Read 'NWB' format

Life cycle: experimental. Read "Neurodata Without Borders" ('NWB' format) file. Unlike other readers read_nwb returns low-level 'Python' class handler via pynwb module.

Usage

read_nwb(file, mode = c("r", "w", "r+", "a", "w-", "x"), ...)

Arguments

file

path to 'NWB' file

mode

file open mode; default is 'r' (read-only)

...

passed to NWBHDF5IO initialize function

Value

A NWBHDF5IO instance

Examples

if(ieegio_sample_data("nwb_sample.nwb", test = TRUE)) {
  file <- ieegio_sample_data("nwb_sample.nwb")

  # Create NWBIO container
  container <- read_nwb(file)

  # Open connection
  container$open()

  # read meta data
  data <- container$read()
  data

  # get `test_timeseries` data
  ts_data <- data$get_acquisition("test_timeseries")
  ts_data

  # read timeseries data into memory
  ts_arr <- ts_data$data[]
  ts_arr

  # Convert Python array to R
  # using `rpymat::py_to_r(ts_arr)` or
  as.numeric(ts_arr)

  # Make sure you close the connection
  container$close()

}


# Requires setting up Python environment
# run `ieegio::install_pynwb()` to set up environment first

if (FALSE) { # \dontrun{


# Replicating tutorial
# https://pynwb.readthedocs.io/en/stable/tutorials/general/plot_file.html

library(rpymat)

# Load Python module
pynwb <- import("pynwb")
uuid <- import("uuid")
datetime <- import("datetime")
np <- import("numpy")
tz <- import("dateutil.tz")



# 2018L is 2018 as integer
session_start_time <- datetime$datetime(
  2018L, 4L, 25L, 2L, 30L, 3L,
  tzinfo=tz$gettz("US/Pacific"))

#  ---- Create NWB file object ------------------------
nwbfile <- pynwb$NWBFile(
  session_description="Mouse exploring a closed field",
  identifier=py_str(uuid$uuid4()),
  session_start_time=session_start_time,
  session_id="session_4321",
  experimenter=py_list(c("Baggins, Frodo")),
  lab="Bag End Laboratory",
  institution="University of Middle Earth at the Shire",
  experiment_description="Thank you Bilbo Baggins.",
  keywords=py_list(c("behavior", "exploration"))
)

# ---- Add subject ------------------------------------
subject <- pynwb$file$Subject(
  subject_id="001",
  age="P90D",
  description="mouse 5",
  species="Mus musculus",
  sex="M"
)

nwbfile$subject <- subject

nwbfile

# ---- Add TimeSeries ------------------------------------
data <- seq(100, 190, by = 10)
time_series_with_rate <- pynwb$TimeSeries(
  name="test_timeseries",
  description="an example time series",
  data=data,
  unit="m",
  starting_time=0.0,
  rate=1.0
)
time_series_with_rate

nwbfile$add_acquisition(time_series_with_rate)

# ---- New Spatial positions ------------------------------------
position_data <- cbind(
  seq(0, 10, length.out = 50),
  seq(0, 9, length.out = 50)
)
position_timestamps = seq(0, 49) / 200

spatial_series_obj = pynwb$behavior$SpatialSeries(
  name="SpatialSeries",
  description="(x,y) position in open field",
  data=position_data,
  timestamps=position_timestamps,
  reference_frame="(0,0) is bottom left corner",
)
spatial_series_obj

position_obj = pynwb$behavior$Position(
  spatial_series=spatial_series_obj)
position_obj

# ---- Behavior Processing Module ------------------------------
behavior_module <- nwbfile$create_processing_module(
  name="behavior", description="processed behavioral data"
)
behavior_module$add(position_obj)

nwbfile$processing$behavior

# omit some process

# ---- Write ---------------------------------------------------
f <- normalizePath(tempfile(fileext = ".nwb"),
                   winslash = "/",
                   mustWork = FALSE)
io <- pynwb$NWBHDF5IO(f, mode = "w")
io$write(nwbfile)
io$close()



} # }