toupy package

Subpackages

• toupy.io package
  • Submodules
  • toupy.io.dataio module
    • LoadData
      • LoadData.load()
      • LoadData.load_olddata()
      • LoadData.loadmasks()
      • LoadData.loadshiftstack()
      • LoadData.loadtheta()
    • LoadProjections
      • LoadProjections.check_angles()
      • LoadProjections.check_angles_new()
      • LoadProjections.insert_missing()
      • LoadProjections.load()
      • LoadProjections.loadedf()
    • LoadTomogram
      • LoadTomogram.load()
    • PathName
      • PathName.datafilewcard()
      • PathName.metadatafilewcard()
      • PathName.results_datapath()
      • PathName.results_folder()
      • PathName.search_projections()
    • SaveData
      • SaveData.save()
      • SaveData.saveFSC()
      • SaveData.savecheck()
      • SaveData.savemasks()
    • SaveTomogram
      • SaveTomogram.convert_to_tiff()
      • SaveTomogram.save()
      • SaveTomogram.save_vol_to_h5()
      • SaveTomogram.savecheck()
      • SaveTomogram.tiff_folderpath()
    • remove_extraprojs()
  • toupy.io.filesrw module
    • convert16bitstiff()
    • convert8bitstiff()
    • convertimageto16bits()
    • convertimageto8bits()
    • create_paramsh5()
    • crop_array()
    • load_paramsh5()
    • memmap_volfile()
    • read_cxi()
    • read_edf()
    • read_ptyr()
    • read_recon()
    • read_theta_raw()
    • read_theta_recon()
    • read_tiff()
    • read_tiff_info()
    • read_volfile()
    • write_edf()
    • write_paramsh5()
    • write_tiff()
    • write_tiffmetadata()
  • toupy.io.h5chunk_shape_3D module
    • binlist()
    • chunk_shape_3D()
    • numVals()
    • perturbShape()
• toupy.registration package
  • Submodules
  • toupy.registration.cone_registration module
    • ConeBeamRegistration
      • ConeBeamRegistration.geometry
      • ConeBeamRegistration.align_horizontal()
      • ConeBeamRegistration.align_horizontal_from_parallel()
      • ConeBeamRegistration.align_vertical()
      • ConeBeamRegistration.align_vertical_cone()
      • ConeBeamRegistration.estimate_cor()
      • ConeBeamRegistration.estimate_geometry()
      • ConeBeamRegistration.rebin_to_parallel()
    • rebin_fan_to_parallel()
  • toupy.registration.registration module
    • registration_gd.py
    • alignprojections_horizontal()
    • alignprojections_vertical()
    • center_of_mass_stack()
    • compute_aligned_horizontal()
    • compute_aligned_sino()
    • compute_aligned_stack()
    • estimate_rot_axis()
    • oneslicefordisplay()
    • refine_horizontalalignment()
    • register_2Darrays()
    • tomoconsistency_multiple()
    • vertical_fluctuations()
    • vertical_shift()
  • toupy.registration.shift module
    • ShiftFunc
      • ShiftFunc.__call__()
      • ShiftFunc.shift_fft()
      • ShiftFunc.shift_linear()
      • ShiftFunc.shift_spline_wrap()
• toupy.resolution package
  • Submodules
  • toupy.resolution.FSC module
    • FRCPlot
      • FRCPlot.plot()
    • FSCPlot
      • FSCPlot.fn_res
      • FSCPlot.fn_res_cpx
      • FSCPlot.resolution_full
      • FSCPlot.resolution_half
      • FSCPlot.plot()
    • FourierShellCorr
      • FourierShellCorr.apodization()
      • FourierShellCorr.circle()
      • FourierShellCorr.fouriercorr()
      • FourierShellCorr.nyquist()
      • FourierShellCorr.ringthickness()
      • FourierShellCorr.ssnr()
      • FourierShellCorr.transverse_apodization()
    • LocalFSC
      • LocalFSC.resolution_map
      • LocalFSC.resolution_map_phys
      • LocalFSC.resolution_map_half
      • LocalFSC.resolution_map_phys_half
      • LocalFSC.resolution_median
      • LocalFSC.resolution_mean
      • LocalFSC.resolution_std
      • LocalFSC.resolution_median_half
      • LocalFSC.resolution_mean_half
      • LocalFSC.resolution_std_half
      • LocalFSC.plot()
    • RandomFSC
      • RandomFSC.FSC_obs
      • RandomFSC.FSC_rand
      • RandomFSC.FSC_corr
      • RandomFSC.T
      • RandomFSC.f
      • RandomFSC.fnyquist
      • RandomFSC.cutoff_shell
      • RandomFSC.plot()
    • SSNRPlot
      • SSNRPlot.FSC
      • SSNRPlot.SSNR
      • SSNRPlot.SSNR_T
      • SSNRPlot.f
      • SSNRPlot.fnyquist
      • SSNRPlot.fn_res
      • SSNRPlot.fn_res_cpx
      • SSNRPlot.resolution_full
      • SSNRPlot.resolution_half
      • SSNRPlot.plot()
  • toupy.resolution.FSCtools module
    • compute_2tomograms()
    • compute_2tomograms_splitted()
    • split_dataset()
  • toupy.resolution.MTF module
    • MTFEstimator
      • MTFEstimator.freq
      • MTFEstimator.MTF
      • MTFEstimator.freq_phys
      • MTFEstimator.f50
      • MTFEstimator.f10
      • MTFEstimator.resolution_50
      • MTFEstimator.resolution_10
      • MTFEstimator.plot()
  • toupy.resolution.decorr module
    • ImageDecorr
      • ImageDecorr.r_values
      • ImageDecorr.A
      • ImageDecorr.d
      • ImageDecorr.r_res
      • ImageDecorr.resolution_px
      • ImageDecorr.resolution
      • ImageDecorr.resolutions_px
      • ImageDecorr.resolution_px_mean
      • ImageDecorr.resolution_px_median
      • ImageDecorr.resolution_px_std
      • ImageDecorr.plot()
  • toupy.resolution.localres module
    • LocalResolution
      • LocalResolution.resolution_map
      • LocalResolution.resolution_map_phys
      • LocalResolution.resolution_map_half
      • LocalResolution.resolution_map_phys_half
      • LocalResolution.sigma_noise
      • LocalResolution.freq_bands
      • LocalResolution.mask
      • LocalResolution.resolution_median
      • LocalResolution.resolution_mean
      • LocalResolution.resolution_std
      • LocalResolution.resolution_median_half
      • LocalResolution.resolution_mean_half
      • LocalResolution.resolution_std_half
      • LocalResolution.plot()
• toupy.restoration package
  • Submodules
  • toupy.restoration.GUI_tracker module
    • AmpTracker
      • AmpTracker.apply_all_masks()
      • AmpTracker.apply_mask()
    • PhaseTracker
      • PhaseTracker.add_mask()
      • PhaseTracker.apply_all_masks()
      • PhaseTracker.apply_mask()
      • PhaseTracker.cmvmax()
      • PhaseTracker.cmvmin()
      • PhaseTracker.down()
      • PhaseTracker.draw_mask()
      • PhaseTracker.key_event()
      • PhaseTracker.load_masks()
      • PhaseTracker.mask_all()
      • PhaseTracker.onclose()
      • PhaseTracker.onscroll()
      • PhaseTracker.play()
      • PhaseTracker.remove_all_mask()
      • PhaseTracker.remove_mask()
      • PhaseTracker.remove_ramp()
      • PhaseTracker.remove_rampall()
      • PhaseTracker.save_masks()
      • PhaseTracker.stop_play()
      • PhaseTracker.submit()
      • PhaseTracker.unwrapping_all()
      • PhaseTracker.unwrapping_phase()
      • PhaseTracker.up()
      • PhaseTracker.update()
    • gui_plotamp()
    • gui_plotphase()
    • make_air_mask()
  • toupy.restoration.derivativetools module
    • calculate_derivatives()
    • calculate_derivatives_fft()
    • chooseregiontoderivatives()
    • derivatives()
    • derivatives_fft()
    • derivatives_sino()
    • gradient_axis()
  • toupy.restoration.phase_retrieval module
    • GPU notes
    • ctf_retrieve()
    • iterative_phase_retrieval()
    • suggest_holo_distances()
    • tie_hom()
  • toupy.restoration.ramptools module
    • normalize_projections_phase()
    • rmair()
    • rmlinearphase()
    • rmphaseramp()
  • toupy.restoration.ring_correction module
    • GPU notes
    • remove_rings_stack()
    • remove_rings_titarenko()
    • remove_rings_wavelet_fft()
  • toupy.restoration.unwraptools module
    • chooseregiontounwrap()
    • distance()
    • get_charge()
    • phaseresidues()
    • phaseresiduesStack()
    • phaseresiduesStack_parallel()
    • unwrap_phase_2d()
    • unwrapping_phase()
    • wrap()
    • wraptopi()
  • toupy.restoration.vorticestools module
    • cart2pol()
    • get_object_novort()
    • get_probe_novort()
    • pol2cart()
    • rmvortices_object()
    • rmvortices_probe()
• toupy.simulation package
  • Submodules
  • toupy.simulation.phantom_creator module
    • phantom()
    • phantom3d()
• toupy.tomo package
  • Submodules
  • toupy.tomo.cone_projector module
    • cone_project()
  • toupy.tomo.fdk module
    • Public API
    • fdk_backproject()
    • fdk_filter()
    • fdk_reconstruct()
    • fdk_weight()
  • toupy.tomo.geometry module
    • ConeBeamGeometry
      • ConeBeamGeometry.magnification
      • ConeBeamGeometry.effective_pixel_size
      • ConeBeamGeometry.SDD
      • ConeBeamGeometry.SOD
      • ConeBeamGeometry.angles
      • ConeBeamGeometry.det_pixel_size
      • ConeBeamGeometry.effective_pixel_size
      • ConeBeamGeometry.magnification
      • ConeBeamGeometry.n_u
      • ConeBeamGeometry.n_v
      • ConeBeamGeometry.u_coords()
      • ConeBeamGeometry.v_coords()
      • ConeBeamGeometry.validate()
  • toupy.tomo.iradon module
    • backprojector()
    • compute_angle_weights()
    • compute_filter()
    • mod_iradon()
    • mod_iradon_cuda()
    • reconsSART()
  • toupy.tomo.radon module
    • projector()
    • radon_cuda()
  • toupy.tomo.tomorecons module
    • fdk_tomo_recons()
    • full_tomo_recons()
    • tomo_recons()
  • toupy.tomo.tv_recons module
    • GPU notes
    • chambolle_pock_tv()
    • tv_reconstruction()
• toupy.utils package
  • Submodules
  • toupy.utils.FFT_utils module
    • fastfftn()
    • fastifftn()
    • is_power2()
    • nextpow2()
    • nextpoweroftwo()
    • padfft()
    • padrightside()
    • padwidthbothsides()
  • toupy.utils.array_utils module
    • create_circle()
    • create_mask_borders()
    • crop()
    • cropROI()
    • fract_hanning()
    • fract_hanning_pad()
    • gauss_kern()
    • hanning_apod1D()
    • hanning_apodization()
    • mask_borders()
    • normalize_array()
    • padarray_bothsides()
    • polynomial1d()
    • projectpoly1d()
    • radtap()
    • replace_bad()
    • round_to_even()
    • sharpening_image()
    • smooth1d()
    • smooth2d()
    • smooth_image()
    • sort_array()
  • toupy.utils.converter_utils module
    • convert_to_beta()
    • convert_to_delta()
    • convert_to_mu()
    • convert_to_rhoe()
    • convert_to_rhom()
  • toupy.utils.fit_utils module
    • model_erf()
    • model_tanh()
    • residuals_erf()
    • residuals_tanh()
  • toupy.utils.funcutils module
    • checkhostname()
    • deprecated()
    • downloadURL()
    • downloadURLfile()
    • progress_bar()
    • switch
      • switch.__iter__()
      • switch.match()
    • tqdm
      • tqdm.__iter__()
      • tqdm.clear()
      • tqdm.close()
      • tqdm.display()
      • tqdm.external_write_mode()
      • tqdm.format_dict
      • tqdm.format_interval()
      • tqdm.format_meter()
      • tqdm.format_num()
      • tqdm.format_sizeof()
      • tqdm.get_lock()
      • tqdm.monitor
      • tqdm.monitor_interval
      • tqdm.moveto()
      • tqdm.pandas()
      • tqdm.refresh()
      • tqdm.reset()
      • tqdm.set_description()
      • tqdm.set_description_str()
      • tqdm.set_lock()
      • tqdm.set_postfix()
      • tqdm.set_postfix_str()
      • tqdm.status_printer()
      • tqdm.unpause()
      • tqdm.update()
      • tqdm.wrapattr()
      • tqdm.write()
  • toupy.utils.plot_utils module
    • RegisterPlot
      • RegisterPlot.plotshorizontal()
      • RegisterPlot.plotsvertical()
      • RegisterPlot.updatehorizontal()
      • RegisterPlot.updatevertical()
    • ShowProjections
      • ShowProjections.probe2HSV()
      • ShowProjections.show_projections()
      • ShowProjections.update_show()
    • animated_image()
    • autoscale_y()
    • display_slice()
    • isnotebook()
    • iterative_show()
    • plot_checkangles()
    • show_figure()
    • show_fsc_curve()
    • show_fsc_images()
    • show_linearphase()
    • show_random_fsc_curve()
    • show_resolution_map()
    • show_ssnr_curve()