API reference

Subpackages

• nabu.app package
  • Submodules
    • nabu.app.bootstrap module
      • bootstrap()
      • get_config_template()
    • nabu.app.bootstrap_stitching module
      • guess_tomo_objects()
      • bootstrap_stitching()
    • nabu.app.cast_volume module
      • main()
    • nabu.app.cli_configs module
    • nabu.app.compare_volumes module
      • idx_1d_to_3d()
      • compare_volumes()
      • compare_volumes_cli()
    • nabu.app.composite_cor module
      • NumpyArrayEncoder
      • main()
      • composite_cor_entry_point()
    • nabu.app.correct_rot module
      • main()
    • nabu.app.create_distortion_map_from_poly module
      • create_distortion_maps_entry_point()
      • create_maps_x_and_z()
    • nabu.app.diag_to_pix module
      • transform_images()
      • detailed_merit()
      • merit()
      • build_total_merit_list()
      • main()
    • nabu.app.diag_to_rot module
      • transform_images()
      • total_merit_list()
      • find_best_interpolating_line()
      • main()
      • do_height_by_height()
      • do_linear_interpolation()
    • nabu.app.double_flatfield module
      • DoubleFlatFieldChunks
      • dff_cli()
    • nabu.app.generate_header module
      • decode_bytes()
      • simulate_edf_header()
      • simulate_info_file()
      • get_hst_saturations()
      • simulate_hst_vol_header()
      • format_as_info()
      • generate_merged_info_file_content()
      • str_or_none()
      • generate_merged_info_file()
    • nabu.app.histogram module
      • VolumesHistogram
      • histogram_cli()
    • nabu.app.multicor module
      • get_user_cors()
      • main()
    • nabu.app.nx_z_splitter module
      • NXZSplitter
      • zsplit()
    • nabu.app.parse_reconstruction_log module
      • extract_timings_from_volume_reconstruction_lines()
      • parse_logfile()
      • display_timings_pie()
      • parse_reclog_cli()
    • nabu.app.prepare_weights_double module
      • main()
      • create_heli_maps()
    • nabu.app.reconstruct module
      • update_reconstruction_start_end()
      • get_log_file()
      • get_reconstructor()
      • list_hdf5_entries()
      • main()
    • nabu.app.reconstruct_helical module
      • main_helical()
    • nabu.app.reduce_dark_flat module
      • reduce_dark_flat()
      • main()
    • nabu.app.rotate module
      • HDF5ImagesStackRotation
      • rotate_cli()
    • nabu.app.shrink_dataset module
      • access_nested_dict()
      • set_nested_dict_value()
      • shrink_dataset()
      • shrink_cli()
    • nabu.app.stitching module
      • main()
    • nabu.app.utils module
      • parse_params_values()
      • parse_sections()
    • nabu.app.validator module
      • get_scans()
      • main()
  • Module contents
• nabu.cuda package
  • Submodules
    • nabu.cuda.convolution module
    • nabu.cuda.fft module
    • nabu.cuda.kernel module
      • CudaKernel
    • nabu.cuda.medfilt module
    • nabu.cuda.padding module
    • nabu.cuda.processing module
      • CudaProcessing
    • nabu.cuda.utils module
      • get_cuda_context()
      • count_cuda_devices()
      • get_gpu_memory()
      • is_gpu_usable()
      • detect_cuda_gpus()
      • collect_cuda_gpus()
      • get_nvcc_version()
      • check_textures_availability()
      • cuarray_format_to_dtype()
      • cuarray_shape_dtype()
      • get_shape_dtype()
      • copy_array()
      • copy_big_gpuarray()
      • replace_array_memory()
      • pycuda_to_cupy()
      • cupy_to_pycuda()
  • Module contents
• nabu.estimation package
  • Submodules
    • nabu.estimation.alignment module
      • progress_bar()
      • AlignmentBase
    • nabu.estimation.cor module
      • CenterOfRotation
      • CenterOfRotationSlidingWindow
      • CenterOfRotationGrowingWindow
      • CenterOfRotationAdaptiveSearch
      • CenterOfRotationOctaveAccurate
    • nabu.estimation.cor_sino module
      • SinoCor
      • SinoCorInterface
      • CenterOfRotationFourierAngles
      • CenterOfRotationVo
    • nabu.estimation.distortion module
      • estimate_flat_distortion()
    • nabu.estimation.focus module
      • CameraFocus
    • nabu.estimation.tilt module
      • CameraTilt
    • nabu.estimation.translation module
      • DetectorTranslationAlongBeam
    • nabu.estimation.utils module
      • is_fullturn_scan()
  • Module contents
• nabu.io package
  • Submodules
    • nabu.io.cast_volume module
      • get_default_output_volume()
      • cast_volume()
    • nabu.io.detector_distortion module
      • DetectorDistortionBase
      • DetectorDistortionMapsXZ
    • nabu.io.reader module
      • Reader
      • NPReader
      • EDFReader
      • HDF5Reader
      • HDF5Loader
      • VolReaderBase
      • NXTomoReader
      • NXDarksFlats
      • EDFStackReader
      • load_images_stack_from_hdf5()
      • get_hdf5_dataset_shape()
      • get_hdf5_dataset_dtype()
      • get_entry_from_h5_path()
      • check_virtual_sources_exist()
      • import_h5_to_dict()
    • nabu.io.reader_helical module
      • ChunkReaderHelical
    • nabu.io.utils module
      • get_compacted_dataslices()
      • get_first_hdf5_entry()
      • hdf5_entry_exists()
      • get_h5_value()
      • get_h5_str_value()
      • create_dict_of_indices()
      • convert_dict_values()
      • EntryReader
      • DatasetReader
      • file_format_is_edf()
      • file_format_is_jp2k()
      • file_format_is_tiff()
      • file_format_is_hdf5()
      • get_output_volume()
    • nabu.io.writer module
      • get_datetime()
      • Writer
      • h5_write_object()
      • NXProcessWriter
      • NXVolVolume
      • LegacyNXProcessWriter
      • export_dict_to_h5()
      • create_virtual_layout()
      • merge_hdf5_files()
      • HSTVolWriter
      • HSTVolVolume
  • Module contents
• nabu.misc package
  • Submodules
    • nabu.misc.binning module
      • binning()
      • binning_n_alt()
    • nabu.misc.fftshift module
    • nabu.misc.filters module
      • correct_spikes()
    • nabu.misc.fourier_filters module
      • get_lowpass_filter()
      • get_highpass_filter()
      • get_bandpass_filter()
    • nabu.misc.histogram module
    • nabu.misc.histogram_cuda module
    • nabu.misc.kernel_base module
    • nabu.misc.padding module
      • pad_interpolate()
      • recut()
    • 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
      • rescale_data()
      • get_dtype_range()
      • psnr()
      • ConvolutionInfos
  • Module contents
• nabu.opencl package
  • Submodules
    • nabu.opencl.fft module
    • nabu.opencl.kernel module
      • OpenCLKernel
    • nabu.opencl.memcpy module
      • OpenCLMemcpy2D
    • nabu.opencl.padding module
    • nabu.opencl.processing module
      • OpenCLProcessing
    • nabu.opencl.utils module
      • get_opencl_devices()
      • usable_opencl_devices()
      • detect_opencl_gpus()
      • collect_opencl_gpus()
      • collect_opencl_cpus()
      • get_opencl_context()
      • replace_array_memory()
      • pick_opencl_cpu_platform()
      • allocate_texture()
      • check_textures_availability()
      • copy_to_texture()
  • Module contents
• nabu.pipeline package
  • Subpackages
    • nabu.pipeline.fullfield package
      • Submodules
      • Module contents
    • nabu.pipeline.helical package
      • Submodules
      • Module contents
    • nabu.pipeline.xrdct package
      • Module contents
  • Submodules
    • nabu.pipeline.config module
      • NabuConfigParser
      • parse_nabu_config_file()
      • generate_nabu_configfile()
      • get_default_nabu_config()
      • validate_config()
      • overwrite_config()
    • nabu.pipeline.config_validators module
      • raise_error()
      • validator()
      • convert_to_int()
      • convert_to_float()
      • convert_to_bool()
      • str2bool()
      • convert_to_bool_noerr()
      • name_range_checker()
      • optional_string_validator()
      • file_name_validator()
      • file_location_validator()
      • optional_file_location_validator()
      • optional_values_file_validator()
      • directory_location_validator()
      • optional_directory_location_validator()
      • dataset_location_validator()
      • directory_writeable_validator()
      • optional_output_directory_validator()
      • optional_output_file_path_validator()
      • integer_validator()
      • nonnegative_integer_validator()
      • positive_integer_validator()
      • optional_positive_integer_validator()
      • nonzero_integer_validator()
      • binning_validator()
      • projections_subsampling_validator()
      • optional_file_name_validator()
      • boolean_validator()
      • boolean_or_auto_validator()
      • float_validator()
      • optional_float_validator()
      • optional_nonzero_float_validator()
      • optional_tuple_of_floats_validator()
      • cor_validator()
      • tilt_validator()
      • slice_num_validator()
      • generic_options_validator()
      • cor_options_validator()
      • cor_slice_validator()
      • flatfield_enabled_validator()
      • phase_method_validator()
      • detector_distortion_correction_validator()
      • unsharp_method_validator()
      • padding_mode_validator()
      • reconstruction_method_validator()
      • fbp_filter_name_validator()
      • reconstruction_implementation_validator()
      • optimization_algorithm_name_validator()
      • output_file_format_validator()
      • distribution_method_validator()
      • sino_normalization_validator()
      • sino_deringer_methods()
      • list_of_int_validator()
      • list_of_shift_validator()
      • list_of_tomoscan_identifier()
      • resources_validator()
      • walltime_validator()
      • nonempty_string_validator()
      • logging_validator()
      • exclude_projections_validator()
      • no_validator()
    • nabu.pipeline.datadump module
      • DataDumpManager
    • nabu.pipeline.dataset_validator module
      • DatasetValidatorBase
    • nabu.pipeline.detector_distortion_provider module
      • DetectorDistortionProvider()
    • nabu.pipeline.estimators module
      • estimate_cor()
      • CORFinderBase
      • CORFinder
      • COREstimator
      • SinoCORFinder
      • SinoCOREstimator
      • CompositeCORFinder
      • oversample()
      • CompositeCOREstimator
      • get_default_kwargs()
      • update_func_kwargs()
      • get_class_name()
      • DetectorTiltEstimator
      • TiltFinder
    • nabu.pipeline.params module
    • nabu.pipeline.processconfig module
      • ProcessConfigBase
    • nabu.pipeline.reader module
      • bin_image_stack()
      • NXTomoReaderBinning()
      • apply_distortion_correction_on_images_stack()
      • NXTomoReaderDistortionCorrection()
      • EDFStackReaderBinning()
      • apply_distortion_correction_on_image()
      • EDFStackReaderDistortionCorrection()
      • load_darks_flats()
    • nabu.pipeline.utils module
      • use_options()
      • pipeline_step()
      • get_subregion()
      • EnvSettings
    • nabu.pipeline.writer module
      • WriterManager
  • Module contents
• nabu.preproc package
  • Submodules
    • nabu.preproc.alignment module
    • nabu.preproc.ccd module
      • CCDFilter
      • Log
    • nabu.preproc.ccd_cuda module
      • CudaCCDFilter
      • CudaLog
    • nabu.preproc.ctf module
      • GeoPars
      • CTFPhaseRetrieval
      • CtfFilter
    • nabu.preproc.ctf_cuda module
      • CudaCTFPhaseRetrieval
    • nabu.preproc.distortion module
      • correct_distortion_interpn()
      • DistortionCorrection
    • nabu.preproc.double_flatfield module
      • DoubleFlatField
    • nabu.preproc.double_flatfield_cuda module
      • CudaDoubleFlatField
    • nabu.preproc.double_flatfield_variable_region module
      • DoubleFlatFieldVariableRegion
    • nabu.preproc.flatfield module
      • FlatFieldArrays
      • FlatField
    • nabu.preproc.flatfield_cuda module
      • CudaFlatFieldArrays
      • CudaFlatField
    • nabu.preproc.flatfield_variable_region module
      • FlatFieldArraysVariableRegion
      • FlatFieldDataVariableRegionUrls
    • nabu.preproc.phase module
      • lmicron_to_db()
      • PaganinPhaseRetrieval
      • compute_paganin_margin()
    • nabu.preproc.phase_cuda module
      • CudaPaganinPhaseRetrieval
    • nabu.preproc.shift module
      • VerticalShift
    • nabu.preproc.shift_cuda module
      • CudaVerticalShift
  • Module contents
• nabu.processing package
  • Submodules
    • nabu.processing.azim module
      • azimuthal_integration()
      • do_radial_distribution()
      • azimuthal_integration_skimage()
      • azimuthal_integration_imagej_stack()
      • azimuthal_integration_skimage_stack()
    • nabu.processing.convolution_cuda module
      • Convolution
    • nabu.processing.fft_base module
      • is_fast_axes()
    • nabu.processing.fft_cuda module
      • init_skcuda()
      • SKCUFFT
      • VKCUFFT
      • has_vkfft()
      • has_skcuda()
      • get_fft_class()
      • get_available_fft_implems()
    • nabu.processing.fft_opencl module
      • VKCLFFT
      • has_vkfft()
    • nabu.processing.fftshift module
      • FFTshiftBase
      • OpenCLFFTshift
    • nabu.processing.histogram module
      • PartialHistogram
      • VolumeHistogram
      • hist_as_2Darray()
      • add_last_bin()
    • nabu.processing.histogram_cuda module
      • CudaPartialHistogram
      • CudaVolumeHistogram
    • nabu.processing.kernel_base module
      • KernelBase
    • nabu.processing.medfilt_cuda module
      • MedianFilter
    • nabu.processing.muladd module
      • MulAdd
    • nabu.processing.muladd_cuda module
      • CudaMulAdd
    • nabu.processing.padding_base module
      • PaddingBase
    • nabu.processing.padding_cuda module
      • CudaPadding
    • nabu.processing.padding_opencl module
      • OpenCLPadding
    • nabu.processing.processing_base module
      • ProcessingBase
    • nabu.processing.roll_opencl module
      • OpenCLRoll
    • nabu.processing.rotation module
      • Rotation
    • nabu.processing.rotation_cuda module
      • CudaRotation
    • nabu.processing.transpose module
      • TransposeBase
      • CudaTranspose
      • OpenCLTranspose
      • transpose()
    • nabu.processing.unsharp module
      • UnsharpMask
    • nabu.processing.unsharp_cuda module
      • CudaUnsharpMask
    • nabu.processing.unsharp_opencl module
      • OpenclUnsharpMask
      • OpenCLUnsharpMask
  • Module contents
• nabu.reconstruction package
  • Submodules
    • nabu.reconstruction.cone module
      • ConebeamReconstructor
      • selection_is_centered()
      • roi_is_centered()
      • fdk_preweighting()
    • nabu.reconstruction.fbp module
      • CudaBackprojector
      • Backprojector
      • PolarBackprojector
    • nabu.reconstruction.fbp_base module
      • BackprojectorBase
    • nabu.reconstruction.fbp_opencl module
      • OpenCLBackprojector
    • nabu.reconstruction.filtering module
      • SinoFilter
      • filter_sinogram()
    • nabu.reconstruction.filtering_cuda module
      • CudaSinoFilter
    • nabu.reconstruction.filtering_opencl module
      • OpenCLSinoFilter
    • nabu.reconstruction.hbp module
      • buildConebeamGeometry()
      • HierarchicalBackprojector
      • get_max_grid_size()
      • getGridSize()
    • nabu.reconstruction.mlem module
      • MLEMReconstructor
    • nabu.reconstruction.projection module
      • Projector
    • nabu.reconstruction.reconstructor module
      • Reconstructor
    • nabu.reconstruction.reconstructor_cuda module
      • CudaReconstructor
    • nabu.reconstruction.rings module
      • MunchDeringer
      • VoDeringer
      • SinoMeanDeringer
    • nabu.reconstruction.rings_cuda module
      • CudaMunchDeringer
      • can_use_cuda_deringer()
      • CudaVoDeringer
      • CudaSinoMeanDeringer
    • nabu.reconstruction.sinogram module
      • SinoBuilder
      • SinoMult
      • convert_halftomo()
      • match_half_sinos_parts()
      • get_extended_sinogram_width()
      • prepare_half_tomo_sinogram()
      • SinoNormalization
    • nabu.reconstruction.sinogram_cuda module
      • CudaSinoBuilder
      • CudaSinoMult
      • CudaSinoNormalization
    • nabu.reconstruction.sinogram_opencl module
      • OpenCLSinoMult
  • Module contents
• nabu.resources package
  • Subpackages
    • nabu.resources.cli package
      • Module contents
    • nabu.resources.templates package
      • Module contents
  • Submodules
    • nabu.resources.cor module
    • nabu.resources.dataset_analyzer module
      • DatasetAnalyzer
      • EDFDatasetAnalyzer
      • HDF5DatasetAnalyzer
      • analyze_dataset()
      • get_radio_pair()
    • nabu.resources.gpu module
      • GPUDescription
      • pick_gpus()
      • pick_gpus_auto()
      • pick_gpus_nvidia()
    • nabu.resources.logger module
      • Logger
      • LoggerOrPrint()
      • PrinterLogger
    • nabu.resources.nxflatfield module
      • get_frame_possible_urls()
      • save_reduced_frames()
      • get_metadata_url()
      • tomoscan_load_reduced_frames()
      • data_url_exists()
      • update_dataset_info_flats_darks()
    • nabu.resources.utils module
      • get_values_from_file()
      • get_memory_per_node()
      • get_threads_per_node()
      • extract_parameters()
      • compact_parameters()
      • is_hdf5_extension()
      • get_quantities_and_units()
  • Module contents
• nabu.stitching package
  • Subpackages
    • nabu.stitching.stitcher package
      • Subpackages
      • Submodules
      • Module contents
    • nabu.stitching.utils package
      • Submodules
      • Module contents
  • Submodules
    • nabu.stitching.alignment module
      • AlignmentAxis2
      • AlignmentAxis1
      • align_frame()
      • align_horizontally()
      • PaddedRawData
    • nabu.stitching.config module
      • str_to_shifts()
      • NormalizationBySample
      • SlurmConfig
      • StitchingConfiguration
      • SingleAxisConfigMetaClass
      • SingleAxisStitchingConfiguration
      • PreProcessedSingleAxisStitchingConfiguration
      • PostProcessedSingleAxisStitchingConfiguration
      • identifiers_as_str_to_instances()
      • dict_to_config_obj()
      • get_default_stitching_config()
      • PreProcessedYStitchingConfiguration
      • PreProcessedZStitchingConfiguration
      • PostProcessedZStitchingConfiguration
    • nabu.stitching.definitions module
      • StitchingType
    • nabu.stitching.frame_composition module
      • FrameComposition
    • nabu.stitching.overlap module
      • OverlapStitchingStrategy
      • OverlapKernelBase
      • ImageStichOverlapKernel
      • compute_image_minimum_divergence()
      • compute_image_higher_signal()
      • check_overlaps()
    • nabu.stitching.sample_normalization module
      • SampleSide
      • Method
      • normalize_frame()
    • nabu.stitching.single_axis_stitching module
      • stitching()
    • nabu.stitching.slurm_utils module
      • split_stitching_configuration_to_slurm_job()
      • split_slices()
      • get_working_directory()
    • nabu.stitching.stitcher_2D module
      • stitch_raw_frames()
      • get_overlap_areas()
    • nabu.stitching.y_stitching module
      • y_stitching()
    • nabu.stitching.z_stitching module
      • z_stitching()
  • Module contents
• nabu.thirdparty package
  • Submodules
    • nabu.thirdparty.algotom_convert_sino module
      • extend_sinogram()
    • nabu.thirdparty.pore3d_deringer_munch module
      • munchetal_filter()
    • nabu.thirdparty.tomocupy_remove_stripe module
      • afb1d()
      • sfb1d()
      • DWTForward
      • DWTInverse
      • remove_stripe_fw()
      • remove_stripe_ti()
      • remove_all_stripe()
      • remove_all_stripe_sinos()
      • remove_all_stripe_pycuda()
    • nabu.thirdparty.tomopy_phase module
      • retrieve_phase()
    • nabu.thirdparty.tomwer_load_flats_darks module
      • get_process_entries()
      • is_process_node()
      • get_darks_frm_process_file()
      • get_flats_frm_process_file()
  • Module contents

Submodules

• nabu.tests module
  • get_modules_to_test()
  • nabu_test()
• nabu.testutils module
  • generate_tests_scenarios()
  • get_data()
  • get_array_of_given_shape()
  • get_big_data()
  • uncompress_file()
  • get_file()
  • compare_arrays()
  • gaussian_apodization_window()
  • compare_shifted_images()
  • generate_nx_dataset()
• nabu.utils module
  • nextpow2()
  • previouspow2()
  • updiv()
  • convert_index()
  • get_folder_path()
  • get_cuda_srcfile()
  • get_opencl_srcfile()
  • get_resource_file()
  • indices_to_slices()
  • merge_slices()
  • compacted_views()
  • get_size_from_sliced_dimension()
  • get_shape_from_sliced_dims()
  • get_available_threads()
  • list_match_queries()
  • is_writeable()
  • is_int()
  • is_scalar()
  • safe_format()
  • get_ftype()
  • get_2D_3D_shape()
  • get_subregion()
  • get_3D_subregion()
  • to_3D_array()
  • view_as_images_stack()
  • rescale_integers()
  • merged_shape()
  • is_device_backend()
  • get_decay()
  • generate_powers()
  • calc_padding_lengths1D()
  • calc_padding_lengths()
  • partition_dict()
  • first_dict_item()
  • subsample_dict()
  • compare_dicts()
  • remove_items_from_list()
  • restore_items_in_list()
  • check_supported()
  • check_supported_enum()
  • check_shape()
  • copy_dict_items()
  • recursive_copy_dict()
  • subdivide_into_overlapping_segment()
  • get_num_threads()
  • DictToObj
  • remove_parenthesis_or_brackets()
  • filter_str_def()
  • convert_str_to_tuple()
  • concatenate_dict()
  • BaseClassError
  • MissingComponentError()
  • generate_coords()
  • clip_circle()
  • extend_image_onepixel()
  • median2()
  • measure_time()
  • wip()
  • warning()
  • deprecated()
  • deprecated_class()
  • deprecation_warning()
  • docstring()

Module contents