raveio (version 0.9.0)

LFP_electrode: Definitions of electrode with 'LFP' signal type

Description

Please use a safer new_electrode function to create instances. This documentation is to describe the member methods of the electrode class LFP_electrode

Value

if the reference number if NULL or 'noref', then returns 0, otherwise returns a FileArray-class

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.

Super class

raveio::RAVEAbstarctElectrode -> LFP_electrode

Active bindings

h5_fname

'HDF5' file name

valid

whether current electrode is valid: subject exists and contains current electrode or reference; subject electrode type matches with current electrode type

raw_sample_rate

voltage sample rate

power_sample_rate

power/phase sample rate

preprocess_info

preprocess information

power_file

path to power 'HDF5' file

phase_file

path to phase 'HDF5' file

voltage_file

path to voltage 'HDF5' file

Methods

Public methods

• LFP_electrode$print()

• LFP_electrode$set_reference()

• LFP_electrode$new()

• LFP_electrode$.load_noref_wavelet()

• LFP_electrode$.load_noref_voltage()

• LFP_electrode$.load_wavelet()

• LFP_electrode$.load_voltage()

• LFP_electrode$.load_raw_voltage()

• LFP_electrode$load_data()

• LFP_electrode$load_blocks()

• LFP_electrode$clear_cache()

• LFP_electrode$clear_memory()

• LFP_electrode$clone()

Inherited methods

• raveio::RAVEAbstarctElectrode$set_epoch()

---

Method print()

print electrode summary

Usage

LFP_electrode$print()

---

Method set_reference()

set reference for current electrode

Usage

LFP_electrode$set_reference(reference)

Arguments

reference

either NULL or LFP_electrode instance

---

Method new()

constructor

Usage

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

Arguments

subject, number, quiet

see constructor in RAVEAbstarctElectrode

---

Method .load_noref_wavelet()

load non-referenced wavelet coefficients (internally used)

Usage

LFP_electrode$.load_noref_wavelet(reload = FALSE)

Arguments

reload

whether to reload cache

---

Method .load_noref_voltage()

load non-referenced voltage (internally used)

Usage

LFP_electrode$.load_noref_voltage(reload = FALSE)

Arguments

reload

whether to reload cache

srate

voltage signal sample rate

---

Method .load_wavelet()

load referenced wavelet coefficients (internally used)

Usage

LFP_electrode$.load_wavelet(
  type = c("power", "phase", "wavelet-coefficient"),
  reload = FALSE
)

Arguments

type

type of data to load

reload

whether to reload cache

---

Method .load_voltage()

load referenced voltage (internally used)

Usage

LFP_electrode$.load_voltage(reload = FALSE)

Arguments

reload

whether to reload cache

---

Method .load_raw_voltage()

load raw voltage (no process)

Usage

LFP_electrode$.load_raw_voltage(reload = FALSE)

Arguments

reload

whether to reload cache

---

Method load_data()

method to load electrode data

Usage

LFP_electrode$load_data(
  type = c("power", "phase", "voltage", "wavelet-coefficient", "raw-voltage")
)

Arguments

type

data type such as "power", "phase", "voltage", "wavelet-coefficient", and "raw-voltage". For "power", "phase", and "wavelet-coefficient", 'Wavelet' transforms are required. For "voltage", 'Notch' filters must be applied. All these types except for "raw-voltage" will be referenced. For "raw-voltage", no reference will be performed since the data will be the "raw" signal (no processing).

---

Method load_blocks()

load electrode block-wise data (with no reference), useful when epoch is absent

Usage

LFP_electrode$load_blocks(
  blocks,
  type = c("power", "phase", "voltage", "wavelet-coefficient", "raw-voltage"),
  simplify = TRUE
)

Arguments

blocks

session blocks

type

data type such as "power", "phase", "voltage", "raw-voltage" (with no filters applied, as-is from imported), "wavelet-coefficient". Note that if type is "raw-voltage", then the data only needs to be imported; for "voltage" data, 'Notch' filters must be applied; for all other types, 'Wavelet' transforms are required.

simplify

whether to simplify the result

---

Method clear_cache()

method to clear cache on hard drive

Usage

LFP_electrode$clear_cache(...)

Arguments

...

ignored

---

Method clear_memory()

method to clear memory

Usage

LFP_electrode$clear_memory(...)

Arguments

...

ignored

---

Method clone()

The objects of this class are cloneable with this method.

Usage

LFP_electrode$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Download subject demo/DemoSubject

subject <- as_rave_subject("demo/DemoSubject", strict = FALSE)

if(dir.exists(subject$path)) {

# Electrode 14 in demo/DemoSubject
e <- new_electrode(subject = subject, number = 14, signal_type = "LFP")

# Load CAR reference "ref_13-16,24"
ref <- new_reference(subject = subject, number = "ref_13-16,24",
                     signal_type = "LFP")
e$set_reference(ref)

# Set epoch
e$set_epoch(epoch = 'auditory_onset')

# Set loading window
e$trial_intervals <- list(c(-1, 2))

# Preview
print(e)

# Now epoch power
power <- e$load_data("power")
names(dimnames(power))

# Subset power
subset(power, Time ~ Time < 0, Electrode ~ Electrode == 14)

# Draw baseline
tempfile <- tempfile()
bl <- power_baseline(power, baseline_windows = c(-1, 0),
                     method = "decibel", filebase = tempfile)
collapsed_power <- collapse2(bl, keep = c(2,1))
# Visualize
dname <- dimnames(bl)
image(collapsed_power, x = dname$Time, y = dname$Frequency,
      xlab = "Time (s)", ylab = "Frequency (Hz)",
      main = "Mean power over trial (Baseline: -1~0 seconds)",
      sub = glue('Electrode {e$number} (Reference: {ref$number})'))
abline(v = 0, lty = 2, col = 'blue')
text(x = 0, y = 20, "Audio onset", col = "blue", cex = 0.6)

# clear cache on hard disk
e$clear_cache()
ref$clear_cache()

}