Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Z _ __all__ (in module snake.core) (in module snake.core.engine) (in module snake.core.handlers) (in module snake.core.handlers.activations) (in module snake.core.handlers.motion) (in module snake.core.phantom) (in module snake.core.sampling) (in module snake.mrd_utils) (in module snake.toolkit.reconstructors) __call__() (snake._meta.MethodRegister method) (snake._meta.Singleton method) (snake.core.engine.base.BaseAcquisitionEngine method) (snake.core.parallel.SHM_Wrapper method) __deepcopy__() (snake.core.phantom.static.Phantom method) __engine__ (snake.core.sampling.base.BaseSampler attribute) (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.EVI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.LoadTrajectorySampler attribute) (snake.core.sampling.samplers.NonCartesianAcquisitionSampler attribute) __engine_name__ (snake.core.engine.base.BaseAcquisitionEngine attribute) (snake.core.engine.cartesian.EPIAcquisitionEngine attribute) (snake.core.engine.cartesian.EVIAcquisition attribute) (snake.core.engine.nufft.NufftAcquisitionEngine attribute) __enter__() (snake.mrd_utils.loader.MRDLoader method) __exit__() (snake.mrd_utils.loader.MRDLoader method) __getitem__() (snake._meta.ENVCONFIG class method) (snake._meta.NoCaseEnumMeta method) __handler_name__ (snake.core.handlers.activations.activations.BlockActivationHandler attribute) (snake.core.handlers.base.AbstractHandler attribute) (snake.core.handlers.fov.FOVHandler attribute) (snake.core.handlers.motion.image.RandomMotionImageHandler attribute) (snake.core.handlers.noise.NoiseHandler attribute) __len__() (snake.mrd_utils.loader.MRDLoader method) __mp_mode__ (snake.core.engine.cartesian.EPIAcquisitionEngine attribute) (snake.core.engine.cartesian.EVIAcquisition attribute) (snake.core.engine.nufft.NufftAcquisitionEngine attribute) __new__() (snake._meta.MetaDCRegister method) __post_init__() (snake.core.handlers.activations.activations.BlockActivationHandler method) (snake.core.handlers.motion.image.RandomMotionImageHandler method) (snake.core.simulation.SimConfig method) (snake.toolkit.reconstructors.base.BaseReconstructor method) __reconstructor_name__ (snake.toolkit.reconstructors.base.BaseReconstructor attribute) (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor attribute) __registry__ (snake.core.engine.base.BaseAcquisitionEngine attribute) (snake.core.handlers.base.AbstractHandler attribute) (snake.core.sampling.base.BaseSampler attribute) (snake.toolkit.reconstructors.base.BaseReconstructor attribute) __repr__() (snake.core.phantom.static.Phantom method) __requires__ (snake.toolkit.reconstructors.base.BaseReconstructor attribute) __sampler_name__ (snake.core.sampling.base.BaseSampler attribute) (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.EVI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.LoadTrajectorySampler attribute) (snake.core.sampling.samplers.RotatedStackOfSpiralSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) __str__() (snake.toolkit.reconstructors.pysap.SequentialReconstructor method) __version__ (in module snake._version) __version_tuple__ (in module snake._version) _acquire_ksp_job() (snake.core.engine.base.BaseAcquisitionEngine method) _all_waveform_infos() (snake.mrd_utils.loader.MRDLoader method) _apply_transform() (in module snake.core.handlers.fov) _birdcage_maps() (in module snake.core.smaps) _dataset (snake.mrd_utils.loader.MRDLoader property) _from_waveform() (snake.core.phantom.dynamic.DynamicData class method) _get_axis_properties() (in module snake.toolkit.plotting) _get_chunk_list() (snake.core.engine.base.BaseAcquisitionEngine method) (snake.core.engine.cartesian.EPIAcquisitionEngine method) (snake.core.engine.cartesian.EVIAcquisition method) _get_hdiv_vdiv() (in module snake.toolkit.plotting) _get_image_data() (snake.mrd_utils.loader.MRDLoader method) _init_model_nufft() (snake.core.engine.nufft.NufftAcquisitionEngine static method) _instances (snake._meta.Singleton attribute) _job_get_T2s_decay() (snake.core.engine.base.BaseAcquisitionEngine static method) _job_model_simple() (snake.core.engine.base.BaseAcquisitionEngine static method) (snake.core.engine.cartesian.EPIAcquisitionEngine static method) (snake.core.engine.cartesian.EVIAcquisition static method) (snake.core.engine.nufft.NufftAcquisitionEngine static method) _job_model_T2s() (snake.core.engine.base.BaseAcquisitionEngine static method) (snake.core.engine.cartesian.EPIAcquisitionEngine static method) (snake.core.engine.cartesian.EVIAcquisition static method) (snake.core.engine.nufft.NufftAcquisitionEngine static method) _job_trajectories() (snake.core.engine.base.BaseAcquisitionEngine method) (snake.core.engine.cartesian.EPIAcquisitionEngine method) (snake.core.engine.cartesian.EVIAcquisition method) (snake.core.engine.nufft.NufftAcquisitionEngine method) _mr_relaxation_parameters() (in module snake.core.phantom.shepp_logan) _read_image() (snake.mrd_utils.loader.MRDLoader method) _read_waveform() (snake.mrd_utils.loader.MRDLoader method) _read_xml_header() (snake.mrd_utils.loader.MRDLoader method) _reconstruct_cartesian() (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor method) _reconstruct_cartesian_frame() (in module snake.toolkit.reconstructors.pysap) _reconstruct_frame() (snake.toolkit.reconstructors.pysap.SequentialReconstructor method) _reconstruct_nufft() (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor method) _repr_html_ (snake.core.simulation.GreConfig attribute) (snake.core.simulation.HardwareConfig attribute) (snake.core.simulation.SimConfig attribute) _repr_html_() (in module snake.core.simulation) _single_frame() (snake.core.sampling.base.BaseSampler method) (snake.core.sampling.samplers.EPI3dAcquisitionSampler method) (snake.core.sampling.samplers.EVI3dAcquisitionSampler method) (snake.core.sampling.samplers.LoadTrajectorySampler method) (snake.core.sampling.samplers.StackOfSpiralSampler method) _write_chunk_data() (snake.core.engine.base.BaseAcquisitionEngine method) (snake.core.engine.cartesian.EPIAcquisitionEngine method) (snake.core.engine.cartesian.EVIAcquisition method) (snake.core.engine.nufft.NufftAcquisitionEngine method) A AbstractHandler (class in snake.core.handlers.base) accelz (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) ACQ (class in snake.mrd_utils.utils) acquisition() (in module snake.toolkit.cli.acquisition) acquisition_cli (in module snake.toolkit.cli.acquisition) acsz (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) ActivationMixin (class in snake.core.handlers.activations.activations) add_all_acq_mrd() (snake.core.sampling.base.BaseSampler method) (snake.core.sampling.samplers.EPI3dAcquisitionSampler method) (snake.core.sampling.samplers.EVI3dAcquisitionSampler method) (snake.core.sampling.samplers.NonCartesianAcquisitionSampler method) add_coil_cov_mrd() (in module snake.mrd_utils.writer) add_dynamic_mrd() (in module snake.mrd_utils.writer) add_motion() (in module snake.core.handlers.motion.utils) add_phantom_mrd() (in module snake.mrd_utils.writer) add_tissue() (snake.core.phantom.static.Phantom method) anat_shape (snake.core.phantom.static.Phantom property) AngleRotation (class in snake.core.sampling.factories) angles (snake.core.handlers.fov.FOVHandler attribute) AnyPath (in module snake.core.engine.base) apply() (snake.core.phantom.dynamic.DynamicData method) apply_motion_to_phantom() (in module snake.core.handlers.motion.image) apply_noise() (in module snake.core.handlers.noise) apply_rotation_at_center() (in module snake.core.handlers.motion.utils) apply_shift (in module snake.core.handlers.motion.utils) apply_weights() (in module snake.core.handlers.utils) (snake.core.handlers.activations.activations.ActivationMixin static method) array_from_shm() (in module snake.core.parallel) array_to_shm() (in module snake.core.parallel) ArrayProps (class in snake.core.parallel) axis3dcut() (in module snake.toolkit.plotting) B b64encode2obj() (in module snake.mrd_utils.utils) base_tissue_name (snake.core.handlers.activations.activations.ActivationMixin attribute) BaseAcquisitionEngine (class in snake.core.engine.base) BaseReconstructor (class in snake.toolkit.reconstructors.base) BaseSampler (class in snake.core.sampling.base) block_design() (in module snake.core.handlers.activations.bold) block_off (snake.core.handlers.activations.activations.BlockActivationHandler attribute) block_on (snake.core.handlers.activations.activations.BlockActivationHandler attribute) BlockActivationHandler (class in snake.core.handlers.activations.activations) BRAINWEB_OCCIPITAL_ROI (in module snake.core.handlers.activations.roi) C cache_dir (snake.toolkit.cli.config.ConfigSNAKE attribute) CartesianFrameDataLoader (class in snake.mrd_utils.loader) center (snake.core.handlers.fov.FOVHandler attribute) CENTER_OUT (snake.core.sampling.factories.VDSorder attribute) check_trajectory() (in module snake.core.sampling.factories) chi (snake.core.phantom.static.PropTissueEnum attribute) chunk_size (snake.toolkit.cli.config.EngineConfig attribute) cleanup_cuda() (in module snake.toolkit.cli.config) COLD (snake.toolkit.reconstructors.pysap.RestartStrategy attribute) COMPRESSION1 (snake.mrd_utils.utils.ACQ attribute) COMPRESSION2 (snake.mrd_utils.utils.ACQ attribute) COMPRESSION3 (snake.mrd_utils.utils.ACQ attribute) COMPRESSION4 (snake.mrd_utils.utils.ACQ attribute) compute_backend (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) conf_validator() (in module snake.toolkit.cli.config) ConfigSNAKE (class in snake.toolkit.cli.config) constant (snake.core.sampling.base.BaseSampler attribute) (snake.core.sampling.samplers.LoadTrajectorySampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) copy() (snake.core.phantom.static.Phantom method) cs (in module snake.toolkit.cli.config) D data (snake.core.phantom.dynamic.DynamicData attribute) (snake.core.phantom.dynamic.KspaceDynamicData attribute) default_gre (in module snake.core.simulation) default_hardware (in module snake.core.simulation) delta_r2s (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) density_compensation (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor attribute) dir_cos() (in module snake.core.sampling.samplers) dtype (snake.core.parallel.ArrayProps attribute) dunder_name (snake._meta.MetaDCRegister attribute) (snake.core.engine.base.MetaEngine attribute) (snake.core.handlers.base.MetaHandler attribute) (snake.core.sampling.base.MetaSampler attribute) (snake.toolkit.reconstructors.base.MetaReconstructor attribute) duration (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) dwell_time_ms (snake.core.simulation.HardwareConfig attribute) DynamicData (class in snake.core.phantom.dynamic) E engine (snake.toolkit.cli.config.ConfigSNAKE attribute) engine_model (snake.mrd_utils.loader.MRDLoader property) EngineConfig (class in snake.toolkit.cli.config) ENVCONFIG (class in snake._meta) EnvConfig (in module snake._meta) EPI3dAcquisitionSampler (class in snake.core.sampling.samplers) EPIAcquisitionEngine (class in snake.core.engine.cartesian) EQUISPACED (snake.core.sampling.factories.VDSpdf attribute) event_condition (snake.core.handlers.activations.activations.ActivationMixin attribute) event_name (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) (snake.toolkit.cli.config.StatConfig attribute) EVI3dAcquisitionSampler (class in snake.core.sampling.samplers) evi_factory() (in module snake.core.sampling.factories) EVIAcquisition (class in snake.core.engine.cartesian) extract_rotated_3d_region() (in module snake.core.handlers.fov) F FA (snake.core.simulation.GreConfig attribute) fft() (in module snake.core.engine.utils) (in module snake.toolkit.reconstructors.fourier) field (snake.core.simulation.HardwareConfig attribute) filename (snake.toolkit.cli.config.ConfigSNAKE attribute) FIRST_IN_AVERAGE (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_CONTRAST (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_ENCODE_STEP1 (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_ENCODE_STEP2 (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_PHASE (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_REPETITION (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_SEGMENT (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_SET (snake.mrd_utils.utils.ACQ attribute) FIRST_IN_SLICE (snake.mrd_utils.utils.ACQ attribute) fix_angle_rotation() (snake.core.sampling.samplers.RotatedStackOfSpiralSampler method) flip2center() (in module snake.core.sampling.factories) fov_mm (snake.core.simulation.SimConfig attribute) FOVHandler (class in snake.core.handlers.fov) frame_index (snake.core.sampling.samplers.RotatedStackOfSpiralSampler attribute) from_brainweb() (snake.core.phantom.static.Phantom class method) from_cfg() (snake.core.handlers.base.HandlerList class method) from_guerin_kern() (snake.core.phantom.static.Phantom class method) from_mrd_dataset() (snake.core.phantom.static.Phantom class method) from_shared_memory() (snake.core.phantom.static.Phantom class method) from_shepp_logan() (snake.core.phantom.static.Phantom class method) func (snake.core.phantom.dynamic.DynamicData attribute) (snake.core.phantom.dynamic.KspaceDynamicData attribute) G GAUSSIAN (snake.core.sampling.factories.VDSpdf attribute) get_all_dynamic() (snake.mrd_utils.loader.MRDLoader method) get_bold() (in module snake.core.handlers.activations.bold) get_cartesian_mask() (in module snake.core.sampling.factories) get_coil_cov() (snake.mrd_utils.loader.MRDLoader method) get_contrast_gre() (in module snake.core.engine.utils) get_coolgraywarm() (in module snake.toolkit.plotting) get_dynamic() (snake.core.handlers.activations.activations.ActivationMixin method) (snake.core.handlers.base.AbstractHandler method) (snake.core.handlers.motion.image.RandomMotionImageHandler method) (snake.core.handlers.noise.NoiseHandler method) (snake.mrd_utils.loader.MRDLoader method) get_dynamic_kspace() (snake.core.handlers.base.AbstractHandler method) get_event_ts() (in module snake.core.handlers.activations.bold) get_handler() (in module snake.core.handlers.base) get_ideal_phantom() (in module snake.core.engine.utils) get_indices_inside_ellipsoid() (in module snake.core.handlers.activations.roi) get_kspace_frame() (snake.mrd_utils.loader.CartesianFrameDataLoader method) (snake.mrd_utils.loader.MRDLoader method) (snake.mrd_utils.loader.NonCartesianFrameDataLoader method) get_kspace_slice_loc() (in module snake.core.sampling.factories) get_mask_cuts_mask() (in module snake.toolkit.plotting) get_mrd_header() (in module snake.mrd_utils.writer) get_next_frame() (snake.core.sampling.base.BaseSampler method) (snake.core.sampling.samplers.RotatedStackOfSpiralSampler method) get_noise() (in module snake.core.engine.utils) get_phantom() (snake.mrd_utils.loader.MRDLoader method) get_phantom_state() (in module snake.core.engine.utils) get_reconstructor() (in module snake.toolkit.reconstructors.base) get_sim_conf() (snake.mrd_utils.loader.MRDLoader method) get_smaps() (in module snake.core.smaps) (snake.mrd_utils.loader.MRDLoader method) get_static() (snake.core.handlers.activations.activations.ActivationMixin method) (snake.core.handlers.base.AbstractHandler method) (snake.core.handlers.fov.FOVHandler method) (snake.core.handlers.noise.NoiseHandler method) get_waveform_id() (in module snake.mrd_utils.utils) gmax (snake.core.simulation.HardwareConfig attribute) GOLDEN (snake.core.sampling.factories.AngleRotation attribute) GOLDEN_MRI (snake.core.sampling.factories.AngleRotation attribute) GreConfig (class in snake.core.simulation) H H (in module snake.core.handlers.base) handler (in module snake.core.handlers.base) HandlerList (class in snake.core.handlers.base) handlers (snake.toolkit.cli.config.ConfigSNAKE attribute) hardware (snake.core.simulation.SimConfig attribute) HardwareConfig (class in snake.core.simulation) header() (snake.mrd_utils.loader.MRDLoader method) hrf_model (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) I idx_in_ellipse() (in module snake.core.phantom.shepp_logan) ifft() (in module snake.toolkit.reconstructors.fourier) in_kspace (snake.core.phantom.dynamic.DynamicData attribute) (snake.core.phantom.dynamic.KspaceDynamicData attribute) in_out (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.EVI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.LoadTrajectorySampler attribute) (snake.core.sampling.samplers.NonCartesianAcquisitionSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) in_shared_memory() (snake.core.phantom.static.Phantom method) init_nufft() (in module snake.toolkit.reconstructors.fourier) IS_DUMMYSCAN_DATA (snake.mrd_utils.utils.ACQ attribute) IS_HPFEEDBACK_DATA (snake.mrd_utils.utils.ACQ attribute) IS_NAVIGATION_DATA (snake.mrd_utils.utils.ACQ attribute) IS_NOISE_MEASUREMENT (snake.mrd_utils.utils.ACQ attribute) IS_PARALLEL_CALIBRATION (snake.mrd_utils.utils.ACQ attribute) IS_PARALLEL_CALIBRATION_AND_IMAGING (snake.mrd_utils.utils.ACQ attribute) IS_PHASE_STABILIZATION (snake.mrd_utils.utils.ACQ attribute) IS_PHASE_STABILIZATION_REFERENCE (snake.mrd_utils.utils.ACQ attribute) IS_PHASECORR_DATA (snake.mrd_utils.utils.ACQ attribute) IS_REVERSE (snake.mrd_utils.utils.ACQ attribute) IS_RTFEEDBACK_DATA (snake.mrd_utils.utils.ACQ attribute) IS_SURFACECOILCORRECTIONSCAN_DATA (snake.mrd_utils.utils.ACQ attribute) iter_frames() (snake.mrd_utils.loader.MRDLoader method) K KspaceDynamicData (class in snake.core.phantom.dynamic) L labels (snake.core.phantom.static.Phantom attribute) labels_idx (snake.core.phantom.static.Phantom property) LAST_IN_AVERAGE (snake.mrd_utils.utils.ACQ attribute) LAST_IN_CONTRAST (snake.mrd_utils.utils.ACQ attribute) LAST_IN_ENCODE_STEP1 (snake.mrd_utils.utils.ACQ attribute) LAST_IN_ENCODE_STEP2 (snake.mrd_utils.utils.ACQ attribute) LAST_IN_MEASUREMENT (snake.mrd_utils.utils.ACQ attribute) LAST_IN_PHASE (snake.mrd_utils.utils.ACQ attribute) LAST_IN_REPETITION (snake.mrd_utils.utils.ACQ attribute) LAST_IN_SEGMENT (snake.mrd_utils.utils.ACQ attribute) LAST_IN_SET (snake.mrd_utils.utils.ACQ attribute) LAST_IN_SLICE (snake.mrd_utils.utils.ACQ attribute) list_handlers() (in module snake.core.handlers.base) list_reconstructors() (in module snake.toolkit.reconstructors.base) LoadTrajectorySampler (class in snake.core.sampling.samplers) log (in module snake.core.parallel) (in module snake.core.phantom.dynamic) (in module snake.core.phantom.static) (in module snake.mrd_utils.loader) (in module snake.mrd_utils.writer) (in module snake.toolkit.cli.acquisition) (in module snake.toolkit.cli.reconstruction) (snake._meta.LogMixin property) (snake.core.engine.base.BaseAcquisitionEngine attribute) (snake.core.sampling.base.BaseSampler property) (snake.toolkit.reconstructors.base.BaseReconstructor attribute) logger (in module snake.core.sampling.factories) LogMixin (class in snake._meta) M main() (in module snake.toolkit.cli.main) main_cli (in module snake.toolkit.cli.main) make_base_mrd() (in module snake.mrd_utils.writer) make_hydra_cli() (in module snake.toolkit.cli.config) make_log_property() (in module snake._meta) make_smaps() (snake.core.phantom.static.Phantom method) masks (snake.core.phantom.static.Phantom attribute) max_iter_per_frame (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) max_n_shots (snake.core.simulation.SimConfig property) max_sim_time (snake.core.simulation.SimConfig attribute) MetaDCRegister (class in snake._meta) MetaEngine (class in snake.core.engine.base) MetaHandler (class in snake.core.handlers.base) MetaReconstructor (class in snake.toolkit.reconstructors.base) MetaSampler (class in snake.core.sampling.base) MethodRegister (class in snake._meta) min_onset (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) model (snake.core.engine.base.BaseAcquisitionEngine attribute) (snake.core.engine.cartesian.EPIAcquisitionEngine attribute) (snake.core.engine.cartesian.EVIAcquisition attribute) (snake.core.engine.nufft.NufftAcquisitionEngine attribute) (snake.toolkit.cli.config.EngineConfig attribute) module snake snake._meta snake._version snake.core snake.core.engine snake.core.engine.base snake.core.engine.cartesian snake.core.engine.nufft snake.core.engine.utils snake.core.handlers snake.core.handlers.activations snake.core.handlers.activations.activations snake.core.handlers.activations.bold snake.core.handlers.activations.roi snake.core.handlers.base snake.core.handlers.fov snake.core.handlers.motion snake.core.handlers.motion.image snake.core.handlers.motion.utils snake.core.handlers.noise snake.core.handlers.utils snake.core.parallel snake.core.phantom snake.core.phantom.data snake.core.phantom.dynamic snake.core.phantom.shepp_logan snake.core.phantom.static snake.core.phantom.utils snake.core.sampling snake.core.sampling.base snake.core.sampling.factories snake.core.sampling.samplers snake.core.simulation snake.core.smaps snake.mrd_utils snake.mrd_utils.loader snake.mrd_utils.utils snake.mrd_utils.writer snake.toolkit snake.toolkit.cli snake.toolkit.cli.acquisition snake.toolkit.cli.config snake.toolkit.cli.main snake.toolkit.cli.reconstruction snake.toolkit.plotting snake.toolkit.reconstructors snake.toolkit.reconstructors.base snake.toolkit.reconstructors.fourier snake.toolkit.reconstructors.pysap motion_file (snake.core.handlers.motion.image.RandomMotionImageHandler attribute) motion_file_tr_ms (snake.core.handlers.motion.image.RandomMotionImageHandler attribute) motion_generator() (in module snake.core.handlers.motion.utils) mr_ellipsoid_parameters() (in module snake.core.phantom.shepp_logan) mr_shepp_logan() (in module snake.core.phantom.shepp_logan) MRDLoader (class in snake.mrd_utils.loader) N n_acquisition (snake.mrd_utils.loader.MRDLoader property) n_coils (snake.core.simulation.HardwareConfig attribute) (snake.mrd_utils.loader.MRDLoader property) n_frames (snake.mrd_utils.loader.MRDLoader property) n_jobs (snake.toolkit.cli.config.EngineConfig attribute) (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor attribute) n_sample (snake.mrd_utils.loader.MRDLoader property) n_shot_slices (snake.core.sampling.samplers.StackOfSpiralSampler attribute) n_shots (snake.mrd_utils.loader.MRDLoader property) n_tissues (snake.core.phantom.static.Phantom property) name (snake.core.parallel.ArrayProps attribute) (snake.core.phantom.dynamic.DynamicData attribute) (snake.core.phantom.dynamic.KspaceDynamicData attribute) (snake.core.phantom.static.Phantom attribute) (snake.toolkit.cli.config.PhantomConfig attribute) nb_revolutions (snake.core.sampling.samplers.StackOfSpiralSampler attribute) NoCaseEnum (class in snake._meta) NoCaseEnumMeta (class in snake._meta) NoiseHandler (class in snake.core.handlers.noise) NonCartesianAcquisitionSampler (class in snake.core.sampling.samplers) NonCartesianFrameDataLoader (class in snake.mrd_utils.loader) nufft_backend (snake.toolkit.cli.config.EngineConfig attribute) (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor attribute) nufft_kwargs (snake.toolkit.reconstructors.base.BaseReconstructor attribute) NufftAcquisitionEngine (class in snake.core.engine.nufft) O obj2b64encode() (in module snake.mrd_utils.utils) obs_time_ms (snake.core.sampling.samplers.LoadTrajectorySampler attribute) (snake.core.sampling.samplers.NonCartesianAcquisitionSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) offset (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) optimizer (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) orderz (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) oversampling (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) P parse_sim_conf() (in module snake.mrd_utils.loader) parse_waveform_information() (in module snake.mrd_utils.loader) path (snake.core.sampling.samplers.LoadTrajectorySampler attribute) pdfz (snake.core.sampling.samplers.EPI3dAcquisitionSampler attribute) (snake.core.sampling.samplers.StackOfSpiralSampler attribute) Phantom (class in snake.core.phantom.static) phantom (snake.toolkit.cli.config.ConfigSNAKE attribute) PhantomConfig (class in snake.toolkit.cli.config) plot_frames_activ() (in module snake.toolkit.plotting) props (snake.core.phantom.static.Phantom attribute) PropTissueEnum (class in snake.core.phantom.static) R radial_factory() (in module snake.core.sampling.factories) RANDOM (snake.core.sampling.factories.VDSorder attribute) RandomMotionImageHandler (class in snake.core.handlers.motion.image) raster_time (snake.core.sampling.samplers.LoadTrajectorySampler attribute) raster_time_ms (snake.core.simulation.HardwareConfig attribute) read_mrd_header() (in module snake.mrd_utils.loader) reconstruct() (snake.toolkit.reconstructors.base.BaseReconstructor method) (snake.toolkit.reconstructors.pysap.SequentialReconstructor method) (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor method) reconstruction() (in module snake.toolkit.cli.reconstruction) reconstruction_cli (in module snake.toolkit.cli.reconstruction) reconstructors (snake.toolkit.cli.config.ConfigSNAKE attribute) REFINE (snake.toolkit.reconstructors.pysap.RestartStrategy attribute) registry (snake._meta.MethodRegister attribute) res_mm (snake.core.simulation.SimConfig property) resize_tissues() (in module snake.core.phantom.utils) restart_strategy (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) RestartStrategy (class in snake.toolkit.reconstructors.pysap) result_dir (snake.toolkit.cli.config.ConfigSNAKE attribute) rho (snake.core.phantom.static.PropTissueEnum attribute) rng_seed (snake.core.simulation.SimConfig attribute) roi_threshold (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) (snake.toolkit.cli.config.StatConfig attribute) roi_tissue_name (snake.core.handlers.activations.activations.ActivationMixin attribute) (snake.core.handlers.activations.activations.BlockActivationHandler attribute) (snake.toolkit.cli.config.StatConfig attribute) rotate_angle (snake.core.sampling.samplers.StackOfSpiralSampler attribute) rotate_frame_angle (snake.core.sampling.samplers.RotatedStackOfSpiralSampler attribute) rotate_trajectory() (in module snake.core.sampling.factories) RotatedStackOfSpiralSampler (class in snake.core.sampling.samplers) rotation() (in module snake.core.handlers.motion.utils) rotation2D() (in module snake.core.handlers.motion.utils) rotation3d() (in module snake.core.handlers.motion.utils) rs_std_degs (snake.core.handlers.motion.image.RandomMotionImageHandler attribute) run_parallel() (in module snake.core.parallel) S sampler (snake.toolkit.cli.config.ConfigSNAKE attribute) seq (snake.core.simulation.SimConfig attribute) SequentialReconstructor (class in snake.toolkit.reconstructors.pysap) serialize() (snake.core.handlers.base.HandlerList method) serialize_array() (in module snake.core.phantom.static) (in module snake.mrd_utils.utils) setup() (snake.toolkit.reconstructors.base.BaseReconstructor method) (snake.toolkit.reconstructors.pysap.SequentialReconstructor method) (snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor method) shape (snake.core.parallel.ArrayProps attribute) (snake.core.simulation.SimConfig attribute) (snake.mrd_utils.loader.MRDLoader property) SHM_Wrapper (class in snake.core.parallel) sim_conf (snake.toolkit.cli.config.ConfigSNAKE attribute) sim_tr_ms (snake.core.simulation.SimConfig property) SimConfig (class in snake.core.simulation) Singleton (class in snake._meta) size (snake.core.handlers.fov.FOVHandler attribute) slice_2d (snake.core.engine.base.BaseAcquisitionEngine attribute) (snake.core.engine.cartesian.EPIAcquisitionEngine attribute) (snake.core.engine.nufft.NufftAcquisitionEngine attribute) (snake.mrd_utils.loader.MRDLoader property) (snake.toolkit.cli.config.EngineConfig attribute) SlicerType (in module snake.core.sampling.factories) smaps (snake.core.phantom.static.Phantom attribute) smax (snake.core.simulation.HardwareConfig attribute) snake module snake._meta module snake._version module snake.core module snake.core.engine module snake.core.engine.base module snake.core.engine.cartesian module snake.core.engine.nufft module snake.core.engine.utils module snake.core.handlers module snake.core.handlers.activations module snake.core.handlers.activations.activations module snake.core.handlers.activations.bold module snake.core.handlers.activations.roi module snake.core.handlers.base module snake.core.handlers.fov module snake.core.handlers.motion module snake.core.handlers.motion.image module snake.core.handlers.motion.utils module snake.core.handlers.noise module snake.core.handlers.utils module snake.core.parallel module snake.core.phantom module snake.core.phantom.data module snake.core.phantom.dynamic module snake.core.phantom.shepp_logan module snake.core.phantom.static module snake.core.phantom.utils module snake.core.sampling module snake.core.sampling.base module snake.core.sampling.factories module snake.core.sampling.samplers module snake.core.simulation module snake.core.smaps module snake.mrd_utils module snake.mrd_utils.loader module snake.mrd_utils.utils module snake.mrd_utils.writer module snake.toolkit module snake.toolkit.cli module snake.toolkit.cli.acquisition module snake.toolkit.cli.config module snake.toolkit.cli.main module snake.toolkit.cli.reconstruction module snake.toolkit.plotting module snake.toolkit.reconstructors module snake.toolkit.reconstructors.base module snake.toolkit.reconstructors.fourier module snake.toolkit.reconstructors.pysap module snake_handler_resolver() (in module snake.toolkit.cli.config) SNAKE_HDF5_CHUNK_SIZE (snake._meta.ENVCONFIG attribute) SNAKE_HDF5_CHUNK_WRITE_SIZE (snake._meta.ENVCONFIG attribute) snake_sampler_resolver() (in module snake.toolkit.cli.config) SNAKE_TMP_DIR (snake._meta.ENVCONFIG attribute) snr (snake.core.engine.base.BaseAcquisitionEngine attribute) (snake.core.engine.cartesian.EPIAcquisitionEngine attribute) (snake.core.engine.cartesian.EVIAcquisition attribute) (snake.core.engine.nufft.NufftAcquisitionEngine attribute) (snake.toolkit.cli.config.EngineConfig attribute) spiral_name (snake.core.sampling.samplers.StackOfSpiralSampler attribute) stack_spiral_factory() (in module snake.core.sampling.factories) stacked_epi2d() (in module snake.core.sampling.factories) stacked_epi_factory() (in module snake.core.sampling.factories) StackOfSpiralSampler (class in snake.core.sampling.samplers) StatConfig (class in snake.toolkit.cli.config) stats (snake.toolkit.cli.config.ConfigSNAKE attribute) sub_id (snake.toolkit.cli.config.PhantomConfig attribute) T T (in module snake._meta) (in module snake.core.handlers.base) (in module snake.core.phantom.static) T1 (snake.core.phantom.static.PropTissueEnum attribute) T2 (snake.core.phantom.static.PropTissueEnum attribute) T2s (snake.core.phantom.static.PropTissueEnum attribute) target_res (snake.core.handlers.fov.FOVHandler attribute) TE (snake.core.simulation.GreConfig attribute) ThreeFloats (in module snake._meta) ThreeInts (in module snake._meta) threshold (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) tissue_1T5 (snake.core.phantom.static.TissueFile attribute) tissue_7T (snake.core.phantom.static.TissueFile attribute) tissue_file (snake.toolkit.cli.config.PhantomConfig attribute) tissue_ignore (snake.toolkit.cli.config.PhantomConfig attribute) tissue_select (snake.toolkit.cli.config.PhantomConfig attribute) TissueFile (class in snake.core.phantom.static) to_mrd_dataset() (snake.core.phantom.static.Phantom method) to_yaml() (snake.core.handlers.base.AbstractHandler method) (snake.core.handlers.base.HandlerList method) TOP_DOWN (snake.core.sampling.factories.VDSorder attribute) TR (snake.core.simulation.GreConfig attribute) trajectory_generator() (in module snake.core.sampling.factories) translation() (in module snake.core.handlers.motion.utils) ts_std_mms (snake.core.handlers.motion.image.RandomMotionImageHandler attribute) TYPE_CHECKING (in module snake._version) U UNIFORM (snake.core.sampling.factories.VDSpdf attribute) unserialize_array() (in module snake.core.phantom.static) (in module snake.mrd_utils.utils) USER1 (snake.mrd_utils.utils.ACQ attribute) USER2 (snake.mrd_utils.utils.ACQ attribute) USER3 (snake.mrd_utils.utils.ACQ attribute) USER4 (snake.mrd_utils.utils.ACQ attribute) USER5 (snake.mrd_utils.utils.ACQ attribute) USER6 (snake.mrd_utils.utils.ACQ attribute) USER7 (snake.mrd_utils.utils.ACQ attribute) USER8 (snake.mrd_utils.utils.ACQ attribute) V validate_rng() (in module snake.core.sampling.factories) variance (snake.core.handlers.noise.NoiseHandler attribute) vds_factory() (in module snake.core.sampling.factories) VDSorder (class in snake.core.sampling.factories) VDSpdf (class in snake.core.sampling.factories) version (in module snake._version) version_tuple (in module snake._version) W WARM (snake.toolkit.reconstructors.pysap.RestartStrategy attribute) wavelet (snake.toolkit.reconstructors.pysap.SequentialReconstructor attribute) Z ZERO (snake.core.sampling.factories.AngleRotation attribute) ZeroFilledReconstructor (class in snake.toolkit.reconstructors.pysap)
