Density

The density module provides an abstract representation of N-dimensional densities, facilitating operations and manipulations of multi-dimensional data.

Constructor

Density

Abstract representation of N-dimensional densities.

Attributes and underlying data

Density.data	Returns the value of Density.data.
Density.origin	Returns the value of the instance's Density.origin attribute.
Density.sampling_rate	Returns the value of the instance's Density.sampling_rate attribute.
Density.metadata	Returns the instance's Density.metadata attribute.
Density.shape	Returns the dimensions of Density.data.
Density.empty	Returns a copy of the class instance with all elements in Density.data set to zero.

Serialization

Density.to_file(filename[, gzip])	Writes class instance to disk.
Density.from_file(filename[, subset, use_memmap])	Reads a file into a Density instance.
Density.from_structure(filename_or_structure)	Reads in an atomic structure and converts it into a Density instance.

Conversion

Density.copy()	Create a copy of the class instance.
Density.to_numpy()	Converts Density.data to an in-memory numpy.ndarray.
Density.to_memmap()	Converts Density.data to a numpy.memmap.

Subsetting

Density.pad(new_shape[, center, padding_value])	Density.pad() extends the internal Density.data array of the current Density instance to new_shape and adapts Density.origin accordingly.
Density.trim_box(cutoff[, margin])	Computes a rectangle with sufficient dimension that encloses all values of the internal data array larger than the specified cutoff, expanded by the specified margin.
Density.centered([cutoff])	Shifts the data center of mass to the center of the data array using linear interpolation.
Density.adjust_box(box[, pad_kwargs])	Adjusts Density.data and Density.origin according to the provided box.
Density.minimum_enclosing_box(cutoff[, ...])	Compute the enclosing box that holds all possible rotations of the internal data array.

Computations

Density.rigid_transform(rotation_matrix[, ...])	Performs a rigid transform of the class instance.
Density.to_pointcloud([threshold])	Returns data indices that are larger than the given threshold.
Density.resample(new_sampling_rate[, ...])	Resamples Density.data to new_sampling_rate.
Density.density_boundary(weight[, ...])	Computes the density boundary of the class instance.
Density.surface_coordinates(density_boundaries)	Calculates the surface coordinates of the class instance using different boundary and surface detection methods.
Density.normal_vectors(coordinates)	Calculates the normal vectors for the given coordinates on the densities of the class instance.
Density.core_mask()	Calculates a weighted core mask by performing iterative binary erosion on Density.data.
Density.center_of_mass(arr[, cutoff])	Computes the center of mass of a numpy ndarray instance using all available elements.
Density.match_densities(target, template[, ...])	Aligns two Density instances target and template and returns the aligned template.
Density.match_structure_to_density(target, ...)	Aligns a tme.structure.Structure template to Density target and returns an aligned tme.structure.Structure instance.
Density.fourier_shell_correlation(density1, ...)	Computes the Fourier Shell Correlation (FSC) between two instances of Density.