hyperspy package

Subpackages

• hyperspy._components package
  • Submodules
    • hyperspy._components.arctan module
      • Arctan
    • hyperspy._components.bleasdale module
      • Bleasdale
    • hyperspy._components.doniach module
      • Doniach
    • hyperspy._components.eels_arctan module
      • Arctan
      • EELSArctan
    • hyperspy._components.eels_cl_edge module
      • EELSCLEdge
    • hyperspy._components.eels_double_power_law module
      • DoublePowerLaw
    • hyperspy._components.eels_vignetting module
      • Vignetting
    • hyperspy._components.error_function module
      • Erf
    • hyperspy._components.exponential module
      • Exponential
    • hyperspy._components.expression module
      • Expression
      • _check_parameter_linearity()
    • hyperspy._components.gaussian module
      • Gaussian
    • hyperspy._components.gaussian2d module
      • Gaussian2D
    • hyperspy._components.gaussianhf module
      • GaussianHF
    • hyperspy._components.heaviside module
      • HeavisideStep
    • hyperspy._components.logistic module
      • Logistic
    • hyperspy._components.lorentzian module
      • Lorentzian
    • hyperspy._components.offset module
      • Offset
    • hyperspy._components.pes_core_line_shape module
      • PESCoreLineShape
    • hyperspy._components.pes_see module
      • SEE
    • hyperspy._components.pes_voigt module
      • PESVoigt
      • Voigt
      • voigt()
    • hyperspy._components.polynomial module
      • Polynomial
      • convert_to_polynomial()
    • hyperspy._components.polynomial_deprecated module
      • Polynomial
    • hyperspy._components.power_law module
      • PowerLaw
    • hyperspy._components.rc module
      • RC
    • hyperspy._components.scalable_fixed_pattern module
      • ScalableFixedPattern
    • hyperspy._components.skew_normal module
      • SkewNormal
    • hyperspy._components.split_voigt module
      • SplitVoigt
    • hyperspy._components.voigt module
      • Voigt
    • hyperspy._components.volume_plasmon_drude module
      • VolumePlasmonDrude
  • Module contents
• hyperspy._signals package
  • Submodules
    • hyperspy._signals.common_signal1d module
      • CommonSignal1D
    • hyperspy._signals.common_signal2d module
      • CommonSignal2D
    • hyperspy._signals.complex_signal module
      • ComplexSignal
      • LazyComplexSignal
    • hyperspy._signals.complex_signal1d module
      • ComplexSignal1D
      • LazyComplexSignal1D
    • hyperspy._signals.complex_signal2d module
      • ComplexSignal2D
      • LazyComplexSignal2D
    • hyperspy._signals.dielectric_function module
      • DielectricFunction
      • LazyDielectricFunction
    • hyperspy._signals.eds module
      • EDSSpectrum
      • LazyEDSSpectrum
    • hyperspy._signals.eds_sem module
      • EDSSEMParametersUI
      • EDSSEMSpectrum
      • LazyEDSSEMSpectrum
    • hyperspy._signals.eds_tem module
      • EDSTEMParametersUI
      • EDSTEMSpectrum
      • LazyEDSTEMSpectrum
    • hyperspy._signals.eels module
      • EELSSpectrum
      • EELSTEMParametersUI
      • LazyEELSSpectrum
    • hyperspy._signals.hologram_image module
      • HologramImage
      • LazyHologramImage
      • _estimate_fringe_contrast_statistical()
    • hyperspy._signals.lazy module
      • LazySignal
      • _get_navigation_dimension_chunk_slice()
      • _reshuffle_mixed_blocks()
      • to_array()
    • hyperspy._signals.signal1d module
      • LazySignal1D
      • Signal1D
      • _shift1D()
      • find_peaks_ohaver()
    • hyperspy._signals.signal2d module
      • LazySignal2D
      • Signal2D
      • estimate_image_shift()
      • fft_correlation()
      • hanning2d()
      • triu_indices_minus_diag()
  • Module contents
• hyperspy.datasets package
  • Submodules
    • hyperspy.datasets.artificial_data module
      • get_atomic_resolution_tem_signal2d()
      • get_core_loss_eels_line_scan_signal()
      • get_core_loss_eels_model()
      • get_core_loss_eels_signal()
      • get_low_loss_eels_line_scan_signal()
      • get_low_loss_eels_signal()
      • get_luminescence_signal()
    • hyperspy.datasets.example_signals module
  • Module contents
• hyperspy.docstrings package
  • Submodules
    • hyperspy.docstrings.model module
    • hyperspy.docstrings.parameters module
    • hyperspy.docstrings.plot module
    • hyperspy.docstrings.signal module
    • hyperspy.docstrings.signal1d module
    • hyperspy.docstrings.utils module
  • Module contents
• hyperspy.drawing package
  • Subpackages
    • hyperspy.drawing._markers package
      • Submodules
      • Module contents
    • hyperspy.drawing._widgets package
      • Submodules
      • Module contents
  • Submodules
    • hyperspy.drawing.figure module
    • hyperspy.drawing.image module
    • hyperspy.drawing.marker module
      • MarkerBase
    • hyperspy.drawing.mpl_he module
      • MPL_HyperExplorer
    • hyperspy.drawing.mpl_hie module
    • hyperspy.drawing.mpl_hse module
      • MPL_HyperSignal1D_Explorer
    • hyperspy.drawing.signal module
    • hyperspy.drawing.signal1d module
      • Signal1DFigure
      • Signal1DLine
    • hyperspy.drawing.tiles module
    • hyperspy.drawing.utils module
      • _parse_array()
      • animate_legend()
      • centre_colormap_values()
      • contrast_stretching()
      • create_figure()
      • make_cmap()
      • on_figure_window_close()
      • plot_RGB_map()
      • plot_histograms()
      • plot_images()
      • plot_signals()
      • plot_spectra()
      • set_xaxis_lims()
      • subplot_parameters()
    • hyperspy.drawing.widget module
      • DraggableWidgetBase
      • ResizableDraggableWidgetBase
      • ResizersMixin
      • Widget1DBase
      • Widget2DBase
      • WidgetBase
    • hyperspy.drawing.widgets module
  • Module contents
• hyperspy.io_plugins package
  • Submodules
    • hyperspy.io_plugins._hierarchical module
      • HierarchicalReader
      • HierarchicalWriter
      • get_signal_chunks()
    • hyperspy.io_plugins.blockfile module
      • file_writer()
      • get_default_header()
    • hyperspy.io_plugins.bruker module
      • BCF_reader
      • HyperHeader
      • SFSTreeItem
      • SFS_reader
      • bcf_hyperspectra()
      • bcf_images()
      • bcf_reader()
      • guess_mode()
      • interpret()
      • parse_line()
      • py_parse_hypermap()
    • hyperspy.io_plugins.dens module
    • hyperspy.io_plugins.digital_micrograph module
      • DigitalMicrographReader
      • file_reader()
    • hyperspy.io_plugins.edax module
      • __get_ipr_header()
      • __get_spc_header()
      • _add_spc_metadata()
      • file_reader()
      • get_ipr_dtype_list()
      • get_spc_dtype_list()
      • get_spd_dtype_list()
      • spc_reader()
      • spd_reader()
    • hyperspy.io_plugins.emd module
      • EMD
      • EMD_NCEM
      • FeiEMDReader
      • FeiSpectrumStream
      • file_reader()
      • file_writer()
      • is_EMD_NCEM()
      • is_EMD_Velox()
      • read_emd_version()
    • hyperspy.io_plugins.empad module
    • hyperspy.io_plugins.fei module
      • get_calibration_from_position()
      • readLELong()
      • readLELongLong()
      • readLEShort()
      • ser_reader()
    • hyperspy.io_plugins.hspy module
      • HyperspyReader
      • HyperspyWriter
      • file_reader()
      • file_writer()
    • hyperspy.io_plugins.image module
      • file_reader()
      • file_writer()
    • hyperspy.io_plugins.impulse module
    • hyperspy.io_plugins.jeol module
      • _read_pts()
      • _readcube()
      • _readframe_dense()
      • _readframe_lazy()
      • file_reader()
    • hyperspy.io_plugins.mrc module
    • hyperspy.io_plugins.mrcz module
    • hyperspy.io_plugins.msa module
      • parse_msa_string()
    • hyperspy.io_plugins.netcdf module
    • hyperspy.io_plugins.nexus module
      • _byte_to_string()
      • _extract_hdf_dataset()
      • _find_data()
      • _find_search_keys_in_dict()
      • _fix_exclusion_keys()
      • _get_nav_list()
      • _getlink()
      • _is_int()
      • _is_linear_axis()
      • _is_numeric_data()
      • _load_metadata()
      • _nexus_dataset_to_signal()
      • _parse_from_file()
      • _parse_to_file()
      • _text_split()
      • _write_nexus_attr()
      • _write_nexus_groups()
      • _write_signal()
      • file_reader()
      • file_writer()
      • list_datasets_in_file()
      • read_metadata_from_file()
    • hyperspy.io_plugins.phenom module
    • hyperspy.io_plugins.protochips module
    • hyperspy.io_plugins.ripple module
      • file_reader()
      • parse_ripple()
      • read_raw()
      • write_raw()
    • hyperspy.io_plugins.semper_unf module
      • SemperFormat
      • pack_to_intbytes()
      • unpack_from_intbytes()
    • hyperspy.io_plugins.sur module
      • DigitalSurfHandler
      • file_reader()
    • hyperspy.io_plugins.tiff module
      • _axes_defaults()
      • _build_axes_dictionaries()
      • _get_hamamatsu_streak_description()
      • _get_scale_unit()
      • _get_tags_dict()
      • _imagej_description()
      • _is_streak_hamamatsu()
      • _order_axes_by_name()
      • file_reader()
      • file_writer()
    • hyperspy.io_plugins.tvips module
      • _find_auto_scan_start_stop()
      • _guess_image_mode()
      • _is_valid_first_tvips_file()
      • file_reader()
      • file_writer()
    • hyperspy.io_plugins.usid_hdf5 module
    • hyperspy.io_plugins.zspy module
      • ZspyReader
      • ZspyWriter
      • file_reader()
      • file_writer()
  • Module contents
• hyperspy.learn package
  • Submodules
    • hyperspy.learn.mlpca module
      • mlpca()
    • hyperspy.learn.mva module
      • LearningResults
      • MVA
      • _get_derivative()
      • _normalize_components()
    • hyperspy.learn.ornmf module
      • ORNMF
      • _mrdivide()
      • _thresh()
      • ornmf()
    • hyperspy.learn.orthomax module
      • orthomax()
    • hyperspy.learn.rpca module
      • ORPCA
      • _soft_thresh()
      • orpca()
      • rpca_godec()
    • hyperspy.learn.svd_pca module
      • svd_flip_signs()
      • svd_pca()
      • svd_solve()
    • hyperspy.learn.whitening module
      • whiten_data()
  • Module contents
• hyperspy.misc package
  • Subpackages
    • hyperspy.misc.eds package
      • Submodules
      • Module contents
    • hyperspy.misc.eels package
      • Submodules
      • Module contents
    • hyperspy.misc.holography package
      • Submodules
      • Module contents
    • hyperspy.misc.io package
      • Submodules
      • Module contents
    • hyperspy.misc.machine_learning package
      • Submodules
      • Module contents
  • Submodules
    • hyperspy.misc.array_tools module
      • _linear_bin()
      • _numba_histogram()
      • _requires_linear_rebin()
      • are_aligned()
      • dict2sarray()
      • get_array_memory_size_in_GiB()
      • get_signal_chunk_slice()
      • homogenize_ndim()
      • numba_closest_index_ceil()
      • numba_closest_index_floor()
      • numba_closest_index_round()
      • numba_histogram()
      • rebin()
      • round_half_away_from_zero()
      • round_half_towards_zero()
      • sarray2dict()
    • hyperspy.misc.axis_tools module
      • check_axes_calibration()
    • hyperspy.misc.config_dir module
    • hyperspy.misc.date_time_tools module
      • ISO_format_to_serial_date()
      • datetime_to_serial_date()
      • get_date_time_from_metadata()
      • serial_date_to_ISO_format()
      • serial_date_to_datetime()
      • update_date_time_in_metadata()
    • hyperspy.misc.elements module
    • hyperspy.misc.example_signals_loading module
      • _resolve_dir()
      • load_1D_EDS_SEM_spectrum()
      • load_1D_EDS_TEM_spectrum()
      • load_object_hologram()
      • load_reference_hologram()
    • hyperspy.misc.export_dictionary module
      • export_to_dictionary()
      • load_from_dictionary()
      • reconstruct_object()
    • hyperspy.misc.hist_tools module
      • _freedman_bw_dask()
      • _scott_bw_dask()
      • histogram()
      • histogram_dask()
    • hyperspy.misc.ipython_tools module
      • get_ipython()
    • hyperspy.misc.label_position module
      • SpectrumLabelPosition
    • hyperspy.misc.lowess_smooth module
      • _lowess()
      • lowess()
    • hyperspy.misc.material module
      • _atomic_to_weight()
      • _density_of_mixture()
      • _mass_absorption_mixture()
      • _weight_to_atomic()
      • atomic_to_weight()
      • density_of_mixture()
      • mass_absorption_coefficient()
      • mass_absorption_mixture()
      • weight_to_atomic()
    • hyperspy.misc.math_tools module
      • anyfloatin()
      • check_random_state()
      • get_linear_interpolation()
      • hann_window_nth_order()
      • isfloat()
      • optimal_fft_size()
      • order_of_magnitude()
      • outer_nd()
    • hyperspy.misc.model_tools module
      • _calculate_covariance()
      • _is_iter()
      • _iter_join()
      • _non_iter()
      • current_component_values
      • current_model_values
    • hyperspy.misc.physics_tools module
      • bragg_scattering_angle()
      • effective_Z()
    • hyperspy.misc.rgb_tools module
      • rgbx2regular_array()
    • hyperspy.misc.signal_tools module
      • _check_and_get_longest_axis()
      • broadcast_signals()
    • hyperspy.misc.slicing module
      • _slice_target()
      • copy_slice_from_whitelist()
    • hyperspy.misc.test_utils module
      • assert_deep_almost_equal()
    • hyperspy.misc.tv_denoise module
      • _tv_denoise_1d()
      • _tv_denoise_2d()
      • _tv_denoise_3d()
      • tv_denoise()
    • hyperspy.misc.utils module
      • DictionaryTreeBrowser
      • _get_block_pattern()
      • add_key_value()
      • attrsetter()
      • check_long_string()
      • closest_power_of_two()
      • find_subclasses()
      • fsdict()
      • get_array_module()
      • get_numpy_kwargs()
      • get_object_package_info()
      • guess_output_signal_size()
      • is_binned()
      • is_cupy_array()
      • is_hyperspy_signal()
      • multiply()
      • nested_dictionary_merge()
      • ordinal()
      • parse_quantity()
      • print_html()
      • process_function_blockwise()
      • replace_html_symbols()
      • rollelem()
      • slugify()
      • stack()
      • str2num()
      • swapelem()
      • to_numpy()
      • transpose()
      • underline()
  • Module contents
• hyperspy.models package
  • Submodules
    • hyperspy.models.edsmodel module
      • EDSModel
      • _get_sigma()
    • hyperspy.models.edssemmodel module
      • EDSSEMModel
    • hyperspy.models.edstemmodel module
      • EDSTEMModel
    • hyperspy.models.eelsmodel module
      • EELSModel
    • hyperspy.models.model1d module
      • ComponentFit
      • Model1D
    • hyperspy.models.model2d module
      • Model2D
  • Module contents
• hyperspy.samfire_utils package
  • Subpackages
    • hyperspy.samfire_utils.goodness_of_fit_tests package
      • Submodules
      • Module contents
    • hyperspy.samfire_utils.segmenters package
      • Submodules
      • Module contents
    • hyperspy.samfire_utils.weights package
      • Submodules
      • Module contents
  • Submodules
    • hyperspy.samfire_utils.fit_tests module
    • hyperspy.samfire_utils.global_strategies module
      • HistogramStrategy
    • hyperspy.samfire_utils.local_strategies module
      • ReducedChiSquaredStrategy
      • exp_decay()
    • hyperspy.samfire_utils.samfire_kernel module
    • hyperspy.samfire_utils.samfire_pool module
      • SamfirePool
    • hyperspy.samfire_utils.samfire_worker module
    • hyperspy.samfire_utils.strategy module
      • GlobalStrategy
      • LocalStrategy
      • SamfireStrategy
      • make_sure_ind()
      • nearest_indices()
  • Module contents
• hyperspy.utils package
  • Submodules
    • hyperspy.utils.eds module
    • hyperspy.utils.markers module
    • hyperspy.utils.material module
    • hyperspy.utils.model module
    • hyperspy.utils.model_selection module
      • AIC()
      • BIC()
    • hyperspy.utils.parallel_pool module
      • ParallelPool
    • hyperspy.utils.peakfinders2D module
      • _fast_mean()
      • _fast_std()
      • clean_peaks()
      • find_local_max()
      • find_peaks_dog()
      • find_peaks_log()
      • find_peaks_max()
      • find_peaks_minmax()
      • find_peaks_stat()
      • find_peaks_xc()
      • find_peaks_zaefferer()
    • hyperspy.utils.plot module
    • hyperspy.utils.roi module
    • hyperspy.utils.samfire module
  • Module contents
    • print_known_signal_types()

Submodules

• hyperspy.Release module
• hyperspy._lazy_signals module
• hyperspy.api module
• hyperspy.api_nogui module
• hyperspy.axes module
  • AxesManager
    • AxesManager._get_data_slice()
    • AxesManager._get_iterpath_size()
    • AxesManager._remove_one_axis()
    • AxesManager._set_axis_attribute_values()
    • AxesManager._sort_axes()
    • AxesManager.axes_are_aligned_with_data
    • AxesManager.convert_units()
    • AxesManager.coordinates
    • AxesManager.create_axes()
    • AxesManager.gui()
    • AxesManager.gui_navigation_sliders()
    • AxesManager.indices
    • AxesManager.iterpath
    • AxesManager.key_navigator()
    • AxesManager.navigation_axes
    • AxesManager.navigation_dimension
    • AxesManager.navigation_shape
    • AxesManager.navigation_size
    • AxesManager.remove()
    • AxesManager.set_axis()
    • AxesManager.set_signal_dimension()
    • AxesManager.value
    • AxesManager.signal_axes
    • AxesManager.signal_dimension
    • AxesManager.signal_shape
    • AxesManager.signal_size
    • AxesManager.switch_iterpath()
    • AxesManager.update_axes_attributes_from()
  • BaseDataAxis
    • BaseDataAxis._get_array_slices()
    • BaseDataAxis._is_increasing_order
    • BaseDataAxis._parse_value()
    • BaseDataAxis._parse_value_from_string()
    • BaseDataAxis.convert_to_uniform_axis()
    • BaseDataAxis.gui()
    • BaseDataAxis.update_from()
    • BaseDataAxis.value2index()
    • BaseDataAxis.value_range_to_indices()
  • DataAxis
    • DataAxis._slice_me()
    • DataAxis.crop()
    • DataAxis.update_axis()
    • DataAxis.update_from()
  • FunctionalDataAxis
    • FunctionalDataAxis._slice_me()
    • FunctionalDataAxis.convert_to_non_uniform_axis()
    • FunctionalDataAxis.crop()
    • FunctionalDataAxis.update_from()
  • GeneratorLen
  • UniformDataAxis
    • UniformDataAxis._slice_me()
    • UniformDataAxis.crop()
    • UniformDataAxis.update_from()
    • UniformDataAxis.value2index()
  • _flyback_iter()
  • _serpentine_iter()
  • create_axis()
  • generate_uniform_axis()
  • ndindex_nat
• hyperspy.component module
  • Component
    • Component._compute_constant_term()
    • Component._constant_term
    • Component._load_dictionary()
    • Component.active_is_multidimensional
    • Component.as_dictionary()
    • Component.export()
    • Component.fetch_values_from_array()
    • Component.gui()
    • Component.init_parameters()
    • Component.plot()
    • Component.print_current_values()
    • Component.set_parameters_free()
    • Component.set_parameters_not_free()
  • NoneFloat
    • NoneFloat.default_value
    • NoneFloat.validate()
  • Parameter
    • Parameter.value
    • Parameter.twin
    • Parameter.twin_function_expr
    • Parameter.twin_inverse_function_expr
    • Parameter.twin_function
    • Parameter.twin_inverse_function
    • Parameter.ext_force_positive
    • Parameter.ext_bounded
    • Parameter._create_array()
    • Parameter._load_dictionary()
    • Parameter.as_dictionary()
    • Parameter.as_signal()
    • Parameter.assign_current_value_to_all()
    • Parameter.default_traits_view()
    • Parameter.export()
    • Parameter.fetch()
    • Parameter.gui()
    • Parameter.plot()
    • Parameter.store_current_value_in_array()
  • _get_scaling_factor()
  • convolve_component_values()
• hyperspy.components1d module
  • For more details see each component docstring.
• hyperspy.components2d module
  • For more details see each component docstring.
• hyperspy.conftest module
• hyperspy.decorators module
  • simple_decorator()
• hyperspy.defaults_parser module
  • EDSConfig
  • EELSConfig
  • GUIs
  • GeneralConfig
  • PlotConfig
  • Preferences
    • Preferences.gui()
• hyperspy.events module
  • EventSuppressor
    • EventSuppressor.add()
    • EventSuppressor.suppress()
  • Events
    • Events._update_doc()
    • Events.suppress()
• hyperspy.exceptions module
  • ByteOrderError
  • DM3DataTypeError
  • DM3FileVersionError
  • DM3TagError
  • DM3TagIDError
  • DM3TagTypeError
  • DataDimensionError
  • ImageIDError
  • ImageModeError
  • LazyCupyConversion
  • MissingParametersError
  • MountainsMapFileError
  • NavigationDimensionError
  • NavigationSizeError
  • NoInteractiveError
  • ShapeError
  • SignalDimensionError
  • SignalSizeError
  • VisibleDeprecationWarning
  • WrongObjectError
• hyperspy.extensions module
• hyperspy.interactive module
  • Interactive
  • interactive()
• hyperspy.io module
  • _escape_square_brackets()
  • _infer_file_reader()
  • _parse_path()
  • assign_signal_subclass()
  • dict2signal()
  • load()
  • load_single_file()
  • load_with_reader()
  • save()
• hyperspy.logger module
  • set_log_level()
• hyperspy.model module
  • BaseModel
    • BaseModel.signal
    • BaseModel.chisq
    • BaseModel.dof
    • BaseModel.components
    • BaseModel.plot()
    • BaseModel.set_current_values_to()
    • BaseModel.fit_component()
    • BaseModel._bounds_as_tuple()
    • BaseModel._disable_ext_bounding()
    • BaseModel._enable_ext_bounding()
    • BaseModel._fetch_values_from_p0()
    • BaseModel._free_parameters
    • BaseModel._get_variance()
    • BaseModel._linear_fit()
    • BaseModel._load_dictionary()
    • BaseModel._on_navigating()
    • BaseModel._set_boundaries()
    • BaseModel._set_mpfit_parameters_info()
    • BaseModel._set_p0()
    • BaseModel.active_components
    • BaseModel.append()
    • BaseModel.as_dictionary()
    • BaseModel.as_signal()
    • BaseModel.assign_current_values_to_all()
    • BaseModel.create_samfire()
    • BaseModel.ensure_parameters_in_bounds()
    • BaseModel.export_results()
    • BaseModel.extend()
    • BaseModel.fetch_stored_values()
    • BaseModel.fetch_values_from_array()
    • BaseModel.fit()
    • BaseModel.gui()
    • BaseModel.insert()
    • BaseModel.load_parameters_from_file()
    • BaseModel.multifit()
    • BaseModel.plot_results()
    • BaseModel.print_current_values()
    • BaseModel.red_chisq
    • BaseModel.remove()
    • BaseModel.save()
    • BaseModel.save_parameters2file()
    • BaseModel.set_component_active_value()
    • BaseModel.set_parameters_free()
    • BaseModel.set_parameters_not_free()
    • BaseModel.set_parameters_value()
    • BaseModel.store()
    • BaseModel.store_current_values()
    • BaseModel.suspend_update()
    • BaseModel.update_plot()
  • ModelComponents
  • _check_deprecated_optimizer()
  • _twinned_parameter()
• hyperspy.roi module
  • BaseInteractiveROI
    • BaseInteractiveROI._apply_roi2widget()
    • BaseInteractiveROI._get_widget_type()
    • BaseInteractiveROI._on_widget_change()
    • BaseInteractiveROI._set_default_values()
    • BaseInteractiveROI._set_from_widget()
    • BaseInteractiveROI._update_widgets()
    • BaseInteractiveROI.add_widget()
    • BaseInteractiveROI.interactive()
    • BaseInteractiveROI.remove_widget()
    • BaseInteractiveROI.update()
  • BasePointROI
  • BaseROI
    • BaseROI._get_ranges()
    • BaseROI._make_slices()
    • BaseROI._parse_axes()
    • BaseROI.is_valid()
    • BaseROI.update()
  • CircleROI
    • CircleROI._apply_roi2widget()
    • CircleROI._get_widget_type()
    • CircleROI._set_default_values()
    • CircleROI._set_from_widget()
    • CircleROI.gui()
    • CircleROI.is_valid()
  • Line2DROI
    • Line2DROI._apply_roi2widget()
    • Line2DROI._get_widget_type()
    • Line2DROI._line_profile_coordinates()
    • Line2DROI._set_default_values()
    • Line2DROI._set_from_widget()
    • Line2DROI.angle()
    • Line2DROI.gui()
    • Line2DROI.profile_line()
  • Point1DROI
    • Point1DROI._apply_roi2widget()
    • Point1DROI._get_ranges()
    • Point1DROI._get_widget_type()
    • Point1DROI._set_default_values()
    • Point1DROI._set_from_widget()
    • Point1DROI.gui()
  • Point2DROI
    • Point2DROI._apply_roi2widget()
    • Point2DROI._get_ranges()
    • Point2DROI._get_widget_type()
    • Point2DROI._set_default_values()
    • Point2DROI._set_from_widget()
    • Point2DROI.gui()
  • RectangularROI
    • RectangularROI._apply_roi2widget()
    • RectangularROI._get_ranges()
    • RectangularROI._get_widget_type()
    • RectangularROI._set_default_values()
    • RectangularROI._set_from_widget()
    • RectangularROI.gui()
    • RectangularROI.height
    • RectangularROI.is_valid()
    • RectangularROI.width
    • RectangularROI.x
    • RectangularROI.y
  • SpanROI
    • SpanROI._apply_roi2widget()
    • SpanROI._get_ranges()
    • SpanROI._get_widget_type()
    • SpanROI._set_default_values()
    • SpanROI._set_from_widget()
    • SpanROI.gui()
    • SpanROI.is_valid()
  • _get_central_half_limits_of_axis()
  • _get_mpl_ax()
• hyperspy.samfire module
  • Samfire
    • Samfire.model
    • Samfire.optional_components
    • Samfire.workers
    • Samfire.pool
    • Samfire.strategies
    • Samfire.metadata
    • Samfire.active_strategy
    • Samfire.update_every
    • Samfire.plot_every
    • Samfire.save_every
    • Samfire.random_state
    • Samfire._setup()
    • Samfire.append()
    • Samfire.backup()
    • Samfire.change_strategy()
    • Samfire.extend()
    • Samfire.generate_values()
    • Samfire.log()
    • Samfire.pixels_done
    • Samfire.pixels_left
    • Samfire.plot()
    • Samfire.refresh_database()
    • Samfire.remove()
    • Samfire.start()
    • Samfire.stop()
    • Samfire.update()
  • StrategyList
    • StrategyList.append()
    • StrategyList.extend()
    • StrategyList.remove()
• hyperspy.signal module
  • BaseSetMetadataItems
  • BaseSignal
    • BaseSignal.T
    • BaseSignal._check_navigation_mask()
    • BaseSignal._check_signal_mask()
    • BaseSignal._cycle_signal()
    • BaseSignal._data_aligned_with_axes
    • BaseSignal._deepcopy_with_new_data()
    • BaseSignal._get_navigation_signal()
    • BaseSignal._get_signal_signal()
    • BaseSignal._get_undefined_axes_list()
    • BaseSignal._iterate_signal()
    • BaseSignal._load_dictionary()
    • BaseSignal._map_all()
    • BaseSignal._to_dictionary()
    • BaseSignal._unfold()
    • BaseSignal.add_gaussian_noise()
    • BaseSignal.add_marker()
    • BaseSignal.add_poissonian_noise()
    • BaseSignal.apply_apodization()
    • BaseSignal.as_lazy()
    • BaseSignal.as_signal1D()
    • BaseSignal.as_signal2D()
    • BaseSignal.change_dtype()
    • BaseSignal.copy()
    • BaseSignal.crop()
    • BaseSignal.data
    • BaseSignal.deepcopy()
    • BaseSignal.derivative()
    • BaseSignal.diff()
    • BaseSignal.estimate_poissonian_noise_variance()
    • BaseSignal.fft()
    • BaseSignal.fold()
    • BaseSignal.get_current_signal()
    • BaseSignal.get_dimensions_from_data()
    • BaseSignal.get_histogram()
    • BaseSignal.get_noise_variance()
    • BaseSignal.ifft()
    • BaseSignal.indexmax()
    • BaseSignal.indexmin()
    • BaseSignal.integrate1D()
    • BaseSignal.integrate_simpson()
    • BaseSignal.is_rgb
    • BaseSignal.is_rgba
    • BaseSignal.is_rgbx
    • BaseSignal.map()
    • BaseSignal.max()
    • BaseSignal.mean()
    • BaseSignal.metadata
    • BaseSignal.min()
    • BaseSignal.nanmax()
    • BaseSignal.nanmean()
    • BaseSignal.nanmin()
    • BaseSignal.nanstd()
    • BaseSignal.nansum()
    • BaseSignal.nanvar()
    • BaseSignal.original_metadata
    • BaseSignal.plot()
    • BaseSignal.print_summary_statistics()
    • BaseSignal.rebin()
    • BaseSignal.rollaxis()
    • BaseSignal.save()
    • BaseSignal.set_noise_variance()
    • BaseSignal.set_signal_origin()
    • BaseSignal.set_signal_type()
    • BaseSignal.split()
    • BaseSignal.squeeze()
    • BaseSignal.std()
    • BaseSignal.sum()
    • BaseSignal.swap_axes()
    • BaseSignal.to_device()
    • BaseSignal.to_host()
    • BaseSignal.transpose()
    • BaseSignal.unfold()
    • BaseSignal.unfold_navigation_space()
    • BaseSignal.unfold_signal_space()
    • BaseSignal.unfolded()
    • BaseSignal.update_plot()
    • BaseSignal.valuemax()
    • BaseSignal.valuemin()
    • BaseSignal.var()
  • ModelManager
    • ModelManager.pop()
    • ModelManager.remove()
    • ModelManager.restore()
    • ModelManager.store()
• hyperspy.signal_tools module
  • BackgroundRemoval
    • BackgroundRemoval.gui()
  • ButterworthFilter
    • ButterworthFilter.gui()
  • EdgesRange
    • EdgesRange.gui()
  • ImageContrastEditor
    • ImageContrastEditor.gui()
    • ImageContrastEditor.plot_histogram()
  • IntegrateArea
    • IntegrateArea.gui()
  • LineInSignal1D
    • LineInSignal1D.position
    • LineInSignal1D.on
    • LineInSignal1D.color
  • LineInSignal2D
  • Load
  • PeaksFinder2D
    • PeaksFinder2D.gui()
  • Signal1DCalibration
    • Signal1DCalibration.gui()
  • Signal1DRangeSelector
  • Signal2DCalibration
    • Signal2DCalibration.gui()
  • SimpleMessage
    • SimpleMessage.gui()
  • Smoothing
  • SmoothingLowess
    • SmoothingLowess.gui()
  • SmoothingSavitzkyGolay
    • SmoothingSavitzkyGolay.gui()
  • SmoothingTV
    • SmoothingTV.gui()
  • SpanSelectorInSignal1D
  • SpikesRemovalInteractive
    • SpikesRemovalInteractive.gui()
  • _get_background_estimator()
• hyperspy.signals module
• hyperspy.ui_registry module

Module contents

HyperSpy: a multi-dimensional data analysis package for Python

Documentation is available in the docstrings and online at https://hyperspy.org/hyperspy-doc/current/index.html.

All public packages, functions and classes are in api. All other packages and modules are for internal consumption and should not be needed for data analysis.

When starting HyperSpy using the hyperspy script (e.g. by executing hyperspy in a console, using the context menu entries or using the links in the Start Menu, the api package is imported in the user namespace as hs, i.e. by executing the following:

>>> import hyperspy.api as hs

(Note that code snippets are indicated by three greater-than signs)

We recommend to import the HyperSpy API as above also when doing it manually. The docstring examples assume that hyperspy.api has been imported as hs, numpy as np and matplotlib.pyplot as plt.

More details in the api docstring.