icy.image

Interface ImageProvider

All Known Subinterfaces:

SequenceFileImporter, SequenceIdImporter

All Known Implementing Classes:

AbstractImageProvider, LociImporterPlugin, PluginSequenceFileImporter, PluginSequenceIdImporter

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 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	getImage(int serie, int resolution, java.awt.Rectangle rectangle, int z, int t, int c) Returns the image located at specified position.
loci.formats.ome.OMEXMLMetadataImpl	getMetaData() Returns the image metadata in OME format.
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.
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.
int	getTileWidth(int serie) Returns the (optimal) tile width for the specified serie of the image.

Method Detail

getMetaData

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

Returns the image metadata in OME format.
Metadata give many informations about the image.

Number of serie (mandatory field) :
OMEXMLMetadataImpl.getImageCount()
Dimension (mandatory fields) :
OMEXMLMetadataImpl.getPixelsSizeX(int)
OMEXMLMetadataImpl.getPixelsSizeY(int)
OMEXMLMetadataImpl.getPixelsSizeZ(int)
OMEXMLMetadataImpl.getPixelsSizeT(int)
OMEXMLMetadataImpl.getPixelsSizeC(int)
OMEXMLMetadataImpl.getPixelsSizeX(int)
Internal data type (mandatory field) :
OMEXMLMetadataImpl.getPixelsType(int)

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

Throws:

UnsupportedFormatException

java.io.IOException

getTileWidth

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

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.

Parameters:

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

Returns:

optimal tile width

Throws:

UnsupportedFormatException

java.io.IOException

getTileHeight

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

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.

Parameters:

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

Returns:

optimal tile height

Throws:

UnsupportedFormatException

java.io.IOException

getThumbnail

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

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

Parameters:

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

Returns:

thumbnail image.

Throws:

UnsupportedFormatException

java.io.IOException

getPixels

java.lang.Object getPixels(int serie,
                         int resolution,
                         java.awt.Rectangle rectangle,
                         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:

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

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

Returns the image located at specified position.

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

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

Returns:

image

Throws:

UnsupportedFormatException

java.io.IOException

getImage

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

Returns the image located at specified position.

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

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

Returns the image located at specified position.

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

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

Returns the image located at specified position.

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

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

Returns the image located at specified position.

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

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