============= API reference ============= This reference manual details the public modules, classes, and functions in kikuchipy, as generated from their docstrings. Many of the docstrings contain examples, however, see the user guide for how to use kikuchipy. .. caution:: kikuchipy is in an alpha stage, so there will be some breaking changes with each release. .. module:: kikuchipy The list of top modules and the load function: .. autosummary:: crystallography data detectors draw filters generators indexing io load pattern projections signals simulations .... crystallography =============== .. automodule:: kikuchipy.crystallography .. currentmodule:: kikuchipy.crystallography .. autosummary:: get_direct_structure_matrix get_reciprocal_metric_tensor get_reciprocal_structure_matrix .. autofunction:: get_direct_structure_matrix .. autofunction:: get_reciprocal_metric_tensor .. autofunction:: get_reciprocal_structure_matrix .... data ==== .. currentmodule:: kikuchipy.data .. autosummary:: nickel_ebsd_small nickel_ebsd_large nickel_ebsd_master_pattern_small silicon_ebsd_moving_screen_in silicon_ebsd_moving_screen_out5mm silicon_ebsd_moving_screen_out10mm .. automodule:: kikuchipy.data :members: :undoc-members: .... detectors ========= .. automodule:: kikuchipy.detectors .. currentmodule:: kikuchipy.detectors .. autosummary:: EBSDDetector PCCalibrationMovingScreen EBSDDetector ------------ .. currentmodule:: kikuchipy.detectors.EBSDDetector .. autosummary:: deepcopy pc_bruker pc_emsoft pc_oxford pc_tsl plot .. autoclass:: kikuchipy.detectors.EBSDDetector :members: :undoc-members: :show-inheritance: .. automethod:: __init__ PCCalibrationMovingScreen ------------------------- .. currentmodule:: kikuchipy.detectors.PCCalibrationMovingScreen .. autosummary:: make_lines plot .. autoclass:: kikuchipy.detectors.PCCalibrationMovingScreen :members: :undoc-members: :show-inheritance: .. automethod:: __init__ .... draw ==== .. automodule:: kikuchipy.draw .. currentmodule:: kikuchipy.draw markers ------- .. currentmodule:: kikuchipy.draw.markers .. autosummary:: get_line_segment_list get_point_list get_text_list .. autofunction:: get_line_segment_list .. autofunction:: get_point_list .. autofunction:: get_text_list colors ------ .. automodule:: kikuchipy.draw.colors .... filters ======= .. automodule:: kikuchipy.filters .. currentmodule:: kikuchipy.filters .. autosummary:: distance_to_origin highpass_fft_filter lowpass_fft_filter modified_hann Window .. autofunction:: distance_to_origin .. autofunction:: highpass_fft_filter .. autofunction:: lowpass_fft_filter .. autofunction:: modified_hann Window ------ .. currentmodule:: kikuchipy.filters.Window .. autosummary:: is_valid make_circular plot shape_compatible .. autoclass:: kikuchipy.filters.Window :members: :undoc-members: :show-inheritance: .. automethod:: __init__ .... generators ========== .. automodule:: kikuchipy.generators .. currentmodule:: kikuchipy.generators .. autosummary:: EBSDSimulationGenerator VirtualBSEGenerator virtual_bse_generator.get_rgb_image virtual_bse_generator.normalize_image EBSDSimulationGenerator ----------------------- .. currentmodule:: kikuchipy.generators.EBSDSimulationGenerator .. autosummary:: geometrical_simulation .. autoclass:: kikuchipy.generators.EBSDSimulationGenerator :members: :undoc-members: :show-inheritance: .. automethod:: __init__ VirtualBSEGenerator ------------------- .. currentmodule:: kikuchipy.generators.VirtualBSEGenerator .. autosummary:: get_images_from_grid get_rgb_image plot_grid roi_from_grid .. autoclass:: kikuchipy.generators.VirtualBSEGenerator :members: :undoc-members: :show-inheritance: .. automethod:: __init__ Other functions --------------- .. currentmodule:: kikuchipy.generators.virtual_bse_generator .. autofunction:: get_rgb_image .. autofunction:: normalize_image .... indexing ======== .. automodule:: kikuchipy.indexing .. currentmodule:: kikuchipy.indexing .. autosummary:: compute_refine_orientation_results compute_refine_orientation_projection_center_results compute_refine_projection_center_results orientation_similarity_map merge_crystal_maps similarity_metrics .. autofunction:: compute_refine_orientation_results .. autofunction:: compute_refine_orientation_projection_center_results .. autofunction:: compute_refine_projection_center_results .. autofunction:: orientation_similarity_map .. autofunction:: merge_crystal_maps similarity_metrics ------------------ .. automodule:: kikuchipy.indexing.similarity_metrics .. currentmodule:: kikuchipy.indexing.similarity_metrics .. autosummary:: SimilarityMetric NormalizedCrossCorrelationMetric NormalizedDotProductMetric .. autoclass:: kikuchipy.indexing.similarity_metrics.SimilarityMetric :members: .. automethod:: __init__ .. autoclass:: kikuchipy.indexing.similarity_metrics.NormalizedCrossCorrelationMetric :members: :show-inheritance: .. automethod:: __call__ .. autoclass:: kikuchipy.indexing.similarity_metrics.NormalizedDotProductMetric :members: :show-inheritance: .. automethod:: __call__ .... io === .. automodule:: kikuchipy.io .. currentmodule:: kikuchipy.io .. autosummary:: _io.load plugins .. autofunction:: kikuchipy.io._io.load plugins ------- .. automodule:: kikuchipy.io.plugins .. currentmodule:: kikuchipy.io.plugins .. autosummary:: emsoft_ebsd emsoft_ebsd_master_pattern h5ebsd nordif nordif_calibration_patterns oxford_binary The plugins import patterns and parameters from file formats into :class:`~kikuchipy.signals.EBSD` or :class:`~kikuchipy.signals.EBSDMasterPattern` (or :class:`~kikuchipy.signals.LazyEBSD` or :class:`~kikuchipy.signals.LazyEBSDMasterPattern` if loading lazily) objects. emsoft_ebsd ~~~~~~~~~~~ .. automodule:: kikuchipy.io.plugins.emsoft_ebsd :members: :undoc-members: :show-inheritance: emsoft_ebsd_master_pattern ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: kikuchipy.io.plugins.emsoft_ebsd_master_pattern :members: :undoc-members: :show-inheritance: h5ebsd ~~~~~~ .. automodule:: kikuchipy.io.plugins.h5ebsd :members: :undoc-members: :show-inheritance: nordif ~~~~~~ .. automodule:: kikuchipy.io.plugins.nordif :members: :undoc-members: :show-inheritance: nordif_calibration_patterns ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: kikuchipy.io.plugins.nordif_calibration_patterns :members: :undoc-members: :show-inheritance: oxford_binary ~~~~~~~~~~~~~ .. automodule:: kikuchipy.io.plugins.oxford_binary :members: :undoc-members: :show-inheritance: .... pattern ======= Single and chunk pattern processing used by signals. .. currentmodule:: kikuchipy.pattern .. autosummary:: chunk fft fft_filter fft_frequency_vectors fft_spectrum get_dynamic_background get_image_quality ifft normalize_intensity remove_dynamic_background rescale_intensity Functions operating on single EBSD patterns as :class:`~numpy.ndarray`. .. automodule:: kikuchipy.pattern :members: :undoc-members: chunk ----- Functions for operating on :class:`~numpy.ndarray` or :class:`~dask.array.Array` chunks of EBSD patterns. .. currentmodule:: kikuchipy.pattern.chunk .. autosummary:: adaptive_histogram_equalization average_neighbour_patterns fft_filter get_dynamic_background get_image_quality normalize_intensity remove_dynamic_background remove_static_background rescale_intensity .. automodule:: kikuchipy.pattern.chunk :members: :undoc-members: .... projections =========== .. automodule:: kikuchipy.projections .. currentmodule:: kikuchipy.projections .. autosummary:: ebsd_projections hesse_normal_form.HesseNormalForm spherical_projection.SphericalProjection ebsd_projections ---------------- .. currentmodule:: kikuchipy.projections.ebsd_projections .. autosummary:: detector2direct_lattice detector2reciprocal_lattice detector2sample .. automodule:: kikuchipy.projections.ebsd_projections :members: :undoc-members: HesseNormalForm ----------------- .. automodule:: kikuchipy.projections.hesse_normal_form .. autoclass:: kikuchipy.projections.hesse_normal_form.HesseNormalForm :members: :undoc-members: :show-inheritance: SphericalProjection -------------------- .. automodule:: kikuchipy.projections.spherical_projection .. autoclass:: kikuchipy.projections.spherical_projection.SphericalProjection :members: :undoc-members: :show-inheritance: .... signals ======= .. automodule:: kikuchipy.signals .. currentmodule:: kikuchipy.signals .. autosummary:: EBSD EBSDMasterPattern VirtualBSEImage util EBSD ---- All methods listed here are also available to :class:`~kikuchipy.signals.LazyEBSD` instances. See :class:`̃hyperspy._signals.signal2d.Signal2D` for methods inherited from HyperSpy. .. currentmodule:: kikuchipy.signals.EBSD .. autosummary:: adaptive_histogram_equalization average_neighbour_patterns dictionary_indexing fft_filter get_average_neighbour_dot_product_map get_decomposition_model get_dynamic_background get_image_quality get_neighbour_dot_product_matrices get_virtual_bse_intensity normalize_intensity plot_virtual_bse_intensity refine_orientation refine_orientation_projection_center refine_projection_center remove_dynamic_background remove_static_background rescale_intensity save set_detector_calibration set_experimental_parameters set_phase_parameters set_scan_calibration .. autoclass:: kikuchipy.signals.EBSD :members: :undoc-members: :inherited-members: Signal2D :show-inheritance: These methods are exclusive to LazyEBSD instances. .. currentmodule:: kikuchipy.signals.LazyEBSD .. autosummary:: get_decomposition_model_write .. autoclass:: kikuchipy.signals.LazyEBSD :members: :undoc-members: :show-inheritance: EBSDMasterPattern ----------------- All methods listed here are also available to :class:`~kikuchipy.signals.LazyEBSDMasterPattern` instances. See :class:`~hyperspy._signals.signal2d.Signal2D` for methods inherited from HyperSpy. .. currentmodule:: kikuchipy.signals.EBSDMasterPattern .. autosummary:: get_patterns normalize_intensity rescale_intensity .. autoclass:: kikuchipy.signals.EBSDMasterPattern :members: :inherited-members: Signal2D :show-inheritance: There are no methods exclusive to LazyEBSDMasterPattern instances. .. autoclass:: kikuchipy.signals.LazyEBSDMasterPattern :members: :undoc-members: :show-inheritance: VirtualBSEImage --------------- See :class:`~hyperspy._signals.signal2d.Signal2D` for methods inherited from HyperSpy. .. currentmodule:: kikuchipy.signals.VirtualBSEImage .. autosummary:: normalize_intensity rescale_intensity .. autoclass:: kikuchipy.signals.VirtualBSEImage :members: :undoc-members: :inherited-members: Signal2D util ---- .. currentmodule:: kikuchipy.signals.util .. autosummary:: ebsd_metadata get_chunking get_dask_array metadata_nodes .. automodule:: kikuchipy.signals.util :members: :undoc-members: .... simulations =========== .. automodule:: kikuchipy.simulations .. currentmodule:: kikuchipy.simulations .. autosummary:: GeometricalEBSDSimulation features GeometricalEBSDSimulation ------------------------- .. currentmodule:: kikuchipy.simulations.GeometricalEBSDSimulation .. autosummary:: as_markers bands_as_markers pc_as_markers zone_axes_as_markers zone_axes_labels_as_markers .. autoclass:: kikuchipy.simulations.GeometricalEBSDSimulation :members: :undoc-members: :show-inheritance: .. automethod:: __init__ features -------- .. automodule:: kikuchipy.simulations.features .. currentmodule:: kikuchipy.simulations.features .. autosummary:: KikuchiBand ZoneAxis KikuchiBand ~~~~~~~~~~~ .. autoclass:: kikuchipy.simulations.features.KikuchiBand :members: :undoc-members: :show-inheritance: :exclude-members: from_highest_hkl, from_min_dspacing, symmetrise, unique .. automethod:: __init__ .. automethod:: __getitem__ ZoneAxis ~~~~~~~~ .. autoclass:: kikuchipy.simulations.features.ZoneAxis :members: :undoc-members: :show-inheritance: :exclude-members: from_highest_hkl, from_min_dspacing, symmetrise, unique .. automethod:: __init__ .. automethod:: __getitem__