icy.plugin.abstract_

Class PluginSequenceFileImporter

java.lang.Object

icy.plugin.abstract_.Plugin

icy.plugin.abstract_.PluginSequenceFileImporter

All Implemented Interfaces:

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

Direct Known Subclasses:

LociImporterPlugin

public abstract class PluginSequenceFileImporter
extends Plugin
implements SequenceFileImporter, PluginNoEDTConstructor

Plugin specialized for Sequence file import operation (see the SequenceFileImporter interface)

Author:

Stephane

See Also:

PluginImporter, PluginFileImporter, PluginSequenceIdImporter, PluginSequenceImporter

Constructor Summary

Constructors

Constructor and Description
PluginSequenceFileImporter()

Method Summary

Methods

Modifier and Type	Method and Description
IcyBufferedImage	getImage(int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImage(int serie, int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImage(int serie, int resolution, int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImage(int serie, int resolution, int z, int t, int c) Returns the image located at specified position.
IcyBufferedImage	getImage(int serie, int resolution, java.awt.Rectangle rectangle, int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImageByTile(int serie, int resolution, int z, int t, int c, int tileW, int tileH, ProgressListener listener) See AbstractImageProvider.getImageByTile(int, int, int, int, int, int, int, ProgressListener)
java.lang.Object	getPixels(int serie, int resolution, java.awt.Rectangle rectangle, int z, int t, int c) Returns the pixel data located for specified position of the image.
int	getResolutionFactor(int serie, int wantedSize) See AbstractImageProvider.getResolutionFactor(int, int)
IcyBufferedImage	getThumbnail(int serie) Returns the image thumbnail for the specified serie of the image.
int	getTileHeight(int serie) Returns the (optimal) tile height for the specified serie of the image.
static java.util.List<java.awt.Rectangle>	getTileList(int sizeX, int sizeY, int tileW, int tileH) See AbstractImageProvider.getTileList(int, int, int, int)
int	getTileWidth(int serie) Returns the (optimal) tile width for the specified serie of the image.

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, removeSequence, report, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface icy.file.SequenceFileImporter

acceptFile, getFileFilters, getOpened, open

Methods inherited from interface icy.sequence.SequenceIdImporter

close

Methods inherited from interface icy.image.ImageProvider

getImage, getMetaData

Constructor Detail

PluginSequenceFileImporter

public PluginSequenceFileImporter()

Method Detail

getTileWidth

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

Description copied from interface: ImageProvider

Returns the (optimal) tile width for the specified serie 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

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

Returns:

optimal tile width

Throws:

UnsupportedFormatException

java.io.IOException

getTileHeight

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

Description copied from interface: ImageProvider

Returns the (optimal) tile height for the specified serie 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

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

Returns:

optimal tile height

Throws:

UnsupportedFormatException

java.io.IOException

getThumbnail

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

Description copied from interface: ImageProvider

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

Specified by:

getThumbnail in interface ImageProvider

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

Returns:

thumbnail image.

Throws:

UnsupportedFormatException

java.io.IOException

getPixels

public java.lang.Object getPixels(int serie,
                         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

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

resolution - Wanted resolution level for the image (use 0 if unsure).
The retrieved image resolution is equal to image.resolution / (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.
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

getImage

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

Description copied from interface: ImageProvider

Returns the image located at specified position.

Specified by:

getImage in interface ImageProvider

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

resolution - Wanted resolution level for the image (use 0 if unsure).
The retrieved image resolution is equal to image.resolution / (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.
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

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

getImage

public IcyBufferedImage getImage(int serie,
                        int resolution,
                        int z,
                        int t,
                        int c)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Description copied from interface: ImageProvider

Returns the image located at specified position.

Specified by:

getImage in interface ImageProvider

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

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

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

getImage

public IcyBufferedImage getImage(int serie,
                        int resolution,
                        int z,
                        int t)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Description copied from interface: ImageProvider

Returns the image located at specified position.

Specified by:

getImage in interface ImageProvider

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

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

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

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

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

getImage

public IcyBufferedImage getImage(int serie,
                        int z,
                        int t)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Description copied from interface: ImageProvider

Returns the image located at specified position.

Specified by:

getImage in interface ImageProvider

Parameters:

serie - Serie index for multi serie image (use 0 if unsure).

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

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

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

getImage

public IcyBufferedImage getImage(int z,
                        int t)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Description copied from interface: ImageProvider

Returns the image located at specified position.

Specified by:

getImage in interface ImageProvider

Parameters:

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

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

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

getImageByTile

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

See AbstractImageProvider.getImageByTile(int, int, int, int, int, int, int, ProgressListener)

Throws:

UnsupportedFormatException

java.io.IOException

getTileList

public static java.util.List<java.awt.Rectangle> getTileList(int sizeX,
                                             int sizeY,
                                             int tileW,
                                             int tileH)

See AbstractImageProvider.getTileList(int, int, int, int)

getResolutionFactor

public int getResolutionFactor(int serie,
                      int wantedSize)
                        throws UnsupportedFormatException,
                               java.io.IOException

See AbstractImageProvider.getResolutionFactor(int, int)

Throws:

UnsupportedFormatException

java.io.IOException