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

Field Summary

Fields inherited from interface icy.sequence.SequenceIdImporter

FLAG_METADATA_ALL, FLAG_METADATA_MASK, FLAG_METADATA_MINIMUM

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 series, int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImage(int series, int resolution, int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImage(int series, int resolution, int z, int t, int c) Returns the image located at specified position.
IcyBufferedImage	getImage(int series, int resolution, java.awt.Rectangle rectangle, int z, int t) Returns the image located at specified position.
ome.xml.meta.OMEXMLMetadata	getOMEXMLMetaData() Returns the image metadata in OME format (metadata provides many informations about the image).
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)
int	getResolutionFactor(int series, int wantedSize) See AbstractImageProvider.getResolutionFactor(int, int)
IcyBufferedImage	getThumbnail(int series) Returns the image thumbnail for the specified series of the image.
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	isResolutionAvailable(int series, int resolution) Returns true if the given sub resolution is available from this series.

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

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

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

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

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

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

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

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

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)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Description copied from interface: ImageProvider

Returns the image located at specified position.

Specified by:

getImage in interface ImageProvider

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

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

See Also:

ImageProvider.isResolutionAvailable(int, int)

getImage

public IcyBufferedImage getImage(int series,
                        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:

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...

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)

getImage

public IcyBufferedImage getImage(int series,
                        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:

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...

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

See Also:

ImageProvider.isResolutionAvailable(int, int)

getImage

public IcyBufferedImage getImage(int series,
                        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:

series - Series index for multi series 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

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

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

Throws:

UnsupportedFormatException

java.io.IOException

getResolutionFactor

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

See AbstractImageProvider.getResolutionFactor(int, int)

Throws:

UnsupportedFormatException

java.io.IOException