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Abstract definition of electrode class in 'RAVE'

Source: R/class007-abstract_electrode.R
RAVEAbstarctElectrode.Rd

This class is not intended for direct use. Please create new child classes and implement some key methods.

Super class

ravepipeline::RAVESerializable -> RAVEAbstarctElectrode

Public fields

subject

subject instance (RAVESubject)

number

integer stands for electrode number or reference ID

reference

reference electrode, either NULL for no reference or an electrode instance inherits RAVEAbstarctElectrode

epoch

a RAVEEpoch instance

stitch_events

events to stitch, when loading window is not default to trial onset; must be NULL or a character vector of length 2

Active bindings

type

signal type of the electrode, such as 'LFP', 'Spike', and 'EKG'; default is 'Unknown'

power_enabled

whether the electrode can be used in power analyses such as frequency, or frequency-time analyses; this usually requires transforming the electrode raw voltage signals using signal processing methods such as 'Fourier', 'wavelet', 'Hilbert', 'Multitaper', etc.

is_reference

whether this instance is a reference electrode

location

location type of the electrode, see LOCATION_TYPES for details

exists

whether electrode exists in subject

preprocess_file

path to preprocess 'HDF5' file

power_file

path to power 'HDF5' file

phase_file

path to phase 'HDF5' file

voltage_file

path to voltage 'HDF5' file

reference_name

reference electrode name

epoch_name

current epoch name

cache_root

run-time cache path; NA if epoch or trial intervals are missing

trial_intervals

trial intervals relative to epoch onset

Methods

Public methods

Inherited methods

RAVEAbstarctElectrode$new()

constructor

Usage

RAVEAbstarctElectrode$new(subject, number, quiet = FALSE)

Arguments

subject

character or RAVESubject instance

number

current electrode number or reference ID

quiet

reserved, whether to suppress warning messages

RAVEAbstarctElectrode$set_reference()

set reference for instance

Usage

RAVEAbstarctElectrode$set_reference(reference)

Arguments

reference

NULL or RAVEAbstarctElectrode instance

RAVEAbstarctElectrode$set_epoch()

set epoch instance for the electrode

Usage

RAVEAbstarctElectrode$set_epoch(epoch, stitch_events = NULL)

Arguments

epoch

characters or RAVEEpoch instance. For characters, make sure "epoch_<name>.csv" is in meta folder.

stitch_events

events to stitch, default is NULL, meaning when loading data, the time is relative to the trial onset (column "Time" in the epoch file); set to a character of length 2, representing the events if time is not relative to trial onset. Please remove the prefix. For example, for a column named "Event_name", the event name is "name".

RAVEAbstarctElectrode$clear_cache()

method to clear cache on hard drive

Usage

RAVEAbstarctElectrode$clear_cache(...)

Arguments

...

implemented by child instances

RAVEAbstarctElectrode$clear_memory()

method to clear memory

Usage

RAVEAbstarctElectrode$clear_memory(...)

Arguments

...

implemented by child instances

RAVEAbstarctElectrode$load_data_with_epochs()

method to load electrode data

Usage

RAVEAbstarctElectrode$load_data_with_epochs(type)

Arguments

type

data type such as "power", "phase", "voltage", "wavelet-coefficient", or others depending on child class implementations

RAVEAbstarctElectrode$load_data()

alias of load_data_with_epochs for legacy code

Usage

RAVEAbstarctElectrode$load_data(type)

Arguments

type

see load_data_with_epochs

RAVEAbstarctElectrode$load_dimnames_with_epochs()

get expected dimension names

Usage

RAVEAbstarctElectrode$load_dimnames_with_epochs(type)

Arguments

type

see load_data_with_epochs

RAVEAbstarctElectrode$load_data_with_blocks()

load electrode block-wise data (with reference), useful when epoch is absent

Usage

RAVEAbstarctElectrode$load_data_with_blocks(blocks, type, simplify = TRUE)

Arguments

blocks

session blocks

type

data type such as "power", "phase", "voltage", "wavelet-coefficient".

simplify

whether to simplify the result

Returns

If simplify is enabled, and only one block is loaded, then the result will be a vector (type="voltage") or a matrix (others), otherwise the result will be a named list where the names are the blocks.

RAVEAbstarctElectrode$load_blocks()

alias of load_data_with_blocks for legacy code

Usage

RAVEAbstarctElectrode$load_blocks(blocks, type, simplify = TRUE)

Arguments

blocks, type, simplify

see load_data_with_blocks

RAVEAbstarctElectrode$load_dim_with_blocks()

get expected dimension information for block-based loader

Usage

RAVEAbstarctElectrode$load_dim_with_blocks(blocks, type)

Arguments

blocks, type

see load_data_with_blocks

RAVEAbstarctElectrode$clone()

The objects of this class are cloneable with this method.

Usage

RAVEAbstarctElectrode$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples


if( has_rave_subject("demo/DemoSubject") ) {

# To run this example, please download demo subject (~700 MB) from
# https://github.com/beauchamplab/rave/releases/tag/v0.1.9-beta

generator <- RAVEAbstarctElectrode

# load demo subject electrode 14
e <- generator$new("demo/DemoSubject", number = 14)

# set epoch
e$subject$epoch_names
e$set_epoch("auditory_onset")
head(e$epoch$table)

# set epoch range (-1 to 2 seconds relative to onset)
e$trial_intervals <- c(-1,2)
# or to set multiple ranges
e$trial_intervals <- list(c(-2,-1), c(0, 2))

# set reference
e$subject$reference_names
reference_table <- e$subject$meta_data(
  meta_type = "reference",
  meta_name = "default")
ref_name <- subset(reference_table, Electrode == 14)[["Reference"]]

# the reference is CAR type, mean of electrode 13-16,24
ref_name

# load & set reference
ref <- generator$new(e$subject, ref_name)
e$set_reference(ref)

}