plugins.kernel.importer

Class LociImporterPlugin

java.lang.Object

icy.plugin.abstract_.Plugin

icy.plugin.abstract_.PluginSequenceFileImporter

plugins.kernel.importer.LociImporterPlugin

All Implemented Interfaces:

SequenceFileImporter, ImageProvider, PluginNoEDTConstructor, SequenceIdImporter, java.io.Closeable, java.lang.AutoCloseable

public class LociImporterPlugin
extends PluginSequenceFileImporter

LOCI Bio-Formats library importer class.

Author:

Stephane

Field Summary

Fields inherited from interface icy.sequence.SequenceIdImporter

FLAG_METADATA_ALL, FLAG_METADATA_MASK, FLAG_METADATA_MINIMUM

Constructor Summary

Constructors

Constructor and Description
LociImporterPlugin()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	acceptFile(java.lang.String path) Return true if the specified file can be opened by the importer
void	close() Close the image which has been previously opened with SequenceIdImporter.open(String, int) method.
java.util.List<javax.swing.filechooser.FileFilter>	getFileFilters() Return the supported FileFilter for this importer.
static IcyBufferedImage	getImage(loci.formats.IFormatReader reader, java.awt.Rectangle rect, int z, int t) Load the image located at (Z, T) position from the specified IFormatReader and return it as an IcyBufferedImage.
static IcyBufferedImage	getImage(loci.formats.IFormatReader reader, java.awt.Rectangle rect, int z, int t, int c) Load a single channel sub image at (Z, T, C) position from the specified IFormatReader and returns it as an IcyBufferedImage.
static IcyBufferedImage	getImage(loci.formats.IFormatReader reader, java.awt.Rectangle rect, int z, int t, int c, int downScaleLevel) Load a single channel sub image at (Z, T, C) position from the specified IFormatReader and returns it as an IcyBufferedImage.
IcyBufferedImage	getImage(int series, int resolution, java.awt.Rectangle rectangle, int z, int t, int c) Returns the image located at specified position.
IcyBufferedImage	getImageByTile(int series, int resolution, java.awt.Rectangle region, int z, int t, int c, int tileW, int tileH, ProgressListener listener)
static IcyBufferedImage	getImageCompatible(loci.formats.IFormatReader reader, int z, int t) Load the image located at (Z, T) position from the specified IFormatReader and return it as an IcyBufferedImage (compatible and slower method).
loci.formats.ome.OMEXMLMetadataImpl	getMetaData() Deprecated.
ome.xml.meta.OMEXMLMetadata	getOMEXMLMetaData() Returns the image metadata in OME format (metadata provides many informations about the image).
java.lang.String	getOpened()
java.lang.Object	getPixels(int series, int resolution, java.awt.Rectangle rectangle, int z, int t, int c) Returns the pixel data located for specified position of the image.
java.lang.Object	getPixelsByTile(int series, int resolution, java.awt.Rectangle region, int z, int t, int c, int tileW, int tileH, ProgressListener listener) See AbstractImageProvider.getPixelsByTile(int, int, Rectangle, int, int, int, int, int, ProgressListener)
loci.formats.IFormatReader	getReader() Returns a reader to use for the current thread (allocate it if needed).
boolean	getReadOriginalMetadata() When set to true the importer will also read original metadata (as annotations)
static IcyBufferedImage	getThumbnail(loci.formats.IFormatReader reader, int z, int t) Load a thumbnail version of the image located at (Z, T) position from the specified IFormatReader and returns it as an IcyBufferedImage.
static IcyBufferedImage	getThumbnail(loci.formats.IFormatReader reader, int z, int t, int c) Load a thumbnail version of the image located at (Z, T, C) position from the specified IFormatReader and returns it as an IcyBufferedImage.
IcyBufferedImage	getThumbnail(int series) Returns the image thumbnail for the specified series of the image.
static IcyBufferedImage	getThumbnailCompatible(loci.formats.IFormatReader reader, int z, int t) Load a thumbnail version of the image located at (Z, T) position from the specified IFormatReader and returns it as an IcyBufferedImage.
static IcyBufferedImage	getThumbnailCompatible(loci.formats.IFormatReader reader, int z, int t, int c) Load a thumbnail version of the image located at (Z, T, C) position from the specified IFormatReader and returns it as an IcyBufferedImage.
int	getTileHeight(int series) Returns the (optimal) tile height for the specified series of the image.
int	getTileWidth(int series) Returns the (optimal) tile width for the specified series of the image.
boolean	isGroupFiles() When set to true the importer will try to group files required for the whole dataset.
boolean	isOpen(java.lang.String path)
boolean	isResolutionAvailable(int series, int resolution) Returns true if the given sub resolution is available from this series.
boolean	open(java.lang.String path, int flags) Open the image designed by the specified file path to allow image data / metadata access.
void	releaseReader(loci.formats.IFormatReader r) Release the reader obtained through getReader() to the reader pool.
void	setGroupFiles(boolean value) When set to true the importer will try to group files required for the whole dataset.
void	setReadOriginalMetadata(boolean value) When set to true the importer will also read original metadata (as annotations).

Methods inherited from class icy.plugin.abstract_.PluginSequenceFileImporter

getImage, getImage, getImage, getImage, getImage, getResolutionFactor

Methods inherited from class icy.plugin.abstract_.Plugin

addIcyFrame, addSequence, getActiveImage, getActiveSequence, getActiveViewer, getDescriptor, getFocusedImage, getFocusedSequence, getFocusedViewer, getIconResource, getImageResource, getInstallFolder, getName, getOwnerClassName, getPlugin, getPreferences, getPreferencesRoot, getResource, getResourceAsStream, getResources, getSequences, isBundled, loadLibrary, prepareLibrary, removeSequence, report, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

LociImporterPlugin

public LociImporterPlugin()

Method Detail

getReadOriginalMetadata

public boolean getReadOriginalMetadata()

When set to true the importer will also read original metadata (as annotations)

Returns:

the readAllMetadata state

See Also:

setReadOriginalMetadata(boolean)

setReadOriginalMetadata

public void setReadOriginalMetadata(boolean value)

When set to true the importer will also read original metadata (as annotations).

isGroupFiles

public boolean isGroupFiles()

When set to true the importer will try to group files required for the whole dataset.

Returns:

the groupFiles

setGroupFiles

public void setGroupFiles(boolean value)

When set to true the importer will try to group files required for the whole dataset.

getFileFilters

public java.util.List<javax.swing.filechooser.FileFilter> getFileFilters()

Description copied from interface: SequenceFileImporter

Return the supported FileFilter for this importer.

acceptFile

public boolean acceptFile(java.lang.String path)

Description copied from interface: SequenceFileImporter

Return true if the specified file can be opened by the importer

isOpen

public boolean isOpen(java.lang.String path)

getOpened

public java.lang.String getOpened()

Returns:

The path of the image file of the image currently opened or null otherwise.
Note that path is always returned in generic java path style (see FileUtil.getGenericPath(String) method).

See Also:

SequenceFileImporter.open(String, int), SequenceIdImporter.close()

open

public boolean open(java.lang.String path,
           int flags)
             throws UnsupportedFormatException,
                    java.io.IOException

Description copied from interface: SequenceFileImporter

Open the image designed by the specified file path to allow image data / metadata access.
Calling this method will automatically close the previous opened image.
Don't forget to call SequenceIdImporter.close() to close the image when you're done.

Parameters:

path - Path of the image file to open.

flags - operation flag:

SequenceIdImporter.FLAG_METADATA_MINIMUM = load minimum metadata informations

SequenceIdImporter.FLAG_METADATA_ALL = load all metadata informations

Returns:

true if the operation has succeeded and false otherwise.

Throws:

UnsupportedFormatException

java.io.IOException

close

public void close()
           throws java.io.IOException

Description copied from interface: SequenceIdImporter

Close the image which has been previously opened with SequenceIdImporter.open(String, int) method.

Throws:

java.io.IOException

getReader

public loci.formats.IFormatReader getReader()
                                     throws loci.formats.FormatException,
                                            java.io.IOException

Returns a reader to use for the current thread (allocate it if needed).
Any obtained reader should be released using releaseReader(IFormatReader)

Throws:

loci.formats.FormatException

java.io.IOException

See Also:

releaseReader(IFormatReader)

releaseReader

public void releaseReader(loci.formats.IFormatReader r)

Release the reader obtained through getReader() to the reader pool.

See Also:

getReader()

getOMEXMLMetaData

public ome.xml.meta.OMEXMLMetadata getOMEXMLMetaData()
                                              throws UnsupportedFormatException,
                                                     java.io.IOException

Description copied from interface: ImageProvider

Returns the image metadata in OME format (metadata provides many informations about the image).

Number of series (mandatory field) :
MetaDataUtil.getNumSeries(OMEXMLMetadata)
Dimension (mandatory fields) :
MetaDataUtil.getSizeX(OMEXMLMetadata, int)
MetaDataUtil.getSizeY(OMEXMLMetadata, int)
MetaDataUtil.getSizeZ(OMEXMLMetadata, int)
MetaDataUtil.getSizeT(OMEXMLMetadata, int)
MetaDataUtil.getSizeC(OMEXMLMetadata, int)
Internal data type (mandatory field) :
MetaDataUtil.getDataType(OMEXMLMetadata, int)
Physical and time position (mandatory fields) :
MetaDataUtil.getPositionX(OMEXMLMetadata, int, int, int, int, double)
MetaDataUtil.getPositionY(OMEXMLMetadata, int, int, int, int, double)
MetaDataUtil.getPositionZ(OMEXMLMetadata, int, int, int, int, double)
MetaDataUtil.getPositionT(OMEXMLMetadata, int, long)
MetaDataUtil.getPositionTOffset(OMEXMLMetadata, int, int, int, int, double)

and many others informations depending the available metadata in the image format.

Specified by:

getOMEXMLMetaData in interface ImageProvider

Overrides:

getOMEXMLMetaData in class PluginSequenceFileImporter

Throws:

UnsupportedFormatException

java.io.IOException

getMetaData

@Deprecated
public loci.formats.ome.OMEXMLMetadataImpl getMetaData()
                                                throws UnsupportedFormatException,
                                                       java.io.IOException

Deprecated.

Throws:

UnsupportedFormatException

java.io.IOException

getTileWidth

public int getTileWidth(int series)
                 throws UnsupportedFormatException,
                        java.io.IOException

Description copied from interface: ImageProvider

Returns the (optimal) tile width for the specified series of the image.
This method allow to know the best tile size to use when using the sub region image loading operations.
This method should returns 0 if tile loading is not supported and -1 if any tile size can be used.

Specified by:

getTileWidth in interface ImageProvider

Overrides:

getTileWidth in class PluginSequenceFileImporter

Parameters:

series - Series index for multi series image (use 0 if unsure).

Returns:

optimal tile width

Throws:

UnsupportedFormatException

java.io.IOException

getTileHeight

public int getTileHeight(int series)
                  throws UnsupportedFormatException,
                         java.io.IOException

Description copied from interface: ImageProvider

Returns the (optimal) tile height for the specified series of the image.
This method allow to know the best tile size to use when using the sub region image loading operations.
This method should returns 0 if tile loading is not supported and -1 if any tile size can be used.

Specified by:

getTileHeight in interface ImageProvider

Overrides:

getTileHeight in class PluginSequenceFileImporter

Parameters:

series - Series index for multi series image (use 0 if unsure).

Returns:

optimal tile height

Throws:

UnsupportedFormatException

java.io.IOException

isResolutionAvailable

public boolean isResolutionAvailable(int series,
                            int resolution)
                              throws UnsupportedFormatException,
                                     java.io.IOException

Description copied from interface: ImageProvider

Returns true if the given sub resolution is available from this series.
Note that even if a sub resolution isn't available, the ImageProvider should provide it by generating it manually (using the IcyBufferedImageUtil.downscaleBy2(IcyBufferedImage, boolean, int) method.

Final image resolution can be calculated with: image.originalResolution / (2^resolution)
So resolution 0 is the original resolution and it's always available (should always returns true).
Resolution 1 is half of the original resolution
Resolution 2 is quarter of the original resolution
...

Specified by:

isResolutionAvailable in interface ImageProvider

Overrides:

isResolutionAvailable in class PluginSequenceFileImporter

Parameters:

series - Series index for multi series image (use 0 if unsure).

resolution - Resolution level

Throws:

UnsupportedFormatException

java.io.IOException

getThumbnail

public IcyBufferedImage getThumbnail(int series)
                              throws UnsupportedFormatException,
                                     java.io.IOException

Description copied from interface: ImageProvider

Returns the image thumbnail for the specified series of the image.

Specified by:

getThumbnail in interface ImageProvider

Overrides:

getThumbnail in class PluginSequenceFileImporter

Parameters:

series - Series index for multi series image (use 0 if unsure).

Returns:

thumbnail image.

Throws:

UnsupportedFormatException

java.io.IOException

getPixels

public java.lang.Object getPixels(int series,
                         int resolution,
                         java.awt.Rectangle rectangle,
                         int z,
                         int t,
                         int c)
                           throws UnsupportedFormatException,
                                  java.io.IOException

Description copied from interface: ImageProvider

Returns the pixel data located for specified position of the image.
Data is returned in form of a single dimension array, the type of this array depends from the image data type
which can be retrieve from the metadata (see OMEXMLMetadataImpl.getPixelsType(int)

Specified by:

getPixels in interface ImageProvider

Overrides:

getPixels in class PluginSequenceFileImporter

Parameters:

series - Series index for multi series image (use 0 if unsure).

resolution - Wanted resolution level for the image (use 0 if unsure).
The retrieved image resolution is equal to image.originalResolution / (2^resolution)
So for instance level 0 is the default image resolution while level 1 is base image resolution / 2 and so on...

rectangle - The 2D region we want to retrieve (considering the original image resolution).
If set to null then the whole image is returned.

z - Z position of the image (slice) we want retrieve data from

t - T position of the image (frame) we want retrieve data from

c - C position of the image (channel) we want retrieve (-1 is not accepted here).

Returns:

native type array containing image pixel data.

Throws:

UnsupportedFormatException

java.io.IOException

See Also:

ImageProvider.isResolutionAvailable(int, int)

getImage

public IcyBufferedImage getImage(int series,
                        int resolution,
                        java.awt.Rectangle rectangle,
                        int z,
                        int t,
                        int c)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Description copied from interface: ImageProvider

Returns the image located at specified position.

Parameters:

series - Series index for multi series image (use 0 if unsure).

resolution - Wanted resolution level for the image (use 0 if unsure).
The retrieved image resolution is equal to image.originalResolution / (2^resolution)
So for instance level 0 is the default image resolution while level 1 is base image resolution / 2 and so on...

rectangle - The 2D region we want to retrieve (considering the original image resolution).
If set to null then the whole image is returned.

z - Z position of the image (slice) we want retrieve

t - T position of the image (frame) we want retrieve

c - C position of the image (channel) we want retrieve (-1 means all channel).

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

See Also:

ImageProvider.isResolutionAvailable(int, int)

getImageByTile

public IcyBufferedImage getImageByTile(int series,
                              int resolution,
                              java.awt.Rectangle region,
                              int z,
                              int t,
                              int c,
                              int tileW,
                              int tileH,
                              ProgressListener listener)
                                throws UnsupportedFormatException,
                                       java.io.IOException

Throws:

UnsupportedFormatException

java.io.IOException

getPixelsByTile

public java.lang.Object getPixelsByTile(int series,
                               int resolution,
                               java.awt.Rectangle region,
                               int z,
                               int t,
                               int c,
                               int tileW,
                               int tileH,
                               ProgressListener listener)
                                 throws UnsupportedFormatException,
                                        java.io.IOException

Description copied from class: PluginSequenceFileImporter

See AbstractImageProvider.getPixelsByTile(int, int, Rectangle, int, int, int, int, int, ProgressListener)

Overrides:

getPixelsByTile in class PluginSequenceFileImporter

Throws:

UnsupportedFormatException

java.io.IOException

getThumbnail

public static IcyBufferedImage getThumbnail(loci.formats.IFormatReader reader,
                            int z,
                            int t)
                                     throws java.lang.UnsupportedOperationException,
                                            java.lang.OutOfMemoryError,
                                            loci.formats.FormatException,
                                            java.io.IOException

Load a thumbnail version of the image located at (Z, T) position from the specified IFormatReader and returns it as an IcyBufferedImage.

Parameters:

reader - IFormatReader

z - Z position of the image to load

t - T position of the image to load

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getThumbnail

public static IcyBufferedImage getThumbnail(loci.formats.IFormatReader reader,
                            int z,
                            int t,
                            int c)
                                     throws java.lang.UnsupportedOperationException,
                                            java.lang.OutOfMemoryError,
                                            loci.formats.FormatException,
                                            java.io.IOException

Load a thumbnail version of the image located at (Z, T, C) position from the specified IFormatReader and returns it as an IcyBufferedImage.

Parameters:

reader - IFormatReader

z - Z position of the thumbnail to load

t - T position of the thumbnail to load

c - Channel index

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getThumbnailCompatible

public static IcyBufferedImage getThumbnailCompatible(loci.formats.IFormatReader reader,
                                      int z,
                                      int t)
                                               throws java.lang.UnsupportedOperationException,
                                                      java.lang.OutOfMemoryError,
                                                      loci.formats.FormatException,
                                                      java.io.IOException

Load a thumbnail version of the image located at (Z, T) position from the specified IFormatReader and returns it as an IcyBufferedImage.
Slow compatible version (load the original image and resize it)

Parameters:

reader - IFormatReader

z - Z position of the image to load

t - T position of the image to load

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getThumbnailCompatible

public static IcyBufferedImage getThumbnailCompatible(loci.formats.IFormatReader reader,
                                      int z,
                                      int t,
                                      int c)
                                               throws java.lang.UnsupportedOperationException,
                                                      java.lang.OutOfMemoryError,
                                                      loci.formats.FormatException,
                                                      java.io.IOException

Load a thumbnail version of the image located at (Z, T, C) position from the specified IFormatReader and returns it as an IcyBufferedImage.
Slow compatible version (load the original image and resize it)

Parameters:

reader - IFormatReader

z - Z position of the thumbnail to load

t - T position of the thumbnail to load

c - Channel index

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getImage

public static IcyBufferedImage getImage(loci.formats.IFormatReader reader,
                        java.awt.Rectangle rect,
                        int z,
                        int t,
                        int c,
                        int downScaleLevel)
                                 throws java.lang.UnsupportedOperationException,
                                        java.lang.OutOfMemoryError,
                                        loci.formats.FormatException,
                                        java.io.IOException

Load a single channel sub image at (Z, T, C) position from the specified IFormatReader
and returns it as an IcyBufferedImage.

Parameters:

reader - Reader used to load the image

rect - Define the image rectangular region we want to retrieve data for (considering current selected image resolution).
Set to null to retrieve the whole image.

z - Z position of the image to load

t - T position of the image to load

c - Channel index to load (-1 = all channels)

downScaleLevel - number of downscale to process (scale level = 1/2^downScaleLevel)

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getImage

public static IcyBufferedImage getImage(loci.formats.IFormatReader reader,
                        java.awt.Rectangle rect,
                        int z,
                        int t,
                        int c)
                                 throws java.lang.UnsupportedOperationException,
                                        java.lang.OutOfMemoryError,
                                        loci.formats.FormatException,
                                        java.io.IOException

Load a single channel sub image at (Z, T, C) position from the specified IFormatReader
and returns it as an IcyBufferedImage.

Parameters:

reader - Reader used to load the image

rect - Define the image rectangular region we want to retrieve data for (considering current selected image resolution).
Set to null to retrieve the whole image.

z - Z position of the image to load

t - T position of the image to load

c - Channel index to load (-1 = all channels)

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getImage

public static IcyBufferedImage getImage(loci.formats.IFormatReader reader,
                        java.awt.Rectangle rect,
                        int z,
                        int t)
                                 throws java.lang.UnsupportedOperationException,
                                        java.lang.OutOfMemoryError,
                                        loci.formats.FormatException,
                                        java.io.IOException

Load the image located at (Z, T) position from the specified IFormatReader
and return it as an IcyBufferedImage.

Parameters:

reader - IFormatReader

rect - Define the image rectangular region we want to retrieve data for (considering current selected image resolution).
Set to null to retrieve the whole image.

z - Z position of the image to load

t - T position of the image to load

Returns:

IcyBufferedImage

Throws:

java.lang.UnsupportedOperationException

java.lang.OutOfMemoryError

loci.formats.FormatException

java.io.IOException

getImageCompatible

public static IcyBufferedImage getImageCompatible(loci.formats.IFormatReader reader,
                                  int z,
                                  int t)
                                           throws loci.formats.FormatException,
                                                  java.io.IOException

Load the image located at (Z, T) position from the specified IFormatReader
and return it as an IcyBufferedImage (compatible and slower method).

Parameters:

reader - IFormatReader

z - Z position of the image to load

t - T position of the image to load

Returns:

IcyBufferedImage

Throws:

loci.formats.FormatException

java.io.IOException