org.micromanager.explore

Class ExploreAcquisition

java.lang.Object

org.micromanager.acqj.main.Acquisition

org.micromanager.acqj.main.XYTiledAcquisition

org.micromanager.explore.ExploreAcquisition

All Implemented Interfaces:

org.micromanager.acqj.api.AcquisitionAPI, org.micromanager.acqj.api.XYTiledAcquisitionAPI, org.micromanager.ndviewer.api.NDViewerAcqInterface, PycroManagerCompatibleAcq

public class ExploreAcquisition
extends org.micromanager.acqj.main.XYTiledAcquisition
implements PycroManagerCompatibleAcq, org.micromanager.ndviewer.api.NDViewerAcqInterface

A single time point acquisition that can dynamically expand in X,Y, and Z.

Author:

Henry

Field Summary

Fields inherited from class org.micromanager.acqj.main.XYTiledAcquisition

pixelStageTranslator_, zAxes_

Fields inherited from class org.micromanager.acqj.main.Acquisition

abortRequested_, core_, dataSink_, debugMode_, eventsFinished_, firstDequeue_, slm_, started_, summaryMetadata_, xyStage_, zStage_

Fields inherited from interface org.micromanager.acqj.api.AcquisitionAPI

AFTER_CAMERA_HOOK, AFTER_EXPOSURE_HOOK, AFTER_HARDWARE_HOOK, BEFORE_HARDWARE_HOOK, EVENT_GENERATION_HOOK

Constructor Summary

Constructors

Constructor and Description
ExploreAcquisition(int pixelOverlapX, int pixelOverlapY, double zStep, ChannelGroupSettings channels, org.micromanager.acqj.api.AcqEngJDataSink adapter, Consumer<String> logger)
ExploreAcquisition(int pixelOverlapX, int pixelOverlapY, double zStep, ChannelGroupSettings channels, ExploreAcqUIAndStorage adapter)

Method Summary

Modifier and Type	Method and Description
void	abort()
void	acquireTileAtCurrentLocation()
void	acquireTiles(int r1, int c1, int r2, int c2)
int	getEventPort() Get the port over which the acquisition accepts acquisition events, or -1 if this is not available
org.micromanager.ndtiffstorage.NDTiffAPI	getStorage()
LinkedBlockingQueue<HashMap<String,Object>>	getTilesWaitingToAcquireAtSlice(HashMap<String,Integer> zAxisPositions)
double	getZOrigin(String name)
double	getZStep(String name)
boolean	isFinished()
void	setZLimits(String name, double zTop, double zBottom)
Future	submitEventIterator(Iterator<org.micromanager.acqj.main.AcquisitionEvent> iter) Submit a iterator of acquisition events for execution.

Methods inherited from class org.micromanager.acqj.main.XYTiledAcquisition

getPixelStageTranslator, getZAxes, getZDeviceNames, initialize

Methods inherited from class org.micromanager.acqj.main.Acquisition

abort, addHook, addImageMetadataProcessor, addImageProcessor, addTagsToTaggedImage, addToImageMetadata, addToOutput, anythingAcquired, areEventsFinished, checkForExceptions, finish, getAfterCameraHooks, getAfterExposureHooks, getAfterHardwareHooks, getBeforeHardwareHooks, getDataSink, getEventGenerationHooks, getImageTransferQueueCount, getImageTransferQueueSize, getStartTime_ms, getSummaryMetadata, isAbortRequested, isDebugMode, isPaused, isStarted, markEventsFinished, setDebugMode, setPaused, setStartTime_ms, start, waitForCompletion

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.micromanager.ndviewer.api.NDViewerAcqInterface

isPaused, setPaused, waitForCompletion

Methods inherited from interface org.micromanager.acqj.api.AcquisitionAPI

abort, addHook, addImageMetadataProcessor, addImageProcessor, anythingAcquired, areEventsFinished, checkForExceptions, finish, getDataSink, getSummaryMetadata, isAbortRequested, isDebugMode, isPaused, isStarted, setDebugMode, setPaused, start, waitForCompletion

Constructor Detail

ExploreAcquisition

public ExploreAcquisition(int pixelOverlapX,
                          int pixelOverlapY,
                          double zStep,
                          ChannelGroupSettings channels,
                          ExploreAcqUIAndStorage adapter)
                   throws Exception

Throws:

Exception

ExploreAcquisition

public ExploreAcquisition(int pixelOverlapX,
                          int pixelOverlapY,
                          double zStep,
                          ChannelGroupSettings channels,
                          org.micromanager.acqj.api.AcqEngJDataSink adapter,
                          Consumer<String> logger)
                   throws Exception

Throws:

Exception

Method Detail

getZOrigin

public double getZOrigin(String name)

Overrides:

getZOrigin in class org.micromanager.acqj.main.XYTiledAcquisition

getZStep

public double getZStep(String name)

Overrides:

getZStep in class org.micromanager.acqj.main.XYTiledAcquisition

isFinished

public boolean isFinished()

Specified by:

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

abort

public void abort()

Specified by:

abort in interface org.micromanager.acqj.api.AcquisitionAPI

Specified by:

abort in interface org.micromanager.ndviewer.api.NDViewerAcqInterface

Overrides:

abort in class org.micromanager.acqj.main.Acquisition

submitEventIterator

public Future submitEventIterator(Iterator<org.micromanager.acqj.main.AcquisitionEvent> iter)

Submit a iterator of acquisition events for execution.

Specified by:

submitEventIterator in interface org.micromanager.acqj.api.AcquisitionAPI

Overrides:

submitEventIterator in class org.micromanager.acqj.main.Acquisition

Parameters:

iter - an iterator of acquisition events

Returns:

getTilesWaitingToAcquireAtSlice

public LinkedBlockingQueue<HashMap<String,Object>> getTilesWaitingToAcquireAtSlice(HashMap<String,Integer> zAxisPositions)

Returns:

acquireTileAtCurrentLocation

public void acquireTileAtCurrentLocation()
                                  throws Exception

Throws:

Exception

acquireTiles

public void acquireTiles(int r1,
                         int c1,
                         int r2,
                         int c2)

setZLimits

public void setZLimits(String name,
                       double zTop,
                       double zBottom)

getStorage

public org.micromanager.ndtiffstorage.NDTiffAPI getStorage()

Specified by:

getStorage in interface PycroManagerCompatibleAcq

getEventPort

public int getEventPort()

Description copied from interface: PycroManagerCompatibleAcq

Get the port over which the acquisition accepts acquisition events, or -1 if this is not available

Specified by:

getEventPort in interface PycroManagerCompatibleAcq

Returns: