Index

A

algo_string() (in module pynx.ptycho.ptycho) AP (class in pynx.ptycho.cl_operator) apodization() (pynx.utils.fourier_shell_correlation.FourierShellCorr method) apply_ops_mul() (pynx.ptycho.cl_operator.CLOperatorPtycho method) ApplyAmplitude (class in pynx.cdi.cl_operator) (class in pynx.ptycho.cl_operator)

ApplyPhaseRamp (class in pynx.ptycho.cl_operator) array_derivative() (in module pynx.utils.array) as_numpy_record_array() (pynx.utils.history.History method) (pynx.utils.history.PynxOrderedDict method) AutoCorrelationSupport (class in pynx.cdi.cl_operator) available_gpu_speed() (in module pynx.processing_unit.cuda_device) (in module pynx.processing_unit.opencl_device)

B

BackgroundFilter (class in pynx.ptycho.cl_operator)

BackPropagatePaganin (class in pynx.wavefront.cl_operator) benchmark_fft() (in module pynx.utils.benchmark)

C

Calc2Obs (class in pynx.ptycho.cl_operator) Calc2Obs1 (class in pynx.ptycho.cl_operator) calc_regularisation_scale() (pynx.ptycho.ptycho.Ptycho method) calc_scan_area() (pynx.ptycho.ptycho.Ptycho method) calc_slabs() (pynx.cdi.runner.regrid.Regrid3D method) calc_slicing() (pynx.cdi.runner.regrid.Regrid3D method) calc_throughput() (in module pynx.cdi.cdi) (in module pynx.ptycho.ptycho) CalcIllumination (class in pynx.ptycho.cl_operator) CDI (class in pynx.cdi.cdi) CDIOperatorException CDIRunner (class in pynx.cdi.runner.runner) CDIRunnerException CDIRunnerScan (class in pynx.cdi.runner.runner) center_array_2d() (in module pynx.utils.array) center_crop_data() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) CenterObjProbe (class in pynx.ptycho.cl_operator) CF (class in pynx.cdi.cl_operator) check_mpi() (pynx.cdi.runner.runner.CDIRunner method) check_params() (pynx.cdi.runner.runner.CDIRunner method) (pynx.ptycho.runner.runner.PtychoRunner method) check_params_beamline() (pynx.cdi.runner.runner.CDIRunner method) (pynx.ptycho.runner.runner.PtychoRunner method)

CircularMask (class in pynx.wavefront.cl_operator) cl_device_fft_speed() (in module pynx.processing_unit.opencl_device) cl_device_global_mem_bandwidth() (in module pynx.processing_unit.opencl_device) cl_init_kernel_n() (pynx.ptycho.cl_operator.CLProcessingUnitPtycho method) cl_init_kernels() (pynx.ptycho.cl_operator.CLProcessingUnitPtycho method) clean_slab() (pynx.cdi.runner.regrid.Regrid3D method) CLObsDataStack (class in pynx.ptycho.cl_operator) CLOperatorPtycho (class in pynx.ptycho.cl_operator) CLOperatorPtychoPower (class in pynx.ptycho.cl_operator) CLOperatorPtychoSum (class in pynx.ptycho.cl_operator) CLProcessingUnitPtycho (class in pynx.ptycho.cl_operator) colorwheel() (in module pynx.utils.plot_utils) compile_kernels() (pynx.cdi.runner.regrid.Regrid3D method) complex2rgbalin() (in module pynx.utils.plot_utils) complex2rgbalin_dark() (in module pynx.utils.plot_utils) complex2rgbalog() (in module pynx.utils.plot_utils) copy() (pynx.cdi.cdi.CDI method) (pynx.wavefront.wavefront.Wavefront method) corr_flat_field() (pynx.cdi.runner.runner.CDIRunnerScan method) crop() (in module pynx.utils.array) crop_around_support() (in module pynx.utils.array) cuda_device_fft_speed() (in module pynx.processing_unit.cuda_device) cuda_device_global_mem_bandwidth() (in module pynx.processing_unit.cuda_device)

D

DetwinHIO (class in pynx.cdi.cl_operator) DetwinRAAR (class in pynx.cdi.cl_operator)

DM (class in pynx.ptycho.cl_operator) DM1 (class in pynx.ptycho.cl_operator) DM2 (class in pynx.ptycho.cl_operator)

E

ER (class in pynx.cdi.cl_operator)

EstimatePSF (class in pynx.cdi.cl_operator)

F

f_thomson() (in module pynx.scattering.fthomson) Fhkl_gold() (in module pynx.scattering.fhkl) Fhkl_thread() (in module pynx.scattering.fhkl) fibonacci_urchin() (in module pynx.utils.pattern) fourier_shift() (in module pynx.utils.array) FourierApplyAmplitude (class in pynx.cdi.cl_operator) fouriercorr() (pynx.utils.fourier_shell_correlation.FourierShellCorr method) FourierShellCorr (class in pynx.utils.fourier_shell_correlation) FreePU (class in pynx.cdi.cl_operator) (class in pynx.ptycho.cl_operator) (class in pynx.wavefront.cl_operator)

Fresnel_thread() (in module pynx.wavefront.fresnel) from_pu() (pynx.ptycho.ptycho.Ptycho method) FSCPlot (class in pynx.utils.fourier_shell_correlation) FT (class in pynx.cdi.cl_operator) (class in pynx.ptycho.cl_operator) (class in pynx.wavefront.cl_operator) full_width() (in module pynx.utils.math) FZP_thread() (in module pynx.wavefront.fzp)

G

get() (pynx.wavefront.wavefront.Wavefront method) get_background() (pynx.ptycho.ptycho.Ptycho method) get_bin() (pynx.cdi.cdi.CDI method) get_crop() (pynx.cdi.cdi.CDI method) get_icalc() (in module pynx.ptycho.cl_operator) (pynx.cdi.cl_operator.ShowCDI static method) get_illumination_obj() (pynx.ptycho.ptycho.Ptycho method) get_img() (in module pynx.utils.pattern) get_iobs() (pynx.cdi.cdi.CDI method) (pynx.ptycho.ptycho.Ptycho method) get_llk() (pynx.cdi.cdi.CDI method) (pynx.ptycho.ptycho.Ptycho method) get_llkn() (pynx.cdi.cdi.CDI method) get_obj() (pynx.cdi.cdi.CDI method) (pynx.ptycho.ptycho.Ptycho method)

get_obj_coord() (pynx.ptycho.ptycho.Ptycho method) get_probe() (pynx.ptycho.ptycho.Ptycho method) get_probe_coord() (pynx.ptycho.ptycho.Ptycho method) get_psf() (pynx.cdi.runner.runner.CDIRunnerScan method) get_psi() (pynx.ptycho.ptycho.Ptycho method) get_required_obj_shape() (pynx.ptycho.ptycho.PtychoData method) get_scan_area_obj() (pynx.ptycho.ptycho.Ptycho method) get_scan_area_points() (pynx.ptycho.ptycho.Ptycho method) get_scan_area_probe() (pynx.ptycho.ptycho.Ptycho method) get_slab() (pynx.cdi.runner.regrid.Regrid3D method) get_support() (pynx.cdi.cdi.CDI method) get_upsample() (pynx.cdi.cdi.CDI method) get_x_y() (pynx.wavefront.wavefront.Wavefront method) get_x_y_z() (pynx.cdi.cdi.CDI method) GPS (class in pynx.cdi.cl_operator) Grad (class in pynx.ptycho.cl_operator)

H

HIO (class in pynx.cdi.cl_operator)

History (class in pynx.utils.history)

I

IFT (class in pynx.cdi.cl_operator) (class in pynx.ptycho.cl_operator) (class in pynx.wavefront.cl_operator) in_object_space() (pynx.cdi.cdi.CDI method) init_cl_vobs() (pynx.ptycho.cl_operator.CLOperatorPtycho method) init_free_pixels() (pynx.cdi.cdi.CDI method) init_mask() (pynx.cdi.runner.runner.CDIRunnerScan method) init_object() (pynx.cdi.runner.runner.CDIRunnerScan method)

init_psf() (pynx.cdi.cdi.CDI method) init_run_number() (pynx.ptycho.runner.runner.PtychoRunnerScan method) init_support() (pynx.cdi.runner.runner.CDIRunnerScan method) InitPSF (class in pynx.cdi.cl_operator) insert() (pynx.utils.history.History method) insertColorwheel() (in module pynx.utils.plot_utils) interp_linear() (in module pynx.utils.array) InterpIobsMask (class in pynx.cdi.cl_operator)

L

LLK (class in pynx.cdi.cl_operator) (class in pynx.ptycho.cl_operator) llk_euclidian() (in module pynx.utils.math) llk_gaussian() (in module pynx.utils.math) llk_poisson() (in module pynx.utils.math) LLKSupport (class in pynx.cdi.cl_operator)

load_data() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) load_data_post_process() (pynx.ptycho.runner.runner.PtychoRunnerScan method) load_obj_probe_cxi() (pynx.ptycho.ptycho.Ptycho method) load_scan() (pynx.ptycho.runner.runner.PtychoRunnerScan method) load_scan_post() (pynx.ptycho.runner.runner.PtychoRunnerScan method) LoopStack (class in pynx.ptycho.cl_operator)

M

MemUsage (class in pynx.ptycho.cl_operator) minimize_grad_phase() (in module pynx.utils.phase) ML (class in pynx.cdi.cl_operator) (class in pynx.ptycho.cl_operator) modes() (in module pynx.ptycho.analysis) module pynx.cdi pynx.cdi.cdi pynx.cdi.cl_operator pynx.cdi.runner.regrid pynx.cdi.runner.runner pynx.processing_unit pynx.processing_unit.cuda_device pynx.processing_unit.opencl_device pynx.ptycho pynx.ptycho.analysis pynx.ptycho.cl_operator pynx.ptycho.ptycho pynx.ptycho.runner.runner pynx.scattering pynx.scattering.fhkl pynx.scattering.fthomson pynx.utils pynx.utils.array pynx.utils.benchmark pynx.utils.fourier_shell_correlation pynx.utils.history pynx.utils.math pynx.utils.pattern pynx.utils.phase pynx.utils.phase_retrieval_transfer_function pynx.utils.plot_utils pynx.wavefront pynx.wavefront.cl_operator pynx.wavefront.wavefront

mpi_scan_split() (pynx.ptycho.runner.runner.PtychoRunnerScan method)

N

nyquist() (in module pynx.utils.phase_retrieval_transfer_function) (pynx.utils.fourier_shell_correlation.FourierShellCorr method)

O

ObjConvolve (class in pynx.cdi.cl_operator) ObjProbe2Psi (class in pynx.ptycho.cl_operator) op() (pynx.cdi.cl_operator.ApplyAmplitude method) (pynx.cdi.cl_operator.AutoCorrelationSupport method) (pynx.cdi.cl_operator.CF method) (pynx.cdi.cl_operator.DetwinHIO method) (pynx.cdi.cl_operator.DetwinRAAR method) (pynx.cdi.cl_operator.ER method) (pynx.cdi.cl_operator.EstimatePSF method) (pynx.cdi.cl_operator.FourierApplyAmplitude method) (pynx.cdi.cl_operator.FreePU method) (pynx.cdi.cl_operator.FT method) (pynx.cdi.cl_operator.GPS method) (pynx.cdi.cl_operator.HIO method) (pynx.cdi.cl_operator.IFT method) (pynx.cdi.cl_operator.InitPSF method) (pynx.cdi.cl_operator.InterpIobsMask method) (pynx.cdi.cl_operator.LLK method) (pynx.cdi.cl_operator.LLKSupport method) (pynx.cdi.cl_operator.ML method) (pynx.cdi.cl_operator.ObjConvolve method) (pynx.cdi.cl_operator.PRTF method) (pynx.cdi.cl_operator.RAAR method) (pynx.cdi.cl_operator.ScaleObj method) (pynx.cdi.cl_operator.SupportExpand method) (pynx.cdi.cl_operator.SupportUpdate method) (pynx.cdi.cl_operator.UpdatePSF method) (pynx.ptycho.cl_operator.AP method) (pynx.ptycho.cl_operator.ApplyAmplitude method) (pynx.ptycho.cl_operator.ApplyPhaseRamp method) (pynx.ptycho.cl_operator.BackgroundFilter method) (pynx.ptycho.cl_operator.Calc2Obs method) (pynx.ptycho.cl_operator.Calc2Obs1 method) (pynx.ptycho.cl_operator.CalcIllumination method) (pynx.ptycho.cl_operator.CenterObjProbe method) (pynx.ptycho.cl_operator.DM method) (pynx.ptycho.cl_operator.DM1 method) (pynx.ptycho.cl_operator.DM2 method) (pynx.ptycho.cl_operator.FreePU method) (pynx.ptycho.cl_operator.FT method) (pynx.ptycho.cl_operator.Grad method) (pynx.ptycho.cl_operator.IFT method) (pynx.ptycho.cl_operator.LLK method) (pynx.ptycho.cl_operator.LoopStack method) (pynx.ptycho.cl_operator.MemUsage method) (pynx.ptycho.cl_operator.ML method) (pynx.ptycho.cl_operator.ObjProbe2Psi method) (pynx.ptycho.cl_operator.PropagateApplyAmplitude method) (pynx.ptycho.cl_operator.PropagateNearField method) (pynx.ptycho.cl_operator.Psi2Obj method) (pynx.ptycho.cl_operator.Psi2ObjMerge method) (pynx.ptycho.cl_operator.Psi2PosMerge method) (pynx.ptycho.cl_operator.Psi2PosShift method) (pynx.ptycho.cl_operator.Psi2Probe method) (pynx.ptycho.cl_operator.Psi2ProbeMerge method) (pynx.ptycho.cl_operator.PurgeStacks method) (pynx.ptycho.cl_operator.QuadraticPhase method) (pynx.ptycho.cl_operator.Scale method) (pynx.ptycho.cl_operator.ScaleObjProbe method) (pynx.ptycho.cl_operator.SelectStack method) (pynx.ptycho.cl_operator.SumIntensity1 method) (pynx.ptycho.cl_operator.ZeroPhaseRamp method) (pynx.wavefront.cl_operator.BackPropagatePaganin method) (pynx.wavefront.cl_operator.CircularMask method) (pynx.wavefront.cl_operator.FreePU method) (pynx.wavefront.cl_operator.FT method) (pynx.wavefront.cl_operator.IFT method) (pynx.wavefront.cl_operator.PropagateFarField method) (pynx.wavefront.cl_operator.PropagateFRT method) (pynx.wavefront.cl_operator.PropagateNearField method) (pynx.wavefront.cl_operator.QuadraticPhase method) (pynx.wavefront.cl_operator.RectangularMask method) (pynx.wavefront.cl_operator.Scale method) (pynx.wavefront.cl_operator.ThinLens method)

OperatorCDI (class in pynx.cdi.cdi) OperatorPtycho (class in pynx.ptycho.ptycho) ortho_modes() (in module pynx.utils.math)

P

pad() (in module pynx.utils.array) pad2() (in module pynx.utils.array) parse_arg() (pynx.cdi.runner.runner.CDIRunner method) (pynx.ptycho.runner.runner.PtychoRunner method) parse_arg_beamline() (pynx.cdi.runner.runner.CDIRunner method) (pynx.ptycho.runner.runner.PtychoRunner method) parse_argv() (pynx.cdi.runner.runner.CDIRunner method) parse_bliss_file() (in module pynx.cdi.runner.regrid) parse_parameters_file() (pynx.cdi.runner.runner.CDIRunner method) phase2rgb() (in module pynx.utils.plot_utils) phase_tilt() (in module pynx.utils.phase) pixel_size_object() (pynx.ptycho.ptycho.PtychoData method) plot() (pynx.utils.fourier_shell_correlation.FSCPlot method) plot_prtf() (in module pynx.utils.phase_retrieval_transfer_function) prepare() (pynx.ptycho.runner.runner.PtychoRunnerScan method) prepare_cdi() (pynx.cdi.runner.runner.CDIRunnerScan method) prepare_data() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.cl_operator.CLOperatorPtycho method) (pynx.ptycho.cl_operator.MemUsage method) prepare_processing_unit() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) primes() (in module pynx.utils.math) print() (pynx.cdi.runner.runner.CDIRunner method) (pynx.ptycho.ptycho.Ptycho method) (pynx.ptycho.runner.runner.PtychoRunner method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) print_probe_fwhm() (pynx.ptycho.runner.runner.PtychoRunnerScan method) probe_fwhm() (in module pynx.ptycho.analysis) probe_propagate() (in module pynx.ptycho.analysis) process_all() (pynx.cdi.runner.regrid.Regrid3D method) process_scans() (pynx.cdi.runner.runner.CDIRunner method) (pynx.ptycho.runner.runner.PtychoRunner method) ProcessingUnitException ProcessingUnitWarning project_frames() (pynx.cdi.runner.regrid.Regrid3D method) project_one_frame() (pynx.cdi.runner.regrid.Regrid3D method) PropagateApplyAmplitude (class in pynx.ptycho.cl_operator) PropagateFarField (class in pynx.wavefront.cl_operator) PropagateFRT (class in pynx.wavefront.cl_operator) PropagateNearField (class in pynx.ptycho.cl_operator) (class in pynx.wavefront.cl_operator) PRTF (class in pynx.cdi.cl_operator) prtf() (in module pynx.utils.phase_retrieval_transfer_function) Psi2Obj (class in pynx.ptycho.cl_operator) Psi2ObjMerge (class in pynx.ptycho.cl_operator) Psi2PosMerge (class in pynx.ptycho.cl_operator) Psi2PosShift (class in pynx.ptycho.cl_operator) Psi2Probe (class in pynx.ptycho.cl_operator) Psi2ProbeMerge (class in pynx.ptycho.cl_operator) Ptycho (class in pynx.ptycho.ptycho) PtychoData (class in pynx.ptycho.ptycho) PtychoRunner (class in pynx.ptycho.runner.runner) PtychoRunnerException PtychoRunnerScan (class in pynx.ptycho.runner.runner) PurgeStacks (class in pynx.ptycho.cl_operator) pynx.cdi module

pynx.cdi.cdi module pynx.cdi.cl_operator module pynx.cdi.runner.regrid module pynx.cdi.runner.runner module pynx.processing_unit module pynx.processing_unit.cuda_device module pynx.processing_unit.opencl_device module pynx.ptycho module pynx.ptycho.analysis module pynx.ptycho.cl_operator module pynx.ptycho.ptycho module pynx.ptycho.runner.runner module pynx.scattering module pynx.scattering.fhkl module pynx.scattering.fthomson module pynx.utils module pynx.utils.array module pynx.utils.benchmark module pynx.utils.fourier_shell_correlation module pynx.utils.history module pynx.utils.math module pynx.utils.pattern module pynx.utils.phase module pynx.utils.phase_retrieval_transfer_function module pynx.utils.plot_utils module pynx.wavefront module pynx.wavefront.cl_operator module pynx.wavefront.wavefront module PynxOrderedDict (class in pynx.utils.history)

Q

QuadraticPhase (class in pynx.ptycho.cl_operator) (class in pynx.wavefront.cl_operator)

R

RAAR (class in pynx.cdi.cl_operator) rebin() (in module pynx.utils.array) rebin_data() (pynx.cdi.runner.runner.CDIRunnerScan method) RectangularMask (class in pynx.wavefront.cl_operator) Regrid3D (class in pynx.cdi.runner.regrid) remove_phase_ramp() (in module pynx.utils.phase) reset_history() (pynx.cdi.cdi.CDI method) (pynx.ptycho.ptycho.Ptycho method)

ring_thickness() (in module pynx.utils.phase_retrieval_transfer_function) ringthickness() (pynx.utils.fourier_shell_correlation.FourierShellCorr method) run() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) run_algorithm() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.runner.runner.PtychoRunnerScan method)

S

save() (pynx.ptycho.runner.runner.PtychoRunnerScan method) save_cdi_data_cxi() (in module pynx.cdi.cdi) save_data_cxi() (pynx.cdi.cdi.CDI method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) save_movie() (pynx.ptycho.runner.runner.PtychoRunnerScan method) save_obj_cxi() (pynx.cdi.cdi.CDI method) save_obj_probe_cxi() (in module pynx.ptycho.ptycho) (pynx.ptycho.ptycho.Ptycho method) save_plot() (pynx.cdi.runner.runner.CDIRunnerScan method) (pynx.ptycho.runner.runner.PtychoRunnerScan method) save_ptycho_data_cxi() (in module pynx.ptycho.ptycho) save_result() (pynx.cdi.runner.runner.CDIRunnerScan method) Scale (class in pynx.ptycho.cl_operator) (class in pynx.wavefront.cl_operator) ScaleObj (class in pynx.cdi.cl_operator) ScaleObjProbe (class in pynx.ptycho.cl_operator) SelectStack (class in pynx.ptycho.cl_operator) send_image() (pynx.cdi.runner.regrid.Regrid3D method) send_mask() (pynx.cdi.runner.regrid.Regrid3D method) set() (pynx.wavefront.wavefront.Wavefront method) set_background() (pynx.ptycho.ptycho.Ptycho method) set_bin() (pynx.cdi.cdi.CDI method) set_crop() (pynx.cdi.cdi.CDI method)

set_free_pixel_mask() (pynx.cdi.cdi.CDI method) set_iobs() (pynx.cdi.cdi.CDI method) set_mask() (pynx.cdi.cdi.CDI method) set_obj() (pynx.cdi.cdi.CDI method) (pynx.ptycho.ptycho.Ptycho method) set_obj_zero_phase_mask() (pynx.ptycho.ptycho.Ptycho method) set_probe() (pynx.ptycho.ptycho.Ptycho method) set_stack_size() (pynx.ptycho.cl_operator.CLProcessingUnitPtycho method) set_support() (pynx.cdi.cdi.CDI method) set_upsample() (pynx.cdi.cdi.CDI method) shift_phase_zero() (in module pynx.utils.phase) show_obj_probe() (in module pynx.utils.plot_utils) ShowCDI (class in pynx.cdi.cl_operator) showCplx() (in module pynx.utils.plot_utils) siemens_star() (in module pynx.utils.pattern) smaller_primes() (in module pynx.utils.math) spiral_archimedes() (in module pynx.utils.pattern) spiral_fermat() (in module pynx.utils.pattern) SumIntensity1 (class in pynx.ptycho.cl_operator) SupportExpand (class in pynx.cdi.cl_operator) SupportTooLarge SupportTooSmall SupportUpdate (class in pynx.cdi.cl_operator)

T

test_smaller_primes() (in module pynx.utils.math) ThinLens (class in pynx.wavefront.cl_operator) timestamp_increment() (pynx.cdi.cdi.OperatorCDI method) (pynx.cdi.cl_operator.FreePU method) (pynx.ptycho.cl_operator.Calc2Obs method) (pynx.ptycho.cl_operator.CalcIllumination method) (pynx.ptycho.cl_operator.CLOperatorPtycho method) (pynx.ptycho.cl_operator.FreePU method) (pynx.ptycho.cl_operator.MemUsage method) (pynx.ptycho.ptycho.OperatorPtycho method) (pynx.wavefront.cl_operator.FreePU method)

transverse_apodization() (pynx.utils.fourier_shell_correlation.FourierShellCorr method)

U

unwrap_phase() (in module pynx.utils.phase) update_history() (pynx.cdi.cdi.CDI method) (pynx.ptycho.ptycho.Ptycho method)

UpdatePSF (class in pynx.cdi.cl_operator) upsample() (in module pynx.utils.array) UserWarningWavefrontNearFieldPropagation

V

view_copy() (pynx.ptycho.cl_operator.CLOperatorPtycho method) view_purge() (pynx.ptycho.cl_operator.CLOperatorPtycho method)

view_register() (pynx.ptycho.cl_operator.CLOperatorPtycho method) view_sum() (pynx.ptycho.cl_operator.CLOperatorPtycho method) view_swap() (pynx.ptycho.cl_operator.CLOperatorPtycho method)

W

Wavefront (class in pynx.wavefront.wavefront)

Z

ZeroPhaseRamp (class in pynx.ptycho.cl_operator)