Package sc.fiji.snt.util

Class IOUtils

java.lang.Object

sc.fiji.snt.util.IOUtils

public final class IOUtils
extends Object

Static utilities for file I/O, namely the detection of reconstruction file formats.

Author:

Tiago Ferreira

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	IOUtils.ReconstructionFormat	The reconstruction formats that can be detected by IOUtils

Method Summary

Modifier and Type	Method	Description
static IOUtils.ReconstructionFormat	detectFormat(File file)	Guesses the format of a reconstruction file from its first bytes.
static IOUtils.ReconstructionFormat	detectFormat(InputStream is, boolean closeStreamAfterGuess)	Guesses the format of a reconstruction file from its first bytes (not its extension): gzip magic number, XML (Neurolucida if the header holds an <mbf> root element), JSON ('{'), NDF ('/'), or SWC otherwise.
static String[]	getReconstructionExtensions()	Returns the extensions (lower case, without the leading period) of the supported reconstruction formats that can be identified by name alone, i.e., not including Neurolucida .xml files
static boolean	isReconstructionFile(File file)	Checks if a file is a reconstruction file based on its extension only (SWC, TRACES, JSON or NDF).
static boolean	isReconstructionFile(File file, boolean sniffXml)	Checks if a file is a reconstruction file.
static boolean	isSWCFile(File file)	Checks if a file has an SWC extension, i.e., .swc or .eswc (extended SWC, which holds extra columns that are ignored on import).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

detectFormat

public static IOUtils.ReconstructionFormat detectFormat(InputStream is,
 boolean closeStreamAfterGuess)
                                                 throws IOException

Guesses the format of a reconstruction file from its first bytes (not its extension): gzip magic number, XML (Neurolucida if the header holds an <mbf> root element), JSON ('{'), NDF ('/'), or SWC otherwise.

Parameters:

is - the stream to be inspected. If it supports marking, it is reset after inspection (unless closeStreamAfterGuess is true)

closeStreamAfterGuess - whether is should be closed after inspection

Returns:

the detected format

Throws:

IOException - if an IO error occurs

detectFormat

public static IOUtils.ReconstructionFormat detectFormat(File file)
                                                 throws IOException

Guesses the format of a reconstruction file from its first bytes. See detectFormat(InputStream, boolean)

Parameters:

file - the file to be inspected

Returns:

the detected format

Throws:

IOException - if the file could not be read

getReconstructionExtensions

public static String[] getReconstructionExtensions()

Returns the extensions (lower case, without the leading period) of the supported reconstruction formats that can be identified by name alone, i.e., not including Neurolucida .xml files

Returns:

a new array of extensions, e.g., "swc", "traces", etc.

isSWCFile

public static boolean isSWCFile(File file)

Checks if a file has an SWC extension, i.e., .swc or .eswc (extended SWC, which holds extra columns that are ignored on import). Case-insensitive.

Parameters:

file - the file to be tested

Returns:

true if the file name ends with ".swc" or ".eswc"

isReconstructionFile

public static boolean isReconstructionFile(File file)

Checks if a file is a reconstruction file based on its extension only (SWC, TRACES, JSON or NDF). Neurolucida XML files are not recognized by this method, see isReconstructionFile(File, boolean)

Parameters:

file - the file to be tested

Returns:

true if the extension is that of a supported reconstruction format

isReconstructionFile

public static boolean isReconstructionFile(File file,
 boolean sniffXml)

Checks if a file is a reconstruction file. Apart from the extension-only check, XML files are recognized as Neurolucida reconstructions if sniffXml is true and their header is that of a Neurolucida file. Only the first few KB of XML files are read.

Parameters:

file - the file to be tested

sniffXml - whether .xml files should be inspected

Returns:

true if the file is a supported reconstruction file