Index

A

about_axis() (aspire.utils.rotation.Rotation static method) abs() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) abs2() (in module aspire.utils.misc) acorr() (in module aspire.utils.matrix) adaptive_support() (in module aspire.denoising.adaptive_support) Add (class in aspire.image.xform) add() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) add_xform() (aspire.image.xform.Pipeline method) add_xforms() (aspire.image.xform.Pipeline method) adjoint() (aspire.image.xform.LinearXform method) (aspire.nufft.finufft.FinufftPlan method) ainner() (in module aspire.utils.matrix) align() (aspire.classification.averager2d.AligningAverager2D method) (aspire.classification.averager2d.BFRAverager2D method) (aspire.classification.averager2d.BFSRAverager2D method) (aspire.classification.averager2d.BFSReddyChatterjiAverager2D method) (aspire.classification.averager2d.ReddyChatterjiAverager2D method) align_BO() (in module aspire.utils.bot_align) AligningAverager2D (class in aspire.classification.averager2d) all_backends() (in module aspire.nufft) all_besselj_zeros() (in module aspire.basis.basis_utils) all_pairs() (in module aspire.utils.misc) all_triplets() (in module aspire.utils.misc) amean (aspire.storage.mrc.MrcStats property) amplitudes (aspire.source.image.ImageSource property) analyze_correlations() (aspire.utils.resolution_estimation.FourierCorrelation method) angle_dist() (aspire.utils.rotation.Rotation static method) angles (aspire.source.image.ImageSource property) (aspire.utils.rotation.Rotation property) AnisotropicNoiseEstimator (class in aspire.noise.noise) anorm() (in module aspire.utils.matrix) anufft() (in module aspire.nufft) append() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) Apple (class in aspire.apple.apple) apply() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) apply_kernel() (aspire.covariance.covar.CovarianceEstimator method) (aspire.reconstruction.estimator.Estimator method) (aspire.reconstruction.mean.MeanEstimator method) (aspire.reconstruction.mean.WeightedVolumesEstimator method) apply_registration() (aspire.utils.rotation.Rotation method) arms (aspire.storage.mrc.MrcStats property) ArrayFilter (class in aspire.operators.filters) ArrayImageSource (class in aspire.source.image) ArrayMicrographSource (class in aspire.source.micrograph) as_blk_diag() (aspire.operators.diag_matrix.DiagMatrix method) as_rotvec() (aspire.utils.rotation.Rotation method) asnumpy() (aspire.basis.basis.Coef method) (aspire.image.image.Image method) (aspire.numeric.numpy.Numpy static method) (aspire.operators.diag_matrix.DiagMatrix method) (aspire.sinogram.sinogram.Sinogram method) (aspire.source.micrograph.MicrographSource method) (aspire.volume.volume.Volume method) aspire module aspire.abinitio module 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 aspire.apple module aspire.apple.apple module aspire.apple.helper module aspire.apple.picking module aspire.basis module 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 aspire.basis.pswf_2d module aspire.basis.pswf_3d module aspire.basis.pswf_utils module aspire.basis.steerable module aspire.classification module aspire.classification.averager2d module aspire.classification.class2d module aspire.classification.class_selection module aspire.classification.legacy_implementations module aspire.classification.reddy_chatterji module aspire.classification.rir_class2d module aspire.commands module aspire.commands.apple module aspire.commands.cov3d module aspire.commands.denoise module aspire.commands.estimate_ctf module aspire.commands.extract_particles module aspire.commands.orient3d module aspire.commands.preprocess module

aspire.covariance module aspire.covariance.covar module aspire.covariance.covar2d module aspire.ctf module aspire.ctf.ctf_estimator module aspire.denoising module aspire.denoising.adaptive_support module aspire.denoising.class_avg module aspire.denoising.denoised_src module aspire.denoising.denoiser module aspire.denoising.denoiser_cov2d module aspire.downloader module aspire.downloader.data_fetcher module aspire.downloader.registry module aspire.exceptions module aspire.image module aspire.image.image module aspire.image.image_stacker module aspire.image.xform module aspire.noise module aspire.noise.noise module aspire.nufft module aspire.nufft.finufft module aspire.nufft.utils module aspire.numeric module aspire.numeric.base_fft module aspire.numeric.complex_pca module aspire.numeric.complex_pca.complex_pca module aspire.numeric.complex_pca.validation module aspire.numeric.numpy module aspire.numeric.scipy module aspire.numeric.scipy_fft module aspire.operators module aspire.operators.blk_diag_matrix module aspire.operators.diag_matrix module aspire.operators.filters module aspire.operators.polar_ft module aspire.operators.wemd module aspire.optimization module aspire.optimization.conj_grad module aspire.reconstruction module aspire.reconstruction.estimator module aspire.reconstruction.kernel module aspire.reconstruction.mean module aspire.sinogram module aspire.sinogram.sinogram module aspire.source module aspire.source.coordinates module aspire.source.image module aspire.source.micrograph module aspire.source.relion module aspire.source.simulation module aspire.storage module aspire.storage.mrc module aspire.storage.starfile module aspire.utils module 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 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 aspire.utils.types module aspire.utils.units module aspire.volume module aspire.volume.symmetry_groups module aspire.volume.volume module aspire.volume.volume_synthesis module AspireException astype() (aspire.volume.volume.Volume method) AsymmetricVolume (class in aspire.volume.volume_synthesis) available_downloads() (in module aspire.downloader.data_fetcher) average() (aspire.classification.averager2d.AligningAverager2D method) (aspire.classification.averager2d.Averager2D method) (aspire.classification.averager2d.BFSReddyChatterjiAverager2D method) (aspire.classification.averager2d.ReddyChatterjiAverager2D method) Averager2D (class in aspire.classification.averager2d)

B

backend_available() (in module aspire.nufft) background_subtract_1d() (aspire.ctf.ctf_estimator.CtfEstimator method) background_subtract_2d() (aspire.ctf.ctf_estimator.CtfEstimator method) backproject() (aspire.image.image.Image method) (aspire.sinogram.sinogram.Sinogram method) BandedSNRImageQualityFunction (class in aspire.classification.class_selection) BandpassImageQualityFunction (class in aspire.classification.class_selection) barycentric_interp_sparse() (in module aspire.basis.fle_2d_utils) Basis (class in aspire.basis.basis) basis_mat() (aspire.operators.filters.Filter method) basis_norm_2d() (aspire.basis.fb_2d.FBBasis2D method) basis_norm_3d() (aspire.basis.fb_3d.FBBasis3D method) BasisImage (class in aspire.image.image) BasisVolume (class in aspire.volume.volume) BatchedRotCov2D (class in aspire.covariance.covar2d) besselj_newton() (in module aspire.basis.basis_utils) besselj_zeros() (in module aspire.basis.basis_utils) best_rank1_approximation() (in module aspire.utils.matrix) BFRAverager2D (class in aspire.classification.averager2d) BFSRAverager2D (class in aspire.classification.averager2d)

BFSReddyChatterjiAverager2D (class in aspire.classification.averager2d) bispec_2drot_large() (in module aspire.classification.legacy_implementations) bispec_operator_1() (in module aspire.classification.legacy_implementations) BispecImage (class in aspire.image.image) bispectrum() (aspire.classification.rir_class2d.RIRClass2D method) BispecVolume (class in aspire.volume.volume) blk_diag_cov_shape (aspire.basis.steerable.SteerableBasis2D property) BlkDiagMatrix (class in aspire.operators.blk_diag_matrix) BlueFilter (class in aspire.operators.filters) BlueNoiseAdder (class in aspire.noise.noise) BNMatrix (class in aspire.basis.pswf_utils) BoxesCoordinateSource (class in aspire.source.coordinates) build() (aspire.basis.fspca.FSPCABasis method) build_clmatrix() (aspire.abinitio.commonline_base.CLOrient3D method) (aspire.abinitio.commonline_c2.CLSymmetryC2 method) build_denoiser() (aspire.denoising.denoiser_cov2d.DenoiserCov2D method) bump_3d() (in module aspire.utils.misc) BumpWeightedImageQualityMixin (class in aspire.classification.class_selection) BumpWeightedVarianceImageQualityFunction (class in aspire.classification.class_selection) by_indices() (aspire.basis.basis.Coef method)

C

cache() (aspire.source.image.ImageSource method) calculate_bispectrum() (aspire.basis.fb_2d.FBBasis2D method) (aspire.basis.fspca.FSPCABasis method) (aspire.basis.steerable.SteerableBasis2D method) cart2pol() (in module aspire.utils.coor_trans) cart2sph() (in module aspire.utils.coor_trans) CartesianImage (class in aspire.image.image) CartesianVolume (class in aspire.volume.volume) Cell2D (class in aspire.utils.cell) centered_fft() (aspire.numeric.base_fft.FFT method) centered_fft2() (aspire.numeric.base_fft.FFT method) centered_fftn() (aspire.numeric.base_fft.FFT method) centered_ifft() (aspire.numeric.base_fft.FFT method) centered_ifft2() (aspire.numeric.base_fft.FFT method) centered_ifftn() (aspire.numeric.base_fft.FFT method) CentersCoordinateSource (class in aspire.source.coordinates) cg() (in module aspire.numeric.scipy) check_array() (in module aspire.numeric.complex_pca.validation) check_backends() (in module aspire.nufft) check_besselj_zeros() (in module aspire.basis.basis_utils) check_psd() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) choice() (in module aspire.utils.random) circ() (in module aspire.utils.misc) circularize() (aspire.reconstruction.kernel.FourierKernel method) (aspire.reconstruction.kernel.FourierKernelMatrix method) circularize_1d() (aspire.reconstruction.kernel.FourierKernel method) cl_angles_to_ind() (aspire.abinitio.commonline_c3_c4.CLSymmetryC3C4 static method) Class2D (class in aspire.classification.class2d) class_distances (aspire.denoising.class_avg.ClassAvgSource property) (aspire.source.image.ImageSource property) class_indices (aspire.denoising.class_avg.ClassAvgSource property) (aspire.source.image.ImageSource property) class_refl (aspire.denoising.class_avg.ClassAvgSource property) (aspire.source.image.ImageSource property) ClassAvgSource (class in aspire.denoising.class_avg) ClassAvgSourcev110 (class in aspire.denoising.class_avg) classify() (aspire.classification.class2d.Class2D method) (aspire.classification.rir_class2d.RIRClass2D method) ClassSelector (class in aspire.classification.class_selection) clean_images (aspire.source.micrograph.MicrographSimulation property) (aspire.source.simulation.Simulation property) CLOrient3D (class in aspire.abinitio.commonline_base) CLSymmetryC2 (class in aspire.abinitio.commonline_c2)

CLSymmetryC3C4 (class in aspire.abinitio.commonline_c3_c4) CLSymmetryCn (class in aspire.abinitio.commonline_cn) CLSymmetryD2 (class in aspire.abinitio.commonline_d2) CLSync3N (class in aspire.abinitio.commonline_sync3n) CLSyncVoting (class in aspire.abinitio.commonline_sync) CnSymmetricVolume (class in aspire.volume.volume_synthesis) CnSymmetryGroup (class in aspire.volume.symmetry_groups) Coef (class in aspire.basis.basis) CommLineEV (class in aspire.abinitio.commonline_ev) CommLineGCAR (class in aspire.abinitio.commonline_gcar) CommLineLUD (class in aspire.abinitio.commonline_lud) common_line_from_rots() (in module aspire.utils.coor_trans) common_lines() (aspire.utils.rotation.Rotation method) CommonlineSDP (class in aspire.abinitio.commonline_sdp) complex_rotate() (aspire.basis.steerable.SteerableBasis2D method) complex_type() (in module aspire.utils.types) ComplexCoef (class in aspire.basis.basis) ComplexPCA (class in aspire.numeric.complex_pca.complex_pca) compute_kernel() (aspire.covariance.covar.CovarianceEstimator method) (aspire.reconstruction.estimator.Estimator method) (aspire.reconstruction.mean.MeanEstimator method) (aspire.reconstruction.mean.WeightedVolumesEstimator method) conj_grad() (aspire.covariance.covar.CovarianceEstimator method) (aspire.reconstruction.mean.WeightedVolumesEstimator method) (in module aspire.optimization.conj_grad) convolve_volume() (aspire.reconstruction.kernel.FourierKernel method) (aspire.reconstruction.kernel.FourierKernelMatrix method) convolve_volume_matrix() (aspire.reconstruction.kernel.FourierKernel method) (aspire.reconstruction.kernel.FourierKernelMatrix method) CoordinateSource (class in aspire.source.coordinates) copy() (aspire.basis.basis.Coef method) (aspire.image.image.Image method) (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) (aspire.sinogram.sinogram.Sinogram method) correlations (aspire.utils.resolution_estimation.FourierCorrelation property) covar_true() (aspire.source.simulation.Simulation method) CovarianceEstimator (class in aspire.covariance.covar) crop_pad_2d() (in module aspire.utils.coor_trans) crop_pad_3d() (in module aspire.utils.coor_trans) CtfEstimator (class in aspire.ctf.ctf_estimator) CTFFilter (class in aspire.operators.filters) CustomNoiseAdder (class in aspire.noise.noise) cyclic_rotations() (in module aspire.utils.misc)

D

d_decay_approx_fun() (in module aspire.basis.basis_utils) dct() (aspire.numeric.scipy_fft.ScipyFFT method) DebugClassAvgSource (class in aspire.denoising.class_avg) default_opt (aspire.denoising.denoiser_cov2d.DenoiserCov2D attribute) DefaultClassAvgSource() (in module aspire.denoising.class_avg) denoise (aspire.denoising.denoiser.Denoiser property) denoise() (aspire.volume.volume.Volume method) DenoisedSource (class in aspire.denoising.denoised_src) Denoiser (class in aspire.denoising.denoiser) DenoiserCov2D (class in aspire.denoising.denoiser_cov2d) dense() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) dense_mat() (aspire.basis.pswf_utils.BNMatrix method) diag() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) DiagMatrix (class in aspire.operators.diag_matrix) dict_to_relion_types() (in module aspire.utils.relion_interop)

dim (aspire.utils.resolution_estimation.FourierRingCorrelation attribute) (aspire.utils.resolution_estimation.FourierShellCorrelation attribute) DimensionsIncompatible disabled() (aspire.image.xform.Xform method) DiskMicrographSource (class in aspire.source.micrograph) DistanceClassSelector (class in aspire.classification.class_selection) DnSymmetricVolume (class in aspire.volume.volume_synthesis) DnSymmetryGroup (class in aspire.volume.symmetry_groups) download_all() (in module aspire.downloader.data_fetcher) Downsample (class in aspire.image.xform) downsample() (aspire.image.image.Image method) (aspire.source.image.ImageSource method) (aspire.volume.volume.Volume method) dtype (aspire.abinitio.commonline_cn.MeanOuterProductEstimator attribute) (aspire.utils.rotation.Rotation property) dual() (aspire.operators.filters.Filter method) DualFilter (class in aspire.operators.filters)

E

eigen_images() (aspire.basis.fspca.FSPCABasis method) eigs() (aspire.source.simulation.Simulation method) (in module aspire.utils.matrix) eigvals (aspire.basis.fspca.FSPCABasis property) eigvals() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) elliptical_average() (aspire.ctf.ctf_estimator.CtfEstimator method) EMAverager2D (class in aspire.classification.averager2d) emdb_10835() (in module aspire.downloader.data_fetcher) emdb_14621() (in module aspire.downloader.data_fetcher) emdb_2484() (in module aspire.downloader.data_fetcher) emdb_2660() (in module aspire.downloader.data_fetcher) emdb_2824() (in module aspire.downloader.data_fetcher) emdb_2984() (in module aspire.downloader.data_fetcher) emdb_3645() (in module aspire.downloader.data_fetcher) emdb_4905() (in module aspire.downloader.data_fetcher) emdb_5778() (in module aspire.downloader.data_fetcher) emdb_6287() (in module aspire.downloader.data_fetcher) emdb_6458() (in module aspire.downloader.data_fetcher) emdb_8012() (in module aspire.downloader.data_fetcher) emdb_8511() (in module aspire.downloader.data_fetcher) empty() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) (aspire.operators.diag_matrix.DiagMatrix static method) empty_like() (aspire.volume.volume.Volume static method) enabled() (aspire.image.xform.Xform method) ErrorTooBig estimate() (aspire.abinitio.commonline_ev.CommLineEV method) (aspire.abinitio.commonline_gcar.CommLineGCAR method) (aspire.abinitio.commonline_lud.CommLineLUD method) (aspire.covariance.covar.CovarianceEstimator method) (aspire.noise.noise.AnisotropicNoiseEstimator method) (aspire.noise.noise.NoiseEstimator method) (aspire.noise.noise.WhiteNoiseEstimator method) (aspire.reconstruction.estimator.Estimator method) estimate_ctf() (in module aspire.ctf.ctf_estimator) estimate_noise_power() (aspire.source.image.ImageSource method) estimate_noise_psd() (aspire.noise.noise.AnisotropicNoiseEstimator method) estimate_psd() (aspire.ctf.ctf_estimator.CtfEstimator method) estimate_rotations() (aspire.abinitio.commonline_base.CLOrient3D method) (aspire.abinitio.commonline_c2.CLSymmetryC2 method) (aspire.abinitio.commonline_c3_c4.CLSymmetryC3C4 method) (aspire.abinitio.commonline_cn.CLSymmetryCn method) (aspire.abinitio.commonline_d2.CLSymmetryD2 method) (aspire.abinitio.commonline_sdp.CommonlineSDP method) (aspire.abinitio.commonline_sync.CLSyncVoting method) (aspire.abinitio.commonline_sync3n.CLSync3N method)

estimate_shifts() (aspire.abinitio.commonline_base.CLOrient3D method) estimate_signal_mean_energy() (aspire.source.image.ImageSource method) estimate_signal_power() (aspire.source.image.ImageSource method) estimate_signal_var() (aspire.source.image.ImageSource method) estimate_snr() (aspire.source.image.ImageSource method) Estimator (class in aspire.reconstruction.estimator) eval_clustering() (aspire.source.simulation.Simulation method) eval_coords() (aspire.source.simulation.Simulation method) eval_covar() (aspire.source.simulation.Simulation method) eval_eigs() (aspire.source.simulation.Simulation method) eval_mean() (aspire.source.simulation.Simulation method) eval_vol() (aspire.source.simulation.Simulation method) eval_volmat() (aspire.source.simulation.Simulation method) evaluate() (aspire.basis.basis.Basis method) (aspire.basis.basis.Coef method) (aspire.basis.basis.ComplexCoef method) (aspire.basis.fspca.FSPCABasis method) (aspire.image.image.BasisImage method) (aspire.operators.filters.DualFilter method) (aspire.operators.filters.Filter method) (aspire.volume.volume.BasisVolume method) evaluate_grid() (aspire.operators.filters.ArrayFilter method) (aspire.operators.filters.Filter method) (aspire.operators.filters.PowerFilter method) evaluate_src_filters_on_grid() (in module aspire.operators.filters) evaluate_t() (aspire.basis.basis.Basis method) evaluate_to_image_basis() (aspire.basis.fspca.FSPCABasis method) expand() (aspire.basis.basis.Basis method) (aspire.basis.fspca.FSPCABasis method) (aspire.image.image.BispecImage method) (aspire.image.image.CartesianImage method) (aspire.image.image.PolarImage method) (aspire.volume.volume.BispecVolume method) (aspire.volume.volume.CartesianVolume method) (aspire.volume.volume.PolarVolume method) expand_from_image_basis() (aspire.basis.fspca.FSPCABasis method) extensions (aspire.image.image.Image attribute) extract_particles() (aspire.apple.picking.Picker method) extract_query() (aspire.apple.helper.PickerHelper class method) extract_references() (aspire.apple.helper.PickerHelper class method) extract_windows() (aspire.apple.helper.PickerHelper class method) eye() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) (aspire.operators.diag_matrix.DiagMatrix static method) eye_like() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method)

F

FBBasis2D (class in aspire.basis.fb_2d) FBBasis3D (class in aspire.basis.fb_3d) FBBasisImage (class in aspire.image.image) FBBasisMixin (class in aspire.basis.fb) FBBasisVolume (class in aspire.volume.volume) fetch_data() (in module aspire.downloader.data_fetcher) FFBBasis2D (class in aspire.basis.ffb_2d) FFBBasis3D (class in aspire.basis.ffb_3d) FFT (class in aspire.numeric.base_fft) fft() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) fft2() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) fft_object() (in module aspire.numeric) fftn() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) fftshift() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) fill_struct() (in module aspire.optimization.conj_grad) Filter (class in aspire.operators.filters) filter() (aspire.image.image.Image method) (aspire.utils.logging.LogFilterByCount method) filter_indices (aspire.source.image.ImageSource property) filter_to_basis_mat() (aspire.basis.fb_2d.FBBasis2D method) (aspire.basis.ffb_2d.FFBBasis2D method) (aspire.basis.fle_2d.FLEBasis2D method) (aspire.basis.fpswf_2d.FPSWFBasis2D method) (aspire.basis.fspca.FSPCABasis method) (aspire.basis.pswf_2d.PSWFBasis2D method) (aspire.basis.steerable.SteerableBasis2D method)

FilterXform (class in aspire.image.xform) find_registration() (aspire.utils.rotation.Rotation method) FinufftPlan (class in aspire.nufft.finufft) fix_signs() (in module aspire.utils.matrix) flatten() (aspire.volume.volume.Volume method) FLEBasis2D (class in aspire.basis.fle_2d) flip() (aspire.image.image.Image method) (aspire.volume.volume.Volume method) forward() (aspire.image.xform.Xform method) FourierCorrelation (class in aspire.utils.resolution_estimation) FourierKernel (class in aspire.reconstruction.kernel) FourierKernelMatrix (class in aspire.reconstruction.kernel) FourierRingCorrelation (class in aspire.utils.resolution_estimation) FourierShellCorrelation (class in aspire.utils.resolution_estimation) FPSWFBasis2D (class in aspire.basis.fpswf_2d) FPSWFBasis3D (class in aspire.basis.fpswf_3d) frc() (aspire.image.image.Image method) from_dense() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) from_euler() (aspire.utils.rotation.Rotation static method) from_list() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) from_matrix() (aspire.utils.rotation.Rotation static method) from_rotvec() (aspire.utils.rotation.Rotation static method) from_snr() (aspire.noise.noise.WhiteNoiseAdder class method) from_vec() (aspire.volume.volume.Volume class method) fsc() (aspire.volume.volume.Volume method) FSPCABasis (class in aspire.basis.fspca) FTKAverager2D (class in aspire.classification.averager2d) FunctionFilter (class in aspire.operators.filters) fuzzy_mask() (in module aspire.utils.misc)

G

g_sync() (aspire.abinitio.commonline_c3_c4.CLSymmetryC3C4 static method) gaussian_1d() (in module aspire.utils.misc) gaussian_2d() (in module aspire.utils.misc) gaussian_3d() (in module aspire.utils.misc) gaussian_filter() (aspire.apple.helper.PickerHelper class method) GaussianBlobsVolume (class in aspire.volume.volume_synthesis) gd() (aspire.ctf.ctf_estimator.CtfEstimator method) generate() (aspire.volume.volume_synthesis.GaussianBlobsVolume method) (aspire.volume.volume_synthesis.LegacyVolume method) (aspire.volume.volume_synthesis.SyntheticVolumeBase method) generate_candidate_rots() (aspire.abinitio.commonline_cn.CLSymmetryCn static method) generate_ctf() (aspire.ctf.ctf_estimator.CtfEstimator method) generate_random_rotations() (aspire.utils.rotation.Rotation static method) generate_rotations() (aspire.volume.symmetry_groups.CnSymmetryGroup method) (aspire.volume.symmetry_groups.DnSymmetryGroup method) (aspire.volume.symmetry_groups.OSymmetryGroup method) (aspire.volume.symmetry_groups.SymmetryGroup method) (aspire.volume.symmetry_groups.TSymmetryGroup method) get_aligned_rotations() (in module aspire.utils.coor_trans) get_block_by_index() (aspire.storage.starfile.StarFile method) get_covar() (aspire.covariance.covar2d.BatchedRotCov2D method) (aspire.covariance.covar2d.RotCov2D method)

get_cwf_coefs() (aspire.covariance.covar2d.BatchedRotCov2D method) (aspire.covariance.covar2d.RotCov2D method) get_eig_vectors() (aspire.basis.pswf_utils.BNMatrix method) get_full_version() (in module aspire.utils.logging) get_maps() (aspire.apple.picking.Picker method) get_mean() (aspire.covariance.covar2d.BatchedRotCov2D method) (aspire.covariance.covar2d.RotCov2D method) get_merged_data_block() (aspire.utils.relion_interop.RelionStarFile method) get_metadata() (aspire.source.image.ImageSource method) (aspire.source.image.OrientedSource method) get_micrograph_index() (aspire.source.micrograph.MicrographSimulation method) get_particle_indices() (aspire.source.micrograph.MicrographSimulation method) get_rots_mse() (in module aspire.utils.coor_trans) get_training_set() (aspire.apple.helper.PickerHelper class method) getConsoleLoggingLevel() (in module aspire.utils.logging) getFileLoggingLevel() (in module aspire.utils.logging) GlobalClassSelector (class in aspire.classification.class_selection) GlobalWithRepulsionClassSelector (class in aspire.classification.class_selection) GreedyClassRepulsionMixin (class in aspire.classification.class_selection) grid_1d() (in module aspire.utils.coor_trans) grid_2d() (in module aspire.utils.coor_trans) grid_3d() (in module aspire.utils.coor_trans)

H

half_to_full() (aspire.operators.polar_ft.PolarFT static method) handle_exception() (in module aspire.exceptions)

has_metadata() (aspire.source.image.ImageSource method) heap_ids (aspire.classification.class_selection.GlobalClassSelector property) heap_idx_map (aspire.classification.class_selection.GlobalClassSelector property)

I

idct() (aspire.numeric.scipy_fft.ScipyFFT method) IdentityFilter (class in aspire.operators.filters) IdentitySymmetryGroup (class in aspire.volume.symmetry_groups) ifft() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) ifft2() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) ifftn() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) ifftshift() (aspire.numeric.base_fft.FFT method) (aspire.numeric.scipy_fft.ScipyFFT method) im_backward() (aspire.source.image.ImageSource method) im_to_vec() (in module aspire.utils.matrix) Image (class in aspire.image.image) ImageQualityFunction (class in aspire.classification.class_selection) images (aspire.source.image.ImageSource property) (aspire.source.micrograph.MicrographSource property)

ImageSource (class in aspire.source.image) ImageStacker (class in aspire.image.image_stacker) import_aspire_ctf() (aspire.source.coordinates.CoordinateSource method) import_relion_ctf() (aspire.source.coordinates.CoordinateSource method) importlib_path() (in module aspire.utils.misc) IndexedSource (class in aspire.source.image) IndexedXform (class in aspire.image.xform) indices() (aspire.basis.fb_3d.FBBasis3D method) indices_mask() (aspire.basis.steerable.SteerableBasis2D method) inverse_r() (in module aspire.utils.misc) invert() (aspire.utils.rotation.Rotation method) invert_contrast() (aspire.source.image.ImageSource method) irfft() (aspire.numeric.scipy_fft.ScipyFFT method) is_scalar_type() (in module aspire.operators.blk_diag_matrix) is_square (aspire.operators.blk_diag_matrix.BlkDiagMatrix property) isfinite (aspire.operators.blk_diag_matrix.BlkDiagMatrix property)

J

J_conjugate() (in module aspire.utils.misc)

K

k_operator() (in module aspire.basis.basis_utils)

Kernel (class in aspire.reconstruction.kernel)

L

LambdaFilter (class in aspire.operators.filters) LambdaXform (class in aspire.image.xform) LegacyVolume (class in aspire.volume.volume_synthesis) lgwt() (in module aspire.basis.basis_utils) LinearIndexedXform (class in aspire.image.xform) LinearPipeline (class in aspire.image.xform)

LinearXform (class in aspire.image.xform) load() (aspire.image.image.Image static method) (aspire.volume.volume.Volume class method) load_mrc() (in module aspire.image.image) load_tiff() (in module aspire.image.image) LogFilterByCount (class in aspire.utils.logging) lowpass() (aspire.basis.fle_2d.FLEBasis2D method)

M

m_flatten() (in module aspire.utils.matlab_compat) m_reshape() (in module aspire.utils.matlab_compat) make_psd() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (in module aspire.utils.matrix) make_symmat() (in module aspire.utils.matrix) mat2cell() (aspire.utils.cell.Cell2D method) mat_evaluate() (aspire.basis.basis.Basis method) mat_evaluate_t() (aspire.basis.basis.Basis method) mat_to_vec() (in module aspire.utils.matrix) matmul() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) matrices (aspire.utils.rotation.Rotation property) (aspire.volume.symmetry_groups.SymmetryGroup property) matrix_type (aspire.basis.fle_2d.FLEBasis2D attribute) (aspire.basis.pswf_2d.PSWFBasis2D attribute) (aspire.basis.steerable.SteerableBasis2D attribute) mdim_fftshift() (aspire.numeric.base_fft.FFT method) mdim_ifftshift() (aspire.numeric.base_fft.FFT method) mdim_mat_fun_conj() (in module aspire.utils.matrix) mean_aligned_angular_distance() (in module aspire.utils.coor_trans) mean_angular_distance() (aspire.utils.rotation.Rotation static method) mean_true() (aspire.source.simulation.Simulation method) MeanEstimator (class in aspire.reconstruction.mean) MeanImageStacker (class in aspire.image.image_stacker) MeanOuterProductEstimator (class in aspire.abinitio.commonline_cn) MedianImageStacker (class in aspire.image.image_stacker) mem_based_cpu_suggestion() (in module aspire.utils.multiprocessing) micrograph_to_blocks() (aspire.ctf.ctf_estimator.CtfEstimator method) MicrographSimulation (class in aspire.source.micrograph) MicrographSource (class in aspire.source.micrograph) module aspire aspire.abinitio aspire.abinitio.commonline_base aspire.abinitio.commonline_c2 aspire.abinitio.commonline_c3_c4 aspire.abinitio.commonline_cn aspire.abinitio.commonline_d2 aspire.abinitio.commonline_ev aspire.abinitio.commonline_gcar aspire.abinitio.commonline_lud aspire.abinitio.commonline_sdp aspire.abinitio.commonline_sync aspire.abinitio.commonline_sync3n aspire.abinitio.sync_voting aspire.apple aspire.apple.apple aspire.apple.helper aspire.apple.picking aspire.basis aspire.basis.basis aspire.basis.basis_utils aspire.basis.fb aspire.basis.fb_2d aspire.basis.fb_3d aspire.basis.ffb_2d aspire.basis.ffb_3d aspire.basis.fle_2d aspire.basis.fle_2d_utils aspire.basis.fpswf_2d aspire.basis.fpswf_3d aspire.basis.fspca aspire.basis.pswf_2d aspire.basis.pswf_3d aspire.basis.pswf_utils aspire.basis.steerable aspire.classification aspire.classification.averager2d aspire.classification.class2d aspire.classification.class_selection aspire.classification.legacy_implementations aspire.classification.reddy_chatterji aspire.classification.rir_class2d aspire.commands aspire.commands.apple aspire.commands.cov3d aspire.commands.denoise aspire.commands.estimate_ctf aspire.commands.extract_particles aspire.commands.orient3d aspire.commands.preprocess aspire.covariance aspire.covariance.covar aspire.covariance.covar2d aspire.ctf aspire.ctf.ctf_estimator aspire.denoising aspire.denoising.adaptive_support aspire.denoising.class_avg aspire.denoising.denoised_src aspire.denoising.denoiser aspire.denoising.denoiser_cov2d aspire.downloader aspire.downloader.data_fetcher aspire.downloader.registry aspire.exceptions aspire.image aspire.image.image aspire.image.image_stacker aspire.image.xform aspire.noise aspire.noise.noise aspire.nufft aspire.nufft.finufft aspire.nufft.utils aspire.numeric aspire.numeric.base_fft aspire.numeric.complex_pca aspire.numeric.complex_pca.complex_pca aspire.numeric.complex_pca.validation aspire.numeric.numpy aspire.numeric.scipy aspire.numeric.scipy_fft aspire.operators aspire.operators.blk_diag_matrix aspire.operators.diag_matrix aspire.operators.filters aspire.operators.polar_ft aspire.operators.wemd aspire.optimization aspire.optimization.conj_grad aspire.reconstruction aspire.reconstruction.estimator aspire.reconstruction.kernel aspire.reconstruction.mean aspire.sinogram aspire.sinogram.sinogram aspire.source aspire.source.coordinates aspire.source.image aspire.source.micrograph aspire.source.relion aspire.source.simulation aspire.storage aspire.storage.mrc aspire.storage.starfile aspire.utils aspire.utils.bot_align aspire.utils.cell aspire.utils.coor_trans aspire.utils.logging aspire.utils.matlab_compat aspire.utils.matrix aspire.utils.misc aspire.utils.multiprocessing aspire.utils.random aspire.utils.relion_interop aspire.utils.resolution_estimation aspire.utils.rotation aspire.utils.types aspire.utils.units aspire.volume aspire.volume.symmetry_groups aspire.volume.volume aspire.volume.volume_synthesis

moments() (aspire.apple.helper.PickerHelper class method) morphology_ops() (aspire.apple.picking.Picker method) MrcStats (class in aspire.storage.mrc) mse() (aspire.utils.rotation.Rotation method) msg_cache (aspire.utils.logging.LogFilterByCount attribute) mul() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) MultiplicativeFilter (class in aspire.operators.filters) Multiply (class in aspire.image.xform)

N

n (aspire.denoising.class_avg.ClassAvgSource property) (aspire.source.image.ImageSource property) n_blobs (aspire.volume.volume_synthesis.CnSymmetricVolume property) (aspire.volume.volume_synthesis.DnSymmetricVolume property) (aspire.volume.volume_synthesis.GaussianBlobsVolume property) (aspire.volume.volume_synthesis.OSymmetricVolume property) (aspire.volume.volume_synthesis.TSymmetricVolume property) n_ctf_filters (aspire.source.image.ImageSource property) nearest_rotations() (in module aspire.utils.matrix) neg() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) NeighborVarianceClassSelector (class in aspire.classification.class_selection) NeighborVarianceWithRepulsionClassSelector (class in aspire.classification.class_selection) nextpow2() (in module aspire.nufft.utils) nn_classification() (aspire.classification.rir_class2d.RIRClass2D method) noise_var (aspire.noise.noise.CustomNoiseAdder property) (aspire.noise.noise.NoiseAdder property) (aspire.noise.noise.WhiteNoiseAdder property)

NoiseAdder (class in aspire.noise.noise) NoiseEstimator (class in aspire.noise.noise) norm (aspire.operators.diag_matrix.DiagMatrix property) norm() (aspire.image.image.Image method) (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) norm_assoc_legendre() (in module aspire.basis.basis_utils) normalize_background() (aspire.source.image.ImageSource method) normalize_bg() (in module aspire.image.image) normalize_blocks() (aspire.ctf.ctf_estimator.CtfEstimator method) norms() (aspire.basis.basis.Basis method) (aspire.basis.fb_2d.FBBasis2D method) (aspire.basis.fb_3d.FBBasis3D method) nufft() (in module aspire.nufft) num_procs_suggestion() (in module aspire.utils.multiprocessing) numeric_object() (in module aspire.numeric) Numpy (class in aspire.numeric.numpy)

O

offsets (aspire.source.image.ImageSource property) ones() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) (aspire.operators.diag_matrix.DiagMatrix static method) opt1d() (aspire.ctf.ctf_estimator.CtfEstimator method) OrientedSource (class in aspire.source.image)

OSymmetricVolume (class in aspire.volume.volume_synthesis) OSymmetryGroup (class in aspire.volume.symmetry_groups) output() (aspire.abinitio.commonline_ev.CommLineEV method) (aspire.abinitio.commonline_gcar.CommLineGCAR method) (aspire.abinitio.commonline_lud.CommLineLUD method)

P

p_n() (in module aspire.basis.basis_utils) parse() (aspire.volume.symmetry_groups.SymmetryGroup static method) particle_image() (aspire.apple.apple.Apple method) partition (aspire.operators.blk_diag_matrix.BlkDiagMatrix property) pca() (aspire.classification.rir_class2d.RIRClass2D method) (aspire.ctf.ctf_estimator.CtfEstimator method) pca_y() (in module aspire.classification.legacy_implementations) pf (aspire.abinitio.commonline_base.CLOrient3D property) phase_flip() (aspire.source.image.ImageSource method) physical_core_cpu_suggestion() (in module aspire.utils.multiprocessing) Picker (class in aspire.apple.picking) PickerHelper (class in aspire.apple.helper) PinkFilter (class in aspire.operators.filters) PinkNoiseAdder (class in aspire.noise.noise) Pipeline (class in aspire.image.xform) Plan (class in aspire.nufft) plot() (aspire.utils.resolution_estimation.FourierCorrelation method) PoissonRejectionImageStacker (class in aspire.image.image_stacker) PolarFT (class in aspire.operators.polar_ft) PolarImage (class in aspire.image.image)

PolarVolume (class in aspire.volume.volume) populate_metadata() (aspire.source.relion.RelionSource method) pow() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) PowerFilter (class in aspire.operators.filters) powerset() (in module aspire.utils.misc) precomp_transform_complex_to_real() (in module aspire.basis.fle_2d_utils) preprocess_micrograph() (aspire.ctf.ctf_estimator.CtfEstimator method) process_folder() (aspire.apple.apple.Apple method) process_micrograph() (aspire.apple.apple.Apple method) process_micrograph_centers() (aspire.apple.apple.Apple method) process_micrograph_plots() (aspire.apple.apple.Apple method) project() (aspire.image.image.Image method) (aspire.volume.volume.Volume method) projections (aspire.source.simulation.Simulation property) pswf_func2d() (aspire.basis.pswf_2d.PSWFBasis2D method) PSWFBasis2D (class in aspire.basis.pswf_2d) PSWFBasis3D (class in aspire.basis.pswf_3d) push() (aspire.abinitio.commonline_cn.MeanOuterProductEstimator method) (aspire.storage.mrc.MrcStats method)

Q

qr_vols_forward() (in module aspire.volume.volume)

quality_scores (aspire.classification.class_selection.ClassSelector property) query_score() (aspire.apple.picking.Picker method)

R

radial_convolve() (aspire.basis.fle_2d.FLEBasis2D method) RadialCTFFilter (class in aspire.operators.filters) RampWeightedImageQualityMixin (class in aspire.classification.class_selection) RampWeightedVarianceImageQualityFunction (class in aspire.classification.class_selection) rand() (in module aspire.utils.random) randi() (in module aspire.utils.random) randn() (in module aspire.utils.random) Random (class in aspire.utils.random) random() (in module aspire.utils.random) RandomClassSelector (class in aspire.classification.class_selection) rapply() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) ratio_to_decibel() (in module aspire.utils.units) read_micrograph() (aspire.apple.picking.Picker method) real_sph_harmonic() (in module aspire.basis.basis_utils) real_type() (in module aspire.utils.types) reddy_chatterji_register() (in module aspire.classification.reddy_chatterji) ReddyChatterjiAverager2D (class in aspire.classification.averager2d) reference_size() (aspire.apple.helper.PickerHelper class method) register() (aspire.utils.rotation.Rotation method) register_rotations() (in module aspire.utils.coor_trans) relative_rots_to_cl_indices() (aspire.abinitio.commonline_cn.CLSymmetryCn static method)

RelionSource (class in aspire.source.relion) RelionStarFile (class in aspire.utils.relion_interop) remove_downloads() (in module aspire.downloader.data_fetcher) res (aspire.image.image.Image property) reset() (aspire.image.xform.Pipeline method) reset_cache() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) rfft() (aspire.numeric.scipy_fft.ScipyFFT method) rfftfreq() (aspire.numeric.scipy_fft.ScipyFFT method) RIRClass2D (class in aspire.classification.rir_class2d) RobustChauvenetRejectionImageStacker (class in aspire.image.image_stacker) roll_dim() (in module aspire.utils.matrix) rotate() (aspire.basis.basis.Coef method) (aspire.basis.basis.ComplexCoef method) (aspire.basis.steerable.SteerableBasis2D method) (aspire.image.image.Image method) (aspire.volume.volume.Volume method) rotated_grids() (in module aspire.volume.volume) rotated_grids_3d() (in module aspire.volume.volume) Rotation (class in aspire.utils.rotation) rotations (aspire.source.image.ImageSource property) RotCov2D (class in aspire.covariance.covar2d) rots_to_clmatrix() (in module aspire.utils.coor_trans) run_svm() (aspire.apple.picking.Picker method)

S

save() (aspire.denoising.class_avg.ClassAvgSource method) (aspire.image.image.Image method) (aspire.source.image.ImageSource method) (aspire.source.micrograph.MicrographSimulation method) (aspire.source.micrograph.MicrographSource method) (aspire.volume.volume.Volume method) save_images() (aspire.source.image.ImageSource method) save_metadata() (aspire.source.image.ImageSource method) (aspire.source.image.OrientedSource method) ScalarFilter (class in aspire.operators.filters) scale() (aspire.operators.filters.CTFFilter method) (aspire.operators.filters.Filter method) ScaledFilter (class in aspire.operators.filters) ScipyFFT (class in aspire.numeric.scipy_fft) select() (aspire.classification.class_selection.ClassSelector method) selection_indices (aspire.denoising.class_avg.ClassAvgSource property) (aspire.source.image.ImageSource property) set_angle() (aspire.ctf.ctf_estimator.CtfEstimator method) set_df1() (aspire.ctf.ctf_estimator.CtfEstimator method) set_df2() (aspire.ctf.ctf_estimator.CtfEstimator method) set_metadata() (aspire.source.image.ImageSource method) setConsoleLoggingLevel() (in module aspire.utils.logging) setFileLoggingLevel() (in module aspire.utils.logging) sha256sum() (in module aspire.utils.misc) shape() (aspire.basis.pswf_utils.BNMatrix method) Shift (class in aspire.image.xform) shift() (aspire.basis.basis.Coef method) (aspire.basis.basis.ComplexCoef method) (aspire.basis.fspca.FSPCABasis method) (aspire.basis.steerable.SteerableBasis2D method) (aspire.image.image.Image method) (aspire.volume.volume.Volume method) show() (aspire.image.image.Image method) (aspire.source.micrograph.MicrographSource method) shrink_covar() (in module aspire.covariance.covar2d) shrink_covar_backward() (aspire.covariance.covar2d.RotCov2D method) SigmaRejectionImageStacker (class in aspire.image.image_stacker) sign (aspire.operators.filters.Filter property)

signal_power (aspire.noise.noise.WhiteNoiseAdder property) simulated_channelspin() (in module aspire.downloader.data_fetcher) Simulation (class in aspire.source.simulation) Sinogram (class in aspire.sinogram.sinogram) size (aspire.basis.basis.Coef property) (aspire.image.image.Image property) solve() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) sparse_object() (in module aspire.numeric) sph_bessel() (in module aspire.basis.basis_utils) sph_harm() (in module aspire.basis.basis_utils) sqrt() (aspire.image.image.Image method) src_backward() (aspire.covariance.covar.CovarianceEstimator method) (aspire.reconstruction.mean.WeightedVolumesEstimator method) src_wiener_coords() (in module aspire.denoising.denoiser_cov2d) stable_eigsh() (in module aspire.utils.matlab_compat) stack_reshape() (aspire.basis.basis.Coef method) (aspire.image.image.Image method) (aspire.operators.diag_matrix.DiagMatrix method) (aspire.sinogram.sinogram.Sinogram method) (aspire.volume.volume.Volume method) StarFile (class in aspire.storage.starfile) StarFileError states (aspire.source.image.ImageSource property) SteerableBasis2D (class in aspire.basis.steerable) sub() (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) support_mask() (in module aspire.utils.misc) symmat_to_vec() (in module aspire.utils.matrix) symmat_to_vec_iso() (in module aspire.utils.matrix) SymmetricXform (class in aspire.image.xform) symmetry_group (aspire.source.image.ImageSource property) (aspire.volume.volume.Volume property) (aspire.volume.volume_synthesis.GaussianBlobsVolume property) SymmetryGroup (class in aspire.volume.symmetry_groups) synchronized_mean() (aspire.abinitio.commonline_cn.MeanOuterProductEstimator method) syncmatrix_vote() (aspire.abinitio.commonline_sync.CLSyncVoting method) SyncVotingMixin (class in aspire.abinitio.sync_voting) SyntheticVolumeBase (class in aspire.volume.volume_synthesis)

T

T (aspire.image.image.Image property) (aspire.operators.blk_diag_matrix.BlkDiagMatrix property) (aspire.operators.diag_matrix.DiagMatrix property) (aspire.volume.volume.Volume property) t_radial_part_mat() (in module aspire.basis.basis_utils) t_x_derivative_mat() (in module aspire.basis.basis_utils) t_x_mat() (in module aspire.basis.basis_utils) t_x_mat_dot() (in module aspire.basis.basis_utils) tapers() (aspire.ctf.ctf_estimator.CtfEstimator method) to_complex() (aspire.basis.basis.Coef method) (aspire.basis.basis.ComplexCoef method) (aspire.basis.fspca.FSPCABasis method) (aspire.basis.steerable.SteerableBasis2D method) to_real() (aspire.basis.basis.Coef method) (aspire.basis.basis.ComplexCoef method) (aspire.basis.fspca.FSPCABasis method) (aspire.basis.steerable.SteerableBasis2D method) to_string (aspire.volume.symmetry_groups.CnSymmetryGroup property) (aspire.volume.symmetry_groups.DnSymmetryGroup property) (aspire.volume.symmetry_groups.OSymmetryGroup property) (aspire.volume.symmetry_groups.SymmetryGroup property) (aspire.volume.symmetry_groups.TSymmetryGroup property)

to_vec() (aspire.volume.volume.Volume method) toeplitz() (aspire.reconstruction.kernel.FourierKernel method) (aspire.reconstruction.kernel.FourierKernelMatrix method) TopClassSelector (class in aspire.classification.class_selection) tqdm() (in module aspire.utils.logging) trange() (in module aspire.utils.logging) transform() (aspire.nufft.finufft.FinufftPlan method) (aspire.operators.polar_ft.PolarFT method) transform_complex_to_real() (in module aspire.basis.fle_2d_utils) transpose() (aspire.image.image.Image method) (aspire.operators.blk_diag_matrix.BlkDiagMatrix method) (aspire.operators.diag_matrix.DiagMatrix method) (aspire.volume.volume.Volume method) true_signal_power() (aspire.source.simulation.Simulation method) true_snr() (aspire.source.simulation.Simulation method) TSymmetricVolume (class in aspire.volume.volume_synthesis) TSymmetryGroup (class in aspire.volume.symmetry_groups)

U

uniform_random_angles() (in module aspire.utils.coor_trans) unique_coords_nd() (in module aspire.basis.basis_utils) UnknownFormat

unroll_dim() (in module aspire.utils.matrix) update() (aspire.source.image.ImageSource method) update_header() (aspire.storage.mrc.MrcStats method) utest_tolerance() (in module aspire.utils.types)

V

VarianceImageQualityFunction (class in aspire.classification.class_selection) vec_to_im() (in module aspire.utils.matrix) vec_to_mat() (in module aspire.utils.matrix) vec_to_symmat() (in module aspire.utils.matrix) vec_to_symmat_iso() (in module aspire.utils.matrix) vec_to_vol() (in module aspire.utils.matrix) vecmat_to_volmat() (in module aspire.utils.matrix)

verify_input_values() (aspire.apple.apple.Apple method) virtual_core_cpu_suggestion() (in module aspire.utils.multiprocessing) vol_coords() (aspire.source.simulation.Simulation method) vol_forward() (aspire.source.image.ImageSource method) vol_to_vec() (in module aspire.utils.matrix) volmat_to_vecmat() (in module aspire.utils.matrix) voltage_to_wavelength() (in module aspire.utils.units) Volume (class in aspire.volume.volume)

W

wavelength_to_voltage() (in module aspire.utils.units) WeightedImageQualityMixin (class in aspire.classification.class_selection) WeightedVolumesEstimator (class in aspire.reconstruction.mean) weights() (aspire.classification.class_selection.WeightedImageQualityMixin method) wemd_embed() (in module aspire.operators.wemd) wemd_norm() (in module aspire.operators.wemd)

whiten() (aspire.source.image.ImageSource method) WhiteNoiseAdder (class in aspire.noise.noise) WhiteNoiseEstimator (class in aspire.noise.noise) WinsorizedImageStacker (class in aspire.image.image_stacker) write() (aspire.storage.starfile.StarFile method) write_star() (aspire.ctf.ctf_estimator.CtfEstimator method) WrongInput

X

Xform (class in aspire.image.xform)

Xform.XformActiveContextManager (class in aspire.image.xform)

Z

ZeroFilter (class in aspire.operators.filters) zeros() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) (aspire.operators.diag_matrix.DiagMatrix static method)

zeros_like() (aspire.operators.blk_diag_matrix.BlkDiagMatrix static method) (aspire.volume.volume.Volume static method)