org.micromanager.explore

Class ExploreAcqUIAndStorage

java.lang.Object

org.micromanager.explore.ExploreAcqUIAndStorage

All Implemented Interfaces:

org.micromanager.acqj.api.AcqEngJDataSink, org.micromanager.ndviewer.api.NDViewerDataSource, PycroManagerCompatibleUI

public class ExploreAcqUIAndStorage
extends Object
implements org.micromanager.acqj.api.AcqEngJDataSink, org.micromanager.ndviewer.api.NDViewerDataSource, PycroManagerCompatibleUI

This class links data storage, viewer, and acquisition, acting as an intermediary when neccessary to implement functionality specific to Explore acquisitions. For example, it removes the row and column axes from the data stored on disk before passing to the viewer, so that they display as one contiguous image.

Field Summary

Fields

Modifier and Type	Field and Description
protected ExploreAcquisition	acq_
protected org.micromanager.ndviewer.main.NDViewer	display_
protected ExploreControlsPanel	exploreControlsPanel_
boolean	loadedData_
protected ExploreMouseListener	mouseListener_
protected org.micromanager.ndtiffstorage.MultiresNDTiffAPI	storage_

Constructor Summary

Constructors

Constructor and Description
ExploreAcqUIAndStorage(String dir, Consumer<String> logger)
ExploreAcqUIAndStorage(String dir, String name, boolean showDisplay, ChannelGroupSettings exploreChannels)
ExploreAcqUIAndStorage(String dir, String name, boolean showDisplay, ChannelGroupSettings exploreChannels, Consumer<String> logger)

Method Summary

Modifier and Type	Method and Description
boolean	anythingAcquired()
void	close() The display calls this when its closing.
static ExploreAcqUIAndStorage	create(String dir, String name, int overlapX, int overlapY, double zStep, String channelGroup)
protected ExploreMouseListener	createMouseListener()
protected org.micromanager.ndviewer.api.OverlayerPlugin	createOverlayer()
void	finish() Called when images done arriving.
ExploreAcquisition	getAcquisition()
int[]	getBounds()
String	getDir()
String	getDiskLocation()
mmcorej.org.json.JSONObject	getDisplayJSON() Used for data loaded from disk.
int	getImageBitDepth(HashMap<String,Object> axesPositions)
mmcorej.TaggedImage	getImageForDisplay(HashMap<String,Object> axes, int resolutionindex, double xOffset, double yOffset, int imageWidth, int imageHeight)
Set<HashMap<String,Object>>	getImageKeys()
int	getMaxResolutionIndex()
String	getName()
Point2D.Double	getStageCoordinateOfViewCenter()
org.micromanager.ndtiffstorage.MultiresNDTiffAPI	getStorage()
mmcorej.org.json.JSONObject	getSummaryMD()
Set<Point>	getTileIndicesWithDataAt(String zName, int zIndex)
String	getUniqueAcqName()
org.micromanager.ndviewer.api.NDViewerAPI	getViewer() Get reference to NDViewer displaying this acquisitions data
void	increaseMaxResolutionLevel(int newMaxResolutionLevel)
void	initialize(org.micromanager.acqj.main.Acquisition acq, mmcorej.org.json.JSONObject summaryMetadata)
boolean	isFinished()
void	pan(int dx, int dy)
void	putImage(mmcorej.TaggedImage taggedImg)
void	zoom(double factor, Point mouseLocation)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

storage_

protected org.micromanager.ndtiffstorage.MultiresNDTiffAPI storage_

loadedData_

public final boolean loadedData_

display_

protected org.micromanager.ndviewer.main.NDViewer display_

acq_

protected ExploreAcquisition acq_

mouseListener_

protected ExploreMouseListener mouseListener_

exploreControlsPanel_

protected ExploreControlsPanel exploreControlsPanel_

Constructor Detail

ExploreAcqUIAndStorage

public ExploreAcqUIAndStorage(String dir,
                              String name,
                              boolean showDisplay,
                              ChannelGroupSettings exploreChannels,
                              Consumer<String> logger)

ExploreAcqUIAndStorage

public ExploreAcqUIAndStorage(String dir,
                              String name,
                              boolean showDisplay,
                              ChannelGroupSettings exploreChannels)

ExploreAcqUIAndStorage

public ExploreAcqUIAndStorage(String dir,
                              Consumer<String> logger)
                       throws IOException

Throws:

IOException

Method Detail

create

public static ExploreAcqUIAndStorage create(String dir,
                                            String name,
                                            int overlapX,
                                            int overlapY,
                                            double zStep,
                                            String channelGroup)
                                     throws Exception

Throws:

Exception

getViewer

public org.micromanager.ndviewer.api.NDViewerAPI getViewer()

Description copied from interface: PycroManagerCompatibleUI

Get reference to NDViewer displaying this acquisitions data

Specified by:

getViewer in interface PycroManagerCompatibleUI

getAcquisition

public ExploreAcquisition getAcquisition()

initialize

public void initialize(org.micromanager.acqj.main.Acquisition acq,
                       mmcorej.org.json.JSONObject summaryMetadata)

Specified by:

initialize in interface org.micromanager.acqj.api.AcqEngJDataSink

getStorage

public org.micromanager.ndtiffstorage.MultiresNDTiffAPI getStorage()

pan

public void pan(int dx,
                int dy)

zoom

public void zoom(double factor,
                 Point mouseLocation)

createOverlayer

protected org.micromanager.ndviewer.api.OverlayerPlugin createOverlayer()

createMouseListener

protected ExploreMouseListener createMouseListener()

putImage

public void putImage(mmcorej.TaggedImage taggedImg)

Specified by:

putImage in interface org.micromanager.acqj.api.AcqEngJDataSink

finish

public void finish()

Called when images done arriving.

Specified by:

finish in interface org.micromanager.acqj.api.AcqEngJDataSink

isFinished

public boolean isFinished()

Specified by:

isFinished in interface org.micromanager.acqj.api.AcqEngJDataSink

Specified by:

isFinished in interface org.micromanager.ndviewer.api.NDViewerDataSource

getDiskLocation

public String getDiskLocation()

Specified by:

getDiskLocation in interface org.micromanager.ndviewer.api.NDViewerDataSource

getDisplayJSON

public mmcorej.org.json.JSONObject getDisplayJSON()

Used for data loaded from disk.

Returns:

close

public void close()

The display calls this when its closing.

Specified by:

close in interface org.micromanager.ndviewer.api.NDViewerDataSource

getImageBitDepth

public int getImageBitDepth(HashMap<String,Object> axesPositions)

Specified by:

getImageBitDepth in interface org.micromanager.ndviewer.api.NDViewerDataSource

getSummaryMD

public mmcorej.org.json.JSONObject getSummaryMD()

getBounds

public int[] getBounds()

Specified by:

getBounds in interface org.micromanager.ndviewer.api.NDViewerDataSource

getImageForDisplay

public mmcorej.TaggedImage getImageForDisplay(HashMap<String,Object> axes,
                                              int resolutionindex,
                                              double xOffset,
                                              double yOffset,
                                              int imageWidth,
                                              int imageHeight)

Specified by:

getImageForDisplay in interface org.micromanager.ndviewer.api.NDViewerDataSource

getImageKeys

public Set<HashMap<String,Object>> getImageKeys()

Specified by:

getImageKeys in interface org.micromanager.ndviewer.api.NDViewerDataSource

anythingAcquired

public boolean anythingAcquired()

Specified by:

anythingAcquired in interface org.micromanager.acqj.api.AcqEngJDataSink

getName

public String getName()

getDir

public String getDir()

getUniqueAcqName

public String getUniqueAcqName()

getMaxResolutionIndex

public int getMaxResolutionIndex()

Specified by:

getMaxResolutionIndex in interface org.micromanager.ndviewer.api.NDViewerDataSource

increaseMaxResolutionLevel

public void increaseMaxResolutionLevel(int newMaxResolutionLevel)

Specified by:

increaseMaxResolutionLevel in interface org.micromanager.ndviewer.api.NDViewerDataSource

getTileIndicesWithDataAt

public Set<Point> getTileIndicesWithDataAt(String zName,
                                           int zIndex)

getStageCoordinateOfViewCenter

public Point2D.Double getStageCoordinateOfViewCenter()