Index

A

access_nested_dict() (in module nabu.app.shrink_dataset) accurate() (nabu.estimation.cor_sino.SinoCor method) add_last_bin() (in module nabu.processing.histogram) afb1d() (in module nabu.thirdparty.tomocupy_remove_stripe) align_frame() (in module nabu.stitching.alignment) align_horizontally() (in module nabu.stitching.alignment) alignment_axis_1 (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration attribute) alignment_axis_2 (nabu.stitching.config.SingleAxisStitchingConfiguration attribute) AlignmentAxis1 (class in nabu.stitching.alignment) AlignmentAxis2 (class in nabu.stitching.alignment) AlignmentBase (class in nabu.estimation.alignment) allocate_array() (nabu.processing.processing_base.ProcessingBase method) allocate_texture() (in module nabu.opencl.utils) allowed_axes (nabu.misc.utils.ConvolutionInfos attribute) analyze_dataset() (in module nabu.resources.dataset_analyzer) apply() (nabu.thirdparty.tomocupy_remove_stripe.DWTForward method) (nabu.thirdparty.tomocupy_remove_stripe.DWTInverse method) apply_distortion_correction_on_image() (in module nabu.pipeline.reader) apply_distortion_correction_on_images_stack() (in module nabu.pipeline.reader) apply_double_flatfield() (nabu.preproc.double_flatfield.DoubleFlatField method) (nabu.preproc.double_flatfield_cuda.CudaDoubleFlatField method) apply_double_flatfield_for_sub_regions() (nabu.preproc.double_flatfield_variable_region.DoubleFlatFieldVariableRegion method) apply_filter() (nabu.preproc.phase.PaganinPhaseRetrieval method) (nabu.preproc.phase_cuda.CudaPaganinPhaseRetrieval method) apply_vertical_shifts() (nabu.preproc.shift.VerticalShift method) (nabu.preproc.shift_cuda.CudaVerticalShift method) array_class (nabu.cuda.processing.CudaProcessing attribute) (nabu.opencl.processing.OpenCLProcessing attribute) (nabu.processing.processing_base.ProcessingBase attribute)

avail_methods (nabu.processing.unsharp.UnsharpMask attribute) available_backends (nabu.app.histogram.VolumesHistogram attribute) available_filters (nabu.reconstruction.filtering.SinoFilter attribute) available_padding_modes (nabu.preproc.phase.PaganinPhaseRetrieval attribute) (nabu.reconstruction.filtering.SinoFilter attribute) axis (nabu.stitching.config.SingleAxisStitchingConfiguration property) (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) axis_0_params (nabu.stitching.config.StitchingConfiguration attribute) axis_0_pos_mm (nabu.stitching.config.StitchingConfiguration attribute) axis_0_pos_px (nabu.stitching.config.PostProcessedZStitchingConfiguration attribute) (nabu.stitching.config.PreProcessedYStitchingConfiguration attribute) (nabu.stitching.config.PreProcessedZStitchingConfiguration attribute) (nabu.stitching.config.StitchingConfiguration attribute) axis_1_params (nabu.stitching.config.StitchingConfiguration attribute) axis_1_pos_mm (nabu.stitching.config.StitchingConfiguration attribute) axis_1_pos_px (nabu.stitching.config.PostProcessedZStitchingConfiguration attribute) (nabu.stitching.config.PreProcessedYStitchingConfiguration attribute) (nabu.stitching.config.PreProcessedZStitchingConfiguration attribute) (nabu.stitching.config.StitchingConfiguration attribute) axis_2_params (nabu.stitching.config.StitchingConfiguration attribute) axis_2_pos_mm (nabu.stitching.config.StitchingConfiguration attribute) axis_2_pos_px (nabu.stitching.config.PostProcessedZStitchingConfiguration attribute) (nabu.stitching.config.PreProcessedYStitchingConfiguration attribute) (nabu.stitching.config.PreProcessedZStitchingConfiguration attribute) (nabu.stitching.config.StitchingConfiguration attribute) azimuthal_integration() (in module nabu.processing.azim) azimuthal_integration_imagej_stack() (in module nabu.processing.azim) azimuthal_integration_skimage() (in module nabu.processing.azim) azimuthal_integration_skimage_stack() (in module nabu.processing.azim)

B

BACK (nabu.stitching.alignment.AlignmentAxis1 attribute) backend (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) (nabu.processing.fft_cuda.SKCUFFT attribute) (nabu.processing.fft_cuda.VKCUFFT attribute) (nabu.processing.fft_opencl.VKCLFFT attribute) (nabu.processing.fftshift.FFTshiftBase attribute) (nabu.processing.fftshift.OpenCLFFTshift attribute) (nabu.processing.padding_cuda.CudaPadding attribute) (nabu.processing.padding_opencl.OpenCLPadding attribute) (nabu.processing.transpose.CudaTranspose attribute) (nabu.processing.transpose.OpenCLTranspose attribute) (nabu.processing.transpose.TransposeBase attribute) (nabu.reconstruction.fbp.CudaBackprojector attribute) (nabu.reconstruction.fbp_base.BackprojectorBase attribute) (nabu.reconstruction.fbp_opencl.OpenCLBackprojector attribute) backend_processing_class (nabu.reconstruction.fbp.CudaBackprojector attribute) (nabu.reconstruction.fbp_base.BackprojectorBase attribute) (nabu.reconstruction.fbp_opencl.OpenCLBackprojector attribute) backends (nabu.processing.histogram.PartialHistogram attribute) backproj() (nabu.reconstruction.fbp_base.BackprojectorBase method) (nabu.reconstruction.hbp.HierarchicalBackprojector method) backprojection() (nabu.pipeline.helical.fbp.BackprojectorHelical method)

Backprojector (in module nabu.reconstruction.fbp) BackprojectorBase (class in nabu.reconstruction.fbp_base) BackprojectorHelical (class in nabu.pipeline.helical.fbp) balance_weights() (nabu.pipeline.helical.weight_balancer.WeightBalancer method) BaseClassError (class in nabu.utils) bench_textures module bin_image_stack() (in module nabu.pipeline.reader) bin_width_policies (nabu.processing.histogram.PartialHistogram attribute) binning() (in module nabu.misc.binning) binning_n_alt() (in module nabu.misc.binning) binning_validator() (in module nabu.pipeline.config_validators) binning_x (nabu.pipeline.fullfield.processconfig.ProcessConfig property) binning_z (nabu.pipeline.fullfield.processconfig.ProcessConfig property) boolean_or_auto_validator() (in module nabu.pipeline.config_validators) boolean_validator() (in module nabu.pipeline.config_validators) bootstrap() (in module nabu.app.bootstrap) bootstrap_stitching() (in module nabu.app.bootstrap_stitching) browse() (nabu.stitching.frame_composition.FrameComposition method) browse_data_files() (nabu.io.writer.HSTVolVolume method) (nabu.io.writer.NXVolVolume method) build_processing_steps() (nabu.pipeline.processconfig.ProcessConfigBase method) build_total_merit_list() (in module nabu.app.diag_to_pix) buildConebeamGeometry() (in module nabu.reconstruction.hbp)

C

calc_padding_lengths() (in module nabu.utils) calc_padding_lengths1D() (in module nabu.utils) call() (nabu.cuda.kernel.CudaKernel method) (nabu.opencl.kernel.OpenCLKernel method) CameraFocus (class in nabu.estimation.focus) CameraTilt (class in nabu.estimation.tilt) can_use_cuda_deringer() (in module nabu.reconstruction.rings_cuda) cast_progress_line_from_log() (nabu.stitching.utils.post_processing.SlurmStitchingFollowerThread static method) cast_volume() (in module nabu.io.cast_volume) CCDCorrectionClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) CCDFilter (class in nabu.preproc.ccd) CENTER (nabu.stitching.alignment.AlignmentAxis1 attribute) (nabu.stitching.alignment.AlignmentAxis2 attribute) CENTERED (nabu.stitching.utils.utils.ShiftAlgorithm attribute) CenterOfRotation (class in nabu.estimation.cor) CenterOfRotationAdaptiveSearch (class in nabu.estimation.cor) CenterOfRotationFourierAngles (class in nabu.estimation.cor_sino) CenterOfRotationGrowingWindow (class in nabu.estimation.cor) CenterOfRotationOctaveAccurate (class in nabu.estimation.cor) CenterOfRotationSlidingWindow (class in nabu.estimation.cor) CenterOfRotationVo (class in nabu.estimation.cor_sino) check_array() (nabu.processing.processing_base.ProcessingBase method) check_defined_attribute() (nabu.resources.dataset_analyzer.DatasetAnalyzer method) check_filename_src() (nabu.processing.kernel_base.KernelBase method) check_inputs() (nabu.stitching.stitcher.post_processing.PostProcessingStitching method) (nabu.stitching.stitcher.pre_processing.PreProcessingStitching method) (nabu.stitching.stitcher.z_stitcher.PreProcessingZStitcher method) check_overlaps() (in module nabu.stitching.overlap) check_shape() (in module nabu.utils) check_supported() (in module nabu.utils) check_supported_enum() (in module nabu.utils) check_textures_availability() (in module nabu.cuda.utils) (in module nabu.opencl.utils) check_virtual_sources_exist() (in module nabu.io.reader) ChunkedPipeline (class in nabu.pipeline.fullfield.chunked) ChunkReaderHelical (class in nabu.io.reader_helical) clean_script (nabu.stitching.config.SlurmConfig attribute) clip_circle() (in module nabu.utils) close_last_plot_windows() (nabu.estimation.alignment.AlignmentBase method) close_plot_window() (nabu.estimation.alignment.AlignmentBase method) CLOSEST (nabu.stitching.overlap.OverlapStitchingStrategy attribute) collect_cuda_gpus() (in module nabu.cuda.utils) collect_opencl_cpus() (in module nabu.opencl.utils) collect_opencl_gpus() (in module nabu.opencl.utils) compact_parameters() (in module nabu.resources.utils) compacted_views() (in module nabu.utils) compare_arrays() (in module nabu.testutils) compare_dicts() (in module nabu.utils) compare_shifted_images() (in module nabu.testutils) compare_volumes() (in module nabu.app.compare_volumes) compare_volumes_cli() (in module nabu.app.compare_volumes) compile_kernel_source() (nabu.cuda.kernel.CudaKernel method) (nabu.opencl.kernel.OpenCLKernel method) compose() (nabu.stitching.frame_composition.FrameComposition method) composed_axis (nabu.stitching.frame_composition.FrameComposition attribute) COMPOSITE_COARSE_TO_FINE (nabu.stitching.utils.utils.ShiftAlgorithm attribute) composite_cor_entry_point() (in module nabu.app.composite_cor) CompositeCOREstimator (in module nabu.pipeline.estimators) CompositeCORFinder (class in nabu.pipeline.estimators) compute_angle() (nabu.estimation.tilt.CameraTilt method) compute_double_flatfield() (nabu.app.double_flatfield.DoubleFlatFieldChunks method) (nabu.preproc.double_flatfield.DoubleFlatField method) (nabu.preproc.double_flatfield_cuda.CudaDoubleFlatField method) compute_estimated_shifts() (nabu.stitching.stitcher.post_processing.PostProcessingStitching method) (nabu.stitching.stitcher.pre_processing.PreProcessingStitching method) compute_filter() (nabu.preproc.phase.PaganinPhaseRetrieval method) compute_histogram() (nabu.processing.histogram.PartialHistogram method) compute_image_higher_signal() (in module nabu.stitching.overlap) compute_image_minimum_divergence() (in module nabu.stitching.overlap) compute_paganin_margin() (in module nabu.preproc.phase) compute_raw_frame_compositions() (nabu.stitching.frame_composition.FrameComposition static method) compute_reduced_flats_and_darks() (nabu.stitching.stitcher.pre_processing.PreProcessingStitching method) compute_stitch_frame_composition() (nabu.stitching.frame_composition.FrameComposition static method) compute_volume_histogram() (nabu.processing.histogram.VolumeHistogram method) compute_weights() (nabu.stitching.overlap.ImageStichOverlapKernel method) concatenate_dict() (in module nabu.utils) ConebeamClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) ConebeamReconstructor (class in nabu.reconstruction.cone)

config_renamed_keys (nabu.pipeline.fullfield.processconfig.ProcessConfig attribute) (nabu.pipeline.helical.processconfig.ProcessConfig attribute) (nabu.pipeline.processconfig.ProcessConfigBase attribute) configuration (nabu.stitching.stitcher.dumper.base.DumperBase property) (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) convert_dict_values() (in module nabu.io.utils) convert_halftomo() (in module nabu.reconstruction.sinogram) convert_index() (in module nabu.utils) convert_sino() (nabu.reconstruction.sinogram.SinoBuilder method) convert_str_to_tuple() (in module nabu.utils) convert_to_bool() (in module nabu.pipeline.config_validators) convert_to_bool_noerr() (in module nabu.pipeline.config_validators) convert_to_float() (in module nabu.pipeline.config_validators) convert_to_int() (in module nabu.pipeline.config_validators) Convolution (class in nabu.processing.convolution_cuda) ConvolutionInfos (class in nabu.misc.utils) convolve() (nabu.processing.convolution_cuda.Convolution method) copy_array() (in module nabu.cuda.utils) copy_big_gpuarray() (in module nabu.cuda.utils) copy_dict_items() (in module nabu.utils) copy_to_texture() (in module nabu.opencl.utils) cor_options_validator() (in module nabu.pipeline.config_validators) cor_slice_validator() (in module nabu.pipeline.config_validators) cor_validator() (in module nabu.pipeline.config_validators) COREstimator (in module nabu.pipeline.estimators) CORFinder (class in nabu.pipeline.estimators) CORFinderBase (class in nabu.pipeline.estimators) correct() (nabu.preproc.distortion.DistortionCorrection method) correct_distortion() (nabu.preproc.distortion.DistortionCorrection method) correct_distortion_interpn() (in module nabu.preproc.distortion) correct_spikes() (in module nabu.misc.filters) correction_methods (nabu.preproc.distortion.DistortionCorrection attribute) COSINUS_WEIGHTS (nabu.stitching.overlap.OverlapStitchingStrategy attribute) count_cuda_devices() (in module nabu.cuda.utils) create_dict_of_indices() (in module nabu.io.utils) create_distortion_maps_entry_point() (in module nabu.app.create_distortion_map_from_poly) create_heli_maps() (in module nabu.app.prepare_weights_double) create_maps_x_and_z() (in module nabu.app.create_distortion_map_from_poly) create_output_dataset() (nabu.stitching.stitcher.dumper.base.DumperBase method) (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumper method) (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD method) (nabu.stitching.stitcher.dumper.preprocessing.PreProcessingStitchingDumper method) create_subset_selection() (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD static method) create_virtual_layout() (in module nabu.io.writer) critical() (nabu.resources.logger.Logger method) CtfFilter (in module nabu.preproc.ctf) CTFPhaseRetrieval (class in nabu.preproc.ctf) CTFPhaseRetrievalClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) cuarray_format_to_dtype() (in module nabu.cuda.utils) cuarray_shape_dtype() (in module nabu.cuda.utils) cuda_fname (nabu.reconstruction.fbp.PolarBackprojector attribute) cuda_kernel_name (nabu.reconstruction.fbp.PolarBackprojector attribute) CudaBackprojector (class in nabu.reconstruction.fbp) CudaCCDFilter (class in nabu.preproc.ccd_cuda) CudaChunkedPipeline (class in nabu.pipeline.fullfield.chunked_cuda) CudaCTFPhaseRetrieval (class in nabu.preproc.ctf_cuda) CudaDoubleFlatField (class in nabu.preproc.double_flatfield_cuda) CudaFlatField (in module nabu.preproc.flatfield_cuda) CudaFlatFieldArrays (class in nabu.preproc.flatfield_cuda) CudaKernel (class in nabu.cuda.kernel) CudaLog (class in nabu.preproc.ccd_cuda) CudaMulAdd (class in nabu.processing.muladd_cuda) CudaMunchDeringer (class in nabu.reconstruction.rings_cuda) CudaPadding (class in nabu.processing.padding_cuda) CudaPaganinPhaseRetrieval (class in nabu.preproc.phase_cuda) CudaPartialHistogram (class in nabu.processing.histogram_cuda) CudaProcessing (class in nabu.cuda.processing) CudaReconstructor (class in nabu.reconstruction.reconstructor_cuda) CudaRotation (class in nabu.processing.rotation_cuda) CudaSinoBuilder (class in nabu.reconstruction.sinogram_cuda) CudaSinoFilter (class in nabu.reconstruction.filtering_cuda) CudaSinoMeanDeringer (class in nabu.reconstruction.rings_cuda) CudaSinoMult (class in nabu.reconstruction.sinogram_cuda) CudaSinoNormalization (class in nabu.reconstruction.sinogram_cuda) CudaTranspose (class in nabu.processing.transpose) CudaUnsharpMask (class in nabu.processing.unsharp_cuda) CudaVerticalShift (class in nabu.preproc.shift_cuda) CudaVoDeringer (class in nabu.reconstruction.rings_cuda) CudaVolumeHistogram (class in nabu.processing.histogram_cuda) cupy_to_pycuda() (in module nabu.cuda.utils)

D

darks (nabu.resources.dataset_analyzer.DatasetAnalyzer property) data (nabu.io.reader_helical.ChunkReaderHelical property) data_url_exists() (in module nabu.resources.nxflatfield) DataDumpManager (class in nabu.pipeline.datadump) dataset_hdf5_url (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer property) dataset_location_validator() (in module nabu.pipeline.config_validators) DatasetAnalyzer (class in nabu.resources.dataset_analyzer) DatasetReader (class in nabu.io.utils) DatasetValidatorBase (class in nabu.pipeline.dataset_validator) debug() (nabu.resources.logger.Logger method) decode_bytes() (in module nabu.app.generate_header) default() (nabu.app.composite_cor.NumpyArrayEncoder method) default_advanced_options (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor attribute) default_extra_options (nabu.estimation.alignment.AlignmentBase attribute) (nabu.estimation.cor_sino.CenterOfRotationVo attribute) (nabu.reconstruction.cone.ConebeamReconstructor attribute) (nabu.reconstruction.fbp_base.BackprojectorBase attribute) (nabu.reconstruction.fbp_opencl.OpenCLBackprojector attribute) (nabu.reconstruction.filtering.SinoFilter attribute) (nabu.reconstruction.filtering_cuda.CudaSinoFilter attribute) (nabu.reconstruction.mlem.MLEMReconstructor attribute) DEFAULT_HIGH_FREQUENCY_THRESHOLD (nabu.stitching.overlap.ImageStichOverlapKernel attribute) default_nabu_config (nabu.pipeline.fullfield.processconfig.ProcessConfig attribute) (nabu.pipeline.helical.processconfig.ProcessConfig attribute) (nabu.pipeline.processconfig.ProcessConfigBase attribute) default_padding_mode (nabu.reconstruction.fbp_base.BackprojectorBase attribute) default_tilt_method (nabu.pipeline.estimators.DetectorTiltEstimator attribute) deprecated() (in module nabu.utils) deprecated_class() (in module nabu.utils) deprecation_warning() (in module nabu.utils) detailed_merit() (in module nabu.app.diag_to_pix) detect_cuda_gpus() (in module nabu.cuda.utils) detect_opencl_gpus() (in module nabu.opencl.utils) detector_distortion_correction_validator() (in module nabu.pipeline.config_validators) detector_tilt (nabu.resources.dataset_analyzer.DatasetAnalyzer property) DetectorDistortionBase (class in nabu.io.detector_distortion) DetectorDistortionMapsXZ (class in nabu.io.detector_distortion)

DetectorDistortionProvider() (in module nabu.pipeline.detector_distortion_provider) DetectorTiltEstimator (class in nabu.pipeline.estimators) DetectorTranslationAlongBeam (class in nabu.estimation.translation) dff_cli() (in module nabu.app.double_flatfield) dict_to_config_obj() (in module nabu.stitching.config) DictToObj (class in nabu.utils) directory_location_validator() (in module nabu.pipeline.config_validators) directory_writeable_validator() (in module nabu.pipeline.config_validators) display_timings_pie() (in module nabu.app.parse_reconstruction_log) distance (nabu.resources.dataset_analyzer.DatasetAnalyzer property) DistortionCorrection (class in nabu.preproc.distortion) distribution_method_validator() (in module nabu.pipeline.config_validators) do_halftomo (nabu.pipeline.fullfield.processconfig.ProcessConfig property) do_height_by_height() (in module nabu.app.diag_to_rot) do_linear_interpolation() (in module nabu.app.diag_to_rot) do_radial_distribution() (in module nabu.processing.azim) docstring() (in module nabu.utils) DoubleFlatField (class in nabu.preproc.double_flatfield) DoubleFlatFieldChunks (class in nabu.app.double_flatfield) DoubleFlatFieldClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) DoubleFlatFieldVariableRegion (class in nabu.preproc.double_flatfield_variable_region) dtype (nabu.stitching.alignment.PaddedRawData property) dtype_to_ctype (nabu.processing.fftshift.FFTshiftBase attribute) (nabu.processing.processing_base.ProcessingBase attribute) (nabu.processing.transpose.TransposeBase attribute) dtype_to_ctype() (nabu.cuda.processing.CudaProcessing method) (nabu.opencl.processing.OpenCLProcessing method) (nabu.processing.fftshift.OpenCLFFTshift method) (nabu.processing.transpose.CudaTranspose method) (nabu.processing.transpose.OpenCLTranspose method) dump_data_to_file() (nabu.pipeline.datadump.DataDumpManager method) dump_stitching_config_as_nx_process() (nabu.stitching.utils.post_processing.StitchingPostProcAggregation method) dumper (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) DumperBase (class in nabu.stitching.stitcher.dumper.base) duplicate_data (nabu.stitching.config.StitchingConfiguration attribute) DWTForward (class in nabu.thirdparty.tomocupy_remove_stripe) DWTInverse (class in nabu.thirdparty.tomocupy_remove_stripe)

E

EDFDatasetAnalyzer (class in nabu.resources.dataset_analyzer) EDFReader (class in nabu.io.reader) EDFStackReader (class in nabu.io.reader) EDFStackReaderBinning() (in module nabu.pipeline.reader) EDFStackReaderDistortionCorrection() (in module nabu.pipeline.reader) empty_frame (nabu.stitching.alignment.PaddedRawData property) energy (nabu.resources.dataset_analyzer.DatasetAnalyzer property) EntryReader (class in nabu.io.utils) EnvSettings (class in nabu.pipeline.utils) error() (nabu.resources.logger.Logger method) error_metric() (nabu.pipeline.estimators.CompositeCORFinder method) error_metric_l1() (nabu.pipeline.estimators.CompositeCORFinder method) error_metric_l2() (nabu.pipeline.estimators.CompositeCORFinder method) estimate() (nabu.preproc.distortion.DistortionCorrection method) estimate_and_correct() (nabu.preproc.distortion.DistortionCorrection method) estimate_cor() (in module nabu.pipeline.estimators)

estimate_cor_coarse() (nabu.estimation.cor_sino.SinoCor method) estimate_cor_fine() (nabu.estimation.cor_sino.SinoCor method) estimate_distortion() (nabu.preproc.distortion.DistortionCorrection method) estimate_flat_distortion() (in module nabu.estimation.distortion) estimate_max_chunk_size() (in module nabu.pipeline.fullfield.computations) estimate_required_memory() (in module nabu.pipeline.fullfield.computations) estimation_methods (nabu.preproc.distortion.DistortionCorrection attribute) exclude_projections_validator() (in module nabu.pipeline.config_validators) export_dict_to_h5() (in module nabu.io.writer) extend_image_onepixel() (in module nabu.utils) extend_sinogram() (in module nabu.thirdparty.algotom_convert_sino) extract_parameters() (in module nabu.resources.utils) extract_peak_region_2d() (nabu.estimation.alignment.AlignmentBase static method) extract_peak_regions_1d() (nabu.estimation.alignment.AlignmentBase static method) extract_preprocess_with_flats() (nabu.pipeline.helical.gridded_accumulator.GriddedAccumulator method) extract_timings_from_volume_reconstruction_lines() (in module nabu.app.parse_reconstruction_log)

F

fatal() (nabu.resources.logger.Logger method) fbp() (nabu.reconstruction.fbp_base.BackprojectorBase method) fbp_filter_name_validator() (in module nabu.pipeline.config_validators) FBPClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) fdk_preweighting() (in module nabu.reconstruction.cone) fft() (nabu.processing.fft_cuda.SKCUFFT method) fftshift() (nabu.processing.fftshift.FFTshiftBase method) FFTshiftBase (class in nabu.processing.fftshift) file_format_is_edf() (in module nabu.io.utils) file_format_is_hdf5() (in module nabu.io.utils) file_format_is_jp2k() (in module nabu.io.utils) file_format_is_tiff() (in module nabu.io.utils) file_location_validator() (in module nabu.pipeline.config_validators) file_name_validator() (in module nabu.pipeline.config_validators) file_to_progress_bar (nabu.stitching.utils.post_processing.SlurmStitchingFollowerThread property) files (nabu.resources.dataset_analyzer.EDFDatasetAnalyzer property) filter_sino() (nabu.pipeline.helical.filtering.HelicalSinoFilter method) (nabu.reconstruction.filtering.SinoFilter method) (nabu.reconstruction.filtering_cuda.CudaSinoFilter method) (nabu.reconstruction.filtering_opencl.OpenCLSinoFilter method) filter_sinogram() (in module nabu.reconstruction.filtering) filter_str_def() (in module nabu.utils) filtered_backprojection() (nabu.reconstruction.fbp_base.BackprojectorBase method) finalize_files_saving() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) find_best_interpolating_line() (in module nabu.app.diag_to_rot) find_cor() (nabu.pipeline.estimators.CompositeCORFinder method) (nabu.pipeline.estimators.CORFinder method) (nabu.pipeline.estimators.SinoCORFinder method) find_distance() (nabu.estimation.focus.CameraFocus method) find_frame_relative_shifts() (in module nabu.stitching.utils.utils) find_mirror_indexes() (in module nabu.pipeline.helical.helical_utils) find_projections_relative_shifts() (in module nabu.stitching.utils.utils) find_scintillator_tilt() (nabu.estimation.focus.CameraFocus method) find_shift() (nabu.estimation.cor.CenterOfRotation method) (nabu.estimation.cor.CenterOfRotationAdaptiveSearch method) (nabu.estimation.cor.CenterOfRotationGrowingWindow method) (nabu.estimation.cor.CenterOfRotationOctaveAccurate method) (nabu.estimation.cor.CenterOfRotationSlidingWindow method) (nabu.estimation.cor_sino.CenterOfRotationFourierAngles method) (nabu.estimation.cor_sino.CenterOfRotationVo method) (nabu.estimation.cor_sino.SinoCorInterface method) (nabu.estimation.translation.DetectorTranslationAlongBeam method)

find_shift_correlate() (in module nabu.stitching.utils.utils) find_shift_with_itk() (in module nabu.stitching.utils.utils) find_tilt() (nabu.pipeline.estimators.DetectorTiltEstimator method) find_volumes_relative_shifts() (in module nabu.stitching.utils.utils) first_dict_item() (in module nabu.utils) FlatField (in module nabu.preproc.flatfield) flatfield_enabled_validator() (in module nabu.pipeline.config_validators) FlatFieldArrays (class in nabu.preproc.flatfield) FlatFieldArraysVariableRegion (class in nabu.preproc.flatfield_variable_region) FlatFieldClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) FlatFieldDataVariableRegionUrls (class in nabu.preproc.flatfield_variable_region) flats (nabu.resources.dataset_analyzer.DatasetAnalyzer property) flats_srcurrent (nabu.resources.dataset_analyzer.DatasetAnalyzer property) flip_lr (nabu.stitching.config.StitchingConfiguration attribute) flip_ud (nabu.stitching.config.StitchingConfiguration attribute) FlippingValueError float_validator() (in module nabu.pipeline.config_validators) follow_device_arr() (nabu.cuda.kernel.CudaKernel method) (nabu.opencl.kernel.OpenCLKernel method) (nabu.processing.kernel_base.KernelBase method) follow_progress() (nabu.stitching.utils.post_processing.StitchingPostProcAggregation method) format_as_info() (in module nabu.app.generate_header) FrameComposition (class in nabu.stitching.frame_composition) frames_slices() (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer method) from_dict() (nabu.stitching.config.NormalizationBySample static method) (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration class method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration class method) (nabu.stitching.config.SlurmConfig static method) from_slice_to_n_elements() (in module nabu.stitching.utils.utils) FRONT (nabu.stitching.alignment.AlignmentAxis1 attribute) FullFieldDatasetValidator (class in nabu.pipeline.fullfield.dataset_validator) FullFieldReconstructor (class in nabu.pipeline.fullfield.reconstruction) futures (nabu.stitching.utils.post_processing.StitchingPostProcAggregation property)

G

gaussian() (nabu.estimation.cor_sino.CenterOfRotationFourierAngles method) gaussian_apodization_window() (in module nabu.testutils) generate_coords() (in module nabu.utils) generate_merged_info_file() (in module nabu.app.generate_header) generate_merged_info_file_content() (in module nabu.app.generate_header) generate_metadata() (nabu.io.writer.HSTVolWriter method) generate_nabu_configfile() (in module nabu.pipeline.config) generate_nx_dataset() (in module nabu.testutils) generate_powers() (in module nabu.utils) generate_tests_scenarios() (in module nabu.testutils) generic_options_validator() (in module nabu.pipeline.config_validators) GeoPars (class in nabu.preproc.ctf) get_2D_3D_shape() (in module nabu.utils) get_3D_subregion() (in module nabu.utils) get_actual_shapes_source_target() (nabu.io.detector_distortion.DetectorDistortionBase method) get_adapted_subregion() (nabu.io.detector_distortion.DetectorDistortionBase method) get_array() (nabu.processing.processing_base.ProcessingBase method) get_array_of_given_shape() (in module nabu.testutils) get_available_fft_implems() (in module nabu.processing.fft_cuda) get_available_threads() (in module nabu.utils) get_bandpass_filter() (in module nabu.misc.fourier_filters) get_big_data() (in module nabu.testutils) get_bin_width() (nabu.processing.histogram.PartialHistogram method) get_binning() (nabu.io.reader_helical.ChunkReaderHelical method) get_block_grid() (nabu.opencl.kernel.OpenCLKernel method) (nabu.processing.kernel_base.KernelBase method) get_bunch_of_data() (nabu.stitching.stitcher.pre_processing.PreProcessingStitching static method) get_chunk_info() (nabu.pipeline.helical.span_strategy.SpanStrategy method) get_class_name() (in module nabu.pipeline.estimators) get_compacted_dataslices() (in module nabu.io.utils) get_config_template() (in module nabu.app.bootstrap) get_cuda_context() (in module nabu.cuda.utils) get_cuda_srcfile() (in module nabu.utils) get_dark() (nabu.preproc.flatfield.FlatFieldArrays method) get_darks_frm_process_file() (in module nabu.thirdparty.tomwer_load_flats_darks) get_data() (in module nabu.testutils) (nabu.io.reader.EDFReader method) (nabu.io.reader.HDF5Reader method) (nabu.io.reader.NPReader method) (nabu.io.reader.Reader method) get_data_dump() (nabu.pipeline.datadump.DataDumpManager method) get_data_slices() (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer method) get_datetime() (in module nabu.io.writer) get_decay() (in module nabu.utils) get_default_kwargs() (in module nabu.pipeline.estimators) get_default_nabu_config() (in module nabu.pipeline.config) get_default_output_volume() (in module nabu.io.cast_volume) get_default_stitching_config() (in module nabu.stitching.config) get_description_dict() (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration static method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration static method) (nabu.stitching.config.StitchingConfiguration static method) get_dict() (nabu.pipeline.config.NabuConfigParser method) (nabu.resources.gpu.GPUDescription method) get_doable_span() (nabu.pipeline.helical.span_strategy.SpanStrategy method) get_double_flatfield() (nabu.preproc.double_flatfield.DoubleFlatField method) (nabu.preproc.double_flatfield_cuda.CudaDoubleFlatField method) get_dtype_range() (in module nabu.misc.utils) get_empty_frame() (nabu.stitching.alignment.PaddedRawData static method) get_entry_from_h5_path() (in module nabu.io.reader) get_extended_sinogram_width() (in module nabu.reconstruction.sinogram) get_fft_class() (in module nabu.processing.fft_cuda) get_file() (in module nabu.testutils) get_filename() (nabu.io.writer.Writer method) get_final_axis_positions_in_px() (nabu.stitching.stitcher.single_axis.SingleAxisStitcher method) get_first_fname() (nabu.pipeline.writer.WriterManager static method) get_first_hdf5_entry() (in module nabu.io.utils) get_flat() (nabu.preproc.flatfield.FlatFieldArrays method) get_flats_frm_process_file() (in module nabu.thirdparty.tomwer_load_flats_darks) get_fname() (nabu.pipeline.writer.WriterManager static method) get_folder_path() (in module nabu.utils) get_frame_possible_urls() (in module nabu.resources.nxflatfield) get_frames_indices() (nabu.io.reader.VolReaderBase method) get_ftype() (in module nabu.utils) get_gpu_memory() (in module nabu.cuda.utils) get_h5_str_value() (in module nabu.io.utils) get_h5_value() (in module nabu.io.utils) get_hdf5_dataset_dtype() (in module nabu.io.reader)

get_hdf5_dataset_shape() (in module nabu.io.reader) get_highpass_filter() (in module nabu.misc.fourier_filters) get_histogram() (nabu.app.histogram.VolumesHistogram method) get_histogram_single_volume() (nabu.app.histogram.VolumesHistogram method) get_hst_saturations() (in module nabu.app.generate_header) get_informative_string() (nabu.pipeline.helical.span_strategy.SpanStrategy method) get_kernel() (nabu.opencl.kernel.OpenCLKernel method) get_last_kernel_time() (nabu.cuda.kernel.CudaKernel method) get_log_file() (in module nabu.app.reconstruct) get_lowpass_filter() (in module nabu.misc.fourier_filters) get_max_grid_size() (in module nabu.reconstruction.hbp) get_memory_per_node() (in module nabu.resources.utils) get_metadata_url() (in module nabu.resources.nxflatfield) get_modules_to_test() (in module nabu.tests) get_n_slices_to_stitch() (nabu.stitching.stitcher.single_axis.SingleAxisStitcher method) get_nearest_index() (nabu.preproc.flatfield.FlatFieldArrays static method) get_num_threads() (in module nabu.utils) get_nvcc_version() (in module nabu.cuda.utils) get_obj_constant_side_length() (in module nabu.stitching.stitcher.base) get_opencl_context() (in module nabu.opencl.utils) get_opencl_devices() (in module nabu.opencl.utils) get_opencl_srcfile() (in module nabu.utils) get_output() (nabu.preproc.phase_cuda.CudaPaganinPhaseRetrieval method) get_output_data_type() (nabu.stitching.stitcher.post_processing.PostProcessingStitching method) get_output_object() (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.SingleAxisStitchingConfiguration method) get_output_volume() (in module nabu.io.utils) get_overlap_areas() (in module nabu.stitching.stitcher_2D) get_previous_next_indices() (nabu.preproc.flatfield.FlatFieldArrays static method) get_process_entries() (in module nabu.thirdparty.tomwer_load_flats_darks) get_quantities_and_units() (in module nabu.resources.utils) get_radio() (nabu.pipeline.estimators.CompositeCORFinder method) get_radio_pair() (in module nabu.resources.dataset_analyzer) get_radios_rotation_mode() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) get_raw_current() (nabu.io.reader.NXDarksFlats method) get_raw_darks() (nabu.io.reader.NXDarksFlats method) get_raw_flats() (nabu.io.reader.NXDarksFlats method) get_read_dump_subregion() (nabu.pipeline.datadump.DataDumpManager method) get_reader() (nabu.resources.dataset_analyzer.EDFDatasetAnalyzer method) (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer method) get_reconstruction_space() (in module nabu.pipeline.helical.gridded_accumulator) get_reconstructor() (in module nabu.app.reconstruct) get_reduced_current() (nabu.io.reader.NXDarksFlats method) get_reduced_darks() (nabu.io.reader.NXDarksFlats method) (nabu.resources.dataset_analyzer.EDFDatasetAnalyzer method) (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer method) get_reduced_flats() (nabu.io.reader.NXDarksFlats method) (nabu.resources.dataset_analyzer.EDFDatasetAnalyzer method) (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer method) get_relative_files() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) get_resource_file() (in module nabu.utils) get_save_steps_file() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) get_scans() (in module nabu.app.validator) get_shape_dtype() (in module nabu.cuda.utils) get_shape_from_sliced_dims() (in module nabu.utils) get_sino() (nabu.pipeline.estimators.CompositeCORFinder method) (nabu.reconstruction.sinogram.SinoBuilder method) get_sinos() (nabu.reconstruction.sinogram.SinoBuilder method) get_size_from_sliced_dimension() (in module nabu.utils) get_slice_start_index() (nabu.pipeline.fullfield.chunked.ChunkedPipeline method) get_subregion() (in module nabu.pipeline.utils) (in module nabu.utils) get_threads_per_node() (in module nabu.resources.utils) get_user_cors() (in module nabu.app.multicor) get_values_from_file() (in module nabu.resources.utils) get_working_directory() (in module nabu.stitching.slurm_utils) getGridSize() (in module nabu.reconstruction.hbp) GLOBAL (nabu.stitching.utils.utils.ShiftAlgorithm attribute) global_end (nabu.stitching.frame_composition.FrameComposition attribute) global_start (nabu.stitching.frame_composition.FrameComposition attribute) GPUDescription (class in nabu.resources.gpu) GriddedAccumulator (class in nabu.pipeline.helical.gridded_accumulator) GROWING_WINDOW (nabu.stitching.utils.utils.ShiftAlgorithm attribute) guess_block_size() (nabu.opencl.kernel.OpenCLKernel method) (nabu.processing.kernel_base.KernelBase static method) guess_grid_size() (nabu.processing.kernel_base.KernelBase static method) guess_tomo_objects() (in module nabu.app.bootstrap_stitching)

H

h5_write_object() (in module nabu.io.writer) has_skcuda() (in module nabu.processing.fft_cuda) has_vkfft() (in module nabu.processing.fft_cuda) (in module nabu.processing.fft_opencl) HBPClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) hdf5_entry (nabu.resources.dataset_analyzer.EDFDatasetAnalyzer property) (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer property) hdf5_entry_exists() (in module nabu.io.utils) HDF5DatasetAnalyzer (class in nabu.resources.dataset_analyzer) HDF5ImagesStackRotation (class in nabu.app.rotate) HDF5Loader (class in nabu.io.reader)

HDF5Reader (class in nabu.io.reader) HelicalDatasetValidator (class in nabu.pipeline.helical.dataset_validator) HelicalSinoFilter (class in nabu.pipeline.helical.filtering) HierarchicalBackprojector (class in nabu.reconstruction.hbp) HIGHER_SIGNAL (nabu.stitching.overlap.OverlapStitchingStrategy attribute) hist_as_2Darray() (in module nabu.processing.histogram) histogram_cli() (in module nabu.app.histogram) histogram_methods (nabu.processing.histogram.PartialHistogram attribute) HistogramClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) HSTVolVolume (class in nabu.io.writer) HSTVolWriter (class in nabu.io.writer)

I

identifiers_as_str_to_instances() (in module nabu.stitching.config) idx_1d_to_3d() (in module nabu.app.compare_volumes) ifft() (nabu.processing.fft_cuda.SKCUFFT method) ifftshift() (nabu.processing.fftshift.FFTshiftBase method) image_key_path (nabu.io.reader.NXTomoReader attribute) IMAGE_MINIMUM_DIVERGENCE (nabu.stitching.overlap.OverlapStitchingStrategy attribute) ImageRotationClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) ImageStichOverlapKernel (class in nabu.stitching.overlap) img_2 (nabu.stitching.overlap.ImageStichOverlapKernel property) implem (nabu.processing.fft_cuda.SKCUFFT attribute) (nabu.processing.fft_cuda.VKCUFFT attribute) (nabu.processing.fft_opencl.VKCLFFT attribute) import_h5_to_dict() (in module nabu.io.reader) indices_to_slices() (in module nabu.utils) info() (nabu.resources.logger.Logger method) init_arrays_to_none() (nabu.processing.processing_base.ProcessingBase method) init_skcuda() (in module nabu.processing.fft_cuda)

input_scans (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration attribute) input_volumes (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration attribute) integer_shift_v (nabu.pipeline.helical.span_strategy.SpanStrategy attribute) integer_validator() (in module nabu.pipeline.config_validators) interp() (nabu.preproc.flatfield.FlatFieldArrays static method) is_active() (nabu.stitching.config.NormalizationBySample method) is_before_radios_cropping() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) is_device_backend() (in module nabu.utils) is_fast_axes() (in module nabu.processing.fft_base) is_fullturn_scan() (in module nabu.estimation.utils) is_gpu_usable() (in module nabu.cuda.utils) is_halftomo (nabu.pipeline.dataset_validator.DatasetValidatorBase property) (nabu.resources.dataset_analyzer.DatasetAnalyzer property) is_hdf5_extension() (in module nabu.resources.utils) is_int() (in module nabu.utils) is_process_node() (in module nabu.thirdparty.tomwer_load_flats_darks) is_scalar() (in module nabu.utils) is_writeable() (in module nabu.utils) ITK_IMG_REG_V4 (nabu.stitching.utils.utils.ShiftAlgorithm attribute)

J

join() (nabu.stitching.utils.post_processing.SlurmStitchingFollowerThread method)

K

kernel() (nabu.cuda.processing.CudaProcessing method) (nabu.opencl.processing.OpenCLProcessing method) (nabu.processing.processing_base.ProcessingBase method) kernel_filename (nabu.reconstruction.fbp.CudaBackprojector attribute) (nabu.reconstruction.fbp_base.BackprojectorBase attribute) (nabu.reconstruction.fbp_opencl.OpenCLBackprojector attribute) (nabu.reconstruction.hbp.HierarchicalBackprojector attribute) kernel_name (nabu.reconstruction.fbp_base.BackprojectorBase attribute) KernelBase (class in nabu.processing.kernel_base)

KernelCls (nabu.processing.fftshift.FFTshiftBase attribute) (nabu.processing.fftshift.OpenCLFFTshift attribute) (nabu.processing.transpose.CudaTranspose attribute) (nabu.processing.transpose.OpenCLTranspose attribute) (nabu.processing.transpose.TransposeBase attribute) kind (nabu.resources.dataset_analyzer.DatasetAnalyzer attribute) (nabu.resources.dataset_analyzer.EDFDatasetAnalyzer attribute) (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer attribute) kinds (nabu.reconstruction.sinogram.SinoNormalization attribute)

L

LEFT (nabu.stitching.alignment.AlignmentAxis2 attribute) (nabu.stitching.sample_normalization.SampleSide attribute) LegacyNXProcessWriter (in module nabu.io.writer) LINEAR_WEIGHTS (nabu.stitching.overlap.OverlapStitchingStrategy attribute) list_hdf5_entries() (in module nabu.app.reconstruct) list_match_queries() (in module nabu.utils) list_of_int_validator() (in module nabu.pipeline.config_validators) list_of_shift_validator() (in module nabu.pipeline.config_validators) list_of_tomoscan_identifier() (in module nabu.pipeline.config_validators) lmicron_to_db() (in module nabu.preproc.phase) (nabu.preproc.phase.PaganinPhaseRetrieval method) load_darks_flats() (in module nabu.pipeline.reader)

load_data() (nabu.io.reader.EDFStackReader method) (nabu.io.reader.HDF5Loader method) (nabu.io.reader.NXTomoReader method) (nabu.io.reader_helical.ChunkReaderHelical method) load_files() (nabu.io.reader_helical.ChunkReaderHelical method) load_images_stack_from_hdf5() (in module nabu.io.reader) local_end (nabu.stitching.frame_composition.FrameComposition attribute) local_start (nabu.stitching.frame_composition.FrameComposition attribute) Log (class in nabu.preproc.ccd) Logger (class in nabu.resources.logger) LoggerOrPrint() (in module nabu.resources.logger) logging_validator() (in module nabu.pipeline.config_validators)

M

main() (in module nabu.app.cast_volume) (in module nabu.app.composite_cor) (in module nabu.app.correct_rot) (in module nabu.app.diag_to_pix) (in module nabu.app.diag_to_rot) (in module nabu.app.multicor) (in module nabu.app.prepare_weights_double) (in module nabu.app.reconstruct) (in module nabu.app.reduce_dark_flat) (in module nabu.app.stitching) (in module nabu.app.validator) main_helical() (in module nabu.app.reconstruct_helical) margin (nabu.stitching.config.NormalizationBySample property) match_half_sinos_parts() (in module nabu.reconstruction.sinogram) MEAN (nabu.stitching.overlap.OverlapStitchingStrategy attribute) (nabu.stitching.sample_normalization.Method attribute) measure_time() (in module nabu.utils) medfilt2() (nabu.processing.medfilt_cuda.MedianFilter method) MEDIAN (nabu.stitching.sample_normalization.Method attribute) median2() (in module nabu.utils) median_clip_correction() (nabu.preproc.ccd.CCDFilter method) (nabu.preproc.ccd_cuda.CudaCCDFilter method) median_clip_mask() (nabu.preproc.ccd.CCDFilter method) median_filter() (nabu.preproc.ccd.CCDFilter static method) MedianFilter (class in nabu.processing.medfilt_cuda) mem (nabu.stitching.config.SlurmConfig attribute) merge_data_dumps() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) merge_hdf5_files() (in module nabu.io.writer) merge_hdf5_reconstructions() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) merge_histograms() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) (nabu.processing.histogram.PartialHistogram method) merge_histograms_configurations() (nabu.app.histogram.VolumesHistogram method) merge_slices() (in module nabu.utils) merged_shape() (in module nabu.utils) merit() (in module nabu.app.diag_to_pix) Method (class in nabu.stitching.sample_normalization) method (nabu.stitching.config.NormalizationBySample property) MissingComponentError() (in module nabu.utils) MLEMClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) MLEMReconstructor (class in nabu.reconstruction.mlem) MLogClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) module bench_textures nabu nabu.app nabu.app.bootstrap nabu.app.bootstrap_stitching nabu.app.cast_volume nabu.app.cli_configs nabu.app.compare_volumes nabu.app.composite_cor nabu.app.correct_rot nabu.app.create_distortion_map_from_poly nabu.app.diag_to_pix nabu.app.diag_to_rot nabu.app.double_flatfield nabu.app.generate_header nabu.app.histogram nabu.app.multicor nabu.app.nx_z_splitter nabu.app.parse_reconstruction_log nabu.app.prepare_weights_double nabu.app.reconstruct nabu.app.reconstruct_helical nabu.app.reduce_dark_flat nabu.app.rotate nabu.app.shrink_dataset nabu.app.stitching nabu.app.utils nabu.app.validator nabu.cuda nabu.cuda.convolution nabu.cuda.fft nabu.cuda.kernel nabu.cuda.medfilt nabu.cuda.padding nabu.cuda.processing nabu.cuda.utils nabu.estimation nabu.estimation.alignment nabu.estimation.cor nabu.estimation.cor_sino nabu.estimation.distortion nabu.estimation.focus nabu.estimation.tilt nabu.estimation.translation nabu.estimation.utils nabu.io nabu.io.cast_volume nabu.io.detector_distortion nabu.io.reader nabu.io.reader_helical nabu.io.utils nabu.io.writer nabu.misc nabu.misc.binning nabu.misc.fftshift nabu.misc.filters nabu.misc.fourier_filters nabu.misc.histogram nabu.misc.histogram_cuda nabu.misc.kernel_base nabu.misc.padding nabu.misc.padding_base nabu.misc.processing_base nabu.misc.rotation nabu.misc.rotation_cuda nabu.misc.transpose nabu.misc.unsharp nabu.misc.unsharp_cuda nabu.misc.unsharp_opencl nabu.misc.utils nabu.opencl nabu.opencl.fft nabu.opencl.kernel nabu.opencl.memcpy nabu.opencl.padding nabu.opencl.processing nabu.opencl.utils nabu.pipeline nabu.pipeline.config nabu.pipeline.config_validators nabu.pipeline.datadump nabu.pipeline.dataset_validator nabu.pipeline.detector_distortion_provider nabu.pipeline.estimators nabu.pipeline.fullfield nabu.pipeline.fullfield.chunked nabu.pipeline.fullfield.chunked_cuda nabu.pipeline.fullfield.computations nabu.pipeline.fullfield.dataset_validator nabu.pipeline.fullfield.nabu_config nabu.pipeline.fullfield.processconfig nabu.pipeline.fullfield.reconstruction nabu.pipeline.helical nabu.pipeline.helical.dataset_validator nabu.pipeline.helical.fbp nabu.pipeline.helical.filtering nabu.pipeline.helical.gridded_accumulator nabu.pipeline.helical.helical_utils nabu.pipeline.helical.nabu_config nabu.pipeline.helical.processconfig nabu.pipeline.helical.span_strategy nabu.pipeline.helical.weight_balancer nabu.pipeline.params nabu.pipeline.processconfig nabu.pipeline.reader nabu.pipeline.utils nabu.pipeline.writer nabu.pipeline.xrdct nabu.preproc nabu.preproc.alignment nabu.preproc.ccd nabu.preproc.ccd_cuda nabu.preproc.ctf nabu.preproc.ctf_cuda nabu.preproc.distortion nabu.preproc.double_flatfield nabu.preproc.double_flatfield_cuda nabu.preproc.double_flatfield_variable_region nabu.preproc.flatfield nabu.preproc.flatfield_cuda nabu.preproc.flatfield_variable_region nabu.preproc.phase nabu.preproc.phase_cuda nabu.preproc.shift nabu.preproc.shift_cuda nabu.processing nabu.processing.azim nabu.processing.convolution_cuda nabu.processing.fft_base nabu.processing.fft_cuda nabu.processing.fft_opencl nabu.processing.fftshift nabu.processing.histogram nabu.processing.histogram_cuda nabu.processing.kernel_base nabu.processing.medfilt_cuda nabu.processing.muladd nabu.processing.muladd_cuda nabu.processing.padding_base nabu.processing.padding_cuda nabu.processing.padding_opencl nabu.processing.processing_base nabu.processing.roll_opencl nabu.processing.rotation nabu.processing.rotation_cuda nabu.processing.transpose nabu.processing.unsharp nabu.processing.unsharp_cuda nabu.processing.unsharp_opencl nabu.reconstruction nabu.reconstruction.cone nabu.reconstruction.fbp nabu.reconstruction.fbp_base nabu.reconstruction.fbp_opencl nabu.reconstruction.filtering nabu.reconstruction.filtering_cuda nabu.reconstruction.filtering_opencl nabu.reconstruction.hbp nabu.reconstruction.mlem nabu.reconstruction.projection nabu.reconstruction.reconstructor nabu.reconstruction.reconstructor_cuda nabu.reconstruction.rings nabu.reconstruction.rings_cuda nabu.reconstruction.sinogram nabu.reconstruction.sinogram_cuda nabu.reconstruction.sinogram_opencl nabu.resources nabu.resources.cli nabu.resources.cor nabu.resources.dataset_analyzer nabu.resources.gpu nabu.resources.logger nabu.resources.nxflatfield nabu.resources.templates nabu.resources.utils nabu.stitching nabu.stitching.alignment nabu.stitching.config nabu.stitching.definitions nabu.stitching.frame_composition nabu.stitching.overlap nabu.stitching.sample_normalization nabu.stitching.single_axis_stitching nabu.stitching.slurm_utils nabu.stitching.stitcher nabu.stitching.stitcher.base nabu.stitching.stitcher.dumper nabu.stitching.stitcher.dumper.base nabu.stitching.stitcher.dumper.postprocessing nabu.stitching.stitcher.dumper.preprocessing nabu.stitching.stitcher.post_processing nabu.stitching.stitcher.pre_processing nabu.stitching.stitcher.single_axis nabu.stitching.stitcher.stitcher nabu.stitching.stitcher.y_stitcher nabu.stitching.stitcher.z_stitcher nabu.stitching.stitcher_2D nabu.stitching.utils nabu.stitching.utils.post_processing nabu.stitching.utils.utils nabu.stitching.y_stitching nabu.stitching.z_stitching nabu.tests nabu.testutils nabu.thirdparty nabu.thirdparty.algotom_convert_sino nabu.thirdparty.pore3d_deringer_munch nabu.thirdparty.tomocupy_remove_stripe nabu.thirdparty.tomopy_phase nabu.thirdparty.tomwer_load_flats_darks nabu.utils

modules_to_load (nabu.stitching.config.SlurmConfig attribute) mul_add() (nabu.processing.muladd.MulAdd method) (nabu.processing.muladd_cuda.CudaMulAdd method) MulAdd (class in nabu.processing.muladd) multi_load (nabu.io.reader.EDFReader attribute) (nabu.io.reader.HDF5Reader attribute) (nabu.io.reader.NPReader attribute) multiple_frames_per_file (nabu.io.reader.EDFStackReader attribute) (nabu.io.reader.NXTomoReader attribute) MunchDeringer (class in nabu.reconstruction.rings) MunchDeringerClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) munchetal_filter() (in module nabu.thirdparty.pore3d_deringer_munch)

N

n_angles() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) n_cpu_per_task (nabu.stitching.config.SlurmConfig attribute) n_jobs (nabu.stitching.config.SlurmConfig attribute) n_tasks (nabu.stitching.config.SlurmConfig attribute) nabu module nabu.app module nabu.app.bootstrap module nabu.app.bootstrap_stitching module nabu.app.cast_volume module nabu.app.cli_configs module nabu.app.compare_volumes module nabu.app.composite_cor module nabu.app.correct_rot module nabu.app.create_distortion_map_from_poly module nabu.app.diag_to_pix module nabu.app.diag_to_rot module nabu.app.double_flatfield module nabu.app.generate_header module nabu.app.histogram module nabu.app.multicor module nabu.app.nx_z_splitter module nabu.app.parse_reconstruction_log module nabu.app.prepare_weights_double module nabu.app.reconstruct module nabu.app.reconstruct_helical module nabu.app.reduce_dark_flat module nabu.app.rotate module nabu.app.shrink_dataset module nabu.app.stitching module nabu.app.utils module nabu.app.validator module nabu.cuda module nabu.cuda.convolution module nabu.cuda.fft module nabu.cuda.kernel module nabu.cuda.medfilt module nabu.cuda.padding module nabu.cuda.processing module nabu.cuda.utils module nabu.estimation module nabu.estimation.alignment module nabu.estimation.cor module nabu.estimation.cor_sino module nabu.estimation.distortion module nabu.estimation.focus module nabu.estimation.tilt module nabu.estimation.translation module nabu.estimation.utils module nabu.io module nabu.io.cast_volume module nabu.io.detector_distortion module nabu.io.reader module nabu.io.reader_helical module nabu.io.utils module nabu.io.writer module nabu.misc module nabu.misc.binning module nabu.misc.fftshift module nabu.misc.filters module nabu.misc.fourier_filters module nabu.misc.histogram module nabu.misc.histogram_cuda module nabu.misc.kernel_base module nabu.misc.padding module nabu.misc.padding_base module nabu.misc.processing_base module nabu.misc.rotation module nabu.misc.rotation_cuda module nabu.misc.transpose module nabu.misc.unsharp module nabu.misc.unsharp_cuda module nabu.misc.unsharp_opencl module nabu.misc.utils module nabu.opencl module nabu.opencl.fft module nabu.opencl.kernel module nabu.opencl.memcpy module nabu.opencl.padding module nabu.opencl.processing module nabu.opencl.utils module nabu.pipeline module nabu.pipeline.config module nabu.pipeline.config_validators module nabu.pipeline.datadump module nabu.pipeline.dataset_validator module nabu.pipeline.detector_distortion_provider module nabu.pipeline.estimators module nabu.pipeline.fullfield module nabu.pipeline.fullfield.chunked module nabu.pipeline.fullfield.chunked_cuda module nabu.pipeline.fullfield.computations module nabu.pipeline.fullfield.dataset_validator module nabu.pipeline.fullfield.nabu_config module nabu.pipeline.fullfield.processconfig module nabu.pipeline.fullfield.reconstruction module nabu.pipeline.helical module nabu.pipeline.helical.dataset_validator module nabu.pipeline.helical.fbp module nabu.pipeline.helical.filtering module nabu.pipeline.helical.gridded_accumulator module nabu.pipeline.helical.helical_utils module nabu.pipeline.helical.nabu_config module nabu.pipeline.helical.processconfig module nabu.pipeline.helical.span_strategy module nabu.pipeline.helical.weight_balancer module nabu.pipeline.params module nabu.pipeline.processconfig module nabu.pipeline.reader module nabu.pipeline.utils module nabu.pipeline.writer module nabu.pipeline.xrdct module nabu.preproc module nabu.preproc.alignment module nabu.preproc.ccd module nabu.preproc.ccd_cuda module nabu.preproc.ctf module

nabu.preproc.ctf_cuda module nabu.preproc.distortion module nabu.preproc.double_flatfield module nabu.preproc.double_flatfield_cuda module nabu.preproc.double_flatfield_variable_region module nabu.preproc.flatfield module nabu.preproc.flatfield_cuda module nabu.preproc.flatfield_variable_region module nabu.preproc.phase module nabu.preproc.phase_cuda module nabu.preproc.shift module nabu.preproc.shift_cuda module nabu.processing module nabu.processing.azim module nabu.processing.convolution_cuda module nabu.processing.fft_base module nabu.processing.fft_cuda module nabu.processing.fft_opencl module nabu.processing.fftshift module nabu.processing.histogram module nabu.processing.histogram_cuda module nabu.processing.kernel_base module nabu.processing.medfilt_cuda module nabu.processing.muladd module nabu.processing.muladd_cuda module nabu.processing.padding_base module nabu.processing.padding_cuda module nabu.processing.padding_opencl module nabu.processing.processing_base module nabu.processing.roll_opencl module nabu.processing.rotation module nabu.processing.rotation_cuda module nabu.processing.transpose module nabu.processing.unsharp module nabu.processing.unsharp_cuda module nabu.processing.unsharp_opencl module nabu.reconstruction module nabu.reconstruction.cone module nabu.reconstruction.fbp module nabu.reconstruction.fbp_base module nabu.reconstruction.fbp_opencl module nabu.reconstruction.filtering module nabu.reconstruction.filtering_cuda module nabu.reconstruction.filtering_opencl module nabu.reconstruction.hbp module nabu.reconstruction.mlem module nabu.reconstruction.projection module nabu.reconstruction.reconstructor module nabu.reconstruction.reconstructor_cuda module nabu.reconstruction.rings module nabu.reconstruction.rings_cuda module nabu.reconstruction.sinogram module nabu.reconstruction.sinogram_cuda module nabu.reconstruction.sinogram_opencl module nabu.resources module nabu.resources.cli module nabu.resources.cor module nabu.resources.dataset_analyzer module nabu.resources.gpu module nabu.resources.logger module nabu.resources.nxflatfield module nabu.resources.templates module nabu.resources.utils module nabu.stitching module nabu.stitching.alignment module nabu.stitching.config module nabu.stitching.definitions module nabu.stitching.frame_composition module nabu.stitching.overlap module nabu.stitching.sample_normalization module nabu.stitching.single_axis_stitching module nabu.stitching.slurm_utils module nabu.stitching.stitcher module nabu.stitching.stitcher.base module nabu.stitching.stitcher.dumper module nabu.stitching.stitcher.dumper.base module nabu.stitching.stitcher.dumper.postprocessing module nabu.stitching.stitcher.dumper.preprocessing module nabu.stitching.stitcher.post_processing module nabu.stitching.stitcher.pre_processing module nabu.stitching.stitcher.single_axis module nabu.stitching.stitcher.stitcher module nabu.stitching.stitcher.y_stitcher module nabu.stitching.stitcher.z_stitcher module nabu.stitching.stitcher_2D module nabu.stitching.utils module nabu.stitching.utils.post_processing module nabu.stitching.utils.utils module nabu.stitching.y_stitching module nabu.stitching.z_stitching module nabu.tests module nabu.testutils module nabu.thirdparty module nabu.thirdparty.algotom_convert_sino module nabu.thirdparty.pore3d_deringer_munch module nabu.thirdparty.tomocupy_remove_stripe module nabu.thirdparty.tomopy_phase module nabu.thirdparty.tomwer_load_flats_darks module nabu.utils module NABU_FFT (nabu.stitching.utils.utils.ShiftAlgorithm attribute) nabu_test() (in module nabu.tests) NabuConfigParser (class in nabu.pipeline.config) name_range_checker() (in module nabu.pipeline.config_validators) nextpow2() (in module nabu.utils) no_validator() (in module nabu.pipeline.config_validators) nominal_current (nabu.pipeline.helical.gridded_accumulator.GriddedAccumulator attribute) NONE (nabu.stitching.utils.utils.ShiftAlgorithm attribute) nonempty_string_validator() (in module nabu.pipeline.config_validators) nonnegative_integer_validator() (in module nabu.pipeline.config_validators) nonzero_integer_validator() (in module nabu.pipeline.config_validators) normalization_by_sample (nabu.stitching.config.StitchingConfiguration attribute) NormalizationBySample (class in nabu.stitching.config) normalize() (nabu.reconstruction.sinogram.SinoNormalization method) normalize_frame() (in module nabu.stitching.sample_normalization) normalize_frame_by_sample() (nabu.stitching.stitcher.single_axis.SingleAxisStitcher method) normalize_radios() (nabu.preproc.flatfield.FlatFieldArrays method) (nabu.preproc.flatfield_cuda.CudaFlatFieldArrays method) normalize_single_radio() (nabu.preproc.flatfield.FlatFieldArrays method) NPReader (class in nabu.io.reader) NumpyArrayEncoder (class in nabu.app.composite_cor) NXDarksFlats (class in nabu.io.reader) NXProcessWriter (class in nabu.io.writer) NXTomoReader (class in nabu.io.reader) NXTomoReaderBinning() (in module nabu.pipeline.reader) NXTomoReaderDistortionCorrection() (in module nabu.pipeline.reader) NXVolVolume (class in nabu.io.writer) NXZSplitter (class in nabu.app.nx_z_splitter)

O

on_detector_projection_intervals (nabu.pipeline.helical.span_strategy.SpanStrategy attribute) OpenCLBackprojector (class in nabu.reconstruction.fbp_opencl) OpenCLFFTshift (class in nabu.processing.fftshift) OpenCLKernel (class in nabu.opencl.kernel) OpenCLMemcpy2D (class in nabu.opencl.memcpy) OpenCLPadding (class in nabu.processing.padding_opencl) OpenCLProcessing (class in nabu.opencl.processing) OpenCLRoll (class in nabu.processing.roll_opencl) OpenCLSinoFilter (class in nabu.reconstruction.filtering_opencl) OpenCLSinoMult (class in nabu.reconstruction.sinogram_opencl) OpenCLTranspose (class in nabu.processing.transpose) OpenclUnsharpMask (class in nabu.processing.unsharp_opencl) OpenCLUnsharpMask (in module nabu.processing.unsharp_opencl) operations (nabu.reconstruction.sinogram.SinoNormalization attribute) optimization_algorithm_name_validator() (in module nabu.pipeline.config_validators) optional_directory_location_validator() (in module nabu.pipeline.config_validators) optional_file_location_validator() (in module nabu.pipeline.config_validators) optional_file_name_validator() (in module nabu.pipeline.config_validators) optional_float_validator() (in module nabu.pipeline.config_validators) optional_nonzero_float_validator() (in module nabu.pipeline.config_validators) optional_output_directory_validator() (in module nabu.pipeline.config_validators) optional_output_file_path_validator() (in module nabu.pipeline.config_validators) optional_positive_integer_validator() (in module nabu.pipeline.config_validators) optional_string_validator() (in module nabu.pipeline.config_validators) optional_tuple_of_floats_validator() (in module nabu.pipeline.config_validators) optional_values_file_validator() (in module nabu.pipeline.config_validators)

order_input_tomo_objects() (nabu.stitching.stitcher.post_processing.PostProcessingStitching method) (nabu.stitching.stitcher.pre_processing.PreProcessingStitching method) other_options (nabu.stitching.config.SlurmConfig attribute) output_data_path (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration attribute) output_dataset (nabu.stitching.stitcher.dumper.base.DumperBase property) (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD property) output_file_format_validator() (in module nabu.pipeline.config_validators) output_file_path (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration attribute) output_identifier (nabu.stitching.stitcher.dumper.base.DumperBase property) (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumper property) (nabu.stitching.stitcher.dumper.preprocessing.PreProcessingStitchingDumper property) output_nexus_version (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration attribute) output_shape (nabu.reconstruction.sinogram.SinoBuilder property) output_volume (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration attribute) OutputDatasetContext (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumper attribute) (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD attribute) OutputVolumeContext (class in nabu.stitching.stitcher.dumper.postprocessing) OutputVolumeNoDDContext (class in nabu.stitching.stitcher.dumper.postprocessing) overlap() (nabu.estimation.cor_sino.SinoCor method) overlap_logic() (in module nabu.pipeline.helical.gridded_accumulator) overlap_size (nabu.stitching.overlap.ImageStichOverlapKernel property) OverlapKernelBase (class in nabu.stitching.overlap) OverlapStitchingStrategy (class in nabu.stitching.overlap) oversample() (in module nabu.pipeline.estimators) overwrite_config() (in module nabu.pipeline.config) overwrite_results (nabu.stitching.config.StitchingConfiguration attribute)

P

pad() (nabu.processing.padding_cuda.CudaPadding method) (nabu.processing.padding_opencl.OpenCLPadding method) pad_data() (nabu.preproc.phase.PaganinPhaseRetrieval method) pad_interpolate() (in module nabu.misc.padding) pad_mode (nabu.stitching.config.SingleAxisStitchingConfiguration attribute) pad_with_values() (nabu.preproc.phase.PaganinPhaseRetrieval method) PaddedRawData (class in nabu.stitching.alignment) padding_logic() (in module nabu.pipeline.helical.gridded_accumulator) padding_mode_validator() (in module nabu.pipeline.config_validators) PaddingBase (class in nabu.processing.padding_base) PaganinPhaseRetrieval (class in nabu.preproc.phase) PaganinPhaseRetrievalClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) parse_logfile() (in module nabu.app.parse_reconstruction_log) parse_nabu_config_file() (in module nabu.pipeline.config) parse_params_values() (in module nabu.app.utils) parse_reclog_cli() (in module nabu.app.parse_reconstruction_log) parse_sections() (in module nabu.app.utils) PartialHistogram (class in nabu.processing.histogram) partition (nabu.stitching.config.SlurmConfig attribute) partition_dict() (in module nabu.utils) phase_method_validator() (in module nabu.pipeline.config_validators) pick_gpus() (in module nabu.resources.gpu) pick_gpus_auto() (in module nabu.resources.gpu) pick_gpus_nvidia() (in module nabu.resources.gpu) pick_opencl_cpu_platform() (in module nabu.opencl.utils) pipeline_step() (in module nabu.pipeline.utils) pixel_size (nabu.resources.dataset_analyzer.DatasetAnalyzer property) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration attribute) PolarBackprojector (class in nabu.reconstruction.fbp) pop_context() (nabu.cuda.processing.CudaProcessing method) positive_integer_validator() (in module nabu.pipeline.config_validators) PostProcessedSingleAxisStitchingConfiguration (class in nabu.stitching.config) PostProcessedZStitchingConfiguration (class in nabu.stitching.config) PostProcessingStitching (class in nabu.stitching.stitcher.post_processing) PostProcessingStitchingDumper (class in nabu.stitching.stitcher.dumper.postprocessing) PostProcessingStitchingDumperNoDD (class in nabu.stitching.stitcher.dumper.postprocessing) PostProcessingZStitcher (class in nabu.stitching.stitcher.z_stitcher) PostProcessingZStitcherNoDD (class in nabu.stitching.stitcher.z_stitcher) powers (nabu.preproc.phase.PaganinPhaseRetrieval attribute) pprint_composition() (nabu.stitching.frame_composition.FrameComposition static method) pre_processing_computation() (nabu.stitching.stitcher.pre_processing.PreProcessingStitching method)

prepare() (nabu.cuda.kernel.CudaKernel method) prepare_half_tomo_sinogram() (in module nabu.reconstruction.sinogram) prepare_sino() (nabu.reconstruction.sinogram.SinoMult method) (nabu.reconstruction.sinogram_cuda.CudaSinoMult method) (nabu.reconstruction.sinogram_opencl.OpenCLSinoMult method) PreProcessedSingleAxisStitchingConfiguration (class in nabu.stitching.config) PreProcessedYStitchingConfiguration (class in nabu.stitching.config) PreProcessedZStitchingConfiguration (class in nabu.stitching.config) preprocessing_command (nabu.stitching.config.SlurmConfig attribute) PreProcessingStitching (class in nabu.stitching.stitcher.pre_processing) PreProcessingStitchingDumper (class in nabu.stitching.stitcher.dumper.preprocessing) PreProcessingYStitcher (class in nabu.stitching.stitcher.y_stitcher) PreProcessingZStitcher (class in nabu.stitching.stitcher.z_stitcher) previouspow2() (in module nabu.utils) PrinterLogger (class in nabu.resources.logger) process() (nabu.stitching.utils.post_processing.StitchingPostProcAggregation method) process_chunk() (nabu.pipeline.fullfield.chunked.ChunkedPipeline method) ProcessConfig (class in nabu.pipeline.fullfield.processconfig) (class in nabu.pipeline.helical.processconfig) ProcessConfigBase (class in nabu.pipeline.processconfig) processing_cls (nabu.processing.muladd.MulAdd attribute) (nabu.processing.muladd_cuda.CudaMulAdd attribute) ProcessingBase (class in nabu.processing.processing_base) ProcessingCls (nabu.processing.fft_cuda.SKCUFFT attribute) (nabu.processing.fft_cuda.VKCUFFT attribute) (nabu.processing.fft_opencl.VKCLFFT attribute) (nabu.processing.fftshift.FFTshiftBase attribute) (nabu.processing.fftshift.OpenCLFFTshift attribute) (nabu.processing.transpose.CudaTranspose attribute) (nabu.processing.transpose.OpenCLTranspose attribute) (nabu.processing.transpose.TransposeBase attribute) progress (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) progress_bar() (in module nabu.estimation.alignment) progress_bars (nabu.stitching.utils.post_processing.StitchingPostProcAggregation property) projection() (nabu.reconstruction.projection.Projector method) projections (nabu.resources.dataset_analyzer.DatasetAnalyzer property) projections_srcurrent (nabu.resources.dataset_analyzer.DatasetAnalyzer property) projections_subsampling_validator() (in module nabu.pipeline.config_validators) Projector (class in nabu.reconstruction.projection) projs_indices() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) psnr() (in module nabu.misc.utils) push_context() (nabu.cuda.processing.CudaProcessing method) pycuda_to_cupy() (in module nabu.cuda.utils)

R

radio_shape() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) radios_shape() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) radios_to_sinos() (nabu.reconstruction.sinogram.SinoBuilder method) raise_error() (in module nabu.pipeline.config_validators) raw_data (nabu.stitching.alignment.PaddedRawData property) raw_data_end (nabu.stitching.alignment.PaddedRawData property) raw_data_start (nabu.stitching.alignment.PaddedRawData property) raw_regions_hdf5_dataset (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD property) read() (nabu.io.reader.EDFReader method) Reader (class in nabu.io.reader) rec_delta_z (nabu.pipeline.fullfield.processconfig.ProcessConfig property) rec_roi (nabu.pipeline.fullfield.processconfig.ProcessConfig property) rec_shape (nabu.pipeline.fullfield.processconfig.ProcessConfig property) reconstruct() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) (nabu.reconstruction.cone.ConebeamReconstructor method) (nabu.reconstruction.mlem.MLEMReconstructor method) (nabu.reconstruction.reconstructor.Reconstructor method) (nabu.reconstruction.reconstructor_cuda.CudaReconstructor method) reconstruct_with_textures() (in module bench_textures) reconstruct_without_textures() (in module bench_textures) reconstruction_implementation_validator() (in module nabu.pipeline.config_validators) reconstruction_method_validator() (in module nabu.pipeline.config_validators) Reconstructor (class in nabu.reconstruction.reconstructor) recover_arrays_references() (nabu.processing.processing_base.ProcessingBase method) recursive_copy_dict() (in module nabu.utils) recut() (in module nabu.misc.padding) reduce_dark_flat() (in module nabu.app.reduce_dark_flat) refine_max_position_1d() (nabu.estimation.alignment.AlignmentBase static method) refine_max_position_2d() (nabu.estimation.alignment.AlignmentBase static method) register_callback() (nabu.pipeline.fullfield.chunked.ChunkedPipeline method) release() (nabu.io.reader.HDF5Reader method) (nabu.io.reader.NPReader method) (nabu.io.reader.Reader method) remove_all_stripe() (in module nabu.thirdparty.tomocupy_remove_stripe) remove_all_stripe_pycuda() (in module nabu.thirdparty.tomocupy_remove_stripe) remove_all_stripe_sinos() (in module nabu.thirdparty.tomocupy_remove_stripe) remove_invalid_values() (nabu.preproc.flatfield.FlatFieldArrays method) remove_items_from_list() (in module nabu.utils) remove_parenthesis_or_brackets() (in module nabu.utils) remove_rings() (nabu.reconstruction.rings.MunchDeringer method) (nabu.reconstruction.rings.SinoMeanDeringer method) (nabu.reconstruction.rings.VoDeringer method) (nabu.reconstruction.rings_cuda.CudaVoDeringer method)

remove_rings_radios() (nabu.reconstruction.rings.VoDeringer method) (nabu.reconstruction.rings_cuda.CudaVoDeringer method) remove_rings_sinogram() (nabu.reconstruction.rings.SinoMeanDeringer method) (nabu.reconstruction.rings.VoDeringer method) (nabu.reconstruction.rings_cuda.CudaSinoMeanDeringer method) (nabu.reconstruction.rings_cuda.CudaVoDeringer method) remove_rings_sinograms() (nabu.reconstruction.rings.SinoMeanDeringer method) (nabu.reconstruction.rings.VoDeringer method) (nabu.reconstruction.rings_cuda.CudaSinoMeanDeringer method) (nabu.reconstruction.rings_cuda.CudaVoDeringer method) remove_stripe_fw() (in module nabu.thirdparty.tomocupy_remove_stripe) remove_stripe_ti() (in module nabu.thirdparty.tomocupy_remove_stripe) replace_array_memory() (in module nabu.cuda.utils) (in module nabu.opencl.utils) rescale_data() (in module nabu.misc.utils) rescale_frames (nabu.stitching.config.StitchingConfiguration attribute) rescale_frames() (nabu.stitching.stitcher.single_axis.SingleAxisStitcher method) rescale_integers() (in module nabu.utils) rescale_params (nabu.stitching.config.StitchingConfiguration attribute) reset_rot_center() (nabu.reconstruction.fbp_base.BackprojectorBase method) resources_validator() (in module nabu.pipeline.config_validators) restore_items_in_list() (in module nabu.utils) retrieve_phase() (in module nabu.thirdparty.tomopy_phase) (nabu.preproc.ctf.CTFPhaseRetrieval method) (nabu.preproc.ctf_cuda.CudaCTFPhaseRetrieval method) (nabu.preproc.phase.PaganinPhaseRetrieval method) (nabu.preproc.phase_cuda.CudaPaganinPhaseRetrieval method) retrieve_tomo_objects() (nabu.stitching.utils.post_processing.StitchingPostProcAggregation method) RIGHT (nabu.stitching.sample_normalization.SampleSide attribute) RIGTH (nabu.stitching.alignment.AlignmentAxis2 attribute) roi_is_centered() (in module nabu.reconstruction.cone) rotate() (nabu.processing.rotation.Rotation method) (nabu.processing.rotation_cuda.CudaRotation method) rotate_cli() (in module nabu.app.rotate) rotate_images() (nabu.app.rotate.HDF5ImagesStackRotation method) Rotation (class in nabu.processing.rotation) rotation_angles (nabu.resources.dataset_analyzer.DatasetAnalyzer property) rotation_angles() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) rotation_axis_position() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) run() (nabu.stitching.utils.post_processing.SlurmStitchingFollowerThread method)

S

safe_format() (in module nabu.utils) SampleSide (class in nabu.stitching.sample_normalization) sanitize_metadata() (nabu.io.writer.HSTVolWriter static method) save() (nabu.io.writer.HSTVolVolume method) (nabu.io.writer.NXVolVolume method) save_configuration() (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumper method) (nabu.stitching.stitcher.dumper.preprocessing.PreProcessingStitchingDumper method) save_frame_to_disk() (nabu.stitching.stitcher.dumper.base.DumperBase static method) (nabu.stitching.stitcher.dumper.preprocessing.PreProcessingStitchingDumper method) save_metadata() (nabu.io.writer.HSTVolVolume method) (nabu.io.writer.NXVolVolume method) save_reduced_frames() (in module nabu.resources.nxflatfield) save_stitched_frame() (nabu.stitching.stitcher.dumper.base.DumperBase method) (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD method) schift() (nabu.estimation.cor_sino.SinoCor static method) search_methods (nabu.pipeline.estimators.CompositeCORFinder attribute) (nabu.pipeline.estimators.CORFinder attribute) (nabu.pipeline.estimators.CORFinderBase attribute) (nabu.pipeline.estimators.SinoCORFinder attribute) selection_is_centered() (in module nabu.reconstruction.cone) serie_label (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) (nabu.stitching.stitcher.y_stitcher.PreProcessingYStitcher property) (nabu.stitching.stitcher.z_stitcher.PostProcessingZStitcher property) (nabu.stitching.stitcher.z_stitcher.PostProcessingZStitcherNoDD property) series (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) set_array() (nabu.processing.processing_base.ProcessingBase method) set_automation_params() (nabu.processing.kernel_base.KernelBase method) set_custom_angles_and_axis_corrections() (nabu.pipeline.helical.fbp.BackprojectorHelical method) set_data_buffer() (nabu.io.reader_helical.ChunkReaderHelical method) set_filter() (nabu.reconstruction.filtering.SinoFilter method) (nabu.reconstruction.filtering_cuda.CudaSinoFilter method) (nabu.reconstruction.filtering_opencl.OpenCLSinoFilter method) set_full_transformation() (nabu.io.detector_distortion.DetectorDistortionBase method) set_image() (nabu.reconstruction.projection.Projector method) set_input() (nabu.preproc.ctf_cuda.CudaCTFPhaseRetrieval method) (nabu.preproc.phase_cuda.CudaPaganinPhaseRetrieval method) set_is_active() (nabu.stitching.config.NormalizationBySample method) set_nested_dict_value() (in module nabu.app.shrink_dataset) set_rot_center() (nabu.reconstruction.sinogram.SinoBuilder method) set_sub_region_transformation() (nabu.io.detector_distortion.DetectorDistortionBase method) set_subregion() (nabu.pipeline.fullfield.chunked.ChunkedPipeline method) settle_flips() (nabu.stitching.stitcher.post_processing.PostProcessingStitching method) (nabu.stitching.stitcher.single_axis.SingleAxisStitcher method) settle_input_scans() (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration method) settle_input_volumes() (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration method) settle_inputs() (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.SingleAxisStitchingConfiguration method) settle_slices() (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.SingleAxisStitchingConfiguration method) setup_hbp() (nabu.reconstruction.hbp.HierarchicalBackprojector method) sfb1d() (in module nabu.thirdparty.tomocupy_remove_stripe) shape (nabu.stitching.alignment.PaddedRawData property) shift() (in module nabu.pipeline.helical.weight_balancer) ShiftAlgorithm (class in nabu.stitching.utils.utils) shrink_cli() (in module nabu.app.shrink_dataset) shrink_dataset() (in module nabu.app.shrink_dataset) side (nabu.stitching.config.NormalizationBySample property) sigma_fraction (nabu.estimation.cor.CenterOfRotationAdaptiveSearch attribute) simulate_edf_header() (in module nabu.app.generate_header) simulate_hst_vol_header() (in module nabu.app.generate_header) simulate_info_file() (in module nabu.app.generate_header) SingleAxisConfigMetaClass (class in nabu.stitching.config) SingleAxisStitcher (class in nabu.stitching.stitcher.single_axis) SingleAxisStitchingConfiguration (class in nabu.stitching.config) sinlet() (nabu.estimation.cor_sino.CenterOfRotationFourierAngles method) SINO_COARSE_TO_FINE (nabu.stitching.utils.utils.ShiftAlgorithm attribute) sino_deringer_methods() (in module nabu.pipeline.config_validators) sino_normalization_validator() (in module nabu.pipeline.config_validators) sino_shape (nabu.pipeline.fullfield.chunked.ChunkedPipeline property) sino_shape() (nabu.pipeline.fullfield.processconfig.ProcessConfig method)

SinoBuilder (class in nabu.reconstruction.sinogram) SinoBuilderClass (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) SinoCor (class in nabu.estimation.cor_sino) SinoCOREstimator (in module nabu.pipeline.estimators) SinoCORFinder (class in nabu.pipeline.estimators) SinoCorInterface (class in nabu.estimation.cor_sino) SinoFilter (class in nabu.reconstruction.filtering) SinoFilterClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) (nabu.reconstruction.fbp.CudaBackprojector attribute) (nabu.reconstruction.fbp_base.BackprojectorBase attribute) (nabu.reconstruction.fbp_opencl.OpenCLBackprojector attribute) SinoMeanDeringer (class in nabu.reconstruction.rings) SinoMeanDeringerClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) SinoMult (class in nabu.reconstruction.sinogram) SinoMultClass (nabu.reconstruction.fbp.CudaBackprojector attribute) (nabu.reconstruction.fbp_base.BackprojectorBase attribute) (nabu.reconstruction.fbp_opencl.OpenCLBackprojector attribute) SinoNormalization (class in nabu.reconstruction.sinogram) SinoNormalizationClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) sinos_shape (nabu.pipeline.fullfield.chunked.ChunkedPipeline property) sinos_shape() (nabu.pipeline.fullfield.processconfig.ProcessConfig method) SKCUFFT (class in nabu.processing.fft_cuda) SKIMAGE (nabu.stitching.utils.utils.ShiftAlgorithm attribute) skip_tomoscan_checks (nabu.pipeline.utils.EnvSettings attribute) slice_for_cross_correlation (nabu.stitching.config.StitchingConfiguration attribute) slice_idx_from_str_to_int() (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration method) slice_num_validator() (in module nabu.pipeline.config_validators) slices (nabu.stitching.config.SingleAxisStitchingConfiguration attribute) SLIDING_WINDOW (nabu.stitching.utils.utils.ShiftAlgorithm attribute) slurm_config (nabu.stitching.config.StitchingConfiguration attribute) SlurmConfig (class in nabu.stitching.config) SlurmStitchingFollowerContext (class in nabu.stitching.utils.post_processing) SlurmStitchingFollowerThread (class in nabu.stitching.utils.post_processing) SpanStrategy (class in nabu.pipeline.helical.span_strategy) split_slices() (in module nabu.stitching.slurm_utils) split_stitching_configuration_to_slurm_job() (in module nabu.stitching.slurm_utils) step_fraction (nabu.estimation.cor.CenterOfRotationAdaptiveSearch attribute) stitch() (nabu.stitching.overlap.ImageStichOverlapKernel method) (nabu.stitching.stitcher.single_axis.SingleAxisStitcher method) stitch_frames() (nabu.stitching.stitcher.single_axis.SingleAxisStitcher static method) stitch_raw_frames() (in module nabu.stitching.stitcher_2D) stitched_axis (nabu.stitching.overlap.ImageStichOverlapKernel property) stitching() (in module nabu.stitching.single_axis_stitching) stitching_axis_in_frame_space (nabu.stitching.stitcher.post_processing.PostProcessingStitching property) (nabu.stitching.stitcher.pre_processing.PreProcessingStitching property) (nabu.stitching.stitcher.single_axis.SingleAxisStitcher property) stitching_config (nabu.stitching.utils.post_processing.StitchingPostProcAggregation property) stitching_kernels_extra_params (nabu.stitching.config.StitchingConfiguration attribute) stitching_regions_hdf5_dataset (nabu.stitching.stitcher.dumper.postprocessing.PostProcessingStitchingDumperNoDD property) stitching_strategy (nabu.stitching.config.StitchingConfiguration attribute) (nabu.stitching.overlap.ImageStichOverlapKernel property) stitching_type (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration property) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration property) (nabu.stitching.config.StitchingConfiguration property) StitchingConfiguration (class in nabu.stitching.config) StitchingPostProcAggregation (class in nabu.stitching.utils.post_processing) StitchingType (class in nabu.stitching.definitions) str2bool() (in module nabu.pipeline.config_validators) str_or_none() (in module nabu.app.generate_header) str_to_shifts() (in module nabu.stitching.config) sub_region_xz (nabu.pipeline.fullfield.chunked.ChunkedPipeline property) subdivide_into_overlapping_segment() (in module nabu.utils) subsample_dict() (in module nabu.utils) subsampling (nabu.pipeline.fullfield.processconfig.ProcessConfig property) sunshine_image (nabu.pipeline.helical.span_strategy.SpanStrategy attribute) supported_modes (nabu.processing.padding_base.PaddingBase attribute) (nabu.processing.rotation.Rotation attribute) (nabu.reconstruction.rings.SinoMeanDeringer attribute) supported_paddings (nabu.preproc.phase_cuda.CudaPaganinPhaseRetrieval attribute)

T

take_logarithm() (nabu.preproc.ccd.Log method) (nabu.preproc.ccd_cuda.CudaLog method) tilt_threshold (nabu.pipeline.estimators.DetectorTiltEstimator attribute) tilt_validator() (in module nabu.pipeline.config_validators) TiltFinder (in module nabu.pipeline.estimators) to_3D_array() (in module nabu.utils) to_device() (nabu.processing.processing_base.ProcessingBase method) to_dict() (nabu.stitching.config.NormalizationBySample method) (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.PreProcessedSingleAxisStitchingConfiguration method) (nabu.stitching.config.SingleAxisStitchingConfiguration method) (nabu.stitching.config.SlurmConfig method) (nabu.stitching.config.StitchingConfiguration method)

tomoscan_load_reduced_frames() (in module nabu.resources.nxflatfield) total_merit_list() (in module nabu.app.diag_to_rot) total_view_heights (nabu.pipeline.helical.span_strategy.SpanStrategy attribute) transform() (nabu.io.detector_distortion.DetectorDistortionBase method) transform_images() (in module nabu.app.diag_to_pix) (in module nabu.app.diag_to_rot) transpose() (in module nabu.processing.transpose) TransposeBase (class in nabu.processing.transpose) tukey() (nabu.estimation.cor_sino.CenterOfRotationFourierAngles method)

U

uncompress_file() (in module nabu.testutils) unsharp() (nabu.processing.unsharp.UnsharpMask method) (nabu.processing.unsharp_cuda.CudaUnsharpMask method) (nabu.processing.unsharp_opencl.OpenclUnsharpMask method) unsharp_method_validator() (in module nabu.pipeline.config_validators) UnsharpMask (class in nabu.processing.unsharp) UnsharpMaskClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute)

unstitched_axis (nabu.stitching.overlap.ImageStichOverlapKernel property) update_dataset_info_flats_darks() (in module nabu.resources.nxflatfield) update_func_kwargs() (in module nabu.pipeline.estimators) update_reconstruction_start_end() (in module nabu.app.reconstruct) updiv() (in module nabu.utils) usable_opencl_devices() (in module nabu.opencl.utils) use_cases (nabu.misc.utils.ConvolutionInfos attribute) use_options() (in module nabu.pipeline.utils)

V

validate_config() (in module nabu.pipeline.config) validator() (in module nabu.pipeline.config_validators) variable_idxlen_sort() (in module nabu.pipeline.fullfield.reconstruction) VerticalShift (class in nabu.preproc.shift) VerticalShiftClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) view_as_images_stack() (in module nabu.utils) VKCLFFT (class in nabu.processing.fft_opencl) VKCUFFT (class in nabu.processing.fft_cuda)

vkffs_cls (nabu.processing.fft_cuda.VKCUFFT attribute) (nabu.processing.fft_opencl.VKCLFFT attribute) VoDeringer (class in nabu.reconstruction.rings) VoDeringerClass (nabu.pipeline.fullfield.chunked.ChunkedPipeline attribute) (nabu.pipeline.fullfield.chunked_cuda.CudaChunkedPipeline attribute) VolReaderBase (class in nabu.io.reader) VolumeHistogram (class in nabu.processing.histogram) VolumesHistogram (class in nabu.app.histogram) voxel_size (nabu.stitching.config.PostProcessedSingleAxisStitchingConfiguration attribute)

W

walltime_validator() (in module nabu.pipeline.config_validators) warn() (nabu.resources.logger.Logger method) warning() (in module nabu.utils) (nabu.resources.logger.Logger method) WeightBalancer (class in nabu.pipeline.helical.weight_balancer) weights_img_1 (nabu.stitching.overlap.ImageStichOverlapKernel property) weights_img_2 (nabu.stitching.overlap.ImageStichOverlapKernel property) width (nabu.stitching.config.NormalizationBySample property) wip() (in module nabu.utils)

within_margin_projection_intervals (nabu.pipeline.helical.span_strategy.SpanStrategy attribute) write() (nabu.io.writer.HSTVolWriter method) (nabu.io.writer.NXProcessWriter method) write_data() (nabu.pipeline.writer.WriterManager method) write_double_flatfield() (nabu.app.double_flatfield.DoubleFlatFieldChunks method) write_histogram() (nabu.app.histogram.VolumesHistogram method) (nabu.pipeline.writer.WriterManager method) write_metadata_file() (nabu.pipeline.fullfield.reconstruction.FullFieldReconstructor method) Writer (class in nabu.io.writer) WriterManager (class in nabu.pipeline.writer)

X

x_flips (nabu.stitching.stitcher.pre_processing.PreProcessingStitching property)

x_translation (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer property)

Y

y_flips (nabu.stitching.stitcher.pre_processing.PreProcessingStitching property)

Y_PREPROC (nabu.stitching.definitions.StitchingType attribute) y_stitching() (in module nabu.stitching.y_stitching)

Z

z_min (nabu.pipeline.fullfield.chunked.ChunkedPipeline property) Z_POSTPROC (nabu.stitching.definitions.StitchingType attribute) Z_PREPROC (nabu.stitching.definitions.StitchingType attribute)

z_split() (nabu.app.nx_z_splitter.NXZSplitter method) z_stitching() (in module nabu.stitching.z_stitching) z_translation (nabu.resources.dataset_analyzer.HDF5DatasetAnalyzer property) zsplit() (in module nabu.app.nx_z_splitter)