TRamWAy
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Index
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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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J
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K
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M
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X
_
_avg_distance (tramway.tessellation.gwr.GasMesh attribute)
(tramway.tessellation.kdtree.KDTreeMesh attribute)
_get_roi() (tramway.analyzer.spt_data.HasROI method)
_max_distance (tramway.tessellation.gwr.GasMesh attribute)
_min_distance (tramway.tessellation.gwr.GasMesh attribute)
(tramway.tessellation.kdtree.KDTreeMesh attribute)
_RWAFile (class in tramway.analyzer.spt_data)
_SPTAsciiFile (class in tramway.analyzer.spt_data)
_SPTDataFrame (class in tramway.analyzer.spt_data)
_SPTMatFile (class in tramway.analyzer.spt_data)
_sum (tramway.inference.optimization.SparseFunction attribute)
_trigger_discard_static_trajectories() (tramway.analyzer.spt_data.SPTFile method)
_trigger_reset_origin() (tramway.analyzer.spt_data.SPTFile method)
A
Aborted
active (tramway.core.analyses.auto.AutosaveCapable attribute)
add() (tramway.core.analyses.auto.Analyses method)
(tramway.core.analyses.base.Analyses method)
add_arguments() (in module tramway.core.plugin)
add_collectible() (tramway.analyzer.pipeline.Pipeline method)
(tramway.analyzer.RWAnalyzer method)
add_colorbar() (in module tramway.plot.bokeh.map)
add_metadata() (tramway.analyzer.roi.SupportRegion method)
add_sampling() (tramway.analyzer.roi.SupportRegion method)
add_tracked_data() (tramway.analyzer.spt_data.TrackerOutput method)
adjacency (tramway.inference.base.Distributed attribute)
adjacency_label (tramway.tessellation.base.Tessellation attribute)
,
[1]
(tramway.tessellation.nesting.NestedTessellations attribute)
(tramway.tessellation.time.TimeLattice attribute)
alias (tramway.analyzer.spt_data.SPTFile attribute)
(tramway.analyzer.spt_data.SPTFiles attribute)
aliases (tramway.analyzer.spt_data.SPTFiles attribute)
alpha_risk (tramway.analyzer.tesseller.proxied.GWR attribute)
Analyses (class in tramway.core.analyses.auto)
(class in tramway.core.analyses.base)
(class in tramway.core.analyses.lazy)
analyses (tramway.analyzer.spt_data.SPTDataItem attribute)
(tramway.core.analyses.auto.Analyses attribute)
AnalysesView (class in tramway.core.analyses.base)
animate() (tramway.analyzer.mapper.mpl.Mpl method)
(tramway.analyzer.mapper.mpl.PatchCollection method)
(tramway.analyzer.spt_data.mpl.LineDealer method)
(tramway.analyzer.tesseller.mpl.Mpl method)
animate_map_2d() (in module tramway.plot.animation.map)
animate_map_2d_helper() (in module tramway.helper.animation)
animate_trajectories_2d() (in module tramway.plot.animation.xyt)
animate_trajectories_2d_helper() (in module tramway.helper.animation)
any_cell() (tramway.inference.base.Distributed method)
append_leaf() (in module tramway.core.analyses.base)
append_stage() (tramway.analyzer.pipeline.Pipeline method)
area (tramway.plot.contour.ContourEditor attribute)
args (tramway.inference.optimization.SparseFunction attribute)
ArrayChain (class in tramway.core.chain)
artefact (tramway.core.analyses.base.Analyses attribute)
as_dataframes() (tramway.analyzer.spt_data.SPTData method)
(tramway.analyzer.spt_data.SPTDataIterator method)
as_frames() (tramway.analyzer.images.Images method)
as_individual_roi() (tramway.analyzer.roi.BoundingBoxes method)
(tramway.analyzer.roi.DecentralizedROIManager method)
(tramway.analyzer.roi.ROI method)
(tramway.analyzer.roi.ROIInitializer method)
as_support_regions() (tramway.analyzer.roi.DecentralizedROIManager method)
(tramway.analyzer.roi.ROI method)
(tramway.analyzer.roi.ROIAsciiFile method)
(tramway.analyzer.roi.ROIInitializer method)
(tramway.analyzer.roi.ROIRecoveredFromSampling method)
(tramway.analyzer.roi.SpecializedROI method)
(tramway.analyzer.roi.v1_ROIRecord method)
as_time_segments() (tramway.analyzer.time.DT method)
(tramway.analyzer.time.SlidingWindow method)
(tramway.analyzer.time.Time method)
at() (tramway.core.chain.ArrayChain method)
autoindex() (tramway.core.analyses.base.Analyses method)
autosave (tramway.core.analyses.auto.AutosaveCapable attribute)
autosave_policy (tramway.core.analyses.auto.AutosaveCapable attribute)
AutosaveCapable (class in tramway.core.analyses.auto)
autosaving() (tramway.core.analyses.auto.AutosaveCapable method)
available_slots (tramway.core.parallel.Scheduler attribute)
avg_distance (tramway.analyzer.tesseller.proxied.Hexagons attribute)
(tramway.analyzer.tesseller.proxied.KMeans attribute)
(tramway.analyzer.tesseller.proxied.Squares attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
avg_probability (tramway.analyzer.tesseller.proxied.Hexagons attribute)
(tramway.analyzer.tesseller.proxied.KMeans attribute)
(tramway.analyzer.tesseller.proxied.Squares attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
(tramway.tessellation.kmeans.KMeansMesh attribute)
(tramway.tessellation.random.RandomMesh attribute)
axes (tramway.plot.animation.VideoWriterReader attribute)
(tramway.plot.contour.ContourEditor attribute)
B
BaseRegion (class in tramway.analyzer.roi)
BaseSampler (class in tramway.analyzer.sampler)
batch_size (tramway.analyzer.tesseller.proxied.GWR attribute)
BFGSResult (class in tramway.inference.optimization)
boundary (tramway.inference.base.Local attribute)
bounding_box (tramway.tessellation.base.Partition attribute)
,
[1]
BoundingBox (class in tramway.analyzer.roi)
BoundingBoxes (class in tramway.analyzer.roi)
bounds (tramway.analyzer.spt_data.SPTData attribute)
(tramway.analyzer.spt_data.SPTDataItem attribute)
(tramway.analyzer.spt_data.SPTDataIterator attribute)
(tramway.inference.optimization.SparseFunction attribute)
box_voronoi_2d() (in module tramway.plot.map)
Browser (class in tramway.analyzer.browser)
browser (tramway.analyzer.RWAnalyzer attribute)
ByTranslocationCount (class in tramway.analyzer.tesseller.post.merger)
C
cache (tramway.inference.base.Cell attribute)
,
[1]
calculate_any_lambda_integral() (in module tramway.inference.bayes_factors.calculate_marginalized_integral)
calculate_bayes_factors() (in module tramway.inference.bayes_factors)
(in module tramway.inference.bayes_factors.calculate_bayes_factors)
calculate_bayes_factors_for_one_cell() (in module tramway.inference.bayes_factors)
(in module tramway.inference.bayes_factors.calculate_bayes_factors)
calculate_integral_ratio() (in module tramway.inference.bayes_factors.calculate_marginalized_integral)
calculate_marginalized_integral() (in module tramway.inference.bayes_factors.calculate_marginalized_integral)
calculate_minimal_n() (in module tramway.inference.bayes_factors.calculate_bayes_factors)
calculate_one_1D_posterior_in_2D() (in module tramway.inference.bayes_factors.calculate_posteriors)
calculate_one_1D_prior_in_2D() (in module tramway.inference.bayes_factors.calculate_posteriors)
calculate_one_2D_posterior() (in module tramway.inference.bayes_factors.calculate_posteriors)
ccount (tramway.inference.base.Distributed attribute)
Cell (class in tramway.inference.base)
cell (tramway.plot.contour.ContourEditor attribute)
cell_adjacency (tramway.feature.curl.Curl attribute)
(tramway.plot.contour.ContourEditor attribute)
(tramway.tessellation.base.Tessellation attribute)
,
[1]
(tramway.tessellation.base.Voronoi attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
(tramway.tessellation.nesting.NestedTessellations attribute)
(tramway.tessellation.time.TimeLattice attribute)
cell_centers (tramway.feature.curl.Curl attribute)
(tramway.plot.contour.ContourEditor attribute)
(tramway.tessellation.base.Delaunay attribute)
,
[1]
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
(tramway.tessellation.nesting.NestedTessellations attribute)
(tramway.tessellation.random.RandomMesh attribute)
(tramway.tessellation.time.TimeLattice attribute)
cell_count (tramway.feature.curl.Curl attribute)
(tramway.plot.contour.ContourEditor attribute)
cell_index (tramway.tessellation.base.Partition attribute)
,
[1]
cell_index() (tramway.tessellation.base.Delaunay method)
(tramway.tessellation.base.Tessellation method)
(tramway.tessellation.kdtree.KDTreeMesh method)
(tramway.tessellation.nesting.NestedTessellations method)
(tramway.tessellation.time.TimeLattice method)
(tramway.tessellation.window.SlidingWindow method)
cell_index_by_radius() (in module tramway.tessellation.base)
cell_label (tramway.tessellation.base.Tessellation attribute)
,
[1]
(tramway.tessellation.nesting.NestedTessellations attribute)
(tramway.tessellation.time.TimeLattice attribute)
cell_plot() (in module tramway.helper.tessellation)
(tramway.helper.roi.RoiCollection method)
cell_to_polygon() (in module tramway.plot.map)
cell_to_polygon_() (in module tramway.plot.map)
cell_vertices (tramway.tessellation.base.Voronoi attribute)
,
[1]
cell_volume (tramway.tessellation.base.Voronoi attribute)
,
[1]
(tramway.tessellation.hexagon.HexagonalMesh attribute)
(tramway.tessellation.time.TimeLattice attribute)
cells (tramway.inference.base.Distributed attribute)
(tramway.plot.contour.ContourEditor attribute)
(tramway.plot.tk.contour.TkContourEditor attribute)
CellStats (in module tramway.tessellation.base)
center (tramway.core.scaler.Scaler attribute)
,
[1]
(tramway.inference.base.Local attribute)
,
[1]
central (tramway.inference.base.Distributed attribute)
,
[1]
ChainArray (class in tramway.core.chain)
check_cache() (tramway.analyzer.spt_data.HasAnalysisTree method)
check_dimensionality() (in module tramway.inference.bayes_factors.calculate_bayes_factors)
check_for_nan() (in module tramway.inference.bayes_factors.calculate_bayes_factors)
child_cell_indices() (tramway.tessellation.nesting.NestedTessellations method)
child_factory (tramway.tessellation.nesting.NestedTessellations attribute)
child_factory_arguments (tramway.tessellation.nesting.NestedTessellations attribute)
children (tramway.tessellation.nesting.NestedTessellations attribute)
clabel() (tramway.analyzer.mapper.mpl.Mpl method)
clear_cache() (tramway.analyzer.spt_data.HasAnalysisTree method)
(tramway.inference.base.Cell method)
clear_caches() (tramway.inference.base.Distributed method)
clim (tramway.analyzer.browser.Browser attribute)
close() (tramway.core.parallel.StarConn method)
coerce_labels() (in module tramway.core.analyses.base)
coerce_labels_and_metadata() (in module tramway.core.analyses.base)
collapse_tol (tramway.analyzer.tesseller.proxied.GWR attribute)
collect_results() (tramway.analyzer.env.environments.SlurmOverSSH method)
collectibles (tramway.analyzer.env.EnvironmentInitializer attribute)
colormap (tramway.analyzer.browser.Browser attribute)
columns (tramway.analyzer.spt_data.SPTData attribute)
(tramway.analyzer.spt_data.SPTDataItem attribute)
(tramway.core.scaler.Scaler attribute)
,
[1]
columns() (in module tramway.core.namedcolumns)
combined (tramway.core.chain.ChainArray attribute)
comments (tramway.core.analyses.base.Analyses attribute)
,
[1]
(tramway.core.analyses.lazy.Analyses attribute)
CommentsView (class in tramway.core.analyses.base)
commit_cache() (tramway.analyzer.spt_data.HasAnalysisTree method)
CommonROI (class in tramway.analyzer.roi)
compatible_source() (tramway.analyzer.roi.HasROI method)
(tramway.analyzer.spt_data.HasROI method)
complete_delaunay (tramway.analyzer.tesseller.proxied.GWR attribute)
compute_dtypes() (in module tramway.analyzer.spt_data)
contour() (in module tramway.feature.adjacency)
(tramway.tessellation.base.Tessellation method)
(tramway.tessellation.grid.RegularMesh method)
contour_utility() (in module tramway.plot.tk.contour)
ContourEditingApp (class in tramway.plot.tk.contour)
ContourEditor (class in tramway.plot.contour)
convert_to_list() (in module tramway.tracking.track_non_track.file_processing_loc)
coord_scale (tramway.analyzer.spt_data._SPTMatFile attribute)
(tramway.analyzer.spt_data.SPTMatFiles attribute)
correct_cost_function() (in module tramway.tracking.track_non_track.file_processing_loc)
correct_deficiencies() (in module tramway.tracking.track_non_track.file_processing_loc)
count_per_dim (tramway.analyzer.tesseller.proxied.Squares attribute)
(tramway.tessellation.grid.RegularMesh attribute)
covariate (tramway.inference.optimization.SparseFunction attribute)
create_traj() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
create_widgets() (tramway.plot.tk.contour.ContourEditingApp method)
crop() (in module tramway.core.xyt)
crop_frames() (tramway.analyzer.images.Images method)
(tramway.analyzer.roi.BoundingBox method)
(tramway.analyzer.roi.FullRegion method)
(tramway.analyzer.roi.SupportRegion method)
cropping_utility() (in module tramway.utils.crop)
cumtime (tramway.inference.optimization.BFGSResult attribute)
Curl (class in tramway.feature.curl)
curl() (tramway.plot.contour.ContourEditor method)
curl_integral() (tramway.feature.curl.Curl method)
D
D (tramway.inference.dv.DV attribute)
d_neg_posterior1() (in module tramway.inference.standard_d)
data (tramway.core.analyses.base.Analyses attribute)
(tramway.core.analyses.lazy.Analyses attribute)
(tramway.inference.base.Local attribute)
,
[1]
data_array (tramway.core.parallel.Workspace attribute)
,
[1]
dataframe (tramway.analyzer.spt_data.SPTDataItem attribute)
dd_neg_posterior1() (in module tramway.inference.standard_ddrift)
deal() (tramway.core.parallel.StarQueue method)
debug (tramway.plot.tk.contour.ContourEditingApp attribute)
(tramway.plot.tk.contour.TkContourEditor attribute)
DecentralizedROIManager (class in tramway.analyzer.roi)
deck (tramway.core.parallel.StarQueue attribute)
defattr() (tramway.inference.base.Maps method)
degree (tramway.inference.base.Distributed attribute)
Delaunay (class in tramway.tessellation.base)
delaunay (tramway.plot.contour.ContourEditor attribute)
delete_cell() (tramway.tessellation.kdtree.KDTreeMesh method)
delete_cells() (tramway.tessellation.base.Voronoi method)
delete_temporary_data() (tramway.analyzer.env.environments.SlurmOverSSH method)
delta0() (in module tramway.inference.gradient)
delta0_without_scaling() (in module tramway.inference.gradient)
delta1() (in module tramway.inference.gradient)
descent_subspace (tramway.inference.optimization.SparseFunction attribute)
descriptors() (tramway.tessellation.base.Partition method)
(tramway.tessellation.base.Tessellation method)
(tramway.tessellation.time.TimeLattice method)
destinations (tramway.inference.base.Translocations attribute)
,
[1]
df (tramway.inference.optimization.BFGSResult attribute)
df_neg_posterior1() (in module tramway.inference.standard_df)
diagnosis (tramway.inference.optimization.BFGSResult attribute)
dict_to_sparse() (in module tramway.tessellation.base)
diffusion_gaussian_bump() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
diffusion_gaussian_trap() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
diffusion_linear() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
diffusivity_indices() (tramway.inference.stochastic_dv.LocalDV method)
diffusivity_prior() (tramway.inference.dv.DV method)
(tramway.inference.stochastic_dv.LocalDV method)
diffusivity_spatial_prior() (tramway.inference.stochastic_dv.LocalDV method)
diffusivity_time_prior() (tramway.inference.stochastic_dv.LocalDV method)
DiffusivityWarning
dilation() (in module tramway.feature.adjacency)
dilation_adjacency (tramway.feature.curl.Curl attribute)
(tramway.plot.contour.ContourEditor attribute)
dim (tramway.inference.base.Cell attribute)
(tramway.inference.base.Distributed attribute)
(tramway.inference.base.Local attribute)
dirname (tramway.core.plugin.Plugins attribute)
disable_widgets() (tramway.plot.tk.contour.ContourEditingApp method)
discard_static_trajectories() (in module tramway.core.xyt)
(tramway.analyzer.spt_data.SPTData method)
(tramway.analyzer.spt_data.SPTDataIterator method)
(tramway.analyzer.spt_data.SPTFile method)
(tramway.analyzer.spt_data.SPTParameters method)
(tramway.analyzer.spt_data._SPTDataFrame method)
dispatch() (tramway.analyzer.env.Environment method)
(tramway.analyzer.env.environments.Environment method)
(tramway.analyzer.env.environments.SlurmOverSSH method)
distance_to_roi_center() (in module tramway.analyzer.roi.utils)
Distributed (class in tramway.inference.base)
distributed() (in module tramway.inference.base)
DistributeMerge (class in tramway.inference.base)
dr (tramway.inference.base.Translocations attribute)
draw() (tramway.core.parallel.EpochScheduler method)
(tramway.core.parallel.Scheduler method)
(tramway.plot.contour.ContourEditor method)
DT (class in tramway.analyzer.time)
dt (tramway.analyzer.spt_data.SPTDataIterator attribute)
(tramway.analyzer.spt_data.SPTParameters attribute)
(tramway.analyzer.time.DT attribute)
(tramway.analyzer.time.Time attribute)
(tramway.inference.base.Translocations attribute)
dtype (tramway.core.chain.Matrix attribute)
duration (tramway.analyzer.time.SlidingWindow attribute)
(tramway.tessellation.window.SlidingWindow attribute)
DV (class in tramway.inference.dv)
dv_neg_posterior() (in module tramway.inference.dv)
dv_neg_posterior1() (in module tramway.inference.dv)
dxy (tramway.inference.base.Translocations attribute)
E
early_setup() (tramway.analyzer.env.environments.SlurmOverSSH method)
(tramway.analyzer.pipeline.Pipeline method)
EfficiencyWarning
empty() (tramway.core.parallel.StarConn method)
enable_regularization() (tramway.analyzer.time.DT method)
(tramway.analyzer.time.SlidingWindow method)
enable_widgets() (tramway.plot.tk.contour.ContourEditingApp method)
env (tramway.analyzer.RWAnalyzer attribute)
Environment (class in tramway.analyzer.env)
(class in tramway.analyzer.env.environments)
EnvironmentInitializer (class in tramway.analyzer.env)
EpochScheduler (class in tramway.core.parallel)
eps (tramway.inference.optimization.SparseFunction attribute)
err (tramway.inference.optimization.BFGSResult attribute)
error_count_tol (tramway.analyzer.tesseller.proxied.GWR attribute)
euclidean (tramway.core.scaler.Scaler attribute)
,
[1]
expandcoord() (in module tramway.core.namedcolumns)
export_file() (in module tramway.utils.inferencemap)
export_to_cluster_file() (in module tramway.utils.inferencemap)
export_to_vmesh_file() (in module tramway.utils.inferencemap)
ExtendedWorkspace (class in tramway.core.parallel.abc)
extract() (tramway.feature.curl.Curl method)
extract_analysis() (in module tramway.core.analyses.base)
F
f (tramway.inference.optimization.BFGSResult attribute)
factor (tramway.core.scaler.Scaler attribute)
,
[1]
features (tramway.inference.base.Maps attribute)
field() (tramway.feature.curl.Curl method)
(tramway.plot.contour.ContourEditor method)
field_map_2d() (in module tramway.plot.bokeh.map)
(in module tramway.plot.map)
figure (tramway.plot.animation.VideoWriterReader attribute)
FileChooser (class in tramway.plot.tk.contour)
FileNotFoundWarning
filepath (tramway.analyzer.roi.ROIAsciiFile attribute)
(tramway.analyzer.spt_data.SPTFile attribute)
(tramway.analyzer.spt_data._RWAFile attribute)
filepaths (tramway.analyzer.spt_data.SPTFiles attribute)
filepattern (tramway.analyzer.spt_data.SPTFiles attribute)
files (tramway.analyzer.spt_data.SPTFiles attribute)
fill_slots() (tramway.core.parallel.Scheduler method)
filter_by_source() (tramway.analyzer.spt_data.SPTDataIterator method)
(tramway.analyzer.spt_data.SPTFiles method)
(tramway.analyzer.spt_data.TrackerOutput method)
filter_script_content() (tramway.analyzer.env.environments.SlurmOverSSH method)
find_artefacts() (in module tramway.core.analyses.base)
(in module tramway.core.analyses.lazy)
find_cell() (tramway.plot.contour.ContourEditor method)
find_marginalized_zeta_t_roots() (in module tramway.inference.bayes_factors.find_marginalized_zeta_t_roots)
FiniteElement (in module tramway.inference.base)
FiniteElements (in module tramway.inference.base)
flag_as_modified() (tramway.core.analyses.auto.Analyses method)
flatten() (tramway.inference.base.Distributed method)
force (tramway.core.plugin.Plugins attribute)
force_save (tramway.core.analyses.auto.AutosaveCapable attribute)
format_analyses() (in module tramway.core.analyses.base)
format_cell_index() (in module tramway.tessellation.base)
fps (tramway.plot.animation.VideoWriterReader attribute)
frame_interval (tramway.analyzer.spt_data.SPTData attribute)
(tramway.analyzer.spt_data.SPTDataItem attribute)
(tramway.analyzer.spt_data.SPTDataIterator attribute)
(tramway.analyzer.spt_data.SPTParameters attribute)
(tramway.analyzer.time.DT attribute)
FreeResolutionTesseller (class in tramway.analyzer.tesseller.proxy)
freeze() (tramway.tessellation.base.Partition method)
(tramway.tessellation.base.Tessellation method)
(tramway.tessellation.gwr.GasMesh method)
(tramway.tessellation.kdtree.KDTreeMesh method)
(tramway.tessellation.nesting.NestedTessellations method)
(tramway.tessellation.time.TimeLattice method)
from_ascii_file() (tramway.analyzer.roi.ROIInitializer method)
(tramway.analyzer.spt_data.SPTDataInitializer method)
from_ascii_files() (tramway.analyzer.roi.ROIInitializer method)
(tramway.analyzer.spt_data.SPTDataInitializer method)
from_bounding_boxes() (tramway.analyzer.roi.ROIInitializer method)
from_callable() (tramway.analyzer.tesseller.post.TessellationPostProcessingInitializer method)
(tramway.analyzer.tesseller.TessellerInitializer method)
from_dataframe() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_dataframes() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_dedicated_rwa_record() (tramway.analyzer.roi.ROIInitializer method)
from_dedicated_rwa_records() (tramway.analyzer.roi.ROIInitializer method)
from_maps() (tramway.analyzer.mapper.MapperInitializer method)
from_mat_file() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_mat_files() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_nearest_neighbors() (tramway.analyzer.sampler.SamplerInitializer method)
from_nearest_time_neighbors() (tramway.analyzer.sampler.SamplerInitializer method)
from_non_tracking() (tramway.analyzer.tracker.TrackerInitializer method)
from_rw_generator() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_rwa_file() (tramway.analyzer.spt_data.SPTDataInitializer method)
(tramway.core.analyses.auto.Analyses class method)
from_rwa_files() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_sampling() (tramway.analyzer.time.TimeInitializer method)
from_single_particle() (tramway.analyzer.tracker.TrackerInitializer method)
from_sliding_window() (tramway.analyzer.time.TimeInitializer method)
from_spheres() (tramway.analyzer.sampler.SamplerInitializer method)
from_squares() (tramway.analyzer.roi.ROIInitializer method)
from_tiff_file() (tramway.analyzer.images.ImagesInitializer method)
from_tiff_files() (tramway.analyzer.images.ImagesInitializer method)
from_tracker() (tramway.analyzer.spt_data.SPTDataInitializer method)
from_UNet() (tramway.analyzer.localizer.LocalizerInitializer method)
from_unet() (tramway.analyzer.localizer.LocalizerInitializer method)
from_voronoi() (tramway.analyzer.sampler.SamplerInitializer method)
full() (tramway.core.parallel.StarConn method)
FullRegion (class in tramway.analyzer.roi)
fully_reified (tramway.analyzer.spt_data.SPTFiles attribute)
fun (tramway.inference.optimization.SparseFunction attribute)
fun() (tramway.inference.optimization.SparseFunction method)
function (tramway.core.scaler.Scaler attribute)
,
[1]
future_edge (tramway.tessellation.time.TimeLattice attribute)
fuzzy (tramway.inference.base.Cell attribute)
G
gas (tramway.tessellation.gwr.GasMesh attribute)
GasMesh (class in tramway.tessellation.gwr)
generate_the_actual_trajectories() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
generate_trajectories (class in tramway.helper.simulation.categoricaltrap)
get() (tramway.core.analyses.base.InstancesView method)
(tramway.core.analyses.lazy.InstancesView method)
(tramway.core.chain.ArrayChain method)
(tramway.core.parallel.StarConn method)
(tramway.core.plugin.Plugins method)
get_all_assigment_stack() (in module tramway.tracking.track_non_track.non_tracking_T_0)
get_assigment_matrix_from_reduced_cost() (in module tramway.tracking.track_non_track.file_processing_loc)
get_cells() (tramway.helper.roi.RoiCollection method)
get_cost_function() (in module tramway.tracking.track_non_track.file_processing_loc)
get_D_confidence_interval() (in module tramway.inference.bayes_factors.get_D_posterior)
get_D_posterior() (in module tramway.inference.bayes_factors.get_D_posterior)
get_dt() (in module tramway.tracking.track_non_track.file_processing_loc)
get_grad_kwargs() (in module tramway.inference.gradient)
get_image() (tramway.analyzer.spt_data.SPTFile method)
get_lambda_MAP() (in module tramway.inference.bayes_factors.calculate_posteriors)
get_local_parameters_accessible_elsewhere_in_tramway() (in module tramway.tracking.track_non_track.file_processing_loc)
get_localization_error() (tramway.inference.base.Local method)
get_locations() (in module tramway.inference.base)
get_map() (tramway.helper.roi.RoiCollection method)
get_MAP_D() (in module tramway.inference.bayes_factors.get_D_posterior)
get_nowait() (tramway.core.parallel.StarConn method)
get_processed_step() (tramway.core.parallel.Scheduler method)
get_spatial_segmentation() (tramway.analyzer.time.DT method)
(tramway.analyzer.time.SlidingWindow method)
get_support_region() (tramway.analyzer.roi.SpecializedROI method)
get_task() (tramway.core.parallel.Worker method)
get_tessellation() (tramway.helper.roi.RoiCollection method)
get_time_segments() (tramway.analyzer.time.SlidingWindow method)
get_translocations() (in module tramway.inference.base)
get_workspace() (tramway.core.parallel.abc.JobStep method)
(tramway.core.parallel.JobStep method)
give_diffusion_drift_gamma() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
give_gamma_equilibirum() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
give_gamma_fixed_value() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
glob() (in module tramway.analyzer.spt_data)
GPULab (class in tramway.analyzer.env.environments)
grab_frame() (tramway.plot.animation.VideoWriter method)
(tramway.plot.animation.VideoWriterReader method)
grad() (tramway.inference.base.Distributed method)
grad1() (in module tramway.inference.gradient)
grad_sum() (tramway.inference.base.Distributed method)
gradient_map() (in module tramway.inference.gradient)
gradient_subspace (tramway.inference.optimization.SparseFunction attribute)
gradn() (in module tramway.inference.gradient)
granularity (tramway.analyzer.pipeline.PipelineStage attribute)
group() (tramway.inference.base.Distributed method)
group_roi() (in module tramway.analyzer.roi.utils)
GroupedRegions (class in tramway.helper.roi)
GWR (class in tramway.analyzer.tesseller.proxied)
H
H (tramway.inference.optimization.BFGSResult attribute)
h0 (tramway.inference.optimization.SparseFunction attribute)
handler (tramway.core.analyses.auto.Analyses attribute)
HasAnalysisTree (class in tramway.analyzer.spt_data)
HasROI (class in tramway.analyzer.roi)
(class in tramway.analyzer.spt_data)
helper_cls (tramway.analyzer.tesseller.proxy.TessellerProxy attribute)
(tramway.analyzer.tesseller.TessellerProxy attribute)
hexagon_count (tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
hexagon_radius (tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
HexagonalMesh (class in tramway.tessellation.hexagon)
Hexagons (class in tramway.analyzer.tesseller.proxied)
hooks (tramway.core.analyses.auto.Analyses attribute)
hull (tramway.inference.base.Local attribute)
I
identify_columns() (in module tramway.inference.base)
identify_extensions() (tramway.core.parallel.ProtoWorkspace method)
Image (class in tramway.analyzer.images)
ImageFiles (class in tramway.analyzer.images)
Images (class in tramway.analyzer.images)
images (tramway.analyzer.RWAnalyzer attribute)
ImagesInitializer (class in tramway.analyzer.images)
import_cluster_file() (in module tramway.utils.inferencemap)
import_file() (in module tramway.utils.inferencemap)
import_vmesh_file() (in module tramway.utils.inferencemap)
index (tramway.inference.base.Local attribute)
,
[1]
index_format (tramway.analyzer.roi.BoundingBoxes attribute)
indices (tramway.inference.base.Distributed attribute)
indices() (tramway.inference.stochastic_dv.LocalDV method)
IndividualROI (class in tramway.analyzer.roi)
infer() (in module tramway.analyzer.pipeline.stages)
(in module tramway.helper.inference)
infer0() (in module tramway.helper.inference)
infer1() (in module tramway.helper.inference)
infer_D() (in module tramway.inference.d)
infer_d_conj_prior() (in module tramway.inference.d_conj_prior)
infer_d_map_and_ci() (in module tramway.inference.d_conj_prior)
infer_DD() (in module tramway.inference.ddrift)
infer_density() (in module tramway.inference.density)
infer_DF() (in module tramway.inference.df)
infer_smooth_D() (in module tramway.inference.standard_d)
infer_smooth_DD() (in module tramway.inference.standard_ddrift)
infer_smooth_DF() (in module tramway.inference.standard_df)
infer_stochastic_DV() (in module tramway.inference.stochastic_dv)
inferDV() (in module tramway.inference.dv)
init (tramway.core.scaler.Scaler attribute)
,
[1]
init_func() (tramway.analyzer.mapper.mpl.PatchCollection method)
(tramway.analyzer.spt_data.mpl.LineDealer method)
init_resource_lock() (tramway.core.parallel.Scheduler method)
initial (tramway.analyzer.tesseller.proxied.KMeans attribute)
initializer_method() (in module tramway.analyzer.attribute)
InitializerMethod (class in tramway.analyzer.attribute)
input (tramway.core.parallel.StarConn attribute)
instances (tramway.core.analyses.base.Analyses attribute)
,
[1]
(tramway.core.analyses.lazy.Analyses attribute)
InstancesView (class in tramway.core.analyses.base)
(class in tramway.core.analyses.lazy)
integral() (tramway.plot.contour.ContourEditor method)
interrupt_jobs() (tramway.analyzer.env.environments.LocalHost method)
interruptible_minimize() (in module tramway.inference.standard_d)
IOWarning
isstructured() (in module tramway.core.namedcolumns)
items() (tramway.core.analyses.base.CommentsView method)
(tramway.core.analyses.base.InstancesView method)
(tramway.core.plugin.Plugins method)
(tramway.inference.base.Distributed method)
iter_frames() (in module tramway.core.xyt)
iter_full_trajectories() (in module tramway.core.xyt)
iter_max_reached() (tramway.core.parallel.Scheduler method)
iter_trajectories() (in module tramway.core.xyt)
J
JobStep (class in tramway.core.parallel)
(class in tramway.core.parallel.abc)
join_thread() (tramway.core.parallel.StarConn method)
joinable (tramway.core.parallel.StarConn attribute)
K
KDTreeMesh (class in tramway.tessellation.kdtree)
keys() (tramway.core.analyses.base.Analyses method)
(tramway.core.analyses.base.AnalysesView method)
(tramway.core.plugin.Plugins method)
(tramway.inference.base.Distributed method)
KMeans (class in tramway.analyzer.tesseller.proxied)
KMeansMesh (class in tramway.tessellation.kmeans)
Knn (class in tramway.analyzer.sampler)
knn (tramway.analyzer.sampler.Knn attribute)
(tramway.analyzer.sampler.TimeKnn attribute)
L
label_paths() (in module tramway.core.analyses.base)
(in module tramway.core.analyses.lazy)
labels (tramway.core.analyses.base.Analyses attribute)
Lazy (class in tramway.core.lazy)
lifetime (tramway.analyzer.tesseller.proxied.GWR attribute)
lightcopy() (in module tramway.core.lazy)
LineDealer (class in tramway.analyzer.spt_data.mpl)
list_files() (tramway.analyzer.spt_data.RWAFiles method)
(tramway.analyzer.spt_data.SPTAsciiFiles method)
(tramway.analyzer.spt_data.SPTFiles method)
(tramway.analyzer.spt_data.SPTMatFiles method)
list_plugins() (in module tramway.core.plugin)
load_mat() (in module tramway.core.xyt)
load_rwa() (in module tramway.core.hdf5)
(in module tramway.core.hdf5.store)
load_xyt() (in module tramway.core.xyt)
(in module tramway.tracking.track_non_track.file_processing_loc)
Local (class in tramway.inference.base)
local_curl() (tramway.feature.curl.Curl method)
local_dv_neg_posterior() (in module tramway.inference.stochastic_dv)
local_variation() (tramway.inference.base.Distributed method)
LocalDV (class in tramway.inference.stochastic_dv)
LocalHost (class in tramway.analyzer.env.environments)
localization_error (tramway.analyzer.spt_data.SPTData attribute)
(tramway.analyzer.spt_data.SPTDataItem attribute)
(tramway.analyzer.spt_data.SPTDataIterator attribute)
(tramway.analyzer.spt_data.SPTParameters attribute)
localization_precision (tramway.analyzer.spt_data.SPTParameters attribute)
LocalizationFile (class in tramway.analyzer.spt_data)
localize() (tramway.analyzer.localizer.UNetLocalizer method)
Localizer (class in tramway.analyzer.localizer)
localizer (tramway.analyzer.RWAnalyzer attribute)
LocalizerInitializer (class in tramway.analyzer.localizer)
location_count (tramway.tessellation.base.Partition attribute)
,
[1]
Locations (class in tramway.inference.base)
locations (tramway.inference.base.Locations attribute)
(tramway.tessellation.base.Partition attribute)
lock() (tramway.core.parallel.Scheduler method)
locked() (tramway.core.parallel.Scheduler method)
logger (tramway.inference.stochastic_dv.LocalDV attribute)
lookup (tramway.core.plugin.Plugins attribute)
lookup_space_cells() (in module tramway.inference.stochastic_dv)
lower_bound (tramway.analyzer.tesseller.proxied.Hexagons attribute)
(tramway.analyzer.tesseller.proxied.Squares attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.random.RandomMesh attribute)
M
Maestro (class in tramway.analyzer.env.environments)
main() (in module tramway.utils.inferencemap)
make_job() (tramway.analyzer.env.environments.SlurmOverSSH method)
make_regions() (in module tramway.inference.stochastic_dv)
map (tramway.feature.curl.Curl attribute)
(tramway.plot.contour.ContourEditor attribute)
(tramway.plot.tk.contour.TkContourEditor attribute)
map_analyses() (in module tramway.core.analyses.base)
map_index (tramway.feature.curl.Curl attribute)
map_plot() (in module tramway.helper.inference)
(tramway.helper.roi.RoiCollection method)
map_plot1() (in module tramway.helper.inference)
Mapper (class in tramway.analyzer.mapper)
mapper (tramway.analyzer.RWAnalyzer attribute)
MapperInitializer (class in tramway.analyzer.mapper)
MapperPlugin (class in tramway.analyzer.mapper)
Maps (class in tramway.inference.base)
maps (tramway.inference.base.Maps attribute)
mapviz_utility() (in module tramway.utils.mapviz)
Matrix (class in tramway.core.chain)
max_level (tramway.tessellation.kdtree.KDTreeMesh attribute)
max_probability (tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
(tramway.tessellation.kdtree.KDTreeMesh attribute)
members (tramway.core.chain.ArrayChain attribute)
memoize() (in module tramway.feature.adjacency)
merged (tramway.inference.base.DistributeMerge attribute)
message (tramway.inference.standard_d.Result attribute)
metadata (tramway.core.analyses.base.Analyses attribute)
,
[1]
(tramway.core.analyses.lazy.Analyses attribute)
min_distance (tramway.analyzer.tesseller.proxied.Hexagons attribute)
(tramway.analyzer.tesseller.proxied.KMeans attribute)
(tramway.analyzer.tesseller.proxied.Squares attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
min_growth (tramway.analyzer.tesseller.proxied.GWR attribute)
min_location_count (tramway.analyzer.sampler.BaseSampler attribute)
min_probability (tramway.analyzer.tesseller.proxied.GWR attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.gwr.GasMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
(tramway.tessellation.kdtree.KDTreeMesh attribute)
minimize_sparse_bfgs() (in module tramway.inference.optimization)
minimize_sparse_bfgs0() (in module tramway.inference.optimization)
minimize_sparse_bfgs1() (in module tramway.inference.optimization)
minimum_diffusivity (tramway.inference.dv.DV attribute)
MisplacedAttributeWarning
MissingSupportWarning
modified() (tramway.core.analyses.auto.Analyses method)
modules (tramway.core.plugin.Plugins attribute)
Mpl (class in tramway.analyzer.images.mpl)
(class in tramway.analyzer.mapper.mpl)
(class in tramway.analyzer.tesseller.mpl)
mpl (tramway.analyzer.spt_data._SPTDataFrame attribute)
(tramway.analyzer.tesseller.TessellerInitializer attribute)
(tramway.analyzer.tesseller.TessellerProxy attribute)
(tramway.analyzer.tesseller.proxy.TessellerProxy attribute)
MultipleArgumentError
MultipleRWAnalyses (class in tramway.analyzer.spt_data)
N
n (tramway.inference.base.TrackedMolecules attribute)
,
[1]
n_pi_func() (in module tramway.inference.bayes_factors.convenience_functions)
n_time_segments() (tramway.analyzer.time.DT method)
(tramway.analyzer.time.SlidingWindow method)
name (tramway.analyzer.pipeline.PipelineStage attribute)
NaNInputError
NaNWarning
ncalls (tramway.inference.optimization.BFGSResult attribute)
(tramway.inference.optimization.SparseFunction attribute)
(tramway.inference.standard_d.Result attribute)
nearest_cell() (in module tramway.tessellation.base)
neighbours() (tramway.inference.base.Distributed method)
(tramway.tessellation.base.Tessellation method)
neighbours_per_axis() (in module tramway.inference.gradient)
NestedTessellations (class in tramway.tessellation.nesting)
new_file() (tramway.plot.tk.contour.ContourEditingApp method)
next_task() (tramway.core.parallel.Scheduler method)
niter (tramway.inference.optimization.BFGSResult attribute)
noisify() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
NonTrackingTracker (class in tramway.analyzer.tracker)
NoSolutionError
number_of_cells (tramway.tessellation.base.Partition attribute)
(tramway.tessellation.base.Tessellation attribute)
(tramway.tessellation.time.TimeLattice attribute)
O
onclick() (tramway.plot.tk.contour.TkContourEditor method)
open_input_file() (tramway.plot.tk.contour.FileChooser method)
OptimizationWarning
order (tramway.core.chain.ArrayChain attribute)
(tramway.core.chain.Matrix attribute)
origins (tramway.inference.base.Translocations attribute)
,
[1]
output (tramway.core.parallel.StarConn attribute)
P
p() (in module tramway.inference.bayes_factors.convenience_functions)
pack_indices() (tramway.tessellation.base.Voronoi method)
pack_temporary_rwa_files() (tramway.analyzer.env.environments.SlurmOverSSH method)
package (tramway.core.plugin.Plugins attribute)
param (tramway.tessellation.base.Partition attribute)
,
[1]
parent (tramway.tessellation.nesting.NestedTessellations attribute)
parent_index_arguments (tramway.tessellation.nesting.NestedTessellations attribute)
partially_reified (tramway.analyzer.spt_data.SPTFiles attribute)
Partition (class in tramway.tessellation.base)
pass_count (tramway.analyzer.tesseller.proxied.GWR attribute)
past_edge (tramway.tessellation.time.TimeLattice attribute)
PatchCollection (class in tramway.analyzer.mapper.mpl)
peek (tramway.core.analyses.lazy.InstancesView attribute)
peek_maps() (in module tramway.core.hdf5)
PermissionError
Pipeline (class in tramway.analyzer.pipeline)
pipeline (tramway.analyzer.RWAnalyzer attribute)
PipelineStage (class in tramway.analyzer.pipeline)
pixel_size (tramway.analyzer.spt_data._SPTMatFile attribute)
(tramway.analyzer.spt_data.SPTMatFiles attribute)
play() (tramway.plot.animation.VideoWriterReader method)
plot() (tramway.analyzer.images.mpl.Mpl method)
(tramway.analyzer.mapper.mpl.Mpl method)
(tramway.analyzer.mapper.mpl.PatchCollection method)
(tramway.analyzer.spt_data.mpl.LineDealer method)
(tramway.analyzer.tesseller.mpl.Mpl method)
plot_cell_indices() (in module tramway.plot.mesh)
(tramway.analyzer.tesseller.mpl.Mpl method)
plot_delaunay() (in module tramway.plot.bokeh.map)
(in module tramway.plot.mesh)
plot_distributed() (in module tramway.plot.mesh)
plot_indices() (in module tramway.plot.mesh)
plot_linking_3_from_list() (in module tramway.tracking.track_non_track.file_processing_loc)
plot_linking_from_list() (in module tramway.tracking.track_non_track.file_processing_loc)
plot_linking_two_images() (in module tramway.tracking.track_non_track.file_processing_loc)
plot_points() (in module tramway.plot.bokeh.map)
(in module tramway.plot.mesh)
plot_trajectories() (in module tramway.plot.bokeh.map)
plot_voronoi() (in module tramway.plot.mesh)
Plugins (class in tramway.core.plugin)
point_adjacency_matrix() (in module tramway.tessellation.base)
points (tramway.tessellation.base.Partition attribute)
,
[1]
(tramway.tessellation.kmeans.KMeansMesh attribute)
poke_maps() (in module tramway.core.hdf5)
pop() (tramway.core.analyses.base.InstancesView method)
(tramway.core.analyses.lazy.InstancesView method)
(tramway.core.plugin.Plugins method)
pop_extension_updates() (tramway.core.parallel.abc.ExtendedWorkspace method)
(tramway.core.parallel.ProtoWorkspace method)
pop_updates() (tramway.core.parallel.abc.VehicleJobStep method)
(tramway.core.parallel.UpdateVehicle method)
pop_workspace_update() (tramway.core.parallel.abc.WorkspaceExtension method)
(tramway.inference.stochastic_dv.LocalDV method)
position_and_displacement_from_assignment() (in module tramway.tracking.track_non_track.non_tracking_T_0)
post_load (tramway.core.plugin.Plugins attribute)
postprocess() (tramway.core.analyses.auto.Analyses method)
potential_drift() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
potential_indices() (tramway.inference.stochastic_dv.LocalDV method)
potential_prior() (tramway.inference.dv.DV method)
(tramway.inference.stochastic_dv.LocalDV method)
potential_spatial_prior() (tramway.inference.stochastic_dv.LocalDV method)
potential_time_prior() (tramway.inference.stochastic_dv.LocalDV method)
potential_trap() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
preprocess() (tramway.core.analyses.auto.Analyses method)
print_traj() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
prior_delay (tramway.inference.stochastic_dv.LocalDV attribute)
prior_include (tramway.inference.dv.DV attribute)
projg (tramway.inference.optimization.BFGSResult attribute)
ProtoWorkspace (class in tramway.core.parallel)
proxy_property() (in module tramway.analyzer.tesseller.proxy)
prune (tramway.analyzer.tesseller.proxied.KMeans attribute)
(tramway.tessellation.kmeans.KMeansMesh attribute)
pseudo_stop() (tramway.core.parallel.Scheduler method)
pseudo_worker (tramway.core.parallel.Scheduler attribute)
pull_updates() (tramway.core.parallel.Worker method)
push_extension_updates() (tramway.core.parallel.abc.ExtendedWorkspace method)
(tramway.core.parallel.ProtoWorkspace method)
push_update() (tramway.core.parallel.Worker method)
push_updates() (tramway.core.parallel.abc.VehicleJobStep method)
(tramway.core.parallel.UpdateVehicle method)
push_workspace_update() (tramway.core.parallel.abc.WorkspaceExtension method)
(tramway.inference.stochastic_dv.LocalDV method)
put() (tramway.core.parallel.StarConn method)
put_nowait() (tramway.core.parallel.StarConn method)
Q
qsize() (tramway.core.parallel.StarConn method)
R
r (tramway.inference.base.Locations attribute)
(tramway.inference.base.Translocations attribute)
radius (tramway.analyzer.sampler.SphericalSampler attribute)
random_start() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
random_walk() (in module tramway.helper.simulation.functional)
random_walk_2d() (in module tramway.helper.simulation.categoricaltrap)
RandomMesh (class in tramway.tessellation.random)
range() (tramway.plot.animation.VideoWriter method)
(tramway.plot.animation.VideoWriterReader method)
RawImages (class in tramway.analyzer.images)
RawSPTFile (class in tramway.analyzer.spt_data)
RawSPTFiles (class in tramway.analyzer.spt_data)
ready (tramway.core.scaler.Scaler attribute)
refresh() (tramway.plot.contour.ContourEditor method)
region() (tramway.inference.stochastic_dv.LocalDV method)
region_to_units() (tramway.helper.roi.UnitRegions method)
regions (tramway.inference.stochastic_dv.LocalDV attribute)
regul (tramway.inference.optimization.SparseFunction attribute)
regularize_in_time (tramway.analyzer.time.SlidingWindow attribute)
RegularMesh (class in tramway.tessellation.grid)
reified (tramway.analyzer.roi.ROIAsciiFile attribute)
(tramway.analyzer.roi.ROIRecoveredFromSampling attribute)
(tramway.analyzer.roi.v1_ROIRecord attribute)
reindex_trajectories() (in module tramway.core.xyt)
reload() (in module tramway.analyzer.pipeline.stages)
reload_from_rwa_files() (tramway.analyzer.spt_data.RWAFiles method)
(tramway.analyzer.spt_data.SPTDataIterator method)
require (tramway.core.plugin.Plugins attribute)
requires_mutability (tramway.analyzer.pipeline.PipelineStage attribute)
reset() (tramway.analyzer.pipeline.Pipeline method)
(tramway.analyzer.tesseller.TessellerProxy method)
(tramway.analyzer.tesseller.proxy.TessellerProxy method)
reset_modification_flag() (tramway.core.analyses.auto.Analyses method)
reset_origin() (tramway.analyzer.spt_data.SPTData method)
residual_factor (tramway.analyzer.tesseller.proxied.GWR attribute)
resolution (tramway.analyzer.tesseller.Tesseller attribute)
(tramway.inference.optimization.BFGSResult attribute)
resource_id (tramway.core.parallel.abc.JobStep attribute)
(tramway.core.parallel.JobStep attribute)
resources (tramway.core.parallel.abc.JobStep attribute)
(tramway.core.parallel.JobStep attribute)
resources() (tramway.core.parallel.abc.Workspace method)
(tramway.core.parallel.ProtoWorkspace method)
restore_spt_data() (in module tramway.analyzer.pipeline.stages)
Result (class in tramway.inference.standard_d)
result (tramway.inference.standard_d.Result attribute)
resume() (tramway.analyzer.env.environments.SlurmOverSSH method)
(tramway.analyzer.pipeline.Pipeline method)
reverse (tramway.inference.base.Distributed attribute)
ro_property_assert() (in module tramway.core.lazy)
ROI (class in tramway.analyzer.roi)
roi (tramway.analyzer.roi.HasROI attribute)
(tramway.analyzer.RWAnalyzer attribute)
(tramway.analyzer.spt_data.HasROI attribute)
roi() (tramway.analyzer.images.mpl.Mpl method)
ROIAsciiFile (class in tramway.analyzer.roi)
ROIAsciiFiles (class in tramway.analyzer.roi)
RoiCollection (class in tramway.helper.roi)
RoiCollections (class in tramway.helper.roi)
RoiHelper (class in tramway.helper.roi)
ROIInitializer (class in tramway.analyzer.roi)
ROIRecords (class in tramway.analyzer.roi)
ROIRecoveredFromSampling (class in tramway.analyzer.roi)
run() (tramway.analyzer.pipeline.Pipeline method)
(tramway.analyzer.RWAnalyzer method)
(tramway.core.parallel.Scheduler method)
(tramway.core.parallel.Worker method)
(tramway.inference.base.Distributed method)
run_everywhere (tramway.analyzer.pipeline.PipelineStage attribute)
rwa_file (tramway.core.analyses.auto.Analyses attribute)
RWAFile (class in tramway.analyzer.spt_data)
RWAFileException
RWAFiles (class in tramway.analyzer.spt_data)
RWAnalyses (class in tramway.analyzer.spt_data)
RWAnalyzer (class in tramway.analyzer)
RWGenerator (class in tramway.analyzer.spt_data)
S
sample() (tramway.analyzer.sampler.SamplerInitializer method)
Sampler (class in tramway.analyzer.sampler)
sampler (tramway.analyzer.RWAnalyzer attribute)
SamplerInitializer (class in tramway.analyzer.sampler)
save() (tramway.core.analyses.auto.Analyses method)
(tramway.core.analyses.auto.AutosaveCapable method)
save_on_completion (tramway.core.analyses.auto.AutosaveCapable attribute)
save_on_every_step (tramway.core.analyses.auto.AutosaveCapable attribute)
save_options (tramway.core.analyses.auto.Analyses attribute)
save_rwa() (in module tramway.core.hdf5)
(in module tramway.core.hdf5.store)
saving() (tramway.plot.animation.VideoWriter method)
(tramway.plot.animation.VideoWriterReader method)
scalar_map_2d() (in module tramway.plot.bokeh.map)
(in module tramway.plot.map)
scalar_map_3d() (in module tramway.plot.map)
scale_distance() (tramway.core.scaler.Scaler method)
scale_length() (tramway.core.scaler.Scaler method)
scale_point() (tramway.core.scaler.Scaler method)
scale_size() (tramway.core.scaler.Scaler method)
scale_surface_area() (tramway.core.scaler.Scaler method)
scale_vector() (tramway.core.scaler.Scaler method)
scale_volume() (tramway.core.scaler.Scaler method)
scaled() (tramway.core.scaler.Scaler method)
Scaler (class in tramway.core.scaler)
scaler (tramway.tessellation.base.Tessellation attribute)
,
[1]
(tramway.tessellation.kdtree.KDTreeMesh attribute)
Scheduler (class in tramway.core.parallel)
script (tramway.analyzer.env.Environment attribute)
(tramway.analyzer.RWAnalyzer attribute)
(tramway.analyzer.env.EnvironmentInitializer attribute)
(tramway.analyzer.env.environments.Environment attribute)
segment() (tramway.analyzer.time.SlidingWindow method)
(tramway.analyzer.time.Time method)
segment_label() (tramway.analyzer.time.SlidingWindow method)
self_update() (tramway.analyzer.spt_data.SPTDataIterator method)
send_task() (tramway.core.parallel.Scheduler method)
set() (tramway.core.chain.ArrayChain method)
set_adjacency() (tramway.tessellation.base.Tessellation method)
set_contiguous_time_support_by_count() (in module tramway.analyzer.roi.utils)
set_maps() (tramway.plot.tk.contour.ContourEditingApp method)
set_num_digits() (tramway.analyzer.roi.BoundingBoxes method)
set_precision() (tramway.analyzer.spt_data._SPTDataFrame method)
(tramway.analyzer.spt_data.SPTDataIterator method)
(tramway.analyzer.spt_data.SPTParameters method)
set_workspace() (tramway.core.parallel.abc.JobStep method)
(tramway.core.parallel.JobStep method)
setup() (tramway.analyzer.env.environments.SlurmOverSSH method)
setup_with_grad_arguments() (in module tramway.inference.gradient)
shape (tramway.core.chain.ArrayChain attribute)
(tramway.core.chain.Matrix attribute)
shift (tramway.analyzer.time.SlidingWindow attribute)
(tramway.tessellation.window.SlidingWindow attribute)
short_options() (in module tramway.core.plugin)
show_maps() (tramway.analyzer.browser.Browser method)
SideEffectWarning
,
[1]
simplified_adjacency() (tramway.tessellation.base.Tessellation method)
(tramway.tessellation.time.TimeLattice method)
single_roi_label() (tramway.helper.roi.RoiCollections method)
size (tramway.analyzer.roi.ROIAsciiFile attribute)
(tramway.core.chain.ArrayChain attribute)
(tramway.core.chain.Matrix attribute)
SlidingWindow (class in tramway.analyzer.time)
(class in tramway.tessellation.window)
SlurmOverSSH (class in tramway.analyzer.env.environments)
smooth_d_neg_posterior() (in module tramway.inference.standard_d)
smooth_dd_neg_posterior() (in module tramway.inference.standard_ddrift)
smooth_df_neg_posterior() (in module tramway.inference.standard_df)
smooth_infer_init() (in module tramway.inference.base)
source (tramway.analyzer.spt_data.SPTDataItem attribute)
space_cols (tramway.inference.base.Cell attribute)
(tramway.inference.base.Distributed attribute)
space_data (tramway.inference.base.Cell attribute)
span (tramway.inference.base.Local attribute)
,
[1]
sparse_grad() (in module tramway.inference.optimization)
sparse_to_dict() (in module tramway.tessellation.base)
SparseFunction (class in tramway.inference.optimization)
spatial_mesh (tramway.tessellation.time.TimeLattice attribute)
SpecializedROI (class in tramway.analyzer.roi)
SphericalSampler (class in tramway.analyzer.sampler)
split_frames() (tramway.tessellation.time.TimeLattice method)
split_segments() (tramway.tessellation.time.TimeLattice method)
splitcoord() (in module tramway.core.namedcolumns)
spt_data (tramway.analyzer.RWAnalyzer attribute)
SPTAsciiFile (class in tramway.analyzer.spt_data)
SPTAsciiFiles (class in tramway.analyzer.spt_data)
SPTData (class in tramway.analyzer.spt_data)
SPTDataFrame (class in tramway.analyzer.spt_data)
SPTDataFrames (class in tramway.analyzer.spt_data)
SPTDataInitializer (class in tramway.analyzer.spt_data)
SPTDataItem (class in tramway.analyzer.spt_data)
SPTDataIterator (class in tramway.analyzer.spt_data)
SPTFile (class in tramway.analyzer.spt_data)
SPTFiles (class in tramway.analyzer.spt_data)
SPTMatFile (class in tramway.analyzer.spt_data)
SPTMatFiles (class in tramway.analyzer.spt_data)
SPTParameters (class in tramway.analyzer.spt_data)
Squares (class in tramway.analyzer.tesseller.proxied)
StandaloneDataItem (class in tramway.analyzer.spt_data)
StandaloneRWAFile (class in tramway.analyzer.spt_data)
StandaloneSPTAsciiFile (class in tramway.analyzer.spt_data)
StandaloneSPTDataFrame (class in tramway.analyzer.spt_data)
StandaloneSPTMatFile (class in tramway.analyzer.spt_data)
StarConn (class in tramway.core.parallel)
StarQueue (class in tramway.core.parallel)
start_new_epoch() (tramway.core.parallel.EpochScheduler method)
start_time (tramway.analyzer.time.SlidingWindow attribute)
(tramway.tessellation.window.SlidingWindow attribute)
statefree() (tramway.core.analyses.auto.Analyses method)
step (tramway.plot.contour.ContourEditor attribute)
stop() (tramway.core.parallel.Scheduler method)
sub() (tramway.inference.base.Maps method)
success (tramway.inference.standard_d.Result attribute)
sum() (tramway.plot.contour.ContourEditor method)
sum_series() (in module tramway.inference.bayes_factors.calculate_marginalized_integral)
SupportRegion (class in tramway.analyzer.roi)
SupportRegions (class in tramway.helper.roi)
surface_area() (tramway.feature.curl.Curl method)
(tramway.plot.contour.ContourEditor method)
sync_start_times() (tramway.analyzer.time.SlidingWindow method)
T
t (tramway.inference.base.Locations attribute)
(tramway.inference.base.Translocations attribute)
tangent() (tramway.feature.curl.Curl method)
(tramway.plot.contour.ContourEditor method)
Tars (class in tramway.analyzer.env.environments)
task_done() (tramway.core.parallel.StarConn method)
tau (tramway.analyzer.tesseller.proxied.GWR attribute)
tcount (tramway.inference.base.Cell attribute)
(tramway.inference.base.Distributed attribute)
(tramway.inference.base.Local attribute)
temperature (tramway.analyzer.spt_data.SPTDataIterator attribute)
(tramway.analyzer.spt_data.SPTParameters attribute)
terminate() (tramway.core.analyses.lazy.Analyses method)
tessellate() (in module tramway.analyzer.pipeline.stages)
(in module tramway.helper.tessellation)
(tramway.analyzer.tesseller.TessellerProxy method)
(tramway.analyzer.tesseller.proxied.GWR method)
(tramway.analyzer.tesseller.proxy.TessellerProxy method)
(tramway.tessellation.base.Delaunay method)
(tramway.tessellation.base.Tessellation method)
(tramway.tessellation.grid.RegularMesh method)
(tramway.tessellation.gwr.GasMesh method)
(tramway.tessellation.hexagon.HexagonalMesh method)
(tramway.tessellation.kdtree.KDTreeMesh method)
(tramway.tessellation.kmeans.KMeansMesh method)
(tramway.tessellation.nesting.NestedTessellations method)
(tramway.tessellation.random.RandomMesh method)
(tramway.tessellation.time.TimeLattice method)
tessellate0() (in module tramway.helper.tessellation)
tessellate1() (in module tramway.helper.tessellation)
tessellate_and_infer() (in module tramway.analyzer.pipeline.stages)
Tessellation (class in tramway.tessellation.base)
tessellation (tramway.tessellation.base.Partition attribute)
,
[1]
TessellationPostProcessing (class in tramway.analyzer.tesseller)
TessellationPostProcessingInitializer (class in tramway.analyzer.tesseller.post)
Tesseller (class in tramway.analyzer.tesseller)
tesseller (tramway.analyzer.RWAnalyzer attribute)
tesseller_plugin() (in module tramway.analyzer.tesseller.plugin)
TessellerInitializer (class in tramway.analyzer.tesseller)
TessellerPlugin (class in tramway.analyzer.tesseller)
(class in tramway.analyzer.tesseller.plugin)
TessellerProxy (class in tramway.analyzer.tesseller)
(class in tramway.analyzer.tesseller.proxy)
TiffFiles (class in tramway.analyzer.images)
tilt (tramway.analyzer.tesseller.proxied.Hexagons attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
,
[1]
Time (class in tramway.analyzer.time)
time (tramway.analyzer.RWAnalyzer attribute)
time_col (tramway.inference.base.Cell attribute)
time_data (tramway.inference.base.Cell attribute)
time_dimension (tramway.tessellation.time.TimeLattice attribute)
time_edge (tramway.tessellation.time.TimeLattice attribute)
time_lattice (tramway.tessellation.time.TimeLattice attribute)
time_step (tramway.analyzer.spt_data.SPTDataIterator attribute)
(tramway.analyzer.spt_data.SPTParameters attribute)
(tramway.analyzer.time.DT attribute)
TimeInitializer (class in tramway.analyzer.time)
TimeKnn (class in tramway.analyzer.sampler)
TimeLattice (class in tramway.tessellation.time)
timeout (tramway.core.parallel.Scheduler attribute)
TkContourEditor (class in tramway.plot.tk.contour)
to_ascii_file() (tramway.analyzer.roi.BoundingBoxes method)
(tramway.analyzer.roi.CommonROI method)
(tramway.analyzer.spt_data._SPTDataFrame method)
to_rwa_file() (tramway.analyzer.spt_data._SPTDataFrame method)
toggle_delaunay() (tramway.plot.tk.contour.TkContourEditor method)
tol (tramway.analyzer.tesseller.proxied.KMeans attribute)
(tramway.tessellation.kmeans.KMeansMesh attribute)
topology (tramway.analyzer.tesseller.proxied.GWR attribute)
TrackedMolecules (class in tramway.inference.base)
Tracker (class in tramway.analyzer.tracker)
tracker (tramway.analyzer.RWAnalyzer attribute)
TrackerInitializer (class in tramway.analyzer.tracker)
TrackerOutput (class in tramway.analyzer.spt_data)
traj_duration() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
traj_from_assigment() (in module tramway.tracking.track_non_track.non_tracking_T_0)
trajectories_to_translocations() (in module tramway.core.xyt)
trajviz_utility() (in module tramway.utils.trajviz)
tramway.analyzer (module)
tramway.analyzer.artefact (module)
tramway.analyzer.attribute (module)
tramway.analyzer.browser (module)
tramway.analyzer.env (module)
tramway.analyzer.env.environments (module)
tramway.analyzer.images (module)
tramway.analyzer.images.mpl (module)
tramway.analyzer.localizer (module)
tramway.analyzer.mapper (module)
tramway.analyzer.mapper.mpl (module)
tramway.analyzer.mapper.utils (module)
tramway.analyzer.pipeline (module)
tramway.analyzer.pipeline.stages (module)
tramway.analyzer.roi (module)
tramway.analyzer.roi.utils (module)
tramway.analyzer.sampler (module)
tramway.analyzer.spt_data (module)
tramway.analyzer.spt_data.mpl (module)
tramway.analyzer.tesseller (module)
tramway.analyzer.tesseller.mpl (module)
tramway.analyzer.tesseller.plugin (module)
tramway.analyzer.tesseller.post (module)
tramway.analyzer.tesseller.post.merger (module)
tramway.analyzer.tesseller.proxied (module)
tramway.analyzer.tesseller.proxy (module)
tramway.analyzer.time (module)
tramway.analyzer.tracker (module)
tramway.core (module)
tramway.core.analyses (module)
tramway.core.analyses.auto (module)
tramway.core.analyses.base (module)
tramway.core.analyses.lazy (module)
tramway.core.chain (module)
tramway.core.exceptions (module)
tramway.core.hdf5 (module)
tramway.core.hdf5.compat (module)
tramway.core.hdf5.store (module)
tramway.core.lazy (module)
tramway.core.namedcolumns (module)
tramway.core.parallel (module)
tramway.core.parallel.abc (module)
tramway.core.plugin (module)
tramway.core.scaler (module)
tramway.core.xyt (module)
tramway.feature (module)
tramway.feature.adjacency (module)
tramway.feature.curl (module)
tramway.feature.single_traj (module)
tramway.helper (module)
tramway.helper.animation (module)
tramway.helper.inference (module)
tramway.helper.roi (module)
tramway.helper.simulation (module)
tramway.helper.simulation.categoricaltrap (module)
tramway.helper.simulation.functional (module)
tramway.helper.tessellation (module)
tramway.inference (module)
tramway.inference.base (module)
tramway.inference.bayes_factors (module)
tramway.inference.bayes_factors.calculate_bayes_factors (module)
tramway.inference.bayes_factors.calculate_marginalized_integral (module)
tramway.inference.bayes_factors.calculate_posteriors (module)
tramway.inference.bayes_factors.convenience_functions (module)
tramway.inference.bayes_factors.find_marginalized_zeta_t_roots (module)
tramway.inference.bayes_factors.get_D_posterior (module)
tramway.inference.d (module)
tramway.inference.d_conj_prior (module)
tramway.inference.ddrift (module)
tramway.inference.density (module)
tramway.inference.df (module)
tramway.inference.dv (module)
tramway.inference.gradient (module)
tramway.inference.optimization (module)
tramway.inference.standard_d (module)
tramway.inference.standard_ddrift (module)
tramway.inference.standard_df (module)
tramway.inference.stochastic_dv (module)
tramway.localization (module)
tramway.localization.UNet (module)
tramway.plot (module)
tramway.plot.animation (module)
tramway.plot.animation.map (module)
tramway.plot.animation.xyt (module)
tramway.plot.bokeh (module)
tramway.plot.bokeh.map (module)
tramway.plot.contour (module)
tramway.plot.map (module)
tramway.plot.mesh (module)
tramway.plot.tk.contour (module)
tramway.tessellation (module)
tramway.tessellation.base (module)
tramway.tessellation.grid (module)
tramway.tessellation.gwr (module)
tramway.tessellation.hexagon (module)
tramway.tessellation.kdtree (module)
tramway.tessellation.kmeans (module)
tramway.tessellation.nesting (module)
tramway.tessellation.random (module)
tramway.tessellation.time (module)
tramway.tessellation.window (module)
tramway.tracking (module)
tramway.tracking.track_non_track (module)
tramway.tracking.track_non_track.file_processing_loc (module)
tramway.tracking.track_non_track.non_tracking_T_0 (module)
tramway.utils (module)
tramway.utils.contour (module)
tramway.utils.crop (module)
tramway.utils.inferencemap (module)
tramway.utils.mapviz (module)
tramway.utils.trajviz (module)
translate_types() (in module tramway.core.hdf5.compat)
Translocations (class in tramway.inference.base)
translocations (tramway.inference.base.Translocations attribute)
(tramway.tessellation.base.Partition attribute)
translocations() (in module tramway.core.xyt)
translocations_to_trajectories() (in module tramway.core.xyt)
trust (tramway.analyzer.tesseller.proxied.GWR attribute)
truth() (in module tramway.helper.simulation.functional)
type (tramway.core.analyses.lazy.Analyses attribute)
U
undefined_grad() (tramway.inference.stochastic_dv.LocalDV method)
undefined_time_derivative() (tramway.inference.stochastic_dv.LocalDV method)
UNetLocalizer (class in tramway.analyzer.localizer)
unitrange() (in module tramway.core.scaler)
UnitRegions (class in tramway.helper.roi)
unload() (tramway.core.lazy.Lazy method)
unlock() (tramway.core.parallel.Scheduler method)
unscale_distance() (tramway.core.scaler.Scaler method)
unscale_length() (tramway.core.scaler.Scaler method)
unscale_point() (tramway.core.scaler.Scaler method)
unscale_surface_area() (tramway.core.scaler.Scaler method)
unscale_vector() (tramway.core.scaler.Scaler method)
unscale_volume() (tramway.core.scaler.Scaler method)
unset_workspace() (tramway.core.parallel.abc.JobStep method)
(tramway.core.parallel.JobStep method)
update() (tramway.core.chain.ChainArray method)
(tramway.core.parallel.ProtoWorkspace method)
(tramway.core.parallel.abc.Workspace method)
(tramway.core.plugin.Plugins method)
(tramway.inference.optimization.SparseFunction method)
update_position() (tramway.helper.simulation.categoricaltrap.generate_trajectories method)
UpdateVehicle (class in tramway.core.parallel)
upper_bound (tramway.analyzer.tesseller.proxied.Hexagons attribute)
(tramway.analyzer.tesseller.proxied.Squares attribute)
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.random.RandomMesh attribute)
V
V (tramway.inference.dv.DV attribute)
v1_ROIRecord (class in tramway.analyzer.roi)
v2_ROIRecord (in module tramway.analyzer.roi)
valid_label() (in module tramway.core.analyses.base)
values() (tramway.core.analyses.base.CommentsView method)
(tramway.core.analyses.base.InstancesView method)
(tramway.core.plugin.Plugins method)
(tramway.inference.base.Distributed method)
variable (tramway.plot.contour.ContourEditor attribute)
variables (tramway.feature.curl.Curl attribute)
(tramway.inference.base.Maps attribute)
(tramway.plot.contour.ContourEditor attribute)
(tramway.plot.tk.contour.TkContourEditor attribute)
variant (tramway.core.parallel.StarConn attribute)
VehicleJobStep (class in tramway.core.parallel)
(class in tramway.core.parallel.abc)
verbose (tramway.analyzer.tesseller.proxied.GWR attribute)
(tramway.core.plugin.Plugins attribute)
(tramway.inference.stochastic_dv.LocalDV attribute)
(tramway.plot.animation.VideoWriterReader attribute)
vertex_adjacency (tramway.tessellation.base.Voronoi attribute)
,
[1]
vertices (tramway.tessellation.base.Voronoi attribute)
,
[1]
(tramway.tessellation.grid.RegularMesh attribute)
(tramway.tessellation.hexagon.HexagonalMesh attribute)
VideoReader (class in tramway.plot.animation)
VideoWriter (class in tramway.plot.animation)
VideoWriterReader (class in tramway.plot.animation)
volume (tramway.inference.base.Local attribute)
Voronoi (class in tramway.tessellation.base)
VoronoiSampler (class in tramway.analyzer.sampler)
W
weights_locator (tramway.analyzer.localizer.UNetLocalizer attribute)
whiten() (in module tramway.core.scaler)
window_duration (tramway.analyzer.time.SlidingWindow attribute)
window_shift (tramway.analyzer.time.SlidingWindow attribute)
with_time_lattice() (in module tramway.tessellation.time)
wolfe_line_search() (in module tramway.inference.optimization)
Worker (class in tramway.core.parallel)
worker (tramway.core.parallel.Scheduler attribute)
worker_count (tramway.analyzer.env.environments.LocalHost attribute)
(tramway.core.parallel.Scheduler attribute)
workers_alive() (tramway.core.parallel.Scheduler method)
Workspace (class in tramway.core.parallel)
(class in tramway.core.parallel.abc)
workspace_set (tramway.core.parallel.abc.JobStep attribute)
(tramway.core.parallel.JobStep attribute)
WorkspaceExtension (class in tramway.core.parallel.abc)
X
x (tramway.inference.optimization.BFGSResult attribute)
(tramway.inference.optimization.SparseFunction attribute)
,
[1]
xy (tramway.inference.base.Locations attribute)
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