Reference/API

Baseline-determination

Please refer to the tutorial on baseline-determination for some examples.

`baseline_dt`	Iterative method of baseline-determination based on the dual-tree complex wavelet transform.
`baseline_dwt`	Iterative method of baseline determination, based on the discrete wavelet transform.
`dtcwt`	1D Dual-tree complex wavelet transform [1]_ along an axis.
`idtcwt`	1D Inverse dual-tree complex wavelet transform [1]_ along an axis.
`available_dt_filters`	Iterable of available wavelet filters compatible with the dual-tree complex wavelet transform.
`available_first_stage_filters`	Iterable of available wavelet filters compatible with the first stage of dual-tree complex wavelent transform.

Structure manipulation

Structure manipulation is provided by the crystals library. A summary of the documentation is provided below.

`Crystal`	The `Crystal` class is a set-like container that represent crystalline structures.
`Atom`	Container object for atomic data.

Bases classes

The Lattice class allows for manipulating lattice information separately from atomic information.

`Lattice`	Container class for lattice information and manipulations.
`LatticeSystem`	Lattice system enumeration.
`AtomicStructure`	Base class for atomic structures.

Parsers

Structure parsers are used to build Crystal instances, mostly through Crystal class methods.

`CIFParser`	Collection of methods that parses CIF files based on cif2cell.
`CODParser`	Collection of methods that parses CIF files retrieved from the Crystallography Open Database.
`PDBParser`	Collection of methods that parses Protein DataBank (PDB) files.

Time-series Analysis

Time-series exploration and analysis.

Time-zero tracking

Measurement of time-shifts between physically-equivalent time traces:

`register_time_shift`	Measure the time shift between a time trace and a reference trace by normalized cross correlation.
`register_time_shifts`	Measure the time shifts between time traces and a reference by cross-correlation.

Robust statistics

mad

Element-wise median absolute deviation (MAD) of a signal.

Fitting

`exponential`	Exponential curve with onset.
`biexponential`	Bi-exponential curve with onset.
`with_irf`	This decorator factory that applies a Gaussian impulse response function (IRF) to a fitting function.

Non-uniform Fast Fourier Transform

`nfft`	Non-uniform Fast Fourier Transform (NFFT) computed on a uniform frequency grid.
`nfftfreq`	Compute the frequency range used in nfft for M frequency bins.

Time-series Selections

`Selection`	Abstract base class for time-series selection masks.
`RectSelection`	Rectangular selection mask.
`DiskSelection`	Disk selection mask.
`RingSelection`	Ring selection mask, i.e. 2-torus.
`RingArcSelection`	Selection patch for a partial 2-torus.
`ArbitrarySelection`	Arbirary selection mask, represented by a boolean array.

Image Analysis

Combine the routines below with npstreams to process diffraction data in parallel. Refer to the tutorial on image manipulation for some examples.

Symmetry

`nfold`	Returns an images averaged according to n-fold rotational symmetry.
`reflection`	Symmetrize an image according to a reflection plane.

Polycrystalline diffraction

azimuthal_average

This function returns an azimuthally-averaged pattern computed from an image, e.g.

Calibrations

powder_calq

Determine the scattering vector q corresponding to a polycrystalline diffraction pattern and a known crystal structure.

Center-finding

autocenter

Find the center of a diffraction pattern automatically.

Image alignment

`align`	Align a diffraction image to a reference.
`ialign`	Generator of aligned diffraction images.
`itrack_peak`	Generator function that tracks a diffraction peak in a stream of images.

Image masking

`mask_from_collection`	Determine binary mask from a set of images.
`combine_masks`	Combine multiple pixel masks into one.
`mask_image`	Fill invalid pixels in an image with another value, according to a pixel mask.

Image noise

`snr_from_collection`	Signal-to-noise ratio (SNR) on a per-pixel basis, for images in a collection.
`isnr`	Streaming, pixelwise signal-to-noise ratio (SNR).
`triml`	Trim values in an array that fall below (i.e.
`trimr`	Trim values in an array that fall above (i.e.

Single-crystal indexing

`bragg_peaks`	Extract the position of Bragg peaks in a single-crystal diffraction pattern.
`bragg_peaks_persistence`	Extract the position of Bragg peaks in a single-crystal diffraction pattern using 2D persistence of the image landscape.
`brillouin_zones`	Generate Brillouin zone projections in the particular 2D geometry based on Bragg peak locations.

Simulation

`structure_factor`	Computation of the static structure factor for electron diffraction.
`affe`	Atomic form factors for electrons, for neutral atoms.
`powdersim`	Simulates polycrystalline diffraction pattern.
`kinematicsim`	Propagate a plane wave through a crystal and compute the resulting diffraction pattern, in the kinematic approximation (thin specimen).
`electrostatic`	Electrostatic potential from a crystal calculated on a real-space mesh, assuming an infinite crystal.
`pelectrostatic`	Projected electrostatic potential from a crystal calculated on a real-space mesh, assuming an infinite crystal in x and y.

Visualization

`potential_map`	Compute the electrostatic potential from powder diffraction data.
`potential_synthesis`	Synthesize the electrostatic potential from a list of experimental reflections and associated diffracted intensities.
`patterson`	Computation of the patterson pair-distribution function from azimuthally-averaged diffraction pattern.

Input/Output

General diffraction image I/O and plotting. Note that for diffshow(), the packages PyQtGraph and PyQt5 must be installed.

`diffread`	Load an image from a file.
`diffshow`	Display an image (from an array or from a file) in an interactive window.

Note

You should prefer to use diffread() to the specific format functions like mibread() and dmread()

Digital Micrograph DM3/DM4:

dmread

Read a DM3/DM4 (Digital Micrograph) file into a NumPy array.

Merlin Image Binary (.mib) files:

`mibheader`	Get an image header from a Merlin Image Binary file.
`mibread`	Read a MIB (Merlin Image Binary) file into a NumPy array.
`imibread`	Generator of images contained in a Merlin Image Binary file as NumPy arrays.

Plot Utilities

`spectrum_colors`	Generates a set of RGB colors corresponding to the visible spectrum (i.e.
`spectrum_cmap`	Rainbow-style Matplotlib colormap generated from `skued.spectrum_colors()`.
`rgb_sweep`	Generate a set of RGB colors as a linear sweep between two RGB colors source and dest.
`indices_to_text`	Returns a Matplotlib-compatible string representation of Miller indices, in LaTeX/Mathjax format.

Array Utilities

`mirror`	Reverse array over many axes.
`repeated_array`	Create a composite array from repeated copies of an array
`cart2polar`	Transform cartesian coordinates to polar coordinates.
`polar2cart`	Transform polar coordinates to cartesian coordinates.
`cart2spherical`	Transform cartesian coordinates into spherical coordinates .
`spherical2cart`	Transform spherical coordinates into cartesian coordinates.
`plane_mesh`	Generate a spatial mesh for a plane defined by two vectors.

Electron Properties

`electron_wavelength`	Relativistic wavelength \(\lambda\) of an accelerated electron.
`electron_velocity`	Relativistic velocity \(v_e\) of an accelerated electron.
`interaction_parameter`	Interaction parameter from relativistic electron wavelength.
`lorentz`	Relativistic factor \(\gamma\), defined as \(\gamma = \frac{1}{\sqrt{1 - v^2/c^2}}\)

Thin Film Optical Properties

film_optical_coefficients

Calculate the reflection, transmission, and absorption coefficients of a thin-film (possibly on a substrate).

Voigt Profile

`gaussian`	Unit integral Gaussian function.
`lorentzian`	Unit integral Lorenzian function.
`pseudo_voigt`	Unit integral pseudo-Voigt profile.

Affine Transforms

`affine_map`	Extends 3x3 transform matrices to 4x4, i.e. general affine transforms.
`transform`	Applies a matrix transform on an array.
`change_of_basis`	Returns the matrix that goes from one basis to the other.
`change_basis_mesh`	Changes the basis of meshgrid arrays.
`is_basis`	Returns true if the set of vectors forms a basis.
`is_rotation_matrix`	Checks whether a matrix is orthogonal with unit determinant (1 or -1), properties of rotation matrices.
`minimum_image_distance`	Returns a periodic array according to the minimum image convention.
`rotation_matrix`	Return matrix to rotate about axis defined by direction around the origin [0,0,0].
`translation_matrix`	Return matrix to translate by direction vector.
`translation_rotation_matrix`	Returns a 4x4 matrix that includes a rotation and a translation.