ptypy package

Subpackages

• ptypy.core package
  • Submodules
  • ptypy.core.classes module
    • Base
      • Base.ID
      • Base.calc_mem_usage()
      • Base.numID
      • Base.owner
    • Container
      • Container.ID
      • Container.S
      • Container.Sp
      • Container.V
      • Container.Vp
      • Container.__getitem__()
      • Container.__setitem__()
      • Container.allreduce()
      • Container.clear()
      • Container.copies
      • Container.copy()
      • Container.delete_copy()
      • Container.dtype
      • Container.fill()
      • Container.formatted_report()
      • Container.info()
      • Container.nbytes
      • Container.ndim
      • Container.new_storage()
      • Container.numID
      • Container.owner
      • Container.reformat()
      • Container.report()
      • Container.size
      • Container.storages
      • Container.views
      • Container.views_in_storage()
    • POD
      • POD.DEFAULT_VIEWS
      • POD.ID
      • POD.active
      • POD.bw
      • POD.diff
      • POD.downsample
      • POD.exit
      • POD.fw
      • POD.geometry
      • POD.mask
      • POD.numID
      • POD.object
      • POD.owner
      • POD.pr_view
      • POD.probe
      • POD.upsample
    • Storage
      • Storage.ID
      • Storage.__getitem__()
      • Storage.__setitem__()
      • Storage.allreduce()
      • Storage.center
      • Storage.copy()
      • Storage.data
      • Storage.dtype
      • Storage.fill()
      • Storage.fill_value
      • Storage.formatted_report()
      • Storage.get_view_coverage()
      • Storage.grids()
      • Storage.ndim
      • Storage.numID
      • Storage.origin
      • Storage.owner
      • Storage.psize
      • Storage.reformat()
      • Storage.report()
      • Storage.update()
      • Storage.update_views()
      • Storage.views
      • Storage.zoom_to_psize()
    • View
      • View.DEFAULT_ACCESSRULE
      • View.ID
      • View.active
      • View.coord
      • View.copy()
      • View.data
      • View.dcoord
      • View.dhigh
      • View.dlayer
      • View.dlow
      • View.error
      • View.layer
      • View.ndim
      • View.numID
      • View.owner
      • View.pcoord
      • View.pod
      • View.pods
      • View.psize
      • View.shape
      • View.slice
      • View.sp
      • View.storage
      • View.storageID
  • ptypy.core.data module
    • MoonFlowerScan
      • MoonFlowerScan.DEFAULT
      • MoonFlowerScan.check()
      • MoonFlowerScan.load()
      • MoonFlowerScan.load_positions()
      • MoonFlowerScan.load_weight()
    • PTYD
    • PtyScan
      • PtyScan.CODES
      • PtyScan.DEFAULT
      • PtyScan.EOS
      • PtyScan.METAKEYS
      • PtyScan.WAIT
      • PtyScan.abort
      • PtyScan.auto()
      • PtyScan.check()
      • PtyScan.correct()
      • PtyScan.end_of_scan
      • PtyScan.frames_accessible
      • PtyScan.get_data_chunk()
      • PtyScan.info
      • PtyScan.initialize()
      • PtyScan.load()
      • PtyScan.load_common()
      • PtyScan.load_positions()
      • PtyScan.load_weight()
      • PtyScan.min_frames
      • PtyScan.num_frames
      • PtyScan.post_initialize()
      • PtyScan.report()
    • PtydScan
      • PtydScan.DEFAULT
      • PtydScan.check()
      • PtydScan.load()
      • PtydScan.load_positions()
      • PtydScan.load_weight()
  • ptypy.core.geometry module
    • BasicFarfieldPropagator
      • BasicFarfieldPropagator.bw()
      • BasicFarfieldPropagator.fw()
      • BasicFarfieldPropagator.update()
    • BasicNearfieldPropagator
      • BasicNearfieldPropagator.bw()
      • BasicNearfieldPropagator.fw()
      • BasicNearfieldPropagator.update()
    • Geo
      • Geo.DEFAULT
      • Geo.ID
      • Geo.distance
      • Geo.downsample()
      • Geo.energy
      • Geo.lam
      • Geo.lz
      • Geo.numID
      • Geo.owner
      • Geo.propagator
      • Geo.psize
      • Geo.resolution
      • Geo.shape
      • Geo.update()
      • Geo.upsample()
  • ptypy.core.illumination module
    • aperture()
    • init_storage()
  • ptypy.core.manager module
    • BlockFull
      • BlockFull.DEFAULT
    • BlockOPRModel
      • BlockOPRModel.DEFAULT
    • BlockScanModel
      • BlockScanModel.DEFAULT
      • BlockScanModel.new_data()
    • BlockVanilla
      • BlockVanilla.DEFAULT
    • Bragg3dModel
      • Bragg3dModel.DEFAULT
    • Full
      • Full.DEFAULT
    • ModelManager
      • ModelManager.data_available
      • ModelManager.end_of_scan
      • ModelManager.new_data()
    • OPRModel
      • OPRModel.DEFAULT
    • ScanModel
      • ScanModel.DEFAULT
      • ScanModel.makePtyScan()
      • ScanModel.new_data()
    • Vanilla
      • Vanilla.DEFAULT
  • ptypy.core.paths module
    • DEFAULT
    • Paths
      • Paths.DEFAULT
      • Paths.auto_file()
      • Paths.get_path()
      • Paths.plot_file()
      • Paths.recon_file()
      • Paths.run()
  • ptypy.core.ptycho module
    • Ptycho
      • Ptycho.DEFAULT
      • Ptycho.ID
      • Ptycho.containers
      • Ptycho.copy_state()
      • Ptycho.finalize()
      • Ptycho.init_communication()
      • Ptycho.init_data()
      • Ptycho.init_engine()
      • Ptycho.init_structures()
      • Ptycho.load_run()
      • Ptycho.numID
      • Ptycho.owner
      • Ptycho.plot_overview()
      • Ptycho.pods
      • Ptycho.print_stats()
      • Ptycho.restore_state()
      • Ptycho.run()
      • Ptycho.save_run()
  • ptypy.core.sample module
    • init_storage()
    • simulate()
  • ptypy.core.save_load module
    • from_h5()
    • link()
    • to_h5()
    • unlink()
  • ptypy.core.xy module
    • from_pars()
    • raster_scan()
    • round_scan()
    • spiral_scan()
  • Module contents
• ptypy.engines package
  • Submodules
  • ptypy.engines.projectional module
    • DM
      • DM.DEFAULT
    • RAAR
      • RAAR.DEFAULT
  • ptypy.engines.ML module
    • ML
      • ML.DEFAULT
      • ML.SUPPORTED_MODELS
      • ML.engine_finalize()
      • ML.engine_initialize()
      • ML.engine_iterate()
      • ML.engine_prepare()
  • ptypy.engines.stochastic module
    • EPIE
      • EPIE.DEFAULT
    • SDR
      • SDR.DEFAULT
  • ptypy.engines.base module
    • Base3dBraggEngine
      • Base3dBraggEngine.prepare()
    • BaseEngine
      • BaseEngine.COMPATIBLE_MODELS
      • BaseEngine.engine_finalize()
      • BaseEngine.engine_initialize()
      • BaseEngine.engine_iterate()
      • BaseEngine.engine_prepare()
      • BaseEngine.finalize()
      • BaseEngine.initialize()
      • BaseEngine.iterate()
      • BaseEngine.prepare()
      • BaseEngine.support_constraint()
    • PositionCorrectionEngine
      • PositionCorrectionEngine.POSREF_ENGINES
      • PositionCorrectionEngine.engine_finalize()
      • PositionCorrectionEngine.engine_initialize()
      • PositionCorrectionEngine.position_update()
  • ptypy.engines.utils module
    • Cdot()
    • Cnorm2()
    • basic_fourier_update()
    • basic_fourier_update_LEGACY()
    • dynamic_load()
    • log_likelihood()
    • projection_update_DM_AP()
    • projection_update_generalized()
    • reduce_dimension()
  • Module contents
    • by_name()
    • register()
• ptypy.experiment package
  • Submodules
  • ptypy.experiment.ID16Anfp module
    • ID16AScan
      • ID16AScan.DEFAULT
      • ID16AScan.check()
      • ID16AScan.correct()
      • ID16AScan.load()
      • ID16AScan.load_common()
      • ID16AScan.load_positions()
      • ID16AScan.load_weight()
    • undistort()
  • ptypy.experiment.hdf5_loader module
    • Hdf5Loader
      • Hdf5Loader.DEFAULT
      • Hdf5Loader.compute_scan_mapping_and_trajectory()
      • Hdf5Loader.get_corrected_intensities()
      • Hdf5Loader.load_mapped_and_arbitrary_scan()
      • Hdf5Loader.load_mapped_and_raster_scan()
      • Hdf5Loader.load_unmapped_raster_scan()
      • Hdf5Loader.subtract_dark()
    • Hdf5LoaderFast
      • Hdf5LoaderFast.DEFAULT
      • Hdf5LoaderFast.get_corrected_intensities()
      • Hdf5LoaderFast.load_mapped_and_arbitrary_scan()
      • Hdf5LoaderFast.load_mapped_and_raster_scan()
      • Hdf5LoaderFast.load_multiprocessing()
      • Hdf5LoaderFast.load_unmapped_raster_scan()
      • Hdf5LoaderFast.subtract_dark()
  • ptypy.experiment.optiklabor module
    • FliSpecScanMultexp
      • FliSpecScanMultexp.DEFAULT
      • FliSpecScanMultexp.check()
      • FliSpecScanMultexp.correct()
      • FliSpecScanMultexp.load()
      • FliSpecScanMultexp.load_common()
  • ptypy.experiment.plugin module
    • makeScanPlugin()
  • ptypy.experiment.spec module
    • SpecInfo
      • SpecInfo.parse()
    • SpecScan
    • verbose()
  • Module contents
    • FliSpecScanMultexp
      • FliSpecScanMultexp.DEFAULT
      • FliSpecScanMultexp.check()
      • FliSpecScanMultexp.correct()
      • FliSpecScanMultexp.load()
      • FliSpecScanMultexp.load_common()
    • Hdf5Loader
      • Hdf5Loader.DEFAULT
      • Hdf5Loader.compute_scan_mapping_and_trajectory()
      • Hdf5Loader.get_corrected_intensities()
      • Hdf5Loader.load_mapped_and_arbitrary_scan()
      • Hdf5Loader.load_mapped_and_raster_scan()
      • Hdf5Loader.load_unmapped_raster_scan()
      • Hdf5Loader.subtract_dark()
    • Hdf5LoaderFast
      • Hdf5LoaderFast.DEFAULT
      • Hdf5LoaderFast.get_corrected_intensities()
      • Hdf5LoaderFast.load_mapped_and_arbitrary_scan()
      • Hdf5LoaderFast.load_mapped_and_raster_scan()
      • Hdf5LoaderFast.load_multiprocessing()
      • Hdf5LoaderFast.load_unmapped_raster_scan()
      • Hdf5LoaderFast.subtract_dark()
    • ID16AScan
      • ID16AScan.DEFAULT
      • ID16AScan.check()
      • ID16AScan.correct()
      • ID16AScan.load()
      • ID16AScan.load_common()
      • ID16AScan.load_positions()
      • ID16AScan.load_weight()
    • MoonFlowerScan
      • MoonFlowerScan.DEFAULT
      • MoonFlowerScan.check()
      • MoonFlowerScan.load()
      • MoonFlowerScan.load_positions()
      • MoonFlowerScan.load_weight()
    • PtyScan
      • PtyScan.CODES
      • PtyScan.DEFAULT
      • PtyScan.EOS
      • PtyScan.METAKEYS
      • PtyScan.WAIT
      • PtyScan.abort
      • PtyScan.auto()
      • PtyScan.check()
      • PtyScan.correct()
      • PtyScan.end_of_scan
      • PtyScan.frames_accessible
      • PtyScan.get_data_chunk()
      • PtyScan.info
      • PtyScan.initialize()
      • PtyScan.load()
      • PtyScan.load_common()
      • PtyScan.load_positions()
      • PtyScan.load_weight()
      • PtyScan.min_frames
      • PtyScan.num_frames
      • PtyScan.post_initialize()
      • PtyScan.report()
    • PtydScan
      • PtydScan.DEFAULT
      • PtydScan.check()
      • PtydScan.load()
      • PtydScan.load_positions()
      • PtydScan.load_weight()
    • QuickScan
      • QuickScan.DEFAULT
      • QuickScan.load()
      • QuickScan.load_positions()
      • QuickScan.load_weight()
    • SimScan
      • SimScan.DEFAULT
      • SimScan.load()
      • SimScan.manipulate_ptycho()
• ptypy.io package
  • Submodules
  • ptypy.io.edfIO module
    • edfread()
  • ptypy.io.h5rw module
    • h5append()
    • h5info()
    • h5read()
    • h5write()
  • ptypy.io.imageIO module
    • imread()
  • ptypy.io.image_read module
    • image_read()
  • ptypy.io.interaction module
    • Client
      • Client.DEFAULT
      • Client.activate()
      • Client.avail()
      • Client.do()
      • Client.flush()
      • Client.get()
      • Client.get_now()
      • Client.newdata()
      • Client.poll()
      • Client.set()
      • Client.stop()
      • Client.stop_server()
      • Client.unexpected_ticket()
      • Client.wait()
    • Server
      • Server.DEFAULT
      • Server.activate()
      • Server.make_ID_pool()
      • Server.process_requests()
      • Server.register()
      • Server.send_error()
      • Server.send_warning()
      • Server.stop()
  • ptypy.io.json_rw module
    • jread()
    • jwrite()
  • ptypy.io.rawIO module
    • rawread()
  • Module contents
• ptypy.resources package
  • Module contents
    • flower_obj()
    • moon_pr()
    • tree_obj()
• ptypy.simulations package
  • Submodules
  • ptypy.simulations.detector module
    • Detector
      • Detector.filter()
    • conv()
    • fill2D()
    • shot()
  • ptypy.simulations.ptysim_utils module
    • exp_positions()
  • ptypy.simulations.simscan module
    • SimScan
      • SimScan.DEFAULT
      • SimScan.load()
      • SimScan.manipulate_ptycho()
  • Module contents
• ptypy.utils package
  • Submodules
  • ptypy.utils.array_utils module
    • c_zoom()
    • crop_pad()
    • crop_pad_axis()
    • crop_pad_symmetric_2d()
    • ellipsis()
    • grids()
    • mirror()
    • pad_lr()
    • rebin()
    • rebin_2d()
    • rectangle()
    • shift_zoom()
    • switch_orientation()
    • zoom()
  • ptypy.utils.math_utils module
    • abs2()
    • c_gf()
    • cabs2()
    • delxb()
    • delxc()
    • delxf()
    • gauss_fwhm()
    • gaussian()
    • gaussian2D()
    • gf()
    • gf_2d()
    • norm()
    • norm2()
    • ortho()
    • rl_deconvolution()
    • smooth_step()
  • ptypy.utils.misc module
    • Table
      • Table.add_records()
      • Table.insert_records()
      • Table.modify_add()
      • Table.new_fields()
      • Table.new_table()
      • Table.pull_records()
      • Table.select_func()
      • Table.select_match()
      • Table.select_range()
    • all_subclasses()
    • clean_path()
    • complex_overload()
    • electron_wavelength()
    • expect2()
    • expect3()
    • expectN()
    • isstr()
    • keV2m()
    • keV2nm()
    • m2keV()
    • nm2keV()
    • str2int()
    • str2range()
    • unique_path()
  • ptypy.utils.parallel module
    • LoadManager
      • LoadManager.assign()
      • LoadManager.load
      • LoadManager.rank_of
      • LoadManager.reset()
    • MPInoise2d()
    • MPIrand_normal()
    • MPIrand_uniform()
    • allreduce()
    • barrier()
    • bcast()
    • bcast_dict()
    • gather_dict()
    • gather_list()
    • receive()
    • send()
  • ptypy.utils.parameters module
    • Param
      • Param.__contains__()
      • Param.__dir__()
      • Param.copy()
      • Param.update()
    • asParam()
    • param_from_json()
    • param_from_yaml()
  • ptypy.utils.plot_client module
    • MPLClient
      • MPLClient.DEFAULT
      • MPLClient.loop_plot()
    • MPLplotter
      • MPLplotter.DEFAULT
      • MPLplotter.create_plot_from_tile_list()
      • MPLplotter.draw()
      • MPLplotter.plot_all()
      • MPLplotter.plot_error()
      • MPLplotter.plot_storage()
      • MPLplotter.save()
      • MPLplotter.update_plot_layout()
    • PlotClient
      • PlotClient.ACTIVE
      • PlotClient.DATA
      • PlotClient.STOPPED
      • PlotClient.disconnect()
      • PlotClient.get_data()
      • PlotClient.start()
      • PlotClient.status
      • PlotClient.stop()
    • figure_from_ptycho()
    • figure_from_ptyr()
    • spawn_MPLClient()
  • ptypy.utils.plot_utils module
    • PtyAxis
      • PtyAxis.add_colorbar()
      • PtyAxis.set_channel()
      • PtyAxis.set_clims()
      • PtyAxis.set_cmap()
      • PtyAxis.set_data()
      • PtyAxis.set_mask()
      • PtyAxis.set_psize()
    • complex2hsv()
    • complex2rgb()
    • franzmap()
    • hsv2complex()
    • hsv2rgb()
    • imload()
    • imsave()
    • pause()
    • plot_storage()
    • rgb2complex()
    • rgb2hsv()
    • rmphaseramp()
  • ptypy.utils.scripts module
    • cxro_iref()
    • diversify()
    • hdr_image()
    • load_from_ptyr()
    • mass_center()
    • phase_from_dpc()
    • png2mpg()
    • radial_distribution()
    • remove_hot_pixels()
    • stxm_analysis()
    • stxm_init()
    • xradia_star()
  • ptypy.utils.descriptor module
    • ArgParseDescriptor
      • ArgParseDescriptor.OPTIONS_DEF
      • ArgParseDescriptor.add2argparser()
      • ArgParseDescriptor.choices
      • ArgParseDescriptor.default
      • ArgParseDescriptor.eval()
      • ArgParseDescriptor.help
    • Descriptor
      • Descriptor.OPTIONS_DEF
      • Descriptor.__getitem__()
      • Descriptor.__setitem__()
      • Descriptor.__str__()
      • Descriptor.add_child()
      • Descriptor.children
      • Descriptor.descendants
      • Descriptor.from_string()
      • Descriptor.get()
      • Descriptor.is_child
      • Descriptor.load_conf_parser()
      • Descriptor.load_csv()
      • Descriptor.load_json()
      • Descriptor.name
      • Descriptor.new_child()
      • Descriptor.option_keys
      • Descriptor.options
      • Descriptor.parent
      • Descriptor.path
      • Descriptor.prune_child()
      • Descriptor.root
      • Descriptor.save_conf_parser()
      • Descriptor.save_csv()
      • Descriptor.save_json()
      • Descriptor.to_string()
    • EvalDescriptor
      • EvalDescriptor.OPTIONS_DEF
      • EvalDescriptor.check()
      • EvalDescriptor.create_template()
      • EvalDescriptor.default
      • EvalDescriptor.doc
      • EvalDescriptor.is_evaluable
      • EvalDescriptor.is_symlink
      • EvalDescriptor.is_target
      • EvalDescriptor.limits
      • EvalDescriptor.make_default()
      • EvalDescriptor.make_doc_rst()
      • EvalDescriptor.parse_doc()
      • EvalDescriptor.sanity_check()
      • EvalDescriptor.type
      • EvalDescriptor.userlevel
      • EvalDescriptor.validate()
  • ptypy.utils.verbose module
    • log()
    • report()
    • set_level()
  • Module contents
• ptypy.debug package
  • Submodules
  • ptypy.debug.embedded_shell module
    • ipshell()
  • ptypy.debug.ipython_kernel module
    • IPythonKernelThread
      • IPythonKernelThread.start()
    • start_ipython_kernel()
  • Module contents

Module contents

PTYPY(v0.8.2): A ptychography reconstruction package.

To cite PTYPY in publications, use

@article{ … }

copyright:

Copyright 2018 by the PTYPY team, see AUTHORS.

license:

see LICENSE for details.

version:

0.8.2.dev116a419

status:

development

ptypy.load_all()

ptypy.load_all_ptyscan_modules()

ptypy.load_gpu_engines(arch='cuda')

ptypy.load_ptyscan_module(module)