Module io.scif

Package io.scif.img

Class ImgOpener

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.img.AbstractImgIOComponent

io.scif.img.ImgOpener

All Implemented Interfaces:

SCIFIOPlugin, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

public class ImgOpener
extends AbstractImgIOComponent

Reads images from data sources using SCIFIO.

Author:

Curtis Rueden, Mark Hiner, Stephan Preibisch, Stephan Saalfeld

Constructor Summary

Constructors

Constructor	Description
ImgOpener()
ImgOpener(org.scijava.Context ctx)

Method Summary

Modifier and Type	Method	Description
SCIFIOImgPlus<?>	openImg(Reader reader, SCIFIOConfig config)	Deprecated. Use openImgs(Reader, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	openImg(Reader reader, T type, SCIFIOConfig config)	Deprecated. Use openImgs(Reader, Object, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T>> SCIFIOImgPlus<T>	openImg(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)	Deprecated. Use openImgs(Reader, Object, SCIFIOConfig) or openImgs(Reader, ImgFactory, SCIFIOConfig).
SCIFIOImgPlus<?>	openImg(String source)	Deprecated. Use openImgs(String).
SCIFIOImgPlus<?>	openImg(String source, SCIFIOConfig config)	Deprecated. Use openImgs(String, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	openImg(String source, net.imglib2.img.ImgFactory<T> imgFactory)	Deprecated. Use openImgs(String, ImgFactory).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	openImg(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)	Deprecated. Use openImgs(String, ImgFactory, SCIFIOConfig).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	openImg(String source, net.imglib2.img.ImgFactory<T> imgFactory, T type)	Deprecated. Use openImgs(String, ImgFactory) or openImgs(String, RealType).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	openImg(String source, T type)	Deprecated. Use openImgs(String, RealType).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T>	openImg(String source, T type, SCIFIOConfig config)	Deprecated. Use openImgs(String, RealType, SCIFIOConfig).
List<SCIFIOImgPlus<?>>	openImgs(Reader reader)	Reads in images using the given Reader.
List<SCIFIOImgPlus<?>>	openImgs(Reader reader, SCIFIOConfig config)	Reads in images using the given Reader.
<T> List<SCIFIOImgPlus<T>>	openImgs(Reader reader, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)	Reads in images using the given Reader.
<T> List<SCIFIOImgPlus<T>>	openImgs(Reader reader, T type, SCIFIOConfig config)	Reads in images using the given Reader.
<T extends net.imglib2.type.numeric.RealType<T>> List<SCIFIOImgPlus<T>>	openImgs(Reader reader, T type, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)	Deprecated. Use openImgs(Reader, ImgFactory, SCIFIOConfig).
List<SCIFIOImgPlus<?>>	openImgs(String source)	Reads in images from the given source.
List<SCIFIOImgPlus<?>>	openImgs(String source, SCIFIOConfig config)	Reads in images from the given source.
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	openImgs(String source, net.imglib2.img.ImgFactory<T> imgFactory)	Reads in images from the given source.
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	openImgs(String source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)	Reads in images from the given source.
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	openImgs(String source, net.imglib2.img.ImgFactory<T> imgFactory, T type)	Deprecated. Use openImgs(String, ImgFactory).
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	openImgs(String source, T type)	Reads in images from the given source.
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>>	openImgs(String source, T type, SCIFIOConfig config)	Reads in images from the given source.
List<SCIFIOImgPlus<?>>	openImgs(org.scijava.io.location.Location source)	Reads in images from the given source.
List<SCIFIOImgPlus<?>>	openImgs(org.scijava.io.location.Location source, SCIFIOConfig config)	Reads in images from the given source.
<T> List<SCIFIOImgPlus<T>>	openImgs(org.scijava.io.location.Location source, net.imglib2.img.ImgFactory<T> imgFactory)	Reads in images from the given source.
<T> List<SCIFIOImgPlus<T>>	openImgs(org.scijava.io.location.Location source, net.imglib2.img.ImgFactory<T> imgFactory, SCIFIOConfig config)	Reads in images from the given source.
<T> List<SCIFIOImgPlus<T>>	openImgs(org.scijava.io.location.Location source, T type)	Reads in images from the given source.
<T> List<SCIFIOImgPlus<T>>	openImgs(org.scijava.io.location.Location source, T type, SCIFIOConfig config)	Reads in images from the given source.

Methods inherited from class io.scif.img.AbstractImgIOComponent

utils

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Constructor Detail

ImgOpener

public ImgOpener()

ImgOpener

public ImgOpener(org.scijava.Context ctx)

Method Detail

openImgs

public List<SCIFIOImgPlus<?>> openImgs(String source)
                                throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>> openImgs(String source,
                                                                                                                         T type)
                                                                                                                  throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

type - The Type T of the output ImgPluses.

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public List<SCIFIOImgPlus<?>> openImgs(String source,
                                       SCIFIOConfig config)
                                throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>> openImgs(String source,
                                                                                                                         T type,
                                                                                                                         SCIFIOConfig config)
                                                                                                                  throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

type - The Type T of the output ImgPluses.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>> openImgs(String source,
                                                                                                                         net.imglib2.img.ImgFactory<T> imgFactory)
                                                                                                                  throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the dataset to open

imgFactory - The ImgFactory to use for creating the resultant ImgPlus.

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>> openImgs(String source,
                                                                                                                         net.imglib2.img.ImgFactory<T> imgFactory,
                                                                                                                         SCIFIOConfig config)
                                                                                                                  throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the dataset to open

imgFactory - The ImgFactory to use for creating the resultant ImgPlus.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public List<SCIFIOImgPlus<?>> openImgs(org.scijava.io.location.Location source)
                                throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T> List<SCIFIOImgPlus<T>> openImgs(org.scijava.io.location.Location source,
                                           T type)
                                    throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

type - The Type T of the output ImgPluses.

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public List<SCIFIOImgPlus<?>> openImgs(org.scijava.io.location.Location source,
                                       SCIFIOConfig config)
                                throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T> List<SCIFIOImgPlus<T>> openImgs(org.scijava.io.location.Location source,
                                           T type,
                                           SCIFIOConfig config)
                                    throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the images to open

type - The Type T of the output ImgPluses.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T> List<SCIFIOImgPlus<T>> openImgs(org.scijava.io.location.Location source,
                                           net.imglib2.img.ImgFactory<T> imgFactory)
                                    throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the dataset to open

imgFactory - The ImgFactory to use for creating the resultant ImgPlus.

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T> List<SCIFIOImgPlus<T>> openImgs(org.scijava.io.location.Location source,
                                           net.imglib2.img.ImgFactory<T> imgFactory,
                                           SCIFIOConfig config)
                                    throws ImgIOException

Reads in images from the given source.

Parameters:

source - the location of the dataset to open

imgFactory - The ImgFactory to use for creating the resultant ImgPlus.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public List<SCIFIOImgPlus<?>> openImgs(Reader reader)
                                throws ImgIOException

Reads in images using the given Reader.

Parameters:

reader - An initialized Reader to use for reading image data. Must be wrapped by a PlaneSeparator filter.

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public List<SCIFIOImgPlus<?>> openImgs(Reader reader,
                                       SCIFIOConfig config)
                                throws ImgIOException

Reads in images using the given Reader.

Parameters:

reader - An initialized Reader to use for reading image data. Must be wrapped by a PlaneSeparator filter.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T> List<SCIFIOImgPlus<T>> openImgs(Reader reader,
                                           T type,
                                           SCIFIOConfig config)
                                    throws ImgIOException

Reads in images using the given Reader.

Parameters:

reader - An initialized Reader to use for reading image data. Must be wrapped by a PlaneSeparator filter.

type - The Type T of the output ImgPluses.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

public <T> List<SCIFIOImgPlus<T>> openImgs(Reader reader,
                                           net.imglib2.img.ImgFactory<T> imgFactory,
                                           SCIFIOConfig config)
                                    throws ImgIOException

Reads in images using the given Reader.

Parameters:

reader - An initialized Reader to use for reading image data. Must be wrapped by a PlaneSeparator filter.

imgFactory - The ImgFactory to use for creating the resultant ImgPlus.

config - SCIFIOConfig to use when opening the images

Returns:

the images which were read

Throws:

ImgIOException - if there is a problem reading the image data.

openImgs

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> List<SCIFIOImgPlus<T>> openImgs(String source,
                                                                                                                         net.imglib2.img.ImgFactory<T> imgFactory,
                                                                                                                         T type)
                                                                                                                  throws ImgIOException

Deprecated.

Use openImgs(String, ImgFactory).

Throws:

ImgIOException

openImgs

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T>> List<SCIFIOImgPlus<T>> openImgs(Reader reader,
                                                                                        T type,
                                                                                        net.imglib2.img.ImgFactory<T> imgFactory,
                                                                                        SCIFIOConfig config)
                                                                                 throws ImgIOException

Deprecated.

Use openImgs(Reader, ImgFactory, SCIFIOConfig).

Throws:

ImgIOException

openImg

@Deprecated
public SCIFIOImgPlus<?> openImg(String source)
                         throws ImgIOException

Deprecated.

Use openImgs(String).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T> openImg(String source,
                                                                                                                  T type)
                                                                                                           throws ImgIOException

Deprecated.

Use openImgs(String, RealType).

Throws:

ImgIOException

openImg

@Deprecated
public SCIFIOImgPlus<?> openImg(String source,
                                SCIFIOConfig config)
                         throws ImgIOException

Deprecated.

Use openImgs(String, SCIFIOConfig).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T> openImg(String source,
                                                                                                                  T type,
                                                                                                                  SCIFIOConfig config)
                                                                                                           throws ImgIOException

Deprecated.

Use openImgs(String, RealType, SCIFIOConfig).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T> openImg(String source,
                                                                                                                  net.imglib2.img.ImgFactory<T> imgFactory)
                                                                                                           throws ImgIOException

Deprecated.

Use openImgs(String, ImgFactory).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T> openImg(String source,
                                                                                                                  net.imglib2.img.ImgFactory<T> imgFactory,
                                                                                                                  SCIFIOConfig config)
                                                                                                           throws ImgIOException

Deprecated.

Use openImgs(String, ImgFactory, SCIFIOConfig).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T> openImg(String source,
                                                                                                                  net.imglib2.img.ImgFactory<T> imgFactory,
                                                                                                                  T type)
                                                                                                           throws ImgIOException

Deprecated.

Use openImgs(String, ImgFactory) or openImgs(String, RealType).

Throws:

ImgIOException

openImg

@Deprecated
public SCIFIOImgPlus<?> openImg(Reader reader,
                                SCIFIOConfig config)
                         throws ImgIOException

Deprecated.

Use openImgs(Reader, SCIFIOConfig).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> SCIFIOImgPlus<T> openImg(Reader reader,
                                                                                                                  T type,
                                                                                                                  SCIFIOConfig config)
                                                                                                           throws ImgIOException

Deprecated.

Use openImgs(Reader, Object, SCIFIOConfig).

Throws:

ImgIOException

openImg

@Deprecated
public <T extends net.imglib2.type.numeric.RealType<T>> SCIFIOImgPlus<T> openImg(Reader reader,
                                                                                 T type,
                                                                                 net.imglib2.img.ImgFactory<T> imgFactory,
                                                                                 SCIFIOConfig config)
                                                                          throws ImgIOException

Deprecated.

Use openImgs(Reader, Object, SCIFIOConfig) or openImgs(Reader, ImgFactory, SCIFIOConfig).

Throws:

ImgIOException