loci.formats

Class FilePattern

java.lang.Object

loci.formats.FilePattern

public class FilePattern
extends Object

FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series. Examples:

• C:\data\BillM\sdub<1-12>.pic
• C:\data\Kevin\80<01-59>0<2-3>.pic
• /data/Josiah/cell-Z<0-39>.C<0-1>.tiff

Author:

Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
private FilePatternBlock[]	blocks List of pattern blocks for this file pattern.
private int[]	endIndex Indices into the pattern indicating the end of a numerical block.
private String[]	files File listing for this file pattern.
private boolean	isRegex Whether or not this FilePattern represents a regular expression.
private static org.slf4j.Logger	LOGGER
private String	msg Error message generated during file pattern construction.
private String	pattern The file pattern string.
private int[]	startIndex Indices into the pattern indicating the start of a numerical block.
private boolean	valid The validity of the file pattern.

Constructor Summary

Constructors

Constructor and Description
FilePattern(Location file) Creates a pattern object using the given file as a template.
FilePattern(String pattern) Creates a pattern object for files with the given pattern string.
FilePattern(String name, String dir) Creates a pattern object using the given filename and directory path as a template.

Method Summary

Methods

Modifier and Type	Method and Description
private void	buildFiles(String prefix, int ndx, List<String> fileList) Recursive method for building filenames for the file listing.
static String	findPattern(File file) Identifies the group pattern from a given file within that group.
static String	findPattern(Location file) Identifies the group pattern from a given file within that group.
static String	findPattern(String path) Identifies the group pattern from a given file within that group.
static String	findPattern(String[] names) Generate a pattern from a list of file names.
static String	findPattern(String name, String dir) Identifies the group pattern from a given file within that group.
private static String	findPattern(String name, String[] nameList, int ndx, int end, String p) Recursive method for parsing a fixed-width numerical block.
static String	findPattern(String name, String dir, String[] nameList) Identifies the group pattern from a given file within that group.
static String	findPattern(String name, String dir, String[] nameList, int[] excludeAxes) Identifies the group pattern from a given file within that group.
static String[]	findSeriesPatterns(String base)
static String[]	findSeriesPatterns(String base, String dir, String[] nameList)
private String[]	getAllFiles(String dir)
String	getBlock(int i) Gets the specified numerical block.
String[]	getBlocks() Gets each numerical block.
private static String	getBounds(BigInteger[] numbers, boolean fixed) Gets a string containing start, end and step values for a sorted list of numbers.
int[]	getCount()
String[][]	getElements()
String	getErrorMessage() Gets the file pattern error message, if any.
String[]	getFiles() Gets a listing of all files matching the given file pattern.
BigInteger[]	getFirst()
BigInteger[]	getLast()
String	getPattern() Gets the file pattern string.
String	getPrefix() Gets the pattern's text string before any numerical ranges.
String	getPrefix(int i) Gets the pattern's text string before the given numerical block.
String[]	getPrefixes() Gets the pattern's text string before each numerical block.
BigInteger[]	getStep()
String	getSuffix() Gets the pattern's text string after all numerical ranges.
boolean	isRegex() Returns whether or not this pattern is a regular expression.
boolean	isValid() Gets whether the file pattern string is valid.
static void	main(String[] args) Method for testing file pattern logic.
private static String[]	matchFiles(String[] inFiles, NumberFilter filter) Filters the given list of filenames according to the specified filter.

Methods inherited from class java.lang.Object

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

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

pattern

private String pattern

The file pattern string.

valid

private boolean valid

The validity of the file pattern.

msg

private String msg

Error message generated during file pattern construction.

startIndex

private int[] startIndex

Indices into the pattern indicating the start of a numerical block.

endIndex

private int[] endIndex

Indices into the pattern indicating the end of a numerical block.

blocks

private FilePatternBlock[] blocks

List of pattern blocks for this file pattern.

files

private String[] files

File listing for this file pattern.

isRegex

private boolean isRegex

Whether or not this FilePattern represents a regular expression.

Constructor Detail

FilePattern

public FilePattern(Location file)

Creates a pattern object using the given file as a template.

FilePattern

public FilePattern(String name,
           String dir)

Creates a pattern object using the given filename and directory path as a template.

FilePattern

public FilePattern(String pattern)

Creates a pattern object for files with the given pattern string.

Method Detail

isRegex

public boolean isRegex()

Returns whether or not this pattern is a regular expression.

getPattern

public String getPattern()

Gets the file pattern string.

isValid

public boolean isValid()

Gets whether the file pattern string is valid.

getErrorMessage

public String getErrorMessage()

Gets the file pattern error message, if any.

getFiles

public String[] getFiles()

Gets a listing of all files matching the given file pattern.

getElements

public String[][] getElements()

getCount

public int[] getCount()

getBlock

public String getBlock(int i)

Gets the specified numerical block.

getBlocks

public String[] getBlocks()

Gets each numerical block.

getPrefix

public String getPrefix()

Gets the pattern's text string before any numerical ranges.

getSuffix

public String getSuffix()

Gets the pattern's text string after all numerical ranges.

getPrefix

public String getPrefix(int i)

Gets the pattern's text string before the given numerical block.

getPrefixes

public String[] getPrefixes()

Gets the pattern's text string before each numerical block.

findPattern

public static String findPattern(String path)

Identifies the group pattern from a given file within that group.

Parameters:

path - The file path to use as a template for the match.

findPattern

public static String findPattern(Location file)

Identifies the group pattern from a given file within that group.

Parameters:

file - The file to use as a template for the match.

findPattern

public static String findPattern(File file)

Identifies the group pattern from a given file within that group.

Parameters:

file - The file to use as a template for the match.

findPattern

public static String findPattern(String name,
                 String dir)

Identifies the group pattern from a given file within that group.

Parameters:

name - The filename to use as a template for the match.

dir - The directory in which to search for matching files.

findPattern

public static String findPattern(String name,
                 String dir,
                 String[] nameList)

Identifies the group pattern from a given file within that group.

Parameters:

name - The filename to use as a template for the match.

dir - The directory prefix to use for matching files.

nameList - The names through which to search for matching files.

findPattern

public static String findPattern(String name,
                 String dir,
                 String[] nameList,
                 int[] excludeAxes)

Identifies the group pattern from a given file within that group.

Parameters:

name - The filename to use as a template for the match.

dir - The directory prefix to use for matching files.

nameList - The names through which to search for matching files.

excludeAxes - The list of axis types which should be excluded from the pattern.

findPattern

public static String findPattern(String[] names)

Generate a pattern from a list of file names. The pattern generated will be a regular expression. Currently assumes that all file names are in the same directory.

findSeriesPatterns

public static String[] findSeriesPatterns(String base)

findSeriesPatterns

public static String[] findSeriesPatterns(String base,
                          String dir,
                          String[] nameList)

findPattern

private static String findPattern(String name,
                 String[] nameList,
                 int ndx,
                 int end,
                 String p)

Recursive method for parsing a fixed-width numerical block.

getBounds

private static String getBounds(BigInteger[] numbers,
               boolean fixed)

Gets a string containing start, end and step values for a sorted list of numbers.

matchFiles

private static String[] matchFiles(String[] inFiles,
                  NumberFilter filter)

Filters the given list of filenames according to the specified filter.

buildFiles

private void buildFiles(String prefix,
              int ndx,
              List<String> fileList)

Recursive method for building filenames for the file listing.

getAllFiles

private String[] getAllFiles(String dir)

main

public static void main(String[] args)

Method for testing file pattern logic.

getFirst

public BigInteger[] getFirst()

getLast

public BigInteger[] getLast()

getStep

public BigInteger[] getStep()