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 done through the following classes:

`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.

Utilities¶

To help with fleshing out unit cell atoms from symmetry operators:

`symmetry_expansion`	Generate a set of unique atoms from an asymmetric cell and symmetry operators.
`lattice_system`	Determine the lattice system.

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 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_decay`	Exponential decay curve with onset.
`biexponential_decay`	Bi-exponential decay curve with onset.

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.

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.
`powder_center`	Finds the center of a powder diffraction pattern by comparing the correlation between the input and its image.

Calibrations¶

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

Image alignment¶

`align`	Align a diffraction image to a reference.
`ialign`	Generator of aligned diffraction images.
`diff_register`	Register translation of diffraction patterns by masked normalized cross-correlation.
`shift_image`	Shift an image.
`itrack_peak`	Generator function that tracks a diffraction peak in a stream of images.

Correlations¶

`xcorr`	Cross-correlation between two N-dimensional arrays.
`mnxc2`	Masked normalized cross-correlation (MNXC) between two images or stacks 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.

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.
`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.
`bounded_reflections`	Returns iterable of reflections (hkl) with norm(G) < nG

Visualization¶

potential_map Compute the electrostatic potential from powder diffraction data.

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.
`rgb_sweep`	Generate a set of RGB colors as a linear sweep between two RGB colors source and dest.

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.
`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.