aspire package¶
Subpackages¶
- aspire.abinitio package
- Submodules
- aspire.abinitio.commonline_base module
- aspire.abinitio.commonline_c2 module
- aspire.abinitio.commonline_c3_c4 module
- aspire.abinitio.commonline_cn module
- aspire.abinitio.commonline_d2 module
- aspire.abinitio.commonline_ev module
- aspire.abinitio.commonline_gcar module
- aspire.abinitio.commonline_lud module
- aspire.abinitio.commonline_sdp module
- aspire.abinitio.commonline_sync module
- aspire.abinitio.commonline_sync3n module
- aspire.abinitio.sync_voting module
- Module contents
- aspire.apple package
- aspire.basis package
- Submodules
- aspire.basis.basis module
- aspire.basis.basis_utils module
- aspire.basis.fb module
- aspire.basis.fb_2d module
- aspire.basis.fb_3d module
- aspire.basis.ffb_2d module
- aspire.basis.ffb_3d module
- aspire.basis.fle_2d module
- aspire.basis.fle_2d_utils module
- aspire.basis.fpswf_2d module
- aspire.basis.fpswf_3d module
- aspire.basis.fspca module
FSPCABasis
FSPCABasis.build()
FSPCABasis.calculate_bispectrum()
FSPCABasis.eigen_images()
FSPCABasis.eigvals
FSPCABasis.evaluate()
FSPCABasis.evaluate_to_image_basis()
FSPCABasis.expand()
FSPCABasis.expand_from_image_basis()
FSPCABasis.filter_to_basis_mat()
FSPCABasis.shift()
FSPCABasis.to_complex()
FSPCABasis.to_real()
- aspire.basis.pswf_2d module
- aspire.basis.pswf_3d module
- aspire.basis.pswf_utils module
- aspire.basis.steerable module
SteerableBasis2D
SteerableBasis2D.blk_diag_cov_shape
SteerableBasis2D.calculate_bispectrum()
SteerableBasis2D.complex_rotate()
SteerableBasis2D.filter_to_basis_mat()
SteerableBasis2D.indices_mask()
SteerableBasis2D.matrix_type
SteerableBasis2D.rotate()
SteerableBasis2D.shift()
SteerableBasis2D.to_complex()
SteerableBasis2D.to_real()
- Module contents
- aspire.classification package
- Submodules
- aspire.classification.averager2d module
- aspire.classification.class2d module
- aspire.classification.class_selection module
BandedSNRImageQualityFunction
BandpassImageQualityFunction
BumpWeightedImageQualityMixin
BumpWeightedVarianceImageQualityFunction
ClassSelector
DistanceClassSelector
GlobalClassSelector
GlobalWithRepulsionClassSelector
GreedyClassRepulsionMixin
ImageQualityFunction
NeighborVarianceClassSelector
NeighborVarianceWithRepulsionClassSelector
RampWeightedImageQualityMixin
RampWeightedVarianceImageQualityFunction
RandomClassSelector
TopClassSelector
VarianceImageQualityFunction
WeightedImageQualityMixin
- aspire.classification.legacy_implementations module
- aspire.classification.reddy_chatterji module
- aspire.classification.rir_class2d module
- Module contents
- aspire.commands package
- aspire.covariance package
- aspire.ctf package
- Submodules
- aspire.ctf.ctf_estimator module
CtfEstimator
CtfEstimator.background_subtract_1d()
CtfEstimator.background_subtract_2d()
CtfEstimator.elliptical_average()
CtfEstimator.estimate_psd()
CtfEstimator.gd()
CtfEstimator.generate_ctf()
CtfEstimator.micrograph_to_blocks()
CtfEstimator.normalize_blocks()
CtfEstimator.opt1d()
CtfEstimator.pca()
CtfEstimator.preprocess_micrograph()
CtfEstimator.set_angle()
CtfEstimator.set_df1()
CtfEstimator.set_df2()
CtfEstimator.tapers()
CtfEstimator.write_star()
estimate_ctf()
- Module contents
- aspire.denoising package
- aspire.downloader package
- aspire.image package
- Submodules
- aspire.image.image module
BasisImage
BispecImage
CartesianImage
FBBasisImage
Image
Image.T
Image.asnumpy()
Image.backproject()
Image.copy()
Image.downsample()
Image.extensions
Image.filter()
Image.flip()
Image.frc()
Image.load()
Image.norm()
Image.project()
Image.res
Image.rotate()
Image.save()
Image.shift()
Image.show()
Image.size
Image.sqrt()
Image.stack_reshape()
Image.transpose()
PolarImage
load_mrc()
load_tiff()
normalize_bg()
- aspire.image.image_stacker module
- aspire.image.xform module
- Module contents
- aspire.noise package
- aspire.nufft package
- aspire.numeric package
- aspire.operators package
- Submodules
- aspire.operators.blk_diag_matrix module
BlkDiagMatrix
BlkDiagMatrix.T
BlkDiagMatrix.abs()
BlkDiagMatrix.add()
BlkDiagMatrix.append()
BlkDiagMatrix.apply()
BlkDiagMatrix.check_psd()
BlkDiagMatrix.copy()
BlkDiagMatrix.dense()
BlkDiagMatrix.diag()
BlkDiagMatrix.eigvals()
BlkDiagMatrix.empty()
BlkDiagMatrix.eye()
BlkDiagMatrix.eye_like()
BlkDiagMatrix.from_dense()
BlkDiagMatrix.from_list()
BlkDiagMatrix.is_square
BlkDiagMatrix.isfinite
BlkDiagMatrix.make_psd()
BlkDiagMatrix.matmul()
BlkDiagMatrix.mul()
BlkDiagMatrix.neg()
BlkDiagMatrix.norm()
BlkDiagMatrix.ones()
BlkDiagMatrix.partition
BlkDiagMatrix.pow()
BlkDiagMatrix.rapply()
BlkDiagMatrix.reset_cache()
BlkDiagMatrix.solve()
BlkDiagMatrix.sub()
BlkDiagMatrix.transpose()
BlkDiagMatrix.zeros()
BlkDiagMatrix.zeros_like()
is_scalar_type()
- aspire.operators.diag_matrix module
DiagMatrix
DiagMatrix.T
DiagMatrix.abs()
DiagMatrix.add()
DiagMatrix.apply()
DiagMatrix.as_blk_diag()
DiagMatrix.asnumpy()
DiagMatrix.copy()
DiagMatrix.dense()
DiagMatrix.eigvals()
DiagMatrix.empty()
DiagMatrix.eye()
DiagMatrix.matmul()
DiagMatrix.mul()
DiagMatrix.neg()
DiagMatrix.norm
DiagMatrix.ones()
DiagMatrix.pow()
DiagMatrix.rapply()
DiagMatrix.solve()
DiagMatrix.stack_reshape()
DiagMatrix.sub()
DiagMatrix.transpose()
DiagMatrix.zeros()
- aspire.operators.filters module
- aspire.operators.polar_ft module
- aspire.operators.wemd module
- Module contents
- aspire.optimization package
- aspire.reconstruction package
- aspire.sinogram package
- aspire.source package
- Submodules
- aspire.source.coordinates module
- aspire.source.image module
ArrayImageSource
ImageSource
ImageSource.amplitudes
ImageSource.angles
ImageSource.cache()
ImageSource.class_distances
ImageSource.class_indices
ImageSource.class_refl
ImageSource.downsample()
ImageSource.estimate_noise_power()
ImageSource.estimate_signal_mean_energy()
ImageSource.estimate_signal_power()
ImageSource.estimate_signal_var()
ImageSource.estimate_snr()
ImageSource.filter_indices
ImageSource.get_metadata()
ImageSource.has_metadata()
ImageSource.im_backward()
ImageSource.images
ImageSource.invert_contrast()
ImageSource.n
ImageSource.n_ctf_filters
ImageSource.normalize_background()
ImageSource.offsets
ImageSource.phase_flip()
ImageSource.rotations
ImageSource.save()
ImageSource.save_images()
ImageSource.save_metadata()
ImageSource.selection_indices
ImageSource.set_metadata()
ImageSource.states
ImageSource.symmetry_group
ImageSource.update()
ImageSource.vol_forward()
ImageSource.whiten()
IndexedSource
OrientedSource
- aspire.source.micrograph module
- aspire.source.relion module
- aspire.source.simulation module
Simulation
Simulation.clean_images
Simulation.covar_true()
Simulation.eigs()
Simulation.eval_clustering()
Simulation.eval_coords()
Simulation.eval_covar()
Simulation.eval_eigs()
Simulation.eval_mean()
Simulation.eval_vol()
Simulation.eval_volmat()
Simulation.mean_true()
Simulation.projections
Simulation.true_signal_power()
Simulation.true_snr()
Simulation.vol_coords()
- Module contents
- aspire.storage package
- aspire.utils package
- Submodules
- aspire.utils.bot_align module
- aspire.utils.cell module
- aspire.utils.coor_trans module
- aspire.utils.logging module
- aspire.utils.matlab_compat module
- aspire.utils.matrix module
acorr()
ainner()
anorm()
best_rank1_approximation()
eigs()
fix_signs()
im_to_vec()
make_psd()
make_symmat()
mat_to_vec()
mdim_mat_fun_conj()
nearest_rotations()
roll_dim()
symmat_to_vec()
symmat_to_vec_iso()
unroll_dim()
vec_to_im()
vec_to_mat()
vec_to_symmat()
vec_to_symmat_iso()
vec_to_vol()
vecmat_to_volmat()
vol_to_vec()
volmat_to_vecmat()
- aspire.utils.misc module
- aspire.utils.multiprocessing module
- aspire.utils.random module
- aspire.utils.relion_interop module
- aspire.utils.resolution_estimation module
- aspire.utils.rotation module
Rotation
Rotation.about_axis()
Rotation.angle_dist()
Rotation.angles
Rotation.apply_registration()
Rotation.as_rotvec()
Rotation.common_lines()
Rotation.dtype
Rotation.find_registration()
Rotation.from_euler()
Rotation.from_matrix()
Rotation.from_rotvec()
Rotation.generate_random_rotations()
Rotation.invert()
Rotation.matrices
Rotation.mean_angular_distance()
Rotation.mse()
Rotation.register()
- aspire.utils.types module
- aspire.utils.units module
- Module contents
- aspire.volume package
- Submodules
- aspire.volume.symmetry_groups module
- aspire.volume.volume module
BasisVolume
BispecVolume
CartesianVolume
FBBasisVolume
PolarVolume
Volume
Volume.T
Volume.asnumpy()
Volume.astype()
Volume.denoise()
Volume.downsample()
Volume.empty_like()
Volume.flatten()
Volume.flip()
Volume.from_vec()
Volume.fsc()
Volume.load()
Volume.project()
Volume.rotate()
Volume.save()
Volume.shift()
Volume.stack_reshape()
Volume.symmetry_group
Volume.to_vec()
Volume.transpose()
Volume.zeros_like()
qr_vols_forward()
rotated_grids()
rotated_grids_3d()
- aspire.volume.volume_synthesis module
- Module contents
Submodules¶
aspire.exceptions module¶
- exception aspire.exceptions.AspireException¶
Bases:
Exception
- exception aspire.exceptions.DimensionsIncompatible¶
Bases:
AspireException
- exception aspire.exceptions.ErrorTooBig¶
Bases:
AspireException
- exception aspire.exceptions.UnknownFormat¶
Bases:
AspireException
- exception aspire.exceptions.WrongInput¶
Bases:
AspireException
- aspire.exceptions.handle_exception(exc_type, exc_value, exc_traceback)¶
Handle any top-level unhandled exception. Tries to gather and log additional context information, then re-raises.
- Parameters:
exc_type – Exception type object
exc_value – Exception value object (an instance of type exc_type)
exc_traceback – The Traceback object associated with exc_value (also available as exc_value.__traceback__)
- Returns:
On return, useful diagnostic information has been logged, and the exception re-raised.