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

A

abort() - Method in class org.micromanager.explore.ExploreAcquisition

abort() - Method in class org.micromanager.remote.RemoteAcquisition

abort(Exception) - Method in class org.micromanager.remote.RemoteAcquisition

abort() - Method in class org.micromanager.remote.XYTiledRemoteAcquisition

abort(Exception) - Method in class org.micromanager.remote.XYTiledRemoteAcquisition

acq_ - Variable in class org.micromanager.explore.ExploreAcqUIAndStorage

acq_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

acquireTileAtCurrentLocation() - Method in class org.micromanager.explore.ExploreAcquisition

acquireTiles(int, int, int, int) - Method in class org.micromanager.explore.ExploreAcquisition

acquireTiles() - Method in class org.micromanager.explore.gui.ExploreMouseListener

addExploreToOverlay(Overlay, double, Graphics, Point2D.Double) - Method in class org.micromanager.explore.gui.ExploreOverlayer

addImageToRecons(short[], int) - Method in class org.micromanager.lightsheet.StackResampler

Add images only after first calling initializeProjections.

addToProcessImageQueue(TaggedImage) - Method in class org.micromanager.lightsheet.StackResampler

Deprecated.

addToProcessImageQueue(short[], int) - Method in class org.micromanager.lightsheet.StackResampler

Use this function to add Tagged images to the processing queue.

anythingAcquired() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

awaitCompletion() - Method in class org.micromanager.remote.RemoteStorageMonitor

C

ChannelGroupSettings - Class in org.micromanager.explore

Class to encapsulate a bunch of ChannelsSettings.

ChannelGroupSettings(String) - Constructor for class org.micromanager.explore.ChannelGroupSettings

channels_ - Variable in class org.micromanager.explore.ChannelGroupSettings

close() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

The display calls this when its closing.

close() - Method in class org.micromanager.explore.gui.ExploreControlsPanel

close() - Method in class org.micromanager.internal.zmq.ZMQServer

close() - Method in class org.micromanager.internal.zmq.ZMQSocketWrapper

close() - Method in class org.micromanager.remote.RemoteAcqHook

ColorableScrollbarUI - Class in org.micromanager.explore.gui

What is this thing?

ColorableScrollbarUI(String) - Constructor for class org.micromanager.explore.gui.ColorableScrollbarUI

COLUMN_NAMES - Static variable in class org.micromanager.explore.gui.SimpleChannelTableModel

context_ - Static variable in class org.micromanager.internal.zmq.ZMQSocketWrapper

convertToPrimitiveArray(byte[], Object) - Static method in class org.micromanager.internal.zmq.ZMQUtil

create(String, String, int, int, double, String) - Static method in class org.micromanager.explore.ExploreAcqUIAndStorage

createAcquisition(String, String, boolean, int, boolean) - Method in class org.micromanager.remote.RemoteAcquisitionFactory

createMouseListener() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

createOverlayer() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

createSettingsKey(int, double, double, double, int, int, int) - Static method in class org.micromanager.lightsheet.StackResampler

Creates a String with values used to create a StackResampler.

createTiledAcquisition(String, String, boolean, boolean, int, int, int, int, boolean) - Method in class org.micromanager.remote.RemoteAcquisitionFactory

currentMouseLocation_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

D

darkUI() - Static method in class org.micromanager.remote.HeadlessLauncher

decodeArray(byte[], Class) - Static method in class org.micromanager.internal.zmq.ZMQUtil

deselected() - Method in class org.micromanager.explore.gui.ExploreControlsPanel

deserialize(byte[], Function<JSONObject, ?>) - Static method in class org.micromanager.internal.zmq.ZMQUtil

display_ - Variable in class org.micromanager.explore.ExploreAcqUIAndStorage

drawOverlay(Overlay, Point2D.Double, double, Graphics, HashMap<String, Object>, double, Point2D.Double) - Method in class org.micromanager.explore.gui.ExploreOverlayer

E

encodeArray(Object) - Static method in class org.micromanager.internal.zmq.ZMQUtil

Convert array of primitives to a String

expandZLimitSliders(int) - Method in class org.micromanager.explore.gui.ZAxisLimitControlPanel

ExploreAcqUIAndStorage - Class in org.micromanager.explore

This class links data storage, viewer, and acquisition, acting as an intermediary when neccessary to implement functionality specific to Explore acquisitions.

ExploreAcqUIAndStorage(String, String, boolean, ChannelGroupSettings, Consumer<String>) - Constructor for class org.micromanager.explore.ExploreAcqUIAndStorage

ExploreAcqUIAndStorage(String, String, boolean, ChannelGroupSettings) - Constructor for class org.micromanager.explore.ExploreAcqUIAndStorage

ExploreAcqUIAndStorage(String, Consumer<String>) - Constructor for class org.micromanager.explore.ExploreAcqUIAndStorage

ExploreAcquisition - Class in org.micromanager.explore

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

ExploreAcquisition(int, int, double, ChannelGroupSettings, ExploreAcqUIAndStorage) - Constructor for class org.micromanager.explore.ExploreAcquisition

ExploreAcquisition(int, int, double, ChannelGroupSettings, AcqEngJDataSink, Consumer<String>) - Constructor for class org.micromanager.explore.ExploreAcquisition

ExploreControlsPanel - Class in org.micromanager.explore.gui

ExploreControlsPanel(ExploreAcquisition, OverlayerPlugin, ChannelGroupSettings, HashMap<String, ZAxis>) - Constructor for class org.micromanager.explore.gui.ExploreControlsPanel

Creates new form ExploreChannelsPanel.

exploreControlsPanel_ - Variable in class org.micromanager.explore.ExploreAcqUIAndStorage

exploreEndTile_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

ExploreMouseListener - Class in org.micromanager.explore.gui

ExploreMouseListener(XYTiledAcquisition, NDViewer, Consumer<String>) - Constructor for class org.micromanager.explore.gui.ExploreMouseListener

Mouse Listener class for paning zooming, and clicking to explore tiles

ExploreMouseListenerAPI - Interface in org.micromanager.explore.gui

ExploreOverlayer - Class in org.micromanager.explore.gui

Class that encapsulates calculation of overlays for DisplayPlus.

ExploreOverlayer(NDViewerAPI, ExploreMouseListenerAPI, XYTiledAcquisition) - Constructor for class org.micromanager.explore.gui.ExploreOverlayer

exploreStartTile_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

ExploreZSliders - Class in org.micromanager.explore.gui

This class holds the controls for a single Z axis

ExploreZSliders(ExploreAcquisition, ZAxis) - Constructor for class org.micromanager.explore.gui.ExploreZSliders

externalObjects_ - Variable in class org.micromanager.internal.zmq.ZMQServer

F

finalizeProjections() - Method in class org.micromanager.lightsheet.StackResampler

Call after all images have arrived to finalize the projections.

finish() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

Called when images done arriving.

FULL_VOLUME - Static variable in class org.micromanager.lightsheet.StackResampler

G

getAcquisition() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getBounds() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getChannelGroup() - Method in class org.micromanager.explore.ChannelGroupSettings

getChannelListSetting(int) - Method in class org.micromanager.explore.ChannelGroupSettings

getChannelNames() - Method in class org.micromanager.explore.ChannelGroupSettings

getChannelSetting(String) - Method in class org.micromanager.explore.ChannelGroupSettings

getColumnClass(int) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

getColumnCount() - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

getColumnName(int) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

getConfigName(int) - Method in class org.micromanager.explore.ChannelGroupSettings

getCurrentMouseLocation() - Method in class org.micromanager.explore.gui.ExploreMouseListener

getCurrentMouseLocation() - Method in interface org.micromanager.explore.gui.ExploreMouseListenerAPI

getDir() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getDiskLocation() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getDisplayJSON() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

Used for data loaded from disk.

getEventPort() - Method in class org.micromanager.explore.ExploreAcquisition

getEventPort() - Method in interface org.micromanager.remote.PycroManagerCompatibleAcq

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

getEventPort() - Method in class org.micromanager.remote.RemoteAcquisition

getEventPort() - Method in class org.micromanager.remote.XYTiledRemoteAcquisition

getExploreEndTile() - Method in class org.micromanager.explore.gui.ExploreMouseListener

getExploreEndTile() - Method in interface org.micromanager.explore.gui.ExploreMouseListenerAPI

getExploreStartTile() - Method in class org.micromanager.explore.gui.ExploreMouseListener

getExploreStartTile() - Method in interface org.micromanager.explore.gui.ExploreMouseListenerAPI

getField(Object, JSONObject) - Method in class org.micromanager.internal.zmq.ZMQServer

getFrameNr() - Method in class org.micromanager.lightsheet.StackResampler.ImagePlusSlice

getImageBitDepth(HashMap<String, Object>) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getImageForDisplay(HashMap<String, Object>, int, double, double, int, int) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getImageKeys() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getMasterServer() - Static method in class org.micromanager.internal.zmq.ZMQServer

getMaxResolutionIndex() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getMouseDragStartPointLeft() - Method in class org.micromanager.explore.gui.ExploreMouseListener

getMouseDragStartPointLeft() - Method in interface org.micromanager.explore.gui.ExploreMouseListenerAPI

getName() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getNumChannels() - Method in class org.micromanager.explore.ChannelGroupSettings

getPackageClasses(String) - Method in class org.micromanager.internal.zmq.ZMQUtil

getPackages() - Static method in class org.micromanager.internal.zmq.ZMQUtil

getPackagesFromJars(URLClassLoader) - Static method in class org.micromanager.internal.zmq.ZMQUtil

getPixels() - Method in class org.micromanager.lightsheet.StackResampler.ImagePlusSlice

getPixelStageTranslator() - Method in class org.micromanager.remote.XYTiledRemoteAcquisition

getPort() - Method in class org.micromanager.internal.zmq.ZMQSocketWrapper

getPort() - Method in class org.micromanager.remote.RemoteEventSource

getPort() - Method in class org.micromanager.remote.RemoteStorageMonitor

getPreferredSize() - Method in class org.micromanager.explore.gui.ExploreZSliders

getPullPort() - Method in class org.micromanager.remote.RemoteAcqHook

getPullPort() - Method in class org.micromanager.remote.RemoteImageProcessor

getPushPort() - Method in class org.micromanager.remote.RemoteAcqHook

getPushPort() - Method in class org.micromanager.remote.RemoteCoreCallback

getPushPort() - Method in class org.micromanager.remote.RemoteImageProcessor

getReconstructedVolumeZYX() - Method in class org.micromanager.lightsheet.StackResampler

Returns reconstructed volume.

getReconstructionVoxelSizeUm() - Method in class org.micromanager.lightsheet.StackResampler

getResampledShapeX() - Method in class org.micromanager.lightsheet.StackResampler

Returns the width of the resampled volume in pixels.

getResampledShapeY() - Method in class org.micromanager.lightsheet.StackResampler

Returns the height of the resampled volume.

getResampledShapeZ() - Method in class org.micromanager.lightsheet.StackResampler

Returns the number of frames of the resampled volume.

getRowCount() - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

getSettingsKey() - Method in class org.micromanager.lightsheet.StackResampler

Returns a String unique for this StackResampler.

getStageCoordinateOfViewCenter() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getStorage() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getStorage() - Method in class org.micromanager.explore.ExploreAcquisition

getStorage() - Method in interface org.micromanager.remote.PycroManagerCompatibleAcq

getStorage() - Method in class org.micromanager.remote.RemoteAcquisition

getStorage() - Method in class org.micromanager.remote.XYTiledRemoteAcquisition

getSummaryMD() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getTileIndicesWithDataAt(String, int) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getTilesWaitingToAcquireAtSlice(HashMap<String, Integer>) - Method in class org.micromanager.explore.ExploreAcquisition

getTitle() - Method in class org.micromanager.explore.gui.ExploreControlsPanel

getUniqueAcqName() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getValueAt(int, int) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

getViewer() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

getViewer() - Method in interface org.micromanager.remote.PycroManagerCompatibleUI

Get reference to NDViewer displaying this acquisitions data

getYXProjection() - Method in class org.micromanager.lightsheet.StackResampler

Returns YX projection.

getYZProjection() - Method in class org.micromanager.lightsheet.StackResampler

Returns ZY projection.

getZOrigin(String) - Method in class org.micromanager.explore.ExploreAcquisition

getZStep(String) - Method in class org.micromanager.explore.ExploreAcquisition

getZXProjection() - Method in class org.micromanager.lightsheet.StackResampler

Returns ZX projection.

group_ - Variable in class org.micromanager.explore.ChannelGroupSettings

H

HeadlessLauncher - Class in org.micromanager.remote

HeadlessLauncher() - Constructor for class org.micromanager.remote.HeadlessLauncher

I

ImagePlusSlice(short[], int) - Constructor for class org.micromanager.lightsheet.StackResampler.ImagePlusSlice

imageWritten(IndexEntryData) - Method in class org.micromanager.remote.RemoteStorageMonitor

increaseMaxResolutionLevel(int) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

initialize(Acquisition, JSONObject) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

initialize(int) - Method in class org.micromanager.internal.zmq.ZMQPullSocket

initialize(int) - Method in class org.micromanager.internal.zmq.ZMQPushSocket

initialize(int) - Method in class org.micromanager.internal.zmq.ZMQServer

initialize(int) - Method in class org.micromanager.internal.zmq.ZMQSocketWrapper

initializeProjections() - Method in class org.micromanager.lightsheet.StackResampler

Call this function before any images arrive to initialize the projection and recon arrays.

invert(double[][]) - Static method in class org.micromanager.lightsheet.StackResampler.LinearTransformation

Inverts a matrix.

isCellEditable(int, int) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

isFinished() - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

isFinished() - Method in class org.micromanager.explore.ExploreAcquisition

isFinished() - Method in class org.micromanager.remote.RemoteAcquisition

isFinished() - Method in class org.micromanager.remote.RemoteEventSource

Return true when all events finished and everything shutdown

isFinished() - Method in class org.micromanager.remote.XYTiledRemoteAcquisition

L

lastMouseWheelZoomTime_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

LinearTransformation() - Constructor for class org.micromanager.lightsheet.StackResampler.LinearTransformation

loadClass(String) - Static method in class org.micromanager.internal.zmq.ZMQUtil

loadedData_ - Variable in class org.micromanager.explore.ExploreAcqUIAndStorage

logger_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

M

main(String[]) - Static method in class org.micromanager.remote.HeadlessLauncher

MOUSE_WHEEL_ZOOM_INTERVAL_MS - Static variable in class org.micromanager.explore.gui.ExploreMouseListener

mouseClicked(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseDragged(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseDraggedActions(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseDragStartPointLeft_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

mouseDragStartPointRight_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

mouseEntered(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseEnteredActions(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseExited(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseExitedActions(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseListener_ - Variable in class org.micromanager.explore.ExploreAcqUIAndStorage

mouseMoved(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseMovedActions(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mousePressed(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mousePressedActions(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseReleased(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseReleasedActions(MouseEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseWheelMoved(MouseWheelEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

mouseWheelMovedActions(MouseWheelEvent) - Method in class org.micromanager.explore.gui.ExploreMouseListener

multiply(double[][], double[][]) - Static method in class org.micromanager.lightsheet.StackResampler.LinearTransformation

Multiplies two matrices.

multiply(double[][], double[]) - Static method in class org.micromanager.lightsheet.StackResampler.LinearTransformation

Multiples a matrix with a vector.

N

next() - Method in class org.micromanager.internal.zmq.ZMQPullSocket

nextActiveChannel(String) - Method in class org.micromanager.explore.ChannelGroupSettings

O

onChannelGroupChanged(String) - Method in class org.micromanager.remote.RemoteCoreCallback

onConfigGroupChanged(String, String) - Method in class org.micromanager.remote.RemoteCoreCallback

onDisplayClose() - Method in class org.micromanager.explore.gui.ExploreZSliders

onDisplayClose() - Method in class org.micromanager.explore.gui.ZAxisLimitControlPanel

onExposureChanged(String, double) - Method in class org.micromanager.remote.RemoteCoreCallback

onPixelSizeAffineChanged(double, double, double, double, double, double) - Method in class org.micromanager.remote.RemoteCoreCallback

onPixelSizeChanged(double) - Method in class org.micromanager.remote.RemoteCoreCallback

onPropertiesChanged() - Method in class org.micromanager.remote.RemoteCoreCallback

onPropertyChanged(String, String, String) - Method in class org.micromanager.remote.RemoteCoreCallback

onSLMExposureChanged(String, double) - Method in class org.micromanager.remote.RemoteCoreCallback

onStagePositionChanged(String, double) - Method in class org.micromanager.remote.RemoteCoreCallback

onSystemConfigurationLoaded() - Method in class org.micromanager.remote.RemoteCoreCallback

onXYStagePositionChanged(String, double, double) - Method in class org.micromanager.remote.RemoteCoreCallback

org.micromanager.explore - package org.micromanager.explore

org.micromanager.explore.gui - package org.micromanager.explore.gui

org.micromanager.internal.zmq - package org.micromanager.internal.zmq

org.micromanager.lightsheet - package org.micromanager.lightsheet

org.micromanager.remote - package org.micromanager.remote

ORTHOGONAL_VIEWS - Static variable in class org.micromanager.lightsheet.StackResampler

P

paintThumb(Graphics, JComponent, Rectangle) - Method in class org.micromanager.explore.gui.ColorableScrollbarUI

paintTrack(Graphics, JComponent, Rectangle) - Method in class org.micromanager.explore.gui.ColorableScrollbarUI

pan(int, int) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

parseAndExecuteCommand(JSONObject) - Method in class org.micromanager.internal.zmq.ZMQServer

parseConstructors(String, Function<Class, Object>) - Static method in class org.micromanager.internal.zmq.ZMQUtil

port_ - Variable in class org.micromanager.internal.zmq.ZMQSocketWrapper

portSocketMap_ - Static variable in class org.micromanager.internal.zmq.ZMQSocketWrapper

PRIMITIVE_ARRAY_NAME_CLASS_MAP - Static variable in class org.micromanager.internal.zmq.ZMQUtil

PRIMITIVE_NAME_CLASS_MAP - Static variable in class org.micromanager.internal.zmq.ZMQUtil

PRIMITIVES - Static variable in class org.micromanager.internal.zmq.ZMQUtil

push(T) - Method in class org.micromanager.internal.zmq.ZMQPushSocket

Serialize the object and send it out to any pulling sockets

putImage(TaggedImage) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

PycroManagerCompatibleAcq - Interface in org.micromanager.remote

This interface enables acquisitions created on the Java side to work with different components of pycro-manager.

PycroManagerCompatibleUI - Interface in org.micromanager.remote

R

receiveMessage() - Method in class org.micromanager.internal.zmq.ZMQSocketWrapper

recordTilesForConfirmation(Point) - Method in class org.micromanager.explore.gui.ExploreMouseListener

RemoteAcqHook - Class in org.micromanager.remote

RemoteAcqHook(AcquisitionAPI) - Constructor for class org.micromanager.remote.RemoteAcqHook

RemoteAcquisition - Class in org.micromanager.remote

Class that serves as the java counterpart to a python acquisition

RemoteAcquisition(RemoteEventSource, RemoteViewerStorageAdapter, boolean) - Constructor for class org.micromanager.remote.RemoteAcquisition

RemoteAcquisitionFactory - Class in org.micromanager.remote

RemoteAcquisitionFactory(CMMCore) - Constructor for class org.micromanager.remote.RemoteAcquisitionFactory

RemoteCoreCallback - Class in org.micromanager.remote

Class that connects core callbacks to a ZMQPush socket so they can be dispatched to external clients

RemoteCoreCallback(CMMCore) - Constructor for class org.micromanager.remote.RemoteCoreCallback

RemoteEventSource - Class in org.micromanager.remote

A source of acquisition events that comes from elsewhere via a ZMQ pull socket

RemoteEventSource() - Constructor for class org.micromanager.remote.RemoteEventSource

RemoteImageProcessor - Class in org.micromanager.remote

Implements an ImageProcessor that sends/recieves images from a remote source using ZMQ push/pull sockets.

RemoteImageProcessor() - Constructor for class org.micromanager.remote.RemoteImageProcessor

RemoteStorageMonitor - Class in org.micromanager.remote

A class that broadcasts information about images that have finsihed saving to disk

RemoteStorageMonitor() - Constructor for class org.micromanager.remote.RemoteStorageMonitor

run(AcquisitionEvent) - Method in class org.micromanager.remote.RemoteAcqHook

S

selectAllChannels() - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

selected() - Method in class org.micromanager.explore.gui.ExploreControlsPanel

sendMessage(JSONObject) - Method in class org.micromanager.internal.zmq.ZMQSocketWrapper

Send a json object as a message, removing binary data as needed and sending in multiple parts

SerializableObject - Interface in org.micromanager.internal.zmq

serialize() - Method in interface org.micromanager.internal.zmq.SerializableObject

serialize(ConcurrentHashMap<String, Object>, Object, JSONObject, int) - Method in class org.micromanager.internal.zmq.ZMQUtil

This version serializes primitves, converts lists to JSONArrays, and sends out pointers to Objects

setAcqAndDequeues(AcquisitionAPI, LinkedBlockingDeque<TaggedImage>, LinkedBlockingDeque<TaggedImage>) - Method in class org.micromanager.remote.RemoteImageProcessor

setActive(boolean) - Method in class org.micromanager.explore.gui.ExploreOverlayer

setChannelGroup(String) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

setChannels(ChannelGroupSettings) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

setField(Object, JSONObject) - Method in class org.micromanager.internal.zmq.ZMQServer

setHighlightedIndices(int, int, int) - Method in class org.micromanager.explore.gui.ColorableScrollbarUI

setUseOnAll(boolean) - Method in class org.micromanager.explore.ChannelGroupSettings

setValueAt(Object, int, int) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

setZLimits(String, double, double) - Method in class org.micromanager.explore.ExploreAcquisition

shutdown() - Method in class org.micromanager.remote.RemoteCoreCallback

SimpleChannelTableModel - Class in org.micromanager.explore.gui

SimpleChannelTableModel(ChannelGroupSettings) - Constructor for class org.micromanager.explore.gui.SimpleChannelTableModel

socket_ - Variable in class org.micromanager.internal.zmq.ZMQSocketWrapper

StackResampler - Class in org.micromanager.lightsheet

This class takes a ZYX stack of pixels and resamples it into a new coordinate space.

StackResampler(int, boolean, double, double, double, int, int, int) - Constructor for class org.micromanager.lightsheet.StackResampler

StackResampler constructor.

StackResampler.ImagePlusSlice - Class in org.micromanager.lightsheet

Helper class to store pixels and frameNr in one instance.

StackResampler.LinearTransformation - Class in org.micromanager.lightsheet

Helper class to do matrix calculations.

start() - Method in class org.micromanager.remote.RemoteStorageMonitor

Start pushing out the indices to the other side

STARTING_PORT_NUMBER - Static variable in class org.micromanager.internal.zmq.ZMQSocketWrapper

startPull() - Method in class org.micromanager.remote.RemoteImageProcessor

startPush() - Method in class org.micromanager.remote.RemoteCoreCallback

startPush() - Method in class org.micromanager.remote.RemoteImageProcessor

startStackProcessing() - Method in class org.micromanager.lightsheet.StackResampler

Pull images from the queue and process them in parallel until a full z stack is processed or a null pix null tags stop signal is received.

storage_ - Variable in class org.micromanager.explore.ExploreAcqUIAndStorage

storageMonitoringComplete() - Method in class org.micromanager.remote.RemoteStorageMonitor

Called by the python side to signal that the final shutdown signal has been received and that the push socket can be closed

storeValuesInPrefs() - Method in class org.micromanager.explore.ChannelGroupSettings

submitEventIterator(Iterator<AcquisitionEvent>) - Method in class org.micromanager.explore.ExploreAcquisition

Submit a iterator of acquisition events for execution.

synchronizeExposures() - Method in class org.micromanager.explore.ChannelGroupSettings

synchronizeExposures() - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

T

tableChanged(TableModelEvent) - Method in class org.micromanager.explore.gui.SimpleChannelTableModel

toJSON(Object) - Static method in class org.micromanager.internal.zmq.ZMQUtil

Convert objects that will be serialized into JSON.

type_ - Variable in class org.micromanager.internal.zmq.ZMQSocketWrapper

U

updateChannelGroup(String) - Method in class org.micromanager.explore.ChannelGroupSettings

updateGUIToReflectHardwareZPosition(String, Integer) - Method in class org.micromanager.explore.gui.ExploreControlsPanel

updateZDrivelocation(Integer) - Method in class org.micromanager.explore.gui.ExploreZSliders

updateZDrivelocation(Integer) - Method in class org.micromanager.explore.gui.ZAxisLimitControlPanel

V

VERSION - Static variable in class org.micromanager.internal.zmq.ZMQServer

viewer_ - Variable in class org.micromanager.explore.gui.ExploreMouseListener

X

XYTiledRemoteAcquisition - Class in org.micromanager.remote

XYTiled acquisition that accepts events froma remote source Class that serves as the java counterpart to a python acquisition

XYTiledRemoteAcquisition(RemoteEventSource, RemoteViewerStorageAdapter, boolean) - Constructor for class org.micromanager.remote.XYTiledRemoteAcquisition

Y

YX_PROJECTION - Static variable in class org.micromanager.lightsheet.StackResampler

Z

ZAxisLimitControlPanel - Class in org.micromanager.explore.gui

ZAxisLimitControlPanel(ExploreAcquisition, ZAxis) - Constructor for class org.micromanager.explore.gui.ZAxisLimitControlPanel

ZMQPullSocket<T> - Class in org.micromanager.internal.zmq

Does not run on its own thread

ZMQPullSocket(Function<JSONObject, T>) - Constructor for class org.micromanager.internal.zmq.ZMQPullSocket

ZMQPushSocket<T> - Class in org.micromanager.internal.zmq

ZMQPushSocket(Function<T, JSONObject>) - Constructor for class org.micromanager.internal.zmq.ZMQPushSocket

ZMQServer - Class in org.micromanager.internal.zmq

implements request reply server (ie the reply part) ecompasses both the master server and the

ZMQServer() - Constructor for class org.micromanager.internal.zmq.ZMQServer

This constructor used if making a new server on a different port and all the classloader info already parsed

ZMQServer(Collection<ClassLoader>, Function<Class, Object>, String[], Consumer<String>) - Constructor for class org.micromanager.internal.zmq.ZMQServer

ZMQServer(Collection<ClassLoader>, Function<Class, Object>, String[], Consumer<String>, int) - Constructor for class org.micromanager.internal.zmq.ZMQServer

ZMQSocketWrapper - Class in org.micromanager.internal.zmq

ZMQSocketWrapper(SocketType, int) - Constructor for class org.micromanager.internal.zmq.ZMQSocketWrapper

ZMQSocketWrapper(SocketType) - Constructor for class org.micromanager.internal.zmq.ZMQSocketWrapper

ZMQUtil - Class in org.micromanager.internal.zmq

ZMQUtil(Collection<ClassLoader>, String[]) - Constructor for class org.micromanager.internal.zmq.ZMQUtil

zoom(double, Point) - Method in class org.micromanager.explore.ExploreAcqUIAndStorage

ZOOM_FACTOR_MOUSE - Static variable in class org.micromanager.explore.gui.ExploreMouseListener

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