API#
- Density
- Constructor
- Density
Density
- Density.data
- Density.empty
- Density.metadata
- Density.origin
- Density.sampling_rate
- Density.shape
- Density.adjust_box
- Density.center_of_mass
- Density.centered
- Density.copy
- Density.core_mask
- Density.density_boundary
- Density.fourier_shell_correlation
- Density.from_file
- Density.from_structure
- Density.match_densities
- Density.match_structure_to_density
- Density.minimum_enclosing_box
- Density.normal_vectors
- Density.pad
- Density.resample
- Density.rigid_transform
- Density.surface_coordinates
- Density.to_file
- Density.to_memmap
- Density.to_numpy
- Density.to_pointcloud
- Density.trim_box
- Density
- Attributes and underlying data
- Serialization
- Conversion
- Subsetting
- Computations
- Constructor
- Structure
- Constructor
- Structure
Structure
- Structure.record_type
- Structure.atom_serial_number
- Structure.atom_name
- Structure.atom_coordinate
- Structure.alternate_location_indicator
- Structure.residue_name
- Structure.chain_identifier
- Structure.residue_sequence_number
- Structure.code_for_residue_insertion
- Structure.occupancy
- Structure.temperature_factor
- Structure.segment_identifier
- Structure.element_symbol
- Structure.charge
- Structure.metadata
- Structure.align_structures
- Structure.center_of_mass
- Structure.centered
- Structure.compare_structures
- Structure.copy
- Structure.from_file
- Structure.rigid_transform
- Structure.subset_by_chain
- Structure.subset_by_range
- Structure.to_file
- Structure.to_volume
- Structure
- Attributes and underlying data
- Structure.record_type
- Structure.atom_serial_number
- Structure.atom_name
- Structure.atom_coordinate
- Structure.alternate_location_indicator
- Structure.residue_name
- Structure.chain_identifier
- Structure.residue_sequence_number
- Structure.code_for_residue_insertion
- Structure.occupancy
- Structure.temperature_factor
- Structure.segment_identifier
- Structure.element_symbol
- Structure.charge
- Structure.metadata
- Serialization
- Conversion
- Subsetting
- Computations
- Constructor
- MatchingData
- Constructor
- MatchingData
MatchingData
- MatchingData.rotations
- MatchingData.target
- MatchingData.target_filter
- MatchingData.target_mask
- MatchingData.template
- MatchingData.template_filter
- MatchingData.template_mask
- MatchingData.fourier_padding
- MatchingData.subset_array
- MatchingData.subset_by_slice
- MatchingData.target_padding
- MatchingData.to_backend
- MatchingData
- Conversion
- Attributes and underlying data
- Utilities
- Constructor
- Preprocessor
- Constructor
- Preprocessor
Preprocessor
- Preprocessor.apply_method
- Preprocessor.bandpass_filter
- Preprocessor.bandpass_mask
- Preprocessor.blob_filter
- Preprocessor.continuous_wedge_mask
- Preprocessor.difference_of_gaussian_filter
- Preprocessor.edge_gaussian_filter
- Preprocessor.gaussian_filter
- Preprocessor.hamming_filter
- Preprocessor.interpolate_box
- Preprocessor.kaiserb_filter
- Preprocessor.local_gaussian_alignment_filter
- Preprocessor.local_gaussian_filter
- Preprocessor.mean_filter
- Preprocessor.median_filter
- Preprocessor.method_to_id
- Preprocessor.mipmap_filter
- Preprocessor.rank_filter
- Preprocessor.step_wedge_mask
- Preprocessor
- Filters
- Preprocessor.continuous_wedge_mask
- Preprocessor.step_wedge_mask
- Preprocessor.gaussian_filter
- Preprocessor.difference_of_gaussian_filter
- Preprocessor.bandpass_filter
- Preprocessor.local_gaussian_alignment_filter
- Preprocessor.local_gaussian_filter
- Preprocessor.edge_gaussian_filter
- Preprocessor.mean_filter
- Preprocessor.rank_filter
- Preprocessor.mipmap_filter
- Preprocessor.kaiserb_filter
- Preprocessor.blob_filter
- Preprocessor.hamming_filter
- Utilities
- Constructor
- Composable Filters
- Specification
- Aggregator
- Frequency Filters
- CryoEM Filters
- CTF
CTF
- CTF.acceleration_voltage
- CTF.amplitude_contrast
- CTF.angles
- CTF.correct_defocus_gradient
- CTF.defocus_angle
- CTF.defocus_y
- CTF.flip_phase
- CTF.opening_axis
- CTF.phase_shift
- CTF.return_real_fourier
- CTF.sampling_rate
- CTF.spherical_aberration
- CTF.tilt_axis
- CTF.shape
- CTF.defocus_x
- CTF.from_file
- CTF.weight
- Wedge
- WedgeReconstructed
- CTF
- Reconstruction
- ReconstructFromTilt
- Exhaustive
- Non-exhaustive
- FLC
- CrossCorrelation
- LaplaceCrossCorrelation
- NormalizedCrossCorrelation
- NormalizedCrossCorrelationMean
- MaskedCrossCorrelation
- PartialLeastSquareDifference
- Chamfer
- MutualInformation
- Envelope
- NormalVectorScore
- Chamfer
- NormalVectorScore
- create_score_object
- optimize_match
- Analyzers
- Memory
- Utilities
- Masks
- Rotations
- Subsetting
- Serialization
- Utilities
- Backends
- Backend Manager
- Abstract Base Backend
- MatchingBackend
MatchingBackend
- MatchingBackend.abs
- MatchingBackend.add
- MatchingBackend.arange
- MatchingBackend.argsort
- MatchingBackend.astype
- MatchingBackend.build_fft
- MatchingBackend.clip
- MatchingBackend.compute_convolution_shapes
- MatchingBackend.concatenate
- MatchingBackend.datatype_bytes
- MatchingBackend.device_count
- MatchingBackend.divide
- MatchingBackend.einsum
- MatchingBackend.eps
- MatchingBackend.extract_center
- MatchingBackend.fill
- MatchingBackend.free_cache
- MatchingBackend.from_sharedarr
- MatchingBackend.full
- MatchingBackend.get_available_memory
- MatchingBackend.get_fundamental_dtype
- MatchingBackend.indices
- MatchingBackend.max
- MatchingBackend.max_filter_coordinates
- MatchingBackend.maximum
- MatchingBackend.mean
- MatchingBackend.min
- MatchingBackend.minimum
- MatchingBackend.mod
- MatchingBackend.multiply
- MatchingBackend.power
- MatchingBackend.repeat
- MatchingBackend.reverse
- MatchingBackend.rigid_transform
- MatchingBackend.roll
- MatchingBackend.set_device
- MatchingBackend.size
- MatchingBackend.sqrt
- MatchingBackend.square
- MatchingBackend.stack
- MatchingBackend.std
- MatchingBackend.subtract
- MatchingBackend.sum
- MatchingBackend.to_backend_array
- MatchingBackend.to_cpu_array
- MatchingBackend.to_numpy_array
- MatchingBackend.to_sharedarr
- MatchingBackend.tobytes
- MatchingBackend.topk_indices
- MatchingBackend.topleft_pad
- MatchingBackend.transpose
- MatchingBackend.tril_indices
- MatchingBackend.unique
- MatchingBackend.unravel_index
- MatchingBackend.where
- MatchingBackend.zeros
- Array operations
- Array initialization
- Template matching
- Conversion
- Auxiliary
- MatchingBackend
- Supported Backends
- NumpyFFTWBackend
NumpyFFTWBackend
- NumpyFFTWBackend.abs
- NumpyFFTWBackend.add
- NumpyFFTWBackend.arange
- NumpyFFTWBackend.argsort
- NumpyFFTWBackend.astype
- NumpyFFTWBackend.build_fft
- NumpyFFTWBackend.center_of_mass
- NumpyFFTWBackend.clip
- NumpyFFTWBackend.compute_convolution_shapes
- NumpyFFTWBackend.concatenate
- NumpyFFTWBackend.datatype_bytes
- NumpyFFTWBackend.device_count
- NumpyFFTWBackend.divide
- NumpyFFTWBackend.dot
- NumpyFFTWBackend.einsum
- NumpyFFTWBackend.eps
- NumpyFFTWBackend.extract_center
- NumpyFFTWBackend.fill
- NumpyFFTWBackend.free_cache
- NumpyFFTWBackend.from_sharedarr
- NumpyFFTWBackend.full
- NumpyFFTWBackend.get_available_memory
- NumpyFFTWBackend.get_fundamental_dtype
- NumpyFFTWBackend.identity
- NumpyFFTWBackend.indices
- NumpyFFTWBackend.max
- NumpyFFTWBackend.max_filter_coordinates
- NumpyFFTWBackend.max_score_over_rotations
- NumpyFFTWBackend.maximum
- NumpyFFTWBackend.mean
- NumpyFFTWBackend.min
- NumpyFFTWBackend.minimum
- NumpyFFTWBackend.mod
- NumpyFFTWBackend.multiply
- NumpyFFTWBackend.norm_scores
- NumpyFFTWBackend.power
- NumpyFFTWBackend.repeat
- NumpyFFTWBackend.reshape
- NumpyFFTWBackend.reverse
- NumpyFFTWBackend.rigid_transform
- NumpyFFTWBackend.roll
- NumpyFFTWBackend.set_device
- NumpyFFTWBackend.size
- NumpyFFTWBackend.sqrt
- NumpyFFTWBackend.square
- NumpyFFTWBackend.stack
- NumpyFFTWBackend.std
- NumpyFFTWBackend.subtract
- NumpyFFTWBackend.sum
- NumpyFFTWBackend.to_backend_array
- NumpyFFTWBackend.to_cpu_array
- NumpyFFTWBackend.to_numpy_array
- NumpyFFTWBackend.to_sharedarr
- NumpyFFTWBackend.tobytes
- NumpyFFTWBackend.topk_indices
- NumpyFFTWBackend.topleft_pad
- NumpyFFTWBackend.transpose
- NumpyFFTWBackend.tril_indices
- NumpyFFTWBackend.unique
- NumpyFFTWBackend.unravel_index
- NumpyFFTWBackend.where
- NumpyFFTWBackend.zeros
- PytorchBackend
PytorchBackend
- PytorchBackend.abs
- PytorchBackend.add
- PytorchBackend.arange
- PytorchBackend.argsort
- PytorchBackend.astype
- PytorchBackend.build_fft
- PytorchBackend.center_of_mass
- PytorchBackend.clip
- PytorchBackend.compute_convolution_shapes
- PytorchBackend.concatenate
- PytorchBackend.datatype_bytes
- PytorchBackend.device_count
- PytorchBackend.divide
- PytorchBackend.dot
- PytorchBackend.einsum
- PytorchBackend.eps
- PytorchBackend.extract_center
- PytorchBackend.fill
- PytorchBackend.flip
- PytorchBackend.free_cache
- PytorchBackend.from_sharedarr
- PytorchBackend.full
- PytorchBackend.get_available_memory
- PytorchBackend.get_fundamental_dtype
- PytorchBackend.identity
- PytorchBackend.indices
- PytorchBackend.max
- PytorchBackend.max_filter_coordinates
- PytorchBackend.max_score_over_rotations
- PytorchBackend.maximum
- PytorchBackend.mean
- PytorchBackend.min
- PytorchBackend.minimum
- PytorchBackend.mod
- PytorchBackend.multiply
- PytorchBackend.norm_scores
- PytorchBackend.power
- PytorchBackend.repeat
- PytorchBackend.reshape
- PytorchBackend.reverse
- PytorchBackend.rigid_transform
- PytorchBackend.roll
- PytorchBackend.set_device
- PytorchBackend.size
- PytorchBackend.sqrt
- PytorchBackend.square
- PytorchBackend.stack
- PytorchBackend.std
- PytorchBackend.subtract
- PytorchBackend.sum
- PytorchBackend.to_backend_array
- PytorchBackend.to_cpu_array
- PytorchBackend.to_numpy_array
- PytorchBackend.to_sharedarr
- PytorchBackend.tobytes
- PytorchBackend.topk_indices
- PytorchBackend.topleft_pad
- PytorchBackend.transpose
- PytorchBackend.tril_indices
- PytorchBackend.unique
- PytorchBackend.unravel_index
- PytorchBackend.where
- PytorchBackend.zeros
- CupyBackend
CupyBackend
- CupyBackend.abs
- CupyBackend.add
- CupyBackend.arange
- CupyBackend.argsort
- CupyBackend.astype
- CupyBackend.build_fft
- CupyBackend.center_of_mass
- CupyBackend.clip
- CupyBackend.compute_convolution_shapes
- CupyBackend.concatenate
- CupyBackend.datatype_bytes
- CupyBackend.device_count
- CupyBackend.divide
- CupyBackend.dot
- CupyBackend.einsum
- CupyBackend.eps
- CupyBackend.extract_center
- CupyBackend.fill
- CupyBackend.free_cache
- CupyBackend.from_sharedarr
- CupyBackend.full
- CupyBackend.get_available_memory
- CupyBackend.get_fundamental_dtype
- CupyBackend.identity
- CupyBackend.indices
- CupyBackend.max
- CupyBackend.max_filter_coordinates
- CupyBackend.max_score_over_rotations
- CupyBackend.maximum
- CupyBackend.mean
- CupyBackend.min
- CupyBackend.minimum
- CupyBackend.mod
- CupyBackend.multiply
- CupyBackend.norm_scores
- CupyBackend.power
- CupyBackend.repeat
- CupyBackend.reshape
- CupyBackend.reverse
- CupyBackend.rigid_transform
- CupyBackend.roll
- CupyBackend.set_device
- CupyBackend.size
- CupyBackend.sqrt
- CupyBackend.square
- CupyBackend.stack
- CupyBackend.std
- CupyBackend.subtract
- CupyBackend.sum
- CupyBackend.to_backend_array
- CupyBackend.to_cpu_array
- CupyBackend.to_numpy_array
- CupyBackend.to_sharedarr
- CupyBackend.tobytes
- CupyBackend.topk_indices
- CupyBackend.topleft_pad
- CupyBackend.transpose
- CupyBackend.tril_indices
- CupyBackend.unique
- CupyBackend.unravel_index
- CupyBackend.var
- CupyBackend.where
- CupyBackend.zeros
- MLXBackend
MLXBackend
- MLXBackend.abs
- MLXBackend.add
- MLXBackend.arange
- MLXBackend.argsort
- MLXBackend.astype
- MLXBackend.build_fft
- MLXBackend.center_of_mass
- MLXBackend.clip
- MLXBackend.compute_convolution_shapes
- MLXBackend.concatenate
- MLXBackend.datatype_bytes
- MLXBackend.device_count
- MLXBackend.divide
- MLXBackend.dot
- MLXBackend.einsum
- MLXBackend.eps
- MLXBackend.extract_center
- MLXBackend.fill
- MLXBackend.free_cache
- MLXBackend.from_sharedarr
- MLXBackend.full
- MLXBackend.get_available_memory
- MLXBackend.get_fundamental_dtype
- MLXBackend.identity
- MLXBackend.indices
- MLXBackend.max
- MLXBackend.max_filter_coordinates
- MLXBackend.max_score_over_rotations
- MLXBackend.maximum
- MLXBackend.mean
- MLXBackend.min
- MLXBackend.minimum
- MLXBackend.mod
- MLXBackend.multiply
- MLXBackend.norm_scores
- MLXBackend.power
- MLXBackend.repeat
- MLXBackend.reshape
- MLXBackend.reverse
- MLXBackend.rigid_transform
- MLXBackend.roll
- MLXBackend.set_device
- MLXBackend.size
- MLXBackend.sqrt
- MLXBackend.square
- MLXBackend.stack
- MLXBackend.std
- MLXBackend.subtract
- MLXBackend.sum
- MLXBackend.to_backend_array
- MLXBackend.to_cpu_array
- MLXBackend.to_numpy_array
- MLXBackend.to_sharedarr
- MLXBackend.tobytes
- MLXBackend.topk_indices
- MLXBackend.topleft_pad
- MLXBackend.transpose
- MLXBackend.tril_indices
- MLXBackend.unique
- MLXBackend.unravel_index
- MLXBackend.where
- MLXBackend.zeros
- JaxBackend
JaxBackend
- JaxBackend.abs
- JaxBackend.add
- JaxBackend.arange
- JaxBackend.argsort
- JaxBackend.astype
- JaxBackend.build_fft
- JaxBackend.center_of_mass
- JaxBackend.clip
- JaxBackend.compute_convolution_shapes
- JaxBackend.concatenate
- JaxBackend.datatype_bytes
- JaxBackend.device_count
- JaxBackend.divide
- JaxBackend.dot
- JaxBackend.einsum
- JaxBackend.eps
- JaxBackend.extract_center
- JaxBackend.fill
- JaxBackend.free_cache
- JaxBackend.from_sharedarr
- JaxBackend.full
- JaxBackend.get_available_memory
- JaxBackend.get_fundamental_dtype
- JaxBackend.identity
- JaxBackend.indices
- JaxBackend.max
- JaxBackend.max_filter_coordinates
- JaxBackend.max_score_over_rotations
- JaxBackend.maximum
- JaxBackend.mean
- JaxBackend.min
- JaxBackend.minimum
- JaxBackend.mod
- JaxBackend.multiply
- JaxBackend.norm_scores
- JaxBackend.power
- JaxBackend.repeat
- JaxBackend.reshape
- JaxBackend.reverse
- JaxBackend.rigid_transform
- JaxBackend.roll
- JaxBackend.set_device
- JaxBackend.size
- JaxBackend.sqrt
- JaxBackend.square
- JaxBackend.stack
- JaxBackend.std
- JaxBackend.subtract
- JaxBackend.sum
- JaxBackend.to_backend_array
- JaxBackend.to_cpu_array
- JaxBackend.to_numpy_array
- JaxBackend.to_sharedarr
- JaxBackend.tobytes
- JaxBackend.topk_indices
- JaxBackend.topleft_pad
- JaxBackend.transpose
- JaxBackend.tril_indices
- JaxBackend.unique
- JaxBackend.unravel_index
- JaxBackend.where
- JaxBackend.zeros
- NumpyFFTWBackend
- Orientations
- Utilities