mpicbg.imglib.io

Class ImageOpener

java.lang.Object

mpicbg.imglib.io.ImageOpener

All Implemented Interfaces:

loci.common.StatusReporter

public class ImageOpener
extends Object
implements loci.common.StatusReporter

Reads in an imglib Image using Bio-Formats.

Author:

Stephan Preibisch, Stephan Saalfeld, Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
static String	CHANNEL
static String	TIME
static String	X
static String	Y
static String	Z

Constructor Summary

Constructors

Constructor and Description
ImageOpener()

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener l) Adds a listener to those informed when progress occurs.
static String	decodeName(String name) Converts the given image name back to a list of dimensional axis types.
static String[]	decodeTypes(String name) Converts the given image name back to a list of dimensional axis types.
static PlanarAccess<ArrayDataAccess<?>>	getPlanarAccess(Image<?> im) Obtains planar access instance backing the given image, if any.
static ArrayDataAccess<?>	makeArray(Object array) Wraps raw primitive array in imglib Array object.
static <T extends RealType<T>> T	makeType(int pixelType) Converts Bio-Formats pixel type to imglib Type object.
void	notifyListeners(loci.common.StatusEvent e) Notifies registered listeners of progress.
<T extends RealType<T>> Image<T>	openImage(IFormatReader r, ImageFactory<T> imageFactory) Reads in an imglib Image from the given initialized IFormatReader, using the given ImageFactory.
<T extends RealType<T>> Image<T>	openImage(String id) Reads in an imglib Image from the given source (e.g., file on disk).
<T extends RealType<T>> Image<T>	openImage(String id, ContainerFactory containerFactory) Reads in an imglib Image from the given source (e.g., file on disk), using the given ContainerFactory to construct the Image.
<T extends RealType<T>> Image<T>	openImage(String id, ImageFactory<T> imageFactory) Reads in an imglib Image from the given source (e.g., file on disk), using the given ImageFactory to construct the Image.
void	removeStatusListener(loci.common.StatusListener l) Removes a listener from those informed when progress occurs.

Methods inherited from class java.lang.Object

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

Field Detail

X

public static final String X

See Also:

Constant Field Values

Y

public static final String Y

See Also:

Constant Field Values

Z

public static final String Z

See Also:

Constant Field Values

TIME

public static final String TIME

See Also:

Constant Field Values

CHANNEL

public static final String CHANNEL

See Also:

Constant Field Values

Constructor Detail

ImageOpener

public ImageOpener()

Method Detail

openImage

public <T extends RealType<T>> Image<T> openImage(String id)
                                           throws FormatException,
                                                  IOException

Reads in an imglib Image from the given source (e.g., file on disk).

Throws:

FormatException

IOException

openImage

public <T extends RealType<T>> Image<T> openImage(String id,
                                                  ContainerFactory containerFactory)
                                           throws FormatException,
                                                  IOException

Reads in an imglib Image from the given source (e.g., file on disk), using the given ContainerFactory to construct the Image.

Throws:

FormatException

IOException

openImage

public <T extends RealType<T>> Image<T> openImage(String id,
                                                  ImageFactory<T> imageFactory)
                                           throws FormatException,
                                                  IOException

Reads in an imglib Image from the given source (e.g., file on disk), using the given ImageFactory to construct the Image.

Throws:

FormatException

IOException

openImage

public <T extends RealType<T>> Image<T> openImage(IFormatReader r,
                                                  ImageFactory<T> imageFactory)
                                           throws FormatException,
                                                  IOException

Reads in an imglib Image from the given initialized IFormatReader, using the given ImageFactory.

Throws:

FormatException

IOException

getPlanarAccess

public static PlanarAccess<ArrayDataAccess<?>> getPlanarAccess(Image<?> im)

Obtains planar access instance backing the given image, if any.

makeType

public static <T extends RealType<T>> T makeType(int pixelType)

Converts Bio-Formats pixel type to imglib Type object.

makeArray

public static ArrayDataAccess<?> makeArray(Object array)

Wraps raw primitive array in imglib Array object.

decodeName

public static String decodeName(String name)

Converts the given image name back to a list of dimensional axis types.

decodeTypes

public static String[] decodeTypes(String name)

Converts the given image name back to a list of dimensional axis types.

addStatusListener

public void addStatusListener(loci.common.StatusListener l)

Adds a listener to those informed when progress occurs.

Specified by:

addStatusListener in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener l)

Removes a listener from those informed when progress occurs.

Specified by:

removeStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Notifies registered listeners of progress.

Specified by:

notifyListeners in interface loci.common.StatusReporter