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Getting started

  • Installing pyxem
  • Using Jupyter Lab
  • Loading Data
  • Big Data
  • GPU Computing

Usage

  • Tutorials
    • Data Inspection- Preprocessing - Unsupervised ML
    • Phase/Orientation Mapping
    • Calibrations
    • Azimuthal Integral
    • Strain Mapping
    • Nanocrystal Segmentation
    • PDF Analysis Tutorial
    • Angular Correlations of Amorphous Materials
    • Analysing magnetic materials using STEM-DPC
    • Fast template matching
    • Orientation mapping for Molecular Glasses
    • Conventions and interoperability
  • Gallery of Examples

Resources

  • API reference
    • data
      • au_grating
      • pdnip_glass
      • zrnb_precipitate
      • twinned_nanowire
      • sample_with_g
      • mgo_nanocrystals
      • tilt_boundary_data
      • si_phase
      • si_tilt
      • si_grains
      • si_grains_simple
      • si_rotations_line
      • simulated_stripes
      • fe_multi_phase_grains
      • fe_fcc_phase
      • fe_bcc_phase
      • cuag_orientations
      • organic_semiconductor
      • feal_stripes
      • sped_ag
      • pdcusi_insitu
      • simulated_constant_shift_magnitude
      • au_grating_20cm
      • small_ptychography
      • au_phase
      • simulated_overlap
      • simulated_strain
      • simulated_pn_junction
    • components
      • ReducedIntensityCorrectionComponent
        • trait_added
        • trait_modified
        • function
      • ScatteringFitComponentLobato
        • trait_added
        • trait_modified
        • function
      • ScatteringFitComponentXTables
        • trait_added
        • trait_modified
        • function
    • generators
      • get_DisplacementGradientMap
      • get_single_DisplacementGradientTensor
      • CalibrationGenerator
        • get_correction_matrix
        • get_diffraction_calibration
        • get_distortion_residuals
        • get_elliptical_distortion
        • get_navigation_calibration
        • get_rotation_calibration
        • plot_calibrated_data
        • plot_corrected_diffraction_pattern
      • IndexationGenerator
      • VectorIndexationGenerator
        • index_vectors
        • refine_best_orientation
        • refine_n_best_orientations
      • TemplateIndexationGenerator
      • ProfileIndexationGenerator
        • index_peaks
      • AcceleratedIndexationGenerator
        • correlate
      • IntegrationGenerator
        • extract_intensities
        • extract_intensities_summation_method
      • PDFGenerator1D
        • get_pdf
      • ReducedIntensityGenerator1D
        • fit_atomic_scattering
        • get_reduced_intensity
        • mask_from_bkgd_pattern
        • mask_reduced_intensity
        • set_diffraction_calibration
        • set_diffraction_offset
        • set_s_cutoff
        • subtract_bkgd_pattern
      • SubpixelrefinementGenerator
        • center_of_mass_method
        • conventional_xc
        • local_gaussian_method
        • reference_xc
      • VarianceGenerator
        • get_diffraction_variance
        • get_image_variance
      • VirtualImageGenerator
        • get_concentric_virtual_images
        • get_virtual_images_from_mesh
        • set_ROI_mesh
      • VirtualDarkFieldGenerator
        • get_virtual_dark_field_images
    • libraries
      • CalibrationDataLibrary
        • plot_calibration_data
    • signals
      • CommonDiffraction
        • unit
        • add_navigation_signal
        • get_integrated_intensity
        • get_virtual_image
        • plot_integrated_intensity
        • to_device
        • to_host
      • Correlation2D
        • get_angular_power
        • get_summed_angular_power
        • get_symmetry_coefficient
      • LazyCorrelation2D
      • BeamShift
        • beam_energy
        • calibrate_electric_shifts
        • get_bivariate_histogram
        • get_color_signal
        • get_linear_plane
        • get_magnitude_phase_signal
        • get_magnitude_signal
        • get_phase_signal
        • make_linear_plane
        • phase_retrieval
        • pixels_to_calibrated_units
        • rotate_beam_shifts
        • rotate_scan_dimensions
      • LazyBeamShift
      • DPCSignal1D
        • to_beamshift
      • DPCSignal2D
        • to_beamshift
      • LazyDPCSignal1D
      • LazyDPCSignal2D
      • DiffractionVariance1D
      • DiffractionVariance2D
      • ImageVariance
      • DiffractionVectors
        • center
        • column_names
        • detector_shape
        • has_navigation_axis
        • num_columns
        • num_rows
        • offsets
        • pixel_calibration
        • pixel_vectors
        • scales
        • units
        • calculate_cartesian_coordinates
        • cluster
        • filter_basis
        • filter_detector_edge
        • filter_magnitude
        • flatten_diffraction_vectors
        • from_peaks
        • get_diffracting_pixels_map
        • get_magnitude_histogram
        • get_magnitudes
        • get_pixel_vectors
        • get_strain_maps
        • get_unique_vectors
        • plot_diffraction_vectors
        • plot_diffraction_vectors_on_signal
        • subpixel_refine
        • to_markers
        • to_mask
        • to_polar
      • DiffractionVectors1D
        • flatten_diffraction_vectors
        • plot
      • DiffractionVectors2D
        • has_navigation_axis
        • filter_detector_edge
        • from_peaks
        • get_unique_vectors
        • to_roi
      • Diffraction1D
      • LazyDiffraction1D
      • LazyDiffraction2D
      • Diffraction2D
        • add_ellipse_array_as_markers
        • add_interactive_line_profile
        • add_peak_array_as_markers
        • angular_mask
        • apply_affine_transformation
        • apply_gain_normalisation
        • center_direct_beam
        • correct_bad_pixels
        • filter
        • find_dead_pixels
        • find_hot_pixels
        • flip_diffraction_x
        • flip_diffraction_y
        • get_azimuthal_integral1d
        • get_azimuthal_integral2d
        • get_diffraction_vectors
        • get_direct_beam_mask
        • get_direct_beam_position
        • get_variance
        • intensity_peaks
        • make_probe_navigation
        • peak_position_refinement_com
        • plot
        • rotate_diffraction
        • shift_diffraction
        • subtract_diffraction_background
        • template_match
        • template_match_disk
        • template_match_ring
        • template_match_with_binary_image
        • threshold_and_mask
      • ElectronDiffraction1D
        • curve_fit
        • model2camera_length
        • model2theta_scale
        • model_simulation1d
        • set_diffraction_calibration
        • set_experimental_parameters
        • set_scan_calibration
      • LazyElectronDiffraction1D
      • LazyElectronDiffraction2D
      • ElectronDiffraction2D
        • beam_energy
        • camera_length
        • diffraction_calibration
        • scan_calibration
        • set_diffraction_calibration
        • set_experimental_parameters
        • set_scan_calibration
      • VectorMatchingResults
        • get_crystallographic_map
        • get_indexed_diffraction_vectors
      • PairDistributionFunction1D
        • normalise_signal
      • PolarDiffraction2D
        • get_angular_correlation
        • get_angular_power
        • get_full_pearson_correlation
        • get_orientation
        • get_pearson_correlation
        • get_resolved_pearson_correlation
        • subtract_diffraction_background
      • LazyPolarDiffraction2D
      • PolarVectors
        • has_delta_phi
        • get_angles
        • to_cartesian
        • to_markers
      • LazyPolarVectors
      • Power2D
        • get_map
        • plot_symmetries
      • LazyPower2D
      • ReducedIntensity1D
        • damp_exponential
        • damp_extrapolate_to_zero
        • damp_lorch
        • damp_low_q_region_erfc
        • damp_updated_lorch
        • fit_thermal_multiple_scattering_correction
      • LearningSegment
        • correlate_learning_segments
        • get_ncc_matrix
        • separate_learning_segments
      • VDFSegment
        • correlate_vdf_segments
        • get_ncc_matrix
        • get_virtual_electron_diffraction
      • StrainMap
        • plot
        • rotate_strain_basis
      • Correlation1D
        • get_symmetry_coefficient
      • LazyCorrelation1D
      • DisplacementGradientMap
        • get_strain_maps
        • polar_decomposition
      • VirtualDarkFieldImage
        • vectors
        • get_vdf_segments
      • InSituDiffraction2D
        • correct_real_space_drift
        • correct_real_space_drift_fast
        • get_drift_vectors
        • get_g2_2d_kresolved
        • get_time_series
        • roll_time_axis
      • LabeledDiffractionVectors2D
        • is_clustered
        • cluster_labeled_vectors
        • map_vectors
        • plot_clustered
        • to_markers
      • OrientationMap
        • num_rows
        • simulation
        • deepcopy
        • get_simulation_arrays
        • plot_over_signal
        • to_crystal_map
        • to_ipf_colormap
        • to_ipf_correlation_heatmap_markers
        • to_ipf_markers
        • to_markers
        • to_phase_index
        • to_phase_map
        • to_polar_markers
        • to_rotation
        • to_single_phase_orientations
        • to_single_phase_polar_markers
        • to_single_phase_vectors
        • to_vectors
    • utils
      • plotting
        • plot_template_over_pattern
      • ransac_ellipse_tools
        • is_ellipse_good
        • make_ellipse_data_points
        • ellipse_to_markers
        • get_ellipse_model_ransac
        • get_ellipse_model_ransac_single_frame
        • determine_ellipse
      • vectors
        • detector_to_fourier
        • calculate_norms
        • calculate_norms_ragged
        • filter_vectors_ragged
        • filter_vectors_edge_ragged
        • normalize_or_zero
        • get_rotation_matrix_between_vectors
        • get_npeaks
        • get_angle_cartesian_vec
        • get_angle_cartesian
        • filter_vectors_near_basis
        • vectors_to_polar
        • to_cart_three_angles
        • polar_to_cartesian
        • get_vectors_mesh
        • get_angles
        • get_filtered_combinations
        • convert_to_markers
        • points_to_polygon
        • points_to_poly_collection
        • column_mean
        • vectors2image
        • get_three_angles
      • diffraction
        • apply_transformation
        • center_of_mass_from_image
        • circular_mask
        • convert_affine_to_transform
        • ellipse_perimeter
        • fftconvolve
        • find_beam_center_blur
        • find_beam_center_interpolate
        • find_beam_offset_cross_correlation
        • find_center_of_mass
        • find_hot_pixels
        • gain_normalise
        • investigate_dog_background_removal_interactive
        • is_cupy_array
        • match_template
        • match_template_dilate
        • normalize_template_match
        • peaks_as_gvectors
        • phase_cross_correlation
        • reference_circle
        • regional_filter
        • remove_bad_pixels
        • remove_dead
        • Version
        • deprecated
        • interp1d
        • tqdm
      • calibration
        • find_diffraction_calibration
        • get_electron_wavelength
        • index_dataset_with_template_rotation
        • value2node
        • value2standard_units
        • Calibration
        • DictionaryTreeBrowser
        • UniformDataAxis
        • deprecated
      • find_diffraction_calibration
      • plot_template_over_pattern
      • determine_ellipse
  • Bibliography
  • Citing pyxem
  • Related projects
  • License
  • Where do I start?
  • Gallery of Examples
  • Standards

Standards#

Below is a gallery of examples showing different standards in pyxem

Coordinates in Pyxem

Coordinates in Pyxem

Flat Ewald’s Sphere Assumption

Flat Ewald's Sphere Assumption

previous

Determining Elliptic Distortion

next

Coordinates in Pyxem
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