.. currentmodule:: arpes This page documents the PyARPES API by generation from signatures and docstrings. You can use this and the source code to supplement the remainder of the PyARPES documentation. Please note that this is not a complete API documentation page. Less used and internal APIs are not documented here. .. contents:: Data-loading functions ====================== .. autosummary:: :toctree: generated/ io.load_data io.load_example_data io.example_data Xarray_extensions ================= Establishes the PyARPES data model by extending the `xarray` types. This is another core part of PyARPES. It provides a lot of extensions to what comes out of the box in xarray. Some of these are useful generics, generally on the .T extension, others collect and manipulate metadata, interface with plotting routines, provide functional programming utilities, etc. If `f` is an ARPES spectrum, then `f.S` should provide a nice representation of your data in a Jupyter cell. This is a complement to the text based approach that merely printing `f` offers. Note, as of PyARPES v3.x.y, the xarray version has been bumped and this representation is no longer necessary as one is provided upstream. The main accessors are .S, .G, and .F. The `.S` accessor: The `.S` accessor contains functionality related to spectroscopy. Utilities which only make sense in this context should be placed here, while more generic tools should be placed elsewhere. The `.G.` accessor: This a general purpose collection of tools which exists to provide conveniences over what already exists in the xarray data model. As an example, there are various tools for simultaneous iteration of data and coordinates here, as well as for vectorized application of functions to data or coordinates. The `.F` accessor: This is an accessor which contains tools related to interpreting curve fitting results. In particular there are utilities for vectorized extraction of parameters, for plotting several curve fits, or for selecting "worst" or "best" fits according to some measure. The .S accessor ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESAngleProperty :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESPhysicalProperty :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESInfoProperty :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESProvenanceProperty :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESOffsetProperty :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESPropertyBase :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.property.ARPESProperty :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.base.ARPESDataArrayAccessorBase :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.spectroscopy.ARPESDataArrayAccessor :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.spectroscopy.ARPESDatasetAccessor :members: :show-inheritance: The .G accessor ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Available as methods via ``.G`` accessor. .. autoclass:: arpes.xarray_extensions.accessor.base.GenericAccessorBase :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.general.GenericDatasetAccessor :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.general.GenericDataArrayAccessor :members: :show-inheritance: The .F accessor ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Available as methods via ``.F`` accessor. .. autoclass:: arpes.xarray_extensions.accessor.fit.ARPESDatasetFitToolAccessor :members: :show-inheritance: .. autoclass:: arpes.xarray_extensions.accessor.fit.ARPESFitToolsAccessor :members: :show-inheritance: Momentum Conversion =================== Small-Angle Approximated and Volumetric Related ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ utilities.conversion.api.convert_to_kspace analysis.forward_conversion.convert_coordinate_forward analysis.forward_conversion.convert_through_angular_point analysis.forward_conversion.convert_through_angular_pair Exact Forward Transforms ~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.forward_conversion.convert_coordinates_to_kspace_forward Utilities ~~~~~~~~~ .. autosummary:: :toctree: generated/ utilities.conversion.fast_interp.Interpolator utilities.conversion.bounds_calculations.full_angles_to_k Conversion Implementations ~~~~~~~~~~~~~~~~~~~~~~~~~~ You do not need to call these directly, but they are good references for anyone looking to implement a different kind of coordinate transform. .. autosummary:: :toctree: generated/ utilities.conversion.base.CoordinateConverter utilities.conversion.kx_ky_conversion.ConvertKp utilities.conversion.kx_ky_conversion.ConvertKxKy utilities.conversion.kz_conversion.ConvertKpKz General Analysis ================ Axis Methods ~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.general.rebin analysis.general.symmetrize_axis analysis.general.condense preparation.axis.normalize_dim preparation.axis.sort_axis Experimental Resolution Modeling ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.resolution.total_resolution_estimate analysis.resolution.thermal_broadening_estimate analysis.resolution.beamline_resolution_estimate analysis.resolution.analyzer_resolution_estimate Self-Energy ~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.self_energy.to_self_energy analysis.self_energy.fit_for_self_energy analysis.self_energy.estimate_bare_band analysis.self_energy.quasiparticle_lifetime Time-Resolved ARPES Related ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.tarpes.find_t_for_max_intensity analysis.tarpes.relative_change analysis.tarpes.build_crosscorrelation analysis.tarpes.delaytime_fs analysis.tarpes.position_mm_to_delaytime_fs Spin-ARPES Related ~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.sarpes.to_intensity_polarization analysis.sarpes.to_up_down analysis.sarpes.normalize_sarpes_photocurrent Fermi Edge Related ~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.gap.symmetrize analysis.gap.determine_broadened_fermi_distribution Derivatives ~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.derivative.dn_along_axis analysis.derivative.curvature analysis.derivative.minimum_gradient Smoothing and Filtering ~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.filters.gaussian_filter_arr analysis.filters.boxcar_filter_arr analysis.filters.savitzky_golay_filter analysis.filters.savgol_filter_multi Deconvolution ~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.deconvolution.deconvolve_ice analysis.deconvolution.deconvolve_rl analysis.deconvolution.make_psf1d analysis.deconvolution.make_psf Masks ~~~~~ .. autosummary:: :toctree: generated/ analysis.mask.apply_mask analysis.mask.apply_mask_to_coords analysis.mask.polys_to_mask analysis.mask.raw_poly_to_mask Fermi Surface Pockets ~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.pocket.curves_along_pocket analysis.pocket.edcs_along_pocket analysis.pocket.radial_edcs_along_pocket analysis.pocket.pocket_parameters Background Removal ~~~~~~~~~~~~~~~~~~ Shirley Backgrounds ------------------- .. autosummary:: :toctree: generated/ analysis.shirley.calculate_shirley_background analysis.shirley.remove_shirley_background Convex Hull Backgrounds ----------------------- .. autosummary:: :toctree: generated/ analysis.background.calculate_background_hull analysis.background.remove_background_hull Incoherent Backgrounds ---------------------- .. autosummary:: :toctree: generated/ correction.background.remove_incoherent_background correction.coords.shift_by Array Alignment ~~~~~~~~~~~~~~~ Subpixel Correlation Based Alignment ------------------------------------ .. autosummary:: :toctree: generated/ analysis.align.align Machine Learning ================ ML Based Decompositions ~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ analysis.decomposition.decomposition_along analysis.decomposition.pca_along analysis.decomposition.nmf_along analysis.decomposition.factor_analysis_along analysis.decomposition.ica_along Deep Learning and PyTorch ~~~~~~~~~~~~~~~~~~~~~~~~~ Utilities for interpretation of results akin to those in fast.ai. .. autosummary:: :toctree: generated/ deep_learning.interpret.Interpretation deep_learning.interpret.InterpretationItem IO tools. .. autosummary:: :toctree: generated/ deep_learning.io.from_portable_bin deep_learning.io.to_portable_bin Transform pipelines. .. autosummary:: :toctree: generated/ deep_learning.transforms.Identity deep_learning.transforms.ReversibleLambda deep_learning.transforms.ComposeBoth Data Generation ~~~~~~~~~~~~~~~ Here are tools for simulating ARPES from theoretical models, including finite statistics, resolution modeling, and detector effects. .. autosummary:: :toctree: generated/ simulation.sample_from_distribution simulation.cloud_to_arr simulation.SpectralFunctionMFL simulation.SpectralFunctionPhaseCoherent simulation.DetectorEffect simulation.NonlinearDetectorEffect Data Loading Plugins ==================== .. autosummary:: :toctree: generated/ endstations.plugin.ALG_main.ALGMainChamber endstations.plugin.ALG_spin_ToF.SpinToFEndstation endstations.plugin.ANTARES.ANTARESEndstation endstations.plugin.Elettra_spectromicroscopy.SpectromicroscopyElettraEndstation endstations.plugin.example_data.ExampleDataEndstation endstations.plugin.fallback.FallbackEndstation endstations.plugin.HERS.HERSEndstation endstations.plugin.igor_export.IgorExportEndstation endstations.plugin.igor_plugin.IgorEndstation endstations.plugin.kaindl.KaindlEndstation endstations.plugin.MAESTRO.MAESTROMicroARPESEndstation endstations.plugin.MAESTRO.MAESTRONanoARPESEndstation endstations.plugin.MBS.MBSEndstation endstations.plugin.merlin.BL403ARPESEndstation endstations.plugin.SToF_DLD.SToFDLDEndstation endstations.plugin.SPD_main.SPDEndstation endstations.plugin.DSNP_UMCS.DSNP_UMCSEndstation Curve Fitting ============= General Curve Fitting Utilities ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ fits.utilities.result_to_hints Models ~~~~~~ .. automodule:: arpes.fits :members: .. autosummary:: :toctree: generated/ :recursive: fit_models.fermi_edge fit_models.dirac fit_models.bands fit_models.functional_forms fit_models.misc fit_models.two_dimensional Plotting ======== Interactive Utilities: holoviews Based ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: arpes.plotting .. autosummary:: :toctree: generated/ ui.concat_along_phi_ui ui.profile_view ui.fit_inspection ui.smoothing.SmoothingApp ui.smoothing.DifferentiateApp General Utilities/Matplotlib Quality of Life ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ An incomplete list of useful plotting utilities from ``arpes.utilities.plotting``. .. autosummary:: :toctree: generated/ utils.path_for_plot utils.savefig utils.simple_ax_grid utils.invisible_axes utils.remove_colorbars utils.frame_with utils.unchanged_limits utils.plot_arr utils.imshow_mask utils.latex_escape utils.fancy_labels utils.summarize Interactive Utilities: Matplotlib Based ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Stack Plots ~~~~~~~~~~~ .. autosummary:: :toctree: generated/ stack_plot.stack_dispersion_plot stack_plot.flat_stack_plot stack_plot.offset_scatter_plot Spin-ARPES Plots ~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ spin.spin_polarized_spectrum spin.spin_colored_spectrum spin.spin_difference_spectrum Count-based and ToF Plots ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ tof.plot_with_std tof.scatter_with_std Reference Plots ~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ spatial.plot_spatial_reference spatial.reference_scan_spatial Curve Fitting Plots ~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ fits.plot_fit fits.plot_fits parameter.plot_parameter False Color Plots ~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ false_color.false_color_plot Plotting with Brillouin Zones ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ bz.plot_data_to_bz bz.overplot_standard bz.plot_plane_to_bz Plot Annotations ~~~~~~~~~~~~~~~~ .. autosummary:: :toctree: generated/ annotations.annotate_cuts annotations.annotate_point annotations.annotate_experimental_conditions