Index

_

__init__() (cdiutils.facetanalysis.FacetAnalysisProcessor method) (cdiutils.Geometry method), [1] (cdiutils.interactive.Plotter method) (cdiutils.interactive.ThreeDViewer method) (cdiutils.interactive.VolumeViewer method), [1] (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIExplorer method) (cdiutils.io.CXIFile method) (cdiutils.io.id01.ID01Loader method) (cdiutils.io.id01.SpecLoader method) (cdiutils.io.ID01Loader method) (cdiutils.io.Loader method) (cdiutils.io.loader.H5TypeLoader method) (cdiutils.io.loader.Loader method) (cdiutils.io.nanomax.NanoMAXLoader method) (cdiutils.io.p10.P10Loader method) (cdiutils.io.P10Loader method) (cdiutils.io.sixs.SIXSLoader method) (cdiutils.io.SIXSLoader method) (cdiutils.io.vtk.VtkImportError method) (cdiutils.pipeline.base.LoggerWriter method) (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.bcdi.PyNXScriptError method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) (cdiutils.process.phaser.PhasingResultAnalyser method) (cdiutils.process.phaser.PyNXImportError method) (cdiutils.process.phaser.PyNXPhaser method) (cdiutils.process.PhasingResultAnalyser method) (cdiutils.process.PyNXPhaser method) (cdiutils.simulation.BCDISimulator method) (cdiutils.SpaceConverter method), [1]

A

add_colorbar() (in module cdiutils.plot) (in module cdiutils.plot.formatting) add_colorwheel() (in module cdiutils.plot.formatting) add_displacement_field() (in module cdiutils.simulation) add_labels() (in module cdiutils.plot.formatting) add_linear_phase() (in module cdiutils.simulation) add_noise() (in module cdiutils.simulation), [1] add_quadratic_phase() (in module cdiutils.simulation) add_random_phase() (in module cdiutils.simulation) adjust_to_valid_shape() (in module cdiutils.utils) alien_mask (cdiutils.io.Loader attribute) (cdiutils.io.loader.Loader attribute) all_angles (cdiutils.simulation.BCDISimulator attribute) amplitude_based_metrics() (cdiutils.process.phaser.PhasingResultAnalyser static method) (cdiutils.process.PhasingResultAnalyser static method) analyse_phasing_results() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.process.phaser.PhasingResultAnalyser method) (cdiutils.process.PhasingResultAnalyser method)

angle() (in module cdiutils.utils) angle_names (cdiutils.io.id01.ID01Loader attribute), [1] (cdiutils.io.id01.SpecLoader attribute) (cdiutils.io.ID01Loader attribute), [1] (cdiutils.io.nanomax.NanoMAXLoader attribute), [1] (cdiutils.io.p10.P10Loader attribute), [1] (cdiutils.io.P10Loader attribute), [1] (cdiutils.io.sixs.SIXSLoader attribute) (cdiutils.io.SIXSLoader attribute) angles (cdiutils.pipeline.bcdi.BcdiPipeline attribute) angular_spectrum_propagation() (in module cdiutils.wavefront) apodize() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) authorised_detector_names (cdiutils.io.id01.ID01Loader attribute), [1] (cdiutils.io.ID01Loader attribute), [1] (cdiutils.io.nanomax.NanoMAXLoader attribute), [1] (cdiutils.io.p10.P10Loader attribute), [1] (cdiutils.io.P10Loader attribute), [1] (cdiutils.io.sixs.SIXSLoader attribute) (cdiutils.io.SIXSLoader attribute)

B

BcdiPipeline (class in cdiutils.pipeline) (class in cdiutils.pipeline.bcdi) BCDISimulator (class in cdiutils.simulation) beam_direction (cdiutils.Geometry attribute), [1] bin_along_axis() (in module cdiutils.utils)

bin_flat_mask() (cdiutils.io.Loader static method) (cdiutils.io.loader.Loader static method) bin_rocking_angle_values() (cdiutils.io.Loader static method) (cdiutils.io.loader.Loader static method) bragg_angle_to_lattice_parameter() (cdiutils.simulation.BCDISimulator method)

C

cancel_job() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) cdiutils.analysis.stats module cdiutils.facetanalysis module cdiutils.io.cxi module cdiutils.io.id01 module cdiutils.io.loader module cdiutils.io.nanomax module cdiutils.io.p10 module cdiutils.io.sixs module cdiutils.io.vtk module cdiutils.pipeline.base module cdiutils.pipeline.bcdi module cdiutils.pipeline.parameters module cdiutils.pipeline.pipeline_plotter module cdiutils.plot.colormap module cdiutils.plot.formatting module cdiutils.plot.slice module cdiutils.plot.volume module cdiutils.process.phaser module cdiutils.process.postprocessor module

cdiutils.simulation module cdiutils.utils module center() (in module cdiutils.utils) chain_centring() (cdiutils.utils.CroppingHandler class method) check_previous_data() (cdiutils.facetanalysis.FacetAnalysisProcessor method) class_isosurface (cdiutils.pipeline.bcdi.BcdiPipeline attribute) (cdiutils.pipeline.BcdiPipeline attribute) close() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIExplorer method) (cdiutils.io.CXIFile method) clustering() (cdiutils.facetanalysis.FacetAnalysisProcessor method) cmap (cdiutils.interactive.Plotter attribute), [1] cmap_options (cdiutils.interactive.ThreeDViewer attribute) collect_keys() (in module cdiutils.pipeline.parameters) complex_to_rgb() (in module cdiutils.plot.colormap) compute_angles() (cdiutils.simulation.BCDISimulator method) compute_corrected_angles() (in module cdiutils.utils) compute_distance_from_com() (in module cdiutils.utils) convert_np_arrays() (in module cdiutils.pipeline.parameters) converter (cdiutils.pipeline.bcdi.BcdiPipeline attribute) copy() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) create_cxi_dataset() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) create_cxi_group() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) create_cxi_image() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) create_group() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) crop_at_center() (in module cdiutils.utils) cropped_detector_data (cdiutils.pipeline.bcdi.BcdiPipeline attribute) CroppingHandler (class in cdiutils.utils) current_entry (cdiutils.io.cxi.CXIFile property) (cdiutils.io.CXIFile property) cxi (cdiutils.io.CXIExplorer attribute) cxi_to_xu() (cdiutils.Geometry method), [1] CXIExplorer (class in cdiutils.io) CXIFile (class in cdiutils.io) (class in cdiutils.io.cxi)

D

data_array (cdiutils.interactive.Plotter attribute), [1] def_edge_corner() (cdiutils.facetanalysis.FacetAnalysisProcessor method) def_index() (cdiutils.facetanalysis.FacetAnalysisProcessor method) def_label() (cdiutils.facetanalysis.FacetAnalysisProcessor method) def_list_facet_analysis() (cdiutils.facetanalysis.FacetAnalysisProcessor method) def_mean_strain() (cdiutils.facetanalysis.FacetAnalysisProcessor method) def_smooth_dir_facet_edge_corner() (cdiutils.facetanalysis.FacetAnalysisProcessor method) def_smooth_supp_dir() (cdiutils.facetanalysis.FacetAnalysisProcessor method) det_calib_params (cdiutils.simulation.BCDISimulator attribute) detector_axis0_orientation (cdiutils.Geometry attribute), [1] detector_axis1_orientation (cdiutils.Geometry attribute), [1] detector_circles (cdiutils.Geometry attribute), [1]

detector_data (cdiutils.pipeline.bcdi.BcdiPipeline attribute) detector_data() (cdiutils.pipeline.pipeline_plotter.PipelinePlotter class method) detector_name (cdiutils.io.Loader attribute) (cdiutils.io.loader.Loader attribute) (cdiutils.simulation.BCDISimulator attribute) detector_shape (cdiutils.simulation.BCDISimulator attribute) detector_to_q_matrix (cdiutils.simulation.BCDISimulator attribute) diffractometer_angles (cdiutils.simulation.BCDISimulator attribute) direct_lab_voxel_size (cdiutils.SpaceConverter property), [1] distance_clustering() (cdiutils.facetanalysis.FacetAnalysisProcessor method) do_transition() (cdiutils.SpaceConverter static method), [1] dspacing() (cdiutils.SpaceConverter static method), [1]

E

energy (cdiutils.simulation.BCDISimulator attribute) energy_to_wavelength() (in module cdiutils.utils) ensure_pynx_shape() (in module cdiutils.utils) entry_counters (cdiutils.io.cxi.CXIFile property) (cdiutils.io.CXIFile property)

explore() (cdiutils.io.CXIExplorer method) extra_info (cdiutils.pipeline.bcdi.BcdiPipeline attribute) extract_reduced_shape() (in module cdiutils.utils) extract_run_info() (in module cdiutils.process.phaser)

F

facet_analysis() (cdiutils.facetanalysis.FacetAnalysisProcessor method) (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) FacetAnalysisProcessor (class in cdiutils.facetanalysis) figsize (cdiutils.interactive.Plotter attribute), [1] filename (cdiutils.interactive.Plotter attribute) fill_up_support() (in module cdiutils.utils) find_edges() (cdiutils.facetanalysis.FacetAnalysisProcessor method) find_hull() (in module cdiutils.utils) find_isosurface() (in module cdiutils.analysis.stats) find_max_pos() (in module cdiutils.utils) find_phasing_results() (cdiutils.process.phaser.PhasingResultAnalyser method) (cdiutils.process.PhasingResultAnalyser method) find_suitable_array_shape() (in module cdiutils.utils) flat_field (cdiutils.io.Loader attribute) (cdiutils.io.loader.Loader attribute)

flip_reconstruction() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) flush() (cdiutils.pipeline.base.LoggerWriter method) focus_probe() (in module cdiutils.wavefront) fontsize (cdiutils.interactive.Plotter attribute), [1] force_centred_cropping() (cdiutils.utils.CroppingHandler class method) format_scanned_counters() (cdiutils.io.Loader static method) (cdiutils.io.loader.Loader static method) from_dict() (cdiutils.Geometry class method), [1] from_file() (cdiutils.pipeline.bcdi.BcdiPipeline class method) (cdiutils.pipeline.BcdiPipeline class method) (cdiutils.SpaceConverter class method), [1] from_setup() (cdiutils.Geometry class method), [1] (cdiutils.io.Loader class method) (cdiutils.io.loader.Loader class method)

G

generate_support_from() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) genetic_phasing() (cdiutils.process.phaser.PyNXPhaser method) (cdiutils.process.PyNXPhaser method) geometry (cdiutils.simulation.BCDISimulator attribute) Geometry (class in cdiutils), [1] get_alien_mask() (cdiutils.io.Loader method) (cdiutils.io.loader.Loader method) get_angular_offsets() (cdiutils.simulation.BCDISimulator method) get_centred_slices() (in module cdiutils.utils) get_data_array() (cdiutils.interactive.Plotter method) get_detector_angles() (cdiutils.simulation.BCDISimulator method) get_detector_name() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) (cdiutils.io.Loader method) (cdiutils.io.loader.Loader method) get_direct_lab_regular_grid() (cdiutils.SpaceConverter method), [1] get_displacement() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) get_displacement_gradient() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) get_explorer() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) get_extent() (in module cdiutils.plot.formatting) get_figure_size() (in module cdiutils.plot) (in module cdiutils.plot.formatting) get_focal_distances() (in module cdiutils.wavefront) get_het_normal_strain() (cdiutils.process.PostProcessor class method) (cdiutils.process.postprocessor.PostProcessor class method) get_histogram() (in module cdiutils.analysis.stats)

get_job_state() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) get_mappable() (in module cdiutils.plot.formatting) get_mask() (cdiutils.io.Loader class method) (cdiutils.io.loader.Loader class method) get_masked_data() (cdiutils.utils.CroppingHandler class method) get_node() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) get_oversampling_ratios() (in module cdiutils.utils) get_params_from_variables() (in module cdiutils.pipeline.parameters) get_plot_configs() (in module cdiutils.plot.formatting) get_position() (cdiutils.utils.CroppingHandler static method) get_prime_factors() (in module cdiutils.utils) get_q_lab_regular_grid() (cdiutils.SpaceConverter method), [1] get_q_norm_histogram() (cdiutils.SpaceConverter method), [1] get_q_space_transitions() (cdiutils.SpaceConverter method), [1] get_realistic_detector_data() (cdiutils.simulation.BCDISimulator method) get_reciprocal_voxel_size() (in module cdiutils.utils) get_rocking_angle() (cdiutils.io.Loader static method) (cdiutils.io.loader.Loader static method) get_rocking_angles() (cdiutils.simulation.BCDISimulator static method) get_roi() (cdiutils.utils.CroppingHandler class method) get_start_time() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) get_structural_properties() (cdiutils.process.PostProcessor class method) (cdiutils.process.postprocessor.PostProcessor class method) get_transformation_matrix() (cdiutils.SpaceConverter method), [1] get_width_metrics() (in module cdiutils.wavefront) get_x_y_limits_extents() (in module cdiutils.plot.formatting) get_xu_q_lab_regular_grid() (cdiutils.SpaceConverter method), [1]

H

h5_safe_load() (in module cdiutils.io.loader) H5TypeLoader (class in cdiutils.io.loader) hemisphere_projection() (in module cdiutils.plot.volume)

hkl (cdiutils.simulation.BCDISimulator attribute) hot_pixel_filter() (in module cdiutils.utils) hybrid_gradient() (in module cdiutils.utils)

I

ID01Loader (class in cdiutils.io) (class in cdiutils.io.id01) IMAGE_MEMBERS (cdiutils.io.cxi.CXIFile attribute) (cdiutils.io.CXIFile attribute) index_cropped_det_to_index_of_q_lab() (cdiutils.SpaceConverter method), [1] index_cropped_det_to_q_lab() (cdiutils.SpaceConverter method), [1] index_det_to_index_of_q_lab() (cdiutils.SpaceConverter method), [1] index_det_to_q_lab() (cdiutils.SpaceConverter method), [1] init_cdi() (cdiutils.process.phaser.PyNXPhaser method) (cdiutils.process.PyNXPhaser method)

init_interpolator() (cdiutils.SpaceConverter method), [1] init_plot() (cdiutils.interactive.Plotter method) init_q_space() (cdiutils.SpaceConverter method), [1] intensity (cdiutils.simulation.BCDISimulator attribute) is_cxi (cdiutils.Geometry attribute), [1] is_job_running() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) is_valid_shape() (in module cdiutils.utils) isparameter() (in module cdiutils.pipeline.parameters)

J

job() (in module cdiutils.pipeline.base)

JobCancelledError JobFailedError

K

kde_from_histogram() (in module cdiutils.analysis.stats)

L

lattice_parameter (cdiutils.simulation.BCDISimulator attribute) lattice_parameter() (cdiutils.SpaceConverter class method), [1] lattice_parameter_to_bragg_angle() (cdiutils.simulation.BCDISimulator method) load_angles() (cdiutils.io.loader.H5TypeLoader method) load_cxi() (in module cdiutils.io) (in module cdiutils.io.cxi) load_det_calib_params() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.id01.SpecLoader method) (cdiutils.io.ID01Loader method) (cdiutils.io.Loader method) (cdiutils.io.loader.Loader method) (cdiutils.io.nanomax.NanoMAXLoader method) (cdiutils.io.p10.P10Loader method) (cdiutils.io.P10Loader method) (cdiutils.io.sixs.SIXSLoader method) (cdiutils.io.SIXSLoader method) load_detector_data() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.id01.SpecLoader method) (cdiutils.io.ID01Loader method) (cdiutils.io.nanomax.NanoMAXLoader method) (cdiutils.io.p10.P10Loader method) (cdiutils.io.P10Loader method) (cdiutils.io.sixs.SIXSLoader method) (cdiutils.io.SIXSLoader method) load_detector_shape() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.id01.SpecLoader method) (cdiutils.io.ID01Loader method) (cdiutils.io.Loader method) (cdiutils.io.loader.Loader method) (cdiutils.io.nanomax.NanoMAXLoader method) (cdiutils.io.p10.P10Loader method) (cdiutils.io.P10Loader method) (cdiutils.io.sixs.SIXSLoader method) (cdiutils.io.SIXSLoader method) load_energy() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.id01.SpecLoader method) (cdiutils.io.ID01Loader method) (cdiutils.io.Loader method) (cdiutils.io.loader.Loader method) (cdiutils.io.nanomax.NanoMAXLoader method) (cdiutils.io.p10.P10Loader method) (cdiutils.io.P10Loader method) (cdiutils.io.sixs.SIXSLoader method) (cdiutils.io.SIXSLoader method)

load_from_cxi() (cdiutils.pipeline.bcdi.BcdiPipeline class method) (cdiutils.pipeline.BcdiPipeline class method) load_instrument_parameters() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) load_measurement_parameters() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) load_motor_positions() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.id01.SpecLoader method) (cdiutils.io.ID01Loader method) (cdiutils.io.nanomax.NanoMAXLoader method) (cdiutils.io.p10.P10Loader method) (cdiutils.io.P10Loader method) (cdiutils.io.sixs.SIXSLoader method) (cdiutils.io.SIXSLoader method) load_parameters() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) load_plotselect_parameter() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) load_sample_parameters() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) load_vtk() (in module cdiutils.io.vtk) Loader (class in cdiutils.io) (class in cdiutils.io.loader) log (cdiutils.interactive.Plotter attribute), [1] LoggerWriter (class in cdiutils.pipeline.base)

M

make_box() (in module cdiutils.simulation) make_colorwheel() (in module cdiutils.plot.formatting) make_cylinder() (in module cdiutils.simulation) make_dump_dir() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) make_ellipsoid() (in module cdiutils.simulation) make_support() (in module cdiutils.utils), [1] mask (cdiutils.pipeline.bcdi.BcdiPipeline attribute) (cdiutils.simulation.BCDISimulator attribute) max_number_of_values_printed (cdiutils.io.CXIExplorer attribute) metrics (cdiutils.process.phaser.PhasingResultAnalyser property) (cdiutils.process.PhasingResultAnalyser property) mode_decomposition() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.process.phaser.PhasingResultAnalyser method) (cdiutils.process.PhasingResultAnalyser method) module cdiutils.analysis.stats cdiutils.facetanalysis cdiutils.io.cxi cdiutils.io.id01 cdiutils.io.loader cdiutils.io.nanomax cdiutils.io.p10 cdiutils.io.sixs cdiutils.io.vtk cdiutils.pipeline.base cdiutils.pipeline.bcdi cdiutils.pipeline.parameters cdiutils.pipeline.pipeline_plotter cdiutils.plot.colormap cdiutils.plot.formatting cdiutils.plot.slice cdiutils.plot.volume cdiutils.process.phaser cdiutils.process.postprocessor cdiutils.simulation cdiutils.utils

monitor_job() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method)

N

name (cdiutils.Geometry attribute), [1] nan_center_of_mass() (in module cdiutils.utils) nan_to_zero() (in module cdiutils.utils) NanoMAXLoader (class in cdiutils.io.nanomax)

normalise() (in module cdiutils.utils) normalise_complex_array() (in module cdiutils.utils) num_frames (cdiutils.simulation.BCDISimulator attribute) num_to_nan() (in module cdiutils.utils)

O

obj (cdiutils.simulation.BCDISimulator attribute) open() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) ortho_detector_data() (cdiutils.pipeline.pipeline_plotter.PipelinePlotter static method)

orthogonalise_to_direct_lab() (cdiutils.SpaceConverter method), [1] orthogonalise_to_q_lab() (cdiutils.SpaceConverter method), [1] orthogonalised_intensity (cdiutils.pipeline.bcdi.BcdiPipeline attribute) oversampling_from_diffraction() (in module cdiutils.utils)

P

P10Loader (class in cdiutils.io) (class in cdiutils.io.p10) paths (cdiutils.io.CXIExplorer attribute) phase_factor (cdiutils.simulation.BCDISimulator attribute) phase_offset_to_zero() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) phase_retrieval() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) phase_retrieval_gui() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) PhasingResultAnalyser (class in cdiutils.process) (class in cdiutils.process.phaser) Pipeline (class in cdiutils.pipeline) (class in cdiutils.pipeline.base) PipelinePlotter (class in cdiutils.pipeline.pipeline_plotter) plot (cdiutils.interactive.Plotter attribute), [1] plot_3d_isosurface() (in module cdiutils.interactive) plot_3d_object() (in module cdiutils.plot.volume) plot_3d_surface_projections() (in module cdiutils.plot.volume) plot_3d_vector_field() (in module cdiutils.plot.volume) plot_3d_voxels() (in module cdiutils.plot.volume) plot_background() (in module cdiutils.plot.formatting) plot_cdi() (cdiutils.process.phaser.PyNXPhaser static method) (cdiutils.process.PyNXPhaser static method) plot_contour() (in module cdiutils.plot.slice) plot_detector_data() (cdiutils.io.Loader static method) (cdiutils.io.loader.Loader static method) plot_final_object_fft() (cdiutils.pipeline.pipeline_plotter.PipelinePlotter static method)

plot_histogram() (in module cdiutils.analysis.stats) plot_multiple_volume_slices() (in module cdiutils.plot.slice) plot_phasing_result() (cdiutils.process.phaser.PhasingResultAnalyser static method) (cdiutils.process.PhasingResultAnalyser static method) plot_propagated_probe() (in module cdiutils.wavefront) plot_slices() (in module cdiutils.plot.slice) plot_volume_slices() (in module cdiutils.plot.slice) Plotter (class in cdiutils.interactive) postprocess() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) PostProcessor (class in cdiutils.process) (class in cdiutils.process.postprocessor) prepare_volume() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) preprocess() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) pretty_print() (cdiutils.pipeline.base.Pipeline static method) (cdiutils.pipeline.BcdiPipeline static method) (cdiutils.pipeline.Pipeline static method) probe_focus_sweep() (in module cdiutils.wavefront) probe_metrics() (in module cdiutils.wavefront) process() (cdiutils.pipeline.base.Pipeline static method) (cdiutils.pipeline.BcdiPipeline static method) (cdiutils.pipeline.Pipeline static method) PyNXImportError PyNXPhaser (class in cdiutils.process) (class in cdiutils.process.phaser) PyNXScriptError

Q

q_to_detector_matrix (cdiutils.simulation.BCDISimulator attribute)

q_voxel_size (cdiutils.simulation.BCDISimulator attribute)

R

read_cxi_dataset() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) read_instructions() (cdiutils.process.phaser.PyNXPhaser class method) (cdiutils.process.PyNXPhaser class method) reconstruction (cdiutils.pipeline.bcdi.BcdiPipeline attribute) remove_phase_ramp() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method) result_analyser (cdiutils.pipeline.bcdi.BcdiPipeline attribute)

rocking_angle (cdiutils.io.Loader attribute) (cdiutils.io.loader.Loader attribute) roi_list_to_slices() (cdiutils.utils.CroppingHandler static method) run() (cdiutils.process.phaser.PyNXPhaser method) (cdiutils.process.PyNXPhaser method) run_detector_calibration() (cdiutils.SpaceConverter static method), [1] run_multiple_instances() (cdiutils.process.phaser.PyNXPhaser method) (cdiutils.process.PyNXPhaser method)

S

safe() (in module cdiutils.io.id01) sample_circles (cdiutils.Geometry attribute), [1] sample_name (cdiutils.io.Loader attribute) (cdiutils.io.loader.Loader attribute) sample_orientation (cdiutils.Geometry property), [1] sample_surface_normal (cdiutils.Geometry attribute), [1] save_as_cxi() (in module cdiutils.io.cxi) save_as_vti() (in module cdiutils.io.vtk) save_fig() (in module cdiutils.plot.formatting) save_json_cmap() (in module cdiutils.plot.colormap) scan (cdiutils.io.Loader attribute) (cdiutils.io.loader.Loader attribute) search() (cdiutils.io.CXIExplorer method) select_best_candidates() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.process.phaser.PhasingResultAnalyser method) (cdiutils.process.PhasingResultAnalyser method) set_data() (cdiutils.interactive.ThreeDViewer method) set_entry() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) set_measurement_params() (cdiutils.simulation.BCDISimulator method) set_object() (cdiutils.simulation.BCDISimulator method) set_plot_configs() (in module cdiutils.plot.formatting) set_x_y_limits_extents() (in module cdiutils.plot.formatting) shape (cdiutils.SpaceConverter property), [1] shape_for_safe_centred_cropping() (in module cdiutils.utils) shift_to_target_pixel() (cdiutils.simulation.BCDISimulator method) show() (cdiutils.interactive.ThreeDViewer method) (cdiutils.io.CXIExplorer method) show_3d_final_result() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method)

show_scan_attributes() (cdiutils.io.id01.ID01Loader method) (cdiutils.io.ID01Loader method) simulate_diffraction() (in module cdiutils.simulation) simulate_object() (cdiutils.simulation.BCDISimulator method) SIXSLoader (class in cdiutils.io) (class in cdiutils.io.sixs) size_up_support() (in module cdiutils.utils) soft_links (cdiutils.io.CXIExplorer attribute) softlink() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) sorted_phasing_results (cdiutils.process.phaser.PhasingResultAnalyser property) (cdiutils.process.PhasingResultAnalyser property) SpaceConverter (class in cdiutils), [1] SpecLoader (class in cdiutils.io.id01) stamp() (cdiutils.io.cxi.CXIFile method) (cdiutils.io.CXIFile method) strain_statistics() (cdiutils.pipeline.pipeline_plotter.PipelinePlotter static method) stream_job_output() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) structural_props (cdiutils.pipeline.bcdi.BcdiPipeline attribute) structure (cdiutils.simulation.BCDISimulator attribute) submit_job() (cdiutils.pipeline.base.Pipeline method) (cdiutils.pipeline.BcdiPipeline method) (cdiutils.pipeline.Pipeline method) summarise() (cdiutils.io.CXIExplorer method) summary_plot() (cdiutils.pipeline.pipeline_plotter.PipelinePlotter static method) support_transfer() (cdiutils.SpaceConverter method), [1] swap_convention() (cdiutils.Geometry static method), [1] symmetric_pad() (in module cdiutils.utils)

T

tabbed_print() (cdiutils.io.CXIExplorer method) target_peak_position (cdiutils.simulation.BCDISimulator attribute) ThreeDViewer (class in cdiutils.interactive) title (cdiutils.interactive.Plotter attribute), [1] to_bool() (in module cdiutils.utils) to_detector_frame() (cdiutils.simulation.BCDISimulator method) to_dict() (cdiutils.Geometry method), [1] (cdiutils.SpaceConverter method), [1]

to_file() (cdiutils.SpaceConverter method), [1] transform_volume() (in module cdiutils.utils) tree() (cdiutils.io.CXIExplorer method) tree_max_array_size (cdiutils.io.CXIExplorer attribute) tree_max_string_length (cdiutils.io.CXIExplorer attribute) twin_image_checkup() (cdiutils.process.phaser.PhasingResultAnalyser static method) (cdiutils.process.PhasingResultAnalyser static method) two_spine_frameless_ax() (in module cdiutils.plot.formatting)

U

unit_vector() (in module cdiutils.utils) unwrap_phase() (cdiutils.process.PostProcessor static method) (cdiutils.process.postprocessor.PostProcessor static method)

update_from_file() (cdiutils.pipeline.bcdi.BcdiPipeline method) (cdiutils.pipeline.BcdiPipeline method) update_plot_params() (in module cdiutils.plot.formatting)

V

v1_to_v2_rotation_matrix() (in module cdiutils.utils) valid_args_only() (in module cdiutils.utils) validate_and_fill_params() (in module cdiutils.pipeline.parameters) visualisation() (cdiutils.facetanalysis.FacetAnalysisProcessor method)

VolumeViewer (class in cdiutils.interactive), [1] voxel_pos (cdiutils.pipeline.bcdi.BcdiPipeline attribute) (cdiutils.pipeline.BcdiPipeline attribute) voxel_size (cdiutils.simulation.BCDISimulator attribute) VtkImportError

W

wavelength (cdiutils.simulation.BCDISimulator attribute) wavelength_to_energy() (in module cdiutils.utils)

white_interior_ticks_labels() (in module cdiutils.plot.formatting) write() (cdiutils.pipeline.base.LoggerWriter method)

X

x_y_lim_from_support() (in module cdiutils.plot.formatting)

Z

zero_to_nan() (in module cdiutils.utils)