Convert neuron morphology files to standard SWC format

This function takes neuron morphology files and converts them into standardised SWC files. It can take 23 different, common file types as input. The user gets a .zip file downloaded and a data frame of any errors or corrections made to the files.

xyz2swc_convert(
  source_dir = NULL,
  source_file = NULL,
  target_zip = file.path(getwd(), "xyz2swc.zip"),
  get_logs = TRUE,
  neuromorpho_url = "https://neuromorpho.org",
  folder = paste0(sample(letters, 10, replace = TRUE), collapse = ""),
  ...
)

Arguments

source_dir

A character string indicating the directory containing the source files.

source_file

A character string indicating the full path to the source file.

target_zip

A character string indicating the full path and filename for the resulting .zip file.

get_logs

A logical indicating whether to create a log file of any errors or corrections made to the files.

neuromorpho_url

A character string indicating the URL of the Neuromorpho website.

folder

A character string indicating the name of the folder to store the converted files on the server.

...

Additional arguments to pass to `neuromorpho_fetch`.

Value

A data frame of any errors or corrections made to the files.

See also

xyz2swc_check for a function to validate SWC files.

Examples

if (FALSE) {
# Convert a single file
xyz2swc_convert(source_file = "path/to/source/file")

# Convert all files in a directory
xyz2swc_convert(source_dir = "path/to/source/directory")

# Specify a custom URL
xyz2swc_convert(source_file = "path/to/source/file", neuromorpho_url = "https://mycustomurl.com")
}