API

Data Structures

• Density
  • Constructor
    • Density
      • Density
      • Density.data
        • Density.data
      • Density.empty
        • Density.empty
      • Density.metadata
        • Density.metadata
      • Density.origin
        • Density.origin
      • Density.sampling_rate
        • Density.sampling_rate
      • Density.shape
        • Density.shape
      • Density.adjust_box
        • Density.adjust_box()
      • Density.align_to_axis
        • Density.align_to_axis()
      • Density.center_of_mass
        • Density.center_of_mass()
      • Density.centered
        • Density.centered()
      • Density.copy
        • Density.copy()
      • Density.core_mask
        • Density.core_mask()
      • Density.density_boundary
        • Density.density_boundary()
      • Density.from_file
        • Density.from_file()
      • Density.from_structure
        • Density.from_structure()
      • Density.match_densities
        • Density.match_densities()
      • Density.match_structure_to_density
        • Density.match_structure_to_density()
      • Density.minimum_enclosing_box
        • Density.minimum_enclosing_box()
      • Density.normal_vectors
        • Density.normal_vectors()
      • Density.pad
        • Density.pad()
      • Density.resample
        • Density.resample()
      • Density.rigid_transform
        • Density.rigid_transform()
      • Density.surface_coordinates
        • Density.surface_coordinates()
      • Density.to_file
        • Density.to_file()
      • Density.to_memmap
        • Density.to_memmap()
      • Density.to_numpy
        • Density.to_numpy()
      • Density.to_pointcloud
        • Density.to_pointcloud()
      • Density.trim_box
        • Density.trim_box()
  • Attributes and underlying data
    • Density.data
      • Density.data
    • Density.origin
      • Density.origin
    • Density.sampling_rate
      • Density.sampling_rate
    • Density.metadata
      • Density.metadata
    • Density.shape
      • Density.shape
    • Density.empty
      • Density.empty
  • Serialization
    • Density.to_file
      • Density.to_file()
    • Density.from_file
      • Density.from_file()
    • Density.from_structure
      • Density.from_structure()
  • Conversion
    • Density.copy
      • Density.copy()
    • Density.to_numpy
      • Density.to_numpy()
    • Density.to_memmap
      • Density.to_memmap()
  • Subsetting
    • Density.pad
      • Density.pad()
    • Density.trim_box
      • Density.trim_box()
    • Density.centered
      • Density.centered()
    • Density.adjust_box
      • Density.adjust_box()
    • Density.minimum_enclosing_box
      • Density.minimum_enclosing_box()
  • Computations
    • Density.rigid_transform
      • Density.rigid_transform()
    • Density.to_pointcloud
      • Density.to_pointcloud()
    • Density.resample
      • Density.resample()
    • Density.density_boundary
      • Density.density_boundary()
    • Density.surface_coordinates
      • Density.surface_coordinates()
    • Density.normal_vectors
      • Density.normal_vectors()
    • Density.core_mask
      • Density.core_mask()
    • Density.center_of_mass
      • Density.center_of_mass()
    • Density.match_densities
      • Density.match_densities()
    • Density.match_structure_to_density
      • Density.match_structure_to_density()
• Structure
  • Constructor
    • Structure
      • Structure
      • Structure.record_type
        • Structure.record_type
      • Structure.atom_serial_number
        • Structure.atom_serial_number
      • Structure.atom_name
        • Structure.atom_name
      • Structure.atom_coordinate
        • Structure.atom_coordinate
      • Structure.alternate_location_indicator
        • Structure.alternate_location_indicator
      • Structure.residue_name
        • Structure.residue_name
      • Structure.chain_identifier
        • Structure.chain_identifier
      • Structure.residue_sequence_number
        • Structure.residue_sequence_number
      • Structure.code_for_residue_insertion
        • Structure.code_for_residue_insertion
      • Structure.occupancy
        • Structure.occupancy
      • Structure.temperature_factor
        • Structure.temperature_factor
      • Structure.segment_identifier
        • Structure.segment_identifier
      • Structure.element_symbol
        • Structure.element_symbol
      • Structure.charge
        • Structure.charge
      • Structure.metadata
        • Structure.metadata
      • Structure.align_structures
        • Structure.align_structures()
      • Structure.align_to_axis
        • Structure.align_to_axis()
      • Structure.center_of_mass
        • Structure.center_of_mass()
      • Structure.centered
        • Structure.centered()
      • Structure.compare_structures
        • Structure.compare_structures()
      • Structure.copy
        • Structure.copy()
      • Structure.from_file
        • Structure.from_file()
      • Structure.rigid_transform
        • Structure.rigid_transform()
      • Structure.subset_by_chain
        • Structure.subset_by_chain()
      • Structure.subset_by_range
        • Structure.subset_by_range()
      • Structure.to_file
        • Structure.to_file()
      • Structure.to_volume
        • Structure.to_volume()
  • Attributes and underlying data
    • Structure.record_type
      • Structure.record_type
    • Structure.atom_serial_number
      • Structure.atom_serial_number
    • Structure.atom_name
      • Structure.atom_name
    • Structure.atom_coordinate
      • Structure.atom_coordinate
    • Structure.alternate_location_indicator
      • Structure.alternate_location_indicator
    • Structure.residue_name
      • Structure.residue_name
    • Structure.chain_identifier
      • Structure.chain_identifier
    • Structure.residue_sequence_number
      • Structure.residue_sequence_number
    • Structure.code_for_residue_insertion
      • Structure.code_for_residue_insertion
    • Structure.occupancy
      • Structure.occupancy
    • Structure.temperature_factor
      • Structure.temperature_factor
    • Structure.segment_identifier
      • Structure.segment_identifier
    • Structure.element_symbol
      • Structure.element_symbol
    • Structure.charge
      • Structure.charge
    • Structure.metadata
      • Structure.metadata
  • Serialization
    • Structure.to_file
      • Structure.to_file()
    • Structure.from_file
      • Structure.from_file()
  • Conversion
    • Structure.to_volume
      • Structure.to_volume()
  • Subsetting
    • Structure.copy
      • Structure.copy()
    • Structure.subset_by_chain
      • Structure.subset_by_chain()
    • Structure.subset_by_range
      • Structure.subset_by_range()
  • Computations
    • Structure.rigid_transform
      • Structure.rigid_transform()
    • Structure.align_structures
      • Structure.align_structures()
    • Structure.compare_structures
      • Structure.compare_structures()
    • Structure.center_of_mass
      • Structure.center_of_mass()
    • Structure.centered
      • Structure.centered()
• MatchingData
  • Constructor
    • MatchingData
      • MatchingData
      • MatchingData.rotations
        • MatchingData.rotations
      • MatchingData.target
        • MatchingData.target
      • MatchingData.target_filter
        • MatchingData.target_filter
      • MatchingData.target_mask
        • MatchingData.target_mask
      • MatchingData.template
        • MatchingData.template
      • MatchingData.template_filter
        • MatchingData.template_filter
      • MatchingData.template_mask
        • MatchingData.template_mask
      • MatchingData.computation_schedule
        • MatchingData.computation_schedule()
      • MatchingData.fourier_padding
        • MatchingData.fourier_padding()
      • MatchingData.set_matching_dimension
        • MatchingData.set_matching_dimension()
      • MatchingData.subset_array
        • MatchingData.subset_array()
      • MatchingData.subset_by_slice
        • MatchingData.subset_by_slice()
      • MatchingData.target_padding
        • MatchingData.target_padding()
      • MatchingData.to_backend
        • MatchingData.to_backend()
  • Conversion
    • MatchingData.to_backend
      • MatchingData.to_backend()
  • Attributes and underlying data
    • MatchingData.target
      • MatchingData.target
    • MatchingData.template
      • MatchingData.template
    • MatchingData.target_mask
      • MatchingData.target_mask
    • MatchingData.template_mask
      • MatchingData.template_mask
    • MatchingData.rotations
      • MatchingData.rotations
  • Utilities
    • MatchingData.subset_array
      • MatchingData.subset_array()
    • MatchingData.subset_by_slice
      • MatchingData.subset_by_slice()
    • MatchingData.set_matching_dimension
      • MatchingData.set_matching_dimension()

Preprocessing

• Preprocessor
  • Constructor
    • Preprocessor
      • Preprocessor
      • Preprocessor.apply_method
        • Preprocessor.apply_method()
      • Preprocessor.bandpass_filter
        • Preprocessor.bandpass_filter()
      • Preprocessor.bandpass_mask
        • Preprocessor.bandpass_mask()
      • Preprocessor.blob_filter
        • Preprocessor.blob_filter()
      • Preprocessor.continuous_wedge_mask
        • Preprocessor.continuous_wedge_mask()
      • Preprocessor.difference_of_gaussian_filter
        • Preprocessor.difference_of_gaussian_filter()
      • Preprocessor.edge_gaussian_filter
        • Preprocessor.edge_gaussian_filter()
      • Preprocessor.gaussian_filter
        • Preprocessor.gaussian_filter()
      • Preprocessor.hamming_filter
        • Preprocessor.hamming_filter()
      • Preprocessor.interpolate_box
        • Preprocessor.interpolate_box()
      • Preprocessor.kaiserb_filter
        • Preprocessor.kaiserb_filter()
      • Preprocessor.local_gaussian_alignment_filter
        • Preprocessor.local_gaussian_alignment_filter()
      • Preprocessor.local_gaussian_filter
        • Preprocessor.local_gaussian_filter()
      • Preprocessor.mean_filter
        • Preprocessor.mean_filter()
      • Preprocessor.median_filter
        • Preprocessor.median_filter()
      • Preprocessor.method_to_id
        • Preprocessor.method_to_id()
      • Preprocessor.mipmap_filter
        • Preprocessor.mipmap_filter()
      • Preprocessor.rank_filter
        • Preprocessor.rank_filter()
      • Preprocessor.step_wedge_mask
        • Preprocessor.step_wedge_mask()
  • Filters
    • Preprocessor.continuous_wedge_mask
      • Preprocessor.continuous_wedge_mask()
    • Preprocessor.step_wedge_mask
      • Preprocessor.step_wedge_mask()
    • Preprocessor.gaussian_filter
      • Preprocessor.gaussian_filter()
    • Preprocessor.difference_of_gaussian_filter
      • Preprocessor.difference_of_gaussian_filter()
    • Preprocessor.bandpass_filter
      • Preprocessor.bandpass_filter()
    • Preprocessor.local_gaussian_alignment_filter
      • Preprocessor.local_gaussian_alignment_filter()
    • Preprocessor.local_gaussian_filter
      • Preprocessor.local_gaussian_filter()
    • Preprocessor.edge_gaussian_filter
      • Preprocessor.edge_gaussian_filter()
    • Preprocessor.mean_filter
      • Preprocessor.mean_filter()
    • Preprocessor.rank_filter
      • Preprocessor.rank_filter()
    • Preprocessor.mipmap_filter
      • Preprocessor.mipmap_filter()
    • Preprocessor.kaiserb_filter
      • Preprocessor.kaiserb_filter()
    • Preprocessor.blob_filter
      • Preprocessor.blob_filter()
    • Preprocessor.hamming_filter
      • Preprocessor.hamming_filter()
  • Utilities
    • Preprocessor.interpolate_box
      • Preprocessor.interpolate_box()
• Composable Filters
  • Specification
    • ComposableFilter
      • ComposableFilter
      • ComposableFilter.__call__
        • ComposableFilter.__call__()
  • Aggregator
    • Compose
      • Compose
      • Compose.__call__
        • Compose.__call__()
  • Frequency Filters
    • BandPass
      • BandPass
      • BandPass.highpass
        • BandPass.highpass
      • BandPass.lowpass
        • BandPass.lowpass
      • BandPass.opening_axis
        • BandPass.opening_axis
      • BandPass.return_real_fourier
        • BandPass.return_real_fourier
      • BandPass.sampling_rate
        • BandPass.sampling_rate
      • BandPass.shape
        • BandPass.shape
      • BandPass.tilt_axis
        • BandPass.tilt_axis
      • BandPass.use_gaussian
        • BandPass.use_gaussian
      • BandPass.angles
        • BandPass.angles
      • BandPass.__call__
        • BandPass.__call__()
    • BandPassReconstructed
      • BandPassReconstructed
      • BandPassReconstructed.highpass
        • BandPassReconstructed.highpass
      • BandPassReconstructed.lowpass
        • BandPassReconstructed.lowpass
      • BandPassReconstructed.opening_axis
        • BandPassReconstructed.opening_axis
      • BandPassReconstructed.return_real_fourier
        • BandPassReconstructed.return_real_fourier
      • BandPassReconstructed.sampling_rate
        • BandPassReconstructed.sampling_rate
      • BandPassReconstructed.shape
        • BandPassReconstructed.shape
      • BandPassReconstructed.tilt_axis
        • BandPassReconstructed.tilt_axis
      • BandPassReconstructed.use_gaussian
        • BandPassReconstructed.use_gaussian
      • BandPassReconstructed.__call__
        • BandPassReconstructed.__call__()
    • LinearWhiteningFilter
      • LinearWhiteningFilter
      • LinearWhiteningFilter.__call__
        • LinearWhiteningFilter.__call__()
  • Cryo-EM Filters
    • CTF
      • CTF
      • CTF.acceleration_voltage
        • CTF.acceleration_voltage
      • CTF.amplitude_contrast
        • CTF.amplitude_contrast
      • CTF.angles
        • CTF.angles
      • CTF.correct_defocus_gradient
        • CTF.correct_defocus_gradient
      • CTF.defocus_angle
        • CTF.defocus_angle
      • CTF.defocus_x
        • CTF.defocus_x
      • CTF.defocus_y
        • CTF.defocus_y
      • CTF.flip_phase
        • CTF.flip_phase
      • CTF.opening_axis
        • CTF.opening_axis
      • CTF.phase_shift
        • CTF.phase_shift
      • CTF.return_real_fourier
        • CTF.return_real_fourier
      • CTF.sampling_rate
        • CTF.sampling_rate
      • CTF.shape
        • CTF.shape
      • CTF.spherical_aberration
        • CTF.spherical_aberration
      • CTF.tilt_axis
        • CTF.tilt_axis
      • CTF.__call__
        • CTF.__call__()
      • CTF.from_file
        • CTF.from_file()
      • CTF.weight
        • CTF.weight()
    • CTFReconstructed
      • CTFReconstructed
      • CTFReconstructed.acceleration_voltage
        • CTFReconstructed.acceleration_voltage
      • CTFReconstructed.amplitude_contrast
        • CTFReconstructed.amplitude_contrast
      • CTFReconstructed.angles
        • CTFReconstructed.angles
      • CTFReconstructed.correct_defocus_gradient
        • CTFReconstructed.correct_defocus_gradient
      • CTFReconstructed.defocus_angle
        • CTFReconstructed.defocus_angle
      • CTFReconstructed.defocus_x
        • CTFReconstructed.defocus_x
      • CTFReconstructed.defocus_y
        • CTFReconstructed.defocus_y
      • CTFReconstructed.flip_phase
        • CTFReconstructed.flip_phase
      • CTFReconstructed.opening_axis
        • CTFReconstructed.opening_axis
      • CTFReconstructed.phase_shift
        • CTFReconstructed.phase_shift
      • CTFReconstructed.return_real_fourier
        • CTFReconstructed.return_real_fourier
      • CTFReconstructed.sampling_rate
        • CTFReconstructed.sampling_rate
      • CTFReconstructed.shape
        • CTFReconstructed.shape
      • CTFReconstructed.spherical_aberration
        • CTFReconstructed.spherical_aberration
      • CTFReconstructed.tilt_axis
        • CTFReconstructed.tilt_axis
      • CTFReconstructed.__call__
        • CTFReconstructed.__call__()
      • CTFReconstructed.from_file
        • CTFReconstructed.from_file()
      • CTFReconstructed.weight
        • CTFReconstructed.weight()
    • Wedge
      • Wedge
      • Wedge.angles
        • Wedge.angles
      • Wedge.frequency_cutoff
        • Wedge.frequency_cutoff
      • Wedge.opening_axis
        • Wedge.opening_axis
      • Wedge.sampling_rate
        • Wedge.sampling_rate
      • Wedge.shape
        • Wedge.shape
      • Wedge.tilt_axis
        • Wedge.tilt_axis
      • Wedge.weight_type
        • Wedge.weight_type
      • Wedge.weights
        • Wedge.weights
      • Wedge.__call__
        • Wedge.__call__()
      • Wedge.from_file
        • Wedge.from_file()
      • Wedge.weight_angle
        • Wedge.weight_angle()
      • Wedge.weight_grigorieff
        • Wedge.weight_grigorieff()
      • Wedge.weight_relion
        • Wedge.weight_relion()
    • WedgeReconstructed
      • WedgeReconstructed
      • WedgeReconstructed.angles
        • WedgeReconstructed.angles
      • WedgeReconstructed.create_continuous_wedge
        • WedgeReconstructed.create_continuous_wedge
      • WedgeReconstructed.frequency_cutoff
        • WedgeReconstructed.frequency_cutoff
      • WedgeReconstructed.opening_axis
        • WedgeReconstructed.opening_axis
      • WedgeReconstructed.reconstruction_filter
        • WedgeReconstructed.reconstruction_filter
      • WedgeReconstructed.tilt_axis
        • WedgeReconstructed.tilt_axis
      • WedgeReconstructed.weight_wedge
        • WedgeReconstructed.weight_wedge
      • WedgeReconstructed.weights
        • WedgeReconstructed.weights
      • WedgeReconstructed.__call__
        • WedgeReconstructed.__call__()
      • WedgeReconstructed.continuous_wedge
        • WedgeReconstructed.continuous_wedge()
      • WedgeReconstructed.step_wedge
        • WedgeReconstructed.step_wedge()
  • Reconstruction
    • ReconstructFromTilt
      • ReconstructFromTilt
      • ReconstructFromTilt.angles
        • ReconstructFromTilt.angles
      • ReconstructFromTilt.interpolation_order
        • ReconstructFromTilt.interpolation_order
      • ReconstructFromTilt.opening_axis
        • ReconstructFromTilt.opening_axis
      • ReconstructFromTilt.reconstruction_filter
        • ReconstructFromTilt.reconstruction_filter
      • ReconstructFromTilt.return_real_fourier
        • ReconstructFromTilt.return_real_fourier
      • ReconstructFromTilt.shape
        • ReconstructFromTilt.shape
      • ReconstructFromTilt.tilt_axis
        • ReconstructFromTilt.tilt_axis
      • ReconstructFromTilt.__call__
        • ReconstructFromTilt.__call__()
      • ReconstructFromTilt.reconstruct
        • ReconstructFromTilt.reconstruct()

Template Matching

• Exhaustive
  • Methods
    • scan
      • scan()
    • scan_subsets
      • scan_subsets()
  • Setup functions
    • cc_setup
      • cc_setup()
    • lcc_setup
      • lcc_setup()
    • corr_setup
      • corr_setup()
    • cam_setup
      • cam_setup()
    • flc_setup
      • flc_setup()
    • flcSphericalMask_setup
      • flcSphericalMask_setup()
    • mcc_setup
      • mcc_setup()
  • Scoring functions
    • corr_scoring
      • corr_scoring()
    • flc_scoring
      • flc_scoring()
    • mcc_scoring
      • mcc_scoring()
  • Adding Custom Methods
    • register_matching_exhaustive
      • register_matching_exhaustive()
• Non-exhaustive
  • FLC
    • FLC
    • FLC.__call__
      • FLC.__call__()
    • FLC.rotate_array
      • FLC.rotate_array()
    • FLC.score
      • FLC.score()
    • FLC.score_angles
      • FLC.score_angles()
    • FLC.score_translation
      • FLC.score_translation()
  • CrossCorrelation
    • CrossCorrelation
    • CrossCorrelation.__call__
      • CrossCorrelation.__call__()
    • CrossCorrelation.grad
      • CrossCorrelation.grad()
    • CrossCorrelation.rotate_array
      • CrossCorrelation.rotate_array()
    • CrossCorrelation.score
      • CrossCorrelation.score()
    • CrossCorrelation.score_angles
      • CrossCorrelation.score_angles()
    • CrossCorrelation.score_translation
      • CrossCorrelation.score_translation()
  • LaplaceCrossCorrelation
    • LaplaceCrossCorrelation
    • LaplaceCrossCorrelation.__call__
      • LaplaceCrossCorrelation.__call__()
    • LaplaceCrossCorrelation.grad
      • LaplaceCrossCorrelation.grad()
    • LaplaceCrossCorrelation.rotate_array
      • LaplaceCrossCorrelation.rotate_array()
    • LaplaceCrossCorrelation.score
      • LaplaceCrossCorrelation.score()
    • LaplaceCrossCorrelation.score_angles
      • LaplaceCrossCorrelation.score_angles()
    • LaplaceCrossCorrelation.score_translation
      • LaplaceCrossCorrelation.score_translation()
  • NormalizedCrossCorrelation
    • NormalizedCrossCorrelation
    • NormalizedCrossCorrelation.__call__
      • NormalizedCrossCorrelation.__call__()
    • NormalizedCrossCorrelation.grad
      • NormalizedCrossCorrelation.grad()
    • NormalizedCrossCorrelation.rotate_array
      • NormalizedCrossCorrelation.rotate_array()
    • NormalizedCrossCorrelation.score
      • NormalizedCrossCorrelation.score()
    • NormalizedCrossCorrelation.score_angles
      • NormalizedCrossCorrelation.score_angles()
    • NormalizedCrossCorrelation.score_translation
      • NormalizedCrossCorrelation.score_translation()
  • NormalizedCrossCorrelationMean
    • NormalizedCrossCorrelationMean
    • NormalizedCrossCorrelationMean.__call__
      • NormalizedCrossCorrelationMean.__call__()
    • NormalizedCrossCorrelationMean.grad
      • NormalizedCrossCorrelationMean.grad()
    • NormalizedCrossCorrelationMean.rotate_array
      • NormalizedCrossCorrelationMean.rotate_array()
    • NormalizedCrossCorrelationMean.score
      • NormalizedCrossCorrelationMean.score()
    • NormalizedCrossCorrelationMean.score_angles
      • NormalizedCrossCorrelationMean.score_angles()
    • NormalizedCrossCorrelationMean.score_translation
      • NormalizedCrossCorrelationMean.score_translation()
  • MaskedCrossCorrelation
    • MaskedCrossCorrelation
    • MaskedCrossCorrelation.__call__
      • MaskedCrossCorrelation.__call__()
    • MaskedCrossCorrelation.rotate_array
      • MaskedCrossCorrelation.rotate_array()
    • MaskedCrossCorrelation.score
      • MaskedCrossCorrelation.score()
    • MaskedCrossCorrelation.score_angles
      • MaskedCrossCorrelation.score_angles()
    • MaskedCrossCorrelation.score_translation
      • MaskedCrossCorrelation.score_translation()
  • PartialLeastSquareDifference
    • PartialLeastSquareDifference
    • PartialLeastSquareDifference.__call__
      • PartialLeastSquareDifference.__call__()
    • PartialLeastSquareDifference.rotate_array
      • PartialLeastSquareDifference.rotate_array()
    • PartialLeastSquareDifference.score
      • PartialLeastSquareDifference.score()
    • PartialLeastSquareDifference.score_angles
      • PartialLeastSquareDifference.score_angles()
    • PartialLeastSquareDifference.score_translation
      • PartialLeastSquareDifference.score_translation()
  • Chamfer
    • Chamfer
    • Chamfer.__call__
      • Chamfer.__call__()
    • Chamfer.rotate_array
      • Chamfer.rotate_array()
    • Chamfer.score
      • Chamfer.score()
    • Chamfer.score_angles
      • Chamfer.score_angles()
    • Chamfer.score_translation
      • Chamfer.score_translation()
  • MutualInformation
    • MutualInformation
    • MutualInformation.__call__
      • MutualInformation.__call__()
    • MutualInformation.rotate_array
      • MutualInformation.rotate_array()
    • MutualInformation.score
      • MutualInformation.score()
    • MutualInformation.score_angles
      • MutualInformation.score_angles()
    • MutualInformation.score_translation
      • MutualInformation.score_translation()
  • Envelope
    • Envelope
    • Envelope.__call__
      • Envelope.__call__()
    • Envelope.rotate_array
      • Envelope.rotate_array()
    • Envelope.score
      • Envelope.score()
    • Envelope.score_angles
      • Envelope.score_angles()
    • Envelope.score_translation
      • Envelope.score_translation()
  • NormalVectorScore
    • NormalVectorScore
    • NormalVectorScore.__call__
      • NormalVectorScore.__call__()
    • NormalVectorScore.rotate_array
      • NormalVectorScore.rotate_array()
    • NormalVectorScore.score
      • NormalVectorScore.score()
    • NormalVectorScore.score_angles
      • NormalVectorScore.score_angles()
    • NormalVectorScore.score_translation
      • NormalVectorScore.score_translation()
  • Chamfer
    • Chamfer
    • Chamfer.__call__
      • Chamfer.__call__()
    • Chamfer.rotate_array
      • Chamfer.rotate_array()
    • Chamfer.score
      • Chamfer.score()
    • Chamfer.score_angles
      • Chamfer.score_angles()
    • Chamfer.score_translation
      • Chamfer.score_translation()
  • NormalVectorScore
    • NormalVectorScore
    • NormalVectorScore.__call__
      • NormalVectorScore.__call__()
    • NormalVectorScore.rotate_array
      • NormalVectorScore.rotate_array()
    • NormalVectorScore.score
      • NormalVectorScore.score()
    • NormalVectorScore.score_angles
      • NormalVectorScore.score_angles()
    • NormalVectorScore.score_translation
      • NormalVectorScore.score_translation()
  • create_score_object
    • create_score_object()
  • optimize_match
    • optimize_match()
• Memory
  • Memory usage helpers
    • estimate_memory_usage
      • estimate_memory_usage()
  • Abstract Base
    • MatchingMemoryUsage
      • MatchingMemoryUsage
      • MatchingMemoryUsage.base_usage
        • MatchingMemoryUsage.base_usage()
      • MatchingMemoryUsage.per_fork
        • MatchingMemoryUsage.per_fork()
  • Memory usage classes
    • CCMemoryUsage
      • CCMemoryUsage
      • CCMemoryUsage.base_usage
        • CCMemoryUsage.base_usage()
      • CCMemoryUsage.per_fork
        • CCMemoryUsage.per_fork()
    • LCCMemoryUsage
      • LCCMemoryUsage
      • LCCMemoryUsage.base_usage
        • LCCMemoryUsage.base_usage()
      • LCCMemoryUsage.per_fork
        • LCCMemoryUsage.per_fork()
    • CORRMemoryUsage
      • CORRMemoryUsage
      • CORRMemoryUsage.base_usage
        • CORRMemoryUsage.base_usage()
      • CORRMemoryUsage.per_fork
        • CORRMemoryUsage.per_fork()
    • CAMMemoryUsage
      • CAMMemoryUsage
      • CAMMemoryUsage.base_usage
        • CAMMemoryUsage.base_usage()
      • CAMMemoryUsage.per_fork
        • CAMMemoryUsage.per_fork()
    • FLCSphericalMaskMemoryUsage
      • FLCSphericalMaskMemoryUsage
      • FLCSphericalMaskMemoryUsage.base_usage
        • FLCSphericalMaskMemoryUsage.base_usage()
      • FLCSphericalMaskMemoryUsage.per_fork
        • FLCSphericalMaskMemoryUsage.per_fork()
    • FLCMemoryUsage
      • FLCMemoryUsage
      • FLCMemoryUsage.base_usage
        • FLCMemoryUsage.base_usage()
      • FLCMemoryUsage.per_fork
        • FLCMemoryUsage.per_fork()
    • MCCMemoryUsage
      • MCCMemoryUsage
      • MCCMemoryUsage.base_usage
        • MCCMemoryUsage.base_usage()
      • MCCMemoryUsage.per_fork
        • MCCMemoryUsage.per_fork()
    • MaxScoreOverRotationsMemoryUsage
      • MaxScoreOverRotationsMemoryUsage
      • MaxScoreOverRotationsMemoryUsage.base_usage
        • MaxScoreOverRotationsMemoryUsage.base_usage()
      • MaxScoreOverRotationsMemoryUsage.per_fork
        • MaxScoreOverRotationsMemoryUsage.per_fork()
    • PeakCallerMaximumFilterMemoryUsage
      • PeakCallerMaximumFilterMemoryUsage
      • PeakCallerMaximumFilterMemoryUsage.base_usage
        • PeakCallerMaximumFilterMemoryUsage.base_usage()
      • PeakCallerMaximumFilterMemoryUsage.per_fork
        • PeakCallerMaximumFilterMemoryUsage.per_fork()
    • CupyBackendMemoryUsage
      • CupyBackendMemoryUsage
      • CupyBackendMemoryUsage.base_usage
        • CupyBackendMemoryUsage.base_usage()
      • CupyBackendMemoryUsage.per_fork
        • CupyBackendMemoryUsage.per_fork()
• Utilities
  • Masks
    • box_mask
      • box_mask()
    • create_mask
      • create_mask()
    • tube_mask
      • tube_mask()
    • elliptical_mask
      • elliptical_mask()
  • Subsetting
    • centered
      • centered()
    • split_shape
      • split_shape()
    • centered_mask
      • centered_mask()
    • apply_convolution_mode
      • apply_convolution_mode()
    • compute_full_convolution_index
      • compute_full_convolution_index()
    • compute_parallelization_schedule
      • compute_parallelization_schedule()
  • Serialization
    • load_pickle
      • load_pickle()
    • write_pickle
      • write_pickle()
  • Utilities
    • scramble_phases
      • scramble_phases()
    • rigid_transform
      • rigid_transform()
    • array_to_memmap
      • array_to_memmap()
    • memmap_to_array
      • memmap_to_array()
    • normalize_template
      • normalize_template()
    • conditional_execute
      • conditional_execute()
    • minimum_enclosing_box
      • minimum_enclosing_box()
    • generate_tempfile_name
      • generate_tempfile_name()
  • Rotations
    • align_to_axis
      • align_to_axis()
    • align_vectors
      • align_vectors()
    • euler_to_rotationmatrix
      • euler_to_rotationmatrix()
    • euler_from_rotationmatrix
      • euler_from_rotationmatrix()
    • get_cone_rotations
      • get_cone_rotations()
    • get_rotation_matrices
      • get_rotation_matrices()

Analyzer

• Specification
  • AbstractAnalyzer
    • AbstractAnalyzer
    • AbstractAnalyzer.shareable
      • AbstractAnalyzer.shareable
    • AbstractAnalyzer.__call__
      • AbstractAnalyzer.__call__()
    • AbstractAnalyzer.init_state
      • AbstractAnalyzer.init_state()
    • AbstractAnalyzer.merge
      • AbstractAnalyzer.merge()
    • AbstractAnalyzer.result
      • AbstractAnalyzer.result()
• How Analyzers Work
• Template Matching Integration
• State Management
• Parallel Processing
• Custom Analyzer Implementation
• Score Aggregation
  • MaxScoreOverRotations
    • MaxScoreOverRotations
    • MaxScoreOverRotations.shareable
      • MaxScoreOverRotations.shareable
    • MaxScoreOverRotations.__call__
      • MaxScoreOverRotations.__call__()
    • MaxScoreOverRotations.init_state
      • MaxScoreOverRotations.init_state()
    • MaxScoreOverRotations.merge
      • MaxScoreOverRotations.merge()
    • MaxScoreOverRotations.result
      • MaxScoreOverRotations.result()
  • MaxScoreOverTranslations
    • MaxScoreOverTranslations
    • MaxScoreOverTranslations.shareable
      • MaxScoreOverTranslations.shareable
    • MaxScoreOverTranslations.__call__
      • MaxScoreOverTranslations.__call__()
    • MaxScoreOverTranslations.init_state
      • MaxScoreOverTranslations.init_state()
    • MaxScoreOverTranslations.merge
      • MaxScoreOverTranslations.merge()
    • MaxScoreOverTranslations.result
      • MaxScoreOverTranslations.result()
  • MaxScoreOverRotationsConstrained
    • MaxScoreOverRotationsConstrained
    • MaxScoreOverRotationsConstrained.shareable
      • MaxScoreOverRotationsConstrained.shareable
    • MaxScoreOverRotationsConstrained.__call__
      • MaxScoreOverRotationsConstrained.__call__()
    • MaxScoreOverRotationsConstrained.init_state
      • MaxScoreOverRotationsConstrained.init_state()
    • MaxScoreOverRotationsConstrained.merge
      • MaxScoreOverRotationsConstrained.merge()
    • MaxScoreOverRotationsConstrained.result
      • MaxScoreOverRotationsConstrained.result()
• Peak Calling
  • PeakCaller
    • PeakCaller
    • PeakCaller.shareable
      • PeakCaller.shareable
    • PeakCaller.__call__
      • PeakCaller.__call__()
    • PeakCaller.call_peaks
      • PeakCaller.call_peaks()
    • PeakCaller.init_state
      • PeakCaller.init_state()
    • PeakCaller.merge
      • PeakCaller.merge()
    • PeakCaller.oversample_peaks
      • PeakCaller.oversample_peaks()
    • PeakCaller.result
      • PeakCaller.result()
  • PeakCallerSort
    • PeakCallerSort
    • PeakCallerSort.shareable
      • PeakCallerSort.shareable
    • PeakCallerSort.__call__
      • PeakCallerSort.__call__()
    • PeakCallerSort.call_peaks
      • PeakCallerSort.call_peaks()
    • PeakCallerSort.init_state
      • PeakCallerSort.init_state()
    • PeakCallerSort.merge
      • PeakCallerSort.merge()
    • PeakCallerSort.oversample_peaks
      • PeakCallerSort.oversample_peaks()
    • PeakCallerSort.result
      • PeakCallerSort.result()
  • PeakCallerMaximumFilter
    • PeakCallerMaximumFilter
    • PeakCallerMaximumFilter.shareable
      • PeakCallerMaximumFilter.shareable
    • PeakCallerMaximumFilter.__call__
      • PeakCallerMaximumFilter.__call__()
    • PeakCallerMaximumFilter.call_peaks
      • PeakCallerMaximumFilter.call_peaks()
    • PeakCallerMaximumFilter.init_state
      • PeakCallerMaximumFilter.init_state()
    • PeakCallerMaximumFilter.merge
      • PeakCallerMaximumFilter.merge()
    • PeakCallerMaximumFilter.oversample_peaks
      • PeakCallerMaximumFilter.oversample_peaks()
    • PeakCallerMaximumFilter.result
      • PeakCallerMaximumFilter.result()
  • PeakCallerFast
    • PeakCallerFast
    • PeakCallerFast.shareable
      • PeakCallerFast.shareable
    • PeakCallerFast.__call__
      • PeakCallerFast.__call__()
    • PeakCallerFast.call_peaks
      • PeakCallerFast.call_peaks()
    • PeakCallerFast.init_state
      • PeakCallerFast.init_state()
    • PeakCallerFast.merge
      • PeakCallerFast.merge()
    • PeakCallerFast.oversample_peaks
      • PeakCallerFast.oversample_peaks()
    • PeakCallerFast.result
      • PeakCallerFast.result()
  • PeakCallerRecursiveMasking
    • PeakCallerRecursiveMasking
    • PeakCallerRecursiveMasking.shareable
      • PeakCallerRecursiveMasking.shareable
    • PeakCallerRecursiveMasking.__call__
      • PeakCallerRecursiveMasking.__call__()
    • PeakCallerRecursiveMasking.call_peaks
      • PeakCallerRecursiveMasking.call_peaks()
    • PeakCallerRecursiveMasking.init_state
      • PeakCallerRecursiveMasking.init_state()
    • PeakCallerRecursiveMasking.merge
      • PeakCallerRecursiveMasking.merge()
    • PeakCallerRecursiveMasking.oversample_peaks
      • PeakCallerRecursiveMasking.oversample_peaks()
    • PeakCallerRecursiveMasking.result
      • PeakCallerRecursiveMasking.result()
  • PeakCallerScipy
    • PeakCallerScipy
    • PeakCallerScipy.shareable
      • PeakCallerScipy.shareable
    • PeakCallerScipy.__call__
      • PeakCallerScipy.__call__()
    • PeakCallerScipy.call_peaks
      • PeakCallerScipy.call_peaks()
    • PeakCallerScipy.init_state
      • PeakCallerScipy.init_state()
    • PeakCallerScipy.merge
      • PeakCallerScipy.merge()
    • PeakCallerScipy.oversample_peaks
      • PeakCallerScipy.oversample_peaks()
    • PeakCallerScipy.result
      • PeakCallerScipy.result()

Flexible Backends

• Backends
  • Backend Manager
    • BackendManager
      • BackendManager
      • BackendManager.add_backend
        • BackendManager.add_backend()
      • BackendManager.available_backends
        • BackendManager.available_backends()
      • BackendManager.change_backend
        • BackendManager.change_backend()
  • Supported Backends
    • NumpyFFTWBackend
      • NumpyFFTWBackend
      • NumpyFFTWBackend.abs
        • NumpyFFTWBackend.abs()
      • NumpyFFTWBackend.add
        • NumpyFFTWBackend.add()
      • NumpyFFTWBackend.addat
        • NumpyFFTWBackend.addat()
      • NumpyFFTWBackend.arange
        • NumpyFFTWBackend.arange()
      • NumpyFFTWBackend.argsort
        • NumpyFFTWBackend.argsort()
      • NumpyFFTWBackend.astype
        • NumpyFFTWBackend.astype()
      • NumpyFFTWBackend.at
        • NumpyFFTWBackend.at()
      • NumpyFFTWBackend.build_fft
        • NumpyFFTWBackend.build_fft()
      • NumpyFFTWBackend.center_of_mass
        • NumpyFFTWBackend.center_of_mass()
      • NumpyFFTWBackend.clip
        • NumpyFFTWBackend.clip()
      • NumpyFFTWBackend.compute_convolution_shapes
        • NumpyFFTWBackend.compute_convolution_shapes()
      • NumpyFFTWBackend.concatenate
        • NumpyFFTWBackend.concatenate()
      • NumpyFFTWBackend.copy
        • NumpyFFTWBackend.copy()
      • NumpyFFTWBackend.datatype_bytes
        • NumpyFFTWBackend.datatype_bytes()
      • NumpyFFTWBackend.device_count
        • NumpyFFTWBackend.device_count()
      • NumpyFFTWBackend.divide
        • NumpyFFTWBackend.divide()
      • NumpyFFTWBackend.dot
        • NumpyFFTWBackend.dot()
      • NumpyFFTWBackend.einsum
        • NumpyFFTWBackend.einsum()
      • NumpyFFTWBackend.eps
        • NumpyFFTWBackend.eps()
      • NumpyFFTWBackend.extract_center
        • NumpyFFTWBackend.extract_center()
      • NumpyFFTWBackend.fill
        • NumpyFFTWBackend.fill()
      • NumpyFFTWBackend.free_cache
        • NumpyFFTWBackend.free_cache()
      • NumpyFFTWBackend.from_sharedarr
        • NumpyFFTWBackend.from_sharedarr()
      • NumpyFFTWBackend.full
        • NumpyFFTWBackend.full()
      • NumpyFFTWBackend.get_available_memory
        • NumpyFFTWBackend.get_available_memory()
      • NumpyFFTWBackend.get_fundamental_dtype
        • NumpyFFTWBackend.get_fundamental_dtype()
      • NumpyFFTWBackend.identity
        • NumpyFFTWBackend.identity()
      • NumpyFFTWBackend.indices
        • NumpyFFTWBackend.indices()
      • NumpyFFTWBackend.irfftn
        • NumpyFFTWBackend.irfftn()
      • NumpyFFTWBackend.max
        • NumpyFFTWBackend.max()
      • NumpyFFTWBackend.max_filter_coordinates
        • NumpyFFTWBackend.max_filter_coordinates()
      • NumpyFFTWBackend.max_score_over_rotations
        • NumpyFFTWBackend.max_score_over_rotations()
      • NumpyFFTWBackend.maximum
        • NumpyFFTWBackend.maximum()
      • NumpyFFTWBackend.mean
        • NumpyFFTWBackend.mean()
      • NumpyFFTWBackend.min
        • NumpyFFTWBackend.min()
      • NumpyFFTWBackend.minimum
        • NumpyFFTWBackend.minimum()
      • NumpyFFTWBackend.mod
        • NumpyFFTWBackend.mod()
      • NumpyFFTWBackend.multiply
        • NumpyFFTWBackend.multiply()
      • NumpyFFTWBackend.norm_scores
        • NumpyFFTWBackend.norm_scores()
      • NumpyFFTWBackend.power
        • NumpyFFTWBackend.power()
      • NumpyFFTWBackend.repeat
        • NumpyFFTWBackend.repeat()
      • NumpyFFTWBackend.reshape
        • NumpyFFTWBackend.reshape()
      • NumpyFFTWBackend.reverse
        • NumpyFFTWBackend.reverse()
      • NumpyFFTWBackend.rfftn
        • NumpyFFTWBackend.rfftn()
      • NumpyFFTWBackend.rigid_transform
        • NumpyFFTWBackend.rigid_transform()
      • NumpyFFTWBackend.roll
        • NumpyFFTWBackend.roll()
      • NumpyFFTWBackend.set_device
        • NumpyFFTWBackend.set_device()
      • NumpyFFTWBackend.size
        • NumpyFFTWBackend.size()
      • NumpyFFTWBackend.sqrt
        • NumpyFFTWBackend.sqrt()
      • NumpyFFTWBackend.square
        • NumpyFFTWBackend.square()
      • NumpyFFTWBackend.stack
        • NumpyFFTWBackend.stack()
      • NumpyFFTWBackend.std
        • NumpyFFTWBackend.std()
      • NumpyFFTWBackend.subtract
        • NumpyFFTWBackend.subtract()
      • NumpyFFTWBackend.sum
        • NumpyFFTWBackend.sum()
      • NumpyFFTWBackend.to_backend_array
        • NumpyFFTWBackend.to_backend_array()
      • NumpyFFTWBackend.to_cpu_array
        • NumpyFFTWBackend.to_cpu_array()
      • NumpyFFTWBackend.to_numpy_array
        • NumpyFFTWBackend.to_numpy_array()
      • NumpyFFTWBackend.to_sharedarr
        • NumpyFFTWBackend.to_sharedarr()
      • NumpyFFTWBackend.tobytes
        • NumpyFFTWBackend.tobytes()
      • NumpyFFTWBackend.topk_indices
        • NumpyFFTWBackend.topk_indices()
      • NumpyFFTWBackend.topleft_pad
        • NumpyFFTWBackend.topleft_pad()
      • NumpyFFTWBackend.transpose
        • NumpyFFTWBackend.transpose()
      • NumpyFFTWBackend.tril_indices
        • NumpyFFTWBackend.tril_indices()
      • NumpyFFTWBackend.unique
        • NumpyFFTWBackend.unique()
      • NumpyFFTWBackend.unravel_index
        • NumpyFFTWBackend.unravel_index()
      • NumpyFFTWBackend.where
        • NumpyFFTWBackend.where()
      • NumpyFFTWBackend.zeros
        • NumpyFFTWBackend.zeros()
    • PytorchBackend
      • PytorchBackend
      • PytorchBackend.abs
        • PytorchBackend.abs()
      • PytorchBackend.add
        • PytorchBackend.add()
      • PytorchBackend.addat
        • PytorchBackend.addat()
      • PytorchBackend.arange
        • PytorchBackend.arange()
      • PytorchBackend.argsort
        • PytorchBackend.argsort()
      • PytorchBackend.astype
        • PytorchBackend.astype()
      • PytorchBackend.at
        • PytorchBackend.at()
      • PytorchBackend.build_fft
        • PytorchBackend.build_fft()
      • PytorchBackend.center_of_mass
        • PytorchBackend.center_of_mass()
      • PytorchBackend.clip
        • PytorchBackend.clip()
      • PytorchBackend.compute_convolution_shapes
        • PytorchBackend.compute_convolution_shapes()
      • PytorchBackend.concatenate
        • PytorchBackend.concatenate()
      • PytorchBackend.copy
        • PytorchBackend.copy()
      • PytorchBackend.datatype_bytes
        • PytorchBackend.datatype_bytes()
      • PytorchBackend.device_count
        • PytorchBackend.device_count()
      • PytorchBackend.divide
        • PytorchBackend.divide()
      • PytorchBackend.dot
        • PytorchBackend.dot()
      • PytorchBackend.einsum
        • PytorchBackend.einsum()
      • PytorchBackend.eps
        • PytorchBackend.eps()
      • PytorchBackend.extract_center
        • PytorchBackend.extract_center()
      • PytorchBackend.eye
        • PytorchBackend.eye()
      • PytorchBackend.fill
        • PytorchBackend.fill()
      • PytorchBackend.flip
        • PytorchBackend.flip()
      • PytorchBackend.free_cache
        • PytorchBackend.free_cache()
      • PytorchBackend.from_sharedarr
        • PytorchBackend.from_sharedarr()
      • PytorchBackend.full
        • PytorchBackend.full()
      • PytorchBackend.get_available_memory
        • PytorchBackend.get_available_memory()
      • PytorchBackend.get_fundamental_dtype
        • PytorchBackend.get_fundamental_dtype()
      • PytorchBackend.identity
        • PytorchBackend.identity()
      • PytorchBackend.indices
        • PytorchBackend.indices()
      • PytorchBackend.irfftn
        • PytorchBackend.irfftn()
      • PytorchBackend.max
        • PytorchBackend.max()
      • PytorchBackend.max_filter_coordinates
        • PytorchBackend.max_filter_coordinates()
      • PytorchBackend.max_score_over_rotations
        • PytorchBackend.max_score_over_rotations()
      • PytorchBackend.maximum
        • PytorchBackend.maximum()
      • PytorchBackend.mean
        • PytorchBackend.mean()
      • PytorchBackend.min
        • PytorchBackend.min()
      • PytorchBackend.minimum
        • PytorchBackend.minimum()
      • PytorchBackend.mod
        • PytorchBackend.mod()
      • PytorchBackend.multiply
        • PytorchBackend.multiply()
      • PytorchBackend.norm_scores
        • PytorchBackend.norm_scores()
      • PytorchBackend.power
        • PytorchBackend.power()
      • PytorchBackend.repeat
        • PytorchBackend.repeat()
      • PytorchBackend.reshape
        • PytorchBackend.reshape()
      • PytorchBackend.reverse
        • PytorchBackend.reverse()
      • PytorchBackend.rfftn
        • PytorchBackend.rfftn()
      • PytorchBackend.rigid_transform
        • PytorchBackend.rigid_transform()
      • PytorchBackend.roll
        • PytorchBackend.roll()
      • PytorchBackend.set_device
        • PytorchBackend.set_device()
      • PytorchBackend.size
        • PytorchBackend.size()
      • PytorchBackend.sqrt
        • PytorchBackend.sqrt()
      • PytorchBackend.square
        • PytorchBackend.square()
      • PytorchBackend.stack
        • PytorchBackend.stack()
      • PytorchBackend.std
        • PytorchBackend.std()
      • PytorchBackend.subtract
        • PytorchBackend.subtract()
      • PytorchBackend.sum
        • PytorchBackend.sum()
      • PytorchBackend.to_backend_array
        • PytorchBackend.to_backend_array()
      • PytorchBackend.to_cpu_array
        • PytorchBackend.to_cpu_array()
      • PytorchBackend.to_numpy_array
        • PytorchBackend.to_numpy_array()
      • PytorchBackend.to_sharedarr
        • PytorchBackend.to_sharedarr()
      • PytorchBackend.tobytes
        • PytorchBackend.tobytes()
      • PytorchBackend.topk_indices
        • PytorchBackend.topk_indices()
      • PytorchBackend.topleft_pad
        • PytorchBackend.topleft_pad()
      • PytorchBackend.transpose
        • PytorchBackend.transpose()
      • PytorchBackend.tril_indices
        • PytorchBackend.tril_indices()
      • PytorchBackend.triu_indices
        • PytorchBackend.triu_indices()
      • PytorchBackend.unique
        • PytorchBackend.unique()
      • PytorchBackend.unravel_index
        • PytorchBackend.unravel_index()
      • PytorchBackend.where
        • PytorchBackend.where()
      • PytorchBackend.zeros
        • PytorchBackend.zeros()
    • CupyBackend
      • CupyBackend
      • CupyBackend.abs
        • CupyBackend.abs()
      • CupyBackend.add
        • CupyBackend.add()
      • CupyBackend.addat
        • CupyBackend.addat()
      • CupyBackend.arange
        • CupyBackend.arange()
      • CupyBackend.argsort
        • CupyBackend.argsort()
      • CupyBackend.astype
        • CupyBackend.astype()
      • CupyBackend.at
        • CupyBackend.at()
      • CupyBackend.build_fft
        • CupyBackend.build_fft()
      • CupyBackend.center_of_mass
        • CupyBackend.center_of_mass()
      • CupyBackend.clip
        • CupyBackend.clip()
      • CupyBackend.compute_convolution_shapes
        • CupyBackend.compute_convolution_shapes()
      • CupyBackend.concatenate
        • CupyBackend.concatenate()
      • CupyBackend.copy
        • CupyBackend.copy()
      • CupyBackend.datatype_bytes
        • CupyBackend.datatype_bytes()
      • CupyBackend.device_count
        • CupyBackend.device_count()
      • CupyBackend.divide
        • CupyBackend.divide()
      • CupyBackend.dot
        • CupyBackend.dot()
      • CupyBackend.einsum
        • CupyBackend.einsum()
      • CupyBackend.eps
        • CupyBackend.eps()
      • CupyBackend.extract_center
        • CupyBackend.extract_center()
      • CupyBackend.fill
        • CupyBackend.fill()
      • CupyBackend.free_cache
        • CupyBackend.free_cache()
      • CupyBackend.from_sharedarr
        • CupyBackend.from_sharedarr()
      • CupyBackend.full
        • CupyBackend.full()
      • CupyBackend.get_available_memory
        • CupyBackend.get_available_memory()
      • CupyBackend.get_fundamental_dtype
        • CupyBackend.get_fundamental_dtype()
      • CupyBackend.identity
        • CupyBackend.identity()
      • CupyBackend.indices
        • CupyBackend.indices()
      • CupyBackend.irfftn
        • CupyBackend.irfftn()
      • CupyBackend.max
        • CupyBackend.max()
      • CupyBackend.max_filter_coordinates
        • CupyBackend.max_filter_coordinates()
      • CupyBackend.max_score_over_rotations
        • CupyBackend.max_score_over_rotations()
      • CupyBackend.maximum
        • CupyBackend.maximum()
      • CupyBackend.mean
        • CupyBackend.mean()
      • CupyBackend.min
        • CupyBackend.min()
      • CupyBackend.minimum
        • CupyBackend.minimum()
      • CupyBackend.mod
        • CupyBackend.mod()
      • CupyBackend.multiply
        • CupyBackend.multiply()
      • CupyBackend.norm_scores
        • CupyBackend.norm_scores()
      • CupyBackend.power
        • CupyBackend.power()
      • CupyBackend.repeat
        • CupyBackend.repeat()
      • CupyBackend.reshape
        • CupyBackend.reshape()
      • CupyBackend.reverse
        • CupyBackend.reverse()
      • CupyBackend.rfftn
        • CupyBackend.rfftn()
      • CupyBackend.rigid_transform
        • CupyBackend.rigid_transform()
      • CupyBackend.roll
        • CupyBackend.roll()
      • CupyBackend.set_device
        • CupyBackend.set_device()
      • CupyBackend.size
        • CupyBackend.size()
      • CupyBackend.sqrt
        • CupyBackend.sqrt()
      • CupyBackend.square
        • CupyBackend.square()
      • CupyBackend.stack
        • CupyBackend.stack()
      • CupyBackend.std
        • CupyBackend.std()
      • CupyBackend.subtract
        • CupyBackend.subtract()
      • CupyBackend.sum
        • CupyBackend.sum()
      • CupyBackend.to_backend_array
        • CupyBackend.to_backend_array()
      • CupyBackend.to_cpu_array
        • CupyBackend.to_cpu_array()
      • CupyBackend.to_numpy_array
        • CupyBackend.to_numpy_array()
      • CupyBackend.to_sharedarr
        • CupyBackend.to_sharedarr()
      • CupyBackend.tobytes
        • CupyBackend.tobytes()
      • CupyBackend.topk_indices
        • CupyBackend.topk_indices()
      • CupyBackend.topleft_pad
        • CupyBackend.topleft_pad()
      • CupyBackend.transpose
        • CupyBackend.transpose()
      • CupyBackend.tril_indices
        • CupyBackend.tril_indices()
      • CupyBackend.unique
        • CupyBackend.unique()
      • CupyBackend.unravel_index
        • CupyBackend.unravel_index()
      • CupyBackend.var
        • CupyBackend.var()
      • CupyBackend.where
        • CupyBackend.where()
      • CupyBackend.zeros
        • CupyBackend.zeros()
    • MLXBackend
      • MLXBackend
      • MLXBackend.abs
        • MLXBackend.abs()
      • MLXBackend.add
        • MLXBackend.add()
      • MLXBackend.addat
        • MLXBackend.addat()
      • MLXBackend.arange
        • MLXBackend.arange()
      • MLXBackend.argsort
        • MLXBackend.argsort()
      • MLXBackend.astype
        • MLXBackend.astype()
      • MLXBackend.at
        • MLXBackend.at()
      • MLXBackend.build_fft
        • MLXBackend.build_fft()
      • MLXBackend.center_of_mass
        • MLXBackend.center_of_mass()
      • MLXBackend.clip
        • MLXBackend.clip()
      • MLXBackend.compute_convolution_shapes
        • MLXBackend.compute_convolution_shapes()
      • MLXBackend.concatenate
        • MLXBackend.concatenate()
      • MLXBackend.copy
        • MLXBackend.copy()
      • MLXBackend.datatype_bytes
        • MLXBackend.datatype_bytes()
      • MLXBackend.device_count
        • MLXBackend.device_count()
      • MLXBackend.divide
        • MLXBackend.divide()
      • MLXBackend.dot
        • MLXBackend.dot()
      • MLXBackend.einsum
        • MLXBackend.einsum()
      • MLXBackend.eps
        • MLXBackend.eps()
      • MLXBackend.extract_center
        • MLXBackend.extract_center()
      • MLXBackend.fill
        • MLXBackend.fill()
      • MLXBackend.free_cache
        • MLXBackend.free_cache()
      • MLXBackend.from_sharedarr
        • MLXBackend.from_sharedarr()
      • MLXBackend.full
        • MLXBackend.full()
      • MLXBackend.get_available_memory
        • MLXBackend.get_available_memory()
      • MLXBackend.get_fundamental_dtype
        • MLXBackend.get_fundamental_dtype()
      • MLXBackend.identity
        • MLXBackend.identity()
      • MLXBackend.indices
        • MLXBackend.indices()
      • MLXBackend.irfftn
        • MLXBackend.irfftn()
      • MLXBackend.max
        • MLXBackend.max()
      • MLXBackend.max_filter_coordinates
        • MLXBackend.max_filter_coordinates()
      • MLXBackend.max_score_over_rotations
        • MLXBackend.max_score_over_rotations()
      • MLXBackend.maximum
        • MLXBackend.maximum()
      • MLXBackend.mean
        • MLXBackend.mean()
      • MLXBackend.min
        • MLXBackend.min()
      • MLXBackend.minimum
        • MLXBackend.minimum()
      • MLXBackend.mod
        • MLXBackend.mod()
      • MLXBackend.multiply
        • MLXBackend.multiply()
      • MLXBackend.norm_scores
        • MLXBackend.norm_scores()
      • MLXBackend.power
        • MLXBackend.power()
      • MLXBackend.repeat
        • MLXBackend.repeat()
      • MLXBackend.reshape
        • MLXBackend.reshape()
      • MLXBackend.reverse
        • MLXBackend.reverse()
      • MLXBackend.rfftn
        • MLXBackend.rfftn()
      • MLXBackend.rigid_transform
        • MLXBackend.rigid_transform()
      • MLXBackend.roll
        • MLXBackend.roll()
      • MLXBackend.set_device
        • MLXBackend.set_device()
      • MLXBackend.size
        • MLXBackend.size()
      • MLXBackend.sqrt
        • MLXBackend.sqrt()
      • MLXBackend.square
        • MLXBackend.square()
      • MLXBackend.stack
        • MLXBackend.stack()
      • MLXBackend.std
        • MLXBackend.std()
      • MLXBackend.subtract
        • MLXBackend.subtract()
      • MLXBackend.sum
        • MLXBackend.sum()
      • MLXBackend.to_backend_array
        • MLXBackend.to_backend_array()
      • MLXBackend.to_cpu_array
        • MLXBackend.to_cpu_array()
      • MLXBackend.to_numpy_array
        • MLXBackend.to_numpy_array()
      • MLXBackend.to_sharedarr
        • MLXBackend.to_sharedarr()
      • MLXBackend.tobytes
        • MLXBackend.tobytes()
      • MLXBackend.topk_indices
        • MLXBackend.topk_indices()
      • MLXBackend.topleft_pad
        • MLXBackend.topleft_pad()
      • MLXBackend.transpose
        • MLXBackend.transpose()
      • MLXBackend.tril_indices
        • MLXBackend.tril_indices()
      • MLXBackend.unique
        • MLXBackend.unique()
      • MLXBackend.unravel_index
        • MLXBackend.unravel_index()
      • MLXBackend.where
        • MLXBackend.where()
      • MLXBackend.zeros
        • MLXBackend.zeros()
    • JaxBackend
      • JaxBackend
      • JaxBackend.abs
        • JaxBackend.abs()
      • JaxBackend.add
        • JaxBackend.add()
      • JaxBackend.addat
        • JaxBackend.addat()
      • JaxBackend.arange
        • JaxBackend.arange()
      • JaxBackend.argsort
        • JaxBackend.argsort()
      • JaxBackend.astype
        • JaxBackend.astype()
      • JaxBackend.at
        • JaxBackend.at()
      • JaxBackend.build_fft
        • JaxBackend.build_fft()
      • JaxBackend.center_of_mass
        • JaxBackend.center_of_mass()
      • JaxBackend.clip
        • JaxBackend.clip()
      • JaxBackend.compute_convolution_shapes
        • JaxBackend.compute_convolution_shapes()
      • JaxBackend.concatenate
        • JaxBackend.concatenate()
      • JaxBackend.copy
        • JaxBackend.copy()
      • JaxBackend.datatype_bytes
        • JaxBackend.datatype_bytes()
      • JaxBackend.device_count
        • JaxBackend.device_count()
      • JaxBackend.divide
        • JaxBackend.divide()
      • JaxBackend.dot
        • JaxBackend.dot()
      • JaxBackend.einsum
        • JaxBackend.einsum()
      • JaxBackend.eps
        • JaxBackend.eps()
      • JaxBackend.extract_center
        • JaxBackend.extract_center()
      • JaxBackend.fill
        • JaxBackend.fill()
      • JaxBackend.free_cache
        • JaxBackend.free_cache()
      • JaxBackend.from_sharedarr
        • JaxBackend.from_sharedarr()
      • JaxBackend.full
        • JaxBackend.full()
      • JaxBackend.get_available_memory
        • JaxBackend.get_available_memory()
      • JaxBackend.get_fundamental_dtype
        • JaxBackend.get_fundamental_dtype()
      • JaxBackend.identity
        • JaxBackend.identity()
      • JaxBackend.indices
        • JaxBackend.indices()
      • JaxBackend.irfftn
        • JaxBackend.irfftn()
      • JaxBackend.max
        • JaxBackend.max()
      • JaxBackend.max_filter_coordinates
        • JaxBackend.max_filter_coordinates()
      • JaxBackend.max_score_over_rotations
        • JaxBackend.max_score_over_rotations()
      • JaxBackend.maximum
        • JaxBackend.maximum()
      • JaxBackend.mean
        • JaxBackend.mean()
      • JaxBackend.min
        • JaxBackend.min()
      • JaxBackend.minimum
        • JaxBackend.minimum()
      • JaxBackend.mod
        • JaxBackend.mod()
      • JaxBackend.multiply
        • JaxBackend.multiply()
      • JaxBackend.norm_scores
        • JaxBackend.norm_scores()
      • JaxBackend.power
        • JaxBackend.power()
      • JaxBackend.repeat
        • JaxBackend.repeat()
      • JaxBackend.reshape
        • JaxBackend.reshape()
      • JaxBackend.reverse
        • JaxBackend.reverse()
      • JaxBackend.rfftn
        • JaxBackend.rfftn()
      • JaxBackend.rigid_transform
        • JaxBackend.rigid_transform()
      • JaxBackend.roll
        • JaxBackend.roll()
      • JaxBackend.scan
        • JaxBackend.scan()
      • JaxBackend.set_device
        • JaxBackend.set_device()
      • JaxBackend.size
        • JaxBackend.size()
      • JaxBackend.sqrt
        • JaxBackend.sqrt()
      • JaxBackend.square
        • JaxBackend.square()
      • JaxBackend.stack
        • JaxBackend.stack()
      • JaxBackend.std
        • JaxBackend.std()
      • JaxBackend.subtract
        • JaxBackend.subtract()
      • JaxBackend.sum
        • JaxBackend.sum()
      • JaxBackend.to_backend_array
        • JaxBackend.to_backend_array()
      • JaxBackend.to_cpu_array
        • JaxBackend.to_cpu_array()
      • JaxBackend.to_numpy_array
        • JaxBackend.to_numpy_array()
      • JaxBackend.to_sharedarr
        • JaxBackend.to_sharedarr()
      • JaxBackend.tobytes
        • JaxBackend.tobytes()
      • JaxBackend.topk_indices
        • JaxBackend.topk_indices()
      • JaxBackend.topleft_pad
        • JaxBackend.topleft_pad()
      • JaxBackend.transpose
        • JaxBackend.transpose()
      • JaxBackend.tril_indices
        • JaxBackend.tril_indices()
      • JaxBackend.unique
        • JaxBackend.unique()
      • JaxBackend.unravel_index
        • JaxBackend.unravel_index()
      • JaxBackend.where
        • JaxBackend.where()
      • JaxBackend.zeros
        • JaxBackend.zeros()
  • Abstract Base Backend
    • MatchingBackend
      • MatchingBackend
      • MatchingBackend.abs
        • MatchingBackend.abs()
      • MatchingBackend.add
        • MatchingBackend.add()
      • MatchingBackend.arange
        • MatchingBackend.arange()
      • MatchingBackend.argsort
        • MatchingBackend.argsort()
      • MatchingBackend.astype
        • MatchingBackend.astype()
      • MatchingBackend.at
        • MatchingBackend.at()
      • MatchingBackend.build_fft
        • MatchingBackend.build_fft()
      • MatchingBackend.clip
        • MatchingBackend.clip()
      • MatchingBackend.compute_convolution_shapes
        • MatchingBackend.compute_convolution_shapes()
      • MatchingBackend.concatenate
        • MatchingBackend.concatenate()
      • MatchingBackend.datatype_bytes
        • MatchingBackend.datatype_bytes()
      • MatchingBackend.device_count
        • MatchingBackend.device_count()
      • MatchingBackend.divide
        • MatchingBackend.divide()
      • MatchingBackend.einsum
        • MatchingBackend.einsum()
      • MatchingBackend.eps
        • MatchingBackend.eps()
      • MatchingBackend.extract_center
        • MatchingBackend.extract_center()
      • MatchingBackend.fill
        • MatchingBackend.fill()
      • MatchingBackend.free_cache
        • MatchingBackend.free_cache()
      • MatchingBackend.from_sharedarr
        • MatchingBackend.from_sharedarr()
      • MatchingBackend.full
        • MatchingBackend.full()
      • MatchingBackend.get_available_memory
        • MatchingBackend.get_available_memory()
      • MatchingBackend.get_fundamental_dtype
        • MatchingBackend.get_fundamental_dtype()
      • MatchingBackend.indices
        • MatchingBackend.indices()
      • MatchingBackend.max
        • MatchingBackend.max()
      • MatchingBackend.max_filter_coordinates
        • MatchingBackend.max_filter_coordinates()
      • MatchingBackend.maximum
        • MatchingBackend.maximum()
      • MatchingBackend.mean
        • MatchingBackend.mean()
      • MatchingBackend.min
        • MatchingBackend.min()
      • MatchingBackend.minimum
        • MatchingBackend.minimum()
      • MatchingBackend.mod
        • MatchingBackend.mod()
      • MatchingBackend.multiply
        • MatchingBackend.multiply()
      • MatchingBackend.power
        • MatchingBackend.power()
      • MatchingBackend.repeat
        • MatchingBackend.repeat()
      • MatchingBackend.reverse
        • MatchingBackend.reverse()
      • MatchingBackend.rigid_transform
        • MatchingBackend.rigid_transform()
      • MatchingBackend.roll
        • MatchingBackend.roll()
      • MatchingBackend.set_device
        • MatchingBackend.set_device()
      • MatchingBackend.size
        • MatchingBackend.size()
      • MatchingBackend.sqrt
        • MatchingBackend.sqrt()
      • MatchingBackend.square
        • MatchingBackend.square()
      • MatchingBackend.stack
        • MatchingBackend.stack()
      • MatchingBackend.std
        • MatchingBackend.std()
      • MatchingBackend.subtract
        • MatchingBackend.subtract()
      • MatchingBackend.sum
        • MatchingBackend.sum()
      • MatchingBackend.to_backend_array
        • MatchingBackend.to_backend_array()
      • MatchingBackend.to_cpu_array
        • MatchingBackend.to_cpu_array()
      • MatchingBackend.to_numpy_array
        • MatchingBackend.to_numpy_array()
      • MatchingBackend.to_sharedarr
        • MatchingBackend.to_sharedarr()
      • MatchingBackend.tobytes
        • MatchingBackend.tobytes()
      • MatchingBackend.topk_indices
        • MatchingBackend.topk_indices()
      • MatchingBackend.topleft_pad
        • MatchingBackend.topleft_pad()
      • MatchingBackend.transpose
        • MatchingBackend.transpose()
      • MatchingBackend.tril_indices
        • MatchingBackend.tril_indices()
      • MatchingBackend.unique
        • MatchingBackend.unique()
      • MatchingBackend.unravel_index
        • MatchingBackend.unravel_index()
      • MatchingBackend.where
        • MatchingBackend.where()
      • MatchingBackend.zeros
        • MatchingBackend.zeros()
    • Array operations
    • Array initialization
    • Template matching
    • Conversion
    • Auxiliary

Miscellaneous

• Orientations
  • Constructor
    • Orientations
      • Orientations
      • Orientations.translations
        • Orientations.translations
      • Orientations.rotations
        • Orientations.rotations
      • Orientations.scores
        • Orientations.scores
      • Orientations.details
        • Orientations.details
      • Orientations.copy
        • Orientations.copy()
      • Orientations.from_file
        • Orientations.from_file()
      • Orientations.get_extraction_slices
        • Orientations.get_extraction_slices()
      • Orientations.to_file
        • Orientations.to_file()
  • Attributes and underlying data
  • Serialization
  • Subsetting
• Utilities
  • Extensions
    • absolute_minimum_deviation()
    • find_candidate_coordinates()
    • find_candidate_indices()
    • max_euclidean_distance()
    • max_index_by_label()
    • online_statistics()
  • Parser
    • Constructor
      • Parser
        • Parser
        • Parser.get
          • Parser.get()
        • Parser.items
          • Parser.items()
        • Parser.keys
          • Parser.keys()
        • Parser.parse_input
          • Parser.parse_input()
        • Parser.values
          • Parser.values()
    • Attributes
      • Parser.get
        • Parser.get()
      • Parser.keys
        • Parser.keys()
      • Parser.values
        • Parser.values()
      • Parser.items
        • Parser.items()
      • Parser.parse_input
        • Parser.parse_input()
    • Supported formats
      • PDBParser
        • PDBParser
        • PDBParser.get
          • PDBParser.get()
        • PDBParser.items
          • PDBParser.items()
        • PDBParser.keys
          • PDBParser.keys()
        • PDBParser.parse_input
          • PDBParser.parse_input()
        • PDBParser.values
          • PDBParser.values()
      • MMCIFParser
        • MMCIFParser
        • MMCIFParser.get
          • MMCIFParser.get()
        • MMCIFParser.items
          • MMCIFParser.items()
        • MMCIFParser.keys
          • MMCIFParser.keys()
        • MMCIFParser.parse_input
          • MMCIFParser.parse_input()
        • MMCIFParser.values
          • MMCIFParser.values()