fileutils: Various file utility functions used by ZooImage

In zooimage: Analysis of Numerical Plankton Images

Description

These functions are usually not called directly by the user, but they are interesting for developers. They help to manage files in the context of ZooImage processes.

Usage

extensionPattern(extension = "r", add.dot = !grepl("[.]", extension))
hasExtension(file, extension = "r", pattern = extensionPattern(extension))
noExtension(file)

listFilesExt(dir, extension = "r", pattern = extensionPattern(extension), ... )
zimList(dir, ...)
zimDatList(dir, ...)
zipList(dir, ...)
zidList(dir, ...)
zidbList(dir, ...)
jpgList(dir, ...)
pngList(dir, ...)

checkFileExists(file, extension, message = "file not found: %s",
    force.file = FALSE)
checkDirExists(dir, message = 'Path "%s" does not exist or is not a directory')
checkEmptyDir(dir, message = 'dir "%s" is not empty')
forceDirCreate(dir)

checkFirstLine(file, expected = c("ZI1", "ZI2", "ZI3", "ZI4", "ZI5"), 
    message = 'file "%s" is not a valid ZooImage version <= 5 file')

Arguments

extension	lowercase version of the extension (the pattern will be constructed to be case-insensitive).
add.dot	if a dot is not provided, it is added by default in front of the pattern.
file	one or more file names or file paths to check.
pattern	a pattern matching a given file extension.
...	further arguments passed to the function. Currently, not in use.
dir	the directory to work with.
message	a warning message to provide (file/dirname replacement using %s).
force.file	make sure the item is a file, not a directory.
expected	the expected content of the first line of the file.

Details

All these function issue only warnings, no errors. Those functions that return TRUE or FALSE are designed to be used in batch mode.

Value

A string with suitable pattern to match a file extension for extensionPattern().

The function noExtension() return base filenames without extensions.

A list of files with given extension for listFilesExt(), and xxxList() functions.

The other functions return TRUE or FALSE, depending if the tested condition is met or not.

Author(s)

Philippe Grosjean <[e-mail]>

See Also

sampleInfo

Examples

# Construct a suitable pattern to match extensions of TIFF image files
extensionPattern("tif")
# Test if file names match given extensions (first 2 items only)
hasExtension(c("test1.tif", "test2.TIF", "test3.R"), "tif")
noExtension(c("test1.tif", "test2.TIF", "test3.R"))

# List all files with a given extension in a directory
ziDir <- system.file("examples", package = "zooimage")
listFilesExt(ziDir, "zid")
zidList(ziDir) # Idem

# Check that a file or a directory exists
checkDirExists(ziDir)
zisFile <- file.path(ziDir, "Description.zis")
checkFileExists(zisFile)

# Is this directory empty? (no)
checkEmptyDir(ziDir)

# force (re)creation of a directory
tmpDir <- file.path(tempdir(), "testdir")
forceDirCreate(tmpDir)
file.info(tmpDir)$isdir # yes
checkEmptyDir(tmpDir)   # yes
file.remove(tmpDir)
file.exists(tmpDir)

# Every .zis file must start with ZI1-5 => check this...
checkFirstLine(zisFile)

# Clean up
rm(ziDir, zisFile, tmpDir)

zooimage documentation built on May 2, 2019, 3:43 p.m.