# 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.

 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.

## 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.