.. include:: references.txt .. _api: ************* Reference/API ************* .. currentmodule:: skued ====================== Baseline-determination ====================== Please refer to the :ref:`tutorial on baseline-determination ` for some examples. .. autosummary:: :toctree: functions/ :nosignatures: baseline_dt baseline_dwt dtcwt idtcwt available_dt_filters available_first_stage_filters ====================== Structure manipulation ====================== .. currentmodule:: crystals Structure manipulation is provided by the `crystals `_ library. A summary of the documentation is provided below. .. 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 Parsers ------- Structure parsers are used to build :class:`Crystal` instances, mostly through :class:`Crystal` class methods. .. 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 biexponential with_irf Non-uniform Fast Fourier Transform ---------------------------------- .. autosummary:: :toctree: functions/ :nosignatures: nfft nfftfreq Time-series Selections ---------------------- .. autosummary:: :toctree: classes/ :nosignatures: Selection RectSelection DiskSelection RingSelection RingArcSelection ArbitrarySelection ============== Image Analysis ============== Combine the routines below with `npstreams`_ to process diffraction data in parallel. Refer to the :ref:`tutorial on image manipulation ` for some examples. Symmetry -------- .. autosummary:: :toctree: functions/ :nosignatures: nfold reflection Polycrystalline diffraction --------------------------- .. autosummary:: :toctree: functions/ :nosignatures: azimuthal_average Calibrations ------------ .. autosummary:: :toctree: functions/ :nosignatures: powder_calq Center-finding -------------- .. autosummary:: :toctree: functions/ :nosignatures: autocenter Image alignment --------------- .. autosummary:: :toctree: functions/ :nosignatures: align ialign itrack_peak 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 Single-crystal indexing ----------------------- .. autosummary:: :toctree: functions/ :nosignatures: bragg_peaks bragg_peaks_persistence brillouin_zones ========== Simulation ========== .. autosummary:: :toctree: functions/ :nosignatures: structure_factor affe powdersim kinematicsim electrostatic pelectrostatic ============= Visualization ============= .. autosummary:: :toctree: functions/ :nosignatures: potential_map potential_synthesis patterson ============ 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 spectrum_cmap rgb_sweep indices_to_text =============== 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