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

A

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

anythingAcquired() - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

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

C

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

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

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

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

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

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

D

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

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

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

E

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

Convert array of primitives to a String

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

F

finish() - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

G

getBounds() - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

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

getDiskLocation() - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

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

Called by python side

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

Called by python side

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

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

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

getImageKeys() - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

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

getMaxResolutionIndex() - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

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

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

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

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

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

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

H

HeadlessLauncher - Class in org.micromanager.remote

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

I

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

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

initialize(Acquisition, JSONObject) - Method in class org.micromanager.remote.RemoteViewerStorageAdapter

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.RemoteViewerStorageAdapter

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

L

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

M

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

N

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

O

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

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

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

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

P

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

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.remote.RemoteViewerStorageAdapter

R

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

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

RemoteViewerStorageAdapter - Class in org.micromanager.remote

The class is the glue needed in order for Acquisition engine, viewer, and data storage to be able to be used together, since they are independent libraries that do not know about one another.

RemoteViewerStorageAdapter(boolean, String, String, boolean, int, int, Integer, int) - Constructor for class org.micromanager.remote.RemoteViewerStorageAdapter

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

S

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(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

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

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

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

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

T

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

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

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

V

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

X

XYTiledRemoteAcquisition - Class in org.micromanager.remote

Class that serves as the java counterpart to a python acquisition

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

Z

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

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