerance (degrees), and shift tolerance (distance)

scale_translation
(s)¶ Experimental API . Return a copy of the transform with scaled shift.

shift_and_angle
(center)¶ Experimental API . Return the shift distance and rotation angle for the transform. The rotation angle is in radians the same as returned by rotation_angle(), and the shift is the distance the given center point is moved by the transformation.

translation
()¶ Experimental API . Return the transformation shift vector, or equivalently the coordinate system origin.

transpose
()¶ Experimental API . Return a copy of the transform with the linear part transposed.

update_normals
(xyz, pure=False)¶ Experimental API . Apply inverse transpose of transform with zero shift to an array of normal vectors, modifying the vectors in place. Optimize if pure rotation.

update_vectors
(xyz)¶ Experimental API . Apply transform with zero shift to an array of vectors, modifying the vectors in place.

z_axis
()¶ Experimental API . Return the coordinate system z axis.

zero_translation
()¶ Experimental API . Return a copy of the transform with zero shift.


class
Places
(places=None, place_array=None, shift_and_scale=None, opengl_array=None)¶ Bases:
object
The Places class represents a list of 0 or more Place objects. The advantage of Places over using a list of Place objects is that it doesn’t need to create a separate Python Place object for each position, instead it is able to represent for example 10,000 atom positions as a numpy array of positioning matrices. So this class is primarily to allow efficient handling of large numbers of positions.

opengl_matrices
()¶ Experimental API . Return array of 4x4 matrices with columnmajor order.

transform_coordinates
(csys)¶ Experimental API . csys maps new coordinates to old coordinates.


cross_product
(u)¶ Experimental API . Return the transform representing vector crossproduct with vector u (on the left) and zero shift.

identity
()¶ Experimental API . Return the identity transform.

interpolate_rotation
(place1, place2, fraction)¶ Experimental API . Interpolate the rotation parts of place1 and place2. The rotation axis taking one coordinate frame to the other is linearly interpolated. The translations are ignored and the returned Place has translation set to zero.

look_at
(from_pt, to_pt, up)¶ Experimental API . Return a Place object that represents looking from ‘from_pt’ to ‘to_pt’ with ‘up’ pointing up.

orthonormal_frame
(zaxis, ydir=None, xdir=None, origin=None)¶ Experimental API . Return a Place object with the specified z axis. Any rotation about that z axis is allowed, unless a vector ydir is given in which case the y axis will be in the plane define by the z axis and ydir.

product
(plist)¶ Experimental API . Product of a sequence of Place transforms.

rotation
(axis, angle, center=(0, 0, 0))¶ Experimental API . Return a transform which is a rotation about the specified center and axis by the given angle (degrees).

scale
(s)¶ Experimental API . Return a transform which is a scale by factor s.

skew_axes
(cell_angles)¶ Experimental API . Return a Place object representing the skewing with cell angles alpha, beta and gamma (degrees). The first axis is (1, 0, 0), the second axis makes angle gamma with the first and is in the xy plane, and the third axis makes angle beta with the first and angle alpha with the second axes. The axes are unit length and form a right handed coordinate system. The angles alpha, beta and gamma are the angles between yz, xz, and xy axes.

transform_planes
(coord_sys, planes)¶ Experimental API . Planes are given by 4 vectors v defining plane v0*x + v1*y + v2*z + v3 = 0. Returns planes in new coordinate system.

translation
(v)¶ Experimental API . Return a transform which is a shift by vector v.

vector_rotation
(u, v)¶ Experimental API . Return a rotation transform taking vector u to vector v by rotation about an axis perpendicular to u and v. The vectors can have any length and the transform maps the direction of u to the direction of v.

z_align
(pt1, pt2)¶ Experimental API . Return a Place object that puts the pt1>pt2 vector on the Z axis
vector: Point and vector operations¶
These are convenience functions that act on points and vectors which are onedimensional numpy arrays of 3 elements, or for multiple points and vectors twodimensional numpy arrays of size N by 3. Vectors of any dimensions are allowed, not just 3dimensional, except where noted. Coordinate values can be 32 or 64bit floating point numbers.

distance
(p, q)¶ Experimental API . Return the distance between two points.

norm
(u)¶ Experimental API . Return the length of a vector.

normalize_vector
(v)¶ Experimental API . Return a unit vector in the same direction as v.

normalize_vectors
(v)¶ Experimental API . Modify an array of vectors, making each have unit length.

vector_sum
(weights, vectors)¶ Experimental API . Return a vector which is a linear combination of vectors with specified weights.

cross_product
(u, v)¶ Experimental API . Return the crossproduct of two vectors. Vectors must be 3dimensonal.

inner_product
(u, v)¶ Experimental API . Return the inner product of two vectors.

inner_product_64
(u, v) → float64¶ Experimental API . Return the innerproduct of two vectors accumulated as a 64bit floating point value even if the vector components are 32bit values. Input arrays are 1dimensional with any value type.
bounds: Bounding boxes¶
Compute bounding boxes for objects in scene. The bounds of no object is represented as None rather than a Bounds object.

class
Bounds
(xyz_min, xyz_max)¶ Bases:
object
Bounding box specified by minimum and maximum x,y,z coordinates.

center
()¶ Experimental API . Center of bounding box.

radius
()¶ Experimental API . Radius of sphere containing bounding box.

size
()¶ Experimental API . Size of box along x,y,z axes.

width
()¶ Experimental API . Maximum of size of box x,y,z axes.

xyz_max
= None¶ Experimental API . Maximum x,y,z bounds as numpy float32 array.

xyz_min
= None¶ Experimental API . Minimum x,y,z bounds as numpy float32 array.


clip_bounds
(b, planes)¶ Experimental API . Clip a bounding box using planes each given as a plane point and normal.

copies_bounding_box
(bounds, positions)¶ Experimental API . Return
Bounds
that covers a specified bounding box replicated atPlaces
.

copy_tree_bounds
(bounds, positions_list)¶ Experimental API . Return
Bounds
that covers a specified bounding box replicated at a hierarchy ofPlaces
.

point_bounds
(xyz, placements=None)¶ Experimental API . Return
Bounds
for a set of points, optionally multiple positions given by aPlaces
instance.

sphere_bounds
(centers, radii)¶ Experimental API . Return
Bounds
containing a set of spheres.

union_bounds
(blist)¶ Experimental API . Return
Bounds
that is the union of a list ofBounds
. The list can contain None elements which are ignored. If the list contains noBounds
then None is returned.
Miscellaneous Routines¶

align_points
(xyz, ref_xyz)¶ Experimental API . Computes rotation and translation to align one set of points with another. The sum of the squares of the distances between corresponding positions is minimized.
Parameters:  xyz : numpy float n by 3 array
 ref_xyz : numpy float n by 3 array
Returns:  place :
Place
transformation taking xyz onto ref_xyz.
 rms : float
root mean square (RMS) value calculated from distances between aligned points.

closest_cylinder_intercept
(base1, base2, radii, xyz1, xyz2) → f, cnum¶ Experimental API . Find first cylinder intercept along line segment from xyz1 to xyz2. Cylinder endcaps are not considered. Implemented in C++.
Parameters:  base1, base2 : n by 3 float arrays
x,y,z cylinder end center coordinates.
 radii : float array
cylinder radii.
 xyz1, xyz2 : float 3tuples
x,y,z coordinates of line segment endpoints.
Returns:  f : float
fraction of distance from xyz1 to xyz2. None if no intercept.
 cnum : int
cylinder number, or None if no intercept.

closest_sphere_intercept
(centers, radii, xyz1, xyz2) → f, snum¶ Experimental API . Find first sphere intercept along line segment from xyz1 to xyz2. Implemented in C++.
Parameters:  centers : n by 3 float array
x,y,z sphere center coordinates.
 radii : length n float array
sphere radii.
 xyz1, xyz2 : float 3tuples
x,y,z coordinates of line segment endpoints.
Returns:  f : float
fraction of distance from xyz1 to xyz2. None if no intercept.
 snum : int
sphere number, or None if no intercept.

closest_triangle_intercept
(vertices, tarray, xyz1, xyz2) → f, tnum¶ Experimental API . Find first triangle intercept along line segment from xyz1 to xyz2. Implemented in C++.
Parameters:  vertices : n by 3 float array
triangle vertex x,y,z coordinates.
 triangles : m by 3 int array
vertex indices specifying 3 vertices for each triangle.
 xyz1, xyz2 : float 3tuples
x,y,z coordinates of line segment endpoints.
Returns:  f : float
fraction of distance from xyz1 to xyz2. None if no intercept.
 tnum : int
triangle number, or None if no intercept.

find_close_points
(xyz1, xyz2, max_distance) → i1, i2¶ Experimental API . Find close points between two sets of points, returning indices for each point that is close to some point in the other set. It does not report all pairs of close points, only which points have some close neighbor in the other set. The calculation is optimized for specified maximum distance small compared to the extent of the point sets, so that only positions close to a point need to be considered. Implemented in C++.
Parameters:  xyz1 : n by 3 float array
 xyz2 : m by 3 float array
 max_distance : float
consider only points less than this distance away.
Returns:  i1, i2 : numpy int32 arrays
Two arrays of indices into the xyz1 and xyz2 arrays. The index arrays are generally not of the same length.

find_closest_points
(xyz1, xyz2, max_distance[, scale2]) → i1, i2, near1¶ Experimental API . Find close points between two sets of points, returning indices for each point that is close to some point in the other set, and also return the closest point in set 2 for each point in set 1. The calculation is optimized for specified maximum distance small compared to the extent of the point sets, so that only positions close to a point need to be considered. Implemented in C++.
Parameters:  xyz1 : n by 3 float array
 xyz2 : m by 3 float array
 max_distance : float
consider only points less than this distance away.
 scale2 : length m float array
Optional argument giving a distance scale factor for each point in set 2. The scale factor is only used for determining the closest point, and causes the closest scaled distance to be used. This is an obscure feature.
Returns:  i1, i2 : numpy int32 array
Two arrays of indices into the xyz1 and xyz2 arrays for points that are within the maximum distance of some other point in the other set.
 near1 : numpy int32 array
A third array is returned that gives the index in set 2 of the closest for each point in set 1. This array has length equal to the number of points in set 1. If a set 1 point has no point from set 2 within the distance range then index returned is 1.

find_close_points_sets
(tp1, tp2, max_distance) → i1, i2¶ Experimental API . Find close points between two sets of points, returning indices for each point that is close to some point in the other set. Each set of points is defined by a list of pairs, each pair being an array of points and an affine transform to apply to those points. The calculation is optimized for specified maximum distance small compared to the extent of the point sets, so that only positions close to a point need to be considered. Implemented in C++.
Parameters:  tp1, tp2 : list of (n by 3 float array, 3 by 4 float array)
The first array of each pair are x,y,z point coordinates, and the second array is an affine transformation with the first 3 columns being a 3 by 3 matrix to applied (left multiplied) to each point and the last column being a translation (added to the point) applied after the matrix multiplication.
 max_distance : float
consider only points less than this distance away.
Returns:  i1, i2 : tuples of numpy int32 arrays
Two tuples of arrays of indices with lengths matching the lengths of the tp1 and tp2 arguments. Each index array list indices into the corresponding transformed point array for points that have some nearby point in the other set.

natural_cubic_spline
(path, segment_subdivisions) → spath, tangents¶ Experimental API . Compute a natural cubic spline through path points in 3 dimensions, producing a finer set of points and tangent vectors at those points. Implemented in C++.
Parameters:  path : n by 3 float array
points that spline will pass through.
 segment_subdivisions : int
place this number of additional points between every two consecutive path points.
Returns:  spath : m by 3 float array
points on cubic spline including original points and subdivision points.
 tangents : m by 3 float array
tangent vector at point of returned path.