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Spike Sorting
Bayes Optimal Template Matching
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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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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
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W
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X
A
ABOTMNode (in module botmpy.nodes.spike_sorting)
activate() (FilterBankNode method)
AdaptiveBayesOptimalTemplateMatchingNode (class in botmpy.nodes.spike_sorting)
AlignmentNode (class in botmpy.nodes.alignment)
AmplitudeHistogram (class in botmpy.common.amplitude_histogram)
append() (MxRingBuffer method)
append_bin() (AmplitudeHistogram method)
append_data_all() (AmplitudeHistogram method)
append_data_peaks() (AmplitudeHistogram method)
append_xi_buf() (FilterNode method)
ArtifactDetectorNode (class in botmpy.nodes.artifact_detector)
AtfFile (class in botmpy.common.datafile.atf)
B
BaseTimeSeriesCovarianceEstimator (class in botmpy.common.covariance_estimator)
BayesOptimalTemplateMatchingNode (class in botmpy.nodes.spike_sorting)
BOTMNode (in module botmpy.nodes.spike_sorting)
botmpy.__init__ (module)
botmpy.common (module)
botmpy.common.amplitude_histogram (module)
botmpy.common.covariance_estimator (module)
botmpy.common.datafile (module)
botmpy.common.datafile.atf (module)
botmpy.common.datafile.datafile (module)
botmpy.common.datafile.gdf (module)
botmpy.common.datafile.nas (module)
botmpy.common.datafile.wri (module)
botmpy.common.datafile.xpd (module)
botmpy.common.funcs_filterutil (module)
botmpy.common.funcs_general (module)
botmpy.common.funcs_spike (module)
botmpy.common.matrix_ops (module)
botmpy.common.mcfilter (module)
botmpy.common.mcfilter.mcfilter_py (module)
botmpy.common.ringbuffer (module)
botmpy.common.spike_alignment (module)
botmpy.common.util (module)
botmpy.nodes (module)
botmpy.nodes.alignment (module)
botmpy.nodes.artifact_detector (module)
botmpy.nodes.base_nodes (module)
botmpy.nodes.cluster (module)
botmpy.nodes.filter_bank (module)
botmpy.nodes.linear_filter (module)
botmpy.nodes.prewhiten (module)
botmpy.nodes.smoothing (module)
botmpy.nodes.spike_detection (module)
botmpy.nodes.spike_sorting (module)
build_block_toeplitz_from_xcorrs() (in module botmpy.common.covariance_estimator)
build_idx_set() (in module botmpy.common.covariance_estimator)
C
calc_filter() (FilterNode method)
capacity (MxRingBuffer attribute)
ce (FilterBankNode attribute)
(FilterNode attribute)
check_nas_file() (NasFile static method)
chunk_data() (in module botmpy.common.funcs_spike)
clear() (MxRingBuffer method)
close() (DataFile method)
closed() (DataFile method)
ClusteringNode (class in botmpy.nodes.cluster)
cmx_init() (TimeSeriesCovE static method)
coloured_loading() (in module botmpy.common.matrix_ops)
component_divergence() (BayesOptimalTemplateMatchingNode method)
convert_dict_to_matrix() (GdfFile static method)
convert_matrix_to_dict() (GdfFile static method)
copy (BayesOptimalTemplateMatchingNode attribute)
copy() (Node method)
create_filter() (FilterBankNode method)
cs (FilterBankNode attribute)
D
DataFile (class in botmpy.common.datafile.datafile)
DataFileError
DataFileMetaclass (class in botmpy.common.datafile.datafile)
deactivate() (FilterBankNode method)
det (AdaptiveBayesOptimalTemplateMatchingNode attribute)
diagonal_loading() (in module botmpy.common.matrix_ops)
dict_list_to_ndarray() (in module botmpy.common.funcs_general)
dict_sort_ndarrays() (in module botmpy.common.funcs_general)
dimension (MxRingBuffer attribute)
DOC_METHODS (DataFileMetaclass attribute)
dtype (Node attribute)
E
EnergyNotCalculatedError
epochs_from_binvec() (in module botmpy.common.funcs_spike)
epochs_from_spiketrain() (in module botmpy.common.funcs_spike)
epochs_from_spiketrain_set() (in module botmpy.common.funcs_spike)
events (ThresholdDetectorNode attribute)
execute() (AdaptiveBayesOptimalTemplateMatchingNode method)
(AlignmentNode method)
(ArtifactDetectorNode method)
(FilterBankNode method)
(FilterBankSortingNode method)
(FilterNode method)
(HomoscedasticClusteringNode method)
(Node method)
(PCANode method)
(PrewhiteningNode method)
(PrewhiteningNode2 method)
(SmoothingNode method)
(SpectrumArtifactDetector method)
(ThresholdDetectorNode method)
extend() (MxRingBuffer method)
extend_xi_buf() (FilterNode method)
extract_spikes() (in module botmpy.common.funcs_spike)
F
f (FilterNode attribute)
f_conc (FilterNode attribute)
filename() (DataFile method)
fill() (MxRingBuffer method)
fill_xi_buf() (FilterNode method)
filter_calculation() (botmpy.nodes.linear_filter.FilterNode class method)
(botmpy.nodes.linear_filter.MatchedFilterNode class method)
(botmpy.nodes.linear_filter.NormalisedMatchedFilterNode class method)
filter_set (FilterBankNode attribute)
FilterBankError
FilterBankNode (class in botmpy.nodes.filter_bank)
FilterBankSortingNode (class in botmpy.nodes.spike_sorting)
FilterError
FilterNode (class in botmpy.nodes.linear_filter)
flush() (MxRingBuffer method)
force_new_bin() (AmplitudeHistogram method)
G
gauss_heat_kernel() (HomoscedasticClusteringNode static method)
GdfFile (class in botmpy.common.datafile.gdf)
get_aligned_spikes() (in module botmpy.common.spike_alignment)
get_available_tetrodes() (XpdFile method)
get_capacity() (MxRingBuffer method)
get_ce() (FilterBankNode method)
(FilterNode method)
get_chan_set() (FilterBankNode method)
(TimeSeriesCovE method)
get_channel_hist() (AmplitudeHistogram method)
get_cmx() (BaseTimeSeriesCovarianceEstimator method)
get_cmx_loaded() (BaseTimeSeriesCovarianceEstimator method)
get_cols() (NasFile static method)
get_cond() (BaseTimeSeriesCovarianceEstimator method)
get_current_train_phase() (Node method)
get_cut() (in module botmpy.common.funcs_spike)
get_data() (AtfFile method)
(DataFile method)
(GdfFile method)
(WriFile method)
(XpdFile method)
get_det() (AdaptiveBayesOptimalTemplateMatchingNode method)
get_dimension() (MxRingBuffer method)
get_dtype() (Node method)
get_epochs() (ThresholdDetectorNode method)
get_events() (ThresholdDetectorNode method)
get_explained_variance() (PCANode method)
get_extracted_events() (ThresholdDetectorNode method)
get_f() (FilterNode method)
get_f_conc() (FilterNode method)
get_filter_set() (FilterBankNode method)
get_fragmentation() (ArtifactDetectorNode method)
get_gdf() (NasFile static method)
get_has_plot() (VERBOSE method)
get_has_print() (VERBOSE method)
get_hist() (AmplitudeHistogram method)
get_icmx() (BaseTimeSeriesCovarianceEstimator method)
get_icmx_loaded() (BaseTimeSeriesCovarianceEstimator method)
get_idx() (in module botmpy.common.funcs_general)
get_idx_for() (FilterBankNode method)
get_input_dim() (Node method)
get_is_full() (MxRingBuffer method)
get_is_verbose() (VERBOSE method)
get_n_data_points() (NasFile method)
get_nc() (FilterBankNode method)
(FilterNode method)
(TimeSeriesCovE method)
get_nf() (FilterBankNode method)
get_noise_prior() (BayesOptimalTemplateMatchingNode method)
get_nonartefact_epochs() (ArtifactDetectorNode method)
(SpectrumArtifactDetector method)
get_output_dim() (Node method)
get_projmatrix() (PCANode method)
get_recmatrix() (PCANode method)
get_remaining_train_phase() (Node method)
get_snr() (FilterNode method)
get_spike_prior() (BayesOptimalTemplateMatchingNode method)
get_spike_prior_bias() (BayesOptimalTemplateMatchingNode method)
get_supported_dtypes() (Node method)
get_svd() (BaseTimeSeriesCovarianceEstimator method)
get_tau_align_energy() (in module botmpy.common.spike_alignment)
get_tau_align_max() (in module botmpy.common.spike_alignment)
get_tau_align_min() (in module botmpy.common.spike_alignment)
get_tau_for_alignment() (in module botmpy.common.spike_alignment)
get_template_set() (FilterBankNode method)
get_tf() (FilterBankNode method)
(FilterNode method)
get_tf_max() (TimeSeriesCovE method)
get_timepoints() (NasFile static method)
get_whitening_op() (BaseTimeSeriesCovarianceEstimator method)
get_xcorrs() (FilterBankNode method)
get_xcorrs_at() (FilterBankNode method)
get_xi() (FilterNode method)
get_xi_conc() (FilterNode method)
H
has_multiple_training_phases() (Node method)
has_plot (VERBOSE attribute)
has_print (VERBOSE attribute)
HomoscedasticClusteringNode (class in botmpy.nodes.cluster)
I
input_dim (Node attribute)
inverse() (Node method)
(PCANode method)
invert_epochs() (in module botmpy.common.funcs_spike)
is_cond_ok() (BaseTimeSeriesCovarianceEstimator method)
is_full (MxRingBuffer attribute)
is_initialised() (BaseTimeSeriesCovarianceEstimator method)
is_invertable() (AlignmentNode method)
(ClusteringNode method)
(SmoothingNode method)
is_invertible() (FilterBankNode method)
(FilterNode method)
(Node static method)
(PrewhiteningNode static method)
(PrewhiteningNode2 static method)
(ThresholdDetectorNode method)
is_trainable() (AlignmentNode method)
(ClusteringNode method)
(FilterBankNode method)
(FilterNode method)
(Node static method)
(PrewhiteningNode static method)
(PrewhiteningNode2 static method)
(SmoothingNode method)
(ThresholdDetectorNode method)
is_training() (Node method)
is_verbose (VERBOSE attribute)
K
kteo() (in module botmpy.common.funcs_filterutil)
M
MatchedFilterNode (class in botmpy.nodes.linear_filter)
matrix_argmax() (in module botmpy.common.matrix_ops)
matrix_argmin() (in module botmpy.common.matrix_ops)
matrix_cond() (in module botmpy.common.matrix_ops)
mcfilter() (in module botmpy.common.mcfilter)
mcfilter_hist() (in module botmpy.common.mcfilter)
mcvec_from_conc() (in module botmpy.common.funcs_general)
mcvec_to_conc() (in module botmpy.common.funcs_general)
mean() (MxRingBuffer method)
merge_epochs() (in module botmpy.common.funcs_spike)
mteo() (in module botmpy.common.funcs_filterutil)
MxRingBuffer (class in botmpy.common.ringbuffer)
N
NasFile (class in botmpy.common.datafile.nas)
nc (FilterBankNode attribute)
(FilterNode attribute)
(TimeSeriesCovE attribute)
new_chan_set() (TimeSeriesCovE method)
nf (FilterBankNode attribute)
Node (class in botmpy.nodes.base_nodes)
noise_prior (BayesOptimalTemplateMatchingNode attribute)
NONE (VERBOSE attribute)
NormalisedMatchedFilterNode (class in botmpy.nodes.linear_filter)
O
output_dim (Node attribute)
overlaps() (in module botmpy.common.funcs_spike)
P
PCANode (class in botmpy.nodes.base_nodes)
PLOT (VERBOSE attribute)
plot() (HomoscedasticClusteringNode method)
(ThresholdDetectorNode method)
plot_ampl_hist() (AmplitudeHistogram method)
plot_buffer_to_axis() (FilterNode method)
plot_filter_set() (FilterBankNode method)
plot_sorting() (FilterBankSortingNode method)
plot_sorting_waveforms() (FilterBankSortingNode method)
plot_template_set() (FilterBankNode method)
plot_template_set2() (FilterBankNode method)
plot_xvft() (FilterBankNode method)
posterior_prob() (BayesOptimalTemplateMatchingNode method)
PrewhiteningNode (class in botmpy.nodes.prewhiten)
PrewhiteningNode2 (class in botmpy.nodes.prewhiten)
PRINT (VERBOSE attribute)
R
range() (AmplitudeHistogram static method)
read_data() (NasFile static method)
read_gdf() (GdfFile static method)
resampled_mean_dist() (AdaptiveBayesOptimalTemplateMatchingNode method)
reset() (BaseTimeSeriesCovarianceEstimator method)
(TrainingResetMixin method)
(XcorrStore method)
reset_history() (FilterBankNode method)
(FilterNode method)
reset_rates() (FilterBankNode method)
ResetNode (class in botmpy.nodes.base_nodes)
rm_chan_set() (TimeSeriesCovE method)
S
save() (Node method)
SDAbsNode (class in botmpy.nodes.spike_detection)
SDIntraNode (class in botmpy.nodes.spike_detection)
SDKteoNode (class in botmpy.nodes.spike_detection)
SDMteoNode (class in botmpy.nodes.spike_detection)
SDPeakNode (class in botmpy.nodes.spike_detection)
SDSqrNode (class in botmpy.nodes.spike_detection)
set_capacity() (MxRingBuffer method)
set_ce() (FilterBankNode method)
(FilterNode method)
set_chan_set() (FilterBankNode method)
set_dtype() (Node method)
set_events() (ThresholdDetectorNode method)
set_input_dim() (Node method)
set_noise_prior() (BayesOptimalTemplateMatchingNode method)
set_output_dim() (Node method)
set_spike_prior() (BayesOptimalTemplateMatchingNode method)
set_spike_prior_bias() (BayesOptimalTemplateMatchingNode method)
set_tf_max() (TimeSeriesCovE method)
shifted_matrix_sub() (in module botmpy.common.funcs_general)
sinc_interp1d() (in module botmpy.common.spike_alignment)
smooth() (in module botmpy.nodes.smoothing)
SmoothingNode (class in botmpy.nodes.smoothing)
snr (FilterNode attribute)
snr_maha() (in module botmpy.common.funcs_spike)
snr_peak() (in module botmpy.common.funcs_spike)
snr_power() (in module botmpy.common.funcs_spike)
sorting2gdf() (FilterBankSortingNode method)
sortrows() (in module botmpy.common.funcs_general)
SpectrumArtifactDetector (class in botmpy.nodes.artifact_detector)
spike_prior (BayesOptimalTemplateMatchingNode attribute)
spike_prior_bias (BayesOptimalTemplateMatchingNode attribute)
spikes_u() (FilterBankSortingNode method)
stop_training() (Node method)
(PCANode method)
(ThresholdDetectorNode method)
supported_dtypes (Node attribute)
T
template_set (FilterBankNode attribute)
ten2vec() (in module botmpy.common.funcs_general)
tf (FilterBankNode attribute)
(FilterNode attribute)
tf_max (TimeSeriesCovE attribute)
threshold_detection() (in module botmpy.common.funcs_spike)
ThresholdDetectorNode (class in botmpy.nodes.spike_detection)
TimeSeriesCovE (class in botmpy.common.covariance_estimator)
tolist() (MxRingBuffer method)
train() (Node method)
(PCANode method)
(ThresholdDetectorNode method)
TrainingResetMixin (class in botmpy.nodes.base_nodes)
U
update() (BaseTimeSeriesCovarianceEstimator method)
(PrewhiteningNode method)
V
vec2ten() (in module botmpy.common.funcs_general)
VERBOSE (class in botmpy.common.util)
W
white_noise_init() (TimeSeriesCovE static method)
WriFile (class in botmpy.common.datafile.wri)
write_gdf() (GdfFile static method)
write_header() (NasFile method)
write_row() (NasFile method)
X
xcorr() (in module botmpy.common.funcs_general)
xcorrs (FilterBankNode attribute)
XcorrStore (class in botmpy.common.covariance_estimator)
xi (FilterNode attribute)
xi_conc (FilterNode attribute)
xi_vs_f() (in module botmpy.common.funcs_filterutil)
XpdFile (class in botmpy.common.datafile.xpd)
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