cedalion
Contents
Getting started
Examples
API
References
cedalion
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
|
W
A
add() (cedalion.dataclasses.accessors.PointsAccessor method)
add_hrf_to_od() (in module cedalion.sim.synthetic_hrf)
add_hrf_to_vertices() (in module cedalion.sim.synthetic_hrf)
add_number_to_name() (in module cedalion.io.snirf)
affine_transform_from_numpy() (in module cedalion.dataclasses.geometry)
align_and_snap_to_scalp() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method)
,
[1]
apply_mask() (in module cedalion.xrutils)
apply_transform() (cedalion.dataclasses.accessors.PointsAccessor method)
(cedalion.dataclasses.geometry.Surface method)
(cedalion.dataclasses.geometry.TrimeshSurface method)
(cedalion.dataclasses.geometry.VTKSurface method)
(cedalion.imagereco.forward_model.TwoSurfaceHeadModel method)
,
[1]
aux_obj (cedalion.dataclasses.recording.Recording attribute)
aux_ts (cedalion.dataclasses.recording.Recording attribute)
B
beer_lambert() (in module cedalion.nirs)
BFI (cedalion.io.snirf.DataTypeLabel attribute)
brain (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
build() (cedalion.geometry.landmarks.LandmarksBuilder1010 method)
build_blob() (in module cedalion.sim.synthetic_hrf)
build_labeled_points() (in module cedalion.dataclasses.schemas)
build_stim_dataframe() (in module cedalion.dataclasses.schemas)
build_stim_df() (in module cedalion.sim.synthetic_hrf)
build_timeseries() (in module cedalion.dataclasses.schemas)
C
calculate_cos_sin_mtx() (in module cedalion.sigdecomp.ERBM)
cedalion
module
cedalion.data
module
cedalion.dataclasses
module
cedalion.dataclasses.accessors
module
cedalion.dataclasses.geometry
module
cedalion.dataclasses.recording
module
cedalion.dataclasses.schemas
module
cedalion.datasets
module
cedalion.geometry
module
cedalion.geometry.landmarks
module
cedalion.geometry.photogrammetry
module
cedalion.geometry.photogrammetry.processors
module
cedalion.geometry.registration
module
cedalion.geometry.segmentation
module
cedalion.geometry.utils
module
cedalion.imagereco
module
cedalion.imagereco.forward_model
module
cedalion.imagereco.solver
module
cedalion.imagereco.tissue_properties
module
cedalion.imagereco.utils
module
cedalion.io
module
cedalion.io.anatomy
module
cedalion.io.bids
module
cedalion.io.forward_model
module
cedalion.io.photogrammetry
module
cedalion.io.probe_geometry
module
cedalion.io.snirf
module
cedalion.models
module
cedalion.models.glm
module
cedalion.nirs
module
cedalion.plots
module
cedalion.sigdecomp
module
cedalion.sigdecomp.dummy
module
cedalion.sigdecomp.ERBM
module
cedalion.sigdecomp.ICA_EBM
module
cedalion.sigproc
module
cedalion.sigproc.artifact
module
cedalion.sigproc.frequency
module
cedalion.sigproc.quality
module
cedalion.sigproc.tasks
module
cedalion.sim
module
cedalion.sim.synthetic_hrf
module
cedalion.tasks
module
cedalion.typing
module
cedalion.validators
module
cedalion.vtktutils
module
cedalion.xrutils
module
CedalionAccessor (class in cedalion.dataclasses.accessors)
cell_coordinates() (in module cedalion.geometry.segmentation)
(in module cedalion.io.anatomy)
cfg_colors (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
channel_distances() (in module cedalion.nirs)
check_dimensionality() (in module cedalion.validators)
cluster_circles (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
cluster_colors (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
cluster_coords (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
cnstd_and_gain() (in module cedalion.sigdecomp.ERBM)
ColoredStickerProcessor (class in cedalion.geometry.photogrammetry.processors)
ColoredStickerProcessorDetails (class in cedalion.geometry.photogrammetry.processors)
common_labels() (cedalion.dataclasses.accessors.PointsAccessor method)
compute_fluence() (cedalion.imagereco.forward_model.ForwardModel method)
,
[1]
compute_sensitivity() (cedalion.imagereco.forward_model.ForwardModel method)
,
[1]
compute_sensitivity_all() (cedalion.imagereco.forward_model.ForwardModel method)
compute_stacked_sensitivity() (cedalion.imagereco.forward_model.ForwardModel static method)
convolve() (in module cedalion.xrutils)
coords (cedalion.dataclasses.schemas.DataArraySchema attribute)
create_mock_activation_below_point() (in module cedalion.imagereco.utils)
crs (cedalion.dataclasses.accessors.PointsAccessor property)
(cedalion.dataclasses.geometry.Surface attribute)
(cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
(cedalion.imagereco.forward_model.TwoSurfaceHeadModel property)
CSF (cedalion.imagereco.tissue_properties.TissueType attribute)
CW_AMPLITUDE (cedalion.io.snirf.DataType attribute)
CW_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute)
D
DataArraySchema (class in cedalion.dataclasses.schemas)
DataType (class in cedalion.io.snirf)
DataTypeLabel (class in cedalion.io.snirf)
DCS_BFI (cedalion.io.snirf.DataType attribute)
DCS_G2 (cedalion.io.snirf.DataType attribute)
decimate() (cedalion.dataclasses.geometry.TrimeshSurface method)
(cedalion.dataclasses.geometry.VTKSurface method)
denormalize_measurement_list() (in module cedalion.io.snirf)
DETECTOR (cedalion.dataclasses.geometry.PointType attribute)
detector_labels (cedalion.dataclasses.recording.Recording property)
dims (cedalion.dataclasses.schemas.DataArraySchema attribute)
DM (cedalion.imagereco.tissue_properties.TissueType attribute)
DMEAN (cedalion.io.snirf.DataTypeLabel attribute)
DOD (cedalion.io.snirf.DataTypeLabel attribute)
DSKEW (cedalion.io.snirf.DataTypeLabel attribute)
DVAR (cedalion.io.snirf.DataTypeLabel attribute)
E
ERBM() (in module cedalion.sigdecomp.ERBM)
F
FD_AC_AMPLITUDE (cedalion.io.snirf.DataType attribute)
FD_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute)
FD_FLUORESCENCE_PHASE (cedalion.io.snirf.DataType attribute)
FD_PHASE (cedalion.io.snirf.DataType attribute)
fix_vertex_normals() (cedalion.dataclasses.geometry.TrimeshSurface method)
ForwardModel (class in cedalion.imagereco.forward_model)
freq_filter() (cedalion.dataclasses.accessors.CedalionAccessor method)
(in module cedalion.sigproc.frequency)
from_segmentation() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel class method)
(cedalion.imagereco.forward_model.TwoSurfaceHeadModel method)
from_trimeshsurface() (cedalion.dataclasses.geometry.VTKSurface class method)
from_vtksurface() (cedalion.dataclasses.geometry.TrimeshSurface class method)
G
generate_hrf() (in module cedalion.sim.synthetic_hrf)
geo3d (cedalion.dataclasses.recording.Recording attribute)
geometry_from_probe() (in module cedalion.io.snirf)
get_colin27_headmodel() (in module cedalion.datasets)
get_colin27_segmentation() (in module cedalion.datasets)
get_colors() (in module cedalion.sim.synthetic_hrf)
get_extinction_coefficients() (in module cedalion.nirs)
get_fingertapping() (in module cedalion.datasets)
get_fingertapping_snirf_path() (in module cedalion.datasets)
get_imagereco_example_fluence() (in module cedalion.datasets)
get_mask() (cedalion.dataclasses.recording.Recording method)
get_multisubject_fingertapping_path() (in module cedalion.datasets)
get_multisubject_fingertapping_snirf_paths() (in module cedalion.datasets)
get_photogrammetry_example_scan() (in module cedalion.datasets)
get_snirf_test_data() (in module cedalion.datasets)
get_timeseries() (cedalion.dataclasses.recording.Recording method)
get_timeseries_type() (cedalion.dataclasses.recording.Recording method)
get_tissue_properties() (in module cedalion.imagereco.tissue_properties)
get_vertex_normals() (cedalion.dataclasses.geometry.TrimeshSurface method)
GM (cedalion.imagereco.tissue_properties.TissueType attribute)
H
H2O (cedalion.io.snirf.DataTypeLabel attribute)
has_channel() (in module cedalion.validators)
has_positions() (in module cedalion.validators)
has_time() (in module cedalion.validators)
has_wavelengths() (in module cedalion.validators)
HBO (cedalion.io.snirf.DataTypeLabel attribute)
HBR (cedalion.io.snirf.DataTypeLabel attribute)
HBT (cedalion.io.snirf.DataTypeLabel attribute)
head_model (cedalion.dataclasses.recording.Recording attribute)
(cedalion.imagereco.forward_model.ForwardModel attribute)
HRF_BFI (cedalion.io.snirf.DataTypeLabel attribute)
HRF_DMEAN (cedalion.io.snirf.DataTypeLabel attribute)
HRF_DOD (cedalion.io.snirf.DataTypeLabel attribute)
HRF_DSKEW (cedalion.io.snirf.DataTypeLabel attribute)
HRF_DVAR (cedalion.io.snirf.DataTypeLabel attribute)
HRF_HBO (cedalion.io.snirf.DataTypeLabel attribute)
HRF_HBR (cedalion.io.snirf.DataTypeLabel attribute)
HRF_HBT (cedalion.io.snirf.DataTypeLabel attribute)
hrf_to_long_channels() (in module cedalion.sim.synthetic_hrf)
hrfs_from_image_reco() (in module cedalion.sim.synthetic_hrf)
I
ICA_EBM() (in module cedalion.sigdecomp.ICA_EBM)
id_motion() (in module cedalion.sigproc.artifact)
id_motion_refine() (in module cedalion.sigproc.artifact)
int2od() (in module cedalion.nirs)
(in module cedalion.sigproc.tasks)
inv_sqrtmH() (in module cedalion.sigdecomp.ERBM)
(in module cedalion.sigdecomp.ICA_EBM)
is_quantified() (in module cedalion.validators)
K
kdtree (cedalion.dataclasses.geometry.Surface property)
L
labels_and_positions() (in module cedalion.io.snirf)
LANDMARK (cedalion.dataclasses.geometry.PointType attribute)
landmarks (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
LandmarksBuilder1010 (class in cedalion.geometry.landmarks)
lfc() (in module cedalion.sigdecomp.ERBM)
LIPID (cedalion.io.snirf.DataTypeLabel attribute)
load() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel class method)
(cedalion.imagereco.forward_model.TwoSurfaceHeadModel method)
load_Adot() (in module cedalion.io.forward_model)
M
m_rot() (in module cedalion.geometry.utils)
m_scale1() (in module cedalion.geometry.utils)
m_scale3() (in module cedalion.geometry.utils)
m_trans() (in module cedalion.geometry.utils)
map_segmentation_mask_to_surface() (in module cedalion.imagereco.utils)
mask() (in module cedalion.xrutils)
masks (cedalion.dataclasses.recording.Recording attribute)
mean_amp() (in module cedalion.sigproc.quality)
measurement_list (cedalion.imagereco.forward_model.ForwardModel attribute)
measurement_list_from_stacked() (in module cedalion.io.snirf)
measurement_list_to_dataframe() (in module cedalion.io.snirf)
mesh (cedalion.dataclasses.geometry.Surface attribute)
(cedalion.dataclasses.geometry.TrimeshSurface attribute)
(cedalion.dataclasses.geometry.VTKSurface attribute)
meta_data (cedalion.dataclasses.recording.Recording attribute)
meta_data_tags_to_dict() (in module cedalion.io.snirf)
minEnclosingCircle() (in module cedalion.geometry.photogrammetry.processors)
module
cedalion
cedalion.data
cedalion.dataclasses
cedalion.dataclasses.accessors
cedalion.dataclasses.geometry
cedalion.dataclasses.recording
cedalion.dataclasses.schemas
cedalion.datasets
cedalion.geometry
cedalion.geometry.landmarks
cedalion.geometry.photogrammetry
cedalion.geometry.photogrammetry.processors
cedalion.geometry.registration
cedalion.geometry.segmentation
cedalion.geometry.utils
cedalion.imagereco
cedalion.imagereco.forward_model
cedalion.imagereco.solver
cedalion.imagereco.tissue_properties
cedalion.imagereco.utils
cedalion.io
cedalion.io.anatomy
cedalion.io.bids
cedalion.io.forward_model
cedalion.io.photogrammetry
cedalion.io.probe_geometry
cedalion.io.snirf
cedalion.models
cedalion.models.glm
cedalion.nirs
cedalion.plots
cedalion.sigdecomp
cedalion.sigdecomp.dummy
cedalion.sigdecomp.ERBM
cedalion.sigdecomp.ICA_EBM
cedalion.sigproc
cedalion.sigproc.artifact
cedalion.sigproc.frequency
cedalion.sigproc.quality
cedalion.sigproc.tasks
cedalion.sim
cedalion.sim.synthetic_hrf
cedalion.tasks
cedalion.typing
cedalion.validators
cedalion.vtktutils
cedalion.xrutils
MUA (cedalion.io.snirf.DataTypeLabel attribute)
MUSP (cedalion.io.snirf.DataTypeLabel attribute)
N
nfaces (cedalion.dataclasses.geometry.Surface property)
(cedalion.dataclasses.geometry.TrimeshSurface property)
(cedalion.dataclasses.geometry.VTKSurface property)
norm() (in module cedalion.xrutils)
normal_hrf() (in module cedalion.imagereco.utils)
nvertices (cedalion.dataclasses.geometry.Surface property)
(cedalion.dataclasses.geometry.TrimeshSurface property)
(cedalion.dataclasses.geometry.VTKSurface property)
O
od2conc() (in module cedalion.nirs)
(in module cedalion.sigproc.tasks)
opt_fid_to_xr() (in module cedalion.io.photogrammetry)
optode_dir (cedalion.imagereco.forward_model.ForwardModel attribute)
optode_pos (cedalion.imagereco.forward_model.ForwardModel attribute)
OTHER (cedalion.imagereco.tissue_properties.TissueType attribute)
P
parse_data_type() (in module cedalion.io.snirf)
parse_data_type_label() (in module cedalion.io.snirf)
pca() (in module cedalion.geometry.photogrammetry.processors)
pinv() (in module cedalion.xrutils)
plot() (cedalion.geometry.landmarks.LandmarksBuilder1010 method)
plot3d() (in module cedalion.plots)
plot_blob() (in module cedalion.sim.synthetic_hrf)
plot_cluster_circles() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails method)
plot_labeled_points() (in module cedalion.plots)
plot_montage3D() (in module cedalion.plots)
plot_surface() (in module cedalion.plots)
plot_vector_field() (in module cedalion.plots)
plot_vertex_colors() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails method)
PointsAccessor (class in cedalion.dataclasses.accessors)
PointType (class in cedalion.dataclasses.geometry)
pre_processing() (in module cedalion.sigdecomp.ERBM)
(in module cedalion.sigdecomp.ICA_EBM)
process() (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessor method)
(cedalion.geometry.photogrammetry.processors.ScanProcessor method)
PROCESSED (cedalion.io.snirf.DataType attribute)
prune_ch() (in module cedalion.sigproc.quality)
pseudo_inverse_stacked() (in module cedalion.imagereco.solver)
pyvista_polydata_to_trimesh() (in module cedalion.vtktutils)
R
RAW_NIRX (cedalion.io.snirf.DataTypeLabel attribute)
RAW_SATORI (cedalion.io.snirf.DataTypeLabel attribute)
read_aux() (in module cedalion.io.snirf)
read_data_elements() (in module cedalion.io.snirf)
read_digpts() (in module cedalion.io.probe_geometry)
read_einstar() (in module cedalion.io.photogrammetry)
read_einstar_obj() (in module cedalion.io.probe_geometry)
read_events_from_tsv() (in module cedalion.io.bids)
read_mrk_json() (in module cedalion.io.probe_geometry)
read_nirs_element() (in module cedalion.io.snirf)
read_photogrammetry_einstar() (in module cedalion.io.photogrammetry)
read_segmentation_masks() (in module cedalion.io.anatomy)
read_snirf() (in module cedalion.io.snirf)
Recording (class in cedalion.dataclasses.recording)
reduce_ndim_sourceLabels() (in module cedalion.io.snirf)
register_icp() (in module cedalion.geometry.registration)
register_trans_rot() (in module cedalion.geometry.registration)
register_trans_rot_isoscale() (in module cedalion.geometry.registration)
remove() (cedalion.dataclasses.accessors.PointsAccessor method)
rename() (cedalion.dataclasses.accessors.PointsAccessor method)
rename_events() (cedalion.dataclasses.accessors.StimAccessor method)
S
sampling_rate (cedalion.dataclasses.accessors.CedalionAccessor property)
sampling_rate() (in module cedalion.sigproc.frequency)
save() (cedalion.imagereco.forward_model.TwoSurfaceHeadModel method)
,
[1]
save_Adot() (in module cedalion.io.forward_model)
scalp (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
ScanProcessor (class in cedalion.geometry.photogrammetry.processors)
sci() (in module cedalion.sigproc.quality)
sd_dist() (in module cedalion.sigproc.quality)
(in module cedalion.sigproc.tasks)
segmentation_masks (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
set_crs() (cedalion.dataclasses.accessors.PointsAccessor method)
set_mask() (cedalion.dataclasses.recording.Recording method)
set_timeseries() (cedalion.dataclasses.recording.Recording method)
simplified_ppval() (in module cedalion.sigdecomp.ERBM)
(in module cedalion.sigdecomp.ICA_EBM)
SKIN (cedalion.imagereco.tissue_properties.TissueType attribute)
SKULL (cedalion.imagereco.tissue_properties.TissueType attribute)
smooth() (cedalion.dataclasses.geometry.TrimeshSurface method)
snap() (cedalion.dataclasses.geometry.Surface method)
snr() (in module cedalion.sigproc.quality)
(in module cedalion.sigproc.tasks)
SOURCE (cedalion.dataclasses.geometry.PointType attribute)
source_labels (cedalion.dataclasses.recording.Recording property)
split_frequency_bands() (in module cedalion.sigdecomp.dummy)
stim (cedalion.dataclasses.recording.Recording attribute)
stim_to_dataframe() (in module cedalion.io.snirf)
StimAccessor (class in cedalion.dataclasses.accessors)
Surface (class in cedalion.dataclasses.geometry)
surface_from_segmentation() (in module cedalion.geometry.segmentation)
symdecor() (in module cedalion.sigdecomp.ICA_EBM)
T
t_ijk2ras (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
t_ras2ijk (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
task() (in module cedalion.tasks)
TDG_AMPLITUDE (cedalion.io.snirf.DataType attribute)
TDG_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute)
TDM_AMPLITUDE (cedalion.io.snirf.DataType attribute)
TDM_FLUORESCENCE_AMPLITUDE (cedalion.io.snirf.DataType attribute)
timeseries (cedalion.dataclasses.recording.Recording attribute)
tissue_properties (cedalion.imagereco.forward_model.ForwardModel attribute)
TissueType (class in cedalion.imagereco.tissue_properties)
to_epochs() (cedalion.dataclasses.accessors.CedalionAccessor method)
to_homogeneous() (cedalion.dataclasses.accessors.PointsAccessor method)
trial_types (cedalion.dataclasses.recording.Recording property)
trimesh_to_vtk_polydata() (in module cedalion.vtktutils)
TrimeshSurface (class in cedalion.dataclasses.geometry)
TwoSurfaceHeadModel (class in cedalion.imagereco.forward_model)
U
unitinmm (cedalion.imagereco.forward_model.ForwardModel attribute)
units (cedalion.dataclasses.geometry.Surface attribute)
UNKNOWN (cedalion.dataclasses.geometry.PointType attribute)
V
validate() (cedalion.dataclasses.schemas.DataArraySchema method)
validate_schemas() (in module cedalion.dataclasses.schemas)
validate_stim_schema() (in module cedalion.dataclasses.schemas)
ValidationError
vertex_colors (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
vertex_hue (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
vertex_value (cedalion.geometry.photogrammetry.processors.ColoredStickerProcessorDetails attribute)
vertices (cedalion.dataclasses.geometry.Surface property)
(cedalion.dataclasses.geometry.TrimeshSurface property)
(cedalion.dataclasses.geometry.VTKSurface property)
volume (cedalion.imagereco.forward_model.ForwardModel attribute)
voxel_to_vertex_brain (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
voxel_to_vertex_scalp (cedalion.imagereco.forward_model.TwoSurfaceHeadModel attribute)
,
[1]
VTKSurface (class in cedalion.dataclasses.geometry)
W
wavelengths (cedalion.dataclasses.recording.Recording property)
WM (cedalion.imagereco.tissue_properties.TissueType attribute)
write_snirf() (in module cedalion.io.snirf)