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CLASS ndi.probe

ndi.probe - the base class for PROBES -- measurement or stimulation devices

In NDI, a PROBE is an instance of an instrument that can be used to MEASURE or to STIMULATE.

Typically, a probe is associated with an ndi.daq.system that performs data acquisition or even control of a stimulator.

A probe is uniquely identified by 3 fields and an session: session- the session where the probe is used name - the name of the probe reference - the reference number of the probe type - the type of probe (see type ndi.fun.probetype2objectinit)

Examples: A multichannel extracellular electrode might be named 'extra', have a reference of 1, and a type of 'n-trode'.

 If the electrode is moved, one should change the name or the reference to indicate that 
 the data should not be attempted to be combined across the two positions. One might change
 the reference number to 2.

How to make a probe: (Talk about epochprobemap records of devices, probes are created from these elements.)

Documentation for ndi.probe
   doc ndi.probe

Superclasses

ndi.element, ndi.ido, ndi.epoch.epochset, ndi.documentservice

Properties

Property Description
session
name
type
reference
underlying_element
direct
subject_id
dependencies
identifier

Methods

Method Description
addepoch add an epoch to the ndi.element
buildepochgraph compute the epochgraph among epochs for an ndi.epoch.epochset object
buildepochtable build the epoch table for an ndi.probe.*
cached_epochgraph return the cached epoch graph of an ndi.epoch.epochset object
cached_epochtable return the cached epochtable of an ndi.epoch.epochset object
doc_unique_id return the document unique reference for an ndi.element object
elementstring Produce a human-readable element string
epoch2str convert an epoch number or id to a string
epochclock return the ndi.time.clocktype objects for an epoch
epochgraph graph of the mapping and cost of converting time among epochs
epochid Get the epoch identifier for a particular epoch
epochnodes return all epoch nodes from an ndi.epoch.epochset object
epochprobemapmatch does an epochprobemap record match our probe?
epochsetname the name of the ndi.probe.* object, for EPOCHNODES
epochtable Return an epoch table that relates the current object's epochs to underlying epochs
epochtableentry return the entry of the EPOCHTABLE that corresonds to an EPOCHID
eq are 2 ndi.probe objects equal?
getcache return the NDI_CACHE and key for ndi.element
getchanneldevinfo GETCHANNELDEVINFO = Get the device, channeltype, and channellist for a given epoch for ndi.probe.*
id return the document unique identifier for an ndi.element object
issyncgraphroot should this object be a root in an ndi.time.syncgraph epoch graph?
load_all_element_docs load all of the ndi.element objects from an session database
load_element_doc load a element doc from the session database
loadaddedepochs load the added epochs from an ndi.element
matchedepochtable compare a hash number from an epochtable to the current version
ndi_unique_id Generate a unique ID number for NDI projects
newdocument return a new database document of type ndi.document based on a element
numepochs Number of epochs of ndi.epoch.epochset
probe create a new ndi.probe object
probestring Produce a human-readable probe string
resetepochtable clear an ndi.epoch.epochset epochtable in memory and force it to be re-read from disk
searchquery return a search query for an ndi.document based on this element
t0_t1
underlyingepochnodes find all the underlying epochnodes of a given epochnode

Methods help

addepoch - add an epoch to the ndi.element

[NDI_ELEMENT_OBJ, EPOCHDOC] = ADDEPOCH(NDI_ELEMENT_OBJ, EPOCHID, EPOCHCLOCK, T0_T1)

Registers the data for an epoch with the NDI_ELEMENT_OBJ.

Inputs: NDI_ELEMENT_OBJ: The ndi.element object to modify EPOCHID: The name of the epoch to add; should match the name of an epoch from the probe EPOCHCLOCK: The epoch clock; must be a single clock type that matches one of the clock types of the probe T0_T1: The starting time and ending time of the existence of information about the ELEMENT on the probe, in units of the epock clock

Help for ndi.probe/addepoch is inherited from superclass NDI.ELEMENT


buildepochgraph - compute the epochgraph among epochs for an ndi.epoch.epochset object

[COST,MAPPING] = BUILDEPOCHGRAPH(NDI_EPOCHSET_OBJ)

Compute the cost and the mapping among epochs in the EPOCHTABLE for an ndi.epoch.epochset object

COST is an MxM matrix where M is the number of EPOCHNODES. For example, if there is one epoch with clock types 'dev_local_time' and 'utc', then M is 2. Each entry COST(i,j) indicates whether there is a mapping between (epoch, clocktype) i to j. The cost of each transformation is normally 1 operation. MAPPING is the ndi.time.timemapping object that describes the mapping.

In the abstract class, the following NDI_CLOCKTYPEs, if they exist, are linked across epochs with a cost of 1 and a linear mapping rule with shift 1 and offset 0: 'utc' -> 'utc' 'utc' -> 'approx_utc' 'exp_global_time' -> 'exp_global_time' 'exp_global_time' -> 'approx_exp_global_time' 'dev_global_time' -> 'dev_global_time' 'dev_global_time' -> 'approx_dev_global_time'

See also: ndi.time.clocktype, ndi.time.clocktype/ndi.time.clocktype, ndi.time.timemapping, ndi.time.timemapping/ndi.time.timemapping, ndi.probe/EPOCHNODES

Help for ndi.probe/buildepochgraph is inherited from superclass NDI.EPOCH.EPOCHSET


buildepochtable - build the epoch table for an ndi.probe.*

ET = BUILDEPOCHTABLE(NDI_PROBE_OBJ)

ET is a structure array with the following fields: Fieldname: | Description


'epoch_number' | The number of the epoch (may change) 'epoch_id' | The epoch ID code (will never change once established) | This uniquely specifies the epoch. 'epoch_session_id' | The ID of the session 'epochprobemap' | The epochprobemap object from each epoch 'epoch_clock' | A cell array of ndi.time.clocktype objects that describe the type of clocks available 't0_t1' | A cell array of ordered pairs [t0 t1] that indicates, for each ndi.time.clocktype, the start and stop | time of this epoch. The time units of t0_t1{i} match epoch_clock{i}. 'underlying_epochs' | A structure array of the ndi.epoch.epochset objects that comprise these epochs. | It contains fields 'underlying', 'epoch_number', and 'epoch_id'


cached_epochgraph - return the cached epoch graph of an ndi.epoch.epochset object

[COST,MAPPING] = CACHED_EPOCHGRAPH(NDI_EPOCHSET_OBJ)

Return the cached version of the epoch graph, if it exists and is up-to-date (that is, the hash number from the EPOCHTABLE of NDI_EPOCHSET_OBJ has not changed). If there is no cached version, or if it is not up-to-date, COST and MAPPING will be empty. If the cached epochgraph is present and not up-to-date, it is deleted.

See also: NDI_EPOCHSET_OBJ/EPOCHGRAPH, NDI_EPOCHSET_OBJ/BUILDEPOCHGRAPH

Help for ndi.probe/cached_epochgraph is inherited from superclass NDI.EPOCH.EPOCHSET


cached_epochtable - return the cached epochtable of an ndi.epoch.epochset object

[ET, HASHVALUE] = CACHED_EPOCHTABLE(NDI_EPOCHSET_OBJ)

Return the cached version of the epochtable, if it exists, along with its HASHVALUE (a hash number generated from the table). If there is no cached version, ET and HASHVALUE will be empty.

Help for ndi.probe/cached_epochtable is inherited from superclass NDI.EPOCH.EPOCHSET


doc_unique_id - return the document unique reference for an ndi.element object

UNIQUE_REF = DOC_UNIQUE_REF(NDI_ELEMENT_OBJ)

Returns the document unique reference for NDI_ELEMENT_OBJ. If there is no associated document for the element, then empty is returned.

Help for ndi.probe/doc_unique_id is inherited from superclass NDI.ELEMENT


elementstring - Produce a human-readable element string

ELEMENTSTR = ELEMENTSTRING(NDI_ELEMENT_OBJ)

Returns the name as a human-readable string.

For ndi.element objects, this is the string 'element: ' followed by its name

Help for ndi.probe/elementstring is inherited from superclass NDI.ELEMENT


epoch2str - convert an epoch number or id to a string

S = EPOCH2STR(NDI_EPOCHSET_OBJ, NUMBER)

Returns the epoch NUMBER in the form of a string. If it is a simple integer, then INT2STR is used to produce a string. If it is an epoch identifier string, then it is returned.

Help for ndi.probe/epoch2str is inherited from superclass NDI.EPOCH.EPOCHSET


epochclock - return the ndi.time.clocktype objects for an epoch

EC = EPOCHCLOCK(NDI_PROBE_OBJ, EPOCH_NUMBER)

Return the clock types available for this epoch.

The ndi.probe class always returns the clock type(s) of the device it is based on


epochgraph - graph of the mapping and cost of converting time among epochs

[COST, MAPPING] = EPOCHGRAPH(NDI_EPOCHSET_OBJ)

Compute the cost and the mapping among epochs in the EPOCHTABLE for an ndi.epoch.epochset object

COST is an MxM matrix where M is the number of ordered pairs of (epochs, clocktypes). For example, if there is one epoch with clock types 'dev_local_time' and 'utc', then M is 2. Each entry COST(i,j) indicates whether there is a mapping between (epoch, clocktype) i to j. The cost of each transformation is normally 1 operation. MAPPING is the ndi.time.timemapping object that describes the mapping.

Help for ndi.probe/epochgraph is inherited from superclass NDI.EPOCH.EPOCHSET


epochid - Get the epoch identifier for a particular epoch

ID = EPOCHID (NDI_EPOCHSET_OBJ, EPOCH_NUMBER)

Returns the epoch identifier string for the epoch EPOCH_NUMBER. If it doesn't exist, it should be created. EPOCH_NUMBER can be a number of an EPOCH ID string.

The abstract class just queries the EPOCHTABLE. Most classes that manage epochs themselves (ndi.file.navigator, ndi.daq.system) will override this method.

Help for ndi.probe/epochid is inherited from superclass NDI.EPOCH.EPOCHSET


epochnodes - return all epoch nodes from an ndi.epoch.epochset object

[NODES,UNDERLYINGNODES] = EPOCHNODES(NDI_EPOCHSET_OBJ)

Return all EPOCHNODES for an ndi.epoch.epochset. EPOCHNODES consist of the following fields: Fieldname: | Description


'epoch_id' | The epoch ID code (will never change once established, though it may be deleted.) | This epoch ID uniquely specifies the epoch within the session. 'epoch_session_id' | The ID of the session that contains the epoch 'epochprobemap' | Any contents information for each epoch, usually of type ndi.epoch.epochprobemap or empty. 'epoch_clock' | A SINGLE ndi.time.clocktype entry that describes the clock type of this node. 't0_t1' | The times [t0 t1] of the beginning and end of the epoch in units of 'epoch_clock' 'underlying_epochs' | A structure array of the ndi.epoch.epochset objects that comprise these epochs. | It contains fields 'underlying', 'epoch_id', and 'epochprobemap' 'objectname' | A string containing the 'name' field of NDI_EPOCHSET_OBJ, if it exists. If there is no | 'name' field, then 'unknown' is used. 'objectclass' | The object class name of the NDI_EPOCHSET_OBJ.

EPOCHNODES are related to EPOCHTABLE entries, except a) only 1 ndi.time.clocktype is permitted per epoch node. If an entry in epoch table contains multiple ndi.time.clocktype entries, then each one will have its own epoch node. This aids in the construction of the EPOCHGRAPH that helps the system map time from one epoch to another. b) EPOCHNODES contain identifying information (objectname and objectclass) to help in identifying the epoch nodes across ndi.epoch.epochset objects.

UNDERLYINGNODES are nodes that are directly linked to this ndi.epoch.epochset's node via 'underlying' epochs.

Help for ndi.probe/epochnodes is inherited from superclass NDI.EPOCH.EPOCHSET


epochprobemapmatch - does an epochprobemap record match our probe?

B = EPOCHPROBEMAPMATCH(NDI_PROBE_OBJ, EPOCHPROBEMAP)

Returns 1 if the ndi.epoch.epochprobemap object EPOCHPROBEMAP is a match for the NDI_PROBE_OBJ probe and 0 otherwise.


epochsetname - the name of the ndi.probe. object, for EPOCHNODES*

NAME = EPOCHSETNAME(NDI_PROBE_OBJ)

Returns the object name that is used when creating epoch nodes.

For ndi.probe objects, this is the string 'probe: ' followed by PROBESTRING(NDI_PROBE_OBJ).


epochtable - Return an epoch table that relates the current object's epochs to underlying epochs

[ET,HASHVALUE] = EPOCHTABLE(NDI_EPOCHSET_OBJ)

ET is a structure array with the following fields: Fieldname: | Description


'epoch_number' | The number of the epoch. The number may change as epochs are added and subtracted. 'epoch_id' | The epoch ID code (will never change once established, though it may be deleted.) | This epoch ID uniquely specifies the epoch. 'epoch_session_id' | The session ID that contains this epoch 'epochprobemap' | Any contents information for each epoch, usually of type ndi.epoch.epochprobemap or empty. 'epoch_clock' | A cell array of ndi.time.clocktype objects that describe the type of clocks available 't0_t1' | A cell array of ordered pairs [t0 t1] that indicates, for each ndi.time.clocktype, the start and stop | time of this epoch. The time units of t0_t1{i} match epoch_clock{i}. 'underlying_epochs' | A structure array of the ndi.epoch.epochset objects that comprise these epochs. | It contains fields 'underlying', 'epoch_number', 'epoch_id', and 'epochprobemap'

HASHVALUE is the hashed value of the epochtable. One can check to see if the epochtable has changed with ndi.epoch.epochset/MATCHEDEPOCHTABLE.

After it is read from disk once, the ET is stored in memory and is not re-read from disk unless the user calls ndi.epoch.epochset/RESETEPOCHTABLE.

Help for ndi.probe/epochtable is inherited from superclass NDI.EPOCH.EPOCHSET


epochtableentry - return the entry of the EPOCHTABLE that corresonds to an EPOCHID

ET_ENTRY = EPOCHTABLEENTRY(NDI_EPOCHSET_OBJ, EPOCH_NUMBER_OR_ID)

Returns the EPOCHTABLE entry associated with the ndi.epoch.epochset object that corresponds to EPOCH_NUMBER_OR_ID, which can be the number of the epoch or the EPOCHID of the epoch.

Help for ndi.probe/epochtableentry is inherited from superclass NDI.EPOCH.EPOCHSET


eq - are 2 ndi.probe objects equal?

Returns 1 if the objects share an object class, session, and probe string.


getcache - return the NDI_CACHE and key for ndi.element

[CACHE,KEY] = GETCACHE(NDI_ELEMENT_OBJ)

Returns the CACHE and KEY for the ndi.element object.

The CACHE is returned from the associated session. The KEY is the probe's ELEMENTSTRING plus the TYPE of the ELEMENT.

See also: ndi.file.navigator

Help for ndi.probe/getcache is inherited from superclass NDI.ELEMENT


getchanneldevinfo - GETCHANNELDEVINFO = Get the device, channeltype, and channellist for a given epoch for ndi.probe.*

[DEV, DEVNAME, DEVEPOCH, CHANNELTYPE, CHANNELLIST] = GETCHANNELDEVINFO(NDI_PROBE_OBJ, EPOCH_NUMBER_OR_ID)

Given an ndi.probe.* object and an EPOCH number, this function returns the corresponding channel and device info. Suppose there are C channels corresponding to a probe. Then the outputs are DEV is a 1xC cell array of ndi.daq.system objects for each channel DEVNAME is a 1xC cell array of the names of each device in DEV DEVEPOCH is a 1xC array with the epoch id of the probe's EPOCH on each device CHANNELTYPE is a cell array of the type of each channel CHANNELLIST is the channel number of each channel.


id - return the document unique identifier for an ndi.element object

UNIQUE_REF = ID(NDI_ELEMENT_OBJ)

Returns the document unique reference for NDI_ELEMENT_OBJ. If there is no associated document for the element, then an error is returned.

Help for ndi.probe/id is inherited from superclass NDI.ELEMENT


issyncgraphroot - should this object be a root in an ndi.time.syncgraph epoch graph?

B = ISSYNCGRAPHROOT(NDI_EPOCHSET_OBJ)

This function tells an ndi.time.syncgraph object whether it should continue adding the 'underlying' epochs to the graph, or whether it should stop at this level.

For ndi.epoch.epochset and ndi.probe.* this returns 0 so that the underlying ndi.daq.system epochs are added.


load_all_element_docs - load all of the ndi.element objects from an session database

ELEMENT_DOCS = LOAD_ALL_ELEMENT_DOCS(NDI_ELEMENT_OBJ)

Loads the ndi.document that is based on the ndi.element object and any associated epoch documents.

Help for ndi.probe/load_all_element_docs is inherited from superclass NDI.ELEMENT


load_element_doc - load a element doc from the session database

ELEMENT_DOC = LOAD_ELEMENT_DOC(NDI_ELEMENT_OBJ)

Load an ndi.document that is based on the ndi.element object.

Returns empty if there is no such document.

Help for ndi.probe/load_element_doc is inherited from superclass NDI.ELEMENT


loadaddedepochs - load the added epochs from an ndi.element

[ET_ADDED, EPOCHDOCS] = LOADADDEDEOPCHS(NDI_ELEMENT_OBJ)

Load the EPOCHTABLE that consists of added/registered epochs that provide information about the ndi.element.

Help for ndi.probe/loadaddedepochs is inherited from superclass NDI.ELEMENT


matchedepochtable - compare a hash number from an epochtable to the current version

B = MATCHEDEPOCHTABLE(NDI_EPOCHSET_OBJ, HASHVALUE)

Returns 1 if the current hashed value of the cached epochtable is identical to HASHVALUE. Otherwise, it returns 0.

Help for ndi.probe/matchedepochtable is inherited from superclass NDI.EPOCH.EPOCHSET


ndi_unique_id - Generate a unique ID number for NDI projects

ID = NDI_UNIQUE_ID

Generates a unique ID character array based on the current time and a random number. It is a hexidecimal representation of the serial date number in UTC Leap Seconds time. The serial date number is the number of days since January 0, 0000 at 0:00:00. The integer portion of the date is the whole number of days and the fractional part of the date number is the fraction of days.

ID = [NUM2HEX(SERIAL_DATE_NUMBER) '_' NUM2HEX(RAND)]

See also: NUM2HEX, NOW, RAND

Help for ndi.probe.ndi_unique_id is inherited from superclass NDI.IDO


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

NDI_DOCUMENT_OBJ = NEWDOCUMENT(NDI_ELEMENT_OBJ)

Fill out the fields of an NDI_DOCUMENT_OBJ of type 'ndi_document_element' with the corresponding 'name' and 'type' fields of the element NDI_ELEMENT_OBJ and the 'name', 'type', and 'reference' fields of its underlying NDI_PROBE_OBJ. If EPOCHID is provided, then an EPOCHID field is filled out as well in accordance to 'ndi_document_epochid'.

When the document is created, it is automatically added to the session.

Help for ndi.probe/newdocument is inherited from superclass NDI.ELEMENT


numepochs - Number of epochs of ndi.epoch.epochset

N = NUMEPOCHS(NDI_EPOCHSET_OBJ)

Returns the number of epochs in the ndi.epoch.epochset object NDI_EPOCHSET_OBJ.

See also: EPOCHTABLE

Help for ndi.probe/numepochs is inherited from superclass NDI.EPOCH.EPOCHSET


probe - create a new ndi.probe object

OBJ = ndi.probe(SESSION, NAME, REFERENCE, TYPE, SUBJECT_ID) or OBJ = ndi.probe(SESSION, NDI_DOCUMENT_OBJ)

Creates an ndi.probe associated with an ndi.session object SESSION and with name NAME (a string that must start with a letter and contain no white space), reference number equal to REFERENCE (a non-negative integer), the TYPE of the probe (a string that must start with a letter and contain no white space).

ndi.probe is a essentially an abstract class, and a specific implementation must be called.


probestring - Produce a human-readable probe string

PROBESTR = PROBESTRING(NDI_PROBE_OBJ)

Returns the name and reference of a probe as a human-readable string.

This is simply PROBESTR = [NDI_PROBE_OBJ.name ' _ ' in2str(NDI_PROBE_OBJ.reference)]


resetepochtable - clear an ndi.epoch.epochset epochtable in memory and force it to be re-read from disk

NDI_EPOCHSET_OBJ = RESETEPOCHTABLE(NDI_EPOCHSET_OBJ)

This function clears the internal cached memory of the epochtable, forcing it to be re-read from disk at the next request.

See also: ndi.probe/EPOCHTABLE

Help for ndi.probe/resetepochtable is inherited from superclass NDI.EPOCH.EPOCHSET


searchquery - return a search query for an ndi.document based on this element

SQ = SEARCHQUERY(NDI_ELEMENT_OBJ, [EPOCHID])

Returns a search query for the fields of an NDI_DOCUMENT_OBJ of type 'ndi_document_element' with the corresponding 'name' and 'type' fields of the element NDI_ELEMENT_OBJ.

Help for ndi.probe/searchquery is inherited from superclass NDI.ELEMENT


t0_t1 - **

T0_T1 - return the t0_t1 (beginning and end) epoch times for an epoch

T0T1 = T0_T1(NDI_EPOCHSET_OBJ, EPOCH_NUMBER)

Return the beginning (t0) and end (t1) times of the epoch EPOCH_NUMBER in the same units as the ndi.time.clocktype objects returned by EPOCHCLOCK.

The abstract class always returns {[NaN NaN]}.

See also: ndi.time.clocktype, EPOCHCLOCK

TODO: this must be a bug, it's just self-referential

Help for ndi.probe/t0_t1 is inherited from superclass NDI.ELEMENT


underlyingepochnodes - find all the underlying epochnodes of a given epochnode

[UNODES, COST, MAPPING] = UNDERLYINGEPOCHNODES(NDI_EPOCHSET_OBJ, EPOCHNODE)

Traverse the underlying nodes of a given EPOCHNODE until we get to the roots (an ndi.epoch.epochset object with ISSYNGRAPHROOT that returns 1).

Note that the EPOCHNODE itself is returned as the first 'underlying' node.

See also: ISSYNCGRAPHROOT

Help for ndi.probe/underlyingepochnodes is inherited from superclass NDI.EPOCH.EPOCHSET