ScriptInterface

```
public interface ScriptInterface
```
Interface to execute commands in the main panel. Implemented by MMStudio and available as the gui object in the Beanshell scripting panel. Most functions throw MMScriptException

Method Summary

All Methods Instance Methods Abstract Methods Deprecated Methods
Modifier and Type	Method and Description
`java.lang.Boolean`	`acquisitionExists(java.lang.String name)` Checks whether an acquisition with the given name already exists.
`void`	`addImageProcessor(DataProcessor<mmcorej.TaggedImage> processor)` Adds an image processor to the DataProcessor pipeline.
`void`	`addImageToAcquisition(java.lang.String name, int frame, int channel, int slice, int position, mmcorej.TaggedImage taggedImg)` Inserts image into the data set.
`void`	`addMMBackgroundListener(java.awt.Component frame)` Lets Components register themselves so that their background can be manipulated by the Micro-Manager UI.
`void`	`addMMListener(MMListenerInterface newL)` Allows MMListeners to register themselves so that they will receive alerts as defined in the MMListenerInterface
`void`	`addToAlbum(mmcorej.TaggedImage image)` Add a TaggedImage to an album; creates a new album if the image and current album do not match in image dimensions, bits per pixel, bytes per pixel, or number of channels.
`void`	`attachRunnable(int frame, int position, int channel, int slice, java.lang.Runnable runnable)` Attach a runnable to the acquisition engine.
`void`	`autostretchCurrentWindow()` Autostretch each histogram for the currently-active window, as if the "Auto" button had been clicked for each one.
`void`	`clearMessageWindow()` Clears scripting console output window.
`void`	`clearRunnables()` Remove runnables from the acquisition engine
`void`	`closeAcquisition(java.lang.String name)` Closes the acquisition.
`void`	`closeAcquisitionWindow(java.lang.String acquisitionName)` Closes the image window corresponding to the acquisition.
`void`	`closeAllAcquisitions()` Closes all currently open acquisitions.
`java.lang.String`	`createAcquisition(org.json.JSONObject summaryMetadata, boolean diskCached, boolean displayOff)` Deprecated. Use openAcquisition() instead.
`boolean`	`displayImage(mmcorej.TaggedImage image)` Show a TaggedImage in the snap/live window (uses current camera settings to figure out the shape of the image)
`void`	`enableLiveMode(boolean b)` Turn live mode on or off (equivalent to pressing the Live mode button).
`void`	`enableRoiButtons(boolean enabled)` Enabled or disable the ROI buttons on the main window.
`org.micromanager.dialogs.AcqControlDlg`	`getAcqDlg()` Deprecated. Use the get/setAcquisitionSettings() interface instead.
`org.micromanager.acquisition.MMAcquisition`	`getAcquisition(java.lang.String name)` Deprecated. Because it returns an internal object that is subject to change.
`IAcquisitionEngine2010`	`getAcquisitionEngine2010()`
`int`	`getAcquisitionImageBitDepth(java.lang.String acqName)` Returns the number of bits used per pixel
`int`	`getAcquisitionImageByteDepth(java.lang.String acqName)` Returns the number of bytes used per pixel
`ImageCache`	`getAcquisitionImageCache(java.lang.String acquisitionName)` Get a reference to the ImageCache object associated with the acquisition.
`int`	`getAcquisitionImageHeight(java.lang.String acqName)` Returns the width (in pixels) of images in this acquisition
`int`	`getAcquisitionImageWidth(java.lang.String acqName)` Returns the width (in pixels) of images in this acquisition
`int`	`getAcquisitionMultiCamNumChannels(java.lang.String acqName)` Returns boolean specifying whether multiple cameras used in this acquisition
`java.lang.String[]`	`getAcquisitionNames()` Gets an Array with names of all open acquisitions
`java.lang.String`	`getAcquisitionPath()` Return the current acquisition path, or null if not applicable
`SequenceSettings`	`getAcquisitionSettings()` Return current acquisition settings
`Autofocus`	`getAutofocus()` Currently active autofocus device (can be either a Java or C++ coded device).
`org.micromanager.utils.AutofocusManager`	`getAutofocusManager()`
`java.awt.Color`	`getBackgroundColor()` Returns the current color of the main window so that it can be used in derived windows/plugins as well
`java.lang.String`	`getBackgroundStyle()`
`ImageCache`	`getCacheForWindow(ij.gui.ImageWindow window)` Given an ImageWindow, return the ImageCache associated with it.
`double`	`getChannelExposureTime(java.lang.String channelGroup, java.lang.String channel, double defaultExp)` Returns exposure time for the desired preset in the given channelgroup Acquires its info from the preferences Same thing is used in MDA window, but this class keeps its own copy
`java.lang.String`	`getCurrentAlbum()` Returns the name of the current album (i.e.
`boolean`	`getHideMDADisplayOption()`
`java.util.List<DataProcessor<mmcorej.TaggedImage>>`	`getImageProcessorPipeline()` Retrieve a copy of the current DataProcessor pipeline.
`mmcorej.CMMCore`	`getMMCore()` Provides access to the Core and its functionality.
`PositionList`	`getPositionList()` Returns a copy of the current PositionList, the one used by the Acquisition Protocol
`java.awt.Rectangle`	`getROI()` Get the default camera's ROI -- a convenience function.
`ij.gui.ImageWindow`	`getSnapLiveWin()` Returns the ImageJ ImageWindow instance that is used for Snap and Live display.
`java.lang.String`	`getUniqueAcquisitionName(java.lang.String stem)` Returns a name beginning with stem that is not yet used.
`java.lang.String`	`getVersion()`
`org.micromanager.positionlist.PositionListDlg`	`getXYPosListDlg()` Deprecated. Use the get/setPositionList() interface instead.
`java.lang.String`	`getXYStageName()` There can be multiple XY stage devices in a system.
`java.awt.geom.Point2D.Double`	`getXYStagePosition()` Obtain the current XY stage position.
`void`	`initializeAcquisition(java.lang.String name, int width, int height, int bytesPerPixel, int bitDepth)` Set up image physical dimensions for the data set that has already been opened.
`java.lang.String`	`installAutofocusPlugin(java.lang.String className)` Installs an autofocus plugin class from the class path.
`boolean`	`isAcquisitionRunning()` Returns true when an acquisition is currently running (note: this function will not return true if live mode, snap, or "Camera --> Album" is currently running
`boolean`	`isLiveModeOn()` Determines whether live mode is currently running.
`boolean`	`isPaused()` Returns true if the acquisition is currently paused.
`void`	`loadAcquisition(java.lang.String path)` Loads setting for Acquisition Dialog from file Will open Acquisition Dialog when it is not open yet
`void`	`logError(java.lang.Exception e)` Writes a stacktrace to the Micro-Manager log.
`void`	`logError(java.lang.Exception e, java.lang.String msg)` Writes the stacktrace and a message to the Micro-Manager log (Corelog.txt).
`void`	`logError(java.lang.String msg)` Writes an error to the Micro-Manager log (same as logMessage).
`void`	`logMessage(java.lang.String msg)` Adds a message to the Micro-Manager log (found in Corelogtxt).
`void`	`logStartupProperties()` Write various properties of MM and the OS to the log.
`void`	`makeActive()`
`void`	`markCurrentPosition()` Opens the XYPositionList when it is not opened.
`void`	`message(java.lang.String text)` Displays text in the scripting console output window.
`void`	`openAcquisition(java.lang.String name, java.lang.String rootDir, int nrFrames, int nrChannels, int nrSlices, int nrPositions, boolean show, boolean save)` Opens a new acquisition data set
`java.lang.String`	`openAcquisitionData(java.lang.String location, boolean inRAM)` Open an existing data set.
`java.lang.String`	`openAcquisitionData(java.lang.String location, boolean inRAM, boolean show)` Open an existing data set.
`void`	`promptToSaveAcquisition(java.lang.String name, boolean prompt)` Display dialog to save data for one of the currently open acquisitions
`void`	`refreshGUI()` Brings GUI up to date with the recent changes in the mmcore.
`void`	`refreshGUIFromCache()` Brings GUI up to date with the recent changes in the mmcore.
`void`	`registerForEvents(java.lang.Object obj)` Request that the given object be added to our EventBus for notification of events occurring.
`void`	`registerProcessorClass(java.lang.Class<? extends DataProcessor<mmcorej.TaggedImage>> processorClass, java.lang.String name)` Register a new DataProcessor class with the Acquisition Engine.
`void`	`removeImageProcessor(DataProcessor<mmcorej.TaggedImage> taggedImageProcessor)` Removes an image processor from the DataProcessor pipeline.
`void`	`removeMMBackgroundListener(java.awt.Component frame)` Lets Components remove themselves from the list whose background gets changed by the Micro-Manager UI.
`void`	`removeMMListener(MMListenerInterface oldL)` Allows MMListeners to remove themselves
`java.lang.String`	`runAcquisition()` Executes Acquisition with current settings Will open the Acquisition Dialog when it is not open yet Returns after Acquisition finishes Note that this function should not be executed on the EDT (which is the thread running the UI).
`java.lang.String`	`runAcquisition(java.lang.String name, java.lang.String root)` Executes Acquisition with current settings but allows for changing the data path.
`void`	`saveConfigPresets()` Save current configuration
`void`	`setAcquisitionAddImageAsynchronous(java.lang.String name)` Change an acquisition so that adding images to it is done asynchronously.
`void`	`setAcquisitionProperty(java.lang.String acqName, java.lang.String propertyName, java.lang.String value)` Sets custom property attached to the acquisition summary
`void`	`setAcquisitionSettings(SequenceSettings settings)` Apply new acquisition settings
`void`	`setBackgroundStyle(java.lang.String backgroundType)` Sets the background color of the GUI and all its registered components to the selected backGroundType
`void`	`setChannelColor(java.lang.String title, int channel, java.awt.Color color)` Sets the color of the specified channel in the image viewer.
`void`	`setChannelContrast(java.lang.String title, int channel, int min, int max)` Sets min (black) and max (white or the channel's color) pixel value clipping levels for each channel.
`void`	`setChannelExposureTime(java.lang.String channelGroup, java.lang.String channel, double exposure)` Updates the exposure time associated with the given preset If the channelgroup and channel name match the current state the exposure time will also be updated
`void`	`setChannelName(java.lang.String title, int channel, java.lang.String name)` Sets the channel name (label)
`void`	`setConfigChanged(boolean status)` lets the GUI know that the current configuration has been changed.
`void`	`setContrastBasedOnFrame(java.lang.String title, int frame, int slice)` Autoscales contrast for each channel at the current position based on pixel values at the current slice and frame
`void`	`setImageProcessorPipeline(java.util.List<DataProcessor<mmcorej.TaggedImage>> pipeline)` Replace the current DataProcessor pipeline with the provided one.
`void`	`setImageProperty(java.lang.String acqName, int frame, int channel, int slice, java.lang.String propName, java.lang.String value)` Sets property attached to an individual image.
`void`	`setImageSavingFormat(java.lang.Class imageSavingClass)` Set the format for saving images to disk.
`void`	`setPause(boolean state)` Pause/Unpause a running acquistion
`void`	`setPositionList(PositionList pl)` Makes this the 'current' PositionList, i.e., the one used by the Acquisition Protocol Replaces the list in the PositionList Window It will open a position list dialog if it was not already open.
`void`	`setRelativeStagePosition(double z)` Move default Focus (Z) relative to current position and block until done
`void`	`setRelativeXYStagePosition(double x, double y)` Move default XY stage relative to current position and block until done.
`void`	`setROI(java.awt.Rectangle r)` Set the default camera's ROI -- a convenience function.
`void`	`setStagePosition(double z)` Move default Focus (Z) and block until done
`void`	`setXYOrigin(double x, double y)` Assigns the current stage position of the default xy-stage to be (x,y), thereby offseting the coordinates of all other positions.
`void`	`setXYStagePosition(double x, double y)` Move default XY stage and block until done.
`void`	`showAutofocusDialog()` Shows the dialog with options for the currently active autofocus device.
`void`	`showError(java.lang.Exception e)` Shows and logs a Java exception.
`void`	`showError(java.lang.Exception e, java.awt.Component parent)` Shows and logs a Java exception.
`void`	`showError(java.lang.Exception e, java.lang.String msg)` Shows an error in the UI and logs stacktrace to the Micro-Manager log.
`void`	`showError(java.lang.Exception e, java.lang.String msg, java.awt.Component parent)` Shows an error in the UI and logs stacktrace to the Micro-Manager log.
`void`	`showError(java.lang.String msg)` Shows an error message in the UI and logs to the Micro-Manager log.
`void`	`showError(java.lang.String msg, java.awt.Component parent)` Shows an error message in the UI and logs to the Micro-Manager log.
`void`	`showMessage(java.lang.String msg)` Shows a message in the UI.
`void`	`showMessage(java.lang.String msg, java.awt.Component parent)` Shows a message in the UI.
`void`	`showXYPositionList()` shows the position list dialog
`void`	`sleep(long ms)` Request a pause in script execution for the specified number of milliseconds.
`void`	`snapAndAddImage(java.lang.String name, int frame, int channel, int z, int position)` Snaps an image with the current settings and places pixels in the specified position of the Micro-Manager Image viewer
`void`	`snapSingleImage()` Snaps image and displays in AcqWindow.
`void`	`unregisterForEvents(java.lang.Object obj)` Unregister the given object from EventBus notfications
`boolean`	`versionLessThan(java.lang.String version)` Displays an error message and returns true if the run-time Micro-Manager version is less than the one specified.

- Method Detail
  - sleep
```
void sleep(long ms)
    throws org.micromanager.utils.MMScriptException
```
    Request a pause in script execution for the specified number of milliseconds. Most systems will guarantee a pause of at least the desired duration, but may wait longer than requested before continuing execution.
    
    Parameters:
    
    ms - Time in millisecond that the script should pause
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - message
```
void message(java.lang.String text)
      throws org.micromanager.utils.MMScriptException
```
    Displays text in the scripting console output window.
    
    Parameters:
    
    text -
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - clearMessageWindow
```
void clearMessageWindow()
                 throws org.micromanager.utils.MMScriptException
```
    Clears scripting console output window.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - refreshGUI
```
void refreshGUI()
```
    Brings GUI up to date with the recent changes in the mmcore.
  - refreshGUIFromCache
```
void refreshGUIFromCache()
```
    Brings GUI up to date with the recent changes in the mmcore. Does not communicate with hardware, only checks Cache
  - snapSingleImage
```
void snapSingleImage()
```
    Snaps image and displays in AcqWindow. Opens a new AcqWindow when current one is not open. Calling this function is the same as pressing the "Snap" button on the main Micro-manager GUI
  - openAcquisition
```
void openAcquisition(java.lang.String name,
                     java.lang.String rootDir,
                     int nrFrames,
                     int nrChannels,
                     int nrSlices,
                     int nrPositions,
                     boolean show,
                     boolean save)
              throws org.micromanager.utils.MMScriptException
```
    Opens a new acquisition data set
    
    Parameters:
    
    name - - Name of the data set
    
    rootDir - - Directory where the new data set is going to be created
    
    nrFrames - - Number of Frames (time points) in this acquisition
    
    nrChannels - - Number of Channels in this acquisition
    
    nrSlices - - Number of Slices (Z-positions) in this acquisition
    
    nrPositions - Number of (XY) Positions in this acquisition.
    
    show - Whether or not to show this acquisition.
    
    save - Whether or not save data during acquisition.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - createAcquisition
```
@Deprecated
java.lang.String createAcquisition(org.json.JSONObject summaryMetadata,
                                               boolean diskCached,
                                               boolean displayOff)
```
    Deprecated. Use openAcquisition() instead.
    
    Another way to create data set, an alternative to the openAcquisition(String name, String rootDir, int nrFrames, int nrChannels, int nrSlices, int nrPositions, boolean show, boolean save) The caller is responsible for providing all required metadata within the summaryMetadata argument
    
    Parameters:
    
    summaryMetadata - The metadata describing the acquisition parameters
    
    diskCached - True if images are cached on disk; false if they are kept in RAM only.
    
    displayOff - True if no display is to be created or shown.
    
    Returns:
  - initializeAcquisition
```
void initializeAcquisition(java.lang.String name,
                           int width,
                           int height,
                           int bytesPerPixel,
                           int bitDepth)
                    throws org.micromanager.utils.MMScriptException
```
    Set up image physical dimensions for the data set that has already been opened. Once dimensions of the image has been set, they can't be changed, i.e. subsequent calls to this method will generate an error. Typically there is no need to call this method, except when display options have to be set before the first image is inserted. If this method is not explicitly called after openAcquisition(), the image dimensions will be automatically initialized based on the first image inserted in the data set.
    
    Parameters:
    
    name - - Name of the data set
    
    width - - Image width in pixels
    
    height - - Image height in pixels
    
    bytesPerPixel - - Number of bytes per pixel
    
    bitDepth - - Dynamic range in bits per pixel
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - addImageToAcquisition
```
void addImageToAcquisition(java.lang.String name,
                           int frame,
                           int channel,
                           int slice,
                           int position,
                           mmcorej.TaggedImage taggedImg)
                    throws org.micromanager.utils.MMScriptException
```
    Inserts image into the data set.
    
    Parameters:
    
    name - - data set name
    
    frame - - 0 based frame number
    
    channel - - 0 based channel number
    
    slice - - 0 based (z) slice number
    
    position - - 0 based position number
    
    taggedImg - Tagged Image (image with associated metadata)
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setAcquisitionAddImageAsynchronous
```
void setAcquisitionAddImageAsynchronous(java.lang.String name)
                                 throws org.micromanager.utils.MMScriptException
```
    Change an acquisition so that adding images to it is done asynchronously. All calls to e.g. addImageToAcquisition() and other similar functions will return nearly-instantly.
    
    Parameters:
    
    name - of acquisition
    
    Throws:
    
    org.micromanager.utils.MMScriptException - if the specified acquisition does not exist.
  - snapAndAddImage
```
void snapAndAddImage(java.lang.String name,
                     int frame,
                     int channel,
                     int z,
                     int position)
              throws org.micromanager.utils.MMScriptException
```
    Snaps an image with the current settings and places pixels in the specified position of the Micro-Manager Image viewer
    
    Parameters:
    
    name - Name of the acquisition.
    
    frame - Frame number (time point, 0-based) in which this image should be inserted.
    
    channel - Channel number (0-based) in which this image should be inserted.
    
    z - Slice number (0-based) in which this image should be inserted.
    
    position - Position number (0-based) in which this image should be inserted.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisition
```
@Deprecated
org.micromanager.acquisition.MMAcquisition getAcquisition(java.lang.String name)
                                                               throws org.micromanager.utils.MMScriptException
```
    Deprecated. Because it returns an internal object that is subject to change.
    
    Provides access to the data set through the MMAcquisition interface. Typically there is no need to use this low-level method and interfere with the default acquisition execution. Intended use is within advanced plugins.
    
    Parameters:
    
    name - - data set name
    
    Returns:
    
    MMAcqusition object
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getUniqueAcquisitionName
```
java.lang.String getUniqueAcquisitionName(java.lang.String stem)
```
    Returns a name beginning with stem that is not yet used.
    
    Parameters:
    
    stem - Base name from which a unique name will be constructed
    
    Returns:
    
    a name beginning with stem that is not yet used
  - getCurrentAlbum
```
java.lang.String getCurrentAlbum()
```
    Returns the name of the current album (i.e. the most recently created one) In addition to their use through the scripting interface, Albums are used by the "Camera --> Album" button in the main window of Micro-Manager and the "--> Album" button on the snap/live window
    
    Returns:
    
    Name of the current Album.
  - addToAlbum
```
void addToAlbum(mmcorej.TaggedImage image)
         throws org.micromanager.utils.MMScriptException
```
    Add a TaggedImage to an album; creates a new album if the image and current album do not match in image dimensions, bits per pixel, bytes per pixel, or number of channels. The current album is the most recently created one Albums are also used by the "Camera --> Album" button in the main window of Micro-Manager and the "--> Album" button on the snap/live window
    
    Parameters:
    
    image - - TaggedImage to be added to album
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - acquisitionExists
```
java.lang.Boolean acquisitionExists(java.lang.String name)
```
    Checks whether an acquisition with the given name already exists.
    
    Parameters:
    
    name - name to be tested for existence
    
    Returns:
    
    true when name already exists
  - closeAcquisition
```
void closeAcquisition(java.lang.String name)
               throws org.micromanager.utils.MMScriptException
```
    Closes the acquisition. After this command metadata is complete, all the references to this data set are cleaned-up, and no additional images can be added to the acquisition Does not close the window in which the acquisition data is displayed
    
    Parameters:
    
    name - name of acquisition to be closed
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - closeAllAcquisitions
```
void closeAllAcquisitions()
```
    Closes all currently open acquisitions.
  - getAcquisitionNames
```
java.lang.String[] getAcquisitionNames()
```
    Gets an Array with names of all open acquisitions
    
    Returns:
    
    Arrays with names of all acquisitions that are currently open
  - getAcquisitionImageWidth
```
int getAcquisitionImageWidth(java.lang.String acqName)
                      throws org.micromanager.utils.MMScriptException
```
    Returns the width (in pixels) of images in this acquisition
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisitionImageHeight
```
int getAcquisitionImageHeight(java.lang.String acqName)
                       throws org.micromanager.utils.MMScriptException
```
    Returns the width (in pixels) of images in this acquisition
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisitionImageBitDepth
```
int getAcquisitionImageBitDepth(java.lang.String acqName)
                         throws org.micromanager.utils.MMScriptException
```
    Returns the number of bits used per pixel
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisitionImageByteDepth
```
int getAcquisitionImageByteDepth(java.lang.String acqName)
                          throws org.micromanager.utils.MMScriptException
```
    Returns the number of bytes used per pixel
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisitionMultiCamNumChannels
```
int getAcquisitionMultiCamNumChannels(java.lang.String acqName)
                               throws org.micromanager.utils.MMScriptException
```
    Returns boolean specifying whether multiple cameras used in this acquisition
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setAcquisitionProperty
```
void setAcquisitionProperty(java.lang.String acqName,
                            java.lang.String propertyName,
                            java.lang.String value)
                     throws org.micromanager.utils.MMScriptException
```
    Sets custom property attached to the acquisition summary
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setImageProperty
```
void setImageProperty(java.lang.String acqName,
                      int frame,
                      int channel,
                      int slice,
                      java.lang.String propName,
                      java.lang.String value)
               throws org.micromanager.utils.MMScriptException
```
    Sets property attached to an individual image.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - runAcquisition
```
java.lang.String runAcquisition()
                         throws org.micromanager.utils.MMScriptException
```
    Executes Acquisition with current settings Will open the Acquisition Dialog when it is not open yet Returns after Acquisition finishes Note that this function should not be executed on the EDT (which is the thread running the UI).
    
    Returns:
    
    The name of the acquisition created.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - runAcquisition
```
java.lang.String runAcquisition(java.lang.String name,
                                java.lang.String root)
                         throws org.micromanager.utils.MMScriptException
```
    Executes Acquisition with current settings but allows for changing the data path. Will open the Acquisition Dialog when it is not open yet. Returns after Acquisition finishes. Note that this function should not be executed on the EDT (which is the thread running the UI).
    
    Parameters:
    
    name - Name of this acquisition.
    
    root - Place in the file system where data can be stored.
    
    Returns:
    
    The name of the acquisition created
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - loadAcquisition
```
void loadAcquisition(java.lang.String path)
              throws org.micromanager.utils.MMScriptException
```
    Loads setting for Acquisition Dialog from file Will open Acquisition Dialog when it is not open yet
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setPositionList
```
void setPositionList(PositionList pl)
              throws org.micromanager.utils.MMScriptException
```
    Makes this the 'current' PositionList, i.e., the one used by the Acquisition Protocol Replaces the list in the PositionList Window It will open a position list dialog if it was not already open.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getPositionList
```
PositionList getPositionList()
                      throws org.micromanager.utils.MMScriptException
```
    Returns a copy of the current PositionList, the one used by the Acquisition Protocol
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setChannelColor
```
void setChannelColor(java.lang.String title,
                     int channel,
                     java.awt.Color color)
              throws org.micromanager.utils.MMScriptException
```
    Sets the color of the specified channel in the image viewer. Only has an effect for images with 2 or more channels
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setChannelName
```
void setChannelName(java.lang.String title,
                    int channel,
                    java.lang.String name)
             throws org.micromanager.utils.MMScriptException
```
    Sets the channel name (label)
    
    Parameters:
    
    title - - acquisition name
    
    channel - - channel index
    
    name - - channel label
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setChannelExposureTime
```
void setChannelExposureTime(java.lang.String channelGroup,
                            java.lang.String channel,
                            double exposure)
```
    Updates the exposure time associated with the given preset If the channelgroup and channel name match the current state the exposure time will also be updated
    
    Parameters:
    
    channelGroup - -
    
    channel - - preset for which to change exposure time
    
    exposure - - desired exposure time
  - setChannelContrast
```
void setChannelContrast(java.lang.String title,
                        int channel,
                        int min,
                        int max)
                 throws org.micromanager.utils.MMScriptException
```
    Sets min (black) and max (white or the channel's color) pixel value clipping levels for each channel.
    
    Parameters:
    
    title - - acquisition name
    
    channel - - channel index (use 0 if there is only a single channel)
    
    min - - black clipping level
    
    max - - white clipping level
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setContrastBasedOnFrame
```
void setContrastBasedOnFrame(java.lang.String title,
                             int frame,
                             int slice)
                      throws org.micromanager.utils.MMScriptException
```
    Autoscales contrast for each channel at the current position based on pixel values at the current slice and frame
    
    Parameters:
    
    title - - acquisition name
    
    frame - - frame number
    
    slice - - slice number
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getChannelExposureTime
```
double getChannelExposureTime(java.lang.String channelGroup,
                              java.lang.String channel,
                              double defaultExp)
```
    Returns exposure time for the desired preset in the given channelgroup Acquires its info from the preferences Same thing is used in MDA window, but this class keeps its own copy
    
    Parameters:
    
    channelGroup -
    
    channel - -
    
    defaultExp - - default value
    
    Returns:
    
    exposure time
  - closeAcquisitionWindow
```
void closeAcquisitionWindow(java.lang.String acquisitionName)
                     throws org.micromanager.utils.MMScriptException
```
    Closes the image window corresponding to the acquisition. If being used along with closeAcquisitiion, this method should be called first
    
    Parameters:
    
    acquisitionName - - Name of the acquisition
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getXYStagePosition
```
java.awt.geom.Point2D.Double getXYStagePosition()
                                         throws org.micromanager.utils.MMScriptException
```
    Obtain the current XY stage position. Returns a point in device coordinates in microns.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setStagePosition
```
void setStagePosition(double z)
               throws org.micromanager.utils.MMScriptException
```
    Move default Focus (Z) and block until done
    
    Parameters:
    
    z - absolute z position
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setRelativeStagePosition
```
void setRelativeStagePosition(double z)
                       throws org.micromanager.utils.MMScriptException
```
    Move default Focus (Z) relative to current position and block until done
    
    Parameters:
    
    z -
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setXYStagePosition
```
void setXYStagePosition(double x,
                        double y)
                 throws org.micromanager.utils.MMScriptException
```
    Move default XY stage and block until done.
    
    Parameters:
    
    x - - coordinate in um
    
    y - - coordinate in um
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setRelativeXYStagePosition
```
void setRelativeXYStagePosition(double x,
                                double y)
                         throws org.micromanager.utils.MMScriptException
```
    Move default XY stage relative to current position and block until done.
    
    Parameters:
    
    x - - coordinate in um
    
    y - - coordinate in um
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getXYStageName
```
java.lang.String getXYStageName()
```
    There can be multiple XY stage devices in a system. This function returns the name of the currently active one
    
    Returns:
    
    Name of the active XYStage device
  - setXYOrigin
```
void setXYOrigin(double x,
                 double y)
          throws org.micromanager.utils.MMScriptException
```
    Assigns the current stage position of the default xy-stage to be (x,y), thereby offseting the coordinates of all other positions.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - saveConfigPresets
```
void saveConfigPresets()
```
    Save current configuration
  - getSnapLiveWin
```
ij.gui.ImageWindow getSnapLiveWin()
```
    Returns the ImageJ ImageWindow instance that is used for Snap and Live display.
  - getCacheForWindow
```
ImageCache getCacheForWindow(ij.gui.ImageWindow window)
                      throws java.lang.IllegalArgumentException
```
    Given an ImageWindow, return the ImageCache associated with it.
    
    Throws:
    
    java.lang.IllegalArgumentException
  - installAutofocusPlugin
```
java.lang.String installAutofocusPlugin(java.lang.String className)
```
    Installs an autofocus plugin class from the class path.
  - getMMCore
```
mmcorej.CMMCore getMMCore()
```
    Provides access to the Core and its functionality.
    
    Returns:
    
    Micro-Manager core object.
  - getAutofocus
```
Autofocus getAutofocus()
```
    Currently active autofocus device (can be either a Java or C++ coded device).
    
    Returns:
    
    currently active autofocus device
  - showAutofocusDialog
```
void showAutofocusDialog()
```
    Shows the dialog with options for the currently active autofocus device.
  - logMessage
```
void logMessage(java.lang.String msg)
```
    Adds a message to the Micro-Manager log (found in Corelogtxt).
    
    Parameters:
    
    msg - - message to be added to the log
  - showMessage
```
void showMessage(java.lang.String msg)
```
    Shows a message in the UI.
    
    Parameters:
    
    msg - - message to be shown
  - showMessage
```
void showMessage(java.lang.String msg,
                 java.awt.Component parent)
```
    Shows a message in the UI.
    
    Parameters:
    
    msg - - message to be shown
    
    parent - - parent component over which this message should be centered
  - logError
```
void logError(java.lang.Exception e,
              java.lang.String msg)
```
    Writes the stacktrace and a message to the Micro-Manager log (Corelog.txt).
    
    Parameters:
    
    e - - Java exception to be logged
    
    msg - - message to be shown
  - logError
```
void logError(java.lang.Exception e)
```
    Writes a stacktrace to the Micro-Manager log.
    
    Parameters:
    
    e - - Java exception to be logged
  - logError
```
void logError(java.lang.String msg)
```
    Writes an error to the Micro-Manager log (same as logMessage).
    
    Parameters:
    
    msg - - message to be logged
  - showError
```
void showError(java.lang.Exception e,
               java.lang.String msg)
```
    Shows an error in the UI and logs stacktrace to the Micro-Manager log.
    
    Parameters:
    
    e - - Java exception to be shown and logged
    
    msg - - Error message to be shown and logged
  - showError
```
void showError(java.lang.Exception e)
```
    Shows and logs a Java exception.
    
    Parameters:
    
    e - - Java excpetion to be shown and logged
  - showError
```
void showError(java.lang.String msg)
```
    Shows an error message in the UI and logs to the Micro-Manager log.
    
    Parameters:
    
    msg - - error message to be shown and logged
  - showError
```
void showError(java.lang.Exception e,
               java.lang.String msg,
               java.awt.Component parent)
```
    Shows an error in the UI and logs stacktrace to the Micro-Manager log.
    
    Parameters:
    
    e - - Java exception to be shown and logged
    
    msg - - Error message to be shown and logged
    
    parent - - frame in which to show dialog, or null for caller
  - showError
```
void showError(java.lang.Exception e,
               java.awt.Component parent)
```
    Shows and logs a Java exception.
    
    Parameters:
    
    e - - Java exception to be shown and logged
    
    parent - - frame in which to show dialog, or null for caller
  - showError
```
void showError(java.lang.String msg,
               java.awt.Component parent)
```
    Shows an error message in the UI and logs to the Micro-Manager log.
    
    Parameters:
    
    msg - - error message to be shown and logged
    
    parent - - frame in which to show dialog, or null for caller
  - addMMListener
```
void addMMListener(MMListenerInterface newL)
```
    Allows MMListeners to register themselves so that they will receive alerts as defined in the MMListenerInterface
    
    Parameters:
    
    newL -
  - removeMMListener
```
void removeMMListener(MMListenerInterface oldL)
```
    Allows MMListeners to remove themselves
    
    Parameters:
    
    oldL -
  - addMMBackgroundListener
```
void addMMBackgroundListener(java.awt.Component frame)
```
    Lets Components register themselves so that their background can be manipulated by the Micro-Manager UI.
    
    Parameters:
    
    frame - Component to which the listener should be added.
  - removeMMBackgroundListener
```
void removeMMBackgroundListener(java.awt.Component frame)
```
    Lets Components remove themselves from the list whose background gets changed by the Micro-Manager UI.
    
    Parameters:
    
    frame - Component from which the listener should be removed.
  - getBackgroundColor
```
java.awt.Color getBackgroundColor()
```
    Returns the current color of the main window so that it can be used in derived windows/plugins as well
    
    Returns:
    
    Current backgroundColor
  - displayImage
```
boolean displayImage(mmcorej.TaggedImage image)
```
    Show a TaggedImage in the snap/live window (uses current camera settings to figure out the shape of the image)
    
    Parameters:
    
    image - TaggedImage (pixel data and metadata tags) to be displayed
  - isLiveModeOn
```
boolean isLiveModeOn()
```
    Determines whether live mode is currently running.
    
    Returns:
    
    when true, live mode is running, when false live mode is not running.
  - enableLiveMode
```
void enableLiveMode(boolean b)
```
    Turn live mode on or off (equivalent to pressing the Live mode button).
    
    Parameters:
    
    b - true starts live mode, false stops live mode.
  - getROI
```
java.awt.Rectangle getROI()
                   throws org.micromanager.utils.MMScriptException
```
    Get the default camera's ROI -- a convenience function.
    
    Returns:
    
    default camera's ROI
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - setROI
```
void setROI(java.awt.Rectangle r)
     throws org.micromanager.utils.MMScriptException
```
    Set the default camera's ROI -- a convenience function.
    
    Parameters:
    
    r -
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisitionImageCache
```
ImageCache getAcquisitionImageCache(java.lang.String acquisitionName)
                             throws org.micromanager.utils.MMScriptException
```
    Get a reference to the ImageCache object associated with the acquisition.
    
    Parameters:
    
    acquisitionName - Name of the acquisition
    
    Returns:
    
    ImageCache object associated with the acquisition
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - markCurrentPosition
```
void markCurrentPosition()
```
    Opens the XYPositionList when it is not opened. Adds the current position to the list (same as pressing the "Mark" button in the XYPositionList)
  - getAcqDlg
```
@Deprecated
org.micromanager.dialogs.AcqControlDlg getAcqDlg()
```
    Deprecated. Use the get/setAcquisitionSettings() interface instead.
    
    Returns the Multi-Dimensional Acquisition Window. To show the window, call: AcqControlDlg dlg = gui.getAcqDlg(); dlg.setVisible(true);
    
    Returns:
    
    Handle to the MDA acquisition dialog
  - getXYPosListDlg
```
@Deprecated
org.micromanager.positionlist.PositionListDlg getXYPosListDlg()
```
    Deprecated. Use the get/setPositionList() interface instead.
    
    Returns the PositionList Dialog. If the Dialog did not yet exist, it will be created. The Dialog will not necessarily be shown, call the setVisibile method of the dialog to do so
    
    Returns:
    
    Handle to the positionList Dialog
  - isAcquisitionRunning
```
boolean isAcquisitionRunning()
```
    Returns true when an acquisition is currently running (note: this function will not return true if live mode, snap, or "Camera --> Album" is currently running
  - versionLessThan
```
boolean versionLessThan(java.lang.String version)
                 throws org.micromanager.utils.MMScriptException
```
    Displays an error message and returns true if the run-time Micro-Manager version is less than the one specified. Versions in Micro-Manager are of the format: major.minor.minute date where ' date' can be omitted Examples: 1.4.6 1.4.6 20110831 When a date is appended to a version number, it will be newer than the same version without a date
    
    Parameters:
    
    version - - minimum version needen to run this code
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - logStartupProperties
```
void logStartupProperties()
```
    Write various properties of MM and the OS to the log.
  - makeActive
```
void makeActive()
```
  - getAutofocusManager
```
org.micromanager.utils.AutofocusManager getAutofocusManager()
```
    Returns:
    
    the currently selected AutoFocusManger object
  - getBackgroundStyle
```
java.lang.String getBackgroundStyle()
```
    Returns:
    
    the current Micro-Manager background style--"Day" or "Night"
  - getVersion
```
java.lang.String getVersion()
```
    Returns:
    
    the currently running Micro-Manager version
  - setBackgroundStyle
```
void setBackgroundStyle(java.lang.String backgroundType)
```
    Sets the background color of the GUI and all its registered components to the selected backGroundType
    
    Parameters:
    
    backgroundType - either "Day" or "Night"
  - setConfigChanged
```
void setConfigChanged(boolean status)
```
    lets the GUI know that the current configuration has been changed. Activates the save button it status is true
    
    Parameters:
    
    status -
  - showXYPositionList
```
void showXYPositionList()
```
    shows the position list dialog
  - openAcquisitionData
```
java.lang.String openAcquisitionData(java.lang.String location,
                                     boolean inRAM)
                              throws org.micromanager.utils.MMScriptException
```
    Open an existing data set. Shows the acquisition in a window.
    
    Returns:
    
    The acquisition object.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - openAcquisitionData
```
java.lang.String openAcquisitionData(java.lang.String location,
                                     boolean inRAM,
                                     boolean show)
                              throws org.micromanager.utils.MMScriptException
```
    Open an existing data set.
    
    Returns:
    
    The name of the acquisition object.
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - enableRoiButtons
```
void enableRoiButtons(boolean enabled)
```
    Enabled or disable the ROI buttons on the main window.
  - setImageSavingFormat
```
void setImageSavingFormat(java.lang.Class imageSavingClass)
                   throws org.micromanager.utils.MMScriptException
```
    Set the format for saving images to disk. Images can be written to disk one per a file or multiple images per file. Using multiple images per file should be faster on most systems
    
    Parameters:
    
    imageSavingClass - use either org.micromanager.acquisition.TaggedImageStorageDiskDefault.class for single-image files of org.micromanager.acquisition.TaggedImageStorageMultipageTiff.class for multi-image files
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - getAcquisitionEngine2010
```
IAcquisitionEngine2010 getAcquisitionEngine2010()
```
  - getHideMDADisplayOption
```
boolean getHideMDADisplayOption()
```
  - addImageProcessor
```
void addImageProcessor(DataProcessor<mmcorej.TaggedImage> processor)
```
    Adds an image processor to the DataProcessor pipeline.
  - removeImageProcessor
```
void removeImageProcessor(DataProcessor<mmcorej.TaggedImage> taggedImageProcessor)
```
    Removes an image processor from the DataProcessor pipeline.
  - getImageProcessorPipeline
```
java.util.List<DataProcessor<mmcorej.TaggedImage>> getImageProcessorPipeline()
```
    Retrieve a copy of the current DataProcessor pipeline.
  - setImageProcessorPipeline
```
void setImageProcessorPipeline(java.util.List<DataProcessor<mmcorej.TaggedImage>> pipeline)
```
    Replace the current DataProcessor pipeline with the provided one.
  - registerProcessorClass
```
void registerProcessorClass(java.lang.Class<? extends DataProcessor<mmcorej.TaggedImage>> processorClass,
                            java.lang.String name)
```
    Register a new DataProcessor class with the Acquisition Engine. For example, if your processor class is named MyProcessor, then you would call this function as: gui.registerProcessorClass(MyProcessor.class, "My Processor");
  - setPause
```
void setPause(boolean state)
```
    Pause/Unpause a running acquistion
  - isPaused
```
boolean isPaused()
```
    Returns true if the acquisition is currently paused.
  - attachRunnable
```
void attachRunnable(int frame,
                    int position,
                    int channel,
                    int slice,
                    java.lang.Runnable runnable)
```
    Attach a runnable to the acquisition engine. Each index (f, p, c, s) can be specified. Passing a value of -1 should result in the runnable being attached at all values of that index. For example, if the first argument is -1, then the runnable should execute at every frame.
  - clearRunnables
```
void clearRunnables()
```
    Remove runnables from the acquisition engine
  - getAcquisitionSettings
```
SequenceSettings getAcquisitionSettings()
```
    Return current acquisition settings
  - setAcquisitionSettings
```
void setAcquisitionSettings(SequenceSettings settings)
```
    Apply new acquisition settings
  - getAcquisitionPath
```
java.lang.String getAcquisitionPath()
```
    Return the current acquisition path, or null if not applicable
  - promptToSaveAcquisition
```
void promptToSaveAcquisition(java.lang.String name,
                             boolean prompt)
                      throws org.micromanager.utils.MMScriptException
```
    Display dialog to save data for one of the currently open acquisitions
    
    Throws:
    
    org.micromanager.utils.MMScriptException
  - registerForEvents
```
void registerForEvents(java.lang.Object obj)
```
    Request that the given object be added to our EventBus for notification of events occurring. The available event types that subscribers can listen for is in the org.micromanager.api.events package.
  - unregisterForEvents
```
void unregisterForEvents(java.lang.Object obj)
```
    Unregister the given object from EventBus notfications
  - autostretchCurrentWindow
```
void autostretchCurrentWindow()
```
    Autostretch each histogram for the currently-active window, as if the "Auto" button had been clicked for each one.

Interface ScriptInterface

Method Summary

Method Detail

sleep

message

clearMessageWindow

refreshGUI

refreshGUIFromCache

snapSingleImage

openAcquisition

createAcquisition

initializeAcquisition

addImageToAcquisition

setAcquisitionAddImageAsynchronous

snapAndAddImage

getAcquisition

getUniqueAcquisitionName

getCurrentAlbum

addToAlbum

acquisitionExists

closeAcquisition

closeAllAcquisitions

getAcquisitionNames

getAcquisitionImageWidth

getAcquisitionImageHeight

getAcquisitionImageBitDepth

getAcquisitionImageByteDepth

getAcquisitionMultiCamNumChannels

setAcquisitionProperty

setImageProperty

runAcquisition

runAcquisition

loadAcquisition

setPositionList

getPositionList

setChannelColor

setChannelName

setChannelExposureTime

setChannelContrast

setContrastBasedOnFrame

getChannelExposureTime

closeAcquisitionWindow

getXYStagePosition

setStagePosition

setRelativeStagePosition

setXYStagePosition

setRelativeXYStagePosition

getXYStageName

setXYOrigin

saveConfigPresets

getSnapLiveWin

getCacheForWindow

installAutofocusPlugin

getMMCore

getAutofocus

showAutofocusDialog

logMessage

showMessage

showMessage

logError

logError

logError

showError

showError

showError

showError

showError

showError

addMMListener

removeMMListener

addMMBackgroundListener

removeMMBackgroundListener

getBackgroundColor

displayImage

isLiveModeOn

enableLiveMode

getROI

setROI

getAcquisitionImageCache

markCurrentPosition