nabu.stitching package

Submodules

• nabu.stitching.alignment module
  • AlignmentAxis2
    • AlignmentAxis2.CENTER
    • AlignmentAxis2.LEFT
    • AlignmentAxis2.RIGTH
  • AlignmentAxis1
    • AlignmentAxis1.FRONT
    • AlignmentAxis1.CENTER
    • AlignmentAxis1.BACK
  • align_horizontally()
  • PaddedRawData
    • PaddedRawData.get_empty_frame()
    • PaddedRawData.empty_frame
    • PaddedRawData.shape
    • PaddedRawData.raw_data
    • PaddedRawData.raw_data_start
    • PaddedRawData.raw_data_end
    • PaddedRawData.dtype
• nabu.stitching.config module
  • str_to_shifts()
  • NormalizationBySample
    • NormalizationBySample.is_active()
    • NormalizationBySample.set_is_active()
    • NormalizationBySample.method
    • NormalizationBySample.margin
    • NormalizationBySample.side
    • NormalizationBySample.width
    • NormalizationBySample.from_dict()
    • NormalizationBySample.to_dict()
  • SlurmConfig
    • SlurmConfig.partition
    • SlurmConfig.mem
    • SlurmConfig.n_jobs
    • SlurmConfig.other_options
    • SlurmConfig.preprocessing_command
    • SlurmConfig.modules_to_load
    • SlurmConfig.clean_script
    • SlurmConfig.n_tasks
    • SlurmConfig.n_cpu_per_task
    • SlurmConfig.to_dict()
    • SlurmConfig.from_dict()
  • StitchingConfiguration
    • StitchingConfiguration.axis_0_pos_px
    • StitchingConfiguration.axis_1_pos_px
    • StitchingConfiguration.axis_2_pos_px
    • StitchingConfiguration.axis_0_pos_mm
    • StitchingConfiguration.axis_1_pos_mm
    • StitchingConfiguration.axis_2_pos_mm
    • StitchingConfiguration.axis_0_params
    • StitchingConfiguration.axis_1_params
    • StitchingConfiguration.axis_2_params
    • StitchingConfiguration.slurm_config
    • StitchingConfiguration.flip_lr
    • StitchingConfiguration.flip_ud
    • StitchingConfiguration.overwrite_results
    • StitchingConfiguration.stitching_strategy
    • StitchingConfiguration.stitching_kernels_extra_params
    • StitchingConfiguration.slice_for_cross_correlation
    • StitchingConfiguration.rescale_frames
    • StitchingConfiguration.rescale_params
    • StitchingConfiguration.normalization_by_sample
    • StitchingConfiguration.stitching_type
    • StitchingConfiguration.get_description_dict()
    • StitchingConfiguration.to_dict()
  • ZStitchingConfiguration
    • ZStitchingConfiguration.slices
    • ZStitchingConfiguration.alignment_axis_2
    • ZStitchingConfiguration.pad_mode
    • ZStitchingConfiguration.settle_inputs()
    • ZStitchingConfiguration.settle_slices()
    • ZStitchingConfiguration.get_output_object()
    • ZStitchingConfiguration.to_dict()
  • PreProcessedZStitchingConfiguration
    • PreProcessedZStitchingConfiguration.input_scans
    • PreProcessedZStitchingConfiguration.output_file_path
    • PreProcessedZStitchingConfiguration.output_data_path
    • PreProcessedZStitchingConfiguration.output_nexus_version
    • PreProcessedZStitchingConfiguration.pixel_size
    • PreProcessedZStitchingConfiguration.stitching_type
    • PreProcessedZStitchingConfiguration.get_output_object()
    • PreProcessedZStitchingConfiguration.settle_inputs()
    • PreProcessedZStitchingConfiguration.settle_input_scans()
    • PreProcessedZStitchingConfiguration.slice_idx_from_str_to_int()
    • PreProcessedZStitchingConfiguration.settle_slices()
    • PreProcessedZStitchingConfiguration.to_dict()
    • PreProcessedZStitchingConfiguration.get_description_dict()
    • PreProcessedZStitchingConfiguration.from_dict()
  • PostProcessedZStitchingConfiguration
    • PostProcessedZStitchingConfiguration.input_volumes
    • PostProcessedZStitchingConfiguration.output_volume
    • PostProcessedZStitchingConfiguration.voxel_size
    • PostProcessedZStitchingConfiguration.alignment_axis_1
    • PostProcessedZStitchingConfiguration.stitching_type
    • PostProcessedZStitchingConfiguration.get_output_object()
    • PostProcessedZStitchingConfiguration.settle_inputs()
    • PostProcessedZStitchingConfiguration.settle_input_volumes()
    • PostProcessedZStitchingConfiguration.slice_idx_from_str_to_int()
    • PostProcessedZStitchingConfiguration.settle_slices()
    • PostProcessedZStitchingConfiguration.from_dict()
    • PostProcessedZStitchingConfiguration.to_dict()
    • PostProcessedZStitchingConfiguration.get_description_dict()
  • identifiers_as_str_to_instances()
  • dict_to_config_obj()
  • get_default_stitching_config()
• nabu.stitching.definitions module
  • StitchingType
    • StitchingType.Z_PREPROC
    • StitchingType.Z_POSTPROC
• nabu.stitching.frame_composition module
  • ZFrameComposition
    • ZFrameComposition.local_start_y
    • ZFrameComposition.local_end_y
    • ZFrameComposition.global_start_y
    • ZFrameComposition.global_end_y
    • ZFrameComposition.browse()
    • ZFrameComposition.compose()
    • ZFrameComposition.compute_raw_frame_compositions()
    • ZFrameComposition.compute_stitch_frame_composition()
    • ZFrameComposition.pprint_z_stitching()
• nabu.stitching.overlap module
  • OverlapStitchingStrategy
    • OverlapStitchingStrategy.MEAN
    • OverlapStitchingStrategy.COSINUS_WEIGHTS
    • OverlapStitchingStrategy.LINEAR_WEIGHTS
    • OverlapStitchingStrategy.CLOSEST
    • OverlapStitchingStrategy.IMAGE_MINIMUM_DIVERGENCE
    • OverlapStitchingStrategy.HIGHER_SIGNAL
  • OverlapKernelBase
  • ZStichOverlapKernel
    • ZStichOverlapKernel.DEFAULT_HIGH_FREQUENCY_THRESHOLD
    • ZStichOverlapKernel.overlap_size
    • ZStichOverlapKernel.img_2
    • ZStichOverlapKernel.weights_img_1
    • ZStichOverlapKernel.weights_img_2
    • ZStichOverlapKernel.stitching_strategy
    • ZStichOverlapKernel.compute_weights()
    • ZStichOverlapKernel.stitch()
  • compute_image_minimum_divergence()
  • compute_image_higher_signal()
  • check_overlaps()
• nabu.stitching.sample_normalization module
  • SampleSide
    • SampleSide.LEFT
    • SampleSide.RIGHT
  • Method
    • Method.MEAN
    • Method.MEDIAN
  • normalize_frame()
• nabu.stitching.slurm_utils module
  • split_stitching_configuration_to_slurm_job()
  • split_slices()
  • get_working_directory()
• nabu.stitching.utils module
  • ShiftAlgorithm
    • ShiftAlgorithm.NABU_FFT
    • ShiftAlgorithm.SKIMAGE
    • ShiftAlgorithm.ITK_IMG_REG_V4
    • ShiftAlgorithm.NONE
    • ShiftAlgorithm.CENTERED
    • ShiftAlgorithm.GLOBAL
    • ShiftAlgorithm.SLIDING_WINDOW
    • ShiftAlgorithm.GROWING_WINDOW
    • ShiftAlgorithm.SINO_COARSE_TO_FINE
    • ShiftAlgorithm.COMPOSITE_COARSE_TO_FINE
  • test_overlap_stitching_strategy()
  • find_frame_relative_shifts()
  • find_volumes_relative_shifts()
  • find_projections_relative_shifts()
  • find_shift_correlate()
  • find_shift_with_itk()
• nabu.stitching.z_stitching module
  • z_stitching()
  • ZStitcher
    • ZStitcher.param_is_auto()
    • ZStitcher.frame_composition
    • ZStitcher.get_final_axis_positions_in_px()
    • ZStitcher.from_abs_pos_to_rel_pos()
    • ZStitcher.from_rel_pos_to_abs_pos()
    • ZStitcher.stitch()
    • ZStitcher.settle_flips()
    • ZStitcher.z_serie
    • ZStitcher.configuration
    • ZStitcher.progress
    • ZStitcher.get_overlap_areas()
    • ZStitcher.rescale_frames()
    • ZStitcher.normalize_frame_by_sample()
    • ZStitcher.stitch_frames()
  • PreProcessZStitcher
    • PreProcessZStitcher.reading_orders
    • PreProcessZStitcher.x_flips
    • PreProcessZStitcher.y_flips
    • PreProcessZStitcher.stitch()
  • PostProcessZStitcher
    • PostProcessZStitcher.stitch()
    • PostProcessZStitcher.get_output_data_type()
  • stitch_vertically_raw_frames()
  • StitchingPostProcAggregation
    • StitchingPostProcAggregation.futures
    • StitchingPostProcAggregation.retrieve_tomo_objects()
    • StitchingPostProcAggregation.dump_stiching_config_as_nx_process()
    • StitchingPostProcAggregation.stitching_config
    • StitchingPostProcAggregation.process()
  • get_obj_width()

Module contents