Index

_

_abc_impl (DualGapCost attribute), [1] (GenericCost attribute), [1] _add_observer() (Observable method) _adj_op() (DictionaryLearning method) (HOTV method) (HOTV_3D method) (LinearBase method) (Radon2D method) (Radon3D method) (WaveletN method) (WaveletPywt method) (WaveletUD2 method) _analysis() (ISAPWaveletTransformBase method) (PyWaveletTransformBase method) (WaveletTransformBase method) _auto_thresh() (AutoWeightedSparseThreshold method), [1] _calc_cost() (DualGapCost method), [1] (GenericCost method), [1] _check_python_versions() (in module pysap.configure) _class_cleanups (DenoiseTestCase attribute) (NoiseTestCase attribute) (WaveletTestCase attribute) _classSetupFailed (DenoiseTestCase attribute) (NoiseTestCase attribute) (WaveletTestCase attribute) _compute_fsvd_coefficients() (in module mri.operators.fourier.utils.orc_coefficients) _compute_mfi_coefficients() (in module mri.operators.fourier.utils.orc_coefficients) _compute_mti_coefficients() (in module mri.operators.fourier.utils.orc_coefficients) _compute_svd_coefficients() (in module mri.operators.fourier.utils.orc_coefficients) _compute_transformation_parameters() (WaveletTransformBase method) _cost_method() (OWL method), [1] _create_histogram() (in module mri.operators.fourier.utils.orc_coefficients) _create_variable_density() (in module mri.operators.fourier.utils.orc_coefficients) _default_spacing() (Image method) _get_allowed_signals() (Observable method) _get_analysis_data() (WaveletTransformBase method) _get_analysis_header() (WaveletTransformBase method) _get_data() (WaveletTransformBase method) _get_dtype() (Image method) _get_filters() (WaveletUD2 method) _get_info() (WaveletTransformBase method) _get_linear_band() (WaveletTransformBase method) _get_ndim() (Image method) _get_scroll_axis() (Image method) _get_shape() (Image method) _get_spacing() (Image method) _getitem_current() (Column2DKspaceGenerator method) _getitem_line() (Column2DKspaceGenerator method) _getitem_memory() (Column2DKspaceGenerator method) _has_run (WaveletUD2 attribute) _id (bior11 attribute) (bior13 attribute) (bior15 attribute) (bior22 attribute) (bior24 attribute) (bior26 attribute) (bior28 attribute) (bior31 attribute) (bior33 attribute) (bior35 attribute) (bior37 attribute) (bior39 attribute) (bior44 attribute) (bior55 attribute) (bior68 attribute) (cgau1 attribute) (cgau2 attribute) (cgau3 attribute) (cgau4 attribute) (cgau5 attribute) (cgau6 attribute) (cgau7 attribute) (cgau8 attribute) (cmor attribute) (coif1 attribute) (coif10 attribute) (coif11 attribute) (coif12 attribute) (coif13 attribute) (coif14 attribute) (coif15 attribute) (coif16 attribute) (coif17 attribute) (coif2 attribute) (coif3 attribute) (coif4 attribute) (coif5 attribute) (coif6 attribute) (coif7 attribute) (coif8 attribute) (coif9 attribute) (db1 attribute) (db10 attribute) (db11 attribute) (db12 attribute) (db13 attribute) (db14 attribute) (db15 attribute) (db16 attribute) (db17 attribute) (db18 attribute) (db19 attribute) (db2 attribute) (db20 attribute) (db21 attribute) (db22 attribute) (db23 attribute) (db24 attribute) (db25 attribute) (db26 attribute) (db27 attribute) (db28 attribute) (db29 attribute) (db3 attribute) (db30 attribute) (db31 attribute) (db32 attribute) (db33 attribute) (db34 attribute) (db35 attribute) (db36 attribute) (db37 attribute) (db38 attribute) (db4 attribute) (db5 attribute) (db6 attribute) (db7 attribute) (db8 attribute) (db9 attribute) (dmey attribute) (fbsp attribute) (gaus1 attribute) (gaus2 attribute) (gaus3 attribute) (gaus4 attribute) (gaus5 attribute) (gaus6 attribute) (gaus7 attribute) (gaus8 attribute) (haar attribute) (mexh attribute) (morl attribute) (rbio11 attribute) (rbio13 attribute) (rbio15 attribute) (rbio22 attribute) (rbio24 attribute) (rbio26 attribute) (rbio28 attribute) (rbio31 attribute) (rbio33 attribute) (rbio35 attribute) (rbio37 attribute) (rbio39 attribute) (rbio44 attribute) (rbio55 attribute) (rbio68 attribute) (shan attribute) (sym10 attribute) (sym11 attribute) (sym12 attribute) (sym13 attribute) (sym14 attribute) (sym15 attribute) (sym16 attribute) (sym17 attribute) (sym18 attribute) (sym19 attribute) (sym2 attribute) (sym20 attribute) (sym3 attribute) (sym4 attribute) (sym5 attribute) (sym6 attribute) (sym7 attribute) (sym8 attribute) (sym9 attribute) _init_transform() (ISAPWaveletTransformBase method) (PyWaveletTransformBase method) (WaveletTransformBase method) _is_allowed_signal() (Observable method) _mkdtemp_isap() (TempDir method) _op() (DictionaryLearning method) (HOTV method) (HOTV_3D method) (LinearBase method) (Radon2D method) (Radon3D method) (WaveletN method) (WaveletPywt method) (WaveletUD2 method) _op_method() (AutoWeightedSparseThreshold method), [1] (GradSelfCalibrationAnalysis method) (GradSelfCalibrationSynthesis method) (GradSynthesis method), [1] (OWL method), [1] _organize_pysap() (PyWaveletTransformBase method) _organize_pywt() (PyWaveletTransformBase method) _oscar_weights() (OWL static method), [1] _pywt_func (bior11 attribute) (bior13 attribute) (bior15 attribute) (bior22 attribute) (bior24 attribute) (bior26 attribute) (bior28 attribute) (bior31 attribute) (bior33 attribute) (bior35 attribute) (bior37 attribute) (bior39 attribute) (bior44 attribute) (bior55 attribute) (bior68 attribute) (cgau1 attribute) (cgau2 attribute) (cgau3 attribute) (cgau4 attribute) (cgau5 attribute) (cgau6 attribute) (cgau7 attribute) (cgau8 attribute) (cmor attribute) (coif1 attribute) (coif10 attribute) (coif11 attribute) (coif12 attribute) (coif13 attribute) (coif14 attribute) (coif15 attribute) (coif16 attribute) (coif17 attribute) (coif2 attribute) (coif3 attribute) (coif4 attribute) (coif5 attribute) (coif6 attribute) (coif7 attribute) (coif8 attribute) (coif9 attribute) (db1 attribute) (db10 attribute) (db11 attribute) (db12 attribute) (db13 attribute) (db14 attribute) (db15 attribute) (db16 attribute) (db17 attribute) (db18 attribute) (db19 attribute) (db2 attribute) (db20 attribute) (db21 attribute) (db22 attribute) (db23 attribute) (db24 attribute) (db25 attribute) (db26 attribute) (db27 attribute) (db28 attribute) (db29 attribute) (db3 attribute) (db30 attribute) (db31 attribute) (db32 attribute) (db33 attribute) (db34 attribute) (db35 attribute) (db36 attribute) (db37 attribute) (db38 attribute) (db4 attribute) (db5 attribute) (db6 attribute) (db7 attribute) (db8 attribute) (db9 attribute) (dmey attribute) (fbsp attribute) (gaus1 attribute) (gaus2 attribute) (gaus3 attribute) (gaus4 attribute) (gaus5 attribute) (gaus6 attribute) (gaus7 attribute) (gaus8 attribute) (haar attribute) (mexh attribute) (morl attribute) (rbio11 attribute) (rbio13 attribute) (rbio15 attribute) (rbio22 attribute) (rbio24 attribute) (rbio26 attribute) (rbio28 attribute) (rbio31 attribute) (rbio33 attribute) (rbio35 attribute) (rbio37 attribute) (rbio39 attribute) (rbio44 attribute) (rbio55 attribute) (rbio68 attribute) (shan attribute) (sym10 attribute) (sym11 attribute) (sym12 attribute) (sym13 attribute) (sym14 attribute) (sym15 attribute) (sym16 attribute) (sym17 attribute) (sym18 attribute) (sym19 attribute) (sym2 attribute) (sym20 attribute) (sym3 attribute) (sym4 attribute) (sym5 attribute) (sym6 attribute) (sym7 attribute) (sym8 attribute) (sym9 attribute)

_pywt_name (bior11 attribute) (bior13 attribute) (bior15 attribute) (bior22 attribute) (bior24 attribute) (bior26 attribute) (bior28 attribute) (bior31 attribute) (bior33 attribute) (bior35 attribute) (bior37 attribute) (bior39 attribute) (bior44 attribute) (bior55 attribute) (bior68 attribute) (cgau1 attribute) (cgau2 attribute) (cgau3 attribute) (cgau4 attribute) (cgau5 attribute) (cgau6 attribute) (cgau7 attribute) (cgau8 attribute) (cmor attribute) (coif1 attribute) (coif10 attribute) (coif11 attribute) (coif12 attribute) (coif13 attribute) (coif14 attribute) (coif15 attribute) (coif16 attribute) (coif17 attribute) (coif2 attribute) (coif3 attribute) (coif4 attribute) (coif5 attribute) (coif6 attribute) (coif7 attribute) (coif8 attribute) (coif9 attribute) (db1 attribute) (db10 attribute) (db11 attribute) (db12 attribute) (db13 attribute) (db14 attribute) (db15 attribute) (db16 attribute) (db17 attribute) (db18 attribute) (db19 attribute) (db2 attribute) (db20 attribute) (db21 attribute) (db22 attribute) (db23 attribute) (db24 attribute) (db25 attribute) (db26 attribute) (db27 attribute) (db28 attribute) (db29 attribute) (db3 attribute) (db30 attribute) (db31 attribute) (db32 attribute) (db33 attribute) (db34 attribute) (db35 attribute) (db36 attribute) (db37 attribute) (db38 attribute) (db4 attribute) (db5 attribute) (db6 attribute) (db7 attribute) (db8 attribute) (db9 attribute) (dmey attribute) (fbsp attribute) (gaus1 attribute) (gaus2 attribute) (gaus3 attribute) (gaus4 attribute) (gaus5 attribute) (gaus6 attribute) (gaus7 attribute) (gaus8 attribute) (haar attribute) (mexh attribute) (morl attribute) (rbio11 attribute) (rbio13 attribute) (rbio15 attribute) (rbio22 attribute) (rbio24 attribute) (rbio26 attribute) (rbio28 attribute) (rbio31 attribute) (rbio33 attribute) (rbio35 attribute) (rbio37 attribute) (rbio39 attribute) (rbio44 attribute) (rbio55 attribute) (rbio68 attribute) (shan attribute) (sym10 attribute) (sym11 attribute) (sym12 attribute) (sym13 attribute) (sym14 attribute) (sym15 attribute) (sym16 attribute) (sym17 attribute) (sym18 attribute) (sym19 attribute) (sym2 attribute) (sym20 attribute) (sym3 attribute) (sym4 attribute) (sym5 attribute) (sym6 attribute) (sym7 attribute) (sym8 attribute) (sym9 attribute) _remove_observer() (Observable method) _reshape_band_based() (OWL method), [1] _reshape_scale_based() (OWL method), [1] _set_analysis_data() (WaveletTransformBase method) _set_analysis_header() (WaveletTransformBase method) _set_data() (WaveletTransformBase method) _set_linear_band() (WaveletTransformBase method) _set_scroll_axis() (Image method) _set_spacing() (Image method) _set_transformation_parameters() (FastCurveletTransform method) (FeauveauWaveletTransform method) (ISAPWaveletTransformBase method) (LineColumnWaveletTransform1D1D method) (WaveletTransformBase method) _sigma_mad() (in module mri.operators.proximity.weighted) _sure_est() (in module mri.operators.proximity.weighted) _synthesis() (ISAPWaveletTransformBase method) (PyWaveletTransformBase method) (WaveletTransformBase method) _TestCase (class in mri.scripts.gridsearch) _thresh_select() (in module mri.operators.proximity.weighted) _trans_op_method() (GradSelfCalibrationAnalysis method) (GradSelfCalibrationSynthesis method) (GradSynthesis method), [1] _update_default_transformation_parameters() (ISAPWaveletTransformBase method) (NonOrthogonalUndecimatedTransform method) (OnLine44AndOnColumn53 method) (OnLine53AndOnColumn44 method) (UndecimatedBiOrthogonalTransform method) (UndecimatedDiadicWaveletTransform method)

A

add_observer() (Observable method) adj_op() (ColumnFFT method) (DictionaryLearning method) (FFT method) (FourierBase method) (FourierOperatorBase method) (gpuNUFFT method) (LinearBase method) (NonCartesianFFT method) (NUFFT2 method) (OperatorBase method) (ORCFFTWrapper method) (Radon2D method) (Radon3D method) (RadonBase method) (WaveletN method) (WaveletUD2 method) allowed_extensions (FITS attribute) (LoaderBase attribute) (MAT attribute) (NIFTI attribute) (npBinary attribute) (TIF attribute) allowed_signals (Observable property) analysis() (WaveletTransformBase method) analysis_data (WaveletTransformBase property)

analysis_header (WaveletTransformBase property) astro module astro.deconvolution module astro.deconvolution.deconvolve module astro.deconvolution.linear module astro.deconvolution.wavelet_filters module astro.denoising module astro.denoising.denoise module astro.denoising.noise module astro.denoising.wavelet module astro.tests module astro.tests.test_denoising module ATrou3D (class in pysap.extensions.transform) AutoWeightedSparseThreshold (class in mri.operators.proximity) (class in mri.operators.proximity.weighted)

B

backend (WaveletN attribute) band_at() (WaveletTransformBase method) bands_lengths (WaveletTransformBase attribute) bands_names (WaveletTransformBase attribute) bands_shapes (WaveletTransformBase attribute) bands_shapes() (WaveletTransformBase class method) bior11 (class in pysap.extensions.transform) bior13 (class in pysap.extensions.transform) bior15 (class in pysap.extensions.transform) bior22 (class in pysap.extensions.transform) bior24 (class in pysap.extensions.transform)

bior26 (class in pysap.extensions.transform) bior28 (class in pysap.extensions.transform) bior31 (class in pysap.extensions.transform) bior33 (class in pysap.extensions.transform) bior35 (class in pysap.extensions.transform) bior37 (class in pysap.extensions.transform) bior39 (class in pysap.extensions.transform) bior44 (class in pysap.extensions.transform) bior55 (class in pysap.extensions.transform) bior68 (class in pysap.extensions.transform) BiOrthogonalTransform3D (class in pysap.extensions.transform) BsplineWaveletTransformATrousAlgorithm (class in pysap.extensions.transform)

C

CalibrationlessReconstructor (class in mri.reconstructors.calibrationless) can_load() (LoaderBase method) can_save() (LoaderBase method) cgau1 (class in pysap.extensions.transform) cgau2 (class in pysap.extensions.transform) cgau3 (class in pysap.extensions.transform) cgau4 (class in pysap.extensions.transform) cgau5 (class in pysap.extensions.transform) cgau6 (class in pysap.extensions.transform) cgau7 (class in pysap.extensions.transform) cgau8 (class in pysap.extensions.transform) check_if_fourier_op_uses_sense() (in module mri.operators.fourier.utils.processing) check_lipschitz_cst() (in module mri.operators.gradient.utils) cmor (class in pysap.extensions.transform) coif1 (class in pysap.extensions.transform) coif10 (class in pysap.extensions.transform) coif11 (class in pysap.extensions.transform) coif12 (class in pysap.extensions.transform) coif13 (class in pysap.extensions.transform) coif14 (class in pysap.extensions.transform)

coif15 (class in pysap.extensions.transform) coif16 (class in pysap.extensions.transform) coif17 (class in pysap.extensions.transform) coif2 (class in pysap.extensions.transform) coif3 (class in pysap.extensions.transform) coif4 (class in pysap.extensions.transform) coif5 (class in pysap.extensions.transform) coif6 (class in pysap.extensions.transform) coif7 (class in pysap.extensions.transform) coif8 (class in pysap.extensions.transform) coif9 (class in pysap.extensions.transform) Column2DKspaceGenerator (class in mri.generators.cartesian) ColumnFFT (class in mri.operators.fourier.online) compute_orc_coefficients() (in module mri.operators.fourier.utils.orc_coefficients) condatvu() (in module etomo.optimizers.primal_dual) (in module mri.optimizers.primal_dual) condatvu_logo() (in module pysap.utils) convert_locations_to_mask() (in module mri.operators.fourier.utils.processing) convert_mask_to_locations() (in module mri.operators.fourier.utils.processing) copy_file() (in module pysap.data)

D

data (WaveletTransformBase property) db1 (class in pysap.extensions.transform) db10 (class in pysap.extensions.transform) db11 (class in pysap.extensions.transform) db12 (class in pysap.extensions.transform) db13 (class in pysap.extensions.transform) db14 (class in pysap.extensions.transform) db15 (class in pysap.extensions.transform) db16 (class in pysap.extensions.transform) db17 (class in pysap.extensions.transform) db18 (class in pysap.extensions.transform) db19 (class in pysap.extensions.transform) db2 (class in pysap.extensions.transform) db20 (class in pysap.extensions.transform) db21 (class in pysap.extensions.transform) db22 (class in pysap.extensions.transform) db23 (class in pysap.extensions.transform) db24 (class in pysap.extensions.transform) db25 (class in pysap.extensions.transform) db26 (class in pysap.extensions.transform) db27 (class in pysap.extensions.transform) db28 (class in pysap.extensions.transform) db29 (class in pysap.extensions.transform) db3 (class in pysap.extensions.transform) db30 (class in pysap.extensions.transform) db31 (class in pysap.extensions.transform) db32 (class in pysap.extensions.transform)

db33 (class in pysap.extensions.transform) db34 (class in pysap.extensions.transform) db35 (class in pysap.extensions.transform) db36 (class in pysap.extensions.transform) db37 (class in pysap.extensions.transform) db38 (class in pysap.extensions.transform) db4 (class in pysap.extensions.transform) db5 (class in pysap.extensions.transform) db6 (class in pysap.extensions.transform) db7 (class in pysap.extensions.transform) db8 (class in pysap.extensions.transform) db9 (class in pysap.extensions.transform) decimated() (ISAPWaveletTransformBase class method) decompose() (in module astro.denoising.wavelet) DecompositionOnScalingFunction (class in pysap.extensions.transform) Deconvolve (class in pysap.extensions.sparse2d) deconvolve() (Deconvolve method) denoise() (in module astro.denoising.denoise) DenoiseTestCase (class in astro.tests.test_denoising) DictionaryLearning (class in mri.operators.linear.dictionary) discard_frequency_outliers() (in module mri.operators.fourier.utils.processing) dmey (class in pysap.extensions.transform) download_file() (in module pysap.data) dtype (Image property) (KspaceGeneratorBase property) DualGapCost (class in etomo.optimizers.utils.cost) (class in mri.optimizers.utils.cost)

E

estimate_density_compensation() (in module etomo.operators.fourier.utils) (in module mri.operators.fourier.utils.processing) etomo module etomo.info module etomo.operators module etomo.operators.fourier module etomo.operators.fourier.fourier module etomo.operators.fourier.utils module etomo.operators.gradient module etomo.operators.gradient.gradient module etomo.operators.linear module etomo.operators.linear.base module etomo.operators.linear.HOTV module etomo.operators.linear.utils module etomo.operators.linear.wavelet module

etomo.operators.radon module etomo.operators.radon.radon module etomo.operators.utils module etomo.optimizers module etomo.optimizers.forward_backward module etomo.optimizers.primal_dual module etomo.optimizers.utils module etomo.optimizers.utils.cost module etomo.optimizers.utils.reweight module etomo.reconstructors module etomo.reconstructors.base module etomo.reconstructors.forwardtomo module Exception extract_k_space_center_and_locations() (in module mri.reconstructors.utils.extract_sensitivity_maps) extract_patches_from_2d_images() (in module mri.operators.linear.utils)

F

FastCurveletTransform (class in pysap.extensions.transform) fbsp (class in pysap.extensions.transform) FeauveauWaveletTransform (class in pysap.extensions.transform) FeauveauWaveletTransformWithoutUndersampling (class in pysap.extensions.transform) FFT (class in mri.operators.fourier.cartesian) Filter (class in pysap.extensions.sparse2d) filter() (Filter method) find_module() (PluginsMetaImportHook method) fista() (in module etomo.optimizers.forward_backward) (in module mri.optimizers.forward_backward) fista_logo() (in module pysap.utils) FITS (class in pysap.base.loaders.fits)

flatten() (in module etomo.operators.linear.utils) (in module pysap.base.utils) flatten_decimated_1_bands() (in module pysap.extensions.formating) flatten_decimated_3_bands() (in module pysap.extensions.formating) flatten_decimated_feauveau() (in module pysap.extensions.formating) flatten_fct (WaveletTransformBase attribute) flatten_swtn() (in module etomo.operators.linear.utils) flatten_undecimated_n_bands() (in module pysap.extensions.formating) flatten_vector() (in module pysap.extensions.formating) flatten_wave() (in module etomo.operators.linear.utils) FourierBase (class in etomo.operators.fourier.fourier) FourierOperatorBase (class in mri.operators.fourier.base)

G

gather_result() (in module mri.scripts.gridsearch) gaus1 (class in pysap.extensions.transform) gaus2 (class in pysap.extensions.transform) gaus3 (class in pysap.extensions.transform) gaus4 (class in pysap.extensions.transform) gaus5 (class in pysap.extensions.transform) gaus6 (class in pysap.extensions.transform) gaus7 (class in pysap.extensions.transform) gaus8 (class in pysap.extensions.transform) generate_flat_patches() (in module mri.operators.linear.utils) generate_kspace_etomo_2D() (in module etomo.operators.fourier.utils) generate_locations_etomo_2D() (in module etomo.operators.fourier.utils) GenericCost (class in etomo.optimizers.utils.cost) (class in mri.optimizers.utils.cost) get_coeff() (WaveletPywt method) get_cospy_filters() (in module astro.deconvolution.wavelet_filters) get_hb() (in module pysap.extensions.formating) get_hbl() (in module pysap.extensions.formating) get_hbr() (in module pysap.extensions.formating) get_hl() (in module pysap.extensions.formating)

get_hr() (in module pysap.extensions.formating) get_ht() (in module pysap.extensions.formating) get_htl() (in module pysap.extensions.formating) get_htr() (in module pysap.extensions.formating) get_loader() (in module pysap.base.io) get_sample_data() (in module pysap.data) get_saver() (in module pysap.base.io) get_Smaps() (in module mri.reconstructors.utils.extract_sensitivity_maps) get_smaps() (SelfCalibrationReconstructor method) get_weights() (in module astro.deconvolution.deconvolve) gpuNUFFT (class in etomo.operators.fourier.fourier) GradAnalysis (class in etomo.operators.gradient.gradient) (class in mri.operators.gradient.gradient) GradBaseMRI (class in mri.operators.gradient.base) GradSelfCalibrationAnalysis (class in mri.operators.gradient.gradient) GradSelfCalibrationSynthesis (class in mri.operators.gradient.gradient) GradSynthesis (class in etomo.operators.gradient.gradient) (class in mri.operators.gradient.gradient) gridded_inverse_fourier_transform_nd() (in module mri.operators.fourier.utils.processing) gridded_inverse_fourier_transform_stack() (in module mri.operators.fourier.utils.processing)

H

haar (class in pysap.extensions.transform) HaarWaveletTransform (class in pysap.extensions.transform) HalfPyramidalTransform (class in pysap.extensions.transform)

histogram() (in module pysap.plotting.utils) HOTV (class in etomo.operators.linear.HOTV) HOTV_3D (class in etomo.operators.linear.HOTV) http_error_206() (ResumeURLOpener method)

I

Image (class in pysap.base.image) inflated_decimated_1_bands() (in module pysap.extensions.formating) inflated_decimated_3_bands() (in module pysap.extensions.formating) inflated_decimated_feauveau() (in module pysap.extensions.formating) inflated_undecimated_n_bands() (in module pysap.extensions.formating) inflated_vector() (in module pysap.extensions.formating)

info (WaveletTransformBase property) info() (in module pysap.configure) initialize_gradient_op() (ReconstructorBase method), [1] is_decimated (WaveletTransformBase attribute) isap_transform_id (WaveletTransformBase attribute) ISAPWaveletTransformBase (class in pysap.extensions.transform) IsotropicAndCompactSupportWaveletInFourierSpace (class in pysap.extensions.transform)

K

KspaceGeneratorBase (class in mri.generators.base)

L

l2norm() (DictionaryLearning method) (HOTV method) (HOTV_3D method) (LinearBase method) (WaveletN method) (WaveletUD2 method) launch_grid() (in module mri.scripts.gridsearch) learn_dictionary() (in module mri.operators.linear.utils) LinearBase (class in etomo.operators.linear.base) LinearWaveletTransformATrousAlgorithm (class in pysap.extensions.transform) LineColumnWaveletTransform1D1D (class in pysap.extensions.transform)

load() (FITS method) (in module pysap.base.io) (LoaderBase method) (MAT method) (NIFTI method) (npBinary method) (TIF method) load_image() (in module pysap.utils) load_module() (PluginsMetaImportHook method) load_transform() (in module pysap.utils) LoaderBase (class in pysap.base.loaders.loader_base) logo() (in module pysap.utils)

M

MallatWaveletTransform79Filters (class in pysap.extensions.transform) mask (ColumnFFT property) MAT (class in pysap.base.loaders.mat) md5_sum_file() (in module pysap.data) MetaRegister (class in pysap.base.transform) mexh (class in pysap.extensions.transform) MeyerWaveletsCompactInFourierSpace (class in pysap.extensions.transform) min_max_normalize() (in module mri.operators.linear.utils) MixedHalfPyramidalWTAndMedianMethod (class in pysap.extensions.transform) MixedWTAndPMTMethod (class in pysap.extensions.transform) modified() (Image method) module astro astro.deconvolution astro.deconvolution.deconvolve astro.deconvolution.linear astro.deconvolution.wavelet_filters astro.denoising astro.denoising.denoise astro.denoising.noise astro.denoising.wavelet astro.tests astro.tests.test_denoising etomo etomo.info etomo.operators etomo.operators.fourier etomo.operators.fourier.fourier etomo.operators.fourier.utils etomo.operators.gradient etomo.operators.gradient.gradient etomo.operators.linear etomo.operators.linear.base etomo.operators.linear.HOTV etomo.operators.linear.utils etomo.operators.linear.wavelet etomo.operators.radon etomo.operators.radon.radon etomo.operators.utils etomo.optimizers etomo.optimizers.forward_backward etomo.optimizers.primal_dual etomo.optimizers.utils etomo.optimizers.utils.cost etomo.optimizers.utils.reweight etomo.reconstructors etomo.reconstructors.base etomo.reconstructors.forwardtomo mri mri.generators mri.generators.base mri.generators.cartesian mri.info mri.operators mri.operators.base mri.operators.fourier mri.operators.fourier.base mri.operators.fourier.cartesian mri.operators.fourier.non_cartesian mri.operators.fourier.online mri.operators.fourier.orc_wrapper mri.operators.fourier.utils mri.operators.fourier.utils.orc_coefficients mri.operators.fourier.utils.processing mri.operators.gradient mri.operators.gradient.base mri.operators.gradient.gradient mri.operators.gradient.online mri.operators.gradient.utils mri.operators.linear mri.operators.linear.dictionary mri.operators.linear.utils mri.operators.linear.wavelet mri.operators.proximity mri.operators.proximity.ordered_weighted_l1_norm mri.operators.proximity.weighted mri.operators.utils mri.optimizers mri.optimizers.base mri.optimizers.forward_backward mri.optimizers.primal_dual mri.optimizers.utils mri.optimizers.utils.cost mri.optimizers.utils.reweight mri.reconstructors mri.reconstructors.base mri.reconstructors.calibrationless mri.reconstructors.self_calibrating mri.reconstructors.single_channel mri.reconstructors.utils mri.reconstructors.utils.extract_sensitivity_maps mri.scripts mri.scripts.gridsearch pysap pysap.apps pysap.base pysap.base.exceptions pysap.base.image pysap.base.io pysap.base.loaders pysap.base.loaders.fits pysap.base.loaders.loader_base pysap.base.loaders.mat pysap.base.loaders.nifti pysap.base.loaders.numpy_binary pysap.base.loaders.tif pysap.base.observable pysap.base.plugins pysap.base.transform pysap.base.utils pysap.configure pysap.data pysap.extensions pysap.extensions.formating pysap.extensions.sparse2d pysap.extensions.tools pysap.extensions.transform pysap.extensions.wrapper pysap.info pysap.plotting pysap.plotting.image pysap.plotting.transform pysap.plotting.utils pysap.plugins pysap.utils

monkeypatch() (in module pysap.base.utils) morl (class in pysap.extensions.transform) MorphologicalMedianTransform (class in pysap.extensions.transform) MorphologicalMinmaxTransform (class in pysap.extensions.transform) MorphologicalPyramidalMinmaxTransform (class in pysap.extensions.transform) MR2D1D (class in pysap.extensions.sparse2d) mr2d1d_trans() (in module pysap.extensions.tools) mr3d_filter() (in module pysap.extensions.tools) mr3d_recons() (in module pysap.extensions.tools) mr3d_transform() (in module pysap.extensions.tools) mr_deconv() (in module pysap.extensions.tools) mr_filter() (in module pysap.extensions.tools) mr_recons() (in module pysap.extensions.tools) mr_transform() (in module pysap.extensions.tools) mReweight (class in etomo.optimizers.utils.reweight) (class in mri.optimizers.utils.reweight) mri module mri.generators module mri.generators.base module mri.generators.cartesian module mri.info module mri.operators module mri.operators.base module mri.operators.fourier module mri.operators.fourier.base module mri.operators.fourier.cartesian module mri.operators.fourier.non_cartesian module mri.operators.fourier.online module mri.operators.fourier.orc_wrapper module mri.operators.fourier.utils module mri.operators.fourier.utils.orc_coefficients module mri.operators.fourier.utils.processing module mri.operators.gradient module mri.operators.gradient.base module mri.operators.gradient.gradient module mri.operators.gradient.online module mri.operators.gradient.utils module mri.operators.linear module mri.operators.linear.dictionary module mri.operators.linear.utils module mri.operators.linear.wavelet module mri.operators.proximity module mri.operators.proximity.ordered_weighted_l1_norm module mri.operators.proximity.weighted module mri.operators.utils module mri.optimizers module mri.optimizers.base module mri.optimizers.forward_backward module mri.optimizers.primal_dual module mri.optimizers.utils module mri.optimizers.utils.cost module mri.optimizers.utils.reweight module mri.reconstructors module mri.reconstructors.base module mri.reconstructors.calibrationless module mri.reconstructors.self_calibrating module mri.reconstructors.single_channel module mri.reconstructors.utils module mri.reconstructors.utils.extract_sensitivity_maps module mri.scripts module mri.scripts.gridsearch module mu (WeightedSparseThreshold property), [1]

N

n_coils (FFT attribute) (FourierOperatorBase attribute) (FourierOperatorBase property) (gpuNUFFT attribute) (WaveletN attribute) n_jobs (FFT attribute) (WaveletN attribute) name (WaveletTransformBase attribute) nb_band_per_scale (WaveletTransformBase attribute) nb_scale (WaveletN attribute)

ndim (Image property) NIFTI (class in pysap.base.loaders.nifti) noise_est() (in module astro.denoising.noise) NoiseTestCase (class in astro.tests.test_denoising) NonCartesianFFT (class in mri.operators.fourier.non_cartesian) NonOrthogonalUndecimatedTransform (class in pysap.extensions.transform) normalize_frequency_locations() (in module mri.operators.fourier.utils.processing) normalized (NUFFT2 attribute) notify_observers() (Observable method) npBinary (class in pysap.base.loaders.numpy_binary) NUFFT2 (class in etomo.operators.fourier.fourier)

O

obs_data (OnlineGradMixin property) Observable (class in pysap.base.observable) OnLine44AndOnColumn53 (class in pysap.extensions.transform) OnLine53AndOnColumn44 (class in pysap.extensions.transform) OnlineGradAnalysis (class in mri.operators.gradient.online) OnlineGradMixin (class in mri.operators.gradient.online) OnlineGradSynthesis (class in mri.operators.gradient.online) op() (ColumnFFT method) (DictionaryLearning method) (FFT method) (FourierBase method) (FourierOperatorBase method) (gpuNUFFT method) (LinearBase method) (NonCartesianFFT method) (NUFFT2 method) (OperatorBase method) (ORCFFTWrapper method) (Radon2D method) (Radon3D method) (RadonBase method) (WaveletN method) (WaveletUD2 method)

operator (gpuNUFFT attribute) OperatorBase (class in mri.operators.base) ORCFFTWrapper (class in mri.operators.fourier.orc_wrapper) OWL (class in mri.operators.proximity) (class in mri.operators.proximity.ordered_weighted_l1_norm)

P

plot_data() (in module pysap.plotting.image) plot_transform() (in module pysap.plotting.transform) PluginsMetaImportHook (class in pysap.base.plugins) pogm() (in module etomo.optimizers.forward_backward) (in module mri.optimizers.forward_backward) progress_bar() (in module pysap.data) psf_convolve() (in module astro.deconvolution.deconvolve) PyramidalBsplineWaveletTransform (class in pysap.extensions.transform) PyramidalLaplacian (class in pysap.extensions.transform) PyramidalLinearWaveletTransform (class in pysap.extensions.transform) PyramidalMedianTransform (class in pysap.extensions.transform) PyramidalWaveletTransformInFourierSpaceAlgo1 (class in pysap.extensions.transform) PyramidalWaveletTransformInFourierSpaceAlgo2 (class in pysap.extensions.transform) pysap module pysap.apps module pysap.base module pysap.base.exceptions module pysap.base.image module pysap.base.io module pysap.base.loaders module pysap.base.loaders.fits module pysap.base.loaders.loader_base module pysap.base.loaders.mat module pysap.base.loaders.nifti module pysap.base.loaders.numpy_binary module pysap.base.loaders.tif module

pysap.base.observable module pysap.base.plugins module pysap.base.transform module pysap.base.utils module pysap.configure module pysap.data module pysap.extensions module pysap.extensions.formating module pysap.extensions.sparse2d module pysap.extensions.tools module pysap.extensions.transform module pysap.extensions.wrapper module pysap.info module pysap.plotting module pysap.plotting.image module pysap.plotting.transform module pysap.plotting.utils module pysap.plugins module pysap.utils module PyWaveletTransformBase (class in pysap.extensions.transform) pywt_class_factory() (in module pysap.extensions.transform)

R

Radon2D (class in etomo.operators.radon.radon) Radon3D (class in etomo.operators.radon.radon) RadonBase (class in etomo.operators.radon.radon) rbio11 (class in pysap.extensions.transform) rbio13 (class in pysap.extensions.transform) rbio15 (class in pysap.extensions.transform) rbio22 (class in pysap.extensions.transform) rbio24 (class in pysap.extensions.transform) rbio26 (class in pysap.extensions.transform) rbio28 (class in pysap.extensions.transform) rbio31 (class in pysap.extensions.transform) rbio33 (class in pysap.extensions.transform) rbio35 (class in pysap.extensions.transform) rbio37 (class in pysap.extensions.transform) rbio39 (class in pysap.extensions.transform) rbio44 (class in pysap.extensions.transform)

rbio55 (class in pysap.extensions.transform) rbio68 (class in pysap.extensions.transform) recombine() (in module astro.denoising.wavelet) reconstruct() (MR2D1D method) (ReconstructorBase method), [1] (SelfCalibrationReconstructor method) reconstruct_case() (_TestCase method) ReconstructorBase (class in etomo.reconstructors.base) (class in mri.reconstructors.base) REGISTRY (MetaRegister attribute) remove_observer() (Observable method) reset() (KspaceGeneratorBase method) ResumeURLOpener (class in pysap.data) reweight() (mReweight method), [1] run_algorithm() (in module mri.optimizers.base) run_online_algorithm() (in module mri.optimizers.base)

S

samples (FFT attribute) (NUFFT2 attribute) save() (FITS method) (in module pysap.base.io) (LoaderBase method) (MAT method) (NIFTI method) (npBinary method) (TIF method) save_image() (in module pysap.utils) scales_lengths (WaveletTransformBase attribute) scales_padds (WaveletTransformBase attribute) scaling() (in module pysap.plotting.utils) scroll_axis (Image property) SelfCalibrationReconstructor (class in mri.reconstructors.self_calibrating) set_coeff() (WaveletPywt method) set_hb() (in module pysap.extensions.formating) set_hbl() (in module pysap.extensions.formating) set_hbr() (in module pysap.extensions.formating) set_hl() (in module pysap.extensions.formating) set_hr() (in module pysap.extensions.formating) set_ht() (in module pysap.extensions.formating) set_htl() (in module pysap.extensions.formating) set_htr() (in module pysap.extensions.formating) set_smaps() (SelfCalibrationReconstructor method) setUp() (DenoiseTestCase method) (NoiseTestCase method) (WaveletTestCase method) shan (class in pysap.extensions.transform) shape (FFT attribute) (FourierOperatorBase attribute) (FourierOperatorBase property) (gpuNUFFT attribute) (Image property) (KspaceGeneratorBase property) (NUFFT2 attribute)

show() (Deconvolve method) (Filter method) (Image method) (WaveletTransformBase method) sigma_clip() (in module astro.denoising.noise) sigma_scales() (in module astro.denoising.noise) SignalObject (class in pysap.base.observable) SingleChannelReconstructor (class in mri.reconstructors.single_channel) spacing (Image property) Sparse2dConfigurationError Sparse2dError Sparse2dRuntimeError Sparse2dWrapper (class in pysap.extensions.wrapper) sparse_deconv_condatvu() (in module astro.deconvolution.deconvolve) sym10 (class in pysap.extensions.transform) sym11 (class in pysap.extensions.transform) sym12 (class in pysap.extensions.transform) sym13 (class in pysap.extensions.transform) sym14 (class in pysap.extensions.transform) sym15 (class in pysap.extensions.transform) sym16 (class in pysap.extensions.transform) sym17 (class in pysap.extensions.transform) sym18 (class in pysap.extensions.transform) sym19 (class in pysap.extensions.transform) sym2 (class in pysap.extensions.transform) sym20 (class in pysap.extensions.transform) sym3 (class in pysap.extensions.transform) sym4 (class in pysap.extensions.transform) sym5 (class in pysap.extensions.transform) sym6 (class in pysap.extensions.transform) sym7 (class in pysap.extensions.transform) sym8 (class in pysap.extensions.transform) sym9 (class in pysap.extensions.transform) synthesis() (WaveletTransformBase method)

T

tearDown() (DenoiseTestCase method) (NoiseTestCase method) (WaveletTestCase method) TempDir (class in pysap.utils) test_decompose() (WaveletTestCase method) test_denoise() (DenoiseTestCase method) test_noise_est() (NoiseTestCase method) test_recombine() (WaveletTestCase method)

test_sigma_clip() (NoiseTestCase method) test_sigma_scales() (NoiseTestCase method) TIF (class in pysap.base.loaders.tif) timer() (in module mri.operators.linear.utils) TomoReconstructor (class in etomo.reconstructors.forwardtomo) transform() (MR2D1D method) trf (WaveletTransformBase attribute) two_dico (DictionaryLearning attribute)

U

undecimated() (ISAPWaveletTransformBase class method) UndecimatedBiOrthogonalTransform (class in pysap.extensions.transform) UndecimatedDiadicWaveletTransform (class in pysap.extensions.transform) UndecimatedHaarTransformATrousAlgorithm (class in pysap.extensions.transform) unflatten() (in module etomo.operators.linear.utils) (in module pysap.base.utils)

unflatten_fct (WaveletTransformBase attribute) unflatten_swtn() (in module etomo.operators.linear.utils) unflatten_wave() (in module etomo.operators.linear.utils) uses_sense (FourierOperatorBase attribute) (FourierOperatorBase property)

V

verbose (WaveletN attribute)

W

Wavelet3DTransformViaLiftingScheme (class in pysap.extensions.transform) wavelet_noise_estimate() (in module mri.operators.proximity.weighted) wavelet_threshold_estimate() (in module mri.operators.proximity.weighted) WaveletConvolve2 (class in astro.deconvolution.linear) WaveletN (class in mri.operators.linear.wavelet) WaveletPywt (class in etomo.operators.linear.wavelet) WaveletTestCase (class in astro.tests.test_denoising)

WaveletTransformBase (class in pysap.base.transform) WaveletTransformInFourierSpace (class in pysap.extensions.transform) WaveletTransformViaLiftingScheme (class in pysap.extensions.transform) WaveletUD2 (class in mri.operators.linear.wavelet) wavelist() (in module pysap.utils) WeightedSparseThreshold (class in mri.operators.proximity) (class in mri.operators.proximity.weighted) with_metaclass() (in module pysap.base.utils)