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
AcceleratedIndexationGenerator
CalibrationGenerator
CalibrationGenerator.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()
IndexationGenerator
IntegrationGenerator
PDFGenerator1D
ProfileIndexationGenerator
ReducedIntensityGenerator1D
ReducedIntensityGenerator1D.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()
SubpixelrefinementGenerator
TemplateIndexationGenerator
VarianceGenerator
VectorIndexationGenerator
VirtualDarkFieldGenerator
VirtualImageGenerator
get_DisplacementGradientMap()
get_single_DisplacementGradientTensor()
- libraries
- signals
- CommonDiffraction
- Correlation2D
- DPCSignal1D
- DPCSignal2D
DPCSignal2D
DPCSignal2D.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
Diffraction2D
Diffraction2D.add_ellipse_array_as_markers()
Diffraction2D.add_peak_array_as_markers()
Diffraction2D.ai
Diffraction2D.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
ElectronDiffraction2D
ElectronDiffraction2D.beam_energy
ElectronDiffraction2D.camera_length
ElectronDiffraction2D.diffraction_calibration
ElectronDiffraction2D.scan_calibration
ElectronDiffraction2D.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