org.micromanager.data

Interface Datastore

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable, DataProvider

All Known Subinterfaces:

RewritableDatastore

public interface Datastore
extends DataProvider

Read/write access to multi-dimensional image data. Important: Custom Datastore implementations are not supported (consider creating a custom storage instead).

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Datastore.SaveMode The file format to save to.

Method Summary

Modifier and Type	Method and Description
void	freeze() Freeze this Datastore so it cannot be further modified.
Annotation	getAnnotation(java.lang.String tag) Get an annotation, creating it if it doesn't exist
java.lang.String	getSavePath() Get the intended or actual path where the data will be stored.
boolean	hasAnnotation(java.lang.String tag) Return whether an annotation with the given tag exists.
void	putImage(Image image) Insert an image into the Datastore.
boolean	save(java.awt.Component parent) Deprecated. Use save(Component, boolean) instead
java.lang.String	save(java.awt.Component parent, boolean blocking) Saves the datastore to an interactively determined path.
void	save(Datastore.SaveMode mode, java.lang.String path) Saves the datastore to the given path using the given format (SaveMode) Will save synchronously (i.e.
void	save(Datastore.SaveMode mode, java.lang.String path, boolean blocking) Saves the datastore to the given path using the given format (SaveMode)
void	setName(java.lang.String name) Sets the name of the Datastore.
void	setSavePath(java.lang.String path) Set the intended path where the data will be stored.
void	setStorage(Storage storage) Sets the data storage implementation for this Datastore.
void	setSummaryMetadata(SummaryMetadata metadata) Set the SummaryMetadata.

Methods inherited from interface org.micromanager.data.DataProvider

close, getAnyImage, getAxes, getAxisLength, getImage, getImagesIgnoringAxes, getImagesMatching, getMaxIndices, getName, getNextIndex, getNumImages, getSummaryMetadata, getUnorderedImageCoords, hasImage, isFrozen, registerForEvents, unregisterForEvents

Method Detail

setStorage

void setStorage(Storage storage)

Sets the data storage implementation for this Datastore.

Parameters:

storage - data storage to be used henceforth

putImage

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

Insert an image into the Datastore. Posts a NewImageEvent to the event bus.

Parameters:

image - Micro-Manager Image object

Throws:

java.io.IOException - if an IO error occurs

DatastoreFrozenException - if the freeze() method has been called.

DatastoreRewriteException - if an Image with the same coordinates already exists in the Datastore.

java.lang.IllegalArgumentException - if the image's axes do not match the axes of images previously added to the Datastore. All images in a Datastore are required to have the same set of axes in their Coords objects.

setSummaryMetadata

void setSummaryMetadata(SummaryMetadata metadata)
                 throws java.io.IOException

Set the SummaryMetadata. Posts a NewSummaryMetadataEvent to the event bus. This method may only be called once for a given Datastore, and must be called before adding any images.

Parameters:

metadata - Object representing the summary metadata

Throws:

java.io.IOException - if an IO error occurs

DatastoreFrozenException - if the freeze() method has been called.

DatastoreRewriteException - if the Datastore already has SummaryMetadata or already has images.

hasAnnotation

boolean hasAnnotation(java.lang.String tag)
               throws java.io.IOException

Return whether an annotation with the given tag exists.

Parameters:

tag - the tag for the annotation

Returns:

true if the annotation exists; false otherwise

Throws:

java.io.IOException - if an IO error occurs

getAnnotation

Annotation getAnnotation(java.lang.String tag)
                  throws java.io.IOException

Get an annotation, creating it if it doesn't exist

Parameters:

tag - tag for the annotation

Returns:

Annotation for th given tag

Throws:

java.io.IOException - if an IO error occurs

freeze

void freeze()
     throws java.io.IOException

Freeze this Datastore so it cannot be further modified.

Throws:

java.io.IOException - if an IO error occurs

setSavePath

void setSavePath(java.lang.String path)

Set the intended path where the data will be stored.

In the current Micro-Manager file format, this path is used as the enclosing directory.

Parameters:

path - the file path (without extension)

Throws:

java.lang.UnsupportedOperationException - if this is an on-disk datastore

getSavePath

java.lang.String getSavePath()

Get the intended or actual path where the data will be stored.

If this is an in-memory datastore, returns whatever was set by setSavePath(java.lang.String). If this is an on-disk datastore, returns the actual path.

Returns:

the file path where the data is (to be) saved

save

@Deprecated
boolean save(java.awt.Component parent)
                  throws java.io.IOException

Deprecated. Use save(Component, boolean) instead

Parameters:

parent - Window on top of which to display the dialog prompt; may be null.

Returns:

true if data was saved; false if user canceled

Throws:

java.io.IOException - if an IO error occurs

save

java.lang.String save(java.awt.Component parent,
                      boolean blocking)
               throws java.io.IOException

Saves the datastore to an interactively determined path. Opens a file dialog prompting user for a storage location

Parameters:

parent - Window on top of which to display a dialog prompting the user for a location to save. After displaying

blocking - if true will return after saving, otherwise will return quickly and continue saving on another thread

Returns:

Path chosen by user to save the data, null if dialog was canceled

Throws:

java.io.IOException - if an IO error occurs

save

void save(Datastore.SaveMode mode,
          java.lang.String path)
   throws java.io.IOException

Saves the datastore to the given path using the given format (SaveMode) Will save synchronously (i.e. this function will block)

Parameters:

mode - File format to save to

path - File path used to save the data

Throws:

java.io.IOException - if an IO error occurs

save

void save(Datastore.SaveMode mode,
          java.lang.String path,
          boolean blocking)
   throws java.io.IOException

Saves the datastore to the given path using the given format (SaveMode)

Parameters:

mode - File format to save to

path - File path used to save the data

blocking - when true, will block while saving data, otherwise will return immediately

Throws:

java.io.IOException - if an IO error occurs

setName

void setName(java.lang.String name)

Sets the name of the Datastore. Posts a DatastoreNewNameEvent

Parameters:

name - new name of the Datastore