org.micromanager.acqj.main

Class XYTiledAcquisition

java.lang.Object

org.micromanager.acqj.main.Acquisition

org.micromanager.acqj.main.XYTiledAcquisition

All Implemented Interfaces:

AcquisitionAPI, XYTiledAcquisitionAPI

public class XYTiledAcquisition
extends Acquisition
implements XYTiledAcquisitionAPI

Special type of acquisiton that collects tiles in a 2D grid. Used by Micro-Magellan and Pycro-Manager

Field Summary

Fields

Modifier and Type	Field and Description
protected CameraTilingStageTranslator	pixelStageTranslator_
protected HashMap<String,ZAxis>	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
XYTiledAcquisition(AcqEngJDataSink sink, Integer overlapX, Integer overlapY)
XYTiledAcquisition(AcqEngJDataSink sink, Integer overlapX, Integer overlapY, Double zStep, Consumer<mmcorej.org.json.JSONObject> summaryMDAdder)

Method Summary

Modifier and Type	Method and Description
CameraTilingStageTranslator	getPixelStageTranslator()
HashMap<String,ZAxis>	getZAxes()
List<String>	getZDeviceNames()
double	getZOrigin(String name)
double	getZStep(String name)
void	initialize() 1) Get the names of core devices to be used in acquisition.

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

abort, 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, submitEventIterator, 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.acqj.api.AcquisitionAPI

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

Field Detail

pixelStageTranslator_

protected CameraTilingStageTranslator pixelStageTranslator_

zAxes_

protected HashMap<String,ZAxis> zAxes_

Constructor Detail

XYTiledAcquisition

public XYTiledAcquisition(AcqEngJDataSink sink,
                          Integer overlapX,
                          Integer overlapY)

XYTiledAcquisition

public XYTiledAcquisition(AcqEngJDataSink sink,
                          Integer overlapX,
                          Integer overlapY,
                          Double zStep,
                          Consumer<mmcorej.org.json.JSONObject> summaryMDAdder)

Method Detail

initialize

public void initialize()

Description copied from class: Acquisition

1) Get the names of core devices to be used in acquisition. 2) Create Summary metadata. 3) Initialize data sink.

Overrides:

initialize in class Acquisition

getZAxes

public HashMap<String,ZAxis> getZAxes()

getPixelStageTranslator

public CameraTilingStageTranslator getPixelStageTranslator()

Specified by:

getPixelStageTranslator in interface XYTiledAcquisitionAPI

getZStep

public double getZStep(String name)

getZOrigin

public double getZOrigin(String name)

getZDeviceNames

public List<String> getZDeviceNames()