io.scif.util

Class SCIFIOMetadataTools

java.lang.Object

io.scif.util.SCIFIOMetadataTools

public class SCIFIOMetadataTools
extends Object

A utility class for working with Metadata objects.

Author:

Mark Hiner

See Also:

Metadata

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SCIFIOMetadataTools.AxisValue Helper class that pairs an AxisType with a length.

Method Summary

Modifier and Type	Method and Description
static <M extends Metadata> M	castMeta(Metadata meta) Casts the provided Metadata object to the generic type of this method.
static int	guessInterleavedAxisCount(List<net.imagej.axis.CalibratedAxis> axes) Guesses at a reasonable default interleaved axis count for the given list of dimensional axes.
static int	guessPlanarAxisCount(List<net.imagej.axis.CalibratedAxis> axes) Guesses at a reasonable default planar axis count for the given list of dimensional axes.
static String[]	keys(Hashtable<String,Object> meta) Gets a sorted list of keys from the given hashtable.
static void	merge(Map<String,Object> src, Map<String,Object> dest, String prefix) Merges the given lists of metadata, prepending the specified prefix for the destination keys.
static long[]	modifyPlanar(int imageIndex, Metadata meta, long... values) Replaces the first values.length of the provided Metadata's planar axes with the values.
static long[]	modifyPlanar(int imageIndex, Metadata meta, SCIFIOMetadataTools.AxisValue... axes) Iterates over the provided Metadata's planar axes, replacing any instances of axes with the paired values.
static Metadata	unwrapMetadata(Metadata meta) Unwraps the provided Metadata class if it has been wrapped in MetadataWrapper(s).
static void	verifyMinimumPopulated(Metadata src, org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out) Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
static void	verifyMinimumPopulated(Metadata src, org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex) Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
static void	verifyMinimumPopulated(Metadata src, org.scijava.io.location.Location loc)
static void	verifyMinimumPopulated(Metadata src, org.scijava.io.location.Location loc, int imageIndex)
static boolean	wholePlane(int imageIndex, Metadata meta, net.imglib2.Interval bounds) Returns true if the provided axes correspond to a complete image plane
static boolean	wholeRow(int imageIndex, Metadata meta, net.imglib2.Interval bounds) Returns true if the provided axes correspond to a complete image row

Methods inherited from class java.lang.Object

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

Method Detail

wholePlane

public static boolean wholePlane(int imageIndex,
                                 Metadata meta,
                                 net.imglib2.Interval bounds)

Returns true if the provided axes correspond to a complete image plane

wholeRow

public static boolean wholeRow(int imageIndex,
                               Metadata meta,
                               net.imglib2.Interval bounds)

Returns true if the provided axes correspond to a complete image row

modifyPlanar

public static long[] modifyPlanar(int imageIndex,
                                  Metadata meta,
                                  long... values)

Replaces the first values.length of the provided Metadata's planar axes with the values.

modifyPlanar

public static long[] modifyPlanar(int imageIndex,
                                  Metadata meta,
                                  SCIFIOMetadataTools.AxisValue... axes)

Iterates over the provided Metadata's planar axes, replacing any instances of axes with the paired values.

castMeta

public static <M extends Metadata> M castMeta(Metadata meta)

Casts the provided Metadata object to the generic type of this method.

Usage: To cast a Metadata instance to ConcreteMetadata, use: SCIFIOMetadataTools.<ConcreteMetadata>castMeta(meta).

unwrapMetadata

public static Metadata unwrapMetadata(Metadata meta)

Unwraps the provided Metadata class if it has been wrapped in MetadataWrapper(s).

Parameters:

meta - Metadata instance to unwrap

Returns:

If meta is a MetadataWrapper, the tail wrapped Metadata. Otherwise meta is returned directly.

verifyMinimumPopulated

public static void verifyMinimumPopulated(Metadata src,
                                          org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out)
                                   throws FormatException

Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.

Throws:

FormatException - if there is a missing metadata field, or the metadata object is uninitialized

verifyMinimumPopulated

public static void verifyMinimumPopulated(Metadata src,
                                          org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out,
                                          int imageIndex)
                                   throws FormatException

Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.

Throws:

FormatException - if there is a missing metadata field, or the metadata object is uninitialized

verifyMinimumPopulated

public static void verifyMinimumPopulated(Metadata src,
                                          org.scijava.io.location.Location loc)
                                   throws FormatException

Throws:

FormatException

verifyMinimumPopulated

public static void verifyMinimumPopulated(Metadata src,
                                          org.scijava.io.location.Location loc,
                                          int imageIndex)
                                   throws FormatException

Throws:

FormatException

guessPlanarAxisCount

public static int guessPlanarAxisCount(List<net.imagej.axis.CalibratedAxis> axes)

Guesses at a reasonable default planar axis count for the given list of dimensional axes.

The heuristic looks for the first index following both Axes.X and Axes.Y. If the list does not contain both X and Y then the guess will equal the total number of axes.

guessInterleavedAxisCount

public static int guessInterleavedAxisCount(List<net.imagej.axis.CalibratedAxis> axes)

Guesses at a reasonable default interleaved axis count for the given list of dimensional axes.

The heuristic looks for the last index preceding both Axes.X and Axes.Y. If the list does not contain either X or Y then the guess will equal the total number of axes.

merge

public static void merge(Map<String,Object> src,
                         Map<String,Object> dest,
                         String prefix)

Merges the given lists of metadata, prepending the specified prefix for the destination keys.

keys

public static String[] keys(Hashtable<String,Object> meta)

Gets a sorted list of keys from the given hashtable.