Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Exceptions
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Interfaces

Interface and Description
org.micromanager.display.DisplaySettings.ContrastSettings TODO: explain
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder Use DisplaySettings.Builder instead
org.micromanager.data.Metadata.MetadataBuilder Use Metadata.Builder instead
org.micromanager.PropertyMap.PropertyMapBuilder
org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder - Use SummaryMetadata.Builder instead

Deprecated Classes

Class and Description
org.micromanager.events.AutofocusPluginShouldInitializeEvent use
org.micromanager.display.HistogramData an improved API will be provided soon

Deprecated Exceptions

Exceptions and Description
org.micromanager.PropertyMap.TypeMismatchException If necessary, catch ClassCastException instead.

Deprecated Fields

Field and Description
org.micromanager.acquisition.ChannelSpec.camera Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.cameraTimeout use Builder and cameraTimeout() instead
org.micromanager.acquisition.SequenceSettings.channelGroup use Builder and channelGroup() instead
org.micromanager.acquisition.ChannelSpec.channelGroup Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.channels use Builder and channels() instead
org.micromanager.acquisition.ChannelSpec.color Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.comment use Builder and comment() instead
org.micromanager.acquisition.ChannelSpec.config Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.customIntervalsMs use Builder and customIntervalsMs() instead
org.micromanager.acquisition.ChannelSpec.doZStack Use Builder and getters instead
org.micromanager.acquisition.ChannelSpec.exposure Use Builder and getters instead
org.micromanager.display.DisplaySettings.FILENAME
org.micromanager.acquisition.SequenceSettings.intervalMs use Builder and intervalMs() instead
org.micromanager.acquisition.SequenceSettings.keepShutterOpenChannels use Builder and keepShutterOpenChannels() instead
org.micromanager.acquisition.SequenceSettings.keepShutterOpenSlices use Builder and keepShutterOpenSlices() instead
org.micromanager.StagePosition.numAxes Use StagePosition.set1DPosition(java.lang.String, double) or StagePosition.set2DPosition(java.lang.String, double, double) to set; use StagePosition.getNumberOfStageAxes(), StagePosition.is1DStagePosition(), or StagePosition.is2DStagePosition() to access.
org.micromanager.acquisition.SequenceSettings.numFrames use Builder and numFrames() instead
org.micromanager.acquisition.SequenceSettings.prefix use Builder and prefix() instead
org.micromanager.acquisition.SequenceSettings.relativeZSlice use Builder and relativeZSlice() instead
org.micromanager.acquisition.SequenceSettings.root use Builder and root() instead
org.micromanager.acquisition.SequenceSettings.save use Builder and save() instead
org.micromanager.acquisition.SequenceSettings.shouldDisplayImages use Builder and shouldDisplayImages() instead
org.micromanager.acquisition.SequenceSettings.skipAutofocusCount use Builder and skipAutofocusCount() instead
org.micromanager.acquisition.ChannelSpec.skipFactorFrame Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.slices use Builder and slices() instead
org.micromanager.acquisition.SequenceSettings.slicesFirst use Builder and slicesFirst() instead
org.micromanager.StagePosition.stageName Use StagePosition.set1DPosition(java.lang.String, double) or StagePosition.set2DPosition(java.lang.String, double, double) to set; use StagePosition.getStageDeviceLabel() to access.
org.micromanager.data.Coords.TIME Use discouraged because it reads like a physical time rather than the time point index that it is.
org.micromanager.acquisition.SequenceSettings.timeFirst use Builder and timeFirst() instead
org.micromanager.acquisition.SequenceSettings.useAutofocus use Builder and useAutofocus() instead
org.micromanager.acquisition.ChannelSpec.useChannel Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.useCustomIntervals use Builder and useCustomIntervals() instead
org.micromanager.acquisition.SequenceSettings.usePositionList use Builder and usePositionList() instead
org.micromanager.StagePosition.x Use methods instead.
org.micromanager.StagePosition.y Use methods instead.
org.micromanager.StagePosition.z
org.micromanager.acquisition.ChannelSpec.zOffset Use Builder and getters instead
org.micromanager.acquisition.SequenceSettings.zReference use Builder and zReference() instead

Deprecated Methods

Method and Description
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.animationFPS(Double)
org.micromanager.PropertyMap.PropertyMapBuilder.build()
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.build()
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.channelColorMode(DisplaySettings.ColorMode)
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.channelColors(Color[])
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.channelContrastSettings(DisplaySettings.ContrastSettings[])
org.micromanager.acquisition.ChannelSpec.Builder.color(Color) use ChannelDisplaySettings.color() instead
org.micromanager.PropertyMap.copy()
org.micromanager.data.SummaryMetadata.copy() - Use SummaryMetadata.Builder.copyBuilder instead
org.micromanager.data.Coords.copy() Use copyBuilder instead
org.micromanager.data.Metadata.copy() Use the appropriate of the following: Metadata.copyBuilderPreservingUUID(), Metadata.copyBuilderWithNewUUID(), Metadata.copyBuilderRemovingUUID(). This method is equivalent to copyBuilderPreservingUUID.
org.micromanager.display.DisplaySettings.copy()
org.micromanager.acquisition.SequenceSettings.copy() When used correctly, SequenceSettings are immutable. If you really need a copy, use copyBuilder().build();
org.micromanager.data.DataManager.createCoords(String) use of Strings for Coords is discouraged
org.micromanager.display.DisplayManager.createFirstInspector()
org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder.customIntervalsMs(Double[])
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.extremaPercentage(Double)
org.micromanager.display.DisplaySettings.ColorMode.fromInt(int)
org.micromanager.display.DisplayWindow.getAsWindow() use DisplayWindow.getWindow() instead
org.micromanager.data.DataProvider.getAxisLength(String) Use DataProvider.getNextIndex(String) instead.
org.micromanager.data.SummaryMetadata.getAxisOrder() - Use getOrdereddAxes() instead
org.micromanager.UserProfile.getBoolean(Class<?>, String, Boolean) use getSettings(c).getBoolean(key, fallback) instead
org.micromanager.PropertyMap.getBoolean(String)
org.micromanager.PropertyMap.getBoolean(String, Boolean)
org.micromanager.UserProfile.getBooleanArray(Class<?>, String, Boolean[]) use getSettings(c).getBooleanList(key, fallback) instead
org.micromanager.PropertyMap.getBooleanArray(String)
org.micromanager.PropertyMap.getBooleanArray(String, Boolean[])
org.micromanager.CompatibilityInterface.getCameraTransform(String) - Use core.getPixelSizeAffineByID(config) instead
org.micromanager.display.DisplaySettings.getChannelColorMode() - use getColorMode() instead
org.micromanager.display.DisplaySettings.getChannelContrastSettings()
org.micromanager.data.SummaryMetadata.getChannelNames() - Use getChannelNameList() instead
org.micromanager.display.DisplaySettings.ContrastSettings.getContrastGammas()
org.micromanager.display.DisplaySettings.ContrastSettings.getContrastMaxes()
org.micromanager.display.DisplaySettings.ContrastSettings.getContrastMins()
org.micromanager.display.DisplayManager.getContrastSettings(Integer[], Integer[], Double[], Boolean)
org.micromanager.display.DisplayManager.getContrastSettings(Integer, Integer, Double, Boolean) Use DisplaySettings.getAllChannelSettings() instead.
org.micromanager.data.DataManager.getCoordsBuilder() Use DataManager.coordsBuilder() instead
org.micromanager.display.DisplayManager.getCurrentWindow() Use getActiveDataViewer() instead
org.micromanager.data.SummaryMetadata.getCustomIntervalsMs() - Use double[] getCustomIntervalsMsArray() instead
org.micromanager.display.AbstractDataViewer.getDatastore() user code should call getDataProvider
org.micromanager.display.DataViewer.getDatastore() use DataViewer.getDataProvider() instead
org.micromanager.display.DisplaySettingsChangedEvent.getDisplay() use getDataViewer instead
org.micromanager.display.DisplayManager.getDisplays(Datastore) replaced by DisplayManager.getDisplays(DataProvider)
org.micromanager.display.DisplayManager.getDisplaySettingsBuilder() - use displaySettingsBuilder() instead
org.micromanager.UserProfile.getDouble(Class<?>, String, Double) use getSettings(c).getDouble(key, fallback) instead
org.micromanager.PropertyMap.getDouble(String)
org.micromanager.PropertyMap.getDouble(String, Double)
org.micromanager.UserProfile.getDoubleArray(Class<?>, String, Double[]) use getSettings(c).getDoubleList(key, fallback) instead
org.micromanager.PropertyMap.getDoubleArray(String)
org.micromanager.PropertyMap.getDoubleArray(String, Double[])
org.micromanager.data.Metadata.getElapsedTimeMs() - use Double Metadata.getElapsedTimeMs(double) instead
org.micromanager.data.Annotation.getFilename() this is an old name for Annotation.getTag()
org.micromanager.data.Image.getImageJPixelType() Unclear what should be used instead. Do not delete until this is figure out.
org.micromanager.display.DisplayWindow.getImagePlus() 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).
org.micromanager.data.DataProvider.getImagesMatching(Coords) - instead use getImagesIgnoringAxes
org.micromanager.display.DisplaySettings.ColorMode.getIndex()
org.micromanager.UserProfile.getInt(Class<?>, String, Integer) use getSettings(c).getInteger(key, fallback) instead
org.micromanager.PropertyMap.getInt(String)
org.micromanager.PropertyMap.getInt(String, Integer)
org.micromanager.UserProfile.getIntArray(Class<?>, String, Integer[]) use getSettings(c).getIntegerList(key, fallback) instead
org.micromanager.PropertyMap.getIntArray(String)
org.micromanager.PropertyMap.getIntArray(String, Integer[])
org.micromanager.events.ShutdownCommencingEvent.getIsCancelled() use ShutdownCommencingEvent.isCanceled() instead
org.micromanager.SnapLiveManager.getIsLiveModeOn()
org.micromanager.events.ChannelExposureEvent.getIsMainExposureTime() use ChannelExposureEvent.isMainExposureTime() instead
org.micromanager.display.DisplayManager.getIsManaged(DataProvider) use DisplayManager.isManaged(DataProvider) instead
org.micromanager.events.LiveModeEvent.getIsOn() use LiveModeEvent.isOn() instead.
org.micromanager.data.Pipeline.getIsSynchronous() Use Pipeline.isSynchronous() instead.
org.micromanager.display.DisplaySettings.ContrastSettings.getIsVisible() Use DisplaySettings.ContrastSettings.isVisible()
org.micromanager.PropertyMap.getKeys()
org.micromanager.UserProfile.getLong(Class<?>, String, Long) use getSettings(c).getLong(key, fallback) instead
org.micromanager.PropertyMap.getLong(String)
org.micromanager.PropertyMap.getLong(String, Long)
org.micromanager.UserProfile.getLongArray(Class<?>, String, Long[]) use getSettings(c).getLongList(key, fallback) instead
org.micromanager.PropertyMap.getLongArray(String)
org.micromanager.PropertyMap.getLongArray(String, Long[])
org.micromanager.display.DisplayWindow.getMagnification() use DisplayWindow.getZoom() instead
org.micromanager.data.DataProvider.getMaxIndices() Use DataProvider.getNextIndex(String axis) instead
org.micromanager.data.DataManager.getMetadataBuilder() Use DataManager.metadataBuilder() instead
org.micromanager.display.DisplaySettings.ContrastSettings.getNumComponents()
org.micromanager.data.Metadata.getPositionName() Use Metadata.getPositionName(java.lang.String) instead
org.micromanager.PropertyMap.getPropertyMap(String)
org.micromanager.data.DataManager.getPropertyMapBuilder() Use PropertyMaps.builder() instead
org.micromanager.display.DisplayManager.getPropertyMapBuilder() Use PropertyMaps.builder() instead
org.micromanager.PropertyMap.getPropertyType(String)
org.micromanager.display.DisplaySettings.ContrastSettings.getSafeContrastGamma(int, Double)
org.micromanager.display.DisplaySettings.getSafeContrastGamma(int, int, Double)
org.micromanager.display.DisplaySettings.ContrastSettings.getSafeContrastMax(int, Integer)
org.micromanager.display.DisplaySettings.getSafeContrastMax(int, int, Integer)
org.micromanager.display.DisplaySettings.ContrastSettings.getSafeContrastMin(int, Integer)
org.micromanager.display.DisplaySettings.getSafeContrastMin(int, int, Integer)
org.micromanager.display.DisplaySettings.getSafeContrastSettings(int, DisplaySettings.ContrastSettings)
org.micromanager.display.DisplaySettings.getSafeIsVisible(int, Boolean)
org.micromanager.display.DisplaySettings.getShouldSyncChannels()
org.micromanager.data.SummaryMetadata.getStagePositions() - Use getStagePositionList() instead
org.micromanager.UserProfile.getString(Class<?>, String, String) use getSettings(c).getString(key, fallback) instead
org.micromanager.PropertyMap.getString(String)
org.micromanager.UserProfile.getStringArray(Class<?>, String, String[]) use getSettings(c).getStringList(key, fallback) instead
org.micromanager.PropertyMap.getStringArray(String)
org.micromanager.PropertyMap.getStringArray(String, String[])
org.micromanager.data.DataManager.getSummaryMetadataBuilder() Use DataManager.summaryMetadataBuilder() instead
org.micromanager.data.Coords.getTime() Due to looking like the physical time rather than an index. Use getTmePoint
org.micromanager.display.DisplaySettings.ContrastSettings.isVisible() Use isVisible
org.micromanager.data.DataManager.loadPropertyMap(String) use PropertyMaps.loadJSON(File) instead
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.magnification(Double)
org.micromanager.PositionListManager.markCurrentPosition() since this function completely depends on the PositionListDlg.
org.micromanager.data.Coords.matches(Coords) Use equality (after removing specific axes) instead
org.micromanager.PropertyMap.merge(PropertyMap)
org.micromanager.PropertyMap.PropertyMapBuilder.putBoolean(String, Boolean)
org.micromanager.PropertyMap.Builder.putBooleanArray(String, Boolean[]) Use PropertyMap.Builder.putBooleanList(java.lang.String, boolean...) instead.
org.micromanager.PropertyMap.PropertyMapBuilder.putBooleanArray(String, Boolean[])
org.micromanager.PropertyMap.PropertyMapBuilder.putDouble(String, Double)
org.micromanager.PropertyMap.Builder.putDoubleArray(String, Double[]) Use PropertyMap.Builder.putDoubleList(java.lang.String, double...) instead.
org.micromanager.PropertyMap.PropertyMapBuilder.putDoubleArray(String, Double[])
org.micromanager.PropertyMap.Builder.putInt(String, Integer) Use PropertyMap.Builder.putInteger(java.lang.String, java.lang.Integer) instead.
org.micromanager.PropertyMap.PropertyMapBuilder.putInt(String, Integer)
org.micromanager.PropertyMap.Builder.putIntArray(String, Integer[]) Use PropertyMap.Builder.putIntegerList(java.lang.String, int...) instead.
org.micromanager.PropertyMap.PropertyMapBuilder.putIntArray(String, Integer[])
org.micromanager.PropertyMap.PropertyMapBuilder.putLong(String, Long)
org.micromanager.PropertyMap.Builder.putLongArray(String, Long[]) Use PropertyMap.Builder.putLongList(java.lang.String, long...) instead.
org.micromanager.PropertyMap.PropertyMapBuilder.putLongArray(String, Long[])
org.micromanager.PropertyMap.PropertyMapBuilder.putPropertyMap(String, PropertyMap)
org.micromanager.PropertyMap.PropertyMapBuilder.putString(String, String)
org.micromanager.PropertyMap.Builder.putStringArray(String, String[]) Use PropertyMap.Builder.putStringList(java.lang.String, java.lang.String...) instead.
org.micromanager.PropertyMap.PropertyMapBuilder.putStringArray(String, String[])
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.safeUpdateChannelColor(Color, int)
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.safeUpdateContrastSettings(DisplaySettings.ContrastSettings, int)
org.micromanager.data.Datastore.save(Component) Use Datastore.save(Component, boolean) instead
org.micromanager.PropertyMap.save(String)
org.micromanager.UserProfile.setBoolean(Class<?>, String, Boolean) use getSettings(c).putBoolean(key, value) instead
org.micromanager.UserProfile.setBooleanArray(Class<?>, String, Boolean[]) use getSettings(c).putBooleanList(key, value) instead
org.micromanager.CompatibilityInterface.setCameraTransform(AffineTransform, String) - Use core.setPixelSizeAffine(config, DoubleVector transform) instead
org.micromanager.display.AbstractDataViewer.setDisplayedImageTo(Coords) user code should call setDisplayPosition
org.micromanager.display.DataViewer.setDisplayedImageTo(Coords) use DataViewer.setDisplayPosition(Coords) instead
org.micromanager.UserProfile.setDouble(Class<?>, String, Double) use getSettings(c).putDouble(key, value) instead
org.micromanager.UserProfile.setDoubleArray(Class<?>, String, Double[]) use getSettings(c).putDoubleList(key, value) instead
org.micromanager.UserProfile.setInt(Class<?>, String, Integer) use getSettings(c).putInteger(key, value) instead
org.micromanager.UserProfile.setIntArray(Class<?>, String, Integer[]) use getSettings(c).putIntegerList(key, value) instead
org.micromanager.SnapLiveManager.setLiveMode(boolean)
org.micromanager.UserProfile.setLong(Class<?>, String, Long) use getSettings(c).putLong(key, value) instead
org.micromanager.UserProfile.setLongArray(Class<?>, String, Long[]) use getSettings(c).putLongList(key, value) instead
org.micromanager.display.DisplayWindow.setMagnification(double) use DisplayWindow.setZoom(double) instead
org.micromanager.UserProfile.setString(Class<?>, String, String) use getSettings(c).putString(key, value) instead
org.micromanager.UserProfile.setStringArray(Class<?>, String, String[]) use getSettings(c).putStringList(key, value) instead
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.shouldAutostretch(Boolean)
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.shouldScaleWithROI(Boolean)
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.shouldSyncChannels(Boolean)
org.micromanager.data.Coords.Builder.time(int) Due to being confusing with physical time.
org.micromanager.display.DisplayWindow.toggleFullScreen() use DisplayWindow.setFullScreen(boolean) instead
org.micromanager.data.Metadata.Builder.uuid() Use Metadata.Builder.generateUUID().
org.micromanager.data.Metadata.MetadataBuilder.uuid()
org.micromanager.display.DisplaySettings.DisplaySettingsBuilder.zoom(Double)

Deprecated Constructors

Constructor and Description
org.micromanager.acquisition.ChannelSpec() Use Builder.build() instead for a default ChannelSpec
org.micromanager.StagePosition() Use StagePosition.create1D(java.lang.String, double) or StagePosition.create2D(java.lang.String, double, double) instead.
org.micromanager.PropertyMap.TypeMismatchException(String) Constructor should not have been part of API.

Deprecated Enum Constants

Enum Constant and Description
org.micromanager.display.DisplaySettings.ColorMode.SPECTRUM