icy.file

Class SequenceFileGroupImporter

java.lang.Object

icy.image.AbstractImageProvider

icy.file.SequenceFileGroupImporter

All Implemented Interfaces:

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

public class SequenceFileGroupImporter
extends AbstractImageProvider
implements SequenceFileImporter

Special importer able to group a list of path (SequenceFileSticher.SequenceFileGroup) to build a single Sequence out of it.
Note that this importer is limited to single series group, we don't allow group mixing several series.

Field Summary

Fields inherited from class icy.image.AbstractImageProvider

DEFAULT_THUMBNAIL_SIZE

Fields inherited from interface icy.sequence.SequenceIdImporter

FLAG_METADATA_ALL, FLAG_METADATA_MASK, FLAG_METADATA_MINIMUM

Constructor Summary

Constructors

Constructor and Description
SequenceFileGroupImporter()

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.
void	closeInternalsImporters() Close all opened internals importer without closing the Group Importer itself (importer remaing active)
java.util.List<javax.swing.filechooser.FileFilter>	getFileFilters() Return the supported FileFilter for this importer.
IcyBufferedImage	getImage(int series, int resolution, java.awt.Rectangle rectangle, int z, int t, int c) Returns the image located at specified position.
SequenceFileImporter	getImporter(java.lang.String path) Return an opened importer for given path.
loci.formats.ome.OMEXMLMetadataImpl	getMetaData()
ome.xml.meta.OMEXMLMetadata	getOMEXMLMetaData() Returns the image metadata in OME format (metadata provides many informations about the image).
java.lang.String	getOpened() Return the current / last loaded image without the image group
SequenceFileSticher.SequenceFileGroup	getOpenedGroup()
java.lang.String	getPath(int z, int t, int c)
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.
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	isOpen()
boolean	isStitchedImage()
void	open(java.util.Collection<java.lang.String> ids, int flags) Open a list of ids
void	open(SequenceFileSticher.SequenceFileGroup group, int flags) Open a SequenceFileGroup
boolean	open(java.lang.String path, int flags) Deprecated. Better to use open(Collection, int) or #open(SequenceFileGroup, int) for this importer
void	releaseImporter(java.lang.String path, SequenceFileImporter importer) Release the importer obtained through getImporter(String) to the importer pool.

Methods inherited from class icy.image.AbstractImageProvider

getImage, getImage, getImage, getImage, getImage, getPixelsByTile, getResolutionFactor, getResolutionFactor, isResolutionAvailable

Methods inherited from class java.lang.Object

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

Methods inherited from interface icy.image.ImageProvider

getImage, getImage, getImage, getImage, getImage, isResolutionAvailable

Constructor Detail

SequenceFileGroupImporter

public SequenceFileGroupImporter()

Method Detail

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

Specified by:

acceptFile in interface SequenceFileImporter

getFileFilters

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

Description copied from interface: SequenceFileImporter

Return the supported FileFilter for this importer.

Specified by:

getFileFilters in interface SequenceFileImporter

isOpen

public boolean isOpen()

Returns:

true if a opened is currently opened

getOpened

public java.lang.String getOpened()

Return the current / last loaded image without the image group

Specified by:

getOpened in interface SequenceFileImporter

Specified by:

getOpened in interface SequenceIdImporter

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()

getOpenedGroup

public SequenceFileSticher.SequenceFileGroup getOpenedGroup()

Returns:

current opened group

open

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

Deprecated. Better to use open(Collection, int) or #open(SequenceFileGroup, int) for this importer

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.

Specified by:

open in interface SequenceFileImporter

Specified by:

open in interface SequenceIdImporter

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

open

public void open(java.util.Collection<java.lang.String> ids,
        int flags)

Open a list of ids

Parameters:

ids -

open

public void open(SequenceFileSticher.SequenceFileGroup group,
        int flags)

Open a SequenceFileGroup

getImporter

public SequenceFileImporter getImporter(java.lang.String path)
                                 throws java.io.IOException,
                                        UnsupportedFormatException

Return an opened importer for given path.
Note that you should call releaseImporter(String, SequenceFileImporter) when you're done with it.

Throws:

java.io.IOException

UnsupportedFormatException

See Also:

releaseImporter(String, SequenceFileImporter)

releaseImporter

public void releaseImporter(java.lang.String path,
                   SequenceFileImporter importer)

Release the importer obtained through getImporter(String) to the importer pool.

See Also:

getImporter(String)

isStitchedImage

public boolean isStitchedImage()

Returns:

true if this image group requires several images to build a full XY plan image.

getPath

public java.lang.String getPath(int z,
                       int t,
                       int c)

Returns:

file path for the given [z,t,c] position

closeInternalsImporters

public void closeInternalsImporters()
                             throws java.io.IOException

Close all opened internals importer without closing the Group Importer itself (importer remaing active)

Throws:

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.

Specified by:

close in interface SequenceIdImporter

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

getMetaData

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

Specified by:

getMetaData in interface ImageProvider

Throws:

UnsupportedFormatException

java.io.IOException

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 AbstractImageProvider

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 AbstractImageProvider

Parameters:

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

Returns:

optimal tile height

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 AbstractImageProvider

Parameters:

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

Returns:

optimal tile width

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 AbstractImageProvider

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.

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

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)

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 AbstractImageProvider

Parameters:

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

Returns:

thumbnail image.

Throws:

UnsupportedFormatException

java.io.IOException