Utilities

Functions that are used in exhaustive and non-exhaustive template matching or are specific to template matching in general are grouped in the utilities module.

Masks

box_mask(shape, center, height)	Creates a box mask centered around the provided center point.
create_mask(mask_type[, sigma_decay])	Creates a mask of the specified type.
tube_mask(shape, symmetry_axis, base_center, ...)	Creates a tube mask.
elliptical_mask(shape, radius, center)	Creates an ellipsoidal mask.

Rotations

get_rotation_matrices(angular_sampling[, ...])	Returns rotation matrices with desired angular_sampling rate.
euler_to_rotationmatrix(angles[, convention])	Convert Euler angles to a rotation matrix.
rotation_aligning_vectors(initial_vector[, ...])	Compute the rotation matrix or Euler angles required to align an initial vector with a target vector.
euler_from_rotationmatrix(rotation_matrix[, ...])	Convert a rotation matrix to euler angles.
load_quaternions_by_angle(angular_sampling)	Get orientations and weights proportional to the given angular_sampling.
get_rotations_around_vector(cone_angle, ...)	Generate rotations describing the possible placements of a vector in a cone.
quaternion_to_rotation_matrix(quaternions)	Convert quaternions to rotation matrices.

Subsetting

centered(arr, new_shape)	Extract the centered portion of an array based on a new shape.
split_shape(shape, splits[, equal_shape])	Splits shape into equally sized and potentially overlapping subsets.
centered_mask(arr, new_shape)	Mask the centered portion of an array based on a new shape.
apply_convolution_mode(arr, ...[, ...])	Applies convolution_mode to arr.
compute_full_convolution_index(outer_shape, ...)	Computes the position of the convolution of pieces in the full convolution.
compute_parallelization_schedule(shape1, ...)	Computes a parallelization schedule for a given computation.

Serialization

load_pickle(filename)	Load and deserialize data written by write_pickle().
write_pickle(data, filename)	Serialize and write data to a file invalidating the input data.

Utilities

scramble_phases(arr[, noise_proportion, ...])	Perform random phase scrambling of arr.
rigid_transform(coordinates, ...[, ...])	Apply a rigid transformation (rotation and translation) to given coordinates.
array_to_memmap(arr[, filename])	Converts a obj:numpy.ndarray to a obj:numpy.memmap.
memmap_to_array(arr)	Convert a obj:numpy.memmap to a obj:numpy.ndarray and delete the memmap.
normalize_template(template, mask, ...)	Standardizes template to zero mean and unit standard deviation in mask.
conditional_execute(func, execute_operation)	Return the given function or a no-op function based on execute_operation.
minimum_enclosing_box(coordinates[, margin, ...])	Computes the minimal enclosing box around coordinates with margin.
generate_tempfile_name([suffix])	Returns the path to a temporary file with given suffix.