api.rst

Reference/API

.. currentmodule:: skued

Baseline-determination

Please refer to the :ref:`tutorial on baseline-determination <baseline_tutorial>` for some examples.

.. autosummary::
    :toctree: functions/
    :nosignatures:

    baseline_dt
    baseline_dwt
    dtcwt
    idtcwt
    available_dt_filters
    available_first_stage_filters

Structure manipulation

Structure manipulation is done through the following classes:

.. autosummary::
    :toctree: classes/
    :nosignatures:

    Crystal
    Atom

Bases classes

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

.. autosummary::
    :toctree: classes/
    :nosignatures:

    Lattice
    LatticeSystem
    AtomicStructure

Utilities

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

.. autosummary::
    :toctree: functions/
    :nosignatures:

    symmetry_expansion
    lattice_system

Parsers

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

.. currentmodule:: skued.structure

.. autosummary::
    :toctree: classes/
    :nosignatures:

    CIFParser
    CODParser
    PDBParser

.. currentmodule:: skued

Time-series Analysis

Time-series exploration and analysis.

Time-zero tracking

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

.. autosummary::
    :toctree: functions/
    :nosignatures:

    register_time_shift
    register_time_shifts

Robust statistics

.. autosummary::
    :toctree: functions/
    :nosignatures:

    mad

Fitting

.. autosummary::
    :toctree: functions/
    :nosignatures:

    exponential_decay
    biexponential_decay

Non-uniform Fast Fourier Transform

.. autosummary::
    :toctree: functions/
    :nosignatures:

    nfft
    nfftfreq

Image Analysis

Combine the routines below with `npstreams`_ to process diffraction data in parallel. Refer to the :ref:`tutorial on image manipulation <image_analysis_tutorial>` for some examples.

Symmetry

.. autosummary::
    :toctree: functions/
    :nosignatures:

    nfold
    reflection

Polycrystalline diffraction

.. autosummary::
    :toctree: functions/
    :nosignatures:

    azimuthal_average
    powder_center

Calibrations

.. autosummary::
    :toctree: functions/
    :nosignatures:

    powder_calq

Image alignment

.. autosummary::
    :toctree: functions/
    :nosignatures:

    align
    ialign
    diff_register
    shift_image
    itrack_peak

Correlations

.. autosummary::
    :toctree: functions/
    :nosignatures:

    xcorr
    mnxc2

Image masking

.. autosummary::
    :toctree: functions/
    :nosignatures:

    mask_from_collection
    combine_masks
    mask_image

Image noise

.. autosummary::
    :toctree: functions/
    :nosignatures:

    snr_from_collection
    isnr
    triml
    trimr

Simulation

.. autosummary::
    :toctree: functions/
    :nosignatures:

    structure_factor
    affe
    powdersim
    electrostatic
    pelectrostatic
    bounded_reflections

Visualization

.. autosummary::
    :toctree: functions/
    :nosignatures:

    potential_map

Input/Output

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

.. autosummary::
    :toctree: functions/
    :nosignatures:

    diffread
    diffshow

Note

You should prefer to use :func:`diffread` to the specific format functions like :func:`mibread` and :func:`dmread`

Digital Micrograph DM3/DM4:

.. autosummary::
    :toctree: functions/
    :nosignatures:

    dmread

Merlin Image Binary (.mib) files:

.. autosummary::
    :toctree: functions/
    :nosignatures:

    mibheader
    mibread
    imibread

Plot Utilities

.. autosummary::
    :toctree: functions/
    :nosignatures:

    spectrum_colors
    rgb_sweep

Array Utilities

.. autosummary::
    :toctree: functions/
    :nosignatures:

    mirror
    repeated_array
    cart2polar
    polar2cart
    cart2spherical
    spherical2cart
    plane_mesh

Electron Properties

.. autosummary::
    :toctree: functions/
    :nosignatures:

    electron_wavelength
    electron_velocity
    interaction_parameter
    lorentz

Thin Film Optical Properties

.. autosummary::
    :toctree: functions/
    :nosignatures:

    film_optical_coefficients

Voigt Profile

.. autosummary::
    :toctree: functions/
    :nosignatures:

    gaussian
    lorentzian
    pseudo_voigt

Affine Transforms

.. autosummary::
    :toctree: functions/
    :nosignatures:

    affine_map
    transform
    change_of_basis
    change_basis_mesh
    is_basis
    is_rotation_matrix
    minimum_image_distance
    rotation_matrix
    translation_matrix
    translation_rotation_matrix