icy.image

Interface ImageProvider

All Known Subinterfaces:

SequenceFileImporter, SequenceIdImporter

All Known Implementing Classes:

AbstractImageProvider, LociImporterPlugin, PluginSequenceFileImporter, PluginSequenceIdImporter, SequenceFileGroupImporter

public interface ImageProvider

Image provider interface.
This interface is designed to any class capable of delivering image data at different level access.
Takes an uniquely identified resource as input and returns image data at different level access.

Example of possible class implementing this interface:

• LOCI (Bio-Formats) image reader class.
• image database interface.

Author:

Stephane

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 region, int z, int t) Returns the image located at specified position.
IcyBufferedImage	getImage(int series, int resolution, java.awt.Rectangle region, int z, int t, int c) Returns the image located at specified position.
loci.formats.ome.OMEXMLMetadataImpl	getMetaData() Deprecated. Use getOMEXMLMetaData() instead.
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 region, 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	isResolutionAvailable(int series, int resolution) Returns true if the given sub resolution is available from this series.

Method Detail

getOMEXMLMetaData

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

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.

Throws:

UnsupportedFormatException

java.io.IOException

getMetaData

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

Deprecated. Use getOMEXMLMetaData() instead.

Throws:

UnsupportedFormatException

java.io.IOException

getTileWidth

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

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.

Parameters:

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

Returns:

optimal tile width

Throws:

UnsupportedFormatException

java.io.IOException

getTileHeight

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

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.

Parameters:

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

Returns:

optimal tile height

Throws:

UnsupportedFormatException

java.io.IOException

isResolutionAvailable

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

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
...

Parameters:

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

resolution - Resolution level

Throws:

UnsupportedFormatException

java.io.IOException

getThumbnail

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

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

Parameters:

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

Returns:

thumbnail image.

Throws:

UnsupportedFormatException

java.io.IOException

getPixels

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

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)

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...

region - 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:

isResolutionAvailable(int, int)

getImage

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

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...

region - 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:

isResolutionAvailable(int, int)

getImage

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

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...

region - 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:

isResolutionAvailable(int, int)

getImage

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

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...

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:

isResolutionAvailable(int, int)

getImage

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

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...

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:

isResolutionAvailable(int, int)

getImage

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

Returns the image located at specified position.

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

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

Returns the image located at specified position.

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