io.scif.img

Class ImgSaver

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.img.AbstractImgIOComponent

io.scif.img.ImgSaver

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 ImgSaver
extends AbstractImgIOComponent

Writes out an ImgPlus using SCIFIO.

Author:

Mark Hiner, Curtis Rueden

Constructor Summary

Constructors

Constructor and Description
ImgSaver()
ImgSaver(org.scijava.Context context)

Method Summary

Modifier and Type	Method and Description
static String	guessDimOrder(net.imagej.axis.CalibratedAxis[] axes, long[] dimLengths, long[] newLengths) The ImgLib axes structure can contain multiple unknown axes.
Metadata	saveImg(org.scijava.io.location.Location id, net.imglib2.img.Img<?> img) Entry point for saving an ImgPlus.
Metadata	saveImg(org.scijava.io.location.Location id, net.imglib2.img.Img<?> img, SCIFIOConfig config) As saveImg(Location, Img) with configuration options.
Metadata	saveImg(org.scijava.io.location.Location id, SCIFIOImgPlus<?> img, int imageIndex) Location id provided.
Metadata	saveImg(org.scijava.io.location.Location id, SCIFIOImgPlus<?> img, int imageIndex, SCIFIOConfig config) As saveImg(Location, SCIFIOImgPlus, int) with configuration options.
Metadata	saveImg(String destination, net.imglib2.img.Img<?> img) Entry point for saving an ImgPlus.
Metadata	saveImg(String destination, net.imglib2.img.Img<?> img, SCIFIOConfig config) As saveImg(Location, Img) with configuration options.
Metadata	saveImg(String destination, SCIFIOImgPlus<?> img, int imageIndex) Location id provided.
Metadata	saveImg(String destination, SCIFIOImgPlus<?> img, int imageIndex, SCIFIOConfig config) As saveImg(Location, SCIFIOImgPlus, int) with configuration options.
void	saveImg(Writer w, net.imglib2.img.Img<?> img) Writer and Img provided
void	saveImg(Writer w, net.imglib2.img.Img<?> img, SCIFIOConfig config) As saveImg(Writer, Img), with configuration options.
void	saveImg(Writer w, SCIFIOImgPlus<?> img, int imageIndex) Writer provided.
void	saveImg(Writer w, SCIFIOImgPlus<?> img, int imageIndex, SCIFIOConfig config) As saveImg(Writer, SCIFIOImgPlus, int), with configuration options.

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.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Constructor Detail

ImgSaver

public ImgSaver()

ImgSaver

public ImgSaver(org.scijava.Context context)

Method Detail

saveImg

public Metadata saveImg(String destination,
                        net.imglib2.img.Img<?> img)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

Entry point for saving an ImgPlus. The goal is to get to a Writer and ImgPlus which are then passed to writePlanes(io.scif.Writer, int, io.scif.img.SCIFIOImgPlus<?>). These saveImg signatures facilitate multiple pathways to that goal. This method is called when a Location id and Img are provided.

Parameters:

destination -

img -

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(String destination,
                        SCIFIOImgPlus<?> img,
                        int imageIndex)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

Location id provided. ImgPlus provided, or wrapped Img in previous saveImg.

Parameters:

destination -

img -

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(String destination,
                        net.imglib2.img.Img<?> img,
                        SCIFIOConfig config)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

As saveImg(Location, Img) with configuration options.

Parameters:

destination -

img -

config - Configuration information to use for this write.

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(String destination,
                        SCIFIOImgPlus<?> img,
                        int imageIndex,
                        SCIFIOConfig config)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

As saveImg(Location, SCIFIOImgPlus, int) with configuration options.

Parameters:

destination -

img -

config - Configuration information to use for this write.

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(org.scijava.io.location.Location id,
                        net.imglib2.img.Img<?> img)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

Entry point for saving an ImgPlus. The goal is to get to a Writer and ImgPlus which are then passed to writePlanes(io.scif.Writer, int, io.scif.img.SCIFIOImgPlus<?>). These saveImg signatures facilitate multiple pathways to that goal. This method is called when a Location id and Img are provided.

Parameters:

id -

img -

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(org.scijava.io.location.Location id,
                        SCIFIOImgPlus<?> img,
                        int imageIndex)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

Location id provided. ImgPlus provided, or wrapped Img in previous saveImg.

Parameters:

id -

img -

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(org.scijava.io.location.Location id,
                        net.imglib2.img.Img<?> img,
                        SCIFIOConfig config)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

As saveImg(Location, Img) with configuration options.

Parameters:

id -

img -

config - Configuration information to use for this write.

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public Metadata saveImg(org.scijava.io.location.Location id,
                        SCIFIOImgPlus<?> img,
                        int imageIndex,
                        SCIFIOConfig config)
                 throws ImgIOException,
                        net.imglib2.exception.IncompatibleTypeException

As saveImg(Location, SCIFIOImgPlus, int) with configuration options.

Parameters:

id -

img -

config - Configuration information to use for this write.

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public void saveImg(Writer w,
                    net.imglib2.img.Img<?> img)
             throws ImgIOException,
                    net.imglib2.exception.IncompatibleTypeException

Writer and Img provided

Parameters:

w -

img -

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public void saveImg(Writer w,
                    SCIFIOImgPlus<?> img,
                    int imageIndex)
             throws ImgIOException,
                    net.imglib2.exception.IncompatibleTypeException

Writer provided. ImgPlus provided, or wrapped provided Img.

Parameters:

w -

img -

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public void saveImg(Writer w,
                    net.imglib2.img.Img<?> img,
                    SCIFIOConfig config)
             throws ImgIOException,
                    net.imglib2.exception.IncompatibleTypeException

As saveImg(Writer, Img), with configuration options.

Parameters:

w -

img -

config - Configuration information to use for this write.

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

saveImg

public void saveImg(Writer w,
                    SCIFIOImgPlus<?> img,
                    int imageIndex,
                    SCIFIOConfig config)
             throws ImgIOException,
                    net.imglib2.exception.IncompatibleTypeException

As saveImg(Writer, SCIFIOImgPlus, int), with configuration options.

Parameters:

w -

img -

config - Configuration information to use for this write.

Throws:

ImgIOException

net.imglib2.exception.IncompatibleTypeException

guessDimOrder

public static String guessDimOrder(net.imagej.axis.CalibratedAxis[] axes,
                                   long[] dimLengths,
                                   long[] newLengths)

The ImgLib axes structure can contain multiple unknown axes. This method will determine if the provided dimension order, obtained from an ImgLib AxisType array, can be converted to a 5-dimensional sequence compatible with SCIFIO, and returns that sequence if it exists and null otherwise.

Parameters:

newLengths - - updated to hold the lengths of the newly ordered axes