ASPIRE
Contents
Installation
Getting Started - CLI
Class Averaging Architecture
Modules
Authors
Galleries:
Tutorials
Experiments
ASPIRE
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Z
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.dirac
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_clmatrix_cu() (aspire.abinitio.commonline_base.CLOrient3D method)
build_clmatrix_host() (aspire.abinitio.commonline_base.CLOrient3D 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)
clmatrix (aspire.abinitio.commonline_base.CLOrient3D 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.basis.dirac.DiracBasis attribute)
(aspire.basis.dirac.DiracBasis2D attribute)
(aspire.basis.dirac.DiracBasis3D attribute)
(aspire.utils.resolution_estimation.FourierRingCorrelation attribute)
(aspire.utils.resolution_estimation.FourierShellCorrelation attribute)
DimensionsIncompatible
DiracBasis (class in aspire.basis.dirac)
DiracBasis2D (class in aspire.basis.dirac)
DiracBasis3D (class in aspire.basis.dirac)
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_base.CLOrient3D method)
(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.dirac.DiracBasis 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.dirac
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)
(aspire.source.image.OrientedSource 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)
rename_with_timestamp() (in module aspire.utils.misc)
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.abinitio.commonline_base.CLOrient3D property)
(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)
shifts (aspire.abinitio.commonline_base.CLOrient3D property)
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)