Creates a NWBHDF5IO file container

Class definition for 'PyNWB' container; use read_nwb for construction function.

Active bindings

opened

Whether the container is opened.

Methods

Public methods

• NWBHDF5IO$new()

• NWBHDF5IO$get_handler()

• NWBHDF5IO$open()

• NWBHDF5IO$close()

• NWBHDF5IO$close_linked_files()

• NWBHDF5IO$read()

• NWBHDF5IO$with()

• NWBHDF5IO$clone()

---

Method new()

Initialize the class

Usage

NWBHDF5IO$new(path = NULL, mode = c("r", "w", "r+", "a", "w-", "x"), ...)

Arguments

path

Path to a '.nwb' file

mode

Mode for opening the file

...

Other parameters passed to nwb$NWBHDF5IO

---

Method get_handler()

Get internal file handler. Please make sure you close the handler correctly.

Usage

NWBHDF5IO$get_handler()

Returns

File handler, i.e. 'PyNWB' NWBHDF5IO instance.

---

Method open()

Open the connections, must be used together with $close method. For high-level method, see $with

Usage

NWBHDF5IO$open()

Returns

container itself

Examples

\dontrun{

# low-level method to open NWB file, for safer methods, see
# `container$with()` below

container$open()

data <- container$read()

# process data...

# Make sure the container is closed!
container$close()

}

---

Method close()

Close the connections (low-level method, see 'with' method below)

Usage

NWBHDF5IO$close(close_links = TRUE)

Arguments

close_links

Whether to close all files linked to from this file; default is true

Returns

Nothing

---

Method close_linked_files()

Close all opened, linked-to files. 'MacOS' and 'Linux' automatically release the linked-to file after the linking file is closed, but 'Windows' does not, which prevents the linked-to file from being deleted or truncated. Use this method to close all opened, linked-to files.

Usage

NWBHDF5IO$close_linked_files()

Returns

Nothing

---

Method read()

Read the 'NWB' file from the 'IO' source. Please use along with '$with' method

Usage

NWBHDF5IO$read()

Returns

'NWBFile' container

---

Method with()

Safe wrapper for reading and handling 'NWB' file. See class examples.

Usage

NWBHDF5IO$with(expr, quoted = FALSE, envir = parent.frame())

Arguments

expr

R expression to evaluate

quoted

Whether expr is quoted; default is false

envir

environment for expr to evaluate; default is the parent frame (see parent.frame)

Returns

Whatever results generated by expr

Examples

\dontrun{

container$with({
  data <- container$read()
  # process data
})

}

---

Method clone()

The objects of this class are cloneable with this method.

Usage

NWBHDF5IO$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{

# Running this example requires a .nwb file

library(rnwb)
container <- NWBHDF5IO$new(path = file)
container$with({

  data <- container$read()
  electrode_table <- data$electrodes[convert = TRUE]

})

print(electrode_table)

} # }

## ------------------------------------------------
## Method `NWBHDF5IO$open`
## ------------------------------------------------

if (FALSE) { # \dontrun{

# low-level method to open NWB file, for safer methods, see
# `container$with()` below

container$open()

data <- container$read()

# process data...

# Make sure the container is closed!
container$close()

} # }

## ------------------------------------------------
## Method `NWBHDF5IO$with`
## ------------------------------------------------

if (FALSE) { # \dontrun{

container$with({
  data <- container$read()
  # process data
})

} # }