CLASS ndi.app.spikesorter¶

NDI.APP.spikesorter - an app to sort spikewaves found in sessions

NDI.APP.spikesorter_OBJ = ndi.app.spikesorter(SESSION)

Creates a new NDI_APP_spikesorter object that can operate on NDI_SESSIONS. The app is named 'ndi_app_spikesorter'.

Documentation for ndi.app.spikesorter
   doc ndi.app.spikesorter

Superclasses¶

ndi.app, ndi.documentservice

Properties¶

Property	Description
session
name

Methods¶

Method	Description
add_sorting_doc	add sorting parameters document
clear_sort	clear all 'sorted spikes' records for an NDI_PROBE_OBJ from session database
load_spike_clusters_doc	ndi.app.spikesorter/load_spike_clusters_doc is a function.
load_spikes	ndi.app.spikesorter/load_spikes is a function.
load_spiketimes_epoch	ndi.app.spikesorter/load_spiketimes_epoch is a function.
load_spikewaves_epoch	ndi.app.spikesorter/load_spikewaves_epoch is a function.
load_times	ndi.app.spikesorter/load_times is a function.
newdocument	return a new database document of type ndi.document based on an app
searchquery	return a search query for an ndi.document related to this app
spike_sort	method that sorts spikes from specific probes in session to ndi_doc
spikesorter	an app to sort spikewaves found in sessions
spikesorter_gui	load spike waves
varappname	return the name of the application for use in variable creation
version_url	return the app version and url

Methods help¶

add_sorting_doc - add sorting parameters document

SORTING_DOC = ADD_SORTING_DOC(NDI_APP_SPIKESORTER_OBJ, SORT_NAME, SORT_PARAMS)

Given SORT_PARAMS as either a structure or a filename, this function returns SORTING_DOC parameters as an ndi.document and checks its fields. If SORT_PARAMS is empty, then the default parameters are returned. If SORT_NAME is already the name of an existing ndi.document then an error is returned.

SORT_PARAMS should contain the following fields: Fieldname | Description

num_pca_features (10) | Number of PCA features to use in klustakwik k-means clustering interpolation (3) | Interpolation factor

clear_sort - clear all 'sorted spikes' records for an NDI_PROBE_OBJ from session database

B = CLEAR_SORT(NDI_APP_SPIKESORTER_OBJ, NDI_EPOCHSET_OBJ)

Clears all sorting entries from the session database for object NDI_PROBE_OBJ.

Returns 1 on success, 0 otherwise.

load_spike_clusters_doc - ndi.app.spikesorter/load_spike_clusters_doc is a function.

doc = load_spike_clusters_doc(ndi_app_spikesorter_obj, ndi_probe_obj, epoch, sort_name)

load_spikes - ndi.app.spikesorter/load_spikes is a function.

spikes = load_spikes(ndi_app_spikesorter_obj, name, type, epoch, extraction_name)

load_spiketimes_epoch - ndi.app.spikesorter/load_spiketimes_epoch is a function.

times = load_spiketimes_epoch(ndi_app_spikesorter_obj, ndi_timeseries_obj, epoch, extraction_name)

load_spikewaves_epoch - ndi.app.spikesorter/load_spikewaves_epoch is a function.

waveforms = load_spikewaves_epoch(ndi_app_spikesorter_obj, ndi_timeseries_obj, epoch, extraction_name)

load_times - ndi.app.spikesorter/load_times is a function.

spikes = load_times(ndi_app_spikesorter_obj, name, type, epoch, extraction_name)

newdocument - return a new database document of type ndi.document based on an app

NDI_DOCUMENT_OBJ = NEWDOCUMENT(NDI_APP_OBJ)

Creates a blank ndi.document object of type 'ndi_document_app'. The 'app.name' field is filled out with the name of NDI_APP_OBJ.VARAPPNAME().

Help for ndi.app.spikesorter/newdocument is inherited from superclass NDI.APP

searchquery - return a search query for an ndi.document related to this app

C = SEARCHQUERY(NDI_APP_OBJ)

Returns a cell array of strings that allow the creation or searching of an ndi.database document for this app with field 'app' that has subfield 'name' equal to the app's VARAPPNAME.

Help for ndi.app.spikesorter/searchquery is inherited from superclass NDI.APP

spike_sort - method that sorts spikes from specific probes in session to ndi_doc

SPIKE_SORT(SPIKEWAVES, SORT_NAME, SORTING_PARAMS) %%%%%%%%%%%% SORT_NAME name given to save sort to ndi_doc

spikesorter - an app to sort spikewaves found in sessions

NDI.APP.spikesorter_OBJ = ndi.app.spikesorter(SESSION)

Creates a new NDI_APP_spikesorter object that can operate on NDI_SESSIONS. The app is named 'ndi_app_spikesorter'.

spikesorter_gui - load spike waves

varappname - return the name of the application for use in variable creation

AN = VARAPPNAME(NDI_APP_OBJ)

Returns the name of the app modified for use as a variable name, either as a Matlab variable or a name in a document.

Help for ndi.app.spikesorter/varappname is inherited from superclass NDI.APP

version_url - return the app version and url

[V, URL] = VERSION_URL(NDI_APP_OBJ)

Return the version and url for the current app. In the base class, it is assumed that GIT is used and is available from the command line and the version and url are read from the git directory.

Developers should override this method in their own class if they use a different version control system.

Help for ndi.app.spikesorter/version_url is inherited from superclass NDI.APP