org.micromanager.ndviewer.main

Class NDViewer

java.lang.Object

org.micromanager.ndviewer.main.NDViewer

All Implemented Interfaces:

NDViewerAPI

public class NDViewer
extends Object
implements NDViewerAPI

Field Summary

Fields

Modifier and Type	Field and Description
protected NDViewerDataSource	dataSource_
protected DataViewCoords	viewCoords_

Constructor Summary

Constructors

Constructor and Description
NDViewer(NDViewerDataSource cache, NDViewerAcqInterface acq, mmcorej.org.json.JSONObject summaryMD, double pixelSize, boolean rgb)
NDViewer(NDViewerDataSource cache, NDViewerAcqInterface acq, mmcorej.org.json.JSONObject summaryMD, double pixelSize, boolean rgb, String preferencesKey)

Method Summary

Modifier and Type	Method and Description
void	abortAcquisition()
void	addControlPanel(ControlsPanelInterface panel) Add a custom JPanel containing controls to the JTabbedPane on the right side of the image.
void	addSetImageHook(Consumer<HashMap<String,Object>> hook) Add a hook function that runs whenever setImage gets called, either programatically or by someone moving the scrollbars
void	channelSetActive(String channelName, boolean selected)
void	close() Forces the viewer to close, automatically aborting any acquisition in the process.
Object	getAxisPosition(String axis) Get the position that the scrollbar with the given label is currently at.
ViewerCanvas	getCanvas()
JPanel	getCanvasJPanel() Get reference to the JPanel on which image drawing takes place.
List<String>	getChannels()
String	getCurrentT()
String	getCurrentZPosition()
Point2D.Double	getDisplayImageSize() Get the size of the ge displayed on screen.
mmcorej.org.json.JSONObject	getDisplaySettingsJSON() Get the JSON represenation of the internal data structure use for saving display and contrast settings.
DisplaySettings	getDisplaySettingsObject()
Point2D.Double	getFullResSourceDataSize() Pixel size of the region currently being displayed in full resolution pixels.
int	getIntegerPositionFromStringPosition(String axisName, String axisPosition) Convert the position of a string axis to an integer position
double	getMagnification() Return ratio between size of pixels on screen and size of full resolution pixels in the imamge.
double	getPixelSize()
Preferences	getPreferences()
String	getStringPositionFromIntegerPosition(String axisName, int axisPosition)
mmcorej.org.json.JSONObject	getSummaryMD()
Point2D.Double	getViewOffset() get the offset of the top left displayed pixel to relative to top left of the full image (in full resolution coordinates).
void	initializeViewerToLoaded(List<String> channelNames, mmcorej.org.json.JSONObject dispSettings, HashMap<String,Object> axisMins, HashMap<String,Object> axisMaxs) Initialize all controls needed for a dataset loaded from disk where you're not calling newImageArrived each time.
boolean	isAcquisitionPaused()
boolean	isCompositMode()
boolean	isImageXYBounded()
boolean	isIntegerAxis(String axis)
void	newImageArrived(HashMap<String,Object> axesPositions) Signal to viewer that a new image is available.
void	onAnimationToggle(AxisScroller scoller, boolean animate)
void	onCanvasResize(int w, int h)
void	onContrastUpdated()
void	onScollersAdded()
void	onScollPositionChanged(AxisScroller scroller, int value)
void	pan(int dx, int dy) Change the view offset by the specified amount.
void	redrawOverlay() trigger redraw of the image overlay.
void	requestToClose() Called when window is x-ed out by user.
void	setAnimateFPS(double doubleValue)
void	setAxisPosition(String axis, int position) Set the scrollbar with a given axis label to a position.
void	setChannelColor(String channel, Color c) Set display settings for channel with the given name.
void	setCompositeMode(boolean selected)
void	setCustomCanvasMouseListener(CanvasMouseListenerInterface m) Add a custom object to respond to different types of mouse events on the canvas.
void	setImageEvent(HashMap<String,Object> axes, boolean fromHuman) Called when scrollbars move
void	setOverlay(Overlay overlay) Set a custom overlay object to be displayed on top of the image.
void	setOverlayerPlugin(OverlayerPlugin overlayer) Set a custom object to provide overlays.
void	setPausedAction(boolean paused)
void	setReadTimeMetadataFunction(Function<mmcorej.org.json.JSONObject,Long> fn) Optional: Pass in a function that tells how to extract elapsed ms from image metadata, for display purposes.
void	setReadZMetadataFunction(Function<mmcorej.org.json.JSONObject,Double> fn) Optional: Pass in a function that tells how to extract z position in µm from image tags, for display purposes.
void	setViewOffset(double newX, double newY) set the offset of the top left displayed pixel to relative to top left of the full image (in full resolution coordinates).
void	setWindowTitle(String s) Set the text in the windows frame.
void	showFolder()
void	showScaleBar(boolean selected)
void	showTimeLabel(boolean selected)
void	showZPositionLabel(boolean selected)
void	superlockAllScrollers()
void	unlockAllScroller()
void	update() Redraw current image and any overlay
void	zoom(double factor, Point mouseLocation) multiply zoom by given factor, centered at location.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

dataSource_

protected volatile NDViewerDataSource dataSource_

viewCoords_

protected DataViewCoords viewCoords_

Constructor Detail

NDViewer

public NDViewer(NDViewerDataSource cache,
                NDViewerAcqInterface acq,
                mmcorej.org.json.JSONObject summaryMD,
                double pixelSize,
                boolean rgb)

NDViewer

public NDViewer(NDViewerDataSource cache,
                NDViewerAcqInterface acq,
                mmcorej.org.json.JSONObject summaryMD,
                double pixelSize,
                boolean rgb,
                String preferencesKey)

Method Detail

getIntegerPositionFromStringPosition

public int getIntegerPositionFromStringPosition(String axisName,
                                                String axisPosition)

Convert the position of a string axis to an integer position

Parameters:

axisPosition -

getStringPositionFromIntegerPosition

public String getStringPositionFromIntegerPosition(String axisName,
                                                   int axisPosition)

setReadTimeMetadataFunction

public void setReadTimeMetadataFunction(Function<mmcorej.org.json.JSONObject,Long> fn)

Description copied from interface: NDViewerAPI

Optional: Pass in a function that tells how to extract elapsed ms from image metadata, for display purposes.

Specified by:

setReadTimeMetadataFunction in interface NDViewerAPI

setReadZMetadataFunction

public void setReadZMetadataFunction(Function<mmcorej.org.json.JSONObject,Double> fn)

Description copied from interface: NDViewerAPI

Optional: Pass in a function that tells how to extract z position in µm from image tags, for display purposes.

Specified by:

setReadZMetadataFunction in interface NDViewerAPI

setChannelColor

public void setChannelColor(String channel,
                            Color c)

Description copied from interface: NDViewerAPI

Set display settings for channel with the given name.

Specified by:

setChannelColor in interface NDViewerAPI

isImageXYBounded

public boolean isImageXYBounded()

getDisplaySettingsJSON

public mmcorej.org.json.JSONObject getDisplaySettingsJSON()

Description copied from interface: NDViewerAPI

Get the JSON represenation of the internal data structure use for saving display and contrast settings. This can be used to save them and then re load them later on.

Specified by:

getDisplaySettingsJSON in interface NDViewerAPI

Returns:

getPreferences

public Preferences getPreferences()

pan

public void pan(int dx,
                int dy)

Description copied from interface: NDViewerAPI

Change the view offset by the specified amount.

Specified by:

pan in interface NDViewerAPI

onScollersAdded

public void onScollersAdded()

onScollPositionChanged

public void onScollPositionChanged(AxisScroller scroller,
                                   int value)

zoom

public void zoom(double factor,
                 Point mouseLocation)

Description copied from interface: NDViewerAPI

multiply zoom by given factor, centered at location.

Specified by:

zoom in interface NDViewerAPI

mouseLocation - location in display pixel coordinates, or null to zoom in on center

onCanvasResize

public void onCanvasResize(int w,
                           int h)

initializeViewerToLoaded

public void initializeViewerToLoaded(List<String> channelNames,
                                     mmcorej.org.json.JSONObject dispSettings,
                                     HashMap<String,Object> axisMins,
                                     HashMap<String,Object> axisMaxs)

Description copied from interface: NDViewerAPI

Initialize all controls needed for a dataset loaded from disk where you're not calling newImageArrived each time.

Specified by:

initializeViewerToLoaded in interface NDViewerAPI

Parameters:

channelNames - names of all channels

axisMins - map of axis names to miniumum extents (can be negative)

axisMaxs - map of axis names to maximum extents

channelSetActive

public void channelSetActive(String channelName,
                             boolean selected)

setWindowTitle

public void setWindowTitle(String s)

Description copied from interface: NDViewerAPI

Set the text in the windows frame.

Specified by:

setWindowTitle in interface NDViewerAPI

newImageArrived

public void newImageArrived(HashMap<String,Object> axesPositions)

Signal to viewer that a new image is available.

Specified by:

newImageArrived in interface NDViewerAPI

Parameters:

axesPositions - Hashmap of axis labels to positions

addSetImageHook

public void addSetImageHook(Consumer<HashMap<String,Object>> hook)

Description copied from interface: NDViewerAPI

Add a hook function that runs whenever setImage gets called, either programatically or by someone moving the scrollbars

Specified by:

addSetImageHook in interface NDViewerAPI

setAxisPosition

public void setAxisPosition(String axis,
                            int position)

Description copied from interface: NDViewerAPI

Set the scrollbar with a given axis label to a position.

Specified by:

setAxisPosition in interface NDViewerAPI

setImageEvent

public void setImageEvent(HashMap<String,Object> axes,
                          boolean fromHuman)

Called when scrollbars move

onContrastUpdated

public void onContrastUpdated()

onAnimationToggle

public void onAnimationToggle(AxisScroller scoller,
                              boolean animate)

update

public void update()

Description copied from interface: NDViewerAPI

Redraw current image and any overlay

Specified by:

update in interface NDViewerAPI

getCanvas

public ViewerCanvas getCanvas()

superlockAllScrollers

public void superlockAllScrollers()

unlockAllScroller

public void unlockAllScroller()

showFolder

public void showFolder()

setAnimateFPS

public void setAnimateFPS(double doubleValue)

abortAcquisition

public void abortAcquisition()

setPausedAction

public void setPausedAction(boolean paused)

isAcquisitionPaused

public boolean isAcquisitionPaused()

setOverlay

public void setOverlay(Overlay overlay)

Description copied from interface: NDViewerAPI

Set a custom overlay object to be displayed on top of the image. This method can be called an arbitrary number of times by a custom. OverlayerPlugin

Specified by:

setOverlay in interface NDViewerAPI

redrawOverlay

public void redrawOverlay()

Description copied from interface: NDViewerAPI

trigger redraw of the image overlay.

Specified by:

redrawOverlay in interface NDViewerAPI

getMagnification

public double getMagnification()

Description copied from interface: NDViewerAPI

Return ratio between size of pixels on screen and size of full resolution pixels in the imamge.

Specified by:

getMagnification in interface NDViewerAPI

Returns:

getPixelSize

public double getPixelSize()

showScaleBar

public void showScaleBar(boolean selected)

setCompositeMode

public void setCompositeMode(boolean selected)

isCompositMode

public boolean isCompositMode()

getDisplaySettingsObject

public DisplaySettings getDisplaySettingsObject()

getChannels

public List<String> getChannels()

getCanvasJPanel

public JPanel getCanvasJPanel()

Description copied from interface: NDViewerAPI

Get reference to the JPanel on which image drawing takes place.

Specified by:

getCanvasJPanel in interface NDViewerAPI

Returns:

getAxisPosition

public Object getAxisPosition(String axis)

Description copied from interface: NDViewerAPI

Get the position that the scrollbar with the given label is currently at.

Specified by:

getAxisPosition in interface NDViewerAPI

Returns:

getViewOffset

public Point2D.Double getViewOffset()

Description copied from interface: NDViewerAPI

get the offset of the top left displayed pixel to relative to top left of the full image (in full resolution coordinates).

Specified by:

getViewOffset in interface NDViewerAPI

Returns:

getFullResSourceDataSize

public Point2D.Double getFullResSourceDataSize()

Description copied from interface: NDViewerAPI

Pixel size of the region currently being displayed in full resolution pixels.

Specified by:

getFullResSourceDataSize in interface NDViewerAPI

Returns:

setViewOffset

public void setViewOffset(double newX,
                          double newY)

Description copied from interface: NDViewerAPI

set the offset of the top left displayed pixel to relative to top left of the full image (in full resolution coordinates).

Specified by:

setViewOffset in interface NDViewerAPI

showTimeLabel

public void showTimeLabel(boolean selected)

showZPositionLabel

public void showZPositionLabel(boolean selected)

getCurrentT

public String getCurrentT()

getCurrentZPosition

public String getCurrentZPosition()

setCustomCanvasMouseListener

public void setCustomCanvasMouseListener(CanvasMouseListenerInterface m)

Description copied from interface: NDViewerAPI

Add a custom object to respond to different types of mouse events on the canvas.

Specified by:

setCustomCanvasMouseListener in interface NDViewerAPI

getDisplayImageSize

public Point2D.Double getDisplayImageSize()

Description copied from interface: NDViewerAPI

Get the size of the ge displayed on screen.

Specified by:

getDisplayImageSize in interface NDViewerAPI

Returns:

setOverlayerPlugin

public void setOverlayerPlugin(OverlayerPlugin overlayer)

Description copied from interface: NDViewerAPI

Set a custom object to provide overlays.

Specified by:

setOverlayerPlugin in interface NDViewerAPI

addControlPanel

public void addControlPanel(ControlsPanelInterface panel)

Description copied from interface: NDViewerAPI

Add a custom JPanel containing controls to the JTabbedPane on the right side of the image.

Specified by:

addControlPanel in interface NDViewerAPI

isIntegerAxis

public boolean isIntegerAxis(String axis)

requestToClose

public void requestToClose()

Called when window is x-ed out by user.

close

public void close()

Description copied from interface: NDViewerAPI

Forces the viewer to close, automatically aborting any acquisition in the process.

Specified by:

close in interface NDViewerAPI

getSummaryMD

public mmcorej.org.json.JSONObject getSummaryMD()