org.micromanager.data

Interface DataProvider

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Subinterfaces:

Datastore, RewritableDatastore

public interface DataProvider
extends java.io.Closeable

Read-only access to multi-dimensional image data.

Method Summary

Modifier and Type	Method and Description
void	close()
Image	getAnyImage() Retrieve any image from this DataProvider.
java.util.List<java.lang.String>	getAxes() Retrieve the axis currently in use by this DataProvider.
int	getAxisLength(java.lang.String axis) Deprecated. Use getNextIndex(String) instead.
Image	getImage(Coords coords) Returns the image at the given position.
java.util.List<Image>	getImagesIgnoringAxes(Coords coords, java.lang.String... ignoreTheseAxes) Returns a list of image in the DataProvider's collection that have identical coords after removing the given axes from both source and target.
java.util.List<Image>	getImagesMatching(Coords coords) Deprecated. - instead use getImagesIgnoringAxes
Coords	getMaxIndices() Deprecated. Use getNextIndex(String axis) instead
java.lang.String	getName() A dataProvider has a name (not guaranteed to be unique).
int	getNextIndex(java.lang.String axis) Returns the highest index along the given axis plus 1.
int	getNumImages() Provides total number of images that can be accessed through this DataProvider.
SummaryMetadata	getSummaryMetadata() Returns Summary Metadata.
java.lang.Iterable<Coords>	getUnorderedImageCoords()
boolean	hasImage(Coords coords)
boolean	isFrozen() A dataProvider is frozen when no more images can be added.
void	registerForEvents(java.lang.Object obj)
void	unregisterForEvents(java.lang.Object obj)

Method Detail

close

void close()
    throws java.io.IOException

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

Throws:

java.io.IOException

getAnyImage

Image getAnyImage()
           throws java.io.IOException

Retrieve any image from this DataProvider.

Returns:

a random image from the collection kept by the DataProvider

Throws:

java.io.IOException - when error occurs loading the data from storage

getAxes

java.util.List<java.lang.String> getAxes()

Retrieve the axis currently in use by this DataProvider.

Returns:

List with Axis being used in no particular order

getAxisLength

@Deprecated
int getAxisLength(java.lang.String axis)

Deprecated. Use getNextIndex(String) instead.

Returns the highest index plus 1 along the given axis. If the axis is not (yet) represented in the data set, it will return 0.

If the axis is present in the data set, but no Coords with that axes are found (Coords for an axis can not be zero), it will return 1.

Missing images for any given axis are ignored, e.g. if the DataProvider has images 0, 1, 3, 4 for a given axis, it will return 5. Do not expect all images along a given axis to be present in the DataProvider.

Parameters:

axis - Axis for which the next index is requested.

Returns:

Next Index for the given axis.

getNextIndex

int getNextIndex(java.lang.String axis)

Returns the highest index along the given axis plus 1. If the axis is not (yet) represented in the data set, it will return 0.

If the axis is present in the data set, but no Coords with that axes are found (Coords for an axis can not be zero), it will return 1.

Missing images for any given axis are ignored, e.g. if the DataProvider has images 0, 1, 3, 4 for a given axis, it will return 5. Do not expect all images along a given axis to be present in the DataProvider.

Parameters:

axis - Axis for which the next index is requested.

Returns:

Next Index for the given axis.

getImage

Image getImage(Coords coords)
        throws java.io.IOException

Returns the image at the given position.

Parameters:

coords - Coords specifying the multi-dimensional index to the image

Returns:

desired Image

Throws:

java.io.IOException - when error occurs loading the data from storage

getImagesMatching

@Deprecated
java.util.List<Image> getImagesMatching(Coords coords)
                                             throws java.io.IOException

Deprecated. - instead use getImagesIgnoringAxes

Returns a list of images that have coords matching the given one.

Parameters:

coords - specification of multi-dimensional index that needs to be present in the Coords of the images that will be returned

Returns:

Matching Images

Throws:

java.io.IOException - when error occurs loading the data from storage

getImagesIgnoringAxes

java.util.List<Image> getImagesIgnoringAxes(Coords coords,
                                            java.lang.String... ignoreTheseAxes)
                                     throws java.io.IOException

Returns a list of image in the DataProvider's collection that have identical coords after removing the given axes from both source and target.

Parameters:

coords - Coords to look for in the provider's collection

ignoreTheseAxes - Axes that will be removed from copy of Coords in the collection before checking for identity

Returns:

images in the dataProvider's collection with the desired Coords

Throws:

java.io.IOException - when error occurs loading the data from storage

isFrozen

boolean isFrozen()

A dataProvider is frozen when no more images can be added.

Returns:

True if no more images can be added

getMaxIndices

@Deprecated
Coords getMaxIndices()

Deprecated. Use getNextIndex(String axis) instead

Coords with highest possible index along each axis.

Returns:

Coords with highest possible index along each axis

getNumImages

int getNumImages()

Provides total number of images that can be accessed through this DataProvider. TODO: does this include blank images/empty Coords?

Returns:

total number of images that can be accessed through this DataProvider

getSummaryMetadata

SummaryMetadata getSummaryMetadata()

Returns Summary Metadata.

Returns:

summarymetadata of this dataProvides

getUnorderedImageCoords

java.lang.Iterable<Coords> getUnorderedImageCoords()

hasImage

boolean hasImage(Coords coords)

getName

java.lang.String getName()

A dataProvider has a name (not guaranteed to be unique).

Returns:

name of this dataProvider

registerForEvents

void registerForEvents(java.lang.Object obj)

unregisterForEvents

void unregisterForEvents(java.lang.Object obj)