Electrode: R6 Class for Electrode

In beauchamplab/rave: R Analysis and Visualization of 'ECOG/iEEG' Data

R6 Class for Electrode

Description

Stores single electrode or reference signals

Public fields

electrode

electrode number in integer

raw_power

stores pre-epoch power spectrum with no reference

raw_phase

stores pre-epoch phase with no reference

raw_volt

stores pre-epoch analog traces with no reference

phase

stores pre-epoch phase after reference

power

stores pre-epoch power spectrum after reference

volt

stores pre-epoch analog traces after reference

preload

which of the three data are pre-loaded

reference

character or Electrode instance indicating the reference for current electrode

has_power, has_phase, has_volt

whether power, phase, or voltage data exist in file system before and after reference

Active bindings

has_power, has_phase, has_volt

whether power, phase, or voltage data exist in file system before and after reference

blocks

character vector of block names (read-only)

subject_id

character of subject ID (read-only)

reference_electrode

whether this is a reference (read-only)

Methods

Public methods

• Electrode$info()

• Electrode$print()

• Electrode$switch_reference()

• Electrode$referenced()

• Electrode$clean()

• Electrode$new()

• Electrode$epoch()

---

Method info()

print electrode information

Usage

Electrode$info()

Returns

none

---

Method print()

overrides default print method

Usage

Electrode$print(...)

Arguments

...

ignored

Returns

none

---

Method switch_reference()

switch reference (experimental)

Usage

Electrode$switch_reference(new_reference)

Arguments

new_reference

An electrode instance

Returns

none

---

Method referenced()

get referenced data

Usage

Electrode$referenced(type = "power", ram = TRUE)

Arguments

type

which data to reference, default is power

ram

whether to load data to memory

Returns

If ram is true, then returns a list of matrices. The length of the list equals the number of blocks, and each matrix is frequency by time points. If ram is false, then returns an environment with each element a LazyH5 or LazyFST instance.

---

Method clean()

remove data from memory

Usage

Electrode$clean(types = c("power", "phase", "volt"), force = FALSE)

Arguments

types

data types to clean

force

whether to remove pre-loaded data types

Returns

none

---

Method new()

constructor

Usage

Electrode$new(
  subject,
  electrode,
  reference_by = "noref",
  preload = NULL,
  is_reference = FALSE
)

Arguments

subject

Subject instance or characters like "proj/sub"

electrode

number, integer

reference_by

reference signals, choices are character, or Electrode instance; default is "noref", meaning no reference to the electrode

preload

data to load along with constructor

is_reference

is current instance a reference?

Returns

An Electrode instance

---

Method epoch()

epoch electrode

Usage

Electrode$epoch(
  epoch_name,
  pre,
  post,
  types = c("volt", "power", "phase"),
  raw = FALSE,
  hybrid = TRUE
)

Arguments

epoch_name

epoch name, for example, epoch_name="default" refers to epoch file "epoch_default.csv" in subject meta folder

pre

seconds before trial onset to load

post

seconds after trial onset to load

types

characters, data types to load; choices are "volt", "power", and "phase"

raw

whether epoch pre-referenced data?

hybrid

whether to fast-cache the data on hard-drive? See also Tensor

Returns

list of data after epoch

Author(s)

Zhengjia Wang

Examples

## Not run: 
# Electrode with no reference
e1 <- Electrode$new('demo/YAB', electrode = 14, reference_by = 'noref')
e1$reference
#> Subject: demo/YAB
#> Electrode: noref (Reference)

# Add Common Average Reference in rave/data/reference/ref_13-63,65-84.h5
e2 <- Electrode$new('demo/YAB', electrode = 14, 
                    reference_by = 'ref_13-63,65-84')

# Electrode with bipolar reference by another electrode
e3 <- Electrode$new('demo/YAB', electrode = 14, reference_by = 'ref_15')

# Alternative way
reference <- Electrode$new('demo/YAB', electrode = 15, is_reference = TRUE)
e4 <- Electrode$new('demo/YAB', electrode = 14, reference_by = reference)

# e3, e4 are the same in scientific meaning. To test it, epoch them
power3 <- e3$epoch('YABaOutlier', 1, 2, 'power', 
                   raw = FALSE, hybrid = FALSE)$power
power4 <- e4$epoch('YABaOutlier', 1, 2, 'power',
                   raw = FALSE, hybrid = TRUE)$power

# Compare e3 and e4, result difference should be 0
range(power3$get_data() - power4$get_data())
#> 0

# With or without hybrid, the size will be different
# No hybrid, totally in memory
lobstr::obj_size(power3)
#> 12 MB
# Hybrid, data is swapped to hard-drive
lobstr::obj_size(power4)
#> 908 kB

## End(Not run)

beauchamplab/rave documentation built on Feb. 16, 2025, 8:12 p.m.