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agora
extraction
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logfile_parser
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R
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T
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V
_
__init__() (align method)
(alignParameters method)
(autoreg method)
(autoregParameters method)
(BasePlotter method)
(butter method)
(butterParameters method)
(Cache method)
(CellTracker method)
(crosscorr method)
(crosscorrParameters method)
(detrend method)
(detrendParameters method)
(dsignal method)
(dsignalParameters method)
(FeatureCalculator method)
(fft method)
(fftParameters method)
(findpeaks method)
(findpeaksParameters method)
(gpsignal method)
(gpsignalParameters method)
(interpolate method)
(interpolateParameters method)
(mi method)
(miParameters method)
(ParametersABC method)
(Parser method)
(PostProcessABC method)
(ProcessABC method)
(savgol method)
(savgolParameters method)
(standardscaler method)
(standardscalerParameters method)
(StepABC method)
(Template method)
(TemplateParameters method)
A
accumulate() (in module agora.io.utils)
add_index_levels() (in module agora.utils.kymograph)
add_to_collection() (in module agora.abc)
agora
module
agora.abc
module
agora.io
module
agora.io.decorators
module
agora.io.utils
module
agora.logging
module
agora.track_abc
module
agora.utils
module
agora.utils.association
module
agora.utils.cast
module
agora.utils.indexing
module
agora.utils.kymograph
module
agora.utils.merge
module
aliby
module
aliby.bin
module
aliby.io
module
aliby.lineage
module
aliby.tile
module
aliby.tile.traps
module
aliby.track
module
aliby.track.cell_tracker
module
aliby.track.utils
module
aliby.utils
module
align (class in postprocessor.core.multisignal.align)
alignParameters (class in postprocessor.core.multisignal.align)
apply_merges() (in module agora.utils.merge)
area() (in module extraction.core.functions.cell)
assign_lbls() (CellTracker method)
autoreg (class in postprocessor.core.processes.autoreg)
autoreg_periodogram() (autoreg method)
autoregParameters (class in postprocessor.core.processes.autoreg)
B
background_max5() (in module extraction.core.functions.trap)
BasePlotter (class in postprocessor.routines.plottingabc)
bidirectional_retainment_filter() (in module agora.utils.kymograph)
butter (class in postprocessor.core.processes.butter)
butterfilter() (butter method)
butterParameters (class in postprocessor.core.processes.butter)
C
Cache (class in agora.io.utils)
calc_baryangles() (in module aliby.track.utils)
calc_barycentre() (in module aliby.track.utils)
calc_barydists() (in module aliby.track.utils)
calc_dtfeats() (CellTracker method)
calc_feat_ndarray() (CellTracker method)
calc_feats_from_mask() (CellTracker method)
(FeatureCalculator method)
calc_trapfeats() (CellTracker method)
(FeatureCalculator method)
CellTracker (class in aliby.track.cell_tracker)
check_type_recursive() (in module agora.abc)
classical_periodogram() (fft method)
cluster_kymograph() (in module agora.utils.kymograph)
compare_indices() (in module agora.utils.indexing)
compare_pred_truth_lols() (in module aliby.track.utils)
conical_volume() (in module extraction.core.functions.cell)
crosscorr (class in postprocessor.core.multisignal.crosscorr)
crosscorrParameters (class in postprocessor.core.multisignal.crosscorr)
D
detrend (class in postprocessor.core.processes.detrend)
detrendParameters (class in postprocessor.core.processes.detrend)
df_extend_nan() (in module postprocessor.core.multisignal.align)
df_shift() (in module postprocessor.core.multisignal.align)
div0() (in module extraction.core.functions.math_utils)
drop_level() (in module agora.utils.kymograph)
drop_mother_label() (in module agora.utils.kymograph)
dsignal (class in postprocessor.core.processes.dsignal)
dsignalParameters (class in postprocessor.core.processes.dsignal)
E
eccentricity() (in module extraction.core.functions.cell)
estimate_gr() (in module postprocessor.core.processes.gpsignal)
extract_header() (in module logfile_parser.swainlab_parser)
extraction
module
extraction.core
module
extraction.core.functions
module
extraction.core.functions.cell
module
extraction.core.functions.custom
module
extraction.core.functions.custom.localisation
module
extraction.core.functions.distributors
module
extraction.core.functions.loaders
module
extraction.core.functions.math_utils
module
extraction.core.functions.trap
module
extraction.core.functions.versioning
module
extraction.local_data_loaders
module
F
FeatureCalculator (class in agora.track_abc)
fft (class in postprocessor.core.processes.fft)
fftParameters (class in postprocessor.core.processes.fft)
fields_to_dict_or_table() (in module logfile_parser.swainlab_parser)
filt_cluster() (in module agora.utils.kymograph)
findpeaks (class in postprocessor.core.processes.findpeaks)
findpeaksParameters (class in postprocessor.core.processes.findpeaks)
fit_autoreg() (autoreg method)
from_yaml() (alignParameters class method)
(autoregParameters class method)
(butterParameters class method)
(crosscorrParameters class method)
(detrendParameters class method)
(dsignalParameters class method)
(fftParameters class method)
(findpeaksParameters class method)
(gpsignalParameters class method)
(interpolateParameters class method)
(miParameters class method)
(ParametersABC class method)
(savgolParameters class method)
(standardscalerParameters class method)
(TemplateParameters class method)
G
gauss3D() (in module extraction.core.functions.custom.localisation)
generate_palette_map() (in module postprocessor.routines.plot_utils)
get_examples_dir() (in module logfile_parser.legacy)
get_feats2use() (CellTracker method)
get_index_as_np() (in module agora.utils.kymograph)
get_legacy_log_example_interface() (in module logfile_parser.legacy)
get_logfile_grammars_dir() (in module logfile_parser.legacy)
get_mother_ilocs_from_daughters() (in module agora.utils.kymograph)
get_mothers_from_another_df() (in module agora.utils.kymograph)
get_new_lbls() (CellTracker method)
get_nfeats_from_model() (in module aliby.track.cell_tracker)
get_parameters() (in module postprocessor.core.abc)
get_process() (in module postprocessor.core.abc)
get_sha() (in module extraction.core.functions.versioning)
get_store_path() (in module agora.io.utils)
gpsignal (class in postprocessor.core.processes.gpsignal)
gpsignalParameters (class in postprocessor.core.processes.gpsignal)
GrammarNotFound
group_merges() (in module agora.utils.merge)
H
half_ceil() (in module aliby.tile.traps)
half_floor() (in module aliby.tile.traps)
HeaderEndNotFound
heatmap() (in module postprocessor.routines.heatmap)
histogram() (in module postprocessor.routines.histogram)
I
identify_trap_locations() (in module aliby.tile.traps)
imBackground() (in module extraction.core.functions.trap)
imread() (in module agora.io.utils)
interpolate (class in postprocessor.core.processes.interpolate)
interpolateParameters (class in postprocessor.core.processes.interpolate)
intersection_matrix() (in module agora.utils.kymograph)
J
join_tracks_pair() (in module agora.utils.merge)
L
load() (in module extraction.local_data_loaders)
load_1z() (in module extraction.local_data_loaders)
load_cellfuns() (in module extraction.core.functions.loaders)
load_cellfuns_core() (in module extraction.core.functions.loaders)
load_custom_args() (in module extraction.core.functions.loaders)
load_funs() (in module extraction.core.functions.loaders)
load_paired_images() (in module extraction.local_data_loaders)
load_redfuns() (in module extraction.core.functions.loaders)
load_tiled_image() (in module extraction.local_data_loaders)
load_trapfuns() (in module extraction.core.functions.loaders)
logfile_parser
module
logfile_parser.legacy
module
logfile_parser.logfile_parser
module
logfile_parser.swainlab_parser
module
lol_to_adj() (in module aliby.track.utils)
M
matlab_style_gauss2D() (in module extraction.core.functions.custom.localisation)
max2p5pc() (in module extraction.core.functions.cell)
max5px() (in module extraction.core.functions.cell)
mean() (in module extraction.core.functions.cell)
mean_plot() (in module postprocessor.routines.mean_plot)
median() (in module extraction.core.functions.cell)
median_plot() (in module postprocessor.routines.median_plot)
melt_reset() (in module agora.utils.kymograph)
merge_association() (in module agora.utils.merge)
mi (class in postprocessor.core.multisignal.mi)
min_maj_approximation() (in module extraction.core.functions.cell)
miParameters (class in postprocessor.core.multisignal.mi)
module
agora
agora.abc
agora.io
agora.io.decorators
agora.io.utils
agora.logging
agora.track_abc
agora.utils
agora.utils.association
agora.utils.cast
agora.utils.indexing
agora.utils.kymograph
agora.utils.merge
aliby
aliby.bin
aliby.io
aliby.lineage
aliby.tile
aliby.tile.traps
aliby.track
aliby.track.cell_tracker
aliby.track.utils
aliby.utils
extraction
extraction.core
extraction.core.functions
extraction.core.functions.cell
extraction.core.functions.custom
extraction.core.functions.custom.localisation
extraction.core.functions.distributors
extraction.core.functions.loaders
extraction.core.functions.math_utils
extraction.core.functions.trap
extraction.core.functions.versioning
extraction.local_data_loaders
logfile_parser
logfile_parser.legacy
logfile_parser.logfile_parser
logfile_parser.swainlab_parser
postprocessor
postprocessor.core
postprocessor.core.abc
postprocessor.core.functions
postprocessor.core.multisignal
postprocessor.core.multisignal.align
postprocessor.core.multisignal.crosscorr
postprocessor.core.multisignal.mi
postprocessor.core.processes
postprocessor.core.processes.autoreg
postprocessor.core.processes.butter
postprocessor.core.processes.detrend
postprocessor.core.processes.dsignal
postprocessor.core.processes.fft
postprocessor.core.processes.findpeaks
postprocessor.core.processes.gpsignal
postprocessor.core.processes.interpolate
postprocessor.core.processes.savgol
postprocessor.core.processes.standardscaler
postprocessor.core.processes.template
postprocessor.routines
postprocessor.routines.heatmap
postprocessor.routines.histogram
postprocessor.routines.mean_plot
postprocessor.routines.median_plot
postprocessor.routines.plot_utils
postprocessor.routines.plottingabc
postprocessor.routines.single_birth_plot
postprocessor.routines.single_plot
N
non_uniform_savgol() (in module postprocessor.core.processes.savgol)
nuc_conv_3d() (in module extraction.core.functions.custom.localisation)
nuc_est_conv() (in module extraction.core.functions.custom.localisation)
O
optimise_ar_order() (autoreg method)
P
ParametersABC (class in agora.abc)
parametrized() (in module agora.io.utils)
parse() (Parser method)
parse_fields() (in module logfile_parser.swainlab_parser)
parse_from_grammar() (in module logfile_parser.swainlab_parser)
parse_from_swainlab_grammar() (in module logfile_parser.swainlab_parser)
parse_table() (in module logfile_parser.swainlab_parser)
parse_x() (in module logfile_parser.swainlab_parser)
ParseError
Parser (class in logfile_parser.logfile_parser)
pick_baryfun() (in module aliby.track.utils)
plot() (BasePlotter method)
PostProcessABC (class in postprocessor.core.abc)
postprocessor
module
postprocessor.core
module
postprocessor.core.abc
module
postprocessor.core.functions
module
postprocessor.core.multisignal
module
postprocessor.core.multisignal.align
module
postprocessor.core.multisignal.crosscorr
module
postprocessor.core.multisignal.mi
module
postprocessor.core.processes
module
postprocessor.core.processes.autoreg
module
postprocessor.core.processes.butter
module
postprocessor.core.processes.detrend
module
postprocessor.core.processes.dsignal
module
postprocessor.core.processes.fft
module
postprocessor.core.processes.findpeaks
module
postprocessor.core.processes.gpsignal
module
postprocessor.core.processes.interpolate
module
postprocessor.core.processes.savgol
module
postprocessor.core.processes.standardscaler
module
postprocessor.core.processes.template
module
postprocessor.routines
module
postprocessor.routines.heatmap
module
postprocessor.routines.histogram
module
postprocessor.routines.mean_plot
module
postprocessor.routines.median_plot
module
postprocessor.routines.plot_utils
module
postprocessor.routines.plottingabc
module
postprocessor.routines.single_birth_plot
module
postprocessor.routines.single_plot
module
predict_proba_from_ndarray() (CellTracker method)
probabilities_from_impair() (CellTracker method)
ProcessABC (class in agora.abc)
R
reduce_z() (in module extraction.core.functions.distributors)
repr_obj() (in module agora.io.utils)
run() (align method)
(autoreg method)
(butter method)
(crosscorr method)
(detrend method)
(fft method)
(findpeaks method)
(mi method)
(standardscaler method)
run_tp() (CellTracker method)
S
savgol (class in postprocessor.core.processes.savgol)
savgolParameters (class in postprocessor.core.processes.savgol)
scale_feats() (CellTracker method)
(FeatureCalculator method)
segment_traps() (in module aliby.tile.traps)
single_birth_plot() (in module postprocessor.routines.single_birth_plot)
single_plot() (in module postprocessor.routines.single_plot)
slices_from_spans() (in module agora.utils.kymograph)
small_peaks_conv() (in module extraction.core.functions.custom.localisation)
sort_association() (in module agora.utils.merge)
spherical_volume() (in module extraction.core.functions.cell)
split_df() (in module agora.utils.kymograph)
standard_filtering() (in module agora.utils.kymograph)
standardscaler (class in postprocessor.core.processes.standardscaler)
standardscalerParameters (class in postprocessor.core.processes.standardscaler)
std() (in module extraction.core.functions.cell)
StepABC (class in agora.abc)
switch_case_nfeats() (in module aliby.track.cell_tracker)
T
table_to_df() (in module logfile_parser.swainlab_parser)
Template (class in postprocessor.core.processes.template)
TemplateParameters (class in postprocessor.core.processes.template)
timed() (in module agora.io.utils)
timer() (in module agora.logging)
to_dict() (alignParameters method)
(autoregParameters method)
(butterParameters method)
(crosscorrParameters method)
(detrendParameters method)
(dsignalParameters method)
(fftParameters method)
(findpeaksParameters method)
(gpsignalParameters method)
(interpolateParameters method)
(miParameters method)
(ParametersABC method)
(savgolParameters method)
(standardscalerParameters method)
(TemplateParameters method)
to_legacy() (in module logfile_parser.legacy)
to_yaml() (alignParameters method)
(autoregParameters method)
(butterParameters method)
(crosscorrParameters method)
(detrendParameters method)
(dsignalParameters method)
(fftParameters method)
(findpeaksParameters method)
(gpsignalParameters method)
(interpolateParameters method)
(miParameters method)
(ParametersABC method)
(savgolParameters method)
(standardscalerParameters method)
(TemplateParameters method)
trap_apply() (in module extraction.core.functions.distributors)
U
union_find() (in module agora.utils.merge)
update() (alignParameters method)
(autoregParameters method)
(butterParameters method)
(crosscorrParameters method)
(detrendParameters method)
(dsignalParameters method)
(fftParameters method)
(findpeaksParameters method)
(gpsignalParameters method)
(interpolateParameters method)
(miParameters method)
(ParametersABC method)
(savgolParameters method)
(standardscalerParameters method)
(TemplateParameters method)
V
validate_association() (in module agora.utils.indexing)
volume() (in module extraction.core.functions.cell)
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