Index

A

actors (cedalion.plots.OptodeSelector attribute), [1] add() (cedalion.dataclasses.accessors.PointsAccessor method), [1] add_artifact_direct() (in module cedalion.sim.synthetic_artifact), [1] add_artifacts() (in module cedalion.sim.synthetic_artifact), [1] add_chromo_artifacts_2_od() (in module cedalion.sim.synthetic_artifact), [1] add_event_timing() (in module cedalion.sim.synthetic_artifact), [1] (in module cedalion.sim.synthetic_utils) add_hrf_to_od() (in module cedalion.sim.synthetic_hrf), [1] add_hrf_to_vertices() (in module cedalion.sim.synthetic_hrf), [1] add_number_to_name() (in module cedalion.io.snirf), [1] adj (cedalion.dataclasses.geometry.PycortexSurface property), [1] affine_transform_from_numpy() (in module cedalion.dataclasses.geometry), [1] AffineTransform (in module cedalion.typing), [1] AFNIGamma (class in cedalion.models.glm.basis_functions), [1]

align_and_snap_to_scalp() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method), [1], [2], [3] apply_inv_sensitivity() (in module cedalion.imagereco.forward_model), [1] apply_mask() (in module cedalion.xrutils), [1] apply_transform() (cedalion.dataclasses.accessors.PointsAccessor method), [1] (cedalion.dataclasses.geometry.PycortexSurface method), [1] (cedalion.dataclasses.geometry.Surface method), [1] (cedalion.dataclasses.geometry.TrimeshSurface method), [1] (cedalion.dataclasses.geometry.Voxels method), [1] (cedalion.dataclasses.geometry.VTKSurface method), [1] (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method), [1], [2], [3] ArtifactFunction (class in cedalion.sim.synthetic_artifact), [1] aux_obj (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] aux_ts (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] average_short_channel() (in module cedalion.models.glm.design_matrix), [1] avg_edge_length (cedalion.dataclasses.geometry.PycortexSurface property), [1]

B

beer_lambert() (in module cedalion.nirs), [1] BFI (cedalion.io.snirf.DataTypeLabel attribute), [1] binaryMaskGenerator() (in module cedalion.geometry.segmentation), [1] brain (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] build() (cedalion.geometry.landmarks.LandmarksBuilder1010 method), [1] build_blob() (in module cedalion.sim.synthetic_hrf), [1]

build_event_df() (in module cedalion.sim.synthetic_utils) build_labeled_points() (in module cedalion.dataclasses.schemas), [1] build_stim_array() (in module cedalion.models.glm.design_matrix), [1] build_stim_dataframe() (in module cedalion.dataclasses.schemas), [1] build_stim_df() (in module cedalion.sim.synthetic_hrf), [1] build_timeseries() (in module cedalion.dataclasses.schemas), [1]

C

calculate_cos_sin_mtx() (in module cedalion.sigdecomp.ERBM), [1] cart2sph() (in module cedalion.geometry.utils), [1] cedalion module cedalion.data module cedalion.dataclasses module, [1] cedalion.dataclasses.accessors module, [1] cedalion.dataclasses.geometry module, [1] cedalion.dataclasses.recording module, [1] cedalion.dataclasses.schemas module, [1] cedalion.datasets module, [1] cedalion.errors module cedalion.geometry module, [1] cedalion.geometry.landmarks module, [1] cedalion.geometry.photogrammetry module, [1] cedalion.geometry.photogrammetry.processors module, [1] cedalion.geometry.registration module, [1] cedalion.geometry.segmentation module, [1] cedalion.geometry.utils module, [1] cedalion.imagereco module cedalion.imagereco.forward_model module, [1] cedalion.imagereco.solver module, [1] cedalion.imagereco.tissue_properties module, [1] cedalion.imagereco.utils module, [1] cedalion.io module cedalion.io.anatomy module, [1] cedalion.io.bids module, [1] cedalion.io.forward_model module, [1] cedalion.io.nirs module cedalion.io.photogrammetry module, [1] cedalion.io.probe_geometry module, [1] cedalion.io.snirf module, [1] cedalion.models module cedalion.models.glm module, [1] cedalion.models.glm.basis_functions module, [1] cedalion.models.glm.design_matrix module, [1] cedalion.models.glm.solve module, [1] cedalion.nirs module, [1] cedalion.physunits module, [1] cedalion.plots module, [1] cedalion.sigdecomp module cedalion.sigdecomp.dummy module cedalion.sigdecomp.ERBM module, [1]

cedalion.sigdecomp.ICA_EBM module, [1] cedalion.sigproc module cedalion.sigproc.epochs module, [1] cedalion.sigproc.frequency module, [1] cedalion.sigproc.motion_correct module, [1] cedalion.sigproc.quality module, [1] cedalion.sigproc.tasks module cedalion.sim module cedalion.sim.synthetic_artifact module, [1] cedalion.sim.synthetic_hrf module, [1] cedalion.sim.synthetic_utils module cedalion.tasks module cedalion.typing module, [1] cedalion.utils module cedalion.validators module, [1] cedalion.vis module cedalion.vis.plot_probe module, [1] cedalion.vis.plot_sensitivity_matrix module, [1] cedalion.vis.time_series module, [1] cedalion.vtktutils module cedalion.xrutils module, [1] CedalionAccessor (class in cedalion.dataclasses.accessors), [1] cell_coordinates() (in module cedalion.geometry.segmentation), [1] (in module cedalion.io.anatomy), [1] cfg_colors (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] channel_distances() (in module cedalion.nirs), [1] check_dimensionality() (in module cedalion.validators), [1] closest_short_channel() (in module cedalion.models.glm.design_matrix), [1] cluster_circles (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] cluster_colors (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] cluster_coords (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] cnstd_and_gain() (in module cedalion.sigdecomp.ERBM), [1] color (cedalion.plots.OptodeSelector attribute), [1] ColoredStickerProcessor (class in cedalion.geometry.photogrammetry.processors), [1] ColoredStickerProcessorDetails (class in cedalion.geometry.photogrammetry.processors), [1] common_labels() (cedalion.dataclasses.accessors.PointsAccessor method), [1] compute_fluence() (cedalion.imagereco.forward_model.ForwardModel method), [1] compute_fluence_mcx() (cedalion.imagereco.forward_model.ForwardModel method), [1] compute_fluence_nirfaster() (cedalion.imagereco.forward_model.ForwardModel method), [1] compute_sensitivity() (cedalion.imagereco.forward_model.ForwardModel method), [1], [2], [3] compute_stacked_sensitivity() (cedalion.imagereco.forward_model.ForwardModel static method), [1] compute_window() (in module cedalion.sigproc.motion_correct), [1] conc2od() (in module cedalion.nirs), [1] conditions() (cedalion.dataclasses.accessors.StimAccessor method), [1] connected (cedalion.dataclasses.geometry.PycortexSurface property), [1] convolve() (in module cedalion.xrutils), [1] coords (cedalion.dataclasses.schemas.DataArraySchema attribute), [1] coords_from_other() (in module cedalion.xrutils), [1] cotangent_weights (cedalion.dataclasses.geometry.PycortexSurface property), [1] create_mock_activation_below_point() (in module cedalion.imagereco.utils), [1] crs (cedalion.dataclasses.accessors.PointsAccessor property), [1] (cedalion.dataclasses.geometry.PycortexSurface attribute) (cedalion.dataclasses.geometry.Surface attribute), [1] (cedalion.dataclasses.geometry.TrimeshSurface attribute), [1], [2] (cedalion.dataclasses.geometry.Voxels attribute), [1], [2], [3] (cedalion.dataclasses.geometry.VTKSurface attribute) (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1] (cedalion.imagereco.forward_model.TwoSurfaceHeadModel property), [1] CRSMismatchError CSF (cedalion.imagereco.tissue_properties.TissueType attribute), [1] CW_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] CW_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1]

D

DataArraySchema (class in cedalion.dataclasses.schemas), [1] DataType (class in cedalion.io.snirf), [1] DataTypeLabel (class in cedalion.io.snirf), [1] DCS_BFI (cedalion.io.snirf.DataType attribute), [1] DCS_G2 (cedalion.io.snirf.DataType attribute), [1] decimate() (cedalion.dataclasses.geometry.PycortexSurface method), [1] (cedalion.dataclasses.geometry.TrimeshSurface method), [1] (cedalion.dataclasses.geometry.VTKSurface method), [1] denormalize_measurement_list() (in module cedalion.io.snirf), [1] detect_baselineshift() (in module cedalion.sigproc.quality), [1] detect_outliers() (in module cedalion.sigproc.quality), [1]

detect_outliers_grad() (in module cedalion.sigproc.quality), [1] detect_outliers_std() (in module cedalion.sigproc.quality), [1] DETECTOR (cedalion.dataclasses.geometry.PointType attribute), [1] detector_labels (cedalion.dataclasses.recording.Recording property), [1] dims (cedalion.dataclasses.schemas.DataArraySchema attribute), [1] DiracDelta (class in cedalion.models.glm.basis_functions), [1] DM (cedalion.imagereco.tissue_properties.TissueType attribute), [1] DMEAN (cedalion.io.snirf.DataTypeLabel attribute), [1] DOD (cedalion.io.snirf.DataTypeLabel attribute), [1] DSKEW (cedalion.io.snirf.DataTypeLabel attribute), [1] DVAR (cedalion.io.snirf.DataTypeLabel attribute), [1]

E

enable_picking() (cedalion.plots.OptodeSelector method), [1], [2], [3]

ERBM() (in module cedalion.sigdecomp.ERBM), [1]

F

face_areas (cedalion.dataclasses.geometry.PycortexSurface property), [1] face_normals (cedalion.dataclasses.geometry.PycortexSurface property), [1] FD_AC_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] FD_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] FD_FLUORESCENCE_PHASE (cedalion.io.snirf.DataType attribute), [1] FD_PHASE (cedalion.io.snirf.DataType attribute), [1] find_spread_points() (in module cedalion.geometry.registration), [1] find_surface_normal() (cedalion.plots.OptodeSelector method), [1] fit() (in module cedalion.models.glm.solve), [1]

fix_vertex_normals() (cedalion.dataclasses.geometry.TrimeshSurface method), [1] ForwardModel (class in cedalion.imagereco.forward_model), [1] freq_filter() (cedalion.dataclasses.accessors.CedalionAccessor method), [1] (in module cedalion.sigproc.frequency), [1] from_segmentation() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel class method), [1] from_surfaces() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel class method), [1] from_trimeshsurface() (cedalion.dataclasses.geometry.PycortexSurface class method), [1] (cedalion.dataclasses.geometry.VTKSurface class method), [1] from_vtksurface() (cedalion.dataclasses.geometry.PycortexSurface class method), [1] (cedalion.dataclasses.geometry.TrimeshSurface class method), [1]

G

Gamma (class in cedalion.models.glm.basis_functions), [1] GammaDeriv (class in cedalion.models.glm.basis_functions), [1] GaussianKernels (class in cedalion.models.glm.basis_functions), [1] GaussianKernelsWithTails (class in cedalion.models.glm.basis_functions), [1] gen_bl_shift() (in module cedalion.sim.synthetic_artifact), [1] gen_spike() (in module cedalion.sim.synthetic_artifact), [1] gen_xform_from_pts() (in module cedalion.geometry.registration), [1] generate_hrf() (in module cedalion.sim.synthetic_hrf), [1] geo2d (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] geo3d (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] geo3d_from_scan() (in module cedalion.geometry.photogrammetry.processors), [1] geodesic_distance() (cedalion.dataclasses.geometry.PycortexSurface method), [1] geodesic_path() (cedalion.dataclasses.geometry.PycortexSurface method), [1] geometry_from_probe() (in module cedalion.io.snirf), [1] get() (in module cedalion.data) get_colin27_headmodel() (in module cedalion.datasets), [1] get_colin27_segmentation() (in module cedalion.datasets), [1] get_colors() (in module cedalion.sim.synthetic_hrf), [1] get_extinction_coefficients() (in module cedalion.nirs), [1] get_fingertapping() (in module cedalion.datasets), [1] get_fingertapping_snirf_path() (in module cedalion.datasets), [1]

get_fingertappingDOT() (in module cedalion.datasets), [1] get_icbm152_segmentation() (in module cedalion.datasets), [1] get_imagereco_example_fluence() (in module cedalion.datasets), [1] get_mask() (cedalion.dataclasses.recording.Recording method), [1] get_multisubject_fingertapping_path() (in module cedalion.datasets), [1] get_multisubject_fingertapping_snirf_paths() (in module cedalion.datasets), [1] get_ninja_cap_probe() (in module cedalion.datasets), [1] get_ninja_uhd_cap_probe() (in module cedalion.datasets), [1] get_ninjanirs_colin27_precomputed_fluence() (in module cedalion.datasets), [1] get_ninjanirs_colin27_precomputed_sensitivity() (in module cedalion.datasets), [1] get_nn22_resting_state() (in module cedalion.datasets), [1] get_photogrammetry_example_scan() (in module cedalion.datasets), [1] get_precomputed_fluence() (in module cedalion.datasets), [1] get_snirf_test_data() (in module cedalion.datasets), [1] get_timeseries() (cedalion.dataclasses.recording.Recording method), [1] get_timeseries_type() (cedalion.dataclasses.recording.Recording method), [1] get_tissue_properties() (in module cedalion.imagereco.tissue_properties), [1] get_vertex_normals() (cedalion.dataclasses.geometry.PycortexSurface method), [1] (cedalion.dataclasses.geometry.TrimeshSurface method), [1] GM (cedalion.imagereco.tissue_properties.TissueType attribute), [1] gvtd() (in module cedalion.sigproc.quality), [1]

H

H2O (cedalion.io.snirf.DataTypeLabel attribute), [1] has_channel() (in module cedalion.validators), [1] has_positions() (in module cedalion.validators), [1] has_time() (in module cedalion.validators), [1] has_wavelengths() (in module cedalion.validators), [1] HBO (cedalion.io.snirf.DataTypeLabel attribute), [1] HBR (cedalion.io.snirf.DataTypeLabel attribute), [1] HBT (cedalion.io.snirf.DataTypeLabel attribute), [1] head_model (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3]

HRF_BFI (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_DMEAN (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_DOD (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_DSKEW (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_DVAR (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_HBO (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_HBR (cedalion.io.snirf.DataTypeLabel attribute), [1] HRF_HBT (cedalion.io.snirf.DataTypeLabel attribute), [1] hrf_to_long_channels() (in module cedalion.sim.synthetic_hrf), [1] hrfs_from_image_reco() (in module cedalion.sim.synthetic_hrf), [1]

I

ICA_EBM() (in module cedalion.sigdecomp.ICA_EBM), [1] icp_with_full_transform() (in module cedalion.geometry.registration), [1] id_motion() (in module cedalion.sigproc.quality), [1] id_motion_refine() (in module cedalion.sigproc.quality), [1] int2od() (in module cedalion.nirs), [1] (in module cedalion.sigproc.tasks)

inv_sqrtmH() (in module cedalion.sigdecomp.ERBM), [1] (in module cedalion.sigdecomp.ICA_EBM), [1] is_quantified() (in module cedalion.validators), [1] iter_design_matrix() (in module cedalion.models.glm.solve), [1]

K

kdtree (cedalion.dataclasses.geometry.Surface property), [1] (cedalion.dataclasses.geometry.Voxels property), [1]

L

LabeledPointCloud (in module cedalion.typing), [1] labels (cedalion.plots.OptodeSelector attribute), [1] labels_and_positions() (in module cedalion.io.snirf), [1] LANDMARK (cedalion.dataclasses.geometry.PointType attribute), [1] landmarks (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] landmarks_mm (cedalion.geometry.landmarks.LandmarksBuilder1010 attribute), [1] LandmarksBuilder1010 (class in cedalion.geometry.landmarks), [1] laplace_operator (cedalion.dataclasses.geometry.PycortexSurface property), [1]

lfc() (in module cedalion.sigdecomp.ERBM), [1] lines (cedalion.geometry.landmarks.LandmarksBuilder1010 attribute), [1] LIPID (cedalion.io.snirf.DataTypeLabel attribute), [1] load() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel class method), [1] (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method), [1] load_Adot() (in module cedalion.io.forward_model), [1] load_fluence() (in module cedalion.io.forward_model), [1] load_tsv() (in module cedalion.io.probe_geometry), [1]

M

m_rot() (in module cedalion.geometry.utils), [1] m_scale1() (in module cedalion.geometry.utils), [1] m_scale3() (in module cedalion.geometry.utils), [1] m_trans() (in module cedalion.geometry.utils), [1] mad() (in module cedalion.sigproc.motion_correct), [1] Main (class in cedalion.vis.plot_sensitivity_matrix), [1] make_design_matrix() (in module cedalion.models.glm.design_matrix), [1] make_drift_regressors() (in module cedalion.models.glm.design_matrix), [1] make_hrf_regressors() (in module cedalion.models.glm.design_matrix), [1] map_segmentation_mask_to_surface() (in module cedalion.imagereco.utils), [1] mask() (in module cedalion.xrutils), [1] masks (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] max_corr_short_channel() (in module cedalion.models.glm.design_matrix), [1] mean_amp() (in module cedalion.sigproc.quality), [1] measurement_list_from_stacked() (in module cedalion.io.snirf), [1] measurement_list_to_dataframe() (in module cedalion.io.snirf), [1] mesh (cedalion.dataclasses.geometry.PycortexSurface attribute), [1] (cedalion.dataclasses.geometry.Surface attribute), [1] (cedalion.dataclasses.geometry.TrimeshSurface attribute), [1], [2], [3] (cedalion.dataclasses.geometry.VTKSurface attribute), [1] meta_data (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] meta_data_tags_to_dict() (in module cedalion.io.snirf), [1] minEnclosingCircle() (in module cedalion.geometry.photogrammetry.processors), [1] module cedalion cedalion.data cedalion.dataclasses, [1] cedalion.dataclasses.accessors, [1] cedalion.dataclasses.geometry, [1] cedalion.dataclasses.recording, [1] cedalion.dataclasses.schemas, [1] cedalion.datasets, [1] cedalion.errors cedalion.geometry, [1] cedalion.geometry.landmarks, [1] cedalion.geometry.photogrammetry, [1] cedalion.geometry.photogrammetry.processors, [1] cedalion.geometry.registration, [1] cedalion.geometry.segmentation, [1] cedalion.geometry.utils, [1] cedalion.imagereco cedalion.imagereco.forward_model, [1] cedalion.imagereco.solver, [1] cedalion.imagereco.tissue_properties, [1] cedalion.imagereco.utils, [1] cedalion.io cedalion.io.anatomy, [1] cedalion.io.bids, [1] cedalion.io.forward_model, [1] cedalion.io.nirs cedalion.io.photogrammetry, [1] cedalion.io.probe_geometry, [1] cedalion.io.snirf, [1] cedalion.models cedalion.models.glm, [1] cedalion.models.glm.basis_functions, [1] cedalion.models.glm.design_matrix, [1] cedalion.models.glm.solve, [1] cedalion.nirs, [1] cedalion.physunits, [1] cedalion.plots, [1] cedalion.sigdecomp cedalion.sigdecomp.dummy cedalion.sigdecomp.ERBM, [1] cedalion.sigdecomp.ICA_EBM, [1] cedalion.sigproc cedalion.sigproc.epochs, [1] cedalion.sigproc.frequency, [1] cedalion.sigproc.motion_correct, [1] cedalion.sigproc.quality, [1] cedalion.sigproc.tasks cedalion.sim cedalion.sim.synthetic_artifact, [1] cedalion.sim.synthetic_hrf, [1] cedalion.sim.synthetic_utils cedalion.tasks cedalion.typing, [1] cedalion.utils cedalion.validators, [1] cedalion.vis cedalion.vis.plot_probe, [1] cedalion.vis.plot_sensitivity_matrix, [1] cedalion.vis.time_series, [1] cedalion.vtktutils cedalion.xrutils, [1]

motion_correct_PCA() (in module cedalion.sigproc.motion_correct), [1] motion_correct_PCA_recurse() (in module cedalion.sigproc.motion_correct), [1] motion_correct_spline() (in module cedalion.sigproc.motion_correct), [1] motion_correct_splineSG() (in module cedalion.sigproc.motion_correct), [1] motion_correct_wavelet() (in module cedalion.sigproc.motion_correct), [1] MUA (cedalion.io.snirf.DataTypeLabel attribute), [1] MUSP (cedalion.io.snirf.DataTypeLabel attribute), [1]

N

NDTimeSeries (in module cedalion.typing), [1] nfaces (cedalion.dataclasses.geometry.PycortexSurface property), [1] (cedalion.dataclasses.geometry.Surface property), [1] (cedalion.dataclasses.geometry.TrimeshSurface property), [1] (cedalion.dataclasses.geometry.VTKSurface property), [1] norm() (in module cedalion.xrutils), [1] normal_hrf() (in module cedalion.imagereco.utils), [1]

normalize_signal() (in module cedalion.sigproc.motion_correct), [1] normals (cedalion.plots.OptodeSelector attribute), [1] nvertices (cedalion.dataclasses.geometry.PycortexSurface property), [1] (cedalion.dataclasses.geometry.Surface property), [1] (cedalion.dataclasses.geometry.TrimeshSurface property), [1] (cedalion.dataclasses.geometry.Voxels property), [1] (cedalion.dataclasses.geometry.VTKSurface property), [1]

O

od2conc() (in module cedalion.nirs), [1] (in module cedalion.sigproc.tasks) on_pick() (cedalion.plots.OptodeSelector method), [1], [2], [3] opt_fid_to_xr() (in module cedalion.io.photogrammetry), [1]

OptodeSelector (class in cedalion.plots), [1] order_ref_points_6() (in module cedalion.geometry.landmarks), [1] OTHER (cedalion.imagereco.tissue_properties.TissueType attribute), [1] other_dim() (in module cedalion.xrutils), [1] overlaps() (in module cedalion.sim.synthetic_utils)

P

pad_time_axis() (in module cedalion.models.glm.design_matrix), [1] pad_to_power_2() (in module cedalion.sigproc.motion_correct), [1] parse_data_type() (in module cedalion.io.snirf), [1] parse_data_type_label() (in module cedalion.io.snirf), [1] pca() (in module cedalion.geometry.photogrammetry.processors), [1] pick_trial_types() (in module cedalion.sim.synthetic_utils) pinv() (in module cedalion.xrutils), [1] plot() (cedalion.geometry.landmarks.LandmarksBuilder1010 method), [1] (cedalion.plots.OptodeSelector method), [1], [2], [3] (cedalion.vis.plot_sensitivity_matrix.Main method), [1] plot3d() (in module cedalion.plots), [1] plot_blob() (in module cedalion.sim.synthetic_hrf), [1] plot_cluster_circles() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails method), [1] plot_labeled_points() (in module cedalion.plots), [1] plot_montage3D() (in module cedalion.plots), [1] plot_stim_markers() (in module cedalion.plots), [1] plot_surface() (in module cedalion.plots), [1] plot_vector_field() (in module cedalion.plots), [1] plot_vertex_colors() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails method), [1] plot_vertex_colors1() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails method), [1]

plotter (cedalion.plots.OptodeSelector attribute), [1] points (cedalion.plots.OptodeSelector attribute), [1] PointsAccessor (class in cedalion.dataclasses.accessors), [1] PointType (class in cedalion.dataclasses.geometry), [1] pol2cart() (in module cedalion.geometry.utils), [1] polys (cedalion.dataclasses.geometry.SimpleMesh attribute), [1] ppts (cedalion.dataclasses.geometry.PycortexSurface property), [1] pre_processing() (in module cedalion.sigdecomp.ERBM), [1] (in module cedalion.sigdecomp.ICA_EBM), [1] predict() (in module cedalion.models.glm.solve), [1] process() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessor method), [1] (cedalion.geometry.photogrammetry.processors.ScanProcessor method), [1] process_coefficients() (in module cedalion.sigproc.motion_correct), [1] PROCESSED (cedalion.io.snirf.DataType attribute), [1] prune_ch() (in module cedalion.sigproc.quality), [1] pseudo_inverse_stacked() (in module cedalion.imagereco.solver), [1] psp() (in module cedalion.sigproc.quality), [1] pts (cedalion.dataclasses.geometry.SimpleMesh attribute), [1] PycortexSurface (class in cedalion.dataclasses.geometry), [1] pyvista_polydata_to_trimesh() (in module cedalion.vtktutils)

Q

QFrequency (in module cedalion.typing), [1]

QLength (in module cedalion.typing), [1] QTime (in module cedalion.typing), [1]

R

random_events_num() (in module cedalion.sim.synthetic_artifact), [1] random_events_perc() (in module cedalion.sim.synthetic_artifact), [1] RAW_NIRX (cedalion.io.snirf.DataTypeLabel attribute), [1] RAW_SATORI (cedalion.io.snirf.DataTypeLabel attribute), [1] read_aux() (in module cedalion.io.snirf), [1] read_data_elements() (in module cedalion.io.snirf), [1] read_digpts() (in module cedalion.io.probe_geometry), [1] read_einstar() (in module cedalion.io.photogrammetry), [1] read_einstar_obj() (in module cedalion.io.probe_geometry), [1] read_events_from_tsv() (in module cedalion.io.bids), [1] read_mrk_json() (in module cedalion.io.probe_geometry), [1] read_nirs() (in module cedalion.io.nirs) read_nirs_element() (in module cedalion.io.snirf), [1] read_photogrammetry_einstar() (in module cedalion.io.photogrammetry), [1]

read_segmentation_masks() (in module cedalion.io.anatomy), [1] read_snirf() (in module cedalion.io.snirf), [1] Recording (class in cedalion.dataclasses.recording), [1] reduce_ndim_sourceLabels() (in module cedalion.io.snirf), [1] register_icp() (in module cedalion.geometry.registration), [1] register_trans_rot() (in module cedalion.geometry.registration), [1] register_trans_rot_isoscale() (in module cedalion.geometry.registration), [1] register_trans_rot_scale() (in module cedalion.geometry.registration), [1] remove() (cedalion.dataclasses.accessors.PointsAccessor method), [1] rename() (cedalion.dataclasses.accessors.PointsAccessor method), [1] rename_events() (cedalion.dataclasses.accessors.StimAccessor method), [1] repair_amp() (in module cedalion.sigproc.quality), [1] run_vis() (in module cedalion.vis.plot_probe), [1] (in module cedalion.vis.time_series), [1]

S

sampling_rate (cedalion.dataclasses.accessors.CedalionAccessor property), [1] sampling_rate() (in module cedalion.sigproc.frequency), [1] save() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method), [1], [2], [3] save_Adot() (in module cedalion.io.forward_model), [1] save_fluence() (in module cedalion.io.forward_model), [1] save_mrk_json() (in module cedalion.io.probe_geometry), [1] scalp (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] scalp_plot() (in module cedalion.plots), [1] scalp_surface (cedalion.geometry.landmarks.LandmarksBuilder1010 attribute), [1] ScanProcessor (class in cedalion.geometry.photogrammetry.processors), [1] sci() (in module cedalion.sigproc.quality), [1] sd_dist() (in module cedalion.sigproc.quality), [1] (in module cedalion.sigproc.tasks) segmentation_masks (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] segmentation_postprocessing() (in module cedalion.geometry.segmentation), [1] sel_chans_by_opt() (in module cedalion.sim.synthetic_artifact), [1] set_crs() (cedalion.dataclasses.accessors.PointsAccessor method), [1] set_mask() (cedalion.dataclasses.recording.Recording method), [1] set_timeseries() (cedalion.dataclasses.recording.Recording method), [1] simple_scalp_projection() (in module cedalion.geometry.registration), [1] SimpleMesh (class in cedalion.dataclasses.geometry), [1] simplified_ppval() (in module cedalion.sigdecomp.ERBM), [1] (in module cedalion.sigdecomp.ICA_EBM), [1]

sizeOfObject() (in module cedalion.geometry.segmentation), [1] SKIN (cedalion.imagereco.tissue_properties.TissueType attribute), [1] SKULL (cedalion.imagereco.tissue_properties.TissueType attribute), [1] smooth() (cedalion.dataclasses.geometry.TrimeshSurface method), [1] snap() (cedalion.dataclasses.geometry.Surface method), [1] snap_to_scalp_voxels() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method), [1] snr() (in module cedalion.sigproc.quality), [1] (in module cedalion.sigproc.tasks) SOURCE (cedalion.dataclasses.geometry.PointType attribute), [1] source_labels (cedalion.dataclasses.recording.Recording property), [1] split_frequency_bands() (in module cedalion.sigdecomp.dummy) split_long_short_channels() (in module cedalion.nirs), [1] stim (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] stim_to_dataframe() (in module cedalion.io.snirf), [1] StimAccessor (class in cedalion.dataclasses.accessors), [1] stimulus_mask() (in module cedalion.sigproc.quality), [1] surface (cedalion.plots.OptodeSelector attribute), [1] Surface (class in cedalion.dataclasses.geometry), [1] surface_from_segmentation() (in module cedalion.geometry.segmentation), [1] surface_gradient() (cedalion.dataclasses.geometry.PycortexSurface method), [1] symdecor() (in module cedalion.sigdecomp.ICA_EBM), [1]

T

t_ijk2ras (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] t_ras2ijk (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] task() (in module cedalion.tasks) tddr() (in module cedalion.sigproc.motion_correct), [1] TDG_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] TDG_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] TDM_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] TDM_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute), [1] TemporalBasisFunction (class in cedalion.models.glm.basis_functions), [1]

timeseries (cedalion.dataclasses.recording.Recording attribute), [1], [2], [3] TissueType (class in cedalion.imagereco.tissue_properties), [1] to_epochs() (cedalion.dataclasses.accessors.CedalionAccessor method), [1] (in module cedalion.sigproc.epochs), [1] to_homogeneous() (cedalion.dataclasses.accessors.PointsAccessor method), [1] to_xarray() (cedalion.dataclasses.accessors.StimAccessor method), [1] trial_types (cedalion.dataclasses.recording.Recording property), [1] trimesh_to_vtk_polydata() (in module cedalion.vtktutils) TrimeshSurface (class in cedalion.dataclasses.geometry), [1] TwoSurfaceHeadModel (class in cedalion.imagereco.forward_model), [1]

U

unexpected_crs() (cedalion.errors.CRSMismatchError class method) unit_stripping_is_error() (in module cedalion.xrutils), [1] units (cedalion.dataclasses.geometry.PycortexSurface attribute) (cedalion.dataclasses.geometry.Surface attribute), [1] (cedalion.dataclasses.geometry.TrimeshSurface attribute), [1], [2] (cedalion.dataclasses.geometry.Voxels attribute), [1], [2], [3] (cedalion.dataclasses.geometry.VTKSurface attribute)

UNKNOWN (cedalion.dataclasses.geometry.PointType attribute), [1] update_normals() (cedalion.plots.OptodeSelector method), [1] update_visualization() (cedalion.plots.OptodeSelector method), [1], [2], [3]

V

validate() (cedalion.dataclasses.schemas.DataArraySchema method), [1] validate_schemas() (in module cedalion.dataclasses.schemas), [1] validate_stim_schema() (in module cedalion.dataclasses.schemas), [1] ValidationError, [1] vertex_colors (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] vertex_hue (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] vertex_normals (cedalion.dataclasses.geometry.PycortexSurface property), [1] vertex_sat (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] vertex_value (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute), [1] vertices (cedalion.dataclasses.geometry.PycortexSurface property), [1] (cedalion.dataclasses.geometry.Surface property), [1] (cedalion.dataclasses.geometry.TrimeshSurface property), [1] (cedalion.dataclasses.geometry.Voxels property), [1] (cedalion.dataclasses.geometry.VTKSurface property), [1]

voxel_to_vertex_brain (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] voxel_to_vertex_scalp (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute), [1], [2], [3] voxels (cedalion.dataclasses.geometry.Voxels attribute), [1], [2], [3] Voxels (class in cedalion.dataclasses.geometry), [1] voxels_from_segmentation() (in module cedalion.geometry.segmentation), [1] vtk_mesh (cedalion.geometry.landmarks.LandmarksBuilder1010 attribute), [1] VTKSurface (class in cedalion.dataclasses.geometry), [1]

W

wavelengths (cedalion.dataclasses.recording.Recording property), [1] WM (cedalion.imagereco.tissue_properties.TissueType attribute), [1]

write_snirf() (in module cedalion.io.snirf), [1] wrong_transform() (cedalion.errors.CRSMismatchError class method)

Z

zero_padded_numbers() (in module cedalion.utils)