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abortRequest() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Request immediate abort of current task
abortRequest() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
abortRequested() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
abortRequested() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
AboutDlg - Class in org.micromanager.internal.dialogs
Help | About dialog for MMStudio.
AboutDlg() - Constructor for class org.micromanager.internal.dialogs.AboutDlg
 
AbstractAnchorEvent<T> - Class in org.micromanager.display.internal.link.internal
 
AbstractDataViewer - Class in org.micromanager.display
Abstract implementation of the DataViewer interface.
AbstractExponentialSmoothing - Class in org.micromanager.internal.utils.performance
Base implementation for exponential smoothing of time series statistic.
AbstractInspectorPanelController - Class in org.micromanager.display.inspector
A panel containing a section of the inspector window.
AbstractInspectorPanelController() - Constructor for class org.micromanager.display.inspector.AbstractInspectorPanelController
 
AbstractLinkAnchor<T> - Class in org.micromanager.display.internal.link
 
AbstractLinkAnchor() - Constructor for class org.micromanager.display.internal.link.AbstractLinkAnchor
 
AbstractOverlay - Class in org.micromanager.display.overlay
Abstract implementation of Overlay.
AbstractOverlay() - Constructor for class org.micromanager.display.overlay.AbstractOverlay
 
accept(File) - Method in class org.micromanager.internal.utils.ScriptFileFilter
 
ACQ_SETTINGS_FILE - Static variable in class org.micromanager.internal.utils.FileDialogs
 
AcqControlDlg - Class in org.micromanager.internal.dialogs
Time-lapse, channel and z-stack acquisition setup dialog.
AcqControlDlg(AcquisitionWrapperEngine, MMStudio) - Constructor for class org.micromanager.internal.dialogs.AcqControlDlg
Acquisition control dialog box.
AcqControlDlg.CheckBoxPanel - Class in org.micromanager.internal.dialogs
Utility class to make a checkboxPanel with a border with a title.
AcqControlDlg.ComponentTitledPanel - Class in org.micromanager.internal.dialogs
Utility class to make a panel with a border with a title.
AcqControlDlg.LabelPanel - Class in org.micromanager.internal.dialogs
Utility class to make a panel with a title.
acqOrderMode() - Method in class org.micromanager.acquisition.SequenceSettings
Order of the various axes during acquisition as defined in AcqOrderMode.
acqOrderMode(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
Sets acquisition order of axes.
AcqOrderMode - Class in org.micromanager.internal.utils
 
AcqOrderMode(int) - Constructor for class org.micromanager.internal.utils.AcqOrderMode
 
AcqSettingsListener - Interface in org.micromanager.internal.interfaces
 
acquire() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Starts acquisition as defined in the Multi-Dimensional Acquisition Window.
acquire() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
AcquisitionDialogPlugin - Interface in org.micromanager.acquisition.internal
This plugin type allows you to override the Multi-Dimensional Acquisition dialog used to perform data acquisition.
AcquisitionEndedEvent - Interface in org.micromanager.acquisition
This event signifies that an acquisition has been ended.
AcquisitionEngine - Interface in org.micromanager.acquisition.internal
The original Acquisition engine interface.
AcquisitionManager - Interface in org.micromanager.acquisition
This interface provides access to methods related to the acquisition engine for performing experiments.
acquisitions() - Method in class org.micromanager.internal.MMStudio
 
acquisitions() - Method in interface org.micromanager.Studio
Provide access to the AcquisitionManager, for running data acquisition using the Micro-Manager acquisition engine.
AcquisitionSelector - Class in org.micromanager.acquisition.internal
This class provides a JButton that accesses the acquisition dialog -- or, if there is more than one such dialog available, provides a popup menu of dialogs to choose from.
AcquisitionSelector() - Constructor for class org.micromanager.acquisition.internal.AcquisitionSelector
 
AcquisitionSequenceStartedEvent - Interface in org.micromanager.acquisition
This variant of the AcquisitionStartedEvent is used for acquisitions that can be described by a SequenceSettings, it provides access to those SequenceSettings.
AcquisitionSleepEvent - Class in org.micromanager.acquisition.internal
This class signals that the acquisition engine is sleeping.
AcquisitionSleepEvent(double) - Constructor for class org.micromanager.acquisition.internal.AcquisitionSleepEvent
 
AcquisitionStartedEvent - Interface in org.micromanager.acquisition
This class signals that an acquisition is starting, and provides access to the Datastore that images from the acquisition will be put into.
AcquisitionWrapperEngine - Class in org.micromanager.acquisition.internal
 
AcquisitionWrapperEngine() - Constructor for class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
ActionCollRenderer() - Constructor for class org.micromanager.internal.utils.HotKeysDialog.ActionCollRenderer
 
actionPerformed(ActionEvent) - Method in class org.micromanager.internal.dialogs.ProfileSelectionUIController
 
actionPerformed(ActionEvent) - Method in class org.micromanager.internal.utils.ColorEditor
Handles events from the editor button and from the dialog's OK button.
activate(DisplayController) - Method in class org.micromanager.internal.navigation.UiMovesStageManager
Keep track of enabling/disabling click-to-move for this display.
activate() - Method in class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
activate() - Method in class org.micromanager.quickaccess.internal.controls.RefreshButton
 
activate() - Method in class org.micromanager.quickaccess.SimpleButtonPlugin
This method will be called when the button is clicked.
activateAxisTable(boolean) - Method in class org.micromanager.internal.positionlist.PositionListDlg
 
active_ - Static variable in class org.micromanager.internal.utils.HotKeys
 
add(Calibration) - Method in class org.micromanager.internal.utils.CalibrationList
Add one Calibration to the list
add(JMenuItem) - Method in class org.micromanager.internal.utils.SortedMenu
 
add(JMenuItem) - Method in class org.micromanager.internal.utils.SortedPopupMenu
 
add(StagePosition) - Method in class org.micromanager.MultiStagePosition
Add one stage position point.
ADD_TO_ALBUM - Static variable in class org.micromanager.internal.utils.HotKeyAction
 
addActionListener(ActionListener) - Method in class org.micromanager.internal.dialogs.AcqControlDlg.CheckBoxPanel
 
addAlert(DefaultAlert) - Method in class org.micromanager.alerts.internal.AlertsWindow
 
addAndConfigureProcessor(ProcessorPlugin) - Method in interface org.micromanager.data.DataManager
Add a new instance of the given ProcessorPlugin to the current application image processing pipeline.
addAndConfigureProcessor(ProcessorPlugin) - Method in class org.micromanager.data.internal.DefaultDataManager
 
addAndConfigureProcessor(ProcessorPlugin) - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
Add a new entry to the list of processors.
addCategorizedAlert(String) - Method in class org.micromanager.alerts.internal.AlertsWindow
Create an alert that can contain multiple categories of messages.
addChangeListener(ChangeListener) - Method in class org.micromanager.PositionList
Adds a changeListener to this PositionList.
addCheckBoxMenuItem(JMenu, String, String, Runnable, boolean) - Static method in class org.micromanager.internal.utils.GUIUtils
 
addConfigGroup(String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
addConfigPreset(ConfigPreset) - Method in class org.micromanager.internal.hcwizard.ConfigGroup
 
addConfigSetting(String, String, String, String) - Method in class org.micromanager.internal.hcwizard.ConfigGroup
 
addConfiguration(JSONObject, Configuration) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
addConfigurator(ConfiguratorWrapper) - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
addConfiguredProcessor(ProcessorConfigurator, ProcessorPlugin) - Method in interface org.micromanager.data.DataManager
Add the provide ProcessorConfigurator onto the end of the application image processing pipeline.
addConfiguredProcessor(ProcessorConfigurator, ProcessorPlugin) - Method in class org.micromanager.data.internal.DefaultDataManager
 
addConfiguredProcessor(ProcessorConfigurator, ProcessorPlugin) - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
Add a new entry to the list of processors, which has already been configured.
addControl(ControlCell) - Method in class org.micromanager.quickaccess.internal.QuickAccessFrame
Add a control to the grid of controls at the specified location and dimensionality.
addCurrentProfileChangeListener(ChangeListener) - Method in class org.micromanager.profile.internal.UserProfileAdmin
 
addCustomAlert(String, JComponent) - Method in class org.micromanager.alerts.internal.AlertsWindow
Create a custom alert with any contents
addDataViewer(DataViewer) - Method in class org.micromanager.display.internal.DataViewerCollection
 
addDevice(Device) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
addDynamicTextFieldListener(DynamicTextField.Listener) - Method in class org.micromanager.internal.utils.DynamicTextField
 
addEditActionListener(ActionListener) - Method in class org.micromanager.internal.utils.SliderPanel
 
addGroup() - Method in class org.micromanager.internal.ConfigPadButtonPanel
 
addHTMLBreaksForTooltip(String) - Static method in class org.micromanager.internal.utils.TooltipTextMaker
 
addImage(Image) - Method in interface org.micromanager.Album
Add the specified Image to the Album's datastore.
addImage(Image) - Method in class org.micromanager.internal.DefaultAlbum
 
addImages(Collection<Image>) - Method in interface org.micromanager.Album
Add the specified Images to the Album's datastore.
addImages(Collection<Image>) - Method in class org.micromanager.internal.DefaultAlbum
 
addImageTagsToOME(Coords, Metadata, int, String, String, String) - Method in class org.micromanager.data.internal.multipagetiff.OMEMetadata
 
addIndexChangeListener(ChangeListener) - Method in class org.micromanager.profile.internal.UserProfileAdmin
 
addInspector(InspectorController) - Method in class org.micromanager.display.inspector.internal.InspectorCollection
 
addInspectorPanelListener(InspectorPanelListener) - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
 
addInspectorPanelListener(InspectorPanelListener) - Method in interface org.micromanager.display.inspector.InspectorPanelController
 
addLayoutComponent(Component, Object) - Method in class org.micromanager.quickaccess.internal.SparseGridLayout
 
addLayoutComponent(String, Component) - Method in class org.micromanager.quickaccess.internal.SparseGridLayout
 
addListener(DataViewerListener, int) - Method in interface org.micromanager.display.DataViewer
Listeners will be notified of important events of the DataViewer.
addListener(HistogramView.Listener) - Method in class org.micromanager.display.inspector.internal.panels.intensity.HistogramView
 
addListener(AnimationController.Listener) - Method in class org.micromanager.display.internal.animate.AnimationController
 
addListener(DataViewerListener, int) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
addListener(StatsComputeQueue.Listener) - Method in class org.micromanager.display.internal.imagestats.StatsComputeQueue
 
addListener() - Method in class org.micromanager.internal.positionlist.CellEditor
 
addListeners() - Method in class org.micromanager.internal.positionlist.PositionListDlg
 
addMenuItem(JMenu, JMenuItem, String, Runnable) - Static method in class org.micromanager.internal.utils.GUIUtils
Adds a menu item to the specified parent menu.
addMenuItem(JMenu, String, String, Runnable) - Static method in class org.micromanager.internal.utils.GUIUtils
Adds a menu item with given text to the specified parent menu.
addMenuItem(JMenu, String, String, Runnable, String) - Static method in class org.micromanager.internal.utils.GUIUtils
Adds a menu item with given text and icon to the specified parent menu.
addNewCalibration() - Method in class org.micromanager.internal.dialogs.CalibrationListDlg
 
addNewChannel() - Method in class org.micromanager.internal.dialogs.ChannelTableModel
Adds a new channel to the list in the MDA window
addOverlay(Overlay) - Method in interface org.micromanager.display.DisplayWindow
Add a graphical overlay.
addOverlay(Overlay) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
addOverlayListener(OverlayListener) - Method in class org.micromanager.display.overlay.AbstractOverlay
Add a listener.
addOverlayListener(OverlayListener) - Method in interface org.micromanager.display.overlay.Overlay
Add a listener.
addPopupButtonListener(PopupButton.Listener) - Method in class org.micromanager.internal.utils.PopupButton
 
addPosition(MultiStagePosition, String) - Method in class org.micromanager.internal.positionlist.PositionListDlg
 
addPosition(MultiStagePosition) - Method in class org.micromanager.internal.positionlist.PositionListDlg
 
addPosition(MultiStagePosition) - Method in class org.micromanager.PositionList
Adds a new position to the list.
addPosition(int, MultiStagePosition) - Method in class org.micromanager.PositionList
Insert a position into the list.
addPreset() - Method in class org.micromanager.internal.ConfigPadButtonPanel
Add a config to a group (user pressed plus config button).
addRandomUUID(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
AddSelectedPeripherals(CMMCore, Vector<Device>, Vector<String>, Vector<Boolean>) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
addSeparator() - Method in class org.micromanager.internal.utils.SortedPopupMenu
 
addSetting(Setting) - Method in class org.micromanager.internal.hcwizard.ConfigPreset
 
addSettingsListener(AcqSettingsListener) - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
addSettingsListener(AcqSettingsListener) - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
addSetupLabel(Label) - Method in class org.micromanager.internal.hcwizard.Device
 
addSetupLabel(String, Label) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
addSetupProperty(PropertyItem) - Method in class org.micromanager.internal.hcwizard.Device
 
addSetupProperty(String, PropertyItem) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
addSlice(String) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
addSlice(String, Object) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
addSlice(ImageProcessor) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
addSlice(String, ImageProcessor) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
addSlice(String, ImageProcessor, int) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
addSliderMouseListener(MouseAdapter) - Method in class org.micromanager.internal.utils.SliderPanel
 
addSynchroDevice(String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
addText(Class<?>, String) - Method in class org.micromanager.alerts.internal.CategorizedAlert
Add a new label to our contents.
addToGson(JsonObject, PropertyMap) - Method in class org.micromanager.internal.propertymap.NonPropertyMapJSONFormats
 
addUnsorted(JMenuItem) - Method in class org.micromanager.internal.utils.SortedMenu
 
addUnsorted(JMenuItem) - Method in class org.micromanager.internal.utils.SortedPopupMenu
Insert an item whose position will be ignored when sorting items.
addUpdatableAlert(String, String) - Method in class org.micromanager.alerts.internal.AlertsWindow
Create a simple alert with a text message.
addViewer(DataViewer) - Method in interface org.micromanager.display.DisplayManager
Register a DataViewer with the Display Manager.
addViewer(DataViewer) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
adjustmentValueChanged(AdjustmentEvent) - Method in class org.micromanager.display.internal.displaywindow.MDScrollBarPanel
 
adjustZoom(double) - Method in interface org.micromanager.display.DisplayWindow
Multiply the current zoom ratio of the image canvas by the provided factor.
adjustZoom(double) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
advanceAnimationPosition(double) - Method in interface org.micromanager.display.internal.animate.AnimationStateDelegate
Advance the current (last rendered) data position by the given number of frames.
advanceAnimationPosition(double) - Method in class org.micromanager.display.internal.animate.DataCoordsAnimationState
 
AffineEditorPanel - Class in org.micromanager.internal.dialogs
 
AffineEditorPanel(Studio, PixelSizeProvider, DoubleVector) - Constructor for class org.micromanager.internal.dialogs.AffineEditorPanel
 
affineToDouble(AffineTransform) - Static method in class org.micromanager.internal.utils.AffineUtils
 
affineToMeasurements(AffineTransform) - Static method in class org.micromanager.internal.utils.AffineUtils
Convert affine transform to human-interpretable measurements of rotation, scale, and shear
AffineUtils - Class in org.micromanager.internal.utils
Utilities specific to the use of affine transforms in Micro-Manager Mainly concerns itself with translation between the different data formats for affine transform
AffineUtils() - Constructor for class org.micromanager.internal.utils.AffineUtils
 
Album - Interface in org.micromanager
Interface for interacting with the Album, an implicit Datastore that Micro-Manager uses as a "scratch pad" for image data.
album() - Method in class org.micromanager.internal.MMStudio
 
album() - Method in interface org.micromanager.Studio
Provides access to and control of the contents of the Album, the implicit, temporary image storage datastore.
Alert - Interface in org.micromanager.alerts
An Alert is a temporary, undecorated message that is displayed to the user in the Messages window.
AlertClearedEvent - Class in org.micromanager.alerts.internal
This event is posted on the application event bus whenever an alert is dismissed from the Messages window.
AlertClearedEvent(DefaultAlert) - Constructor for class org.micromanager.alerts.internal.AlertClearedEvent
 
AlertManager - Interface in org.micromanager.alerts
The AlertManager allows you to show non-intrusive messages to the user, which will be displayed in a special window, the Messages window.
alerts() - Method in class org.micromanager.internal.MMStudio
 
alerts() - Method in interface org.micromanager.Studio
Provide access to the AlertManager, for creating low-profile, non- interrupting alerts in the user interface.
AlertsWindow - Class in org.micromanager.alerts.internal
 
AlertsWindow(Studio) - Constructor for class org.micromanager.alerts.internal.AlertsWindow
 
alertsWindow() - Method in class org.micromanager.alerts.internal.DefaultAlertManager
 
AlertUpdatedEvent - Class in org.micromanager.alerts.internal
This event is posted on the application event bus whenever an alert is created or updated.
AlertUpdatedEvent(DefaultAlert) - Constructor for class org.micromanager.alerts.internal.AlertUpdatedEvent
 
allowChangesOnlyWhenUsed(boolean) - Method in class org.micromanager.internal.utils.PropertyTableData.Builder
 
allowChangingProperties(boolean) - Method in class org.micromanager.internal.utils.PropertyTableData.Builder
 
allowed - Variable in class org.micromanager.internal.utils.PropertyItem
 
AnalysisWindows2D - Class in org.micromanager.internal.utils.imageanalysis
Code to generate Making Windows (https://en.wikipedia.org/wiki/Window_function) for instance useful when masking edges to avoid Fourier border artefacts
AnalysisWindows2D() - Constructor for class org.micromanager.internal.utils.imageanalysis.AnalysisWindows2D
 
AnchorDidBecomeInSyncEvent<T> - Interface in org.micromanager.display.internal.link
 
AnchorDidBecomeLinkableEvent<T> - Interface in org.micromanager.display.internal.link
 
AnchorDidBecomeOutOfSyncEvent<T> - Interface in org.micromanager.display.internal.link
 
AnchorDidMakeLinkEvent<T> - Interface in org.micromanager.display.internal.link
 
AnchorWillBecomeUnlinkableEvent<T> - Interface in org.micromanager.display.internal.link
 
AnchorWillBreakLinkEvent<T> - Interface in org.micromanager.display.internal.link
 
animationAcknowledgeDataPosition(P) - Method in interface org.micromanager.display.internal.animate.AnimationController.Listener
Update range but don't display
animationAcknowledgeDataPosition(Coords) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
AnimationController<P> - Class in org.micromanager.display.internal.animate
Coordinates and moderates animation of displayed data position.
AnimationController.Listener<P> - Interface in org.micromanager.display.internal.animate
Listeners are notified on an otherwise nonblocking thread owned by the animation controller (never the EDT).
AnimationController.NewPositionHandlingMode - Enum in org.micromanager.display.internal.animate
 
animationDidJumpToNewDataPosition(P) - Method in interface org.micromanager.display.internal.animate.AnimationController.Listener
 
animationDidJumpToNewDataPosition(Coords) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
animationFPS(Double) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder
Deprecated.
animationFPS(Double) - Method in class org.micromanager.display.internal.DefaultDisplaySettings.LegacyBuilder
Deprecated.
 
animationNewDataPositionExpired() - Method in interface org.micromanager.display.internal.animate.AnimationController.Listener
What could this signify? Docs can be useful!
animationNewDataPositionExpired() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
animationShouldDisplayDataPosition(P) - Method in interface org.micromanager.display.internal.animate.AnimationController.Listener
 
animationShouldDisplayDataPosition(Coords) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
AnimationStateDelegate<P> - Interface in org.micromanager.display.internal.animate
An object that computes the next data position to render in an animated display.
animationWillJumpToNewDataPosition(P) - Method in interface org.micromanager.display.internal.animate.AnimationController.Listener
 
animationWillJumpToNewDataPosition(Coords) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
Annotation - Interface in org.micromanager.data
A Annotation is a container for mutable information that is associated with a Datastore.
app() - Method in class org.micromanager.internal.MMStudio
 
app() - Method in interface org.micromanager.Studio
Provides access to the application API for controlling and updating the GUI.
Application - Interface in org.micromanager
Provides access to and control of various aspects of the user interface, allowing code to directly update and control the GUI.
ApplicationSkin - Interface in org.micromanager
Provides access to methods dealing with the "skin" or "look and feel" of the user interface.
ApplicationSkin.SkinMode - Enum in org.micromanager
Available skins used by the application.
ApplicationSkinEvent - Interface in org.micromanager.events
This event is posted when the ApplicationSkin is set via ApplicationSkin.setSkin(org.micromanager.ApplicationSkin.SkinMode).
applyDelaysToHardware(CMMCore) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
applyDisplaySettings(DisplaySettings) - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
applySettings() - Method in interface org.micromanager.AutofocusPlugin
Pushes setting to the hardware or software autofocus.
applySettings() - Method in class org.micromanager.internal.utils.CoreAutofocus
 
applySetupConfigsToHardware(CMMCore) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
Transfer to hardware all configuration settings defined in the setup
applySetupLabelsToHardware(CMMCore) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
Transfer to hardware all labels defined in the setup
arrayFromBuffer(Buffer) - Static method in class org.micromanager.data.internal.BufferTools
 
AsynchronousContext - Class in org.micromanager.data.internal.pipeline
 
AsynchronousContext(Processor, Datastore, DefaultPipeline) - Constructor for class org.micromanager.data.internal.pipeline.AsynchronousContext
 
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
Attach to a data viewer.
attachDataViewer(DataViewer) - Method in interface org.micromanager.display.inspector.InspectorPanelController
 
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.internal.panels.comments.CommentsInspectorPanelController
 
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.internal.panels.intensity.IntensityInspectorPanelController
 
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.internal.panels.metadata.PlaneMetadataInspectorPanelController
 
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.internal.panels.metadata.SummaryMetadataInspectorPanelController
 
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.internal.panels.overlays.OverlaysInspectorPanelController
 
attachRunnable(int, int, int, int, Runnable) - Method in interface org.micromanager.acquisition.AcquisitionManager
Attach a runnable to the acquisition engine.
attachRunnable(int, int, int, int, Runnable) - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
attachRunnable(int, int, int, int, Runnable) - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
attachRunnable(int, int, int, int, Runnable) - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
attachRunnable(int, int, int, int, Runnable) - Method in interface org.micromanager.acquisition.internal.IAcquisitionEngine2010
 
attachToFixedDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.internal.InspectorController
 
attachToFrontmostDataViewer() - Method in class org.micromanager.display.inspector.internal.InspectorController
 
AutofocusBase - Class in org.micromanager.internal.utils
 
AutofocusBase() - Constructor for class org.micromanager.internal.utils.AutofocusBase
 
AutofocusButtons - Class in org.micromanager.quickaccess.internal.controls
Implements the "Autofocus" buttons (one to run autofocus, one to adjust the autofocus options).
AutofocusButtons() - Constructor for class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
AutofocusManager - Interface in org.micromanager
This entity provides access to methods for controlling autofocus of the microscope.
autofocusNow() - Method in class org.micromanager.internal.MMStudio
Executes a full focus from the current autofocus device.
AutofocusPlugin - Interface in org.micromanager
This interface is used for a java-based autofocus plugin.
AutofocusPluginShouldInitializeEvent - Class in org.micromanager.events
Deprecated.
use
AutofocusPluginShouldInitializeEvent() - Constructor for class org.micromanager.events.AutofocusPluginShouldInitializeEvent
Deprecated.
 
AutofocusPropertyEditor - Class in org.micromanager.internal.utils
/** PropertyEditor provides UI for manipulating sets of autofocus properties.
AutofocusPropertyEditor(Studio, DefaultAutofocusManager) - Constructor for class org.micromanager.internal.utils.AutofocusPropertyEditor
Constructs the Autofocus Property Editor.
AutofocusPropertyEditor.PropertyCellEditor - Class in org.micromanager.internal.utils
Cell editing using either JTextField or JComboBox depending on whether the property enforces a set of allowed values.
AutofocusPropertyEditor.PropertyCellRenderer - Class in org.micromanager.internal.utils
Cell rendering for the device property table.
AutomaticCalibrationThread - Class in org.micromanager.internal.pixelcalibrator
 
autoscaleIgnoredPercentile(double) - Method in interface org.micromanager.display.DisplaySettings.Builder
 
autoscaleIgnoredQuantile(double) - Method in interface org.micromanager.display.DisplaySettings.Builder
 
AutoShutterEvent - Interface in org.micromanager.events
This event is posted when autoshutter is enabled or disabled.
autostretch(boolean) - Method in interface org.micromanager.display.DisplaySettings.Builder
Whether to continuously apply autoscale.
autostretch() - Method in interface org.micromanager.display.DisplayWindow
Perform a one-shot autoscaling of intensities.
autostretch() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
AUTOSTRETCH - Static variable in class org.micromanager.internal.utils.HotKeyAction
 
axisOrder(String...) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
axisOrder(Iterable<String>) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
axisOrder(String...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
axisOrder(Iterable<String>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
axisOrder(String...) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
 
AxisPanel(DisplayWindow, ExportMovieDlg) - Constructor for class org.micromanager.display.internal.gearmenu.ExportMovieDlg.AxisPanel
 

B

BaseContext - Class in org.micromanager.data.internal.pipeline
 
BaseContext(Processor, Datastore, DefaultPipeline) - Constructor for class org.micromanager.data.internal.pipeline.BaseContext
 
BeanshellEngine - Class in org.micromanager.internal.script
 
BeanshellEngine(ScriptPanel) - Constructor for class org.micromanager.internal.script.BeanshellEngine
 
BeanshellEngine.EvalThread - Class in org.micromanager.internal.script
 
BEANSHELLSCRIPT - Static variable in class org.micromanager.internal.utils.HotKeyAction
 
beanShellScript_ - Variable in class org.micromanager.internal.utils.HotKeyAction
 
binning(Integer) - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
binning(Integer) - Method in interface org.micromanager.data.Metadata.Builder
 
binning(Integer) - Method in interface org.micromanager.data.Metadata.MetadataBuilder
Deprecated.
 
bitDepth(Integer) - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
bitDepth(Integer) - Method in interface org.micromanager.data.Metadata.Builder
 
bitDepth(Integer) - Method in interface org.micromanager.data.Metadata.MetadataBuilder
Deprecated.
 
BITS_PER_SAMPLE - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
BoofCVImageConverter - Class in org.micromanager.internal.utils.imageanalysis
Collection of static functions that convert between ImageJ, Micro-Manager, and BoofCV images.
BoofCVImageConverter() - Constructor for class org.micromanager.internal.utils.imageanalysis.BoofCVImageConverter
 
boofCVToMM(ImageGray<? extends ImageGray<?>>, Coords, Metadata) - Static method in class org.micromanager.internal.utils.imageanalysis.BoofCVImageConverter
Converts a boofCV image into a MM image Currently only supports GrayU8 and GrayU16, returns null for other types
boofCVToMM(ImageGray<? extends ImageGray<?>>, boolean, Coords, Metadata) - Static method in class org.micromanager.internal.utils.imageanalysis.BoofCVImageConverter
Converts a boofCV image into a MM image Currently only supports GrayU8 and GrayU16, returns null for other types
borderSet_ - Variable in class org.micromanager.internal.dialogs.AcqControlDlg.ComponentTitledPanel
 
bottomHanWindow1DA(int, int) - Static method in class org.micromanager.internal.utils.imageanalysis.ImagePadder
Creates a HanWindow specific for the padPreibisch function Top half is 0, followed by a "half" HanWindow ending at 1.0
boundingBox(MultiStagePosition[], String) - Method in class org.micromanager.internal.positionlist.utils.TileCreator
 
Bounds() - Constructor for class org.micromanager.internal.graph.GraphData.Bounds
 
BoundsRectAndMask - Class in org.micromanager.display.internal.imagestats
 
BppToImageType(long) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
BSH_FILE - Static variable in class org.micromanager.internal.script.ScriptPanel
 
BufferTools - Class in org.micromanager.data.internal
 
BufferTools() - Constructor for class org.micromanager.data.internal.BufferTools
 
build() - Method in class org.micromanager.acquisition.ChannelSpec.Builder
 
build() - Method in class org.micromanager.acquisition.SequenceSettings.Builder
Constructs SequenceSettings.
build() - Method in interface org.micromanager.data.Coords.Builder
 
build() - Method in interface org.micromanager.data.Coords.CoordsBuilder
 
build() - Method in class org.micromanager.data.internal.DefaultCoords.Builder
 
build() - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
build() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
build() - Method in interface org.micromanager.data.Metadata.MetadataBuilder
Deprecated.
Construct a Metadata from the MetadataBuilder.
build() - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
 
build() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
build() - Method in interface org.micromanager.display.ComponentDisplaySettings.Builder
 
build() - Method in interface org.micromanager.display.DisplaySettings.Builder
 
build() - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder
Deprecated.
build() - Method in class org.micromanager.display.internal.DefaultDisplaySettings.LegacyBuilder
Deprecated.
 
build(Studio) - Method in class org.micromanager.display.internal.displaywindow.DisplayController.Builder
 
build() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats.Builder
 
build() - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap.Builder
 
build() - Method in class org.micromanager.internal.utils.PropertyTableData.Builder
 
build() - Method in interface org.micromanager.PropertyMap.Builder
 
build() - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder
Deprecated.
Builder() - Constructor for class org.micromanager.acquisition.ChannelSpec.Builder
 
Builder() - Constructor for class org.micromanager.acquisition.SequenceSettings.Builder
 
Builder(SequenceSettings) - Constructor for class org.micromanager.acquisition.SequenceSettings.Builder
Construct a Builder using the given SequenceSettings (copy builder).
builder() - Static method in class org.micromanager.data.Coordinates
 
Builder() - Constructor for class org.micromanager.data.internal.DefaultCoords.Builder
 
Builder() - Constructor for class org.micromanager.data.internal.DefaultMetadata.Builder
 
Builder() - Constructor for class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
builder() - Static method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
builder() - Static method in class org.micromanager.display.internal.DefaultComponentDisplaySettings
 
builder() - Static method in class org.micromanager.display.internal.DefaultDisplaySettings
 
Builder(DataProvider) - Constructor for class org.micromanager.display.internal.displaywindow.DisplayController.Builder
 
builder() - Static method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
builder() - Static method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
Builder() - Constructor for class org.micromanager.internal.propertymap.DefaultPropertyMap.Builder
 
Builder(Studio) - Constructor for class org.micromanager.internal.utils.PropertyTableData.Builder
 
builder() - Static method in class org.micromanager.PropertyMaps
Returns a builder object for creating PropertyMap instances.
buttonFont - Static variable in class org.micromanager.internal.utils.GUIUtils
 
BYTE_ORDER - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
bytesFromBuffer(ByteBuffer) - Static method in class org.micromanager.data.internal.BufferTools
 

C

c(int) - Method in interface org.micromanager.data.Coords.Builder
Shorthand for channel.
C - Static variable in interface org.micromanager.data.Coords
Axis label for the channel axis (short form).
c(int) - Method in class org.micromanager.data.internal.DefaultCoords.Builder
 
cache() - Method in class org.micromanager.internal.MMStudio
 
calculate() - Method in class org.micromanager.internal.dialogs.AffineEditorPanel
 
Calibration - Class in org.micromanager.internal.utils
 
Calibration() - Constructor for class org.micromanager.internal.utils.Calibration
 
calibrationDone() - Method in class org.micromanager.internal.pixelcalibrator.PixelCalibratorDialog
 
CalibrationEditor - Class in org.micromanager.internal.dialogs
Dialog for editing of a pixel size configuration preset.
CalibrationEditor(Studio, String, String) - Constructor for class org.micromanager.internal.dialogs.CalibrationEditor
 
CalibrationEditor.PropertyCellEditor - Class in org.micromanager.internal.dialogs
Cell editing using either JTextField or JComboBox depending on whether the property enforces a set of allowed values.
CalibrationEditor.PropertyCellRenderer - Class in org.micromanager.internal.dialogs
 
calibrationFailed(boolean) - Method in class org.micromanager.internal.pixelcalibrator.PixelCalibratorDialog
 
CalibrationList - Class in org.micromanager.internal.utils
 
CalibrationList(CMMCore) - Constructor for class org.micromanager.internal.utils.CalibrationList
 
CalibrationListDlg - Class in org.micromanager.internal.dialogs
 
CalibrationListDlg(CMMCore) - Constructor for class org.micromanager.internal.dialogs.CalibrationListDlg
Create the dialog
CalibrationThread - Class in org.micromanager.internal.pixelcalibrator
 
CalibrationThread() - Constructor for class org.micromanager.internal.pixelcalibrator.CalibrationThread
 
camera(String) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
 
camera - Variable in class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder and getters instead
camera() - Method in class org.micromanager.acquisition.ChannelSpec
 
camera(String) - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
camera(String) - Method in interface org.micromanager.data.Metadata.Builder
 
camera(String) - Method in interface org.micromanager.data.Metadata.MetadataBuilder
Deprecated.
 
cameras_ - Variable in class org.micromanager.internal.utils.ShowFlags
 
cameraTimeout(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
 
cameraTimeout - Variable in class org.micromanager.acquisition.SequenceSettings
Deprecated.
use Builder and cameraTimeout() instead
cameraTimeout() - Method in class org.micromanager.acquisition.SequenceSettings
Minimum camera timeout, in ms, for sequence acquisitions (actual timeout depends on exposure time and other factors).
cancelLogCapture() - Method in class org.micromanager.internal.diagnostics.ProblemReport
Stop CoreLog capture and discard captured log.
CancelRequest() - Method in class org.micromanager.internal.hcwizard.DetectorJDialog
 
cancelShutdown() - Method in class org.micromanager.events.internal.DefaultShutdownCommencingEvent
Cancel shutdown.
cancelShutdown() - Method in class org.micromanager.events.internal.InternalShutdownCommencingEvent
Cancel shutdown.
cancelShutdown() - Method in interface org.micromanager.events.ShutdownCommencingEvent
Cancel shutdown.
canCloseViewer(DataViewer) - Method in class org.micromanager.acquisition.internal.MMAcquisition
 
canCloseViewer(DataViewer) - Method in class org.micromanager.display.DataViewerListener
Whether or not the DataViewer can be closed.
canCloseViewer(DataViewer) - Method in class org.micromanager.display.internal.DefaultDisplayManager
Check if this is the last display for a Datastore that we are managing, and verify closing without saving (if appropriate).
canCloseViewer(DataViewer) - Method in class org.micromanager.internal.SnapLiveManager
 
canCloseViewerWithoutPrompting(DataViewer) - Method in class org.micromanager.display.internal.DefaultDisplayManager
Checks if this is the last display for a managed Datastore, and if so, whether that datastore can be closed without prompting Informational only, no actions are taken, so no side effects (unlike canCLoseViewer) *
canFitRect(Rectangle, ControlCell) - Method in class org.micromanager.quickaccess.internal.QuickAccessFrame
Return true if there is room for a control at the desired rect.
canvasDidChangeSize() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
canvasNeedsSwap() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
cascade(Window, Class<?>) - Static method in class org.micromanager.internal.utils.WindowPositioning
Set the location of a window so that it cascades within a series of windows.
CategorizedAlert - Class in org.micromanager.alerts.internal
Subclass of DefaultAlert intended for showing multiple lines of alert texts, broken out into subcategories and using a scrollpane if necessary.
CELL_HEIGHT - Static variable in class org.micromanager.quickaccess.QuickAccessPlugin
The height of a single cell in the Quick-Access Window.
CELL_WIDTH - Static variable in class org.micromanager.quickaccess.QuickAccessPlugin
The width of a single cell in the Quick-Access Window.
CellEditor - Class in org.micromanager.internal.positionlist
Editor component for the position list table
CellEditor(Font) - Constructor for class org.micromanager.internal.positionlist.CellEditor
 
CenterAndDragListener - Class in org.micromanager.internal.navigation
Implementation of the Center And DragListener that lets the user "drag" the stage.
CenterAndDragListener(Studio, XYNavigator) - Constructor for class org.micromanager.internal.navigation.CenterAndDragListener
 
centerFrameWithFrame(Window, Window) - Static method in class org.micromanager.internal.utils.GUIUtils
Center the provided Window within the screen contained by the provided other window.
ChainedMapView<K,V> - Class in org.micromanager.internal.utils
 
changeAxis(String, String) - Method in class org.micromanager.display.internal.gearmenu.ExportMovieDlg
One of our panels is changing from the old axis to the new axis; if the new axis is represented in any other panel, it must be swapped with the old one.
changeDeviceName(String, String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
changedUpdate(DocumentEvent) - Method in class org.micromanager.display.inspector.internal.panels.comments.CommentsInspectorPanelController
 
channel(int) - Method in interface org.micromanager.data.Coords.Builder
Set the channel index.
CHANNEL - Static variable in interface org.micromanager.data.Coords
Axis label for the channel axis.
channel(int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
 
channel(int) - Method in class org.micromanager.data.internal.DefaultCoords.Builder
 
channel(int) - Method in interface org.micromanager.display.DisplaySettings.Builder
Increases the number of ChannelDisplaySettings in this Builder to the given number.
channel(int, ChannelDisplaySettings) - Method in interface org.micromanager.display.DisplaySettings.Builder
Sets the ChannelDisplaySettings for the given channel.
ChannelCellEditor - Class in org.micromanager.internal.dialogs
Cell editing using either JTextField or JComboBox depending on whether the property enforces a set of allowed values.
ChannelCellEditor() - Constructor for class org.micromanager.internal.dialogs.ChannelCellEditor
 
ChannelCellRenderer - Class in org.micromanager.internal.dialogs
Renderer class for the channel table.
ChannelCellRenderer(AcquisitionEngine) - Constructor for class org.micromanager.internal.dialogs.ChannelCellRenderer
 
ChannelColorEvent - Class in org.micromanager.events.internal
Signals that the user assigned a new color to a channel Used to synchronize the color used to display a channel in the UI
ChannelColorEvent(String, String, Color) - Constructor for class org.micromanager.events.internal.ChannelColorEvent
 
channelColorMode(DisplaySettings.ColorMode) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder
Deprecated.
channelColorMode(DisplaySettings.ColorMode) - Method in class org.micromanager.display.internal.DefaultDisplaySettings.LegacyBuilder
Deprecated.
 
channelColors(Color[]) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder
Deprecated.
channelColors(Color[]) - Method in class org.micromanager.display.internal.DefaultDisplaySettings.LegacyBuilder
Deprecated.
 
channelContrastSettings(DisplaySettings.ContrastSettings[]) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder
Deprecated.
channelContrastSettings(DisplaySettings.ContrastSettings[]) - Method in class org.micromanager.display.internal.DefaultDisplaySettings.LegacyBuilder
Deprecated.
 
ChannelDisplaySettings - Interface in org.micromanager.display
Stores the display settings for individual channels Coords of image to be displayed.
ChannelDisplaySettings.Builder - Interface in org.micromanager.display
Builder for ChannelDisplaySettings.
channelDisplaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager
Generates a blank channelDisplaySettings Builder with all null values.
channelDisplaySettingsBuilder() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
ChannelExposureEvent - Interface in org.micromanager.events
This class signals when the exposure time for one of the channels of the current channel group has been changed.
channelGroup(String) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
 
channelGroup - Variable in class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder and getters instead
channelGroup() - Method in class org.micromanager.acquisition.ChannelSpec
 
channelGroup(String) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
 
channelGroup - Variable in class org.micromanager.acquisition.SequenceSettings
Deprecated.
use Builder and channelGroup() instead
channelGroup() - Method in class org.micromanager.acquisition.SequenceSettings
Configuration group used to define channels used in the acquisition.
channelGroup(String) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
channelGroup(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
channelGroup(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
 
ChannelGroupChangedEvent - Interface in org.micromanager.events
Event signaling that the "Channel Group" changed.
ChannelIntensityController - Class in org.micromanager.display.inspector.internal.panels.intensity
 
channelNames(String...) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
channelNames(Iterable<String>) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
channelNames(String...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
channelNames(Iterable<String>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
channelNames(String...) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
 
channels(ArrayList<ChannelSpec>) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
Sets the ChannelSpecs to be used in this builder.
channels - Variable in class org.micromanager.acquisition.SequenceSettings
Deprecated.
use Builder and channels() instead
channels() - Method in class org.micromanager.acquisition.SequenceSettings
List with channel definitions to be used in the acquisition.
channels(Iterable<ChannelDisplaySettings>) - Method in interface org.micromanager.display.DisplaySettings.Builder
Replaces ChannelDisplaySettings with those given.
ChannelSpec - Class in org.micromanager.acquisition
A ChannelSpec is a description of how a specific channel will be used in an MDA (multi-dimensional acquisition).
ChannelSpec() - Constructor for class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder.build() instead for a default ChannelSpec
ChannelSpec.Builder - Class in org.micromanager.acquisition
ChannelSpec Builder.
channelSpecBuilder() - Method in interface org.micromanager.acquisition.AcquisitionManager
Provides and empty ChannelSpec Builder.
channelSpecBuilder() - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
ChannelTableModel - Class in org.micromanager.internal.dialogs
Data representation class for the channels list in the MDA dialog.
ChannelTableModel(Studio, AcquisitionEngine) - Constructor for class org.micromanager.internal.dialogs.ChannelTableModel
 
checkImageSizes(Image, Image) - Static method in class org.micromanager.data.internal.ImageSizeChecker
 
choosePreset(String, String) - Method in class org.micromanager.internal.ConfigPadButtonPanel
Shows select preset OptionPane.
CITATION_TEXT - Static variable in class org.micromanager.internal.dialogs.IntroDlg
 
cleanup(ProcessorContext) - Method in interface org.micromanager.data.Processor
Clean up when processing is finished.
cleanup() - Method in interface org.micromanager.data.ProcessorConfigurator
Remove any GUI resources currently in use.
cleanup() - Method in class org.micromanager.display.internal.gearmenu.GearButton
 
cleanup() - Method in class org.micromanager.internal.dialogs.AffineEditorPanel
 
cleanup() - Method in class org.micromanager.internal.LineProfile
Unregister from display events and dispose of the profile Window.
cleanup() - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
Remove all extant configurator GUIs.
cleanup() - Method in class org.micromanager.internal.utils.AutofocusPropertyEditor
Saves settings to profile, so they can be restored in the next session.
cleanUpConfigurationList() - Method in class org.micromanager.internal.dialogs.ChannelTableModel
Remove all channels from the list which are not compatible with the current acquisition settings
cleanupOnClose() - Method in class org.micromanager.internal.MMUIManager
Closes and cleans up all UI elements.
clear() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Deprecated.
clear() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
Deprecated.
unclear what this should be doing
clear() - Method in class org.micromanager.internal.hcwizard.ConfigGroup
 
clear() - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap.Builder
 
clear() - Method in class org.micromanager.internal.utils.ChainedMapView
 
clear() - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
clear() - Method in interface org.micromanager.PropertyMap.Builder
 
clear() - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
clearAllPositions() - Method in class org.micromanager.PositionList
Empties the list.
ClearCLNioConverters - Class in org.micromanager.internal.utils.imageanalysis
 
ClearCLNioConverters() - Constructor for class org.micromanager.internal.utils.imageanalysis.ClearCLNioConverters
 
clearComponentHighlights() - Method in class org.micromanager.display.inspector.internal.panels.intensity.HistogramView
 
clearExceptions() - Method in class org.micromanager.data.internal.pipeline.DefaultPipeline
 
clearExceptions() - Method in interface org.micromanager.data.Pipeline
Clear the list of exceptions that the pipeline has encountered, allowing insertImage() to be called again.
clearGraphs() - Method in class org.micromanager.display.inspector.internal.panels.intensity.HistogramView
 
clearMessageWindow() - Method in class org.micromanager.internal.script.ScriptPanel
 
clearMessageWindow() - Method in interface org.micromanager.ScriptController
Clears scripting console output window.
clearOutput() - Method in class org.micromanager.internal.script.ScriptPanel
Clears the content of the message window
clearPipeline() - Method in interface org.micromanager.data.DataManager
Clear the current application pipeline, so that no on-the-fly image processing is performed.
clearPipeline() - Method in class org.micromanager.data.internal.DefaultDataManager
 
clearPipeline() - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
Clear the pipeline table.
clearPipeline() - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
clearROI() - Method in class org.micromanager.internal.MMROIManager
Clears the ROI, i.e.
clearRunnables() - Method in interface org.micromanager.acquisition.AcquisitionManager
Remove runnables from the acquisition engine.
clearRunnables() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
clearRunnables() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
clearRunnables() - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
clearRunnables() - Method in interface org.micromanager.acquisition.internal.IAcquisitionEngine2010
 
clearSettingsForAllClasses() - Method in class org.micromanager.profile.internal.DefaultUserProfile
 
clearSettingsForAllClasses() - Method in interface org.micromanager.UserProfile
Reset this user profile, deleting all settings.
clearSynchroDevices() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
clip(double, double, double) - Static method in class org.micromanager.internal.utils.MathFunctions
 
clip(int, int, int) - Static method in class org.micromanager.internal.utils.MathFunctions
 
close() - Method in interface org.micromanager.data.DataProvider
 
close() - Method in class org.micromanager.data.internal.DefaultDatastore
 
close() - Method in class org.micromanager.data.internal.multipagetiff.MultipageTiffReader
Closes this MultipageTIffReader.
close(String, String) - Method in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
Called when entire set of files (i.e.
close() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
Remove open file descriptors.
close() - Method in class org.micromanager.data.internal.SciFIODataProvider
 
close() - Method in class org.micromanager.data.internal.StorageRAM
 
close() - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
close() - Method in interface org.micromanager.data.Storage
Release any resources used by the Storage, for example open file descriptors.
close() - Method in interface org.micromanager.display.DisplayWindow
Close this display window unconditionally.
close() - Method in class org.micromanager.display.inspector.internal.InspectorController
 
close() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
close() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
close() - Method in class org.micromanager.internal.dialogs.AcqControlDlg
Closes a(and disposes) the MDA window.
close() - Method in class org.micromanager.internal.MMUIManager
Close the Main Frame.
close() - Method in class org.micromanager.profile.internal.DefaultUserProfile
Stop autosaving and stop performing migrations.
CloseAllButton - Class in org.micromanager.quickaccess.internal.controls
Implements the "CloseAll" button logic.
CloseAllButton() - Constructor for class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
closeAllDisplayWindows(boolean) - Method in interface org.micromanager.display.DisplayManager
Close all open image windows.
closeAllDisplayWindows(boolean) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
closeDialog() - Method in class org.micromanager.internal.utils.WaitDialog
This static method closes the wait dialog.
closeDisplaysFor(DataProvider) - Method in interface org.micromanager.display.DisplayManager
Given a DataProvider, close any open DisplayWindows for that DataProvider.
closeDisplaysFor(DataProvider) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
closeLinearDialog() - Method in class org.micromanager.internal.dialogs.CustomTimeIntervalsPanel
 
closeLogDialog() - Method in class org.micromanager.internal.dialogs.CustomTimeIntervalsPanel
 
closeOptionsDialog() - Method in class org.micromanager.internal.utils.DefaultAutofocusManager
 
closePanel() - Method in class org.micromanager.internal.script.ScriptPanel
 
closeRequested(ShutdownCommencingEvent) - Method in class org.micromanager.display.inspector.internal.InspectorController
 
closeSequence(boolean) - Method in class org.micromanager.internal.MMStudio
Initiates closing sequence.
CoalescentEDTRunnablePool - Class in org.micromanager.internal.utils
Provide versions of SwingUtilities.invokeLater that coalesce with other outstanding invocations.
CoalescentEDTRunnablePool.CoalescentRunnable - Interface in org.micromanager.internal.utils
A "coalescent" runnable, for use with invokeLaterWithCoalescence.
coalesceWith(CoalescentEDTRunnablePool.CoalescentRunnable) - Method in interface org.micromanager.internal.utils.CoalescentEDTRunnablePool.CoalescentRunnable
Return a new runnable formed by coalescing this instance with another.
color(Color) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
Deprecated.
use ChannelDisplaySettings.color() instead
color - Variable in class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder and getters instead
color() - Method in class org.micromanager.acquisition.ChannelSpec
 
color(Color) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
COLOR_PALETTE - Static variable in class org.micromanager.display.inspector.internal.panels.intensity.IntensityInspectorPanelController
 
COLOR_SWATCH - Static variable in class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
 
colorBlue() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
colorColorBlindFriendly(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
colorCyan() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
ColorEditor - Class in org.micromanager.internal.utils
Color chooser for channel data.
ColorEditor(AbstractTableModel, int) - Constructor for class org.micromanager.internal.utils.ColorEditor
 
colorForMonochromaticWavelenth(double) - Static method in class org.micromanager.internal.utils.ColorPalettes
 
colorGreen() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
colorMagenta() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
ColorMaps - Class in org.micromanager.internal.utils
 
colorMode(DisplaySettings.ColorMode) - Method in interface org.micromanager.display.DisplaySettings.Builder
Color mode or lookup table for displaying the image.
colorModeComposite() - Method in interface org.micromanager.display.DisplaySettings.Builder
 
colorModeGrayscale() - Method in interface org.micromanager.display.DisplaySettings.Builder
 
colorModeHighlightSaturated() - Method in interface org.micromanager.display.DisplaySettings.Builder
 
colorModeSingleColor() - Method in interface org.micromanager.display.DisplaySettings.Builder
 
ColorPalettes - Class in org.micromanager.internal.utils
 
colorRed() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
ColorRenderer - Class in org.micromanager.internal.utils
Color chooser cell renderer.
ColorRenderer(boolean) - Constructor for class org.micromanager.internal.utils.ColorRenderer
 
colorWhite() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
colorYellow() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
COLUMN_NAMES - Variable in class org.micromanager.internal.dialogs.ChannelTableModel
 
columnNames_ - Variable in class org.micromanager.internal.ConfigGroupPad.StateTableData
 
comment(String) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
 
comment - Variable in class org.micromanager.acquisition.SequenceSettings
Deprecated.
use Builder and comment() instead
comment() - Method in class org.micromanager.acquisition.SequenceSettings
Text comment to be attached to the acquired data.
COMMENTS_HEADER - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
COMMENTS_OFFSET_HEADER - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
CommentsHelper - Class in org.micromanager.data.internal
Comments are handled separately from SummaryMetadata and Imagemetadata since the used may change them (add to them) at any point in time.
CommentsHelper() - Constructor for class org.micromanager.data.internal.CommentsHelper
 
CommentsInspectorPanelController - Class in org.micromanager.display.inspector.internal.panels.comments
 
CommentsInspectorPanelPlugin - Class in org.micromanager.display.inspector.internal.panels.comments
 
CommentsInspectorPanelPlugin() - Constructor for class org.micromanager.display.inspector.internal.panels.comments.CommentsInspectorPanelPlugin
 
compare(Device, Device) - Method in class org.micromanager.internal.hcwizard.DeviceSorter
 
compare(String, String) - Method in class org.micromanager.internal.utils.ImageLabelComparator
 
compare(String, String) - Method in class org.micromanager.internal.utils.SortFunctionObjects.DoubleStringComp
 
compare(String, String) - Method in class org.micromanager.internal.utils.SortFunctionObjects.IntStringComp
 
compare(String, String) - Method in class org.micromanager.internal.utils.SortFunctionObjects.NumericPrefixStringComp
 
compareAndSetDisplayPosition(Coords, Coords, boolean) - Method in class org.micromanager.display.AbstractDataViewer
Implements compareAndSetDisplayPosition.
compareAndSetDisplayPosition(Coords, Coords) - Method in class org.micromanager.display.AbstractDataViewer
 
compareAndSetDisplayPosition(Coords, Coords, boolean) - Method in interface org.micromanager.display.DataViewer
Set the display position only if the current position is the expected one.
compareAndSetDisplayPosition(Coords, Coords) - Method in interface org.micromanager.display.DataViewer
Set the display position only if the current position is the expected one.
compareAndSetDisplaySettings(DisplaySettings, DisplaySettings) - Method in class org.micromanager.display.AbstractDataViewer
Implements compareAndSetDisplaySettings.
compareAndSetDisplaySettings(DisplaySettings, DisplaySettings) - Method in interface org.micromanager.display.DataViewer
Set the display settings only if the current settings match the expected one.
compat() - Method in class org.micromanager.internal.MMStudio
 
compat() - Method in interface org.micromanager.Studio
Provides access to the compatibility layer that exposes some old 1.4 API methods.
CompatibilityInterface - Interface in org.micromanager
Legacy interface that implements some methods from the old 1.4 API.
component(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
component(int, ComponentDisplaySettings) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
ComponentDisplaySettings - Interface in org.micromanager.display
Certain cameras (such as RGB cameras) can produce images where each pixel has multiple components.
ComponentDisplaySettings.Builder - Interface in org.micromanager.display
Interface for ComponentDisplaySettings Builder.
componentDisplaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager
Generates a blank componentSettings Builder with all null values.
componentDisplaySettingsBuilder() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
componentHidden(ComponentEvent) - Method in class org.micromanager.internal.utils.PopupButton
 
componentMoved(ComponentEvent) - Method in class org.micromanager.internal.utils.PopupButton
 
componentResized(ComponentEvent) - Method in class org.micromanager.internal.utils.PopupButton
 
componentShown(ComponentEvent) - Method in class org.micromanager.internal.utils.PopupButton
 
ComponentTitledBorder - Class in org.micromanager.internal.dialogs
MySwing: Advanced Swing Utilites Copyright (C) 2005 Santhosh Kumar T
ComponentTitledBorder(Component, JComponent, Border) - Constructor for class org.micromanager.internal.dialogs.ComponentTitledBorder
 
ComponentTitledPanel() - Constructor for class org.micromanager.internal.dialogs.AcqControlDlg.ComponentTitledPanel
 
COMPRESSION - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
compTitledBorder - Variable in class org.micromanager.internal.dialogs.AcqControlDlg.ComponentTitledPanel
 
computerName(String) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
computerName(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
computerName(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
 
computeScore(ImageProcessor) - Method in interface org.micromanager.AutofocusPlugin
Computes a focus score for the given image.
computeScore(ImageProcessor) - Method in class org.micromanager.internal.utils.CoreAutofocus
 
config(String) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
 
config - Variable in class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder and getters instead
config() - Method in class org.micromanager.acquisition.ChannelSpec
 
config - Variable in class org.micromanager.internal.utils.StateItem
 
ConfigDialog - Class in org.micromanager.internal.dialogs
 
ConfigDialog(String, String, Studio, boolean) - Constructor for class org.micromanager.internal.dialogs.ConfigDialog
 
ConfigGroup - Class in org.micromanager.internal.hcwizard
Configuration group encapsulation for use in Configuration Wizard.
ConfigGroup(String) - Constructor for class org.micromanager.internal.hcwizard.ConfigGroup
 
ConfigGroupChangedEvent - Interface in org.micromanager.events
Event signaling that the "active" preset in a config group changed.
ConfigGroupPad - Class in org.micromanager.internal
Preset panel.
ConfigGroupPad(Studio) - Constructor for class org.micromanager.internal.ConfigGroupPad
 
ConfigGroupPad.StateTableData - Class in org.micromanager.internal
Property table data model, representing state devices.
ConfigMenu - Class in org.micromanager.internal.menus
 
ConfigMenu(MMStudio, JMenuBar) - Constructor for class org.micromanager.internal.menus.ConfigMenu
 
ConfigPadButtonPanel - Class in org.micromanager.internal
Buttons under the ConfigPad that let the user add, remove, or edit config groups and configuration within groups.
ConfigPreset - Class in org.micromanager.internal.hcwizard
Encapsulation of the preset data for use in the Configuration Wizard.
ConfigPreset() - Constructor for class org.micromanager.internal.hcwizard.ConfigPreset
 
ConfigPreset(String) - Constructor for class org.micromanager.internal.hcwizard.ConfigPreset
 
ConfigSelectionUIController - Class in org.micromanager.internal.dialogs
 
ConfiguratorWrapper - Class in org.micromanager.internal.pipelineinterface
This class wraps around a ProcessorConfigurator, allowing it to be easily enabled or disabled without having any logic in the plugin side of things.
ConfiguratorWrapper(ProcessorPlugin, ProcessorConfigurator, String) - Constructor for class org.micromanager.internal.pipelineinterface.ConfiguratorWrapper
 
configureBinningCombo() - Method in class org.micromanager.internal.MMUIManager
Sets up teh camera binning dropdown.
configureBinningComboForCamera(String) - Method in class org.micromanager.internal.MainFrame
Dropdown for camera binning.
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.ExposureTime
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.LiveButton
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.MDAButtons
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.ShutterControl
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.SnapButton
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.internal.controls.TextLabel
 
configureControl(Frame) - Method in class org.micromanager.quickaccess.WidgetPlugin
Generate configuration information that can be used to configure a control generated by this plugin.
configureExporter(ImageExporter) - Method in class org.micromanager.display.internal.gearmenu.ExportMovieDlg.AxisPanel
Apply our configuration to the provided ImageExporter, and recurse if appropriate to any contained AxisPanel.
ConfigWizard - Class in org.micromanager.internal.hcwizard
Configuration Wizard main panel.
ConfigWizard(Studio, String) - Constructor for class org.micromanager.internal.hcwizard.ConfigWizard
Create the application
confInclude - Variable in class org.micromanager.internal.utils.PropertyItem
 
consume() - Method in class org.micromanager.display.internal.event.DisplayKeyPressEvent
 
containsAffineTransform(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsAffineTransform(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsAffineTransform(String) - Method in interface org.micromanager.PropertyMap
 
containsAffineTransform(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsAffineTransformList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsAffineTransformList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsAffineTransformList(String) - Method in interface org.micromanager.PropertyMap
 
containsAffineTransformList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsAll(Collection<?>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsAll(Collection<?>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsAll(Collection<?>) - Method in interface org.micromanager.PropertyMap
 
containsAll(Collection<?>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
Return whether all of the given keys are present in this view.
containsBoolean(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsBoolean(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsBoolean(String) - Method in interface org.micromanager.PropertyMap
 
containsBoolean(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsBooleanList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsBooleanList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsBooleanList(String) - Method in interface org.micromanager.PropertyMap
 
containsBooleanList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsByte(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsByte(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsByte(String) - Method in interface org.micromanager.PropertyMap
 
containsByte(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsByteList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsByteList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsByteList(String) - Method in interface org.micromanager.PropertyMap
 
containsByteList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsColor(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsColor(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsColor(String) - Method in interface org.micromanager.PropertyMap
 
containsColor(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsColorList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsColorList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsColorList(String) - Method in interface org.micromanager.PropertyMap
 
containsColorList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsDimension(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsDimension(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsDimension(String) - Method in interface org.micromanager.PropertyMap
 
containsDimension(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsDimensionList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsDimensionList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsDimensionList(String) - Method in interface org.micromanager.PropertyMap
 
containsDimensionList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsDouble(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsDouble(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsDouble(String) - Method in interface org.micromanager.PropertyMap
 
containsDouble(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsDoubleList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsDoubleList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsDoubleList(String) - Method in interface org.micromanager.PropertyMap
 
containsDoubleList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsFloat(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsFloat(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsFloat(String) - Method in interface org.micromanager.PropertyMap
 
containsFloat(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsFloatList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsFloatList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsFloatList(String) - Method in interface org.micromanager.PropertyMap
 
containsFloatList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsInteger(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsInteger(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsInteger(String) - Method in interface org.micromanager.PropertyMap
 
containsInteger(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsIntegerList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsIntegerList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsIntegerList(String) - Method in interface org.micromanager.PropertyMap
 
containsIntegerList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsKey(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsKey(Object) - Method in class org.micromanager.internal.utils.ChainedMapView
 
containsKey(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsKey(String) - Method in interface org.micromanager.PropertyMap
 
containsKey(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
Return whether a given key is present in this view.
containsLong(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsLong(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsLong(String) - Method in interface org.micromanager.PropertyMap
 
containsLong(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsLongList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsLongList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsLongList(String) - Method in interface org.micromanager.PropertyMap
 
containsLongList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsNumber(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsNumber(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsNumber(String) - Method in interface org.micromanager.PropertyMap
 
containsNumber(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsNumberList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsNumberList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsNumberList(String) - Method in interface org.micromanager.PropertyMap
 
containsNumberList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsPoint(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsPoint(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsPoint(String) - Method in interface org.micromanager.PropertyMap
 
containsPoint(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsPointList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsPointList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsPointList(String) - Method in interface org.micromanager.PropertyMap
 
containsPointList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsPropertyMap(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsPropertyMap(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsPropertyMap(String) - Method in interface org.micromanager.PropertyMap
 
containsPropertyMap(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsPropertyMapList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsPropertyMapList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsPropertyMapList(String) - Method in interface org.micromanager.PropertyMap
 
containsPropertyMapList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsRectangle(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsRectangle(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsRectangle(String) - Method in interface org.micromanager.PropertyMap
 
containsRectangle(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsRectangleList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsRectangleList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsRectangleList(String) - Method in interface org.micromanager.PropertyMap
 
containsRectangleList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsShort(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsShort(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsShort(String) - Method in interface org.micromanager.PropertyMap
 
containsShort(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsShortList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsShortList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsShortList(String) - Method in interface org.micromanager.PropertyMap
 
containsShortList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsString(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsString(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsString(String) - Method in interface org.micromanager.PropertyMap
 
containsString(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsStringForEnum(String, Class<E>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsStringForEnum(String, Class<E>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsStringForEnum(String, Class<E>) - Method in interface org.micromanager.PropertyMap
 
containsStringForEnum(String, Class<E>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsStringList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsStringList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsStringList(String) - Method in interface org.micromanager.PropertyMap
 
containsStringList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsStringListForEnumList(String, Class<E>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsStringListForEnumList(String, Class<E>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsStringListForEnumList(String, Class<E>) - Method in interface org.micromanager.PropertyMap
 
containsStringListForEnumList(String, Class<E>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsUUID(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsUUID(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsUUID(String) - Method in interface org.micromanager.PropertyMap
 
containsUUID(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsUUIDList(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
containsUUIDList(String) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
containsUUIDList(String) - Method in interface org.micromanager.PropertyMap
 
containsUUIDList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
containsValue(Object) - Method in class org.micromanager.internal.utils.ChainedMapView
 
ControlCell - Class in org.micromanager.quickaccess.internal
This class represents a single control in the window.
ControlCell(Studio, QuickAccessFrame, QuickAccessPlugin, PropertyMap, Rectangle) - Constructor for class org.micromanager.quickaccess.internal.ControlCell
 
ControlPanel - Class in org.micromanager.internal.diagnostics.gui
Control Panel in ProblemReportFrame.
controlsFactory(DisplayWindowControlsFactory) - Method in class org.micromanager.display.internal.displaywindow.DisplayController.Builder
 
convert(ImageGray<? extends ImageGray<?>>, boolean) - Static method in class org.micromanager.internal.utils.imageanalysis.BoofCVImageConverter
Converts a BoofCV image into an ImageJ ImageProcessor TODO: support other types besides GrayU8 and GrayU16
convert(ImageProcessor, boolean) - Static method in class org.micromanager.internal.utils.imageanalysis.BoofCVImageConverter
Converts an ImageJ ImageProcessor to a BoofCV image
convertAff(AffineTransform) - Static method in class org.micromanager.internal.utils.imageanalysis.BoofCVImageConverter
Converts a Java affine transform into a Georegression Affine transform
convertClearCLBufferToNio(ClearCLImageInterface) - Static method in class org.micromanager.internal.utils.imageanalysis.ClearCLNioConverters
Copies Intensity data from ClearCLBuffer to Java Direct Buffer Input is either ClearCLBuffer or ClearCLImage Caller will also need dimensions: source.getDimensions()
convertNioTiClearCLBuffer(ClearCLContext, Buffer, long[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ClearCLNioConverters
convertNioTiClearCL Author: @nicost 6 2019
convertNioTiClearCLImage(ClearCLContext, Buffer, long[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ClearCLNioConverters
 
convertRGB32BytesToInt(byte[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
Converts a sequence of 4 bytes into an int.
convertRGB32IntToBytes(int[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
convertRGB32UBytesToInt(byte[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
Used to convert unsigned bytes coming from the C++ later into ints that can be used by ImageJ.
convertTaggedImage(TaggedImage) - Method in interface org.micromanager.data.DataManager
Given a TaggedImage input, output an Image based on the TaggedImage.
convertTaggedImage(TaggedImage, Coords, Metadata) - Method in interface org.micromanager.data.DataManager
Given a TaggedImage input, output an Image based on the TaggedImage, but with the Coords and/or Metadata optionally overridden.
convertTaggedImage(TaggedImage) - Method in class org.micromanager.data.internal.DefaultDataManager
 
convertTaggedImage(TaggedImage, Coords, Metadata) - Method in class org.micromanager.data.internal.DefaultDataManager
 
convertToFloat() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
Coordinates - Class in org.micromanager.data
Static helper functions to assist working with Coords.
Coords - Interface in org.micromanager.data
The multi-dimensional coordinate of a 2D image within a dataset.
coords() - Static method in class org.micromanager.internal.propertymap.NonPropertyMapJSONFormats
 
Coords.Builder - Interface in org.micromanager.data
The real Builder for Coords.
Coords.CoordsBuilder - Interface in org.micromanager.data
Not sure why there is a Builder and CoordsBuilder.
coordsBuilder() - Method in interface org.micromanager.data.DataManager
Generate a "blank" CoordsBuilder for use in constructing new Coords instances.
coordsBuilder() - Method in class org.micromanager.data.internal.DefaultDataManager
 
coordsExist(Coords) - Method in interface org.micromanager.display.internal.animate.DataCoordsAnimationState.CoordsProvider
 
coordsExist(Coords) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
coordsToRasterPosition(ImageMetadata, Coords) - Method in class org.micromanager.data.internal.SciFIODataProvider
 
copy() - Method in class org.micromanager.acquisition.SequenceSettings
Deprecated.
When used correctly, SequenceSettings are immutable. If you really need a copy, use copyBuilder().build();
copy() - Method in interface org.micromanager.data.Coords
Deprecated.
Use copyBuilder instead
copy() - Method in class org.micromanager.data.internal.DefaultCoords
Deprecated.
copy() - Method in class org.micromanager.data.internal.DefaultMetadata
Deprecated.
copy() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
Deprecated.
copy() - Method in interface org.micromanager.data.Metadata
Deprecated.
Use the appropriate of the following: Metadata.copyBuilderPreservingUUID(), Metadata.copyBuilderWithNewUUID(), Metadata.copyBuilderRemovingUUID(). This method is equivalent to copyBuilderPreservingUUID.
copy() - Method in interface org.micromanager.data.SummaryMetadata
Deprecated.
- Use SummaryMetadata.Builder.copyBuilder instead
copy() - Method in interface org.micromanager.display.DisplaySettings
Deprecated.
copy() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
Deprecated.
copy() - Method in class org.micromanager.display.internal.imagestats.PowerOf2BinMapper
 
copy() - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
copy(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
copy() - Method in interface org.micromanager.PropertyMap
Deprecated.
copyApplicationPipeline(Datastore, boolean) - Method in interface org.micromanager.data.DataManager
Create a copy of the current application Pipeline as configured in the "Data Processing Pipeline" window.
copyApplicationPipeline(Datastore, boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
copyAtCoords(Coords) - Method in interface org.micromanager.data.Image
Generate a copy of this Image, except with different coordinates.
copyAtCoords(Coords) - Method in class org.micromanager.data.internal.DefaultImage
 
copyBuilder() - Method in class org.micromanager.acquisition.ChannelSpec
 
copyBuilder() - Method in class org.micromanager.acquisition.SequenceSettings
 
copyBuilder() - Method in interface org.micromanager.data.Coords
Provides a Builder pre-loaded with a copy of this Coords.
copyBuilder() - Method in class org.micromanager.data.internal.DefaultCoords
 
copyBuilder() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
copyBuilder() - Method in interface org.micromanager.data.SummaryMetadata
 
copyBuilder() - Method in interface org.micromanager.display.ChannelDisplaySettings
 
copyBuilder() - Method in interface org.micromanager.display.ComponentDisplaySettings
 
copyBuilder() - Method in interface org.micromanager.display.DisplaySettings
 
copyBuilder() - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
copyBuilder() - Method in class org.micromanager.display.internal.DefaultComponentDisplaySettings
 
copyBuilder() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
copyBuilder() - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
copyBuilder() - Method in interface org.micromanager.PropertyMap
 
copyBuilderPreservingUUID() - Method in class org.micromanager.data.internal.DefaultMetadata
 
copyBuilderPreservingUUID() - Method in interface org.micromanager.data.Metadata
Return a builder with the same content, preserving the image UUID.
copyBuilderRemovingUUID() - Method in class org.micromanager.data.internal.DefaultMetadata
 
copyBuilderRemovingUUID() - Method in interface org.micromanager.data.Metadata
Return a builder with the same content but removing the image UUID.
copyBuilderWithChannelSettings(int, ChannelDisplaySettings) - Method in interface org.micromanager.display.DisplaySettings
 
copyBuilderWithChannelSettings(int, ChannelDisplaySettings) - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
copyBuilderWithComponentSettings(int, ComponentDisplaySettings) - Method in interface org.micromanager.display.ChannelDisplaySettings
 
copyBuilderWithComponentSettings(int, int, ComponentDisplaySettings) - Method in interface org.micromanager.display.DisplaySettings
 
copyBuilderWithComponentSettings(int, ComponentDisplaySettings) - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
copyBuilderWithComponentSettings(int, int, ComponentDisplaySettings) - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
copyBuilderWithNewUUID() - Method in class org.micromanager.data.internal.DefaultMetadata
 
copyBuilderWithNewUUID() - Method in interface org.micromanager.data.Metadata
Return a builder with the same content, assigning a new image UUID.
copyComments(Datastore, Datastore) - Static method in class org.micromanager.data.internal.CommentsHelper
 
copyDoubleVector(DoubleVector) - Static method in class org.micromanager.internal.dialogs.AffineEditorPanel
 
copyForRequest(ImageStatsRequest) - Method in class org.micromanager.display.internal.imagestats.ImagesAndStats
 
copyFrom(Datastore, ProgressMonitor) - Method in class org.micromanager.data.internal.DefaultDatastore
Copy all data from the source Datastore into ourselves.
copyLivePipeline(Datastore, boolean) - Method in interface org.micromanager.data.DataManager
Create a copy of the current Live Pipeline as configured in the "Data Processing Pipeline" window.
copyLivePipeline(Datastore, boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
copyMetadata(TaggedImage) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
Generate a new TaggedImage off of the provided one, with copied metadata so that changes elsewhere in the program won't affect this one.
copyRemovingAxes(String...) - Method in interface org.micromanager.data.Coords
Removes the axes provided as varargs from this Coord.
copyRemovingAxes(String...) - Method in class org.micromanager.data.internal.DefaultCoords
 
copyRetainingAxes(String...) - Method in interface org.micromanager.data.Coords
Name of this function is very unclear.
copyRetainingAxes(String...) - Method in class org.micromanager.data.internal.DefaultCoords
 
COPYRIGHT_TEXT - Static variable in class org.micromanager.internal.dialogs.AboutDlg
 
CopyToImageJItem - Class in org.micromanager.display.internal.gearmenu
 
CopyToImageJItem() - Constructor for class org.micromanager.display.internal.gearmenu.CopyToImageJItem
 
copyWith(Coords, Metadata) - Method in interface org.micromanager.data.Image
Generate a copy of this Image, except with different coordinates and metadata.
copyWith(Coords, Metadata) - Method in class org.micromanager.data.internal.DefaultImage
 
copyWithMetadata(Metadata) - Method in interface org.micromanager.data.Image
Generate a copy of this Image, except with different metadata.
copyWithMetadata(Metadata) - Method in class org.micromanager.data.internal.DefaultImage
 
core() - Method in class org.micromanager.internal.MMStudio
 
core() - Method in interface org.micromanager.Studio
Provides access to the Core and its functionality.
CoreAutofocus - Class in org.micromanager.internal.utils
Makes C++ autofocus devices appear similarly to autofocus devices implemented in Java
CoreAutofocus() - Constructor for class org.micromanager.internal.utils.CoreAutofocus
 
CoreEventCallback - Class in org.micromanager.events.internal
Callback to update Java layer when a change happens in the MMCore.
CoreEventCallback(Studio, AcquisitionWrapperEngine) - Constructor for class org.micromanager.events.internal.CoreEventCallback
 
coreStringToDouble(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
coreStringToInt(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
coreStringToLong(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
CPUTimer - Class in org.micromanager.internal.utils.performance
Times CPU usage on the current thread.
create() - Static method in class org.micromanager.display.inspector.internal.InspectorCollection
 
create(Studio, DataViewerCollection) - Static method in class org.micromanager.display.inspector.internal.InspectorController
 
create() - Static method in class org.micromanager.display.inspector.internal.panels.comments.CommentsInspectorPanelController
 
create(DataViewer, int) - Static method in class org.micromanager.display.inspector.internal.panels.intensity.ChannelIntensityController
 
create() - Static method in class org.micromanager.display.inspector.internal.panels.intensity.HistogramView
Instead of constructor, use this static function to create a HistogramView.
create(ImagesAndStats) - Static method in class org.micromanager.display.inspector.internal.panels.intensity.ImageStatsPublisher.ImageStatsChangedEvent
 
create(Studio) - Static method in class org.micromanager.display.inspector.internal.panels.intensity.IntensityInspectorPanelController
 
create() - Static method in class org.micromanager.display.inspector.internal.panels.metadata.PlaneMetadataInspectorPanelController
 
create() - Static method in class org.micromanager.display.inspector.internal.panels.metadata.SummaryMetadataInspectorPanelController
 
create(Studio) - Static method in class org.micromanager.display.inspector.internal.panels.overlays.OverlaysInspectorPanelController
 
create(int, boolean) - Static method in class org.micromanager.display.inspector.internal.VerticalMultiSplitPane
 
create(AnimationStateDelegate<P>) - Static method in class org.micromanager.display.internal.animate.AnimationController
 
create(DataCoordsAnimationState.CoordsProvider) - Static method in class org.micromanager.display.internal.animate.DataCoordsAnimationState
 
create() - Static method in class org.micromanager.display.internal.DataViewerCollection
 
create(DisplayUIController, ImagesAndStats) - Static method in class org.micromanager.display.internal.displaywindow.imagej.ImageJBridge
 
create(ImageJBridge) - Static method in class org.micromanager.display.internal.displaywindow.imagej.MMImagePlus
 
create(DataViewer) - Static method in class org.micromanager.display.internal.event.DataViewerAddedEvent
 
create(DataViewer) - Static method in class org.micromanager.display.internal.event.DataViewerDidBecomeActiveEvent
 
create(DataViewer) - Static method in class org.micromanager.display.internal.event.DataViewerDidBecomeInactiveEvent
 
create(DataViewer) - Static method in class org.micromanager.display.internal.event.DataViewerDidBecomeInvisibleEvent
 
create(DataViewer) - Static method in class org.micromanager.display.internal.event.DataViewerDidBecomeVisibleEvent
 
create(int, int, String[], List<Coords>, List<long[]>) - Static method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
create(DataViewer) - Static method in class org.micromanager.display.internal.event.DataViewerWillCloseEvent
 
create(DataViewer, List<Image>, Image) - Static method in class org.micromanager.display.internal.event.DefaultDisplayDidShowImageEvent
 
create(DataViewer, Coords, Coords) - Static method in class org.micromanager.display.internal.event.DefaultDisplayPositionChangedEvent
 
create(DataViewer, DisplaySettings, DisplaySettings) - Static method in class org.micromanager.display.internal.event.DefaultDisplaySettingsChangedEvent
 
create(DisplayWindow, Overlay) - Static method in class org.micromanager.display.internal.event.DisplayWindowDidAddOverlayEvent
 
create(DisplayWindow, Overlay) - Static method in class org.micromanager.display.internal.event.DisplayWindowDidRemoveOverlayEvent
 
create(InspectorController) - Static method in class org.micromanager.display.internal.event.InspectorDidCloseEvent
 
create(Rectangle, byte[]) - Static method in class org.micromanager.display.internal.imagestats.BoundsRectAndMask
 
create(long, ImageStatsRequest, ImageStats...) - Static method in class org.micromanager.display.internal.imagestats.ImagesAndStats
 
create(int, IntegerComponentStats...) - Static method in class org.micromanager.display.internal.imagestats.ImageStats
 
create() - Static method in class org.micromanager.display.internal.imagestats.ImageStatsProcessor
 
create(Coords, List<Image>, BoundsRectAndMask) - Static method in class org.micromanager.display.internal.imagestats.ImageStatsRequest
 
create(int, int) - Static method in class org.micromanager.display.internal.imagestats.PowerOf2BinMapper
Create a bin mapper covering full range of unsigned integer type.
create() - Static method in class org.micromanager.display.internal.imagestats.StatsComputeQueue
 
create() - Static method in class org.micromanager.display.internal.link.internal.DefaultLinkManager
 
create() - Static method in class org.micromanager.display.internal.link.internal.LinkEndpointPool
 
create() - Static method in class org.micromanager.display.overlay.internal.overlays.PatternOverlay
 
create(UserProfileAdmin) - Static method in class org.micromanager.internal.dialogs.ConfigSelectionUIController
 
create(Application, UserProfileAdmin) - Static method in class org.micromanager.internal.dialogs.ProfileSelectionUIController
 
create(UserProfile) - Static method in class org.micromanager.internal.StartupSettings
 
create(Map<K, V>, Map<K, V>) - Static method in class org.micromanager.internal.utils.ChainedMapView
 
create() - Static method in class org.micromanager.internal.utils.CoalescentEDTRunnablePool
 
create(Studio) - Static method in class org.micromanager.internal.utils.DaytimeNighttime
Look and Feel controller construtor.
create(PerformanceMonitor, String) - Static method in class org.micromanager.internal.utils.performance.gui.PerformanceMonitorUI
 
create(int) - Static method in class org.micromanager.internal.utils.performance.SimpleRunningQuantile
 
create(int) - Static method in class org.micromanager.internal.utils.performance.SkipListRunningQuantile
 
create(int) - Static method in class org.micromanager.internal.utils.performance.TimeIntervalRunningQuantile
 
create() - Static method in class org.micromanager.internal.utils.PopupButton
 
create(String) - Static method in class org.micromanager.internal.utils.PopupButton
 
create(Icon) - Static method in class org.micromanager.internal.utils.PopupButton
 
create(String, JComponent) - Static method in class org.micromanager.internal.utils.PopupButton
 
create(Icon, JComponent) - Static method in class org.micromanager.internal.utils.PopupButton
 
create(String, Icon, JComponent) - Static method in class org.micromanager.internal.utils.PopupButton
 
create(UserProfileAdmin, UUID, PropertyMap) - Static method in class org.micromanager.profile.internal.DefaultUserProfile
 
create(UserProfile, CMMCore) - Static method in class org.micromanager.profile.internal.gui.HardwareConfigurationManager
 
create() - Static method in class org.micromanager.profile.internal.UserProfileAdmin
 
create() - Static method in class org.micromanager.profile.internal.UserProfileChangedEvent
 
create1D(String, double) - Static method in class org.micromanager.StagePosition
Creates a new StapePosition for a 1 axis drive.
create2D(String, double, double) - Static method in class org.micromanager.StagePosition
Creates a new StapePosition for a 2 axis drive.
createAlbumCoords(Image) - Method in class org.micromanager.internal.DefaultAlbum
Creates Coords for the image to be added to the album.
createAlert(AlertsWindow, String) - Static method in class org.micromanager.alerts.internal.CategorizedAlert
Sets up the contents of the alert before passing them to the constructor, so they can in turn be passed to the DefaultAlert constructor.
createApplicationDataPathIfNeeded() - Static method in class org.micromanager.internal.utils.JavaUtils
 
createAxisPanel() - Method in class org.micromanager.display.internal.gearmenu.ExportMovieDlg
Create a row of controls for iterating over an axis.
createBareMessageDialog(Window, String) - Static method in class org.micromanager.internal.utils.GUIUtils
Create an undecorated window centered on the specified parent with the specified text.
createBeanshellREPL() - Method in class org.micromanager.internal.script.ScriptPanel
 
createBlankProcessor(Image) - Static method in class org.micromanager.data.internal.DefaultImageJConverter
Creates an Image ImageProcessor with the pixel type and dimensions of the input Image, but all pixel values set to 0
createButton() - Method in class org.micromanager.internal.ConfigPadButtonPanel
Creates one of the buttons.
createButton(String, String) - Method in class org.micromanager.internal.ConfigPadButtonPanel
Creates a button, ready to be displayed.
createButton() - Method in class org.micromanager.quickaccess.ToggleButtonPlugin
Provide a JToggleButton that will behave as desired by the plugin.
createCalibrationListDlg() - Method in class org.micromanager.internal.MMUIManager
Creates the Pixel Size Calibration Dialog.
createChainedView(PropertyMap) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
createChannelTable() - Method in class org.micromanager.internal.dialogs.AcqControlDlg
Creates the table displaying channels.
createComponents() - Method in class org.micromanager.internal.utils.ShowFlagsPanel
 
createConfigurator(PropertyMap) - Method in interface org.micromanager.data.ProcessorPlugin
Generate any GUI needed to configure the plugin, using the provided settings to initialize the GUI.
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.ExposureTime
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.LiveButton
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.MDAButtons
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.ShutterControl
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.SnapButton
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.internal.controls.TextLabel
 
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.WidgetPlugin
Create the GUI components for this control.
createCoords(String) - Method in interface org.micromanager.data.DataManager
Deprecated.
use of Strings for Coords is discouraged
createCoords(String) - Method in class org.micromanager.data.internal.DefaultDataManager
Deprecated.
createDesktopImage() - Static method in class org.micromanager.internal.utils.ScreenImage
Convenience method to create a BufferedImage of the desktop
createDirectory(String) - Static method in class org.micromanager.internal.utils.JavaUtils
 
createDisplay(DataProvider) - Method in interface org.micromanager.display.DisplayManager
Create a new DisplayWindow for the specified DataProvider and return it.
createDisplay(DataProvider, DisplayWindowControlsFactory) - Method in interface org.micromanager.display.DisplayManager
Create a new DisplayWindow for the specified DataProvider and return it.
createDisplay(DataProvider) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
createDisplay(DataProvider, DisplayWindowControlsFactory) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
createExporter() - Method in interface org.micromanager.display.DisplayManager
Provide an ImagceExporter for generating image sequences.
createExporter() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
createFactory(PropertyMap) - Method in interface org.micromanager.data.ProcessorPlugin
Generate a ProcessorFactory that can be used to generate Processor instances.
createFirstInspector() - Method in interface org.micromanager.display.DisplayManager
Deprecated.
createFirstInspector() - Method in class org.micromanager.display.internal.DefaultDisplayManager
Deprecated.
createImage(Object, int, int, int, int, Coords, Metadata) - Method in interface org.micromanager.data.DataManager
Generate a new Image with the provided pixel data, rules for interpreting that pixel data, coordinates, and metadata.
createImage(ImageProcessor, Coords, Metadata) - Method in interface org.micromanager.data.ImageJConverter
Create a new Image based on the provided ImageProcessor and metadata.
createImage(Object, int, int, int, int, Coords, Metadata) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createImage(ImageProcessor, Coords, Metadata) - Method in class org.micromanager.data.internal.DefaultImageJConverter
 
createImage(JComponent) - Static method in class org.micromanager.internal.utils.ScreenImage
 
createImage(JComponent, Rectangle) - Static method in class org.micromanager.internal.utils.ScreenImage
 
createImage(Component) - Static method in class org.micromanager.internal.utils.ScreenImage
 
createImage(Rectangle) - Static method in class org.micromanager.internal.utils.ScreenImage
Create a BufferedImage from a rectangular region on the screen.
createInspectorForDataViewer(DataViewer) - Method in interface org.micromanager.display.DisplayManager
Create a new Inspector window that shows information for the specified DataViewer, or for the topmost window if the DataViewer is null.
createInspectorForDataViewer(DataViewer) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
createLabel(String) - Method in class org.micromanager.internal.ConfigPadButtonPanel
Creates a label for the button.
createMainWindow() - Method in class org.micromanager.internal.MMUIManager
Creates the Main Frame.
createMenuBar(MMStudio) - Static method in class org.micromanager.internal.menus.MMMenuBar
 
createMenuInMenuBar(JMenuBar, String) - Static method in class org.micromanager.internal.utils.GUIUtils
Adds a menu to the specified menu bar.
createMultipageTIFFDatastore(String, boolean, boolean) - Method in interface org.micromanager.data.DataManager
Generate a new, "blank" Datastore with multipage TIFF-based Storage and return it.
createMultipageTIFFDatastore(Datastore, String, boolean, boolean) - Method in interface org.micromanager.data.DataManager
 
createMultipageTIFFDatastore(String, boolean, boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createMultipageTIFFDatastore(Datastore, String, boolean, boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createNewAnnotation(String) - Method in class org.micromanager.data.internal.DefaultDatastore
I am not sure what this is supposed to do....
createNewPanel() - Method in class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
Create a new, empty panel.
createOverlay() - Method in class org.micromanager.display.overlay.internal.overlays.PatternOverlayPlugin
 
createOverlay() - Method in class org.micromanager.display.overlay.internal.overlays.ScaleBarPlugin
 
createOverlay() - Method in class org.micromanager.display.overlay.internal.overlays.TimestampPlugin
 
createOverlay() - Method in interface org.micromanager.display.overlay.OverlayPlugin
 
createPanelController(Studio) - Method in interface org.micromanager.display.inspector.InspectorPanelPlugin
 
createPanelController(Studio) - Method in class org.micromanager.display.inspector.internal.panels.comments.CommentsInspectorPanelPlugin
 
createPanelController(Studio) - Method in class org.micromanager.display.inspector.internal.panels.intensity.IntensityInspectorPanelPlugin
 
createPanelController(Studio) - Method in class org.micromanager.display.inspector.internal.panels.metadata.PlaneMetadataInspectorPanelPlugin
 
createPanelController(Studio) - Method in class org.micromanager.display.inspector.internal.panels.metadata.SummaryMetadataInspectorPanelPlugin
 
createPanelController(Studio) - Method in class org.micromanager.display.inspector.internal.panels.overlays.OverlaysInspectorPanelPlugin
 
createPipeline(List<ProcessorFactory>, Datastore, boolean) - Method in interface org.micromanager.data.DataManager
Create a new Pipeline using the provided list of ProcessorFactories.
createPipeline(List<ProcessorFactory>, Datastore, boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createPipelineFrame() - Method in class org.micromanager.internal.MMUIManager
Creates the PipelineFrame that lets users set up on the fly proecssing pipelines.
createPluginMenu(JMenuBar) - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
createProcessor(Image) - Method in interface org.micromanager.data.ImageJConverter
Create an ImageProcessor whose image pixel data is derived from the provided Image.
createProcessor(Image) - Method in class org.micromanager.data.internal.DefaultImageJConverter
 
createProcessor(Image, boolean) - Static method in class org.micromanager.data.internal.DefaultImageJConverter
 
createProcessor() - Method in interface org.micromanager.data.ProcessorFactory
Generate a new DataProcessor based on the configuration of the Factory.
createProcessorFromComponent(Image, int) - Method in interface org.micromanager.data.ImageJConverter
Create an ImageProcessor whose image pixel data is derived from a single component of the provided Image.
createProcessorFromComponent(Image, int) - Method in class org.micromanager.data.internal.DefaultImageJConverter
 
createProfile(String) - Method in class org.micromanager.profile.internal.UserProfileAdmin
Create a profile with the given name.
createPropertyEditor() - Method in class org.micromanager.internal.MMUIManager
Creates and displays the Property Browser.
createRAMDatastore() - Method in interface org.micromanager.data.DataManager
Generate a new, "blank" Datastore with RAM-based Storage and return it.
createRAMDatastore(Datastore) - Method in interface org.micromanager.data.DataManager
 
createRAMDatastore() - Method in class org.micromanager.data.internal.DefaultDataManager
 
createRAMDatastore(Datastore) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createResolutionsFromHardware(CMMCore) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
Copy the configuration presets from the hardware and override the current setup data.
createRewritableRAMDatastore() - Method in interface org.micromanager.data.DataManager
Generate a new, "blank" RewritableDatastore with RAM-based Storage and return it.
createRewritableRAMDatastore(Datastore) - Method in interface org.micromanager.data.DataManager
 
createRewritableRAMDatastore() - Method in class org.micromanager.data.internal.DefaultDataManager
 
createRewritableRAMDatastore(Datastore) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createScriptPanel() - Method in class org.micromanager.internal.MMUIManager
 
createSetupConfigsFromHardware(CMMCore) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
Copy the configuration presets from the hardware and override the current setup data.
createSimple(int) - Static method in class org.micromanager.internal.utils.performance.TimeIntervalRunningQuantile
 
createSinglePlaneTIFFSeriesDatastore(String) - Method in interface org.micromanager.data.DataManager
Generate a new, "blank" Datastore whose Storage is a series of single-plane TIFF files.
createSinglePlaneTIFFSeriesDatastore(Datastore, String) - Method in interface org.micromanager.data.DataManager
 
createSinglePlaneTIFFSeriesDatastore(String) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createSinglePlaneTIFFSeriesDatastore(Datastore, String) - Method in class org.micromanager.data.internal.DefaultDataManager
 
createStarted() - Static method in class org.micromanager.internal.utils.performance.CPUTimer
 
createStarted() - Static method in class org.micromanager.internal.utils.performance.WallTimer
 
createSwatch(Color, int) - Static method in class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
Dynamically generate an icon that's a square of the specified color with the specified edge length.
createThreadFactory(String) - Static method in class org.micromanager.internal.utils.ThreadFactoryFactory
 
createTiles(double, TileCreator.OverlapUnitEnum, MultiStagePosition[], double, String, String, StrVector, ZGenerator.Type) - Method in class org.micromanager.internal.positionlist.utils.TileCreator
 
createUnavailable() - Static method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
createWithTimeConstantMs(double) - Static method in class org.micromanager.internal.utils.performance.ExponentialSmoothing
 
createWithTimeConstantMs(double) - Static method in class org.micromanager.internal.utils.performance.PerformanceMonitor
 
createWithTimeConstantMs(double) - Static method in class org.micromanager.internal.utils.performance.TimeIntervalExponentialSmoothing
 
creatingNew_ - Variable in class org.micromanager.internal.hcwizard.MicroscopeModel
 
crop(int, int, int, int, int, int) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
crossCorrelate(ImageProcessor, ImageProcessor) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
Executes ImageJ-based Fourier space cross-correlation This should have the exact same result as the ImageJ FFT - FD Math - Correlate command
CURRENT_METADATA_VERSION - Static variable in class org.micromanager.data.internal.DefaultSummaryMetadata
This is the version string for all metadata as saved in Micro-Manager data files.
currentMemory() - Static method in class org.micromanager.internal.utils.MemoryUtils
Returns the currently allocated memory.
CUSTOM_FILE - Static variable in class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
 
CUSTOM_ICON_STRING - Static variable in class org.micromanager.quickaccess.WidgetPlugin
Key used for custom icon information.
customIntervalsMs(ArrayList<Double>) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
 
customIntervalsMs - Variable in class org.micromanager.acquisition.SequenceSettings
Deprecated.
use Builder and customIntervalsMs() instead
customIntervalsMs() - Method in class org.micromanager.acquisition.SequenceSettings
Time intervals between the starts of time points in milliseconds.
customIntervalsMs(double...) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
customIntervalsMs(Iterable<Double>) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
customIntervalsMs(Double[]) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
Deprecated.
customIntervalsMs(double...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
customIntervalsMs(Iterable<Double>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
customIntervalsMs(Double[]) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
CustomTimeIntervalsPanel - Class in org.micromanager.internal.dialogs
 
CustomTimeIntervalsPanel(AcquisitionEngine, Studio, Window) - Constructor for class org.micromanager.internal.dialogs.CustomTimeIntervalsPanel
 
CustomTimesDialog - Class in org.micromanager.internal.dialogs
This class provides a dialog available from the "Advanced" button on the AcqConrolDlg (MDA setup window) in the timepoints panel.
CustomTimesDialog(AcquisitionEngine, Studio) - Constructor for class org.micromanager.internal.dialogs.CustomTimesDialog
 

D

data() - Method in class org.micromanager.internal.MMStudio
 
data() - Method in interface org.micromanager.Studio
Provide access to the DataManager instance for accessing Micro-Manager data constructs.
DataCoordsAnimationState - Class in org.micromanager.display.internal.animate
Manages the position within a dataset displayed during animated playback.
DataCoordsAnimationState.CoordsProvider - Interface in org.micromanager.display.internal.animate
Interface for the delegate supplying presence/absence of data.
DataManager - Interface in org.micromanager.data
This class provides general utility functions for working with Micro-Manager data.
DataProvider - Interface in org.micromanager.data
Read-only access to multi-dimensional image data.
dataProvider(DataProvider) - Method in class org.micromanager.display.internal.displaywindow.DisplayController.Builder
Sets DataProvider for this DisplayController Builder.
DataProviderHasNewImageEvent - Interface in org.micromanager.data
This class signifies that an image has been added to a DataProvider.
DataProviderHasNewNameEvent - Interface in org.micromanager.data
This event posts when the DataStore gets a new name, i.e.
DataProviderHasNewSummaryMetadataEvent - Interface in org.micromanager.data
This class signifies that new summary metadata has been set for a DataProvider.
Datastore - Interface in org.micromanager.data
Read/write access to multi-dimensional image data.
Datastore.SaveMode - Enum in org.micromanager.data
The file format to save to.
DatastoreClosingEvent - Interface in org.micromanager.data
This class signifies that a Datastore's close() method has been called, and thus that all resources associated with that Datastore, and references to the Datastore, should be removed so that it can be garbage collected.
DatastoreFrozenEvent - Interface in org.micromanager.data
This class signifies that a Datastore has become frozen and can no longer be written to (but read actions may still occur).
DatastoreFrozenException - Exception in org.micromanager.data
An unchecked exception thrown when an attempt is made to modify a Datastore that has been frozen.
DatastoreFrozenException() - Constructor for exception org.micromanager.data.DatastoreFrozenException
 
DatastoreRewriteException - Exception in org.micromanager.data
An unchecked exception thrown when an attempt is made to overwrite data in a non-rewritable datastore.
DatastoreRewriteException() - Constructor for exception org.micromanager.data.DatastoreRewriteException
 
DataViewer - Interface in org.micromanager.display
General interface for any user interface displaying image data.
DataViewerAddedEvent - Class in org.micromanager.display.internal.event
 
DataViewerCollection - Class in org.micromanager.display.internal
The collection of data viewers.
DataViewerDidBecomeActiveEvent - Class in org.micromanager.display.internal.event
TODO: any external dataviewre that likes to be managed needs to be able to create this event.
DataViewerDidBecomeInactiveEvent - Class in org.micromanager.display.internal.event
 
DataViewerDidBecomeInvisibleEvent - Class in org.micromanager.display.internal.event
 
DataViewerDidBecomeVisibleEvent - Class in org.micromanager.display.internal.event
 
DataViewerListener - Class in org.micromanager.display
Simple interface dedicated to the question if a dataviewer can be closed or not.
DataViewerListener() - Constructor for class org.micromanager.display.DataViewerListener
 
DataViewerMousePixelInfoChangedEvent - Class in org.micromanager.display.internal.event
 
DataViewerWillCloseEvent - Class in org.micromanager.display.internal.event
 
DaytimeNighttime - Class in org.micromanager.internal.utils
This class controls the colors of the user interface.
DaytimeNighttime.Table - Class in org.micromanager.internal.utils
Because tables don't obey look and feel color commands, we have this custom table that picks up its background based on the current mode.
deActivate(DataViewer) - Method in class org.micromanager.internal.navigation.UiMovesStageManager
Deactivates all the UI elements that move the stage for the given display.
debugMode() - Method in class org.micromanager.internal.pixelcalibrator.PixelCalibratorDialog
 
deducePixelSize(AffineTransform) - Static method in class org.micromanager.internal.utils.AffineUtils
 
DEFAULT_PRIORITY - Static variable in class org.micromanager.internal.utils.PrioritizedEventBus
 
DefaultAcquisitionEndedEvent - Class in org.micromanager.acquisition.internal
This event signifies that an acquisition has been ended.
DefaultAcquisitionEndedEvent(Datastore, Object) - Constructor for class org.micromanager.acquisition.internal.DefaultAcquisitionEndedEvent
 
DefaultAcquisitionManager - Class in org.micromanager.acquisition.internal
TODO: this class still depends on MMStudio for access to its cache.
DefaultAcquisitionManager(Studio, AcquisitionWrapperEngine, AcqControlDlg) - Constructor for class org.micromanager.acquisition.internal.DefaultAcquisitionManager
Constructor only sets essential member values.
DefaultAcquisitionStartedEvent - Class in org.micromanager.acquisition.internal
* This implementation of this event is posted on the Studio event bus, * so subscribe to this event using EventManager.
DefaultAcquisitionStartedEvent(Datastore, Object, SequenceSettings) - Constructor for class org.micromanager.acquisition.internal.DefaultAcquisitionStartedEvent
 
DefaultAlbum - Class in org.micromanager.internal
Implementation of the Album interface.
DefaultAlbum(Studio) - Constructor for class org.micromanager.internal.DefaultAlbum
 
DefaultAlert - Class in org.micromanager.alerts.internal
 
DefaultAlertManager - Class in org.micromanager.alerts.internal
 
DefaultAlertManager(Studio) - Constructor for class org.micromanager.alerts.internal.DefaultAlertManager
 
DefaultAnchorDidBecomeInSyncEvent<T> - Class in org.micromanager.display.internal.link.internal
 
DefaultAnchorDidBecomeInSyncEvent(LinkAnchor<T>) - Constructor for class org.micromanager.display.internal.link.internal.DefaultAnchorDidBecomeInSyncEvent
 
DefaultAnchorDidBecomeLinkableEvent<T> - Class in org.micromanager.display.internal.link.internal
 
DefaultAnchorDidBecomeLinkableEvent(LinkAnchor<T>) - Constructor for class org.micromanager.display.internal.link.internal.DefaultAnchorDidBecomeLinkableEvent
 
DefaultAnchorDidBecomeOutOfSyncEvent<T> - Class in org.micromanager.display.internal.link.internal
 
DefaultAnchorDidBecomeOutOfSyncEvent(LinkAnchor<T>) - Constructor for class org.micromanager.display.internal.link.internal.DefaultAnchorDidBecomeOutOfSyncEvent
 
DefaultAnchorDidMakeLinkEvent<T> - Class in org.micromanager.display.internal.link.internal
 
DefaultAnchorDidMakeLinkEvent(LinkAnchor<T>) - Constructor for class org.micromanager.display.internal.link.internal.DefaultAnchorDidMakeLinkEvent
 
DefaultAnchorWillBecomeUnlinkableEvent<T> - Class in org.micromanager.display.internal.link.internal
 
DefaultAnchorWillBecomeUnlinkableEvent(LinkAnchor<T>) - Constructor for class org.micromanager.display.internal.link.internal.DefaultAnchorWillBecomeUnlinkableEvent
 
DefaultAnchorWillBreakLinkEvent<T> - Class in org.micromanager.display.internal.link.internal
 
DefaultAnchorWillBreakLinkEvent(LinkAnchor<T>) - Constructor for class org.micromanager.display.internal.link.internal.DefaultAnchorWillBreakLinkEvent
 
DefaultAnnotation - Class in org.micromanager.data.internal
Fairly naive Annotation implementation that stores PropertyMaps as JSON in a plaintext file.
DefaultAnnotation(Datastore, String) - Constructor for class org.micromanager.data.internal.DefaultAnnotation
Annotations are user-provided comments that either pertain to the complete dataset (Summary comments), or per image.
DefaultApplication - Class in org.micromanager.internal
Implementation of the Application interface.
DefaultApplication(Studio, ApplicationSkin) - Constructor for class org.micromanager.internal.DefaultApplication
 
DefaultApplicationSkinEvent - Class in org.micromanager.events.internal
 
DefaultApplicationSkinEvent(ApplicationSkin.SkinMode) - Constructor for class org.micromanager.events.internal.DefaultApplicationSkinEvent
 
DefaultAutofocusManager - Class in org.micromanager.internal.utils
Manages different instances of autofocus devices, both Java plugin and MMCore based.
DefaultAutofocusManager(Studio) - Constructor for class org.micromanager.internal.utils.DefaultAutofocusManager
 
DefaultAutoShutterEvent - Class in org.micromanager.events.internal
This event is posted on the Studio event bus, so subscribe it using EventManager.
DefaultAutoShutterEvent(boolean) - Constructor for class org.micromanager.events.internal.DefaultAutoShutterEvent
 
DefaultChannelDisplaySettings - Class in org.micromanager.display.internal
 
DefaultChannelExposureEvent - Class in org.micromanager.events.internal
 
DefaultChannelExposureEvent(double, String, String, boolean) - Constructor for class org.micromanager.events.internal.DefaultChannelExposureEvent
 
DefaultChannelGroupChangedEvent - Class in org.micromanager.events.internal
Event signaling that the "Channel Group" changed This event is posted on the Studio event bus, so subscribe using EventManager.
DefaultChannelGroupChangedEvent(String) - Constructor for class org.micromanager.events.internal.DefaultChannelGroupChangedEvent
 
DefaultCompatibilityInterface - Class in org.micromanager.internal
Implementation of the Compatibility Interface.
DefaultCompatibilityInterface(Studio) - Constructor for class org.micromanager.internal.DefaultCompatibilityInterface
 
DefaultComponentDisplaySettings - Class in org.micromanager.display.internal
 
DefaultConfigGroupChangedEvent - Class in org.micromanager.events.internal
Event signaling that the "active" preset in a config group changed.
DefaultConfigGroupChangedEvent(String, String) - Constructor for class org.micromanager.events.internal.DefaultConfigGroupChangedEvent
 
DefaultContrastSettings(Integer, Integer, Double, Boolean) - Constructor for class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
Convenience method for single-component settings.
DefaultContrastSettings(Integer[], Integer[], Double[], Boolean) - Constructor for class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
 
DefaultCoords - Class in org.micromanager.data.internal
 
DefaultCoords(DefaultCoords.Builder) - Constructor for class org.micromanager.data.internal.DefaultCoords
 
DefaultCoords.Builder - Class in org.micromanager.data.internal
 
DefaultDataManager - Class in org.micromanager.data.internal
This implementation of the DataManager interface provides general utility access to Micro-Manager's data objects.
DefaultDataManager(MMStudio) - Constructor for class org.micromanager.data.internal.DefaultDataManager
 
DefaultDataSaver - Class in org.micromanager.data.internal
TODO: Not sure if Swingworker is the best implementation.
DefaultDataSaver(Studio, DefaultDatastore, Datastore.SaveMode, String) - Constructor for class org.micromanager.data.internal.DefaultDataSaver
Takes care of most of the dirty work saving data to various targets.
DefaultDatastore - Class in org.micromanager.data.internal
Default implementaton of the Datastore interface.
DefaultDatastore(Studio) - Constructor for class org.micromanager.data.internal.DefaultDatastore
 
DefaultDatastoreClosingEvent - Class in org.micromanager.data.internal
This class signifies that a Datastore's close() method has been called, and thus that all resources associated with that Datastore, and references to the Datastore, should be removed so that it can be garbage collected.
DefaultDatastoreClosingEvent(Datastore) - Constructor for class org.micromanager.data.internal.DefaultDatastoreClosingEvent
 
DefaultDatastoreFrozenEvent - Class in org.micromanager.data.internal
This class signifies that a Datastore has become locked and cannot be written to any more (but read actions can still occur).
DefaultDatastoreFrozenEvent() - Constructor for class org.micromanager.data.internal.DefaultDatastoreFrozenEvent
 
DefaultDisplayDidShowImageEvent - Class in org.micromanager.display.internal.event
This event posts when a DataViewer displays an image(s).
DefaultDisplayManager - Class in org.micromanager.display.internal
 
DefaultDisplayManager(Studio) - Constructor for class org.micromanager.display.internal.DefaultDisplayManager
 
DefaultDisplayPositionChangedEvent - Class in org.micromanager.display.internal.event
This event posts when the position (i.e., Channel, Time, Position, Slice, possibly other Axes) in the display changed.
DefaultDisplaySettings - Class in org.micromanager.display.internal
Implementation of the DisplaySettings interface.
DefaultDisplaySettings.DefaultContrastSettings - Class in org.micromanager.display.internal
Deprecated.
DefaultDisplaySettings.LegacyBuilder - Class in org.micromanager.display.internal
Deprecated.
DefaultDisplaySettingsChangedEvent - Class in org.micromanager.display.internal.event
Standard implementation of NewDisplaySettingsEvent.
DefaultEventManager - Class in org.micromanager.events.internal
 
DefaultEventManager() - Constructor for class org.micromanager.events.internal.DefaultEventManager
DefaultEventManager is basically a pass-through to the Google Eventbus
DefaultExposureChangedEvent - Class in org.micromanager.events.internal
This class signals when the exposure time for a given camera has changed.
DefaultExposureChangedEvent(String, double) - Constructor for class org.micromanager.events.internal.DefaultExposureChangedEvent
 
DefaultGUIRefreshEvent - Class in org.micromanager.events.internal
This event posts whenever the GUI refreshes its state from the Core (e.g.
DefaultGUIRefreshEvent() - Constructor for class org.micromanager.events.internal.DefaultGUIRefreshEvent
 
DefaultHasNewNameEvent - Class in org.micromanager.data.internal
This event posts when the DataStore gets a new name, i.e.
DefaultHasNewNameEvent(String) - Constructor for class org.micromanager.data.internal.DefaultHasNewNameEvent
 
DefaultImage - Class in org.micromanager.data.internal
This class represents a single image from a single camera.
DefaultImage(TaggedImage) - Constructor for class org.micromanager.data.internal.DefaultImage
Generate a DefaultImage from a TaggedImage.
DefaultImage(TaggedImage, Coords, Metadata) - Constructor for class org.micromanager.data.internal.DefaultImage
Generate a DefaultImage from a TaggedImage using the supplied coords and metadata.
DefaultImage(Object, PropertyMap, Coords, Metadata) - Constructor for class org.micromanager.data.internal.DefaultImage
Generates a DefaultImage from pixels, image info in a PropertyMap and the supplied coords and metadata.
DefaultImage(Object, int, int, int, int, Coords, Metadata) - Constructor for class org.micromanager.data.internal.DefaultImage
Generates a DefaultImage from pixels, minimal image info, and the supplied coords and metadata.
DefaultImage(Image, Coords, Metadata) - Constructor for class org.micromanager.data.internal.DefaultImage
Creates a new image object that shares the pixels of the source image Attaches the provided coords and metadata
DefaultImageDeletedEvent - Class in org.micromanager.data.internal
This class signifies that an image has been deleted from a Datastore.
DefaultImageDeletedEvent(Image, Datastore) - Constructor for class org.micromanager.data.internal.DefaultImageDeletedEvent
 
DefaultImageExporter - Class in org.micromanager.display.internal.gearmenu
 
DefaultImageExporter() - Constructor for class org.micromanager.display.internal.gearmenu.DefaultImageExporter
 
DefaultImageExporter.ExporterLoop - Class in org.micromanager.display.internal.gearmenu
This recursive structure represents the "nested loop" approach to exporting.
DefaultImageJConverter - Class in org.micromanager.data.internal
 
DefaultImageJConverter(Studio) - Constructor for class org.micromanager.data.internal.DefaultImageJConverter
 
DefaultImageOverwrittenEvent - Class in org.micromanager.data.internal
This class signifies that an image in a Datastore has been overwritten by a new image.
DefaultImageOverwrittenEvent(Image, Image, Datastore) - Constructor for class org.micromanager.data.internal.DefaultImageOverwrittenEvent
 
DefaultLinkManager - Class in org.micromanager.display.internal.link.internal
 
DefaultLiveModeEvent - Class in org.micromanager.events.internal
This class signals that live mode has been turned on or off.
DefaultLiveModeEvent(boolean) - Constructor for class org.micromanager.events.internal.DefaultLiveModeEvent
 
DefaultMDAPlugin - Class in org.micromanager.acquisition.internal
This built-in plugin provides access to our standard MDA dialog.
DefaultMDAPlugin() - Constructor for class org.micromanager.acquisition.internal.DefaultMDAPlugin
 
DefaultMetadata - Class in org.micromanager.data.internal
This class holds the metadata for ImagePlanes.
DefaultMetadata(PropertyMap) - Constructor for class org.micromanager.data.internal.DefaultMetadata
 
DefaultMetadata.Builder - Class in org.micromanager.data.internal
 
DefaultNewImageEvent - Class in org.micromanager.data.internal
This class signifies that an image has been added to a Datastore.
DefaultNewImageEvent(Image, DataProvider) - Constructor for class org.micromanager.data.internal.DefaultNewImageEvent
 
DefaultNewPipelineEvent - Class in org.micromanager.data.internal
This class signifies that the configuration of the application pipeline has changed, giving entities that use that pipeline an opportunity to make a new copy of it (by invoking DataManager.copyApplicationPipeline()).
DefaultNewPipelineEvent() - Constructor for class org.micromanager.data.internal.DefaultNewPipelineEvent
 
DefaultNewPositionListEvent - Class in org.micromanager.events.internal
This event posts when the application's Stage Position List changes (positions added, removed, or moved).
DefaultNewPositionListEvent(PositionList) - Constructor for class org.micromanager.events.internal.DefaultNewPositionListEvent
 
DefaultNewSummaryMetadataEvent - Class in org.micromanager.data.internal
This class signifies that new summary metadata has been set for a DataProvider.
DefaultNewSummaryMetadataEvent(SummaryMetadata) - Constructor for class org.micromanager.data.internal.DefaultNewSummaryMetadataEvent
 
DefaultPipeline - Class in org.micromanager.data.internal.pipeline
 
DefaultPipeline(List<Processor>, Datastore, boolean) - Constructor for class org.micromanager.data.internal.pipeline.DefaultPipeline
 
DefaultPixelSizeAffineChangedEvent - Class in org.micromanager.events.internal
This event posts when the affine transform, describing the relation between stage movement and camera coordinates, changes.
DefaultPixelSizeAffineChangedEvent(AffineTransform) - Constructor for class org.micromanager.events.internal.DefaultPixelSizeAffineChangedEvent
 
DefaultPixelSizeChangedEvent - Class in org.micromanager.events.internal
This event posts when the pixel size, the size of a camera pixel in the object plane, changes.
DefaultPixelSizeChangedEvent(double) - Constructor for class org.micromanager.events.internal.DefaultPixelSizeChangedEvent
 
DefaultPluginManager - Class in org.micromanager.internal.pluginmanagement
Implementation of the PluginManager API.
DefaultPluginManager(Studio) - Constructor for class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
DefaultPositionListManager - Class in org.micromanager.internal
Default implementation of the PositionListManager.
DefaultPositionListManager(Studio) - Constructor for class org.micromanager.internal.DefaultPositionListManager
 
DefaultPropertiesChangedEvent - Class in org.micromanager.events.internal
This class signals when any property of the microscope has changed.
DefaultPropertiesChangedEvent() - Constructor for class org.micromanager.events.internal.DefaultPropertiesChangedEvent
 
DefaultPropertyChangedEvent - Class in org.micromanager.events.internal
This class provides information when a specific property changes.
DefaultPropertyChangedEvent(String, String, String) - Constructor for class org.micromanager.events.internal.DefaultPropertyChangedEvent
 
DefaultPropertyManager - Class in org.micromanager.internal
Default implementation of the PropertyManager API.
DefaultPropertyManager() - Constructor for class org.micromanager.internal.DefaultPropertyManager
 
DefaultPropertyMap - Class in org.micromanager.internal.propertymap
 
DefaultPropertyMap.Builder - Class in org.micromanager.internal.propertymap
 
DefaultQuickAccessManager - Class in org.micromanager.quickaccess.internal
This class is responsible for managing the different Quick Access Windows.
DefaultQuickAccessManager(Studio) - Constructor for class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
 
DefaultRewritableDatastore - Class in org.micromanager.data.internal
 
DefaultRewritableDatastore(MMStudio) - Constructor for class org.micromanager.data.internal.DefaultRewritableDatastore
 
DefaultShutdownCommencingEvent - Class in org.micromanager.events.internal
This event posts when the user requests the program to shut down.
DefaultShutdownCommencingEvent() - Constructor for class org.micromanager.events.internal.DefaultShutdownCommencingEvent
 
DefaultShutterEvent - Class in org.micromanager.events.internal
This event posts when the shutter opens or closes.
DefaultShutterEvent(boolean) - Constructor for class org.micromanager.events.internal.DefaultShutterEvent
 
DefaultShutterManager - Class in org.micromanager.internal
Default implementation of the ShutterManager API.
DefaultShutterManager(Studio) - Constructor for class org.micromanager.internal.DefaultShutterManager
 
DefaultSLMExposureChangedEvent - Class in org.micromanager.events.internal
This interface posts when the exposure time for a given Spatial Light Modulator (such as a Digital Mirror Device) changes.
DefaultSLMExposureChangedEvent(String, double) - Constructor for class org.micromanager.events.internal.DefaultSLMExposureChangedEvent
 
DefaultStagePositionChangedEvent - Class in org.micromanager.events.internal
This class signals when a single-axis drive has moved.
DefaultStagePositionChangedEvent(String, double) - Constructor for class org.micromanager.events.internal.DefaultStagePositionChangedEvent
 
DefaultStartupCompleteEvent - Class in org.micromanager.events.internal
This event signifies that the system finished starting up.
DefaultStartupCompleteEvent() - Constructor for class org.micromanager.events.internal.DefaultStartupCompleteEvent
 
DefaultSummaryMetadata - Class in org.micromanager.data.internal
 
DefaultSummaryMetadata.Builder - Class in org.micromanager.data.internal
 
DefaultSystemConfigurationLoadedEvent - Class in org.micromanager.events.internal
This interface signals when a configuration file is loaded.
DefaultSystemConfigurationLoadedEvent() - Constructor for class org.micromanager.events.internal.DefaultSystemConfigurationLoadedEvent
 
DefaultTaggedImageSink - Class in org.micromanager.acquisition.internal
This object spawns a new thread that receives images from the acquisition engine and runs them through a Pipeline to the Datastore.
DefaultTaggedImageSink(BlockingQueue<TaggedImage>, Pipeline, Datastore, AcquisitionEngine, EventManager) - Constructor for class org.micromanager.acquisition.internal.DefaultTaggedImageSink
 
DefaultUserProfile - Class in org.micromanager.profile.internal
Implementation of UserProfile.
DefaultXYStagePositionChangedEvent - Class in org.micromanager.events.internal
This class signals when any XY stage changes position.
DefaultXYStagePositionChangedEvent(String, double, double) - Constructor for class org.micromanager.events.internal.DefaultXYStagePositionChangedEvent
 
DelayPage - Class in org.micromanager.internal.hcwizard
Wizard page to set device delays.
DelayPage() - Constructor for class org.micromanager.internal.hcwizard.DelayPage
Create the panel
deleteAllImages() - Method in class org.micromanager.data.internal.DefaultRewritableDatastore
 
deleteAllImages() - Method in interface org.micromanager.data.RewritableDatastore
Delete all images from the Datastore.
deleteConfig(String, String) - Method in class org.micromanager.internal.utils.PropertyTableData
 
deleteFollowing(ExportMovieDlg.AxisPanel) - Method in class org.micromanager.display.internal.gearmenu.ExportMovieDlg
Remove all AxisPanels after the specified panel.
deleteImage(Coords) - Method in class org.micromanager.data.internal.DefaultRewritableDatastore
 
deleteImage(Coords) - Method in class org.micromanager.data.internal.StorageRAM
 
deleteImage(Coords) - Method in interface org.micromanager.data.RewritableDatastore
Delete an image from the Datastore.
deleteImage(Coords) - Method in interface org.micromanager.data.RewritableStorage
Delete an image from the Storage.
deleteImagesMatching(Coords) - Method in class org.micromanager.data.internal.DefaultRewritableDatastore
 
deleteImagesMatching(Coords) - Method in interface org.micromanager.data.RewritableDatastore
Delete all images from the Datastore whose coordinates match the provided Coords object, which may be underspecified.
deleteLastSlice() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
deleteLogFilesDaysOld(int, String) - Static method in class org.micromanager.internal.logging.LogFileManager
 
deletePanel(QuickAccessFrame) - Method in class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
Remove an existing panel.
deleteSlice(int) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
deleteStorage() - Method in class org.micromanager.internal.diagnostics.ProblemReport
Deletes Problem Report files from disk.
descr - Variable in class org.micromanager.internal.utils.StateItem
 
description_ - Variable in enum org.micromanager.internal.positionlist.utils.ZGenerator.Type
 
detachChangeListeners(JSpinner) - Static method in class org.micromanager.internal.utils.GUIUtils
 
detachDataViewer() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
Detach from any currently attached data viewer.
detachDataViewer() - Method in interface org.micromanager.display.inspector.InspectorPanelController
 
detachDataViewer() - Method in class org.micromanager.display.inspector.internal.panels.comments.CommentsInspectorPanelController
 
detachDataViewer() - Method in class org.micromanager.display.inspector.internal.panels.intensity.IntensityInspectorPanelController
 
detachDataViewer() - Method in class org.micromanager.display.inspector.internal.panels.metadata.PlaneMetadataInspectorPanelController
 
detachDataViewer() - Method in class org.micromanager.display.inspector.internal.panels.metadata.SummaryMetadataInspectorPanelController
 
detachDataViewer() - Method in class org.micromanager.display.inspector.internal.panels.overlays.OverlaysInspectorPanelController
 
DetectorJDialog - Class in org.micromanager.internal.hcwizard
 
DetectorJDialog(Dialog, boolean) - Constructor for class org.micromanager.internal.hcwizard.DetectorJDialog
Creates new form DetectorJDialog
Device - Class in org.micromanager.internal.hcwizard
Data structure describing a general MM device.
Device(String, String, String, String, boolean, String, Vector<String>) - Constructor for class org.micromanager.internal.hcwizard.Device
 
Device(String, String, String, String) - Constructor for class org.micromanager.internal.hcwizard.Device
 
Device(String, String, String) - Constructor for class org.micromanager.internal.hcwizard.Device
 
device - Variable in class org.micromanager.internal.utils.PropertyItem
 
deviceName_ - Variable in class org.micromanager.internal.hcwizard.Setting
 
DeviceSetupDlg - Class in org.micromanager.internal.hcwizard
 
DeviceSetupDlg(MicroscopeModel, Studio, Device) - Constructor for class org.micromanager.internal.hcwizard.DeviceSetupDlg
Create the dialog.
DeviceSorter - Class in org.micromanager.internal.hcwizard
 
DeviceSorter() - Constructor for class org.micromanager.internal.hcwizard.DeviceSorter
 
DevicesPage - Class in org.micromanager.internal.hcwizard
Wizard page to add or remove devices.
DevicesPage() - Constructor for class org.micromanager.internal.hcwizard.DevicesPage
Create the panel
DEVLIST_FILE_NAME - Static variable in class org.micromanager.internal.hcwizard.MicroscopeModel
 
directBufferFromArray(Object) - Static method in class org.micromanager.data.internal.BufferTools
 
directBufferFromBytes(byte[]) - Static method in class org.micromanager.data.internal.BufferTools
 
directBufferFromInts(int[]) - Static method in class org.micromanager.data.internal.BufferTools
 
directBufferFromShorts(short[]) - Static method in class org.micromanager.data.internal.BufferTools
 
directBufferFromString(String) - Static method in class org.micromanager.data.internal.BufferTools
 
directory(String) - Method in class org.micromanager.data.internal.DefaultSummaryMetadata.Builder
 
directory(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
 
directory(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder
Deprecated.
 
disabled - Variable in class org.micromanager.internal.utils.PropertyTableData
 
disableExcluded_ - Variable in class org.micromanager.internal.utils.PropertyValueCellEditor
 
DISCLAIMER_TEXT - Static variable in class org.micromanager.internal.dialogs.IntroDlg
 
discoverPeripherals(CMMCore) - Method in class org.micromanager.internal.hcwizard.Device
 
dismiss() - Method in interface org.micromanager.alerts.Alert
Dismiss the Alert, causing it to no longer be visible to the user.
dismiss() - Method in class org.micromanager.alerts.internal.DefaultAlert
 
dispatchKeyEvent(KeyEvent) - Method in class org.micromanager.internal.utils.MMKeyDispatcher
 
DISPLAY_SETTINGS_BYTES_PER_CHANNEL - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
DISPLAY_SETTINGS_HEADER - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
DISPLAY_SETTINGS_OFFSET_HEADER - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
DisplayController - Class in org.micromanager.display.internal.displaywindow
Main controller for the standard image viewer.
DisplayController.Builder - Class in org.micromanager.display.internal.displaywindow
Builder for DisplayController.
DisplayDidShowImageEvent - Interface in org.micromanager.display
This event posts when a DataViewer displays an image(s).
displayError(String) - Method in class org.micromanager.internal.script.ScriptPanel
 
displayError(String, int) - Method in class org.micromanager.internal.script.ScriptPanel
 
DisplayGearMenuPlugin - Interface in org.micromanager.display
DisplayGearMenuPlugins add items to be shown in the "gear menu" shown in each DisplayWindow.
displayImage(Image) - Method in class org.micromanager.internal.SnapLiveManager
Display the provided image.
displayImage(Image) - Method in interface org.micromanager.SnapLiveManager
Insert the provided image into the Datastore, causing it to be displayed in any open Snap/Live DisplayWindows.
DisplayKeyPressEvent - Class in org.micromanager.display.internal.event
Used to propagate key-presses through the Guava bus If a consumer wants others to know that the keyEvent led to action, call the "consumed()" function.
DisplayKeyPressEvent(KeyEvent) - Constructor for class org.micromanager.display.internal.event.DisplayKeyPressEvent
 
DisplayManager - Interface in org.micromanager.display
This interface declares generic display-related methods.
displayMessage(String) - Method in class org.micromanager.internal.script.ScriptPanel
 
DisplayMouseEvent - Class in org.micromanager.display.internal.event
Provides a MouseEvent and the location (in image pixel coordinates) where the event happened
DisplayMouseEvent(MouseEvent, Rectangle, int) - Constructor for class org.micromanager.display.internal.event.DisplayMouseEvent
 
DisplayMouseWheelEvent - Class in org.micromanager.display.internal.event
 
DisplayMouseWheelEvent(MouseWheelEvent) - Constructor for class org.micromanager.display.internal.event.DisplayMouseWheelEvent
 
displayNonBlockingMessage(String) - Static method in class org.micromanager.internal.utils.ReportingUtils
 
DisplayPositionChangedEvent - Interface in org.micromanager.display
This event posts when the position (i.e., Channel, Time, Position, Slice, possibly other Axes) in the display changed.
displays() - Method in class org.micromanager.internal.MMStudio
 
displays() - Method in interface org.micromanager.Studio
Provides access to the DisplayManager instance for accessing Micro-Manager display constructs.
DisplaySettings - Interface in org.micromanager.display
This class defines the parameters that control how a given DisplayWindow displays data from the Datastore.
DisplaySettings.Builder - Interface in org.micromanager.display
Builder for DisplaySettings.
DisplaySettings.ColorMode - Enum in org.micromanager.display
ColorMode enums.
DisplaySettings.ContrastSettings - Interface in org.micromanager.display
Deprecated.
TODO: explain
DisplaySettings.DisplaySettingsBuilder - Interface in org.micromanager.display
Deprecated.
Use DisplaySettings.Builder instead
displaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager
Generate a "blank" DisplaySettings.Builder with all null values.
displaySettingsBuilder() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
DisplaySettingsChangedEvent - Interface in org.micromanager.display
Event used internally by a data viewer to respond to requests to update the display settings.
displayStatusString(String) - Method in interface org.micromanager.display.DisplayWindow
Display a custom string in the window.
displayStatusString(String) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
displayStringToDouble(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
displayStringToInt(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
displayStringToLong(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
displayTimeUnit(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
 
displayTimeUnit() - Method in class org.micromanager.acquisition.SequenceSettings
Time unit, only used to store preferred way to display the time.
DisplayUIController - Class in org.micromanager.display.internal.displaywindow
Manages the JFrame(s) for image displays.
DisplayWindow - Interface in org.micromanager.display
A DisplayWindow is the interface to Micro-Manager's image display windows.
DisplayWindowAPIAdapter - Class in org.micromanager.display.internal.displaywindow
This is to DisplayWindow what AbstractDataViewer is to DataViewer.
DisplayWindowControlsFactory - Interface in org.micromanager.display
A ControlsFactory is used to provide custom controls for a DisplayWindow.
DisplayWindowDidAddOverlayEvent - Class in org.micromanager.display.internal.event
 
DisplayWindowDidRemoveOverlayEvent - Class in org.micromanager.display.internal.event
 
dispose() - Method in class org.micromanager.internal.dialogs.CalibrationListDlg
 
dispose() - Method in class org.micromanager.internal.dialogs.ConfigDialog
 
dispose() - Method in class org.micromanager.internal.dialogs.PixelConfigEditor
 
dispose() - Method in class org.micromanager.internal.dialogs.PixelPresetEditor
 
dispose() - Method in class org.micromanager.internal.dialogs.StageControlFrame
 
dispose() - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
 
dispose() - Method in class org.micromanager.internal.pipelineinterface.ProcessExistingDataDialog
 
dispose() - Method in class org.micromanager.internal.pixelcalibrator.PixelCalibratorDialog
 
dispose() - Method in class org.micromanager.internal.positionlist.TileCreatorDlg
 
dispose() - Method in class org.micromanager.internal.script.ScriptPanel
 
DoubleStringComp() - Constructor for class org.micromanager.internal.utils.SortFunctionObjects.DoubleStringComp
 
doubleStringCoreToDisplay(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
doubleStringDisplayToCore(Object) - Static method in class org.micromanager.internal.utils.NumberUtils
 
doubleToAffine(DoubleVector) - Static method in class org.micromanager.internal.utils.AffineUtils
 
doubleToCoreString(double) - Static method in class org.micromanager.internal.utils.NumberUtils
 
doubleToDisplayString(double) - Static method in class org.micromanager.internal.utils.NumberUtils
 
doubleToDisplayString(double, int) - Static method in class org.micromanager.internal.utils.NumberUtils
TODO: Check if this is thread safe
doZStack(Boolean) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
 
doZStack - Variable in class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder and getters instead
doZStack() - Method in class org.micromanager.acquisition.ChannelSpec
 
DragDropUtil - Class in org.micromanager.internal.utils
DragDropUtil Handler for drop events in Micro-Manager Checks if files or folders are dropped onto Micro-Manager, and tries to open them.
DragDropUtil(Studio) - Constructor for class org.micromanager.internal.utils.DragDropUtil
 
dragEnter(DropTargetDragEvent) - Method in class org.micromanager.internal.utils.DragDropUtil
 
dragExit(DropTargetEvent) - Method in class org.micromanager.internal.utils.DragDropUtil
 
DraggableIcon - Class in org.micromanager.quickaccess.internal
This class represents an icon that can be dragged around the window, for adding or removing controls.
DraggableIcon(Studio, QuickAccessFrame, JComponent, ImageIcon, QuickAccessPlugin, boolean, ControlCell, Dimension) - Constructor for class org.micromanager.quickaccess.internal.DraggableIcon
icon and plugin are both optional.
dragOver(DropTargetDragEvent) - Method in class org.micromanager.internal.utils.DragDropUtil
 
drawCursor(Graphics2D, Rectangle, float) - Method in class org.micromanager.internal.graph.GraphPanel
 
drawMapping(Graphics2D, Rectangle, float, float, double) - Method in class org.micromanager.internal.graph.GraphPanel
 
drawSphere(double, int, int, int) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
drop(DropTargetDropEvent) - Method in class org.micromanager.internal.utils.DragDropUtil
This function does the actual work
dropActionChanged(DropTargetDragEvent) - Method in class org.micromanager.internal.utils.DragDropUtil
 
dropPlugin(QuickAccessPlugin) - Method in class org.micromanager.quickaccess.internal.QuickAccessFrame
Drop the specified plugin into the controlsPanel_ at the current mouse location, creating a new control (and configuring it if necessary).
dump() - Method in class org.micromanager.internal.utils.performance.PerformanceMonitor
 
dump() - Method in class org.micromanager.internal.utils.PropertyItem
 
dumpAllToCoreLog(boolean) - Static method in class org.micromanager.internal.diagnostics.SystemInfo
 
dumpComPortProperties(String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
dumpComPortsSetupProps() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
dumpDeviceProperties(String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
dumpProperties(String) - Method in class org.micromanager.internal.utils.AutofocusBase
 
dumpSetupConf() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
Display report for the current configuration.
duplicate() - Method in interface org.micromanager.display.DisplayWindow
Create a new display window for the same data provider as this one.
duplicate() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
duplicate() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
duplicateChannels() - Method in class org.micromanager.internal.dialogs.ChannelTableModel
reports if the same channel name is used twice
duplicateProfile(UUID, String) - Method in class org.micromanager.profile.internal.UserProfileAdmin
 
DynamicTextField - Class in org.micromanager.internal.utils
A JTextField with a single listener interface for value change.
DynamicTextField() - Constructor for class org.micromanager.internal.utils.DynamicTextField
 
DynamicTextField(Document, String, int) - Constructor for class org.micromanager.internal.utils.DynamicTextField
 
DynamicTextField(int) - Constructor for class org.micromanager.internal.utils.DynamicTextField
 
DynamicTextField(String) - Constructor for class org.micromanager.internal.utils.DynamicTextField
 
DynamicTextField(String, int) - Constructor for class org.micromanager.internal.utils.DynamicTextField
 
DynamicTextField.Listener - Interface in org.micromanager.internal.utils
Listener interface for DynamicTextField

E

editCalibration() - Method in class org.micromanager.internal.dialogs.CalibrationListDlg
 
editGroup() - Method in class org.micromanager.internal.ConfigPadButtonPanel
Edit a group (user clicked the edit group button).
editNameOnly() - Method in class org.micromanager.internal.dialogs.CalibrationEditor
 
editPreset() - Method in class org.micromanager.internal.ConfigPadButtonPanel
Edit a preset.
editPreset(String, String, boolean) - Method in class org.micromanager.internal.dialogs.CalibrationListDlg
 
EDTHangLogger - Class in org.micromanager.internal.diagnostics
Log event dispatch thread hangs to the CoreLog.
EDTHangLogger(CMMCore, long, long) - Constructor for class org.micromanager.internal.diagnostics.EDTHangLogger
 
EDTProfiler - Class in org.micromanager.internal.utils
 
EDTProfiler() - Constructor for class org.micromanager.internal.utils.EDTProfiler
 
elapsedTimeMs(Double) - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
elapsedTimeMs(Double) - Method in interface org.micromanager.data.Metadata.Builder
 
elapsedTimeMs(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder
Deprecated.
 
emptyPropertyMap() - Method in class org.micromanager.internal.DefaultPropertyManager
Returns an empty property map.
emptyPropertyMap() - Method in interface org.micromanager.PropertyManager
Returns an empty property map.
emptyPropertyMap() - Static method in class org.micromanager.PropertyMaps
Return the empty property map.
enable(boolean) - Static method in class org.micromanager.internal.utils.UIMonitor
 
enableContinuousFocus(boolean) - Method in interface org.micromanager.AutofocusPlugin
Turns on continuous autofocus.
enableContinuousFocus(boolean) - Method in class org.micromanager.internal.utils.AutofocusBase
 
enableContinuousFocus(boolean) - Method in class org.micromanager.internal.utils.CoreAutofocus
 
enableEdit(boolean) - Method in class org.micromanager.internal.utils.SliderPanel
 
enableRoiButtons(boolean) - Method in class org.micromanager.internal.MainFrame
 
encode(int) - Static method in class org.micromanager.internal.utils.MMUUEncoder
 
encodeBuffer(InputStream, OutputStream) - Method in class org.micromanager.internal.utils.MMUUEncoder
 
endedEditingPreset(ConfigDialog) - Method in class org.micromanager.internal.dialogs.CalibrationListDlg
 
enforceIntegerTextField(JTextField, int, int) - Static method in class org.micromanager.internal.utils.GUIUtils
 
enforceValidTextField(JTextField, GUIUtils.StringValidator) - Static method in class org.micromanager.internal.utils.GUIUtils
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.DelayPage
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.DevicesPage
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.FinishPage
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.IntroPage
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.LabelsPage
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.PagePanel
 
enterPage(boolean) - Method in class org.micromanager.internal.hcwizard.RolesPage
 
ENTRIES_PER_IFD - Static variable in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
entrySet() - Method in class org.micromanager.internal.utils.ChainedMapView
 
equals(Object) - Method in class org.micromanager.data.internal.DefaultCoords
 
equals(Object) - Method in class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
 
equals(Object) - Method in class org.micromanager.display.internal.imagestats.BoundsRectAndMask
 
equals(Object) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
equals(Object) - Method in class org.micromanager.MultiStagePosition
Compares this MultiStagePosition to another, and returns true if they are equal in all aspects.
equals(Object) - Method in class org.micromanager.StagePosition
Compare us against the provided StagePosition and return true only if we are equal in all respects.
ERROR_MESSAGE - Static variable in exception org.micromanager.data.DatastoreFrozenException
 
ERROR_MESSAGE - Static variable in exception org.micromanager.data.DatastoreRewriteException
 
EvalThread(String) - Constructor for class org.micromanager.internal.script.BeanshellEngine.EvalThread
 
evaluate(String) - Method in class org.micromanager.internal.script.BeanshellEngine
 
evaluate(String) - Method in interface org.micromanager.internal.script.ScriptingEngine
 
evaluateAsync(String) - Method in class org.micromanager.internal.script.BeanshellEngine
 
evaluateAsync(String) - Method in interface org.micromanager.internal.script.ScriptingEngine
 
EventBusExceptionLogger - Class in org.micromanager.internal.utils
 
EventBusExceptionLogger() - Constructor for class org.micromanager.internal.utils.EventBusExceptionLogger
 
EventManager - Interface in org.micromanager.events
This interface provides access to the application-wide EventBus, on which the events in the org.micromanager.events package are posted.
EventPublisher - Interface in org.micromanager
Any object that bears an internal event bus to which other objects can subscribe to receive events.
events() - Method in class org.micromanager.internal.MMStudio
 
events() - Method in interface org.micromanager.Studio
Provides access to the EventManager instance for subscribing to and posting events on the application-wide EventBus.
exceptionOccurred(Exception) - Method in class org.micromanager.data.internal.pipeline.DefaultPipeline
 
execute(Studio) - Static method in class org.micromanager.internal.dialogs.IJVersionCheckDlg
Show the warning dialog, if applicable and user has not opted out.
ExecuteAction() - Method in class org.micromanager.internal.utils.HotKeyAction
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.DelayPage
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.DevicesPage
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.FinishPage
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.IntroPage
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.LabelsPage
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.PagePanel
 
exitPage(boolean) - Method in class org.micromanager.internal.hcwizard.RolesPage
 
ExponentialSmoothing - Class in org.micromanager.internal.utils.performance
Compute rolling exponential average of a time series.
export() - Method in interface org.micromanager.display.ImageExporter
Run the export process.
export() - Method in class org.micromanager.display.internal.gearmenu.DefaultImageExporter
Export images according to the user's setup.
ExporterLoop(String, int, int) - Constructor for class org.micromanager.display.internal.gearmenu.DefaultImageExporter.ExporterLoop
 
ExportImagesItem - Class in org.micromanager.display.internal.gearmenu
 
ExportImagesItem() - Constructor for class org.micromanager.display.internal.gearmenu.ExportImagesItem
 
ExportMovieDlg - Class in org.micromanager.display.internal.gearmenu
This dialog provides an interface for exporting (a portion of) a dataset to an image sequence, complete with all MicroManager overlays.
ExportMovieDlg(Studio, DisplayWindow) - Constructor for class org.micromanager.display.internal.gearmenu.ExportMovieDlg
Show the dialog.
ExportMovieDlg.AxisPanel - Class in org.micromanager.display.internal.gearmenu
A set of controls for selecting a range of values for a single axis of the dataset.
exposure(double) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
 
exposure - Variable in class org.micromanager.acquisition.ChannelSpec
Deprecated.
Use Builder and getters instead
exposure() - Method in class org.micromanager.acquisition.ChannelSpec
 
ExposureChangedEvent - Interface in org.micromanager.events
This class signals when the exposure time for a given camera has changed.
exposureMs(Double) - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
exposureMs(Double) - Method in interface org.micromanager.data.Metadata.Builder
 
exposureMs(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder
Deprecated.
 
ExposureTime - Class in org.micromanager.quickaccess.internal.controls
Allows you to set the exposure time for the currently-selected channel.
ExposureTime() - Constructor for class org.micromanager.quickaccess.internal.controls.ExposureTime
 
extractFromGsonObject(JsonObject, PropertyMap.Builder) - Method in enum org.micromanager.data.internal.PropertyKey
Parse the value stored in the containing JSON object.
extremaPercentage(Double) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder
Deprecated.
extremaPercentage(Double) - Method in class org.micromanager.display.internal.DefaultDisplaySettings.LegacyBuilder
Deprecated.
 

F

FileDialogs - Class in org.micromanager.internal.utils
 
FileDialogs() - Constructor for class org.micromanager.internal.utils.FileDialogs
 
FileDialogs.FileType - Class in org.micromanager.internal.utils
 
FileMenu - Class in org.micromanager.internal.menus
Handles setting up the File menu and its actions.
FileMenu(Studio, JMenuBar) - Constructor for class org.micromanager.internal.menus.FileMenu
 
fileName(String) - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
fileName(String) - Method in interface org.micromanager.data.Metadata.Builder
 
FILENAME - Static variable in interface org.micromanager.display.DisplaySettings
Deprecated.
FileType(String, String, String, boolean, String...) - Constructor for class org.micromanager.internal.utils.FileDialogs.FileType
 
fillInMissingTiffDatas(int, int) - Method in class org.micromanager.data.internal.multipagetiff.OMEMetadata
 
findConfigPreset(String) - Method in class org.micromanager.internal.hcwizard.ConfigGroup
 
findMaxPixel(ImagePlus) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
findMaxPixel(ImageProcessor) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
findPlugins(String) - Static method in class org.micromanager.internal.pluginmanagement.PluginFinder
Find all jars under the given root, check them for the META-INF file that indicates that they're annotated with the @Plugin annotation, and return a list of the corresponding annotated classes.
findPluginsWithLoader(ClassLoader) - Static method in class org.micromanager.internal.pluginmanagement.PluginFinder
 
findProperty(String) - Method in class org.micromanager.internal.hcwizard.Device
 
findSetupProperty(String) - Method in class org.micromanager.internal.hcwizard.Device
 
findTableColumn(JTable, int) - Method in class org.micromanager.internal.dialogs.AcqControlDlg
Returns the TableColumn associated with the specified column index in the model.
finish() - Method in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
Called when there is no more data to be written.
finishCapturingLog() - Method in class org.micromanager.internal.diagnostics.ProblemReport
Stop CoreLog capture and record the captured log as part of the report.
finished() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
Call this function when no more images are expected Finishes writing the metadata file and closes it.
FinishPage - Class in org.micromanager.internal.hcwizard
The last wizard page.
FinishPage() - Constructor for class org.micromanager.internal.hcwizard.FinishPage
Create the panel
fireColorMap() - Static method in class org.micromanager.internal.utils.ColorMaps
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.dialogs.CalibrationEditor.PropertyCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.dialogs.ChannelCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.utils.AutofocusPropertyEditor.PropertyCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.utils.PropertyNameCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.utils.PropertyUsageCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.utils.PropertyValueCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.utils.StateGroupCellRenderer
 
firePropertyChange(String, boolean, boolean) - Method in class org.micromanager.internal.utils.StatePresetCellRenderer
 
fireTableDataChanged() - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
fitToWindow() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMImageCanvas
 
fitWindowInScreen(Window) - Static method in class org.micromanager.internal.utils.WindowPositioning
Move and resize a window so that it is on screen and (to the extent possible) fits in the screen.
fixMissingInfo(DisplaySettings, SummaryMetadata) - Static method in class org.micromanager.display.internal.RememberedDisplaySettings
Some MM versions have stored DisplaySettings without storing ChannelNames This causes the channel names not to be shown in the Intensity Inspector Panels.
FMT0 - Static variable in class org.micromanager.internal.utils.TextUtils
 
FMT1 - Static variable in class org.micromanager.internal.utils.TextUtils
 
FMT2 - Static variable in class org.micromanager.internal.utils.TextUtils
 
FMT3 - Static variable in class org.micromanager.internal.utils.TextUtils
 
focusGained(FocusEvent) - Method in class org.micromanager.internal.positionlist.CellEditor
 
focusLost(FocusEvent) - Method in class org.micromanager.internal.positionlist.CellEditor
 
focusReceived(ImageWindow) - Method in interface org.micromanager.internal.utils.ImageFocusListener
 
forceDataPosition(P) - Method in class org.micromanager.display.internal.animate.AnimationController
 
format(JComponent) - Method in class org.micromanager.internal.ConfigPadButtonPanel
 
format(ProblemReport) - Method in class org.micromanager.internal.diagnostics.ProblemReportFormatter
Generate a formatted report
formatToPropertyMap() - Method in class org.micromanager.data.internal.DefaultImage
 
FpsSpinnerNumberModel - Class in org.micromanager.display.internal.displaywindow
 
FpsSpinnerNumberModel(double, double, double) - Constructor for class org.micromanager.display.internal.displaywindow.FpsSpinnerNumberModel
 
frame() - Method in class org.micromanager.internal.MMUIManager
 
freeMemory() - Static method in class org.micromanager.internal.utils.MemoryUtils
 
freeze() - Method in interface org.micromanager.data.Datastore
Freeze this Datastore so it cannot be further modified.
freeze() - Method in class org.micromanager.data.internal.DefaultDatastore
 
freeze() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
freeze() - Method in class org.micromanager.data.internal.StorageRAM
 
freeze() - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
freeze() - Method in interface org.micromanager.data.Storage
Freeze the Storage, preventing any changes to its contents.
fromAxesAndImages(int, int, String[], List<Image>) - Static method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
fromGson(JsonElement) - Static method in class org.micromanager.internal.propertymap.MM1JSONSerializer
 
fromGson(JsonElement) - Method in class org.micromanager.internal.propertymap.NonPropertyMapJSONFormats
 
fromGson(JsonElement) - Static method in class org.micromanager.internal.propertymap.PropertyMapJSONSerializer
Deserialize from a Gson JsonElement.
fromImage(int, int, Image) - Static method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
fromInt(int) - Static method in enum org.micromanager.display.DisplaySettings.ColorMode
Deprecated.
fromJSON(String) - Method in class org.micromanager.internal.DefaultPropertyManager
Creates a property map from its JSON-serialized form.
fromJSON(String) - Static method in class org.micromanager.internal.propertymap.MM1JSONSerializer
Read an MM1 JSON string into a property map.
fromJSON(String) - Method in class org.micromanager.internal.propertymap.NonPropertyMapJSONFormats
 
fromJSON(String) - Static method in class org.micromanager.internal.propertymap.PropertyMapJSONSerializer
 
fromJSON(String) - Method in interface org.micromanager.PropertyManager
Creates a property map from its JSON-serialized form.
fromJSON(String) - Static method in class org.micromanager.PropertyMaps
Create a property map from its JSON-serialized form.
fromJSON(JSONObject, Studio, QuickAccessFrame) - Static method in class org.micromanager.quickaccess.internal.ControlCell
 
fromJSONStream(String) - Static method in class org.micromanager.acquisition.ChannelSpec
De-serialize from JSON encoded string.
fromJSONStream(String) - Static method in class org.micromanager.acquisition.SequenceSettings
 
fromNormalizedString(String) - Static method in class org.micromanager.data.internal.DefaultCoords
Generate a Coords from a string using the normalized string format.
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.data.Coordinates
Constructs a Coords instance from a PropertyMap.
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.data.internal.DefaultCoords
 
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.data.internal.DefaultMetadata
 
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
fromPropertyMap(PropertyMap, String, String) - Static method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
Restores ChannelDisplaySettings from a PropertyMap, but uses the input channelGroup and channelName rather than the ones in the PropertyMap Needed to gracefully update propertymaps that did not yet store the channelGroup
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
Restores ChannelDisplaySettings from a PropertyMap
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.display.internal.DefaultComponentDisplaySettings
 
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.display.internal.DefaultDisplaySettings
Restore DisplaySettings from a PropertyMap.
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.MultiStagePosition
Generates a multistagePosition from the given PropertyMap.
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.StagePosition
Returns the given PrropertyMap as a StagePosition.
fromString(String) - Static method in enum org.micromanager.ApplicationSkin.SkinMode
Returns skinmode associated with the given string (if any).
fromString(String, Studio) - Static method in class org.micromanager.internal.pipelineinterface.ConfiguratorWrapper
Return a deserialized ConfiguratorWrapper based on the provided string.
fullFocus() - Method in interface org.micromanager.AutofocusPlugin
Runs a full, one-shot autofocus protocol.
fullFocus() - Method in class org.micromanager.internal.utils.CoreAutofocus
 

G

GammaSliderCalculator - Class in org.micromanager.internal.utils
 
GammaSliderCalculator(int, int) - Constructor for class org.micromanager.internal.utils.GammaSliderCalculator
 
gammaToSlider(double) - Method in class org.micromanager.internal.utils.GammaSliderCalculator
 
GearButton - Class in org.micromanager.display.internal.gearmenu
This class provides access to various rarely-used functions (like save or duplicate) via a dropdown menu.
GearButton(DisplayWindow, Studio) - Constructor for class org.micromanager.display.internal.gearmenu.GearButton
 
generateAffineTransformFromPointPairs(Map<Point2D.Double, Point2D.Double>) - Static method in class org.micromanager.internal.utils.MathFunctions
 
generateAffineTransformFromPointPairs(Map<Point2D.Double, Point2D.Double>, double, double) - Static method in class org.micromanager.internal.utils.MathFunctions
 
generateDeviceListFile(StringBuffer, CMMCore) - Static method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
generateFileName(ProblemReport) - Method in class org.micromanager.internal.diagnostics.ProblemReportFormatter
Return a filename for use upon report upload.
generateLabel(int, int, int, int) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
generateLabel() - Method in class org.micromanager.PositionList
Helper method to generate unique label when inserting a new position.
generateLabel(String) - Method in class org.micromanager.PositionList
Generates a label for a new Position.
generateMetadata(Image, boolean) - Method in interface org.micromanager.acquisition.AcquisitionManager
Generate a new Metadata that contains pre-populated fields based on the current state of the program and the provided Image.
generateMetadata(Image, boolean) - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
generateSummaryMetadata() - Method in interface org.micromanager.acquisition.AcquisitionManager
Generate a new SummaryMetadata that contains pre-populated fields based on the current state of the program.
generateSummaryMetadata() - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
generateUUID() - Method in class org.micromanager.data.internal.DefaultMetadata.Builder
 
generateUUID() - Method in interface org.micromanager.data.Metadata.Builder
 
Geometry - Class in org.micromanager.internal.utils
 
get(int) - Method in class org.micromanager.internal.utils.CalibrationList
Returns calibration based on index
get(Object) - Method in class org.micromanager.internal.utils.ChainedMapView
 
get(int) - Method in class org.micromanager.MultiStagePosition
Return stage position based on index.
get(String) - Method in class org.micromanager.MultiStagePosition
Returns position for a specific stage.
get16BitData(Object) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
get1DAxes() - Method in class org.micromanager.internal.positionlist.PositionListDlg
Returns the first selected Drive or null when none is selected
get1DPosition() - Method in class org.micromanager.StagePosition
 
get2DAxis() - Method in class org.micromanager.internal.positionlist.PositionListDlg
Returns the first selected XYDrive or null when none is selected
get2DPositionX() - Method in class org.micromanager.StagePosition
 
get2DPositionY() - Method in class org.micromanager.StagePosition
 
get32BitData(Object) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
get8BitData(Object) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getAcquisitionDatastore() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Return Datastore for current or most recent acquisition, or null if no acquisition has been run yet.
getAcquisitionDatastore() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
getAcquisitionDialogPlugins() - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
getAcquisitionEngine() - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
getAcquisitionEngine() - Method in class org.micromanager.internal.MMStudio
 
getAcquisitionEngine2010() - Method in class org.micromanager.internal.MMStudio
Returns an instance of the AcquisitionEngine2010 object.
getAcquisitionManager() - Method in class org.micromanager.internal.MMStudio
 
getAcquisitionManager() - Method in interface org.micromanager.Studio
Provide access to the AcquisitionManager, for running data acquisition using the Micro-Manager acquisition engine.
getAcquisitionSettings() - Method in interface org.micromanager.acquisition.AcquisitionManager
Return current acquisition settings as shown in the Multi-D Acquisition dialog.
getAcquisitionSettings() - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionManager
 
getAcquisitionWindow() - Method in class org.micromanager.internal.MMUIManager
Returns the singleton instance of the Multi-Dimensional Acquisition Dialog.
getActiveCalibration() - Method in class org.micromanager.internal.utils.CalibrationList
 
getActiveDataViewer() - Method in interface org.micromanager.display.DisplayManager
Returns the currently active data viewer.
getActiveDataViewer() - Method in class org.micromanager.display.internal.DataViewerCollection
 
getActiveDataViewer() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
getAdapterName() - Method in class org.micromanager.internal.hcwizard.Device
 
getAfDevices() - Method in class org.micromanager.internal.utils.DefaultAutofocusManager
Returns a list of available af device names NOTE: we operate based on the "device name" rather than the plugin class name, because the latter is the same for all autofocus device adapters (it's always CoreAutofocus).
getAffineTransform() - Method in class org.micromanager.internal.dialogs.AffineEditorPanel
 
getAffineTransform() - Method in class org.micromanager.internal.dialogs.PixelConfigEditor
 
getAffineTransform() - Method in class org.micromanager.internal.dialogs.PixelPresetEditor
 
getAffineTransform() - Method in interface org.micromanager.internal.dialogs.PixelSizeProvider
Returns the affine transform as currently known by the PixelSizeProvider
getAffineTransform() - Method in class org.micromanager.internal.hcwizard.ConfigPreset
 
getAffineTransform(String, AffineTransform) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAffineTransform(String, AffineTransform) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getAffineTransform(String, AffineTransform) - Method in interface org.micromanager.PropertyMap
 
getAffineTransform(String, AffineTransform) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getAffineTransformList(String, AffineTransform...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAffineTransformList(String, Iterable<AffineTransform>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAffineTransformList(String, AffineTransform...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getAffineTransformList(String, Iterable<AffineTransform>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getAffineTransformList(String, AffineTransform...) - Method in interface org.micromanager.PropertyMap
 
getAffineTransformList(String, Iterable<AffineTransform>) - Method in interface org.micromanager.PropertyMap
 
getAffineTransformList(String, AffineTransform...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getAffineTransformList(String, Iterable<AffineTransform>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getAlbum() - Method in class org.micromanager.internal.MMStudio
 
getAlbum() - Method in interface org.micromanager.Studio
Provides access to and control of the contents of the Album, the implicit, temporary image storage datastore.
getAlert() - Method in class org.micromanager.alerts.internal.AlertClearedEvent
 
getAlert() - Method in class org.micromanager.alerts.internal.AlertUpdatedEvent
 
getAlertManager() - Method in class org.micromanager.internal.MMStudio
 
getAlertManager() - Method in interface org.micromanager.Studio
Provide access to the AlertManager, for creating low-profile, non- interrupting alerts in the user interface.
getAllAsText(boolean) - Static method in class org.micromanager.internal.diagnostics.SystemInfo
 
getAllAutofocusMethods() - Method in interface org.micromanager.AutofocusManager
Return a list of the current valid autofocus names, suitable for use in setAutofocusMethodByName().
getAllAutofocusMethods() - Method in class org.micromanager.internal.utils.DefaultAutofocusManager
 
getAllChannelColors() - Method in interface org.micromanager.display.DisplaySettings
 
getAllChannelColors() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getAllChannelSettings() - Method in interface org.micromanager.display.DisplaySettings
 
getAllChannelSettings() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getAllChannelVisibilities() - Method in interface org.micromanager.display.DisplaySettings
 
getAllChannelVisibilities() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getAllComponentSettings() - Method in interface org.micromanager.display.ChannelDisplaySettings
 
getAllComponentSettings() - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
getAllCoords() - Method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
getAllCoordsSorted() - Method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
getAllDataViewers() - Method in interface org.micromanager.display.DisplayManager
Return all DataViewers that Micro-Manager knows about.
getAllDataViewers() - Method in class org.micromanager.display.internal.DataViewerCollection
 
getAllDataViewers() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
getAllDisplayedCoords() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getAllImageWindows() - Method in interface org.micromanager.display.DisplayManager
Return all active DisplayWindows.
getAllImageWindows() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
getAllInspectors() - Method in class org.micromanager.display.inspector.internal.InspectorCollection
 
getAllKeys() - Method in enum org.micromanager.data.internal.PropertyKey
 
getAllSetupLabels() - Method in class org.micromanager.internal.hcwizard.Device
 
getAllText() - Method in class org.micromanager.alerts.internal.CategorizedAlert
 
getAnchor() - Method in class org.micromanager.display.internal.link.internal.AbstractAnchorEvent
 
getAnchor() - Method in interface org.micromanager.display.internal.link.internal.LinkAnchorEvent
 
getAnchor() - Method in interface org.micromanager.display.internal.link.internal.LinkEndpoint
 
getAnimatedAxes() - Method in interface org.micromanager.display.internal.animate.DataCoordsAnimationState.CoordsProvider
 
getAnimatedAxes() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
getAnimationPosition() - Method in interface org.micromanager.display.internal.animate.AnimationStateDelegate
Get the current data position.
getAnimationPosition() - Method in class org.micromanager.display.internal.animate.DataCoordsAnimationState
 
getAnimationRateFPS() - Method in class org.micromanager.display.internal.animate.AnimationController
 
getAnnotation(String) - Method in interface org.micromanager.data.Datastore
Get an annotation, creating it if it doesn't exist.
getAnnotation(String) - Method in class org.micromanager.data.internal.DefaultDatastore
 
getAnyImage() - Method in interface org.micromanager.data.DataProvider
Retrieve any image from this DataProvider.
getAnyImage() - Method in class org.micromanager.data.internal.DefaultDatastore
 
getAnyImage() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getAnyImage() - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getAnyImage() - Method in class org.micromanager.data.internal.StorageRAM
 
getAnyImage() - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getAnyImage() - Method in interface org.micromanager.data.Storage
Return any Image, or null if there are no images.
getApplication() - Method in class org.micromanager.internal.MMStudio
 
getApplication() - Method in interface org.micromanager.Studio
Provides access to the application API for controlling and updating the GUI.
getApplicationDataPath() - Static method in class org.micromanager.internal.utils.JavaUtils
 
getApplicationPipelineConfigurators(boolean) - Method in interface org.micromanager.data.DataManager
Return a list of the ProcessorConfigurators currently being used by the application pipeline interface.
getApplicationPipelineConfigurators(boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
getApplicationSkin() - Method in interface org.micromanager.Application
Provides access to the application skin API for determining colors for various GUI components.
getApplicationSkin() - Method in class org.micromanager.internal.DefaultApplication
 
getAsNumber(String, Number) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAsNumber(String, Number) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getAsNumber(String, Number) - Method in interface org.micromanager.PropertyMap
Retrieve a numerical value, without checking its specific type.
getAsNumber(String, Number) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getAsNumberList(String, Number...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAsNumberList(String, Iterable<Number>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAsNumberList(String, Number...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getAsNumberList(String, Iterable<Number>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getAsNumberList(String, Number...) - Method in interface org.micromanager.PropertyMap
 
getAsNumberList(String, Iterable<Number>) - Method in interface org.micromanager.PropertyMap
 
getAsNumberList(String, Number...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getAsNumberList(String, Iterable<Number>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getAsOpaqueValue(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getAsOpaqueValue(String) - Method in interface org.micromanager.PropertyMap
 
getAsWindow() - Method in interface org.micromanager.display.DisplayWindow
Deprecated.
getAsWindow() - Method in class org.micromanager.display.internal.displaywindow.DisplayWindowAPIAdapter
Deprecated.
getAutofocusManager() - Method in class org.micromanager.internal.MMStudio
 
getAutofocusManager() - Method in interface org.micromanager.Studio
Provide access to the AutofocusManager, for performing autofocus operations.
getAutofocusMethod() - Method in interface org.micromanager.AutofocusManager
Return the current AutofocusPlugin being used to run autofocus.
getAutofocusMethod() - Method in class org.micromanager.internal.utils.DefaultAutofocusManager
 
getAutofocusPlugins() - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
getAutofocusPlugins() - Method in interface org.micromanager.PluginManager
Return a HashMap that maps plugin class names to AutofocusPlugin instances.
getAutosavingProfile(UUID, ExceptionListener) - Method in class org.micromanager.profile.internal.UserProfileAdmin
 
getAutoscaleIgnoredPercentile() - Method in interface org.micromanager.display.DisplaySettings
When autoscaling, the minimum value will have this fraction of pixels with lower intensities, and the maximum value will have this fraction of pixels with higher intensities.
getAutoscaleIgnoredPercentile() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getAutoscaleIgnoredQuantile() - Method in interface org.micromanager.display.DisplaySettings
When autoscaling, the minimum value will have this fraction of pixels with lower intensities, and the maximum value will have this fraction of pixels with higher intensities.
getAutoscaleIgnoredQuantile() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getAutoscaleMaxForQuantile(double) - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getAutoscaleMinForQuantile(double) - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getAutoShutter() - Method in interface org.micromanager.events.AutoShutterEvent
Returns true when autoshutter is enabled, false otherwise.
getAutoShutter() - Method in class org.micromanager.events.internal.DefaultAutoShutterEvent
 
getAutoShutter() - Method in class org.micromanager.internal.DefaultShutterManager
 
getAutoShutter() - Method in interface org.micromanager.ShutterManager
Return true if autoshutter is enabled.
getAvailableChannels() - Method in class org.micromanager.internal.dialogs.ChannelTableModel
 
getAvailableDevicesCompact() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
Creates a list of devices that are either hubs or don't belong to hubs
getAvailableGroups() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
getAvailableGroups() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
getAvailableHubs() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getAvailableSerialPorts() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getAvailableUnusedMemory() - Static method in class org.micromanager.internal.utils.JavaUtils
Find out how much unused memory (in bytes) is still available for the JVM to use.
getAverage() - Method in class org.micromanager.internal.utils.performance.AbstractExponentialSmoothing
 
getAxes() - Method in interface org.micromanager.data.Coords
Return all axes that this Coords has an index for.
getAxes() - Method in interface org.micromanager.data.DataProvider
Retrieve the axis currently in use by this DataProvider.
getAxes() - Method in class org.micromanager.data.internal.DefaultCoords
 
getAxes() - Method in class org.micromanager.data.internal.DefaultDatastore
 
getAxes() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
TODO: Check that summaryMetadata is a reliable source for this information.
getAxes() - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getAxes() - Method in class org.micromanager.data.internal.StorageRAM
 
getAxes() - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getAxes() - Method in interface org.micromanager.data.Storage
Return a List of all axis names for Images we know about.
getAxis() - Method in class org.micromanager.display.internal.gearmenu.ExportMovieDlg.AxisPanel
 
getAxisLength(String) - Method in interface org.micromanager.data.DataProvider
Deprecated.
getAxisLength(String) - Method in class org.micromanager.data.internal.DefaultDatastore
Deprecated.
getAxisLength(String) - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getAxisLength(String) - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getAxisOrder() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
Deprecated.
use getOrderedAxes instead
getAxisOrder() - Method in interface org.micromanager.data.SummaryMetadata
Deprecated.
- Use getOrdereddAxes() instead
getBackgroundColor() - Method in interface org.micromanager.ApplicationSkin
Return the current background color for normal GUI elements.
getBackgroundColor() - Method in class org.micromanager.internal.utils.DaytimeNighttime
Return the current background color.
getBadLibraries() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getBinCount() - Method in class org.micromanager.display.internal.imagestats.PowerOf2BinMapper
 
getBinMode() - Method in class org.micromanager.internal.MainFrame
Return the current selection from the comboBinning_ menu, or null.
getBinning() - Method in class org.micromanager.data.internal.DefaultMetadata
 
getBinning() - Method in interface org.micromanager.data.Metadata
The binning mode of the camera for this image.
getBinning(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getBinSize() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the number of distinct intensities that fit within each bin of the histogram.
getBitDepth() - Method in class org.micromanager.data.internal.DefaultMetadata
 
getBitDepth() - Method in interface org.micromanager.data.Metadata
The number of bits used to represent each pixel (e.g.
getBitDepth() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the bit depth of the dataset.
getBitDepth() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
getBitDepth(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getBoolean(String, boolean) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getBoolean(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getBoolean(String, Boolean) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getBoolean(Class<?>, String, Boolean) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getBoolean(String, boolean) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getBoolean(String, boolean) - Method in interface org.micromanager.PropertyMap
 
getBoolean(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getBoolean(String, Boolean) - Method in interface org.micromanager.PropertyMap
Deprecated.
getBoolean(String, boolean) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getBoolean(Class<?>, String, Boolean) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getBoolean(key, fallback) instead
getBooleanArray(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getBooleanArray(String, Boolean[]) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getBooleanArray(Class<?>, String, Boolean[]) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getBooleanArray(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getBooleanArray(String, Boolean[]) - Method in interface org.micromanager.PropertyMap
Deprecated.
getBooleanArray(Class<?>, String, Boolean[]) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getBooleanList(key, fallback) instead
getBooleanList(String, boolean...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getBooleanList(String, Iterable<Boolean>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getBooleanList(String, boolean...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getBooleanList(String, Iterable<Boolean>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getBooleanList(String, boolean...) - Method in interface org.micromanager.PropertyMap
 
getBooleanList(String, Iterable<Boolean>) - Method in interface org.micromanager.PropertyMap
 
getBooleanList(String, boolean...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getBooleanList(String, Iterable<Boolean>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getBorder() - Method in class org.micromanager.internal.dialogs.AcqControlDlg.ComponentTitledPanel
 
getBorderInsets(Component) - Method in class org.micromanager.internal.dialogs.ComponentTitledBorder
 
getBounds() - Method in class org.micromanager.display.internal.imagestats.BoundsRectAndMask
 
getBounds() - Method in class org.micromanager.internal.graph.GraphData
 
getBox() - Method in class org.micromanager.internal.graph.GraphPanel
 
getBuildTime() - Static method in class org.micromanager.internal.utils.JavaUtils
 
getButtonIcon() - Method in class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
getButtonIcon() - Method in class org.micromanager.quickaccess.internal.controls.RefreshButton
 
getButtonIcon() - Method in class org.micromanager.quickaccess.SimpleButtonPlugin
Returns an icon to show in the button.
getByte(String, byte) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getByte(String, byte) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getByte(String, byte) - Method in interface org.micromanager.PropertyMap
 
getByte(String, byte) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getByteArray() - Method in interface org.micromanager.data.Image
Regardless of the the value of #getBytesPerPixel return an array of bytes containing raw data for the image.
getByteArray(Buffer) - Static method in class org.micromanager.data.internal.BufferTools
Convert a buffer to an array of `byte` regardless of the underlying data type of the buffer Useful for low-level data manipulation and for efficiently streaming data over a socket.
getByteArray() - Method in class org.micromanager.data.internal.DefaultImage
 
getByteList(String, byte...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getByteList(String, Iterable<Byte>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getByteList(String, byte...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getByteList(String, Iterable<Byte>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getByteList(String, byte...) - Method in interface org.micromanager.PropertyMap
 
getByteList(String, Iterable<Byte>) - Method in interface org.micromanager.PropertyMap
 
getByteList(String, byte...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getByteList(String, Iterable<Byte>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getBytesPerComponent() - Method in interface org.micromanager.data.Image
Return the number of bytes used to represent each pixel component of this image.
getBytesPerComponent() - Method in class org.micromanager.data.internal.DefaultImage
 
getBytesPerComponent() - Method in enum org.micromanager.data.internal.PixelType
 
getBytesPerPixel() - Method in interface org.micromanager.data.Image
Return the number of bytes used to represent each pixel of this image.
getBytesPerPixel() - Method in class org.micromanager.data.internal.DefaultImage
 
getBytesPerPixel() - Method in enum org.micromanager.data.internal.PixelType
 
getBytesPerPixel(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getC() - Method in interface org.micromanager.data.Coords
Shorthand for getChannel.
getC() - Method in class org.micromanager.data.internal.DefaultCoords
 
getCalibratedPixelSize() - Method in class org.micromanager.internal.pixelcalibrator.PixelCalibratorDialog
 
getCalibrationListDlg() - Method in class org.micromanager.internal.MMUIManager
Provides access to the CalibrationListDlg.
getCalibrationsFromCore() - Method in class org.micromanager.internal.utils.CalibrationList
 
getCaller() - Static method in class org.micromanager.internal.utils.ReportingUtils
Return the caller of the method that called getCaller().
getCamera() - Method in class org.micromanager.data.internal.DefaultMetadata
 
getCamera() - Method in interface org.micromanager.data.Metadata
The name of the camera for this image.
getCameraLabel() - Method in class org.micromanager.internal.MMCache
 
getCameraName() - Method in interface org.micromanager.events.ExposureChangedEvent
Camera whose exposure time changed.
getCameraName() - Method in class org.micromanager.events.internal.DefaultExposureChangedEvent
Camera whose exposure time changed.
getCameraTransform(String) - Method in interface org.micromanager.CompatibilityInterface
Deprecated.
- Use core.getPixelSizeAffineByID(config) instead
getCameraTransform(String) - Method in class org.micromanager.internal.DefaultCompatibilityInterface
Deprecated.
getCanCustomizeIcon() - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
getCanCustomizeIcon() - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
getCanCustomizeIcon() - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
getCanCustomizeIcon() - Method in class org.micromanager.quickaccess.WidgetPlugin
Returns true if the widget can accept custom icons (i.e.
getCause() - Method in exception org.micromanager.internal.hcwizard.MMConfigFileException
 
getCause() - Method in exception org.micromanager.internal.utils.MMAutofocusException
 
getCause() - Method in exception org.micromanager.internal.utils.MMScriptException
 
getCause() - Method in exception org.micromanager.internal.utils.MMSerializationException
 
getCell() - Method in class org.micromanager.quickaccess.internal.QuickAccessFrame
Map the current mouse position (relative to the window) into a cell location (in the controlsPanel_).
getCellEditorValue() - Method in class org.micromanager.internal.dialogs.CalibrationEditor.PropertyCellEditor
 
getCellEditorValue() - Method in class org.micromanager.internal.dialogs.ChannelCellEditor
This method is called when editing is completed.
getCellEditorValue() - Method in class org.micromanager.internal.positionlist.CellEditor
 
getCellEditorValue() - Method in class org.micromanager.internal.utils.AutofocusPropertyEditor.PropertyCellEditor
 
getCellEditorValue() - Method in class org.micromanager.internal.utils.ColorEditor
 
getCellEditorValue() - Method in class org.micromanager.internal.utils.HotKeysDialog.HotKeyCol1Editor
 
getCellEditorValue() - Method in class org.micromanager.internal.utils.PropertyUsageCellEditor
 
getCellEditorValue() - Method in class org.micromanager.internal.utils.PropertyValueCellEditor
 
getCellEditorValue() - Method in class org.micromanager.internal.utils.StatePresetCellEditor
 
getCenterLocation() - Method in class org.micromanager.display.internal.event.DisplayMouseEvent
Provides center location in image coordinates Calculates the center of the Rectangle returned in getLocation
getCenterValue(long, T) - Method in class org.micromanager.display.internal.imagestats.PowerOf2BinMapper
 
getChannel() - Method in interface org.micromanager.data.Coords
Get the channel index.
getChannel() - Method in class org.micromanager.data.internal.DefaultCoords
 
getChannel() - Method in interface org.micromanager.events.ChannelExposureEvent
Return the channel whose exposure time has changed.
getChannel() - Method in class org.micromanager.events.internal.ChannelColorEvent
 
getChannel() - Method in class org.micromanager.events.internal.DefaultChannelExposureEvent
Return the channel whose exposure time has changed.
getChannelColor(int) - Method in interface org.micromanager.display.DisplaySettings
 
getChannelColor(int) - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getChannelColor(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getChannelColorMode() - Method in interface org.micromanager.display.DisplaySettings
Deprecated.
- use getColorMode() instead
getChannelColorMode() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
Deprecated.
getChannelConfigs() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Find out which channels are currently available for the selected channel group.
getChannelConfigs() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
Find out which channels are currently available for the selected channel group.
getChannelContrastSettings() - Method in interface org.micromanager.display.DisplaySettings
Deprecated.
getChannelContrastSettings() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
Deprecated.
getChannelExposureTime(String, String, double) - Method in interface org.micromanager.Application
Retrieve the exposure time that has been set for the specified channel.
getChannelExposureTime(String, String, double) - Method in class org.micromanager.internal.DefaultApplication
Returns exposure time for the desired preset in the given channelgroup.
getChannelExposureTime(String, String, double) - Method in class org.micromanager.internal.dialogs.ChannelTableModel
Returns the exposure time of the given preset
getChannelGroup() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Returns the configuration preset group currently selected in the Multi-Dimensional Acquisition Window
getChannelGroup() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
getChannelGroup() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getChannelGroup() - Method in interface org.micromanager.data.SummaryMetadata
The config group that was used to switch between channels.
getChannelGroup() - Method in interface org.micromanager.events.ChannelExposureEvent
Return the name of the channel group in which the modified channel is located.
getChannelGroup() - Method in class org.micromanager.events.internal.ChannelColorEvent
 
getChannelGroup() - Method in class org.micromanager.events.internal.DefaultChannelExposureEvent
Return the name of the channel group in which the modified channel is located.
getChannelGroup(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getChannelIndex(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getChannelName(int) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
Returns name assocaited with given channel index.
getChannelName(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getChannelNameList() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getChannelNameList() - Method in interface org.micromanager.data.SummaryMetadata
 
getChannelNames() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
Deprecated.
getChannelNames() - Method in interface org.micromanager.data.SummaryMetadata
Deprecated.
- Use getChannelNameList() instead
getChannels() - Method in class org.micromanager.internal.dialogs.ChannelTableModel
 
getChannelSettings(int) - Method in interface org.micromanager.display.DisplaySettings.Builder
Returns the ChannelDisplaySettings for the given channel number.
getChannelSettings(int) - Method in interface org.micromanager.display.DisplaySettings
 
getChannelSettings(int) - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getChildDevices(Device) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getCircularBufferSize() - Method in class org.micromanager.internal.MMStudio.MMSettings
Returns current size of the circular buffer.
getCMMCore() - Method in class org.micromanager.internal.MMStudio
Returns instance of the core uManager object.
getCMMCore() - Method in interface org.micromanager.Studio
Provides access to the Core and its functionality.
getCoalescenceClass() - Method in interface org.micromanager.internal.utils.CoalescentEDTRunnablePool.CoalescentRunnable
Return a tag class used to group instances that can be coalesced.
getColor() - Method in interface org.micromanager.display.ChannelDisplaySettings
Color used to represent this channel, i.e., brightest color of the LUT used to display this channel
getColor() - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
getColor() - Method in class org.micromanager.events.internal.ChannelColorEvent
 
getColor(String, Color) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getColor(String, Color) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getColor(String, Color) - Method in interface org.micromanager.PropertyMap
 
getColor(String, Color) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getColorblindFriendlyPalette() - Static method in class org.micromanager.internal.utils.ColorPalettes
 
getColorList(String, Color...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getColorList(String, Iterable<Color>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getColorList(String, Color...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getColorList(String, Iterable<Color>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getColorList(String, Color...) - Method in interface org.micromanager.PropertyMap
 
getColorList(String, Iterable<Color>) - Method in interface org.micromanager.PropertyMap
 
getColorList(String, Color...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getColorList(String, Iterable<Color>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getColorMode() - Method in interface org.micromanager.display.DisplaySettings
Color mode or lookup table for displaying the image.
getColorMode() - Method in class org.micromanager.display.internal.DefaultDisplaySettings
 
getColorModel() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
getColorPlanesFromRGB32(byte[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getColorPlanesFromRGB64(short[]) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getColumnClass(int) - Method in class org.micromanager.internal.dialogs.ChannelTableModel
 
getColumnClass(int) - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
getColumnCount() - Method in class org.micromanager.internal.ConfigGroupPad.StateTableData
 
getColumnCount() - Method in class org.micromanager.internal.dialogs.ChannelTableModel
 
getColumnCount() - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
getColumnCount() - Method in class org.micromanager.internal.utils.HotKeysDialog.ShortCutTableModel
 
getColumnCount() - Method in class org.micromanager.internal.utils.PropertyTableData
 
getColumnName(int) - Method in class org.micromanager.internal.ConfigGroupPad.StateTableData
 
getColumnName(int) - Method in class org.micromanager.internal.dialogs.ChannelTableModel
 
getColumnName(int) - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
getColumnName(int) - Method in class org.micromanager.internal.utils.HotKeysDialog.ShortCutTableModel
 
getColumnName(int) - Method in class org.micromanager.internal.utils.PropertyTableData
 
getComment() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
getComment() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
getComments(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getCompatibilityInterface() - Method in class org.micromanager.internal.MMStudio
 
getCompatibilityInterface() - Method in interface org.micromanager.Studio
Provides access to the compatibility layer that exposes some old 1.4 API methods.
getComponentIntensitiesAt(int, int) - Method in interface org.micromanager.data.Image
Returns the pixel intensity of all components.
getComponentIntensitiesAt(int, int) - Method in class org.micromanager.data.internal.DefaultImage
 
getComponentIntensityAt(int, int, int) - Method in interface org.micromanager.data.Image
Get the intensity of a component of the pixel at the specified position.
getComponentIntensityAt(int, int, int) - Method in class org.micromanager.data.internal.DefaultImage
 
getComponentSampleOffset(int) - Method in enum org.micromanager.data.internal.PixelType
Get the position of a component sample within a pixel .
getComponentScalingMax(int) - Method in class org.micromanager.display.inspector.internal.panels.intensity.HistogramView
 
getComponentScalingMin(int) - Method in class org.micromanager.display.inspector.internal.panels.intensity.HistogramView
 
getComponentSettings(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
 
getComponentSettings(int) - Method in interface org.micromanager.display.ChannelDisplaySettings
 
getComponentSettings(int) - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
getComponentStats(int) - Method in class org.micromanager.display.internal.imagestats.ImageStats
 
getComponentValuesForCoords(Coords) - Method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
getComponentValuesStringForCoords(Coords) - Method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
getComputerName() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getComputerName() - Method in interface org.micromanager.data.SummaryMetadata
The name of the computer the data was collected on.
getConfig() - Method in class org.micromanager.quickaccess.internal.ControlCell
 
getConfig() - Method in class org.micromanager.quickaccess.internal.QuickAccessFrame
Create a JSONObject for storing our settings to the profile.
getConfigFilePaths() - Method in interface org.micromanager.IntroPlugin
Provide a list of paths to config files to include in the config file dropdown menu.
getConfigPad() - Method in class org.micromanager.internal.MainFrame
 
getConfigPresets() - Method in class org.micromanager.internal.hcwizard.ConfigGroup
 
getConfiguration() - Method in class org.micromanager.display.overlay.AbstractOverlay
Return the user-customizable settings for this overlay.
getConfiguration() - Method in class org.micromanager.display.overlay.internal.overlays.PatternOverlay
 
getConfiguration() - Method in class org.micromanager.display.overlay.internal.overlays.ScaleBarOverlay
 
getConfiguration() - Method in class org.micromanager.display.overlay.internal.overlays.TimestampOverlay
 
getConfiguration() - Method in interface org.micromanager.display.overlay.Overlay
Return the user-customizable settings for this overlay.
getConfiguration() - Method in class org.micromanager.internal.utils.Calibration
 
getConfigurationComponent() - Method in class org.micromanager.display.overlay.AbstractOverlay
Return the configuration UI component for this overlay.
getConfigurationComponent() - Method in class org.micromanager.display.overlay.internal.overlays.PatternOverlay
 
getConfigurationComponent() - Method in class org.micromanager.display.overlay.internal.overlays.ScaleBarOverlay
 
getConfigurationComponent() - Method in class org.micromanager.display.overlay.internal.overlays.TimestampOverlay
 
getConfigurationComponent() - Method in interface org.micromanager.display.overlay.Overlay
Return the configuration UI component for this overlay.
getConfigurator() - Method in class org.micromanager.internal.pipelineinterface.ConfiguratorWrapper
 
getConfiguratorEnabled(int) - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
 
getConfiguratorEnabledLive(int) - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
 
getContents() - Method in class org.micromanager.alerts.internal.DefaultAlert
 
getContents(File) - Static method in class org.micromanager.internal.script.ScriptPanel
 
getContrastGammas() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings
Deprecated.
getContrastGammas() - Method in class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
getContrastMaxes() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings
Deprecated.
getContrastMaxes() - Method in class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
getContrastMins() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings
Deprecated.
getContrastMins() - Method in class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
getContrastSettings(Integer, Integer, Double, Boolean) - Method in interface org.micromanager.display.DisplayManager
Deprecated.
getContrastSettings(Integer[], Integer[], Double[], Boolean) - Method in interface org.micromanager.display.DisplayManager
Deprecated. 
getContrastSettings(Integer, Integer, Double, Boolean) - Method in class org.micromanager.display.internal.DefaultDisplayManager
Deprecated.
getContrastSettings(Integer[], Integer[], Double[], Boolean) - Method in class org.micromanager.display.internal.DefaultDisplayManager
Deprecated.
getControlCell() - Method in class org.micromanager.quickaccess.internal.DraggableIcon
 
getCoords() - Method in interface org.micromanager.data.DataProviderHasNewImageEvent
Returns Coords for the image.
getCoords() - Method in interface org.micromanager.data.Image
Retrieve the Coords of this Image.
getCoords() - Method in class org.micromanager.data.internal.DefaultImage
 
getCoords() - Method in class org.micromanager.data.internal.DefaultNewImageEvent
 
getCoordsBuilder() - Method in interface org.micromanager.data.DataManager
Deprecated.
getCoordsBuilder() - Method in class org.micromanager.data.internal.DefaultDataManager
Deprecated.
getCopyright() - Method in class org.micromanager.acquisition.internal.DefaultMDAPlugin
 
getCopyright() - Method in class org.micromanager.display.internal.gearmenu.CopyToImageJItem
 
getCopyright() - Method in class org.micromanager.display.internal.gearmenu.ExportImagesItem
 
getCopyright() - Method in class org.micromanager.display.internal.gearmenu.LineProfileItem
 
getCopyright() - Method in class org.micromanager.internal.utils.CoreAutofocus
 
getCopyright() - Method in interface org.micromanager.MMPlugin
Provide a copyright string.
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.ExposureTime
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.LiveButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.MDAButtons
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.RefreshButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.ShutterControl
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.SnapButton
 
getCopyright() - Method in class org.micromanager.quickaccess.internal.controls.TextLabel
 
getCoreCamera(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getCoreLogLifetimeDays() - Method in class org.micromanager.internal.MMStudio.MMSettings
 
getCount() - Method in class org.micromanager.internal.utils.performance.AbstractExponentialSmoothing
 
getCurrentFocusScore() - Method in interface org.micromanager.AutofocusPlugin
Returns the current focus "score" (goodness of focus).
getCurrentFocusScore() - Method in class org.micromanager.internal.utils.CoreAutofocus
 
getCurrentHardwareConfiguration() - Method in class org.micromanager.profile.internal.gui.HardwareConfigurationManager
 
getCurrentImagesAndStats() - Method in interface org.micromanager.display.inspector.internal.panels.intensity.ImageStatsPublisher
 
getCurrentImagesAndStats() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
getCurrentShutter() - Method in class org.micromanager.internal.DefaultShutterManager
 
getCurrentShutter() - Method in interface org.micromanager.ShutterManager
Return the current shutter device.
getCurrentTime() - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getCurrentValue() - Method in interface org.micromanager.display.internal.link.internal.LinkEndpoint
 
getCurrentValue() - Method in interface org.micromanager.display.internal.link.LinkAnchor
Return the current local value of the linked attribute.
getCurrentWindow() - Method in interface org.micromanager.display.DisplayManager
Deprecated.
Use getActiveDataViewer() instead
getCurrentWindow() - Method in class org.micromanager.display.internal.DefaultDisplayManager
Deprecated.
getCurrentZPos() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
getCurrentZPos() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
getCustomIcon(PropertyMap, Icon) - Method in class org.micromanager.quickaccess.internal.DefaultQuickAccessManager
 
getCustomIcon(PropertyMap, Icon) - Method in interface org.micromanager.quickaccess.QuickAccessManager
Generate an Icon based on information contained in the provided PropertyMap.
getCustomIntervalsMs() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
Deprecated.
getCustomIntervalsMs() - Method in interface org.micromanager.data.SummaryMetadata
Deprecated.
- Use double[] getCustomIntervalsMsArray() instead
getCustomIntervalsMsArray() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getCustomIntervalsMsArray() - Method in interface org.micromanager.data.SummaryMetadata
 
getCustomIntervalsMsList() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getCustomIntervalsMsList() - Method in interface org.micromanager.data.SummaryMetadata
When using a variable amount of time between timepoints, this array has the list of wait times.
getDataManager() - Method in class org.micromanager.internal.MMStudio
 
getDataManager() - Method in interface org.micromanager.Studio
Provide access to the DataManager instance for accessing Micro-Manager data constructs.
getDataProvider() - Method in interface org.micromanager.data.DataProviderHasNewImageEvent
Provides the DataProvider this image was added to; potentially useful for code that listens to events from multiple DataProviders.
getDataProvider() - Method in class org.micromanager.data.internal.DefaultNewImageEvent
Provides the DataProvider this image was added to; potentially useful for code that listens to events from multiple DataProviders.
getDataProvider() - Method in interface org.micromanager.display.DataViewer
Retrieve the data provider backing this viewer.
getDataProvider() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
getDataSetSize() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
Provides size of the dataset in bytes.
getDatastore() - Method in interface org.micromanager.acquisition.AcquisitionStartedEvent
Return the Datastore into which images will be inserted during the acquisition.
getDatastore() - Method in class org.micromanager.acquisition.internal.DefaultAcquisitionStartedEvent
 
getDatastore() - Method in class org.micromanager.acquisition.internal.MMAcquisition
 
getDatastore() - Method in interface org.micromanager.Album
Return the Datastore that currently backs the Album.
getDatastore() - Method in interface org.micromanager.data.Annotation
Return the datastore to which this annotation is associated.
getDatastore() - Method in interface org.micromanager.data.DatastoreClosingEvent
Returns the Datastore that is closing.
getDatastore() - Method in interface org.micromanager.data.ImageDeletedEvent
Provides the Datastore this image was added to; potentially useful for code that listens to events from multiple Datastores.
getDatastore() - Method in interface org.micromanager.data.ImageOverwrittenEvent
Provides the Datastore this image was added to; potentially useful for code that listens to events from multiple Datastores.
getDatastore() - Method in class org.micromanager.data.internal.DefaultAnnotation
 
getDatastore() - Method in class org.micromanager.data.internal.DefaultDatastoreClosingEvent
 
getDatastore() - Method in class org.micromanager.data.internal.DefaultImageDeletedEvent
Provides the Datastore this image was added to; potentially useful for code that listens to events from multiple Datastores.
getDatastore() - Method in class org.micromanager.data.internal.DefaultImageOverwrittenEvent
Provides the Datastore this image was added to; potentially useful for code that listens to events from multiple Datastores.
getDatastore() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getDatastore() - Method in class org.micromanager.data.internal.pipeline.DefaultPipeline
 
getDatastore() - Method in interface org.micromanager.data.Pipeline
Get the output Datastore for this Pipeline.
getDatastore() - Method in class org.micromanager.display.AbstractDataViewer
Deprecated.
user code should call getDataProvider
getDatastore() - Method in interface org.micromanager.display.DataViewer
Deprecated.
getDatastore() - Method in class org.micromanager.internal.DefaultAlbum
 
getDataViewer() - Method in interface org.micromanager.display.DisplayDidShowImageEvent
Returns the Dataviewer displaying the image.
getDataViewer() - Method in interface org.micromanager.display.DisplayPositionChangedEvent
The dataViewer posting this event.
getDataViewer() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent
Get the data viewer.
getDataViewer() - Method in class org.micromanager.display.internal.event.DataViewerAddedEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DataViewerDidBecomeActiveEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DataViewerDidBecomeInactiveEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DataViewerDidBecomeInvisibleEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DataViewerDidBecomeVisibleEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DataViewerWillCloseEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DefaultDisplayDidShowImageEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DefaultDisplayPositionChangedEvent
 
getDataViewer() - Method in class org.micromanager.display.internal.event.DefaultDisplaySettingsChangedEvent
Get the data viewer.
getDefaultPalette() - Static method in class org.micromanager.internal.utils.ColorPalettes
 
getDefaultXYStage() - Method in class org.micromanager.MultiStagePosition
Return the default XY stage, i,e, the one used if no stage is named explicitly.
getDefaultZStage() - Method in class org.micromanager.MultiStagePosition
Returns the Default Z stage, i.e.
getDelay() - Method in class org.micromanager.internal.hcwizard.Device
 
getDesc() - Method in enum org.micromanager.ApplicationSkin.SkinMode
Returns a description of this skin.
getDescription() - Method in enum org.micromanager.data.internal.PropertyKey
 
getDescription() - Method in class org.micromanager.internal.diagnostics.ProblemReport
Gets the user-entered description.
getDescription() - Method in class org.micromanager.internal.hcwizard.Device
 
getDescription() - Method in interface org.micromanager.internal.positionlist.utils.ZGenerator
 
getDescription() - Method in class org.micromanager.internal.utils.ScriptFileFilter
 
getDevice() - Method in class org.micromanager.events.internal.DefaultPropertyChangedEvent
 
getDevice() - Method in interface org.micromanager.events.PropertyChangedEvent
Device to which the changed property belongs.
getDeviceDescription(String, String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getDeviceName() - Method in class org.micromanager.events.internal.DefaultSLMExposureChangedEvent
 
getDeviceName() - Method in class org.micromanager.events.internal.DefaultStagePositionChangedEvent
Name of the stage that moved
getDeviceName() - Method in class org.micromanager.events.internal.DefaultXYStagePositionChangedEvent
Name of the (XYStage) device that change position
getDeviceName() - Method in interface org.micromanager.events.SLMExposureChangedEvent
Returns name of the SLM device.
getDeviceName() - Method in interface org.micromanager.events.StagePositionChangedEvent
Name of the stage.
getDeviceName() - Method in interface org.micromanager.events.XYStagePositionChangedEvent
Name of the (XYStage) device that change position.
getDeviceName() - Method in class org.micromanager.internal.hcwizard.DeviceSetupDlg
 
getDevicePoint(Point2D.Float, Rectangle, float, float) - Method in class org.micromanager.internal.graph.GraphPanel
 
getDevicePointUnclippedXMax(Point2D.Float, Rectangle, float, float) - Method in class org.micromanager.internal.graph.GraphPanel
 
getDevices() - Method in class org.micromanager.events.internal.ShutterDevicesEvent
 
getDevices() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getDeviceSetupProperty(String, String) - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getDimension(String, Dimension) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getDimension(String, Dimension) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getDimension(String, Dimension) - Method in interface org.micromanager.PropertyMap
 
getDimension(String, Dimension) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getDimensionList(String, Dimension...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getDimensionList(String, Iterable<Dimension>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getDimensionList(String, Dimension...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getDimensionList(String, Iterable<Dimension>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getDimensionList(String, Dimension...) - Method in interface org.micromanager.PropertyMap
 
getDimensionList(String, Iterable<Dimension>) - Method in interface org.micromanager.PropertyMap
 
getDimensionList(String, Dimension...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getDimensionList(String, Iterable<Dimension>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getDirectory() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getDirectory() - Method in interface org.micromanager.data.SummaryMetadata
The directory the data was originally saved to.
getDirectory() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
getDisabledBackgroundColor() - Method in interface org.micromanager.ApplicationSkin
Return the current "disabled" background color.
getDisabledBackgroundColor() - Method in class org.micromanager.internal.utils.DaytimeNighttime
Return a proper "disabled" background color based on the current mode.
getDisabledTextColor() - Method in interface org.micromanager.ApplicationSkin
Return the current color for disabled text.
getDisabledTextColor() - Method in class org.micromanager.internal.utils.DaytimeNighttime
Return the current color for disabled text.
getDiskLocation() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getDisplay() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent
Deprecated.
use getDataViewer instead
getDisplay() - Method in class org.micromanager.display.internal.event.DefaultDisplaySettingsChangedEvent
Deprecated.
use getDataViewer instead
getDisplay() - Method in class org.micromanager.internal.SnapLiveManager
 
getDisplay() - Method in interface org.micromanager.SnapLiveManager
Return the DisplayWindow used for snap/live mode.
getDisplayController() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getDisplayedAxisLength(String) - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getDisplayedExposureTime() - Method in class org.micromanager.internal.MainFrame
 
getDisplayedImages() - Method in interface org.micromanager.display.DataViewer
Retrieve the Images currently being displayed.
getDisplayedImages() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
getDisplayedImages() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getDisplayGearMenuPlugins() - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
getDisplayGearMenuPlugins() - Method in interface org.micromanager.PluginManager
Return a HashMap that maps plugin class names to DisplayGearMenuPlugin instances.
getDisplayIntervalQuantile(double) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
Return the DisplayIntervalQuantile.
getDisplayIntervalQuantile(double) - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getDisplayManager() - Method in class org.micromanager.internal.MMStudio
 
getDisplayManager() - Method in interface org.micromanager.Studio
Provides access to the DisplayManager instance for accessing Micro-Manager display constructs.
getDisplayName() - Method in enum org.micromanager.data.internal.PropertyKey
 
getDisplayPosition() - Method in class org.micromanager.display.AbstractDataViewer
Implements getDisplayPosition.
getDisplayPosition() - Method in interface org.micromanager.display.DataViewer
Get the coordinates for the currently displayed images.
getDisplayPosition() - Method in interface org.micromanager.display.DisplayPositionChangedEvent
returns the new display position.
getDisplayPosition() - Method in class org.micromanager.display.internal.event.DefaultDisplayPositionChangedEvent
 
getDisplays(Datastore) - Method in interface org.micromanager.display.DisplayManager
getDisplays(DataProvider) - Method in interface org.micromanager.display.DisplayManager
Return all associated DisplayWindows for the DataProvider.
getDisplays(Datastore) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
getDisplays(DataProvider) - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
getDisplaySettings() - Method in class org.micromanager.display.AbstractDataViewer
Implements getDisplaySettings.
getDisplaySettings() - Method in interface org.micromanager.display.DataViewer
Get the current display settings.
getDisplaySettings() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent
Get the new display settings.
getDisplaySettings() - Method in class org.micromanager.display.internal.event.DefaultDisplaySettingsChangedEvent
Get the new display settings.
getDisplaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager
Deprecated.
- use displaySettingsBuilder() instead
getDisplaySettingsBuilder() - Method in class org.micromanager.display.internal.DefaultDisplayManager
Deprecated.
getDisplayWindow() - Method in class org.micromanager.display.internal.event.DisplayWindowDidAddOverlayEvent
 
getDisplayWindow() - Method in class org.micromanager.display.internal.event.DisplayWindowDidRemoveOverlayEvent
 
getDouble(String, double) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getDouble(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getDouble(String, Double) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getDouble(Class<?>, String, Double) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getDouble(String, double) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getDouble(String, double) - Method in interface org.micromanager.PropertyMap
 
getDouble(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getDouble(String, Double) - Method in interface org.micromanager.PropertyMap
Deprecated.
getDouble(String, double) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getDouble(Class<?>, String, Double) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getDouble(key, fallback) instead
getDoubleArray(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getDoubleArray(String, Double[]) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getDoubleArray(Class<?>, String, Double[]) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getDoubleArray(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getDoubleArray(String, Double[]) - Method in interface org.micromanager.PropertyMap
Deprecated.
getDoubleArray(Class<?>, String, Double[]) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getDoubleList(key, fallback) instead
getDoubleList(String, double...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getDoubleList(String, Iterable<Double>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getDoubleList(String, double...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getDoubleList(String, Iterable<Double>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getDoubleList(String, double...) - Method in interface org.micromanager.PropertyMap
 
getDoubleList(String, Iterable<Double>) - Method in interface org.micromanager.PropertyMap
 
getDoubleList(String, double...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getDoubleList(String, Iterable<Double>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getElapsedTimeMs() - Method in class org.micromanager.data.internal.DefaultMetadata
Deprecated.
getElapsedTimeMs(double) - Method in class org.micromanager.data.internal.DefaultMetadata
 
getElapsedTimeMs() - Method in interface org.micromanager.data.Metadata
Deprecated.
getElapsedTimeMs(double) - Method in interface org.micromanager.data.Metadata
Time in milliseconds since the start of the given data acquisition at which the image was received by Micro-Manager.
getElapsedTimeMs(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getEnabledConfigurators(boolean) - Method in class org.micromanager.internal.pipelineinterface.PipelineTableModel
 
getEnabledLivePipelineConfigurators() - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
Return a list of the live-mode enabled configurators.
getEnabledPipelineConfigurators() - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
Return a list of the enabled configurators.
getEnabledTextColor() - Method in interface org.micromanager.ApplicationSkin
Return the current color for enabled text.
getEnabledTextColor() - Method in class org.micromanager.internal.utils.DaytimeNighttime
Return the current color for enabled text.
getEntries() - Method in class org.micromanager.internal.utils.performance.PerformanceMonitor
 
getError() - Method in class org.micromanager.internal.script.BeanshellEngine.EvalThread
 
getEvent() - Method in class org.micromanager.display.internal.event.DisplayMouseEvent
The MouseEvent as received by the display.
getEvent() - Method in class org.micromanager.display.internal.event.DisplayMouseWheelEvent
 
getEventManager() - Method in class org.micromanager.internal.MMStudio
 
getEventManager() - Method in interface org.micromanager.Studio
Provides access to the EventManager instance for subscribing to and posting events on the application-wide EventBus.
getExample() - Method in class org.micromanager.internal.utils.AcqOrderMode
Generates a string describing the ordering, e.g.
getExceptions() - Method in class org.micromanager.data.internal.pipeline.DefaultPipeline
 
getExceptions() - Method in interface org.micromanager.data.Pipeline
Return a list containing any exceptions that have occurred during processing of images.
getExposureMs() - Method in class org.micromanager.data.internal.DefaultMetadata
 
getExposureMs() - Method in interface org.micromanager.data.Metadata
How long of an exposure was used to collect this image.
getExposureMs(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getFileMenu() - Method in class org.micromanager.internal.menus.MMMenuBar
 
getFilename() - Method in interface org.micromanager.data.Annotation
Deprecated.
this is an old name for Annotation.getTag()
getFilename() - Method in class org.micromanager.data.internal.DefaultAnnotation
Deprecated.
getFileName() - Method in class org.micromanager.data.internal.DefaultMetadata
 
getFileName() - Method in interface org.micromanager.data.Metadata
The name of the file from which the image was loaded, if applicable.
getFileName(int) - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
getFileName() - Method in class org.micromanager.internal.hcwizard.ConfigWizard
 
getFileName() - Method in class org.micromanager.internal.hcwizard.MicroscopeModel
 
getFileName(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getFirstConfigGroup() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
Find out which groups are available
getFirstConfigGroup() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
Get first available config group
getFloat(String, float) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getFloat(String, float) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getFloat(String, float) - Method in interface org.micromanager.PropertyMap
 
getFloat(String, float) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getFloatList(String, float...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getFloatList(String, Iterable<Float>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getFloatList(String, float...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getFloatList(String, Iterable<Float>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getFloatList(String, float...) - Method in interface org.micromanager.PropertyMap
 
getFloatList(String, Iterable<Float>) - Method in interface org.micromanager.PropertyMap
 
getFloatList(String, float...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getFloatList(String, Iterable<Float>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getFocusDirection() - Method in class org.micromanager.internal.hcwizard.Device
 
getFocusDirectionFromHardware(CMMCore) - Method in class org.micromanager.internal.hcwizard.Device
 
getFrame() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getFrameIndex(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getFrameIntervalMs() - Method in interface org.micromanager.acquisition.internal.AcquisitionEngine
 
getFrameIntervalMs() - Method in class org.micromanager.acquisition.internal.AcquisitionWrapperEngine
 
getFromColorblindFriendlyPalette(int) - Static method in class org.micromanager.internal.utils.ColorPalettes
 
getFromDefaultPalette(int) - Static method in class org.micromanager.internal.utils.ColorPalettes
 
getFromPrimaryColorPalette(int) - Static method in class org.micromanager.internal.utils.ColorPalettes
 
getFullScreenBounds(GraphicsConfiguration) - Static method in class org.micromanager.internal.utils.GUIUtils
Get the usable screen area (minus taskbars, etc.) for the specified monitor.
getGearMenu() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
Provide a menu used for miscellaneous controls.
getGearMenu() - Method in interface org.micromanager.display.inspector.InspectorPanelController
 
getGearMenu() - Method in class org.micromanager.display.inspector.internal.panels.intensity.IntensityInspectorPanelController
 
getGeneralAnnotation() - Method in interface org.micromanager.data.Annotation
Return a PropertyMap of information stored by the Annotation that is not specific to any one image.
getGeneralAnnotation() - Method in class org.micromanager.data.internal.DefaultAnnotation
 
getGlobalSettingsWithoutMigration() - Method in class org.micromanager.profile.internal.UserProfileAdmin
 
getGraphBounds() - Method in class org.micromanager.internal.graph.GraphPanel
 
getGraphicsConfigurationBestMatching(Rectangle) - Static method in class org.micromanager.internal.utils.GUIUtils
If a window's top-left corner is off the screen, then getGraphicsConfigurationContaining will return null.
getGraphicsConfigurationContaining(int, int) - Static method in class org.micromanager.internal.utils.GUIUtils
 
getGridColumn() - Method in class org.micromanager.MultiStagePosition
Returns rectangular grid column.
getGridRow() - Method in class org.micromanager.MultiStagePosition
Returns rectangular grid row.
getGroupName() - Method in interface org.micromanager.display.ChannelDisplaySettings
Name of the channelgroup this channel belongs to.
getGroupName() - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
getGroupName() - Method in interface org.micromanager.events.ConfigGroupChangedEvent
Name of the ConfigGroup.
getGroupName() - Method in class org.micromanager.events.internal.DefaultConfigGroupChangedEvent
 
getHaveRegistered(Studio) - Static method in class org.micromanager.internal.dialogs.RegistrationDlg
 
getHeight() - Method in interface org.micromanager.data.Image
Get the height of this image in pixels.
getHeight() - Method in class org.micromanager.data.internal.DefaultImage
 
getHeight() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
getHeight(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getHelpText() - Method in class org.micromanager.acquisition.internal.DefaultMDAPlugin
 
getHelpText() - Method in class org.micromanager.display.internal.gearmenu.CopyToImageJItem
 
getHelpText() - Method in class org.micromanager.display.internal.gearmenu.ExportImagesItem
 
getHelpText() - Method in class org.micromanager.display.internal.gearmenu.LineProfileItem
 
getHelpText() - Method in class org.micromanager.internal.utils.CoreAutofocus
 
getHelpText() - Method in interface org.micromanager.MMPlugin
Provide a longer string describing the purpose of the plugin.
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.ExposureTime
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.LiveButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.MDAButtons
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.RefreshButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.ShutterControl
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.SnapButton
 
getHelpText() - Method in class org.micromanager.quickaccess.internal.controls.TextLabel
 
getHideMDADisplayOption() - Method in class org.micromanager.internal.MMStudio
 
getHistogram() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the histogram, an array of ints counting the number of samples whose intensities fall into each bin.
getHistogramBinCount() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getHistogramBinWidth() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getHistogramRangeMax() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getHistogramRangeMin() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getHistoRangeBits() - Method in interface org.micromanager.display.ChannelDisplaySettings
Range of this histogram displayed for this channel For now, histogram always starts at zero, so this represents the maximum value on the x-axis of the histogram.
getHistoRangeBits() - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
getHistoricalKeys() - Method in enum org.micromanager.data.internal.PropertyKey
 
getIcon() - Method in interface org.micromanager.acquisition.internal.AcquisitionDialogPlugin
Provide an ImageIcon for display in the selection menu.
getIcon() - Method in class org.micromanager.acquisition.internal.DefaultMDAPlugin
 
getIcon() - Method in class org.micromanager.quickaccess.internal.ControlCell
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.ExposureTime
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.LiveButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.MDAButtons
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.RefreshButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.ShutterControl
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.SnapButton
 
getIcon() - Method in class org.micromanager.quickaccess.internal.controls.TextLabel
 
getIcon() - Method in class org.micromanager.quickaccess.internal.DraggableIcon
 
getIcon() - Method in class org.micromanager.quickaccess.QuickAccessPlugin
Provide an icon to use to represent this plugin when configuring the Quick-Access Window.
getID() - Method in class org.micromanager.internal.utils.AcqOrderMode
 
getIJImageCanvas() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
Not ideal, but the Image Exporter needs access to the canvas to grab images
getIJImageCanvas() - Method in class org.micromanager.display.internal.displaywindow.imagej.ImageJBridge
 
getIJImagePlus() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getIJImagePlus() - Method in class org.micromanager.display.internal.displaywindow.imagej.ImageJBridge
 
getIJNumberOfChannels() - Method in class org.micromanager.display.internal.displaywindow.imagej.ImageJBridge
 
getIJType(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getIJZoom() - Method in class org.micromanager.display.internal.displaywindow.imagej.ImageJBridge
 
getImage(Coords) - Method in interface org.micromanager.data.DataProvider
Returns the image at the given position.
getImage() - Method in interface org.micromanager.data.DataProviderHasNewImageEvent
Provides the newly-added image.
getImage() - Method in interface org.micromanager.data.ImageDeletedEvent
Provides the Image that was deleted.
getImage(Coords) - Method in class org.micromanager.data.internal.DefaultDatastore
 
getImage() - Method in class org.micromanager.data.internal.DefaultImageDeletedEvent
Provides the Image that was deleted.
getImage() - Method in class org.micromanager.data.internal.DefaultNewImageEvent
Provides the newly-added image.
getImage(Coords) - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getImage() - Method in class org.micromanager.data.internal.pipeline.ImageWrapper
 
getImage(Coords) - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getImage(Coords) - Method in class org.micromanager.data.internal.StorageRAM
 
getImage(Coords) - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getImage(Coords) - Method in interface org.micromanager.data.Storage
Retrieve the Image located at the specified coordinates.
getImage(int) - Method in class org.micromanager.display.internal.imagestats.ImageStatsRequest
 
getImageAnnotation(Coords) - Method in interface org.micromanager.data.Annotation
Return a PropertyMap of information stored by this Annotation related to the image at the specified coordinates.
getImageAnnotation(Coords) - Method in class org.micromanager.data.internal.DefaultAnnotation
 
getImageArray() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMVirtualStack
 
getImageBitDepth() - Method in class org.micromanager.internal.MMCache
 
getImageComment(Datastore, Coords) - Static method in class org.micromanager.data.internal.CommentsHelper
Returns the comment for the specified Image in the specified Datastore, or empty string if it does not exist.
getImageHeight() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getImageJConverter() - Method in interface org.micromanager.data.DataManager
Provide access to the ImageJConverter() object.
getImageJConverter() - Method in class org.micromanager.data.internal.DefaultDataManager
 
getImageJPixelType() - Method in interface org.micromanager.data.Image
Deprecated.
Unclear what should be used instead. Do not delete until this is figure out.
getImageJPixelType() - Method in class org.micromanager.data.internal.DefaultImage
Deprecated.
getImageNumber() - Method in class org.micromanager.data.internal.DefaultMetadata
 
getImageNumber() - Method in interface org.micromanager.data.Metadata
The sequence number of this image, for sequence acquisitions.
getImagePlus() - Method in interface org.micromanager.display.DisplayWindow
Deprecated.
Directly accessing the ImagePlus of an MMStudio display window will generally result in very fragile code. Consider accessing image data through DataViewer.getDataProvider(). For drawing overlay graphics, see DisplayWindow.addOverlay(org.micromanager.display.overlay.Overlay).
getImagePlus() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
Deprecated.
getImageProcessorType(ImageProcessor) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getImages() - Method in interface org.micromanager.display.DisplayDidShowImageEvent
Returns the images newly displayed.
getImages() - Method in class org.micromanager.display.internal.event.DefaultDisplayDidShowImageEvent
 
getImages() - Method in class org.micromanager.display.internal.imagestats.ImageStatsRequest
 
getImagesAndStats() - Method in class org.micromanager.display.inspector.internal.panels.intensity.ImageStatsPublisher.ImageStatsChangedEvent
 
getImagesIgnoringAxes(Coords, String...) - Method in interface org.micromanager.data.DataProvider
Returns a list of image in the DataProvider's collection that have identical coords after removing the given axes from both source and target.
getImagesIgnoringAxes(Coords, String...) - Method in class org.micromanager.data.internal.DefaultDatastore
 
getImagesIgnoringAxes(Coords, String...) - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getImagesIgnoringAxes(Coords, String...) - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getImagesIgnoringAxes(Coords, String...) - Method in class org.micromanager.data.internal.StorageRAM
Finds images in this storage that match the given coord, but ignore the provided axes (i.e., remove those axes from our images, and then check if the Coord is identical to the one given).
getImagesIgnoringAxes(Coords, String...) - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getImagesIgnoringAxes(Coords, String...) - Method in interface org.micromanager.data.Storage
Retrieve a list of images with Coords identical to the given Coords instance, except for the axes listed in the exception list.
getImageSize(double) - Method in class org.micromanager.internal.positionlist.utils.TileCreator
 
getImagesMatching(Coords) - Method in interface org.micromanager.data.DataProvider
Deprecated.
- instead use getImagesIgnoringAxes
getImagesMatching(Coords) - Method in class org.micromanager.data.internal.DefaultDatastore
 
getImagesMatching(Coords) - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getImagesMatching(Coords) - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getImagesMatching(Coords) - Method in class org.micromanager.data.internal.StorageRAM
 
getImagesMatching(Coords) - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getImagesMatching(Coords) - Method in interface org.micromanager.data.Storage
Retrieve a list of all images whose Coords match the given incomplete Coords instance.
getImageTime(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getImageWidth() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
 
getIndex(String) - Method in interface org.micromanager.data.Coords
Get the index for the given axis.
getIndex(String) - Method in class org.micromanager.data.internal.DefaultCoords
 
getIndex() - Method in enum org.micromanager.display.DisplaySettings.ColorMode
Deprecated.
getIndex() - Method in class org.micromanager.display.internal.imagestats.ImageStats
 
getIndexingAxes() - Method in class org.micromanager.display.internal.event.DataViewerMousePixelInfoChangedEvent
 
getIndexKeys() - Method in class org.micromanager.data.internal.multipagetiff.MultipageTiffReader
Returns the Coords this reader knows about .
getIndexMap() - Method in class org.micromanager.data.internal.multipagetiff.MultipageTiffWriter
 
getIndices(String) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getInfoString(ImagesAndStats) - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
Generates the info string in the top right of the viewer showing: - x-y size in microns - x-y size in pixels - pixelType - Size in k/MB
getInRangeHistogram() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getInspector() - Method in class org.micromanager.display.internal.event.InspectorDidCloseEvent
 
getInspectorPlugins() - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
getInspectorPlugins() - Method in interface org.micromanager.PluginManager
Return a HashMap that maps plugin class names to InspectorPlugin instances.
getInstance() - Static method in class org.micromanager.internal.MMStudio
Returns singleton instance of MMStudio.
getInstance() - Static method in class org.micromanager.internal.utils.EventBusExceptionLogger
 
getInt(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getInt(String, Integer) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getInt(Class<?>, String, Integer) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getInt(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getInt(String, Integer) - Method in interface org.micromanager.PropertyMap
Deprecated.
getInt(Class<?>, String, Integer) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getInteger(key, fallback) instead
getIntArray(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getIntArray(String, Integer[]) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getIntArray(Class<?>, String, Integer[]) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getIntArray(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getIntArray(String, Integer[]) - Method in interface org.micromanager.PropertyMap
Deprecated.
getIntArray(Class<?>, String, Integer[]) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getIntegerList(key, fallback) instead
getInteger(String, int) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getInteger(String, int) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getInteger(String, int) - Method in interface org.micromanager.PropertyMap
 
getInteger(String, int) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getIntegerList(String, int...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getIntegerList(String, Iterable<Integer>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getIntegerList(String, int...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getIntegerList(String, Iterable<Integer>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getIntegerList(String, int...) - Method in interface org.micromanager.PropertyMap
 
getIntegerList(String, Iterable<Integer>) - Method in interface org.micromanager.PropertyMap
 
getIntegerList(String, int...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getIntegerList(String, Iterable<Integer>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getIntendedDimensions() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getIntendedDimensions() - Method in interface org.micromanager.data.SummaryMetadata
The expected number of images along each axis that were to be collected.
getIntendedSize(String) - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
Provides the expected highest index minus one for a given axis.
getIntensityAt(int, int) - Method in interface org.micromanager.data.Image
Retrieve the intensity of the pixel at the specified position.
getIntensityAt(int, int) - Method in class org.micromanager.data.internal.DefaultImage
 
getIntensityStringAt(int, int) - Method in interface org.micromanager.data.Image
Generate a string describing the value(s) of the pixel at the specified location.
getIntensityStringAt(int, int) - Method in class org.micromanager.data.internal.DefaultImage
 
getIntervalMs(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getIntroPlugins() - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
getIntroPlugins() - Method in interface org.micromanager.PluginManager
Return a HashMap that maps plugin class names to IntroPlugin instances.
getIntValue(JTextField) - Static method in class org.micromanager.internal.utils.GUIUtils
 
getIsCancelled() - Method in class org.micromanager.events.internal.DefaultShutdownCommencingEvent
getIsCancelled() - Method in interface org.micromanager.events.ShutdownCommencingEvent
Deprecated.
getIsLiveModeOn() - Method in interface org.micromanager.SnapLiveManager
Deprecated.
getIsMainExposureTime() - Method in interface org.micromanager.events.ChannelExposureEvent
getIsMainExposureTime() - Method in class org.micromanager.events.internal.DefaultChannelExposureEvent
getIsManaged(DataProvider) - Method in interface org.micromanager.display.DisplayManager
getIsOn() - Method in interface org.micromanager.events.LiveModeEvent
Deprecated.
getIsSynchronous() - Method in interface org.micromanager.data.Pipeline
Deprecated.
getIsVisible() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings
getIsVisible() - Method in class org.micromanager.display.internal.DefaultDisplaySettings.DefaultContrastSettings
Deprecated.
getItem(String, String) - Method in class org.micromanager.internal.utils.PropertyTableData
 
getJarPath() - Static method in class org.micromanager.internal.utils.JavaUtils
Return the path of the jar containing this class.
getJSONArrayMember(JSONObject, String) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getKeepShutterOpenChannels() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getKeepShutterOpenChannels() - Method in interface org.micromanager.data.SummaryMetadata
For acquisitions with more than one channel, whether or not the shutter was left open in between each channel.
getKeepShutterOpenSlices() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getKeepShutterOpenSlices() - Method in interface org.micromanager.data.SummaryMetadata
For acquisitions with more than one Z slice, whether or not the shutter was left open in between each slice.
getKeyEvent() - Method in class org.micromanager.display.internal.event.DisplayKeyPressEvent
 
getKeys() - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getKeys(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getKeys() - Method in interface org.micromanager.PropertyMap
Deprecated.
getLabel() - Method in class org.micromanager.internal.utils.Calibration
 
getLabel() - Method in class org.micromanager.internal.utils.CalibrationList
Returns calibration label
getLabel(JSONObject) - Static method in class org.micromanager.internal.utils.MDUtils
Deprecated.
 
getLabel() - Method in class org.micromanager.MultiStagePosition
Returns position label.
getLayoutAlignmentX(Container) - Method in class org.micromanager.quickaccess.internal.SparseGridLayout
 
getLayoutAlignmentY(Container) - Method in class org.micromanager.quickaccess.internal.SparseGridLayout
 
getLegacyLogFileDirectory() - Static method in class org.micromanager.internal.logging.LogFileManager
 
getLegacySerializedObject(String, T) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getLegacySerializedObject(Class<?>, String, T) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getLibrary() - Method in class org.micromanager.internal.hcwizard.Device
 
getLibraryContents(String, CMMCore) - Static method in class org.micromanager.internal.hcwizard.Device
 
getLightBackgroundColor() - Method in interface org.micromanager.ApplicationSkin
Return the current "lighter" background color for highlighted or otherwise differentiated GUI elements.
getLightBackgroundColor() - Method in class org.micromanager.internal.utils.DaytimeNighttime
Return the current "lighter" background color.
getLinkablePeers() - Method in class org.micromanager.display.internal.link.AbstractLinkAnchor
 
getLinkablePeers() - Method in interface org.micromanager.display.internal.link.internal.LinkEndpoint
 
getLinkablePeers() - Method in interface org.micromanager.display.internal.link.LinkAnchor
Get all linkable peer anchors.
getLinkage() - Method in interface org.micromanager.display.internal.link.internal.LinkEndpoint
 
getLinkageGroup() - Method in interface org.micromanager.display.internal.link.internal.LinkEndpoint
 
getLinkageGroup() - Method in interface org.micromanager.display.internal.link.LinkAnchor
Return a tag object designating the linkage group of this anchor.
getLinkedPeers() - Method in class org.micromanager.display.internal.link.AbstractLinkAnchor
 
getLinkedPeers() - Method in interface org.micromanager.display.internal.link.internal.LinkEndpoint
 
getLinkedPeers() - Method in interface org.micromanager.display.internal.link.LinkAnchor
Return the currently linked peers.
getLivePipelineConfigurators(boolean) - Method in interface org.micromanager.data.DataManager
Return a list of the ProcessorConfigurators currently being used by the live pipeline interface.
getLivePipelineConfigurators(boolean) - Method in class org.micromanager.data.internal.DefaultDataManager
 
getLivePipelineFactories() - Method in class org.micromanager.internal.pipelineinterface.PipelineFrame
 
getLocation() - Method in class org.micromanager.display.internal.event.DisplayMouseEvent
Provides location in image coordinates.
getLogFileDirectory() - Static method in class org.micromanager.internal.logging.LogFileManager
 
getLogManager() - Method in class org.micromanager.internal.MMStudio
 
getLogManager() - Method in interface org.micromanager.Studio
Provides access to Micro-Manager's logging functions, like logError(), showMessage(), etc.
getLong(String, long) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getLong(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getLong(String, Long) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getLong(Class<?>, String, Long) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getLong(String, long) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getLong(String, long) - Method in interface org.micromanager.PropertyMap
 
getLong(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getLong(String, Long) - Method in interface org.micromanager.PropertyMap
Deprecated.
getLong(String, long) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getLong(Class<?>, String, Long) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getLong(key, fallback) instead
getLongArray(String) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getLongArray(String, Long[]) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
Deprecated.
getLongArray(Class<?>, String, Long[]) - Method in class org.micromanager.profile.internal.DefaultUserProfile
Deprecated.
getLongArray(String) - Method in interface org.micromanager.PropertyMap
Deprecated.
getLongArray(String, Long[]) - Method in interface org.micromanager.PropertyMap
Deprecated.
getLongArray(Class<?>, String, Long[]) - Method in interface org.micromanager.UserProfile
Deprecated.
use getSettings(c).getLongList(key, fallback) instead
getLongList(String, long...) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getLongList(String, Iterable<Long>) - Method in class org.micromanager.internal.propertymap.DefaultPropertyMap
 
getLongList(String, long...) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getLongList(String, Iterable<Long>) - Method in class org.micromanager.profile.internal.ProfilePropertyMapView
 
getLongList(String, long...) - Method in interface org.micromanager.PropertyMap
 
getLongList(String, Iterable<Long>) - Method in interface org.micromanager.PropertyMap
 
getLongList(String, long...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getLongList(String, Iterable<Long>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
 
getLowerBound(long, T) - Method in class org.micromanager.display.internal.imagestats.PowerOf2BinMapper
 
getMagnification() - Method in interface org.micromanager.display.DisplayWindow
Deprecated.
getMagnification() - Method in class org.micromanager.display.internal.displaywindow.DisplayWindowAPIAdapter
Deprecated.
getMainWindow() - Method in interface org.micromanager.Application
Provide access to the main window of the program.
getMainWindow() - Method in class org.micromanager.internal.DefaultApplication
 
getManagedDataProviders() - Method in interface org.micromanager.display.DisplayManager
Return a list of all DataProviders that MicroManager is managing (see the manage() method for more information).
getManagedDataProviders() - Method in class org.micromanager.display.internal.DefaultDisplayManager
 
getMask() - Method in class org.micromanager.display.internal.imagestats.BoundsRectAndMask
 
getMax(Object) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getMaxBinCountPowerOf2() - Method in class org.micromanager.display.internal.imagestats.ImageStatsRequest
 
getMaxIgnoringOutliers() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the intensity of the brightest sample in the dataset once a fraction of all pixels have been discarded.
getMaximumExtentOfAxis(String) - Method in interface org.micromanager.display.internal.animate.DataCoordsAnimationState.CoordsProvider
 
getMaximumExtentOfAxis(String) - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
getMaxIndex(String) - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getMaxIndex(String) - Method in class org.micromanager.data.internal.StorageRAM
 
getMaxIndex(String) - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getMaxIndex(String) - Method in interface org.micromanager.data.Storage
Return the largest stored position along the specified axis.
getMaxIndices() - Method in interface org.micromanager.data.DataProvider
getMaxIndices() - Method in class org.micromanager.data.internal.DefaultDatastore
Deprecated.
getMaxIndices() - Method in class org.micromanager.data.internal.multipagetiff.StorageMultipageTiff
 
getMaxIndices() - Method in class org.micromanager.data.internal.SciFIODataProvider
Deprecated.
getMaxIndices() - Method in class org.micromanager.data.internal.StorageRAM
 
getMaxIndices() - Method in class org.micromanager.data.internal.StorageSinglePlaneTiffSeries
 
getMaxIndices() - Method in interface org.micromanager.data.Storage
Return a Coords that provides the maximum index along all available axes.
getMaxIntensity() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getMaxVal() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the intensity of the brightest sample in the dataset used to generate the histogram.
getMean() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the mean value of all samples in the dataset.
getMeanIntensity() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getMenuPlugins() - Method in class org.micromanager.internal.pluginmanagement.DefaultPluginManager
 
getMenuPlugins() - Method in interface org.micromanager.PluginManager
Return a HashMap that maps plugin class names to MenuPlugin instances.
getMetadata() - Method in interface org.micromanager.data.Image
Retrieve the Metadata for this Image.
getMetadata() - Method in class org.micromanager.data.internal.DefaultImage
 
getMetadataBuilder() - Method in interface org.micromanager.data.DataManager
Deprecated.
getMetadataBuilder() - Method in class org.micromanager.data.internal.DefaultDataManager
Deprecated.
getMetadataVersion() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getMetadataVersion() - Method in interface org.micromanager.data.SummaryMetadata
The version of the metadata when the data was collected.
getMicroManagerVersion() - Method in class org.micromanager.data.internal.DefaultSummaryMetadata
 
getMicroManagerVersion() - Method in interface org.micromanager.data.SummaryMetadata
The version of Micro-Manager used to collect the data.
getMin(Object) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getMinIgnoringOutliers() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the intensity of the dimmest sample in the dataset once a fraction of all pixels have been discarded.
getMinIntensity() - Method in class org.micromanager.display.internal.imagestats.IntegerComponentStats
 
getMinMax(Object) - Static method in class org.micromanager.internal.utils.imageanalysis.ImageUtils
 
getMinVal() - Method in class org.micromanager.display.HistogramData
Deprecated.
Retrieve the intensity of the dimmest sample in the dataset used to generate the histogram.
getMMPrincipalDisplayedCoords() - Method in class org.micromanager.display.internal.displaywindow.DisplayUIController
Return the coords of selected channel among the displayed images.
getMouseMovesStage() - Method in class org.micromanager.internal.menus.ToolsMenu
 
getMs() - Method in class org.micromanager.internal.utils.performance.CPUTimer
 
getMs() - Method in class org.micromanager.internal.utils.performance.WallTimer
 
getName() - Method in class org.micromanager.acquisition.internal.DefaultMDAPlugin
 
getName() - Method in interface org.micromanager.data.DataProvider
A dataProvider has a name (not guaranteed to be unique).
getName() - Method in class org.micromanager.data.internal.DefaultDatastore
 
getName() - Method in class org.micromanager.data.internal.SciFIODataProvider
 
getName() - Method in interface org.micromanager.display.ChannelDisplaySettings
Returns name of the channel that is displayed.
getName() - Method in interface org.micromanager.display.DataViewer
Return the name of this viewer.
getName() - Method in class org.micromanager.display.internal.DefaultChannelDisplaySettings
 
getName() - Method in class org.micromanager.display.internal.displaywindow.DisplayController
 
getName() - Method in class org.micromanager.display.internal.gearmenu.CopyToImageJItem
 
getName() - Method in class org.micromanager.display.internal.gearmenu.ExportImagesItem
 
getName() - Method in class org.micromanager.display.internal.gearmenu.LineProfileItem
 
getName() - Method in class org.micromanager.internal.hcwizard.ConfigGroup
 
getName() - Method in class org.micromanager.internal.hcwizard.ConfigPreset
 
getName() - Method in class org.micromanager.internal.hcwizard.Device
 
getName() - Method in class org.micromanager.internal.pipelineinterface.ConfiguratorWrapper
 
getName() - Method in class org.micromanager.internal.utils.CoreAutofocus
 
getName() - Method in interface org.micromanager.MMPlugin
Provide a short string identifying the plugin.
getName() - Method in class org.micromanager.quickaccess.internal.controls.AutofocusButtons
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.CloseAllButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.ExposureTime
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.LiveButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.MDAButtons
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.PresetButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.RefreshButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.SavedMDAButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.ScriptButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.ShutterControl
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.SnapButton
 
getName() - Method in class org.micromanager.quickaccess.internal.controls.TextLabel
 
getNChannelsWithoutSideEffect() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMCompositeImage
 
getNChannelsWithoutSideEffect() - Method in class org.micromanager.display.internal.displaywindow.imagej.MMImagePlus
 
getNewChannelGroup() - Method in interface org.micromanager.events.ChannelGroupChangedEvent
Provides the name of the newly selected channel group.
getNewChannelGroup() - Method in class org.micromanager.events.internal.DefaultChannelGroupChangedEvent
Provides the name of the newly selected channel group
getNewConfig() - Method in interface org.micromanager.events.ConfigGroupChangedEvent
Returns the name of the newly selected config in the group.
getNewConfig() - Method in class org.micromanager.events.internal.DefaultConfigGroupChangedEvent
 
getNewExposureTime() - Method in interface org.micromanager.events.ChannelExposureEvent
Return the new exposure time for the channel.
getNewExposureTime() - Method in interface org.micromanager.events.ExposureChangedEvent
New exposure time.
getNewExposureTime() - Method in class org.micromanager.events.internal.DefaultChannelExposureEvent
Return the new exposure time for the channel.
getNewExposureTime() - Method in class org.micromanager.events.internal.DefaultExposureChangedEvent
New exposure time
getNewExposureTime() - Method in class org.micromanager.events.internal.DefaultSLMExposureChangedEvent
 
getNewExposureTime() - Method in interface org.micromanager.events.SLMExposureChangedEvent
Returns new exposure time of the SLM.
getNewImage() - Method in interface org.micromanager.data.ImageOverwrittenEvent
Provides the newly-added image.
getNewImage() - Method in class org.micromanager.data.internal.DefaultImageOverwrittenEvent
Provides the newly-added image.
getNewName() - Method in interface org.micromanager.data.DataProviderHasNewNameEvent
Returns the new name of the DataProvider.
getNewName() - Method in class org.micromanager.data.internal.DefaultHasNewNameEvent
 
getNewPixelSizeAffine() - Method in class org.micromanager.events.internal.DefaultPixelSizeAffineChangedEvent
New affine transform.
getNewPixelSizeAffine() - Method in interface org.micromanager.events.PixelSizeAffineChangedEvent
New affine transform.
getNewPixelSizeUm() - Method in class org.micromanager.events.internal.DefaultPixelSizeChangedEvent
 
getNewPixelSiz