Welcome to pyxem’s documentation!#
Pyxem is an open source project working to bring together tools for the analysis of data from pixelated electron detectors. Based on the HyperSpy project, pyxem has an active community of users and developers who are interested in many different areas including:
Orientation Mapping of Crystals
Strain Mapping
Virtual Dark Field Imaging
Differential Phase Contrast
Structural Characterization of Amorphous Materials
And much, much more!
Where do I start?#
For most cases starting with one of the linked Jupyter notebooks is the correct place to start. If you can either download the notebook and run locally or run the notebooks remotely using Binder.
If you are searching for documentation on some function you can use the API reference or search the documentation.
The following notebooks should provide workflows for analyzing your dataset.
User Guide and Workflows#
User guide
Help
- API reference
- detectors
- generators
AcceleratedIndexationGeneratorCalibrationGeneratorCalibrationGenerator.get_correction_matrix()CalibrationGenerator.get_diffraction_calibration()CalibrationGenerator.get_distortion_residuals()CalibrationGenerator.get_elliptical_distortion()CalibrationGenerator.get_navigation_calibration()CalibrationGenerator.get_rotation_calibration()CalibrationGenerator.plot_calibrated_data()CalibrationGenerator.plot_corrected_diffraction_pattern()CalibrationGenerator.to_ai()
IndexationGeneratorIntegrationGeneratorPDFGenerator1DProfileIndexationGeneratorReducedIntensityGenerator1DReducedIntensityGenerator1D.fit_atomic_scattering()ReducedIntensityGenerator1D.get_reduced_intensity()ReducedIntensityGenerator1D.mask_from_bkgd_pattern()ReducedIntensityGenerator1D.mask_reduced_intensity()ReducedIntensityGenerator1D.set_diffraction_calibration()ReducedIntensityGenerator1D.set_diffraction_offset()ReducedIntensityGenerator1D.set_s_cutoff()ReducedIntensityGenerator1D.subtract_bkgd_pattern()
SubpixelrefinementGeneratorTemplateIndexationGeneratorVarianceGeneratorVectorIndexationGeneratorVirtualDarkFieldGeneratorVirtualImageGeneratorget_DisplacementGradientMap()get_single_DisplacementGradientTensor()
- libraries
- signals
- CommonDiffraction
- Correlation2D
- DPCSignal1D
- DPCSignal2D
DPCSignal2DDPCSignal2D.correct_ramp()DPCSignal2D.flip_axis_90_degrees()DPCSignal2D.gaussian_blur()DPCSignal2D.get_bivariate_histogram()DPCSignal2D.get_color_image_with_indicator()DPCSignal2D.get_color_signal()DPCSignal2D.get_magnitude_signal()DPCSignal2D.get_phase_signal()DPCSignal2D.phase_retrieval()DPCSignal2D.rotate_beam_shifts()DPCSignal2D.rotate_data()DPCSignal2D.to_beamshift()
- DiffractionVariance1D
- DiffractionVariance2D
- Diffraction1D
- Diffraction2D
Diffraction2DDiffraction2D.add_ellipse_array_as_markers()Diffraction2D.add_peak_array_as_markers()Diffraction2D.aiDiffraction2D.angular_mask()Diffraction2D.angular_slice_radial_average()Diffraction2D.angular_slice_radial_integration()Diffraction2D.apply_affine_transformation()Diffraction2D.apply_gain_normalisation()Diffraction2D.center_direct_beam()Diffraction2D.center_of_mass()Diffraction2D.correct_bad_pixels()Diffraction2D.find_dead_pixels()Diffraction2D.find_hot_pixels()Diffraction2D.find_peaks_lazy()Diffraction2D.flip_diffraction_x()Diffraction2D.flip_diffraction_y()Diffraction2D.get_azimuthal_integral1d()Diffraction2D.get_azimuthal_integral2d()Diffraction2D.get_direct_beam_mask()Diffraction2D.get_direct_beam_position()Diffraction2D.get_medfilt1d()Diffraction2D.get_radial_integral()Diffraction2D.get_variance()Diffraction2D.intensity_peaks()Diffraction2D.make_probe_navigation()Diffraction2D.peak_position_refinement_com()Diffraction2D.plot()Diffraction2D.radial_average()Diffraction2D.radial_integration()Diffraction2D.rotate_diffraction()Diffraction2D.set_ai()Diffraction2D.shift_diffraction()Diffraction2D.sigma_clip()Diffraction2D.subtract_diffraction_background()Diffraction2D.template_match()Diffraction2D.template_match_disk()Diffraction2D.template_match_ring()Diffraction2D.template_match_with_binary_image()Diffraction2D.threshold_and_mask()
- ElectronDiffraction1D
- ElectronDiffraction2D
ElectronDiffraction2DElectronDiffraction2D.beam_energyElectronDiffraction2D.camera_lengthElectronDiffraction2D.diffraction_calibrationElectronDiffraction2D.scan_calibrationElectronDiffraction2D.set_ai()ElectronDiffraction2D.set_diffraction_calibration()ElectronDiffraction2D.set_experimental_parameters()ElectronDiffraction2D.set_scan_calibration()
- TemplateMatchingResults
- VectorMatchingResults
- PairDistributionFunction1D
- PolarDiffraction2D
- Power2D
- ReducedIntensity1D
- LearningSegment
- VDFSegment
- StrainMap
- DisplacementGradientMap
- VirtualDarkFieldImage
- utils
- Bibliography
- Contributing
- Open datasets and workflows
- Citing pyxem
- Related projects
- Changelog