org.micromanager.data

Interface Storage

All Known Subinterfaces:

RewritableStorage

public interface Storage

Storages are responsible for providing image data to Datastores when requested. Different Storages may have different mechanisms -- for example, by storing images in a file, or in RAM. In practice you are unlikely to need to implement your own Storage class, and most of its methods are simply "backings" for similar methods in Datastore.

Note that the Storage interface does not expose any "setter" methods (e.g. putImage(), setSummaryMetadata(), etc.). It is expected that any read/write Storage listen for the relevant events published by the Datastore instead.

Method Summary

Modifier and Type	Method and Description
void	close() Release any resources used by the Storage, for example open file descriptors.
void	freeze() Freeze the Storage, preventing any changes to its contents.
Image	getAnyImage() Return any Image, or null if there are no images.
java.util.List<java.lang.String>	getAxes() Return a List of all axis names for Images we know about.
Image	getImage(Coords coords) Retrieve the Image located at the specified coordinates.
java.util.List<Image>	getImagesIgnoringAxes(Coords coords, java.lang.String... ignoreTheseAxes) Retrieve a list of images with Coords identical to the given Coords instance, except for the axes listed in the exception list.
java.util.List<Image>	getImagesMatching(Coords coords) Retrieve a list of all images whose Coords match the given incomplete Coords instance.
int	getMaxIndex(java.lang.String axis) Return the largest stored position along the specified axis.
Coords	getMaxIndices() Return a Coords that provides the maximum index along all available axes.
int	getNumImages() Return the number of images in this dataset.
SummaryMetadata	getSummaryMetadata() Retrieve the SummaryMetadata associated with this dataset.
java.lang.Iterable<Coords>	getUnorderedImageCoords() Return an Iterable that provides access to all image coordinates in the Storage, in arbitrary order.
boolean	hasImage(Coords coords) Returns whether or not an image exists at the specified coordinates.
void	putImage(Image image) Insert an Image into the Storage, so that it may be returned by later getImage() calls.

Method Detail

freeze

void freeze()
     throws java.io.IOException

Freeze the Storage, preventing any changes to its contents.

Throws:

java.io.IOException

putImage

void putImage(Image image)
       throws java.io.IOException

Insert an Image into the Storage, so that it may be returned by later getImage() calls.

Parameters:

image - Image to be inserted.

Throws:

java.io.IOException

getImage

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

Retrieve the Image located at the specified coordinates.

Parameters:

coords - Coordinates specifying which image to retrieve

Returns:

desired Image

Throws:

java.io.IOException

hasImage

boolean hasImage(Coords coords)

Returns whether or not an image exists at the specified coordinates.

Parameters:

coords - Coordinates to test

Returns:

True if an image exists at the coordinates, false otherwise.

getAnyImage

Image getAnyImage()

Return any Image, or null if there are no images. Only really useful if you need a representative image to work with. No guarantees are made about which image will be provided.

Returns:

any Image or null if there are no images

getUnorderedImageCoords

java.lang.Iterable<Coords> getUnorderedImageCoords()

Return an Iterable that provides access to all image coordinates in the Storage, in arbitrary order.

Returns:

Iterable that provides access to all image coordinates in the Storage, in arbitrary order

getImagesMatching

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

Retrieve a list of all images whose Coords match the given incomplete Coords instance. For example, providing a Coords of <"z" = 9> would return all Images whose position along the "z" axis is 9 (note that this means that Images with no defined position along that axis will not be returned). The result may be empty.

Parameters:

coords - Coordinates specifying images to match

Returns:

List with matching Images

Throws:

java.io.IOException

getImagesIgnoringAxes

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

Retrieve a list of images with Coords identical to the given Coords instance, except for the axes listed in the exception list. For instance, given Coords t=1,z=3> and axes "c", the following Coords would match: <t=1, z=3>, <t=1, z=3, c=1>, <t=1, z=3, c=2>.

Parameters:

coords - coord looking for matching images

ignoreTheseAxes - Axes to be ignored in the images collection when looking for matches

Returns:

matching images

Throws:

java.io.IOException - happens with disk based storage

getMaxIndex

int getMaxIndex(java.lang.String axis)

Return the largest stored position along the specified axis. Will be -1 if no images have a position along that axis (or the axis is not present in the Storage)

Parameters:

axis - axis of interest

Returns:

Largest stored position along the specified axis or -1 when no images are found on the given axis

getAxes

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

Return a List of all axis names for Images we know about.

Returns:

List of all axis names for Images we know about

getMaxIndices

Coords getMaxIndices()

Return a Coords that provides the maximum index along all available axes.

Returns:

Coords that provides the maximum index along all available axes

getSummaryMetadata

SummaryMetadata getSummaryMetadata()

Retrieve the SummaryMetadata associated with this dataset.

Returns:

SummaryMetadata associated with this dataset

getNumImages

int getNumImages()

Return the number of images in this dataset.

Returns:

number of images in this dataset

close

void close()
    throws java.io.IOException

Release any resources used by the Storage, for example open file descriptors.

Throws:

java.io.IOException