aspire package

Subpackages

• aspire.abinitio package
  • Submodules
  • aspire.abinitio.commonline_base module
    • CLOrient3D
      • CLOrient3D.build_clmatrix()
      • CLOrient3D.build_clmatrix_cu()
      • CLOrient3D.build_clmatrix_host()
      • CLOrient3D.clmatrix
      • CLOrient3D.estimate()
      • CLOrient3D.estimate_rotations()
      • CLOrient3D.estimate_shifts()
      • CLOrient3D.pf
      • CLOrient3D.rotations
      • CLOrient3D.shifts
  • aspire.abinitio.commonline_c2 module
    • CLSymmetryC2
      • CLSymmetryC2.build_clmatrix()
      • CLSymmetryC2.estimate_rotations()
  • aspire.abinitio.commonline_c3_c4 module
    • CLSymmetryC3C4
      • CLSymmetryC3C4.cl_angles_to_ind()
      • CLSymmetryC3C4.estimate_rotations()
      • CLSymmetryC3C4.g_sync()
  • aspire.abinitio.commonline_cn module
    • CLSymmetryCn
      • CLSymmetryCn.estimate_rotations()
      • CLSymmetryCn.generate_candidate_rots()
      • CLSymmetryCn.relative_rots_to_cl_indices()
    • MeanOuterProductEstimator
      • MeanOuterProductEstimator.dtype
      • MeanOuterProductEstimator.push()
      • MeanOuterProductEstimator.synchronized_mean()
  • aspire.abinitio.commonline_d2 module
    • CLSymmetryD2
      • CLSymmetryD2.estimate_rotations()
  • aspire.abinitio.commonline_ev module
    • CommLineEV
      • CommLineEV.estimate()
      • CommLineEV.output()
  • aspire.abinitio.commonline_gcar module
    • CommLineGCAR
      • CommLineGCAR.estimate()
      • CommLineGCAR.output()
  • aspire.abinitio.commonline_irls module
    • CommonlineIRLS
      • CommonlineIRLS.estimate_rotations()
  • aspire.abinitio.commonline_lud module
    • CommonlineLUD
      • CommonlineLUD.estimate_rotations()
  • aspire.abinitio.commonline_sdp module
    • CommonlineSDP
      • CommonlineSDP.estimate_rotations()
  • aspire.abinitio.commonline_sync module
    • CLSyncVoting
      • CLSyncVoting.estimate_rotations()
      • CLSyncVoting.syncmatrix_vote()
  • aspire.abinitio.commonline_sync3n module
    • CLSync3N
      • CLSync3N.estimate_rotations()
  • aspire.abinitio.sync_voting module
    • SyncVotingMixin
  • Module contents
• aspire.apple package
  • Submodules
  • aspire.apple.apple module
    • Apple
      • Apple.particle_image()
      • Apple.process_folder()
      • Apple.process_micrograph()
      • Apple.process_micrograph_centers()
      • Apple.process_micrograph_plots()
      • Apple.verify_input_values()
  • aspire.apple.helper module
    • PickerHelper
      • PickerHelper.extract_query()
      • PickerHelper.extract_references()
      • PickerHelper.extract_windows()
      • PickerHelper.gaussian_filter()
      • PickerHelper.get_training_set()
      • PickerHelper.moments()
      • PickerHelper.reference_size()
  • aspire.apple.picking module
    • Picker
      • Picker.extract_particles()
      • Picker.get_maps()
      • Picker.morphology_ops()
      • Picker.query_score()
      • Picker.read_micrograph()
      • Picker.run_svm()
  • Module contents
• aspire.basis package
  • Submodules
  • aspire.basis.basis module
    • Basis
      • Basis.evaluate()
      • Basis.evaluate_t()
      • Basis.expand()
      • Basis.mat_evaluate()
      • Basis.mat_evaluate_t()
      • Basis.norms()
    • Coef
      • Coef.asnumpy()
      • Coef.by_indices()
      • Coef.copy()
      • Coef.evaluate()
      • Coef.rotate()
      • Coef.shift()
      • Coef.size
      • Coef.stack_reshape()
      • Coef.to_complex()
      • Coef.to_real()
    • ComplexCoef
      • ComplexCoef.evaluate()
      • ComplexCoef.rotate()
      • ComplexCoef.shift()
      • ComplexCoef.to_complex()
      • ComplexCoef.to_real()
  • aspire.basis.basis_utils module
    • all_besselj_zeros()
    • besselj_newton()
    • besselj_zeros()
    • check_besselj_zeros()
    • d_decay_approx_fun()
    • k_operator()
    • lgwt()
    • norm_assoc_legendre()
    • p_n()
    • real_sph_harmonic()
    • sph_bessel()
    • sph_harm()
    • t_radial_part_mat()
    • t_x_derivative_mat()
    • t_x_mat()
    • t_x_mat_dot()
    • unique_coords_nd()
  • aspire.basis.dirac module
    • DiracBasis
      • DiracBasis.dim
      • DiracBasis.expand()
    • DiracBasis2D
      • DiracBasis2D.dim
    • DiracBasis3D
      • DiracBasis3D.dim
  • aspire.basis.fb module
    • FBBasisMixin
  • aspire.basis.fb_2d module
    • FBBasis2D
      • FBBasis2D.basis_norm_2d()
      • FBBasis2D.calculate_bispectrum()
      • FBBasis2D.filter_to_basis_mat()
      • FBBasis2D.norms()
  • aspire.basis.fb_3d module
    • FBBasis3D
      • FBBasis3D.basis_norm_3d()
      • FBBasis3D.indices()
      • FBBasis3D.norms()
  • aspire.basis.ffb_2d module
    • FFBBasis2D
      • FFBBasis2D.filter_to_basis_mat()
  • aspire.basis.ffb_3d module
    • FFBBasis3D
  • aspire.basis.fle_2d module
    • FLEBasis2D
      • FLEBasis2D.filter_to_basis_mat()
      • FLEBasis2D.lowpass()
      • FLEBasis2D.matrix_type
      • FLEBasis2D.radial_convolve()
  • aspire.basis.fle_2d_utils module
    • barycentric_interp_sparse()
    • precomp_transform_complex_to_real()
    • transform_complex_to_real()
  • aspire.basis.fpswf_2d module
    • FPSWFBasis2D
      • FPSWFBasis2D.filter_to_basis_mat()
  • aspire.basis.fpswf_3d module
    • FPSWFBasis3D
  • aspire.basis.fspca module
    • FSPCABasis
      • FSPCABasis.build()
      • FSPCABasis.calculate_bispectrum()
      • FSPCABasis.eigen_images()
      • FSPCABasis.eigvals
      • FSPCABasis.evaluate()
      • FSPCABasis.evaluate_to_image_basis()
      • FSPCABasis.expand()
      • FSPCABasis.expand_from_image_basis()
      • FSPCABasis.filter_to_basis_mat()
      • FSPCABasis.shift()
      • FSPCABasis.to_complex()
      • FSPCABasis.to_real()
  • aspire.basis.pswf_2d module
    • PSWFBasis2D
      • PSWFBasis2D.filter_to_basis_mat()
      • PSWFBasis2D.matrix_type
      • PSWFBasis2D.pswf_func2d()
  • aspire.basis.pswf_3d module
    • PSWFBasis3D
  • aspire.basis.pswf_utils module
    • BNMatrix
      • BNMatrix.dense_mat()
      • BNMatrix.get_eig_vectors()
      • BNMatrix.shape()
  • aspire.basis.steerable module
    • SteerableBasis2D
      • SteerableBasis2D.blk_diag_cov_shape
      • SteerableBasis2D.calculate_bispectrum()
      • SteerableBasis2D.complex_rotate()
      • SteerableBasis2D.filter_to_basis_mat()
      • SteerableBasis2D.indices_mask()
      • SteerableBasis2D.matrix_type
      • SteerableBasis2D.rotate()
      • SteerableBasis2D.shift()
      • SteerableBasis2D.to_complex()
      • SteerableBasis2D.to_real()
  • Module contents
• aspire.classification package
  • Submodules
  • aspire.classification.averager2d module
    • AligningAverager2D
      • AligningAverager2D.align()
      • AligningAverager2D.average()
    • Averager2D
      • Averager2D.average()
    • BFRAverager2D
      • BFRAverager2D.align()
    • BFSRAverager2D
      • BFSRAverager2D.align()
    • BFSReddyChatterjiAverager2D
      • BFSReddyChatterjiAverager2D.align()
      • BFSReddyChatterjiAverager2D.average()
    • BFTAverager2D
      • BFTAverager2D.align()
    • EMAverager2D
    • FTKAverager2D
    • ReddyChatterjiAverager2D
      • ReddyChatterjiAverager2D.align()
      • ReddyChatterjiAverager2D.average()
    • commute_shift_rot()
  • aspire.classification.class2d module
    • Class2D
      • Class2D.classify()
  • aspire.classification.class_selection module
    • BandedSNRImageQualityFunction
    • BandpassImageQualityFunction
    • BumpWeightedImageQualityMixin
    • BumpWeightedVarianceImageQualityFunction
    • ClassSelector
      • ClassSelector.quality_scores
      • ClassSelector.select()
    • DistanceClassSelector
    • GlobalClassSelector
      • GlobalClassSelector.heap_ids
      • GlobalClassSelector.heap_idx_map
    • GlobalVarianceClassSelector
    • GlobalWithRepulsionClassSelector
    • GreedyClassRepulsionMixin
    • ImageQualityFunction
    • NeighborVarianceClassSelector
    • NeighborVarianceWithRepulsionClassSelector
    • RampWeightedImageQualityMixin
    • RampWeightedVarianceImageQualityFunction
    • RandomClassSelector
    • TopClassSelector
    • VarianceImageQualityFunction
    • WeightedImageQualityMixin
      • WeightedImageQualityMixin.weights()
  • aspire.classification.legacy_implementations module
    • bispec_2drot_large()
    • bispec_operator_1()
    • pca_y()
  • aspire.classification.reddy_chatterji module
    • reddy_chatterji_register()
  • aspire.classification.rir_class2d module
    • RIRClass2D
      • RIRClass2D.bispectrum()
      • RIRClass2D.classify()
      • RIRClass2D.nn_classification()
      • RIRClass2D.pca()
  • Module contents
• aspire.commands package
  • Submodules
  • 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
  • Module contents
• aspire.covariance package
  • Submodules
  • aspire.covariance.covar module
    • CovarianceEstimator
      • CovarianceEstimator.apply_kernel()
      • CovarianceEstimator.compute_kernel()
      • CovarianceEstimator.conj_grad()
      • CovarianceEstimator.estimate()
      • CovarianceEstimator.src_backward()
  • aspire.covariance.covar2d module
    • BatchedRotCov2D
      • BatchedRotCov2D.get_covar()
      • BatchedRotCov2D.get_cwf_coefs()
      • BatchedRotCov2D.get_mean()
    • RotCov2D
      • RotCov2D.get_covar()
      • RotCov2D.get_cwf_coefs()
      • RotCov2D.get_mean()
      • RotCov2D.shrink_covar_backward()
    • shrink_covar()
  • Module contents
• aspire.ctf package
  • Submodules
  • aspire.ctf.ctf_estimator module
    • CtfEstimator
      • CtfEstimator.background_subtract_1d()
      • CtfEstimator.background_subtract_2d()
      • CtfEstimator.elliptical_average()
      • CtfEstimator.estimate_psd()
      • CtfEstimator.gd()
      • CtfEstimator.generate_ctf()
      • CtfEstimator.micrograph_to_blocks()
      • CtfEstimator.normalize_blocks()
      • CtfEstimator.opt1d()
      • CtfEstimator.pca()
      • CtfEstimator.preprocess_micrograph()
      • CtfEstimator.set_angle()
      • CtfEstimator.set_df1()
      • CtfEstimator.set_df2()
      • CtfEstimator.tapers()
      • CtfEstimator.write_star()
    • estimate_ctf()
  • Module contents
• aspire.denoising package
  • Submodules
  • aspire.denoising.adaptive_support module
    • adaptive_support()
  • aspire.denoising.class_avg module
    • ClassAvgSource
      • ClassAvgSource.class_distances
      • ClassAvgSource.class_indices
      • ClassAvgSource.class_refl
      • ClassAvgSource.n
      • ClassAvgSource.save()
      • ClassAvgSource.selection_indices
    • ClassAvgSourcev132
    • ClassAvgSourcev140
    • DebugClassAvgSource
    • DefaultClassAvgSource()
    • LegacyClassAvgSource
  • aspire.denoising.denoised_src module
    • DenoisedSource
  • aspire.denoising.denoiser module
    • Denoiser
      • Denoiser.denoise
  • aspire.denoising.denoiser_cov2d module
    • DenoiserCov2D
      • DenoiserCov2D.build_denoiser()
      • DenoiserCov2D.default_opt
    • src_wiener_coords()
  • Module contents
• aspire.downloader package
  • Submodules
  • aspire.downloader.data_fetcher module
    • available_downloads()
    • download_all()
    • emdb_10835()
    • emdb_14621()
    • emdb_2484()
    • emdb_2660()
    • emdb_2824()
    • emdb_2984()
    • emdb_3645()
    • emdb_4905()
    • emdb_5778()
    • emdb_6287()
    • emdb_6458()
    • emdb_8012()
    • emdb_8511()
    • fetch_data()
    • remove_downloads()
    • simulated_channelspin()
  • aspire.downloader.registry module
  • Module contents
• aspire.image package
  • Submodules
  • aspire.image.image module
    • BasisImage
      • BasisImage.evaluate()
    • BispecImage
      • BispecImage.expand()
    • CartesianImage
      • CartesianImage.expand()
    • FBBasisImage
    • Image
      • Image.T
      • Image.asnumpy()
      • Image.backproject()
      • Image.copy()
      • Image.downsample()
      • Image.extensions
      • Image.filter()
      • Image.flip()
      • Image.frc()
      • Image.legacy_whiten()
      • Image.load()
      • Image.norm()
      • Image.project()
      • Image.res
      • Image.rotate()
      • Image.save()
      • Image.shift()
      • Image.show()
      • Image.size
      • Image.sqrt()
      • Image.stack_reshape()
      • Image.transpose()
    • PolarImage
      • PolarImage.expand()
    • load_mrc()
    • load_tiff()
    • normalize_bg()
  • aspire.image.image_stacker module
    • ImageStacker
    • MeanImageStacker
    • MedianImageStacker
    • PoissonRejectionImageStacker
    • RobustChauvenetRejectionImageStacker
    • SigmaRejectionImageStacker
    • WinsorizedImageStacker
  • aspire.image.xform module
    • Add
    • CropPad
    • Downsample
    • FilterXform
    • IndexedXform
    • LambdaXform
    • LegacyWhiten
    • LinearIndexedXform
    • LinearPipeline
    • LinearXform
      • LinearXform.adjoint()
    • Multiply
    • Pipeline
      • Pipeline.add_xform()
      • Pipeline.add_xforms()
      • Pipeline.reset()
    • Shift
    • SymmetricXform
    • Xform
      • Xform.XformActiveContextManager
      • Xform.disabled()
      • Xform.enabled()
      • Xform.forward()
  • Module contents
• aspire.noise package
  • Submodules
  • aspire.noise.noise module
    • AnisotropicNoiseEstimator
      • AnisotropicNoiseEstimator.estimate()
    • BlueNoiseAdder
    • CustomNoiseAdder
      • CustomNoiseAdder.noise_var
    • LegacyNoiseEstimator
      • LegacyNoiseEstimator.estimate()
    • NoiseAdder
      • NoiseAdder.noise_var
    • NoiseEstimator
      • NoiseEstimator.estimate()
      • NoiseEstimator.filter
    • PinkNoiseAdder
    • WhiteNoiseAdder
      • WhiteNoiseAdder.from_snr()
      • WhiteNoiseAdder.noise_var
      • WhiteNoiseAdder.signal_power
    • WhiteNoiseEstimator
      • WhiteNoiseEstimator.estimate()
  • Module contents
• aspire.nufft package
  • Submodules
  • aspire.nufft.cufinufft module
  • aspire.nufft.finufft module
    • FinufftPlan
      • FinufftPlan.adjoint()
      • FinufftPlan.transform()
  • aspire.nufft.pynfft module
  • aspire.nufft.utils module
    • nextpow2()
  • Module contents
    • Plan
    • all_backends()
    • anufft()
    • backend_available()
    • check_backends()
    • nufft()
• aspire.numeric package
  • Subpackages
    • aspire.numeric.complex_pca package
      • Submodules
      • aspire.numeric.complex_pca.complex_pca module
      • aspire.numeric.complex_pca.validation module
      • Module contents
  • Submodules
  • aspire.numeric.base_fft module
    • FFT
      • FFT.centered_fft()
      • FFT.centered_fft2()
      • FFT.centered_fftn()
      • FFT.centered_ifft()
      • FFT.centered_ifft2()
      • FFT.centered_ifftn()
      • FFT.dct()
      • FFT.fft()
      • FFT.fft2()
      • FFT.fftn()
      • FFT.fftshift()
      • FFT.idct()
      • FFT.ifft()
      • FFT.ifft2()
      • FFT.ifftn()
      • FFT.ifftshift()
      • FFT.irfft()
      • FFT.irfft2()
      • FFT.mdim_fftshift()
      • FFT.mdim_ifftshift()
      • FFT.rfft()
      • FFT.rfft2()
      • FFT.rfftfreq()
  • aspire.numeric.cupy module
  • aspire.numeric.cupy_fft module
  • aspire.numeric.mkl_fft module
  • aspire.numeric.numpy module
    • Numpy
      • Numpy.asnumpy()
  • aspire.numeric.pyfftw_fft module
  • aspire.numeric.scipy module
    • cg()
  • aspire.numeric.scipy_fft module
    • ScipyFFT
      • ScipyFFT.dct()
      • ScipyFFT.fft()
      • ScipyFFT.fft2()
      • ScipyFFT.fftn()
      • ScipyFFT.fftshift()
      • ScipyFFT.idct()
      • ScipyFFT.ifft()
      • ScipyFFT.ifft2()
      • ScipyFFT.ifftn()
      • ScipyFFT.ifftshift()
      • ScipyFFT.irfft()
      • ScipyFFT.irfft2()
      • ScipyFFT.rfft()
      • ScipyFFT.rfft2()
      • ScipyFFT.rfftfreq()
  • Module contents
    • fft_object()
    • numeric_object()
    • sparse_object()
• aspire.operators package
  • Submodules
  • aspire.operators.blk_diag_matrix module
    • BlkDiagMatrix
      • BlkDiagMatrix.T
      • BlkDiagMatrix.abs()
      • BlkDiagMatrix.add()
      • BlkDiagMatrix.append()
      • BlkDiagMatrix.apply()
      • BlkDiagMatrix.check_psd()
      • BlkDiagMatrix.copy()
      • BlkDiagMatrix.dense()
      • BlkDiagMatrix.diag()
      • BlkDiagMatrix.eigvals()
      • BlkDiagMatrix.empty()
      • BlkDiagMatrix.eye()
      • BlkDiagMatrix.eye_like()
      • BlkDiagMatrix.from_dense()
      • BlkDiagMatrix.from_list()
      • BlkDiagMatrix.is_square
      • BlkDiagMatrix.isfinite
      • BlkDiagMatrix.make_psd()
      • BlkDiagMatrix.matmul()
      • BlkDiagMatrix.mul()
      • BlkDiagMatrix.neg()
      • BlkDiagMatrix.norm()
      • BlkDiagMatrix.ones()
      • BlkDiagMatrix.partition
      • BlkDiagMatrix.pow()
      • BlkDiagMatrix.rapply()
      • BlkDiagMatrix.reset_cache()
      • BlkDiagMatrix.solve()
      • BlkDiagMatrix.sub()
      • BlkDiagMatrix.transpose()
      • BlkDiagMatrix.zeros()
      • BlkDiagMatrix.zeros_like()
    • is_scalar_type()
  • aspire.operators.diag_matrix module
    • DiagMatrix
      • DiagMatrix.T
      • DiagMatrix.abs()
      • DiagMatrix.add()
      • DiagMatrix.apply()
      • DiagMatrix.as_blk_diag()
      • DiagMatrix.asnumpy()
      • DiagMatrix.copy()
      • DiagMatrix.dense()
      • DiagMatrix.eigvals()
      • DiagMatrix.empty()
      • DiagMatrix.eye()
      • DiagMatrix.matmul()
      • DiagMatrix.mul()
      • DiagMatrix.neg()
      • DiagMatrix.norm
      • DiagMatrix.ones()
      • DiagMatrix.pow()
      • DiagMatrix.rapply()
      • DiagMatrix.solve()
      • DiagMatrix.stack_reshape()
      • DiagMatrix.sub()
      • DiagMatrix.transpose()
      • DiagMatrix.zeros()
  • aspire.operators.filters module
    • ArrayFilter
      • ArrayFilter.evaluate_grid()
    • BlueFilter
    • CTFFilter
    • DualFilter
      • DualFilter.evaluate()
    • Filter
      • Filter.basis_mat()
      • Filter.dual()
      • Filter.evaluate()
      • Filter.evaluate_grid()
      • Filter.scale()
      • Filter.sign
    • FunctionFilter
    • IdentityFilter
    • LambdaFilter
    • MultiplicativeFilter
    • PinkFilter
    • PowerFilter
      • PowerFilter.evaluate_grid()
    • RadialCTFFilter
    • ScalarFilter
    • ScaledFilter
    • ZeroFilter
    • evaluate_src_filters_on_grid()
  • aspire.operators.polar_ft module
    • PolarFT
      • PolarFT.half_to_full()
      • PolarFT.shift()
      • PolarFT.transform()
  • aspire.operators.wemd module
    • wemd_embed()
    • wemd_norm()
  • Module contents
• aspire.optimization package
  • Submodules
  • aspire.optimization.conj_grad module
    • conj_grad()
    • fill_struct()
  • Module contents
• aspire.reconstruction package
  • Submodules
  • aspire.reconstruction.estimator module
    • Estimator
      • Estimator.apply_kernel()
      • Estimator.compute_kernel()
      • Estimator.estimate()
  • aspire.reconstruction.kernel module
    • FourierKernel
      • FourierKernel.circularize()
      • FourierKernel.circularize_1d()
      • FourierKernel.convolve_volume()
      • FourierKernel.convolve_volume_matrix()
      • FourierKernel.toeplitz()
    • FourierKernelMatrix
      • FourierKernelMatrix.circularize()
      • FourierKernelMatrix.convolve_volume()
      • FourierKernelMatrix.convolve_volume_matrix()
      • FourierKernelMatrix.toeplitz()
    • Kernel
  • aspire.reconstruction.mean module
    • MeanEstimator
      • MeanEstimator.apply_kernel()
      • MeanEstimator.compute_kernel()
    • WeightedVolumesEstimator
      • WeightedVolumesEstimator.apply_kernel()
      • WeightedVolumesEstimator.compute_kernel()
      • WeightedVolumesEstimator.conj_grad()
      • WeightedVolumesEstimator.src_backward()
  • Module contents
• aspire.sinogram package
  • Submodules
  • aspire.sinogram.sinogram module
    • Sinogram
      • Sinogram.asnumpy()
      • Sinogram.backproject()
      • Sinogram.copy()
      • Sinogram.stack_reshape()
  • Module contents
• aspire.source package
  • Submodules
  • aspire.source.coordinates module
    • BoxesCoordinateSource
    • CentersCoordinateSource
    • CoordinateSource
      • CoordinateSource.import_aspire_ctf()
      • CoordinateSource.import_relion_ctf()
  • aspire.source.image module
    • ArrayImageSource
    • ImageSource
      • ImageSource.amplitudes
      • ImageSource.angles
      • ImageSource.cache()
      • ImageSource.class_distances
      • ImageSource.class_indices
      • ImageSource.class_refl
      • ImageSource.crop_pad()
      • ImageSource.downsample()
      • ImageSource.estimate_noise_power()
      • ImageSource.estimate_signal_mean_energy()
      • ImageSource.estimate_signal_power()
      • ImageSource.estimate_signal_var()
      • ImageSource.estimate_snr()
      • ImageSource.filter_indices
      • ImageSource.get_metadata()
      • ImageSource.has_metadata()
      • ImageSource.im_backward()
      • ImageSource.images
      • ImageSource.invert_contrast()
      • ImageSource.legacy_downsample()
      • ImageSource.legacy_normalize_background()
      • ImageSource.legacy_whiten()
      • ImageSource.n
      • ImageSource.n_ctf_filters
      • ImageSource.normalize_background()
      • ImageSource.offsets
      • ImageSource.phase_flip()
      • ImageSource.pixel_size
      • ImageSource.pop_metadata()
      • ImageSource.rotations
      • ImageSource.save()
      • ImageSource.save_images()
      • ImageSource.save_metadata()
      • ImageSource.selection_indices
      • ImageSource.set_metadata()
      • ImageSource.states
      • ImageSource.symmetry_group
      • ImageSource.update()
      • ImageSource.vol_forward()
      • ImageSource.whiten()
    • IndexedSource
    • OrientedSource
      • OrientedSource.get_metadata()
      • OrientedSource.offsets
      • OrientedSource.save_metadata()
  • aspire.source.micrograph module
    • ArrayMicrographSource
    • DiskMicrographSource
    • MicrographSimulation
      • MicrographSimulation.clean_images
      • MicrographSimulation.get_micrograph_index()
      • MicrographSimulation.get_particle_indices()
      • MicrographSimulation.save()
    • MicrographSource
      • MicrographSource.asnumpy()
      • MicrographSource.images
      • MicrographSource.save()
      • MicrographSource.show()
  • aspire.source.relion module
    • RelionSource
      • RelionSource.populate_metadata()
  • aspire.source.simulation module
    • Simulation
      • Simulation.clean_images
      • Simulation.covar_true()
      • Simulation.eigs()
      • Simulation.eval_clustering()
      • Simulation.eval_coords()
      • Simulation.eval_covar()
      • Simulation.eval_eigs()
      • Simulation.eval_mean()
      • Simulation.eval_vol()
      • Simulation.eval_volmat()
      • Simulation.mean_true()
      • Simulation.projections
      • Simulation.true_signal_power()
      • Simulation.true_snr()
      • Simulation.vol_coords()
  • Module contents
• aspire.storage package
  • Submodules
  • aspire.storage.mrc module
    • MrcStats
      • MrcStats.amean
      • MrcStats.arms
      • MrcStats.push()
      • MrcStats.update_header()
  • aspire.storage.starfile module
    • StarFile
      • StarFile.get_block_by_index()
      • StarFile.write()
    • StarFileError
  • Module contents
• aspire.utils package
  • Submodules
  • aspire.utils.bot_align module
    • align_BO()
  • aspire.utils.cell module
    • Cell2D
      • Cell2D.mat2cell()
  • aspire.utils.coor_trans module
    • cart2pol()
    • cart2sph()
    • crop_pad_2d()
    • crop_pad_3d()
    • grid_1d()
    • grid_2d()
    • grid_3d()
    • mean_aligned_angular_distance()
    • rots_to_clmatrix()
  • aspire.utils.logging module
    • LogFilterByCount
      • LogFilterByCount.filter()
      • LogFilterByCount.msg_cache
    • getConsoleLoggingLevel()
    • getFileLoggingLevel()
    • get_full_version()
    • setConsoleLoggingLevel()
    • setFileLoggingLevel()
    • tqdm()
    • trange()
  • aspire.utils.matlab_compat module
    • stable_eigsh()
  • aspire.utils.matrix module
    • acorr()
    • ainner()
    • anorm()
    • best_rank1_approximation()
    • eigs()
    • fix_signs()
    • make_psd()
    • make_symmat()
    • mat_to_vec()
    • mdim_mat_fun_conj()
    • nearest_rotations()
    • symmat_to_vec()
    • symmat_to_vec_iso()
    • vec_to_mat()
    • vec_to_symmat()
    • vec_to_symmat_iso()
  • aspire.utils.misc module
    • J_conjugate()
    • abs2()
    • all_pairs()
    • all_triplets()
    • bump_3d()
    • check_pixel_size()
    • circ()
    • cyclic_rotations()
    • fuzzy_mask()
    • gaussian_1d()
    • gaussian_2d()
    • gaussian_3d()
    • gaussian_window()
    • importlib_path()
    • inverse_r()
    • powerset()
    • rename_with_timestamp()
    • sha256sum()
    • support_mask()
  • aspire.utils.multiprocessing module
    • mem_based_cpu_suggestion()
    • num_procs_suggestion()
    • physical_core_cpu_suggestion()
    • virtual_core_cpu_suggestion()
  • aspire.utils.random module
    • Random
    • choice()
    • matlab_rand()
    • randi()
    • randn()
    • random()
  • aspire.utils.relion_interop module
    • RelionStarFile
      • RelionStarFile.get_merged_data_block()
    • dict_to_relion_types()
  • aspire.utils.resolution_estimation module
    • FourierCorrelation
      • FourierCorrelation.analyze_correlations()
      • FourierCorrelation.correlations
      • FourierCorrelation.plot()
    • FourierRingCorrelation
      • FourierRingCorrelation.dim
    • FourierShellCorrelation
      • FourierShellCorrelation.dim
  • aspire.utils.rotation module
    • Rotation
      • Rotation.about_axis()
      • Rotation.angle_dist()
      • Rotation.angles
      • Rotation.apply_registration()
      • Rotation.as_rotvec()
      • Rotation.common_lines()
      • Rotation.dtype
      • Rotation.find_registration()
      • Rotation.from_euler()
      • Rotation.from_matrix()
      • Rotation.from_rotvec()
      • Rotation.generate_random_rotations()
      • Rotation.invert()
      • Rotation.matrices
      • Rotation.mean_angular_distance()
      • Rotation.mse()
      • Rotation.register()
  • aspire.utils.types module
    • complex_type()
    • real_type()
    • utest_tolerance()
  • aspire.utils.units module
    • ratio_to_decibel()
    • voltage_to_wavelength()
    • wavelength_to_voltage()
  • Module contents
• aspire.volume package
  • Submodules
  • aspire.volume.symmetry_groups module
    • CnSymmetryGroup
      • CnSymmetryGroup.generate_rotations()
      • CnSymmetryGroup.to_string
    • DnSymmetryGroup
      • DnSymmetryGroup.generate_rotations()
      • DnSymmetryGroup.to_string
    • ISymmetryGroup
      • ISymmetryGroup.generate_rotations()
      • ISymmetryGroup.to_string
    • IdentitySymmetryGroup
    • OSymmetryGroup
      • OSymmetryGroup.generate_rotations()
      • OSymmetryGroup.to_string
    • SymmetryGroup
      • SymmetryGroup.generate_rotations()
      • SymmetryGroup.matrices
      • SymmetryGroup.parse()
      • SymmetryGroup.to_string
    • TSymmetryGroup
      • TSymmetryGroup.generate_rotations()
      • TSymmetryGroup.to_string
  • aspire.volume.volume module
    • BasisVolume
      • BasisVolume.evaluate()
    • BispecVolume
      • BispecVolume.expand()
    • CartesianVolume
      • CartesianVolume.expand()
    • FBBasisVolume
    • PolarVolume
      • PolarVolume.expand()
    • Volume
      • Volume.T
      • Volume.asnumpy()
      • Volume.astype()
      • Volume.denoise()
      • Volume.downsample()
      • Volume.empty_like()
      • Volume.flatten()
      • Volume.flip()
      • Volume.from_vec()
      • Volume.fsc()
      • Volume.load()
      • Volume.project()
      • Volume.rotate()
      • Volume.save()
      • Volume.shift()
      • Volume.stack_reshape()
      • Volume.symmetry_group
      • Volume.to_vec()
      • Volume.transpose()
      • Volume.zeros_like()
    • qr_vols_forward()
    • rotated_grids()
    • rotated_grids_3d()
  • aspire.volume.volume_synthesis module
    • AsymmetricVolume
    • CnSymmetricVolume
      • CnSymmetricVolume.n_blobs
    • DnSymmetricVolume
      • DnSymmetricVolume.n_blobs
    • GaussianBlobsVolume
      • GaussianBlobsVolume.generate()
      • GaussianBlobsVolume.n_blobs
      • GaussianBlobsVolume.symmetry_group
    • ISymmetricVolume
      • ISymmetricVolume.n_blobs
    • LegacyVolume
      • LegacyVolume.generate()
    • OSymmetricVolume
      • OSymmetricVolume.n_blobs
    • SyntheticVolumeBase
      • SyntheticVolumeBase.generate()
    • TSymmetricVolume
      • TSymmetricVolume.n_blobs
  • Module contents

Submodules

aspire.exceptions module

exception aspire.exceptions.AspireException

Bases: Exception

exception aspire.exceptions.DimensionsIncompatible

Bases: AspireException

exception aspire.exceptions.ErrorTooBig

Bases: AspireException

exception aspire.exceptions.UnknownFormat

Bases: AspireException

exception aspire.exceptions.WrongInput

Bases: AspireException

aspire.exceptions.handle_exception(exc_type, exc_value, exc_traceback)

Handle any top-level unhandled exception. Tries to gather and log additional context information, then re-raises.

Parameters:

• exc_type – Exception type object

• exc_value – Exception value object (an instance of type exc_type)

• exc_traceback – The Traceback object associated with exc_value (also available as exc_value.__traceback__)

Returns:

On return, useful diagnostic information has been logged, and the exception re-raised.

Module contents