A B C D E F G H I L M N O P R S T U W X Y Z

A

abort() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Cancel any pending events and shutdown

abort(Exception) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Abort, and provide an exception that is the reason for the abort.

abort(Exception) - Method in class org.micromanager.acqj.main.Acquisition

Auto abort caused by an exception during acquisition

abort() - Method in class org.micromanager.acqj.main.Acquisition

abortRequested_ - Variable in class org.micromanager.acqj.main.Acquisition

ACQ_STARTED - Static variable in class org.micromanager.acqj.main.AcqNotification.Acquisition

AcqEngJDataSink - Interface in org.micromanager.acqj.api

Where the acquisition sends data to.

AcqEngMetadata - Class in org.micromanager.acqj.main

Convenience/standardization for Acq Engine metadata

AcqEngMetadata() - Constructor for class org.micromanager.acqj.main.AcqEngMetadata

AcqEventModules - Class in org.micromanager.acqj.util

A utility class with multiple "modules" functions for creating common acquisition functions that can be combined to encode complex behaviors

AcqEventModules() - Constructor for class org.micromanager.acqj.util.AcqEventModules

AcqNotification - Class in org.micromanager.acqj.main

AcqNotification(Class, String, String) - Constructor for class org.micromanager.acqj.main.AcqNotification

AcqNotification.Acquisition - Class in org.micromanager.acqj.main

AcqNotification.Camera - Class in org.micromanager.acqj.main

AcqNotification.Hardware - Class in org.micromanager.acqj.main

AcqNotification.Image - Class in org.micromanager.acqj.main

AcqNotificationListener - Interface in org.micromanager.acqj.api

Acquisition() - Constructor for class org.micromanager.acqj.main.AcqNotification.Acquisition

Acquisition - Class in org.micromanager.acqj.main

This is the main class for using AcqEngJ.

Acquisition(AcqEngJDataSink) - Constructor for class org.micromanager.acqj.main.Acquisition

Primary constructor for creating Acquisitons.

Acquisition(AcqEngJDataSink, Consumer<JSONObject>) - Constructor for class org.micromanager.acqj.main.Acquisition

Version of the constructor that accepts a function that can modify SummaryMetadata as needed

Acquisition(AcqEngJDataSink, boolean) - Constructor for class org.micromanager.acqj.main.Acquisition

Version in which initialization can be handled by a subclass

acquisition_ - Variable in class org.micromanager.acqj.main.AcquisitionEvent

AcquisitionAPI - Interface in org.micromanager.acqj.api

General interface for acquisitions

AcquisitionEvent - Class in org.micromanager.acqj.main

Information about the acquisition of a single image or a sequence of image.

AcquisitionEvent(AcquisitionAPI) - Constructor for class org.micromanager.acqj.main.AcquisitionEvent

AcquisitionEvent(List<AcquisitionEvent>) - Constructor for class org.micromanager.acqj.main.AcquisitionEvent

Constructor used for running a list of events in a sequence.

AcquisitionEventIterator - Class in org.micromanager.acqj.util

Takes a list of iterators representing levels of a tree, where each level is an axis (e.g.

AcquisitionEventIterator(AcquisitionEvent, List<Function<AcquisitionEvent, Iterator<AcquisitionEvent>>>, Function<AcquisitionEvent, AcquisitionEvent>) - Constructor for class org.micromanager.acqj.util.AcquisitionEventIterator

AcquisitionEventIterator(AcquisitionEvent, List<Function<AcquisitionEvent, Iterator<AcquisitionEvent>>>) - Constructor for class org.micromanager.acqj.util.AcquisitionEventIterator

AcquisitionHook - Interface in org.micromanager.acqj.api

addAcqNotificationListener(AcqNotificationListener) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Add a AcqNotificationListener to receive asynchronous notifications about the acquisition

addAcqNotificationListener(AcqNotificationListener) - Method in class org.micromanager.acqj.main.Acquisition

addHook(AcquisitionHook, int) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Add a an arbitrary piece of code (i.e.

addHook(AcquisitionHook, int) - Method in class org.micromanager.acqj.main.Acquisition

addImageMetadata(JSONObject, AcquisitionEvent, long, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

Add the core set of image metadata that should be present in any acquisition

addImageMetadataProcessor(Consumer<JSONObject>) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Add a Consumer that will receive the metadata JSONObject for each image that is generated and modify it as needed.

addImageMetadataProcessor(Consumer<JSONObject>) - Method in class org.micromanager.acqj.main.Acquisition

addImageProcessor(TaggedImageProcessor) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Add an image processor for modifying images before saving or diverting them to some other purpose

addImageProcessor(TaggedImageProcessor) - Method in class org.micromanager.acqj.main.Acquisition

addListener(AcqNotificationListener) - Method in class org.micromanager.acqj.internal.NotificationHandler

addTagsToTaggedImage(JSONObject, HashMap<String, String>) - Method in class org.micromanager.acqj.main.Acquisition

Add provided tags (Key-Value pairs of type String) to the Tagged Image tags.

addToImageMetadata(JSONObject) - Method in class org.micromanager.acqj.main.Acquisition

addToOutput(TaggedImage) - Method in class org.micromanager.acqj.main.Acquisition

addToOutputQueue(TaggedImage) - Method in class org.micromanager.acqj.util.ImageProcessorBase

AFFINE_TRANSFORM - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

AffineTransformUtils - Class in org.micromanager.acqj.internal

AffineTransformUtils() - Constructor for class org.micromanager.acqj.internal.AffineTransformUtils

AFTER_CAMERA_HOOK - Static variable in interface org.micromanager.acqj.api.AcquisitionAPI

AFTER_EXPOSURE_HOOK - Static variable in interface org.micromanager.acqj.api.AcquisitionAPI

AFTER_HARDWARE_HOOK - Static variable in interface org.micromanager.acqj.api.AcquisitionAPI

anythingAcquired() - Method in interface org.micromanager.acqj.api.AcqEngJDataSink

Has putImage been called yet?

anythingAcquired() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Returns true once any data has been acquired

anythingAcquired() - Method in class org.micromanager.acqj.example.BlackHoleDataSink

anythingAcquired() - Method in class org.micromanager.acqj.main.Acquisition

areEventsFinished() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

returns true if all acquisition events have been processed and hardware control is complete.

areEventsFinished() - Method in class org.micromanager.acqj.main.Acquisition

AXES - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

AXES_GRID_COL - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

AXES_GRID_ROW - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

B

BEFORE_HARDWARE_HOOK - Static variable in interface org.micromanager.acqj.api.AcquisitionAPI

BIT_DEPTH - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

BlackHoleDataSink - Class in org.micromanager.acqj.example

This is a minimal implementation of a DataSink meant for demonstration purposes only.

BlackHoleDataSink() - Constructor for class org.micromanager.acqj.example.BlackHoleDataSink

blockUnlessAborted(long) - Method in class org.micromanager.acqj.main.Acquisition

blockUntilEventsFinished(Double) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Blcok until all acquisitions events are finished or timeout is reached

blockUntilEventsFinished(Double) - Method in class org.micromanager.acqj.main.Acquisition

C

Camera() - Constructor for class org.micromanager.acqj.main.AcqNotification.Camera

CameraTilingStageTranslator - Class in org.micromanager.acqj.util.xytiling

Convenience class for using an Affine transform to translate between pixel coordinates and stage coordinates when doing XY tiled imaging

CameraTilingStageTranslator(AffineTransform, String, int, int, int, int) - Constructor for class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

CHANNEL_AXIS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CHANNEL_GROUP - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CHANNEL_NAME - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

channels(List<ChannelSetting>) - Static method in class org.micromanager.acqj.util.AcqEventModules

Make an iterator for events for each active channel

ChannelSetting - Class in org.micromanager.acqj.util

Convenience class that encapsulates a single channel setting

ChannelSetting(String, String, double, double, boolean) - Constructor for class org.micromanager.acqj.util.ChannelSetting

ChannelSetting(String, String, double, double) - Constructor for class org.micromanager.acqj.util.ChannelSetting

checkForDefaultDevices(AcquisitionEvent) - Method in class org.micromanager.acqj.internal.Engine

checkForExceptions() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Throws an exception if an exception occured on a thread managed by the acquisiton

checkForExceptions() - Method in class org.micromanager.acqj.main.Acquisition

close() - Method in interface org.micromanager.acqj.api.AcquisitionHook

Shut down and release all resources

close() - Method in class org.micromanager.acqj.example.WorthlessAcquisitionHook

config_ - Variable in class org.micromanager.acqj.util.ChannelSetting

copy() - Method in class org.micromanager.acqj.internal.ZAxis

copy(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

copy() - Method in class org.micromanager.acqj.main.AcquisitionEvent

core_ - Variable in class org.micromanager.acqj.main.Acquisition

CORE_AUTOFOCUS_DEVICE - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_CAMERA - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_FOCUS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_GALVO - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_IMAGE_PROCESSOR - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_SHUTTER - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_SLM - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

CORE_XYSTAGE - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

coreStringToDouble(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

coreStringToInt(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

coreStringToLong(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

createAcqEventsFinishedNotification() - Static method in class org.micromanager.acqj.main.AcqNotification

createAcqStartedNotification() - Static method in class org.micromanager.acqj.main.AcqNotification

createAcquisitionFinishedEvent(AcquisitionAPI) - Static method in class org.micromanager.acqj.main.AcquisitionEvent

createAcquisitionSequenceEndEvent(AcquisitionAPI) - Static method in class org.micromanager.acqj.main.AcquisitionEvent

createAxes(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

createDataSinkFinishedNotification() - Static method in class org.micromanager.acqj.main.AcqNotification

createImageSavedNotification(String) - Static method in class org.micromanager.acqj.main.AcqNotification

createPositionGrid(int, int, double, double, int, int, int, int) - Static method in class org.micromanager.acqj.internal.AffineTransformUtils

D

DATA_SINK_FINISHED - Static variable in class org.micromanager.acqj.main.AcqNotification.Image

dataSink_ - Variable in class org.micromanager.acqj.main.Acquisition

DATE_TIME - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

debugMode_ - Variable in class org.micromanager.acqj.main.Acquisition

deviceNames - Variable in class org.micromanager.acqj.internal.HardwareSequences

displayStringToDouble(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

displayStringToInt(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

displayStringToLong(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

doubleStringCoreToDisplay(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

doubleStringDisplayToCore(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

doubleToAffine(DoubleVector) - Static method in class org.micromanager.acqj.internal.AffineTransformUtils

doubleToCoreString(double) - Static method in class org.micromanager.acqj.internal.NumUtils

doubleToDisplayString(double) - Static method in class org.micromanager.acqj.internal.NumUtils

E

ELAPSED_TIME_MS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

Engine - Class in org.micromanager.acqj.internal

Engine(CMMCore) - Constructor for class org.micromanager.acqj.internal.Engine

EVENT_GENERATION_HOOK - Static variable in interface org.micromanager.acqj.api.AcquisitionAPI

EVENTS_FINISHED - Static variable in class org.micromanager.acqj.main.AcqNotification.Acquisition

eventsFinished_ - Variable in class org.micromanager.acqj.main.Acquisition

EXPLORE_ACQUISITION - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

exploreLowerZIndexLimit_ - Variable in class org.micromanager.acqj.internal.ZAxis

exploreUpperZIndexLimit_ - Variable in class org.micromanager.acqj.internal.ZAxis

EXPOSURE - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

exposure_ - Variable in class org.micromanager.acqj.util.ChannelSetting

F

finish() - Method in interface org.micromanager.acqj.api.AcqEngJDataSink

Called when no more data will be collected.

finish() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Signal the acquisition to complete once all events are done

finish() - Method in class org.micromanager.acqj.example.BlackHoleDataSink

finish() - Method in class org.micromanager.acqj.main.Acquisition

finishAcquisition(Acquisition) - Method in class org.micromanager.acqj.internal.Engine

No more data to be collected for this acquisition.

firstDequeue_ - Variable in class org.micromanager.acqj.main.Acquisition

fromJSON(JSONObject, AcquisitionAPI) - Static method in class org.micromanager.acqj.main.AcquisitionEvent

Create an event or sequence of events from JSON

FullExample - Class in org.micromanager.acqj.example

This class demonstrates how to setup an acquisition using AcqEngJ

FullExample() - Constructor for class org.micromanager.acqj.example.FullExample

G

GENERIC_UM_INTENDED_SUFFIX - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

getAcqDate(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getAdditonalProperties() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getAffineTransform(double, double) - Static method in class org.micromanager.acqj.internal.AffineTransformUtils

getAffineTransform(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getAffineTransformString(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getAfterCameraHooks() - Method in class org.micromanager.acqj.main.Acquisition

getAfterExposureHooks() - Method in class org.micromanager.acqj.main.Acquisition

getAfterHardwareHooks() - Method in class org.micromanager.acqj.main.Acquisition

getAxes(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getAxesAsJSON(HashMap<String, Object>) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getAxesAsJSONString() - Method in class org.micromanager.acqj.main.AcquisitionEvent

Convert the event's axes to a JSONObject, or if it is a sequence event, then convert to a json array of json objects

getAxisPosition(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getAxisPosition(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

getAxisPositions() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getBeforeHardwareHooks() - Method in class org.micromanager.acqj.main.Acquisition

getBitDepth(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getBytesPerPixel(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCameraDeviceName() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getCameraImageCounts(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

Get the number of images to be acquired on each camera in a sequence event.

getCenter() - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

getChannelGroup(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getConfigGroup() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getConfigPreset() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getCore() - Static method in class org.micromanager.acqj.internal.Engine

getCoreAutofocusDevice(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreCamera(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreFocus(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreGalvo(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreImageProcessor(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreShutter(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreSLM(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCoreXY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getCurrentDateAndTime() - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getDataSink() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Get the DataSink used by this acquisition.

getDataSink() - Method in class org.micromanager.acqj.main.Acquisition

Don't delete, called by python side

getDefinedAxes() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getDepth(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getDeviceAxisName(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

getDisplayedPixel(double, long, long, double, double) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

return the pixel location in coordinates at appropriate res level of the top left pixel for the given row/column

getDisplayPositionCorners() - Method in class org.micromanager.acqj.main.AcquisitionEvent

Get the stage coordinates of the corners of the camera field of view

getDisplayTileCornerStageCoords(XYStagePosition) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getDisplayTileHeight() - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getDisplayTileWidth() - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getElapsedTimeMs(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getEventGenerationHooks() - Method in class org.micromanager.acqj.main.Acquisition

getExposure(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getExposure() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getFullResPositionIndexFromStageCoords(double, double) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getGridCol() - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

getGridRow() - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

getHeight(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getImageTime(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getImageTransferQueueCount() - Method in class org.micromanager.acqj.main.Acquisition

getImageTransferQueueSize() - Method in class org.micromanager.acqj.main.Acquisition

getIndices(String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getInstance() - Static method in class org.micromanager.acqj.internal.Engine

getIntervalMs(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getJSONArrayMember(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getKeys(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getMinimumStartTimeAbsolute() - Method in class org.micromanager.acqj.main.AcquisitionEvent

Get the minimum start time in system time.

getName() - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

getNumberOfComponents(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getPixelCoordsFromStageCoords(double, double) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getPixelOverlapX(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getPixelOverlapY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getPixelSizeUm(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getPixelStageTranslator() - Method in interface org.micromanager.acqj.api.XYTiledAcquisitionAPI

getPixelStageTranslator() - Method in class org.micromanager.acqj.main.XYTiledAcquisition

getPixelType(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getPositionIndices(int[], int[]) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

Return the position indices for the positions at the specified rows, cols.

getPositionList() - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getPositionName(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getPositionName() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getSequence() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getSLMImage() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getStageCoordsFromPixelCoords(long, long) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getStageDeviceNames() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getStageSingleAxisStagePosition(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

getStageX(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getStageXIntended(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getStageY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getStageYIntended(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getStageZIntended(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getStartTime_ms() - Method in class org.micromanager.acqj.main.Acquisition

getSummaryMetadata() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Get the summary metadata for this acquisition

getSummaryMetadata() - Method in class org.micromanager.acqj.main.Acquisition

getTags() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getTileIndicesFromDisplayedPixel(double, int, int, double, double) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getTimeout_ms() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getTIndex() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getVisibleTileCorners(int, int) - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

If positions are laid out in a grid, get the stage coordinates of the corners of the visible part of each tile (i.e.

getWidth(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getXPosition() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getXYPosition(int) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

getYPosition() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getZAxes() - Method in class org.micromanager.acqj.main.XYTiledAcquisition

getZCTOrder(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getZDeviceNames() - Method in class org.micromanager.acqj.main.XYTiledAcquisition

getZIndex() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getZOrigin(String) - Method in class org.micromanager.acqj.main.XYTiledAcquisition

getZPosition() - Method in class org.micromanager.acqj.main.AcquisitionEvent

getZPositionUm(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

getZStep(String) - Method in class org.micromanager.acqj.main.XYTiledAcquisition

getZStepUm(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

group_ - Variable in class org.micromanager.acqj.util.ChannelSetting

H

Hardware() - Constructor for class org.micromanager.acqj.main.AcqNotification.Hardware

HardwareSequences - Class in org.micromanager.acqj.internal

Class for holding data about what hardware sequences are currently being run

HardwareSequences() - Constructor for class org.micromanager.acqj.internal.HardwareSequences

hasAcqDate(JSONObject) - Method in class org.micromanager.acqj.main.AcqEngMetadata

hasAffineTransformString(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasAxis(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasBitDepth(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasChannelGroup(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasConfigGroup() - Method in class org.micromanager.acqj.main.AcquisitionEvent

hasCoreAutofocus(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreCamera(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreFocus(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreGalvo(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreImageProcessor(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreShutter(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreSLM(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasCoreXY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasElapsedTimeMs(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasExposure(JSONObject) - Method in class org.micromanager.acqj.main.AcqEngMetadata

hashCode() - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

hasHeight(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasImageTime(JSONObject) - Method in class org.micromanager.acqj.main.AcqEngMetadata

hasIntervalMs(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasNext() - Method in class org.micromanager.acqj.util.AcquisitionEventIterator

hasPixelOverlapX(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasPixelOverlapY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasPixelSizeUm(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasPixelType(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasPositionName(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasStageX(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasStageXIntended(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasStageY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasStageYIntended(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasStageZIntended(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasWidth(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasZCTOrder(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasZPositionUm(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

hasZStepUm(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

HEIGHT - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

highestExploredZIndex_ - Variable in class org.micromanager.acqj.internal.ZAxis

I

Image() - Constructor for class org.micromanager.acqj.main.AcqNotification.Image

IMAGE_SAVED - Static variable in class org.micromanager.acqj.main.AcqNotification.Image

ImageProcessorBase - Class in org.micromanager.acqj.util

An abstract class that handles a the threading to implement an image processor that runs asynchronously--i.e.

ImageProcessorBase() - Constructor for class org.micromanager.acqj.util.ImageProcessorBase

INITIAL_POS_LIST - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

initialize(Acquisition, JSONObject) - Method in interface org.micromanager.acqj.api.AcqEngJDataSink

Called when the Acquisition is initialized

initialize(Acquisition, JSONObject) - Method in class org.micromanager.acqj.example.BlackHoleDataSink

initialize() - Method in class org.micromanager.acqj.main.Acquisition

1) Get the names of core devices to be used in acquisition.

initialize() - Method in class org.micromanager.acqj.main.XYTiledAcquisition

intStringCoreToDisplay(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

intStringDisplayToCore(Object) - Static method in class org.micromanager.acqj.internal.NumUtils

intToCoreString(long) - Static method in class org.micromanager.acqj.internal.NumUtils

intToDisplayString(int) - Static method in class org.micromanager.acqj.internal.NumUtils

isAbortRequested() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Has abort been called?

isAbortRequested() - Method in class org.micromanager.acqj.main.Acquisition

isAcquisitionEventsFinishedNotification() - Method in class org.micromanager.acqj.main.AcqNotification

isAcquisitionFinishedEvent() - Method in class org.micromanager.acqj.main.AcquisitionEvent

isAcquisitionSequenceEndEvent() - Method in class org.micromanager.acqj.main.AcquisitionEvent

isAffineTransformDefined() - Static method in class org.micromanager.acqj.internal.AffineTransformUtils

isConfigGroupSequenced() - Method in class org.micromanager.acqj.main.AcquisitionEvent

isDataSinkFinishedNotification() - Method in class org.micromanager.acqj.main.AcqNotification

isDebugMode() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Should debug logging be printed

isDebugMode() - Method in class org.micromanager.acqj.main.Acquisition

isExploreAcq(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

isExposureSequenced() - Method in class org.micromanager.acqj.main.AcquisitionEvent

isFinished() - Method in interface org.micromanager.acqj.api.AcqEngJDataSink

Is this sink and all associated resources complete (e.g.

isFinished() - Method in class org.micromanager.acqj.example.BlackHoleDataSink

isGRAY(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

isGRAY16(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

isGRAY8(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

isImageSavedNotification() - Method in class org.micromanager.acqj.main.AcqNotification

isPaused() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

return if acquisition is paused (i.e.

isPaused() - Method in class org.micromanager.acqj.main.Acquisition

isRGB(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

isRGB32(JSONObject) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

isStarted() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

return if acquisition is started by the first call to submitEventIterator

isStarted() - Method in class org.micromanager.acqj.main.Acquisition

isXYSequenced() - Method in class org.micromanager.acqj.main.AcquisitionEvent

isZSequenced() - Method in class org.micromanager.acqj.main.AcquisitionEvent

L

longToCoreString(long) - Static method in class org.micromanager.acqj.internal.NumUtils

longToDisplayString(long) - Static method in class org.micromanager.acqj.internal.NumUtils

lowestExploredZIndex_ - Variable in class org.micromanager.acqj.internal.ZAxis

M

makeSummaryMD(AcquisitionAPI) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

Make the core set of tags needed in summary metadata.

moveStage(String, int, int, double, double) - Static method in class org.micromanager.acqj.util.AcqEventModules

Generic version of a z stack that corresponds to an arbitrary sequence of linearly spaced points along a stage

N

name_ - Variable in class org.micromanager.acqj.internal.ZAxis

next() - Method in class org.micromanager.acqj.util.AcquisitionEventIterator

NotificationHandler - Class in org.micromanager.acqj.internal

Class that handles asynchronous notifications from the acquisition engine Runs a dedicated thread that stores notifications and dispatchems them to listeners

NotificationHandler() - Constructor for class org.micromanager.acqj.internal.NotificationHandler

notificationTypeToString(Class) - Static method in class org.micromanager.acqj.main.AcqNotification

NumUtils - Class in org.micromanager.acqj.internal

NumUtils() - Constructor for class org.micromanager.acqj.internal.NumUtils

O

offset_ - Variable in class org.micromanager.acqj.util.ChannelSetting

org.micromanager.acqj.api - package org.micromanager.acqj.api

org.micromanager.acqj.example - package org.micromanager.acqj.example

org.micromanager.acqj.internal - package org.micromanager.acqj.internal

org.micromanager.acqj.main - package org.micromanager.acqj.main

org.micromanager.acqj.util - package org.micromanager.acqj.util

org.micromanager.acqj.util.xytiling - package org.micromanager.acqj.util.xytiling

OVERLAP_X - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

OVERLAP_Y - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

P

parseDouble(String) - Static method in class org.micromanager.acqj.internal.NumUtils

phase_ - Variable in class org.micromanager.acqj.main.AcqNotification

PIX_SIZE - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

PIX_TYPE - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

PIX_TYPE_GRAY16 - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

PIX_TYPE_GRAY8 - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

pixelCoordsFromStageCoords(double, double, double, Point2D.Double) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

pixelStageTranslator_ - Variable in class org.micromanager.acqj.main.XYTiledAcquisition

POS_NAME - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

POSITION_AXIS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

positions(List<XYStagePosition>) - Static method in class org.micromanager.acqj.util.AcqEventModules

Iterate over an arbitrary list of positions.

POST_EXPOSURE - Static variable in class org.micromanager.acqj.main.AcqNotification.Camera

POST_HARDWARE - Static variable in class org.micromanager.acqj.main.AcqNotification.Hardware

postNotification(AcqNotification) - Method in interface org.micromanager.acqj.api.AcqNotificationListener

postNotification(AcqNotification) - Method in class org.micromanager.acqj.internal.NotificationHandler

postNotification(AcqNotification) - Method in class org.micromanager.acqj.main.Acquisition

PRE_HARDWARE - Static variable in class org.micromanager.acqj.main.AcqNotification.Hardware

PRE_SEQUENCE_STARTED - Static variable in class org.micromanager.acqj.main.AcqNotification.Camera

PRE_SNAP - Static variable in class org.micromanager.acqj.main.AcqNotification.Camera

processImage(TaggedImage) - Method in class org.micromanager.acqj.example.WorthlessImageProcessor

This is a minimal implementation of an ImageProcessor meant for demonstration purposes only.

processImage(TaggedImage) - Method in class org.micromanager.acqj.util.ImageProcessorBase

propertyDeviceNames - Variable in class org.micromanager.acqj.internal.HardwareSequences

propertyNames - Variable in class org.micromanager.acqj.internal.HardwareSequences

putImage(TaggedImage) - Method in interface org.micromanager.acqj.api.AcqEngJDataSink

Add a new image to saving/display etc.

putImage(TaggedImage) - Method in class org.micromanager.acqj.example.BlackHoleDataSink

R

run(AcquisitionEvent) - Method in interface org.micromanager.acqj.api.AcquisitionHook

Called for before/after hardware acquisition hooks

run(AcquisitionEvent) - Method in class org.micromanager.acqj.example.WorthlessAcquisitionHook

S

SAVING_PREFIX - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

setAcqAndDequeues(AcquisitionAPI, LinkedBlockingDeque<TaggedImage>, LinkedBlockingDeque<TaggedImage>) - Method in interface org.micromanager.acqj.api.TaggedImageProcessor

Deprecated.

Use setAcqAndQueues instead

setAcqAndDequeues(AcquisitionAPI, LinkedBlockingDeque<TaggedImage>, LinkedBlockingDeque<TaggedImage>) - Method in class org.micromanager.acqj.util.ImageProcessorBase

setAcqAndQueues(AcquisitionAPI, BlockingQueue<TaggedImage>, BlockingQueue<TaggedImage>) - Method in interface org.micromanager.acqj.api.TaggedImageProcessor

Class for modifying/adding/deleting images after they're acquired before saving.

setAcqAndQueues(AcquisitionAPI, BlockingQueue<TaggedImage>, BlockingQueue<TaggedImage>) - Method in class org.micromanager.acqj.util.ImageProcessorBase

setAcqDate(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setAffineTransformString(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setAxisPosition(JSONObject, String, Object) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setAxisPosition(String, Object) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setBitDepth(JSONObject, int) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCameraDeviceName(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setChannelGroup(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setChannelName(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setConfigGroup(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setConfigPreset(String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setCoreAutofocus(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreCamera(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreFocus(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreGalvo(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreImageProcessor(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreShutter(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreSLM(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setCoreXY(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setDebugMode(boolean) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Activate debug logging

setDebugMode(boolean) - Method in class org.micromanager.acqj.main.Acquisition

Don't delete, called by python side

setElapsedTimeMs(JSONObject, long) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setExploreAcq(JSONObject, boolean) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setExposure(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setExposure(double) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setHeight(JSONObject, int) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setImageTime(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setIntervalMs(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setMinimumStartTime(Long) - Method in class org.micromanager.acqj.main.AcquisitionEvent

Set the minimum start time in ms relative to when the acq started.

setName(String) - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

setPaused(boolean) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Pause or unpause

setPaused(boolean) - Method in class org.micromanager.acqj.main.Acquisition

setPixelOverlapX(JSONObject, int) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setPixelOverlapY(JSONObject, int) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setPixelSizeUm(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setPixelTypeFromByteDepth(JSONObject, int) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setPixelTypeFromString(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setPositionName(JSONObject, String) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setPositions(List<XYStagePosition>) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

Set a grid of XY stage positions, as generated from some external source, so that they can be used to in caculations relating pixel and stage coordinates

setProperty(String, String, String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setStageCoordinate(String, double) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setStageCoordinate(String, double, String) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setStagePositionIntended(JSONObject, String, Double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setStageX(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setStageXIntended(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setStageY(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setStageYIntended(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setStageZIntended(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setStartTime_ms(long) - Method in class org.micromanager.acqj.main.Acquisition

setTags(HashMap<String, String>) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setTimeIndex(int) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setWidth(JSONObject, int) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setX(double) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setY(double) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setZ(Integer, Double) - Method in class org.micromanager.acqj.main.AcquisitionEvent

setZCTOrder(JSONObject, boolean) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setZPositionUm(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

setZStepUm(JSONObject, double) - Static method in class org.micromanager.acqj.main.AcqEngMetadata

shouldAcquireImage() - Method in class org.micromanager.acqj.main.AcquisitionEvent

sink_ - Variable in class org.micromanager.acqj.util.ImageProcessorBase

slm_ - Variable in class org.micromanager.acqj.main.Acquisition

source_ - Variable in class org.micromanager.acqj.util.ImageProcessorBase

stackTraceToString(Exception) - Static method in class org.micromanager.acqj.internal.Engine

stageCoordsFromPixelCoords(int, int, double, Point2D.Double) - Method in class org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

start() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Deprecated.

start() - Method in class org.micromanager.acqj.main.Acquisition

started_ - Variable in class org.micromanager.acqj.main.Acquisition

stringToTransform(String) - Static method in class org.micromanager.acqj.internal.AffineTransformUtils

submitEventIterator(Iterator<AcquisitionEvent>) - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Submit a list of acquisition events for acquisition.

submitEventIterator(Iterator<AcquisitionEvent>) - Method in class org.micromanager.acqj.internal.Engine

Submit a stream of events which will get lazily processed and merged into multi-image hardware sequenced events as needed.

submitEventIterator(Iterator<AcquisitionEvent>) - Method in class org.micromanager.acqj.main.Acquisition

summaryMetadata_ - Variable in class org.micromanager.acqj.main.Acquisition

T

TaggedImageProcessor - Interface in org.micromanager.acqj.api

Image processors are responsible for shutting down and releasing resources automatically, once a TaggedImage(null, null) appears in the source queue.

TAGS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

TIME - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

TIME_AXIS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

timelapse(int, double) - Static method in class org.micromanager.acqj.util.AcqEventModules

TIMELAPSE_INTERVAL - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

toJSON() - Method in class org.micromanager.acqj.main.AcqNotification

toJSON() - Method in class org.micromanager.acqj.main.AcquisitionEvent

Return JSONArray or JSONObject for sequence vs single event

toJSON(String) - Method in class org.micromanager.acqj.util.xytiling.XYStagePosition

toString() - Method in class org.micromanager.acqj.main.AcquisitionEvent

transformToString(AffineTransform) - Static method in class org.micromanager.acqj.internal.AffineTransformUtils

type_ - Variable in class org.micromanager.acqj.main.AcqNotification

U

use_ - Variable in class org.micromanager.acqj.util.ChannelSetting

W

waitForCompletion() - Method in interface org.micromanager.acqj.api.AcquisitionAPI

Block until acquisition finished and all resources complete.

waitForCompletion() - Method in class org.micromanager.acqj.main.Acquisition

WIDTH - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

WorthlessAcquisitionHook - Class in org.micromanager.acqj.example

This is a minimal implementation of an AcquistionHook meant for demonstration purposes only.

WorthlessAcquisitionHook() - Constructor for class org.micromanager.acqj.example.WorthlessAcquisitionHook

WorthlessImageProcessor - Class in org.micromanager.acqj.example

WorthlessImageProcessor() - Constructor for class org.micromanager.acqj.example.WorthlessImageProcessor

X

X_UM - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

X_UM_INTENDED - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

xyStage_ - Variable in class org.micromanager.acqj.main.Acquisition

XYStagePosition - Class in org.micromanager.acqj.util.xytiling

Immutable object representing single XY stage position

XYStagePosition(Point2D.Double) - Constructor for class org.micromanager.acqj.util.xytiling.XYStagePosition

for abitrary positions not neccessarily in a grid

XYStagePosition(Point2D.Double, int, int) - Constructor for class org.micromanager.acqj.util.xytiling.XYStagePosition

XYTiledAcquisition - Class in org.micromanager.acqj.main

Special type of acquisiton that collects tiles in a 2D grid.

XYTiledAcquisition(AcqEngJDataSink, Integer, Integer) - Constructor for class org.micromanager.acqj.main.XYTiledAcquisition

XYTiledAcquisition(AcqEngJDataSink, Integer, Integer, Double, Consumer<JSONObject>) - Constructor for class org.micromanager.acqj.main.XYTiledAcquisition

XYTiledAcquisitionAPI - Interface in org.micromanager.acqj.api

General interface for tiled XY multi-resolution acquisitions

Y

Y_UM - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

Y_UM_INTENDED - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

Z

Z_AXIS - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

Z_STEP_UM - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

Z_UM - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

Z_UM_INTENDED - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

zAxes_ - Variable in class org.micromanager.acqj.main.XYTiledAcquisition

ZAxis - Class in org.micromanager.acqj.internal

ZAxis(String, double, double) - Constructor for class org.micromanager.acqj.internal.ZAxis

ZAxis(String, double, double, int, int, int, int) - Constructor for class org.micromanager.acqj.internal.ZAxis

ZC_ORDER - Static variable in class org.micromanager.acqj.main.AcqEngMetadata

zOrigin_um_ - Variable in class org.micromanager.acqj.internal.ZAxis

zStack(int, int, double, double) - Static method in class org.micromanager.acqj.util.AcqEventModules

zStage_ - Variable in class org.micromanager.acqj.main.Acquisition

zStep_um_ - Variable in class org.micromanager.acqj.internal.ZAxis

A B C D E F G H I L M N O P R S T U W X Y Z