loci.plugins.in

Class ImagePlusReader

java.lang.Object

loci.plugins.in.ImagePlusReader

All Implemented Interfaces:

loci.common.StatusReporter

public class ImagePlusReader
extends java.lang.Object
implements loci.common.StatusReporter

A high-level reader for ImagePlus objects.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<loci.common.StatusListener>	listeners
protected ImportProcess	process Import preparation process managing Bio-Formats readers and other state.
static java.lang.String	PROP_LUT Special property prefix for storing planar LUTs.
static java.lang.String	PROP_SERIES Special property for storing series number associated with the image.
private long	startTime
private long	time

Constructor Summary

Constructors

Constructor and Description
ImagePlusReader() Constructs an ImagePlusReader with the default options.
ImagePlusReader(ImportProcess process) Constructs an ImagePlusReader with the given complete import preparation process.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener l)
private java.util.List<ij.ImagePlus>	applyColors(java.util.List<ij.ImagePlus> imps)
private java.util.List<ij.ImagePlus>	concatenate(java.util.List<ij.ImagePlus> imps)
private java.lang.String	constructImageTitle(IFormatReader r, java.lang.String file, java.lang.String seriesName, boolean groupFiles)
private java.lang.String	constructSliceLabel(int ndx, IFormatReader r, IMetadata meta, int series, int zCount, int cCount, int tCount)
private ij.io.FileInfo	createFileInfo()
static ij.ImagePlus	createImage(java.lang.String title, ij.ImageStack stack, java.util.List<ij.process.LUT> luts) Creates an ImagePlus from the given image stack.
static ij.ImagePlus	createImage(java.lang.String title, java.util.List<ij.process.ImageProcessor> procs) Creates an ImagePlus from the given image processors.
static ij.ImageStack	createStack(java.util.List<ij.process.ImageProcessor> procs, java.util.List<java.lang.String> labels, java.util.List<ij.process.LUT> luts) Creates an image stack from the given image processors.
private ij.ImageStack	createVirtualStack(ImportProcess process, int s, java.util.List<ij.process.LUT> luts)
private void	finishTiming()
private boolean[]	getPlanesToLoad(int s)
void	notifyListeners(loci.common.StatusEvent e)
ij.ImagePlus[]	openImagePlus() Opens one or more ImagePlus objects corresponding to the reader's associated options.
ij.ImagePlus[]	openThumbImagePlus()
private ij.ImagePlus	readImage(int s, boolean thumbnail)
private java.util.List<ij.ImagePlus>	readImages()
private java.util.List<ij.ImagePlus>	readImages(boolean thumbnail)
private ij.ImageStack	readPlanes(ImportProcess process, int s, java.util.List<ij.process.LUT> luts, boolean thumbnail)
private ij.process.ImageProcessor[]	readProcessors(ImportProcess process, int no, loci.common.Region r, boolean thumbnail) HACK: This method mainly exists to prompt the user for a missing LuraWave license code, in the case of LWF-compressed Flex.
private java.util.List<ij.ImagePlus>	readThumbImages()
void	removeStatusListener(loci.common.StatusListener l)
private static void	saveLUTs(ij.ImagePlus imp, java.util.List<ij.process.LUT> luts)
private java.util.List<ij.ImagePlus>	splitDims(java.util.List<ij.ImagePlus> imps)
private void	startTiming()
private static java.lang.String[]	substringsBetween(java.lang.String str, java.lang.String open, java.lang.String close)
private void	updateTiming(int s, int i, int current, int total)

Methods inherited from class java.lang.Object

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

Field Detail

PROP_SERIES

public static final java.lang.String PROP_SERIES

Special property for storing series number associated with the image.

See Also:

Constant Field Values

PROP_LUT

public static final java.lang.String PROP_LUT

Special property prefix for storing planar LUTs.

See Also:

Constant Field Values

process

protected ImportProcess process

Import preparation process managing Bio-Formats readers and other state.

listeners

protected java.util.List<loci.common.StatusListener> listeners

startTime

private long startTime

time

private long time

Constructor Detail

ImagePlusReader

public ImagePlusReader()
                throws java.io.IOException

Constructs an ImagePlusReader with the default options.

Throws:

java.io.IOException - if the default options cannot be determined.

ImagePlusReader

public ImagePlusReader(ImportProcess process)

Constructs an ImagePlusReader with the given complete import preparation process.

Method Detail

openImagePlus

public ij.ImagePlus[] openImagePlus()
                             throws FormatException,
                                    java.io.IOException

Opens one or more ImagePlus objects corresponding to the reader's associated options.

Throws:

FormatException

java.io.IOException

openThumbImagePlus

public ij.ImagePlus[] openThumbImagePlus()
                                  throws FormatException,
                                         java.io.IOException

Throws:

FormatException

java.io.IOException

addStatusListener

public void addStatusListener(loci.common.StatusListener l)

Specified by:

addStatusListener in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener l)

Specified by:

removeStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Specified by:

notifyListeners in interface loci.common.StatusReporter

createImage

public static ij.ImagePlus createImage(java.lang.String title,
                                       java.util.List<ij.process.ImageProcessor> procs)

Creates an ImagePlus from the given image processors.

Parameters:

title - The title for the image.

procs - List of image processors to compile into an image.

createImage

public static ij.ImagePlus createImage(java.lang.String title,
                                       ij.ImageStack stack,
                                       java.util.List<ij.process.LUT> luts)

Creates an ImagePlus from the given image stack.

Parameters:

title - The title for the image.

stack - The image stack containing the image planes.

luts - Optional list of plane-specific LUTs to store as image properties, for later use.

createStack

public static ij.ImageStack createStack(java.util.List<ij.process.ImageProcessor> procs,
                                        java.util.List<java.lang.String> labels,
                                        java.util.List<ij.process.LUT> luts)

Creates an image stack from the given image processors.

Parameters:

procs - List of image processors to compile into a stack.

labels - Optional list of labels, one per plane.

luts - Optional list for storing plane-specific LUTs, for later use.

readImages

private java.util.List<ij.ImagePlus> readImages()
                                         throws FormatException,
                                                java.io.IOException

Throws:

FormatException

java.io.IOException

readThumbImages

private java.util.List<ij.ImagePlus> readThumbImages()
                                              throws FormatException,
                                                     java.io.IOException

Throws:

FormatException

java.io.IOException

readImages

private java.util.List<ij.ImagePlus> readImages(boolean thumbnail)
                                         throws FormatException,
                                                java.io.IOException

Throws:

FormatException

java.io.IOException

readImage

private ij.ImagePlus readImage(int s,
                               boolean thumbnail)
                        throws FormatException,
                               java.io.IOException

Throws:

FormatException

java.io.IOException

createVirtualStack

private ij.ImageStack createVirtualStack(ImportProcess process,
                                         int s,
                                         java.util.List<ij.process.LUT> luts)
                                  throws FormatException,
                                         java.io.IOException

Throws:

FormatException

java.io.IOException

readPlanes

private ij.ImageStack readPlanes(ImportProcess process,
                                 int s,
                                 java.util.List<ij.process.LUT> luts,
                                 boolean thumbnail)
                          throws FormatException,
                                 java.io.IOException

Throws:

FormatException

java.io.IOException

readProcessors

private ij.process.ImageProcessor[] readProcessors(ImportProcess process,
                                                   int no,
                                                   loci.common.Region r,
                                                   boolean thumbnail)
                                            throws FormatException,
                                                   java.io.IOException

HACK: This method mainly exists to prompt the user for a missing LuraWave license code, in the case of LWF-compressed Flex.

Throws:

FormatException

java.io.IOException

See Also:

ImportProcess.setId()

concatenate

private java.util.List<ij.ImagePlus> concatenate(java.util.List<ij.ImagePlus> imps)

applyColors

private java.util.List<ij.ImagePlus> applyColors(java.util.List<ij.ImagePlus> imps)

splitDims

private java.util.List<ij.ImagePlus> splitDims(java.util.List<ij.ImagePlus> imps)

startTiming

private void startTiming()

updateTiming

private void updateTiming(int s,
                          int i,
                          int current,
                          int total)

finishTiming

private void finishTiming()

createFileInfo

private ij.io.FileInfo createFileInfo()

getPlanesToLoad

private boolean[] getPlanesToLoad(int s)

constructImageTitle

private java.lang.String constructImageTitle(IFormatReader r,
                                             java.lang.String file,
                                             java.lang.String seriesName,
                                             boolean groupFiles)

constructSliceLabel

private java.lang.String constructSliceLabel(int ndx,
                                             IFormatReader r,
                                             IMetadata meta,
                                             int series,
                                             int zCount,
                                             int cCount,
                                             int tCount)

substringsBetween

private static java.lang.String[] substringsBetween(java.lang.String str,
                                                    java.lang.String open,
                                                    java.lang.String close)

saveLUTs

private static void saveLUTs(ij.ImagePlus imp,
                             java.util.List<ij.process.LUT> luts)