BigWarp (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bigwarp.BigWarp<T>

```
public class BigWarp<T>
extends Object
```

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`BigWarp.BigWarpData<T>`
`protected class`	`BigWarp.LandmarkModeListener`
`class`	`BigWarp.LandmarkTableListener`
`protected class`	`BigWarp.MouseLandmarkListener`
`class`	`BigWarp.MouseLandmarkTableListener`
`static class`	`BigWarp.SolveThread`
`class`	`BigWarp.WarningTableCellRenderer`
`static class`	`BigWarp.WarpVisType`

Field Summary

Fields
Modifier and Type	Field and Description
`protected VisibilityAndGroupingDialog`	`activeSourcesDialogP`
`protected VisibilityAndGroupingDialog`	`activeSourcesDialogQ`
`protected File`	`autoSaveDirectory`
`protected BigWarpAutoSaver`	`autoSaver`
`protected int`	`baselineModelIndex`
`protected AbstractModel<?>[]`	`baseXfmList`
`protected BookmarksEditor`	`bookmarkEditorP`
`protected BookmarksEditor`	`bookmarkEditorQ`
`protected BrightnessDialog`	`brightnessDialog`
`protected RealPoint`	`currentLandmark`
`protected InvertibleRealTransform`	`currentTransform`
`protected BigWarp.BigWarpData<T>`	`data`
`protected static int`	`DEFAULT_HEIGHT`
`protected static int`	`DEFAULT_WIDTH`
`protected BigWarpDragOverlay`	`dragOverlayP`
`protected BigWarpDragOverlay`	`dragOverlayQ`
`protected boolean`	`firstWarpEstimation`
`static int`	`GRID_SOURCE_ID`
`protected SourceAndConverter<FloatType>`	`gridSource`
`protected HelpDialog`	`helpDialog`
`protected AffineTransform3D`	`initialViewP`
`protected AffineTransform3D`	`initialViewQ`
`protected boolean`	`inLandmarkMode`
`static int`	`JACDET_SOURCE_ID`
`protected SourceAndConverter<FloatType>`	`jacDetSource`
`protected Set<KeyEventPostProcessor>`	`keyEventPostProcessorSet`
`protected BigWarp.MouseLandmarkListener`	`landmarkClickListenerP`
`protected BigWarp.MouseLandmarkListener`	`landmarkClickListenerQ`
`protected BigWarpLandmarkFrame`	`landmarkFrame`
`protected LandmarkTableModel`	`landmarkModel`
`protected BigWarp.LandmarkTableListener`	`landmarkModellistener`
`protected BigWarpLandmarkPanel`	`landmarkPanel`
`protected LandmarkPointMenu`	`landmarkPopupMenu`
`protected JTable`	`landmarkTable`
`protected BigWarp.MouseLandmarkTableListener`	`landmarkTableListener`
`protected File`	`lastDirectory`
`protected File`	`lastLandmarks`
`protected static org.apache.log4j.Logger`	`logger`
`protected BigWarpMessageAnimator`	`message`
`protected int[]`	`movingSourceIndexList`
`protected BigWarpViewerOptions`	`options`
`protected BigWarpOverlay`	`overlayP`
`protected BigWarpOverlay`	`overlayQ`
`protected SetupAssignments`	`setupAssignments`
`protected SourceInfoDialog`	`sourceInfoDialog`
`protected List<SourceAndConverter<T>>`	`sources`
`protected int[]`	`targetSourceIndexList`
`protected AffineTransform3D`	`tmpTransform`
`protected TransformTypeSelectDialog`	`transformSelector`
`protected boolean`	`updateWarpOnPtChange`
`protected BigWarpViewerPanel`	`viewerP`
`protected BigWarpViewerPanel`	`viewerQ`
`protected BigWarpViewerSettings`	`viewerSettings`
`static int`	`WARPMAG_SOURCE_ID`
`protected SourceAndConverter<FloatType>`	`warpMagSource`
`protected WarpVisFrame`	`warpVisDialog`

Constructor Summary

Constructors
Constructor and Description
`BigWarp(BigWarp.BigWarpData<T> data, String windowTitle, BigWarpViewerOptions options, ProgressWriter progressWriter)`
`BigWarp(BigWarp.BigWarpData<T> data, String windowTitle, ProgressWriter progressWriter)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`protected void`	`addDefaultTableMouseListener()`
`void`	`addKeyEventPostProcessor(KeyEventPostProcessor ke)`
`boolean`	`addPoint(double[] ptarray, boolean isMoving)` Updates the global variable ptBack
`String`	`addPoint(double[] ptarray, boolean isMoving, BigWarpViewerPanel viewer)` Updates the global variable ptBack
`void`	`addTransformListener(TransformListener<InvertibleRealTransform> listener)`
`void`	`autoSaveLandmarks()` Saves landmarks to a new File in the user's bigwarp folder.
`void`	`checkBoxInputMaps()`
`void`	`closeAll()`
`static double`	`computeScaleAssumeRigid(AffineTransform3D xfm)`
`protected int`	`detectNumDims()` The display will be in 3d if any of the input sources are 3d.
`static <T> int`	`detectNumDims(List<SourceAndConverter<T>> sources)` The display will be in 3d if any of the input sources are 3d.
`protected void`	`disableTransformHandlers()`
`protected void`	`enableTransformHandlers()`
`void`	`exportAsImagePlus(boolean virtual)`
`void`	`exportAsImagePlus(boolean virtual, String path)`
`void`	`exportWarpField()`
`protected void`	`fitBaselineWarpMagModel()`
`BigWarpAutoSaver`	`getAutoSaver()` Returns the `BigWarpAutoSaver`.
`File`	`getBigwarpSettingsFolder()` Returns the default location for bigwarp settings / auto saved files: ~/.bigwarp
`Bookmarks`	`getBookmarks()`
`BigWarpTransform`	`getBwTransform()`
`BigWarp.BigWarpData<T>`	`getData()`
`BigWarpLandmarkFrame`	`getLandmarkFrame()`
`BigWarpLandmarkPanel`	`getLandmarkPanel()`
`File`	`getLastDirectory()`
`AffineTransform3D`	`getMovingToFixedTransformAsAffineTransform3D()`
`BigWarpOverlay`	`getOverlayP()`
`BigWarpOverlay`	`getOverlayQ()`
`int`	`getSelectedUnpairedRow(boolean isMoving)` Returns the index of the selected row, if it is unpaired, -1 otherwise
`SetupAssignments`	`getSetupAssignments()`
`List<SourceAndConverter<T>>`	`getSources()`
`ThinPlateR2LogRSplineKernelTransform`	`getTransform()` Deprecated.
`String`	`getTransformType()`
`BigWarpViewerFrame`	`getViewerFrameP()`
`BigWarpViewerFrame`	`getViewerFrameQ()`
`void`	`goToBookmark()`
`static void`	`initBrightness(double cumulativeMinCutoff, double cumulativeMaxCutoff, ViewerState state, ConverterSetups converterSetups)` Deprecated. Use `InitializeViewerState` method instead.
`void`	`invertPointCorrespondences()`
`boolean`	`isInLandmarkMode()`
`boolean`	`isMovingDisplayTransformed()`
`boolean`	`isRowIncomplete()` Returns true if the currently selected row in the landmark table is missing on the the landmarks
`boolean`	`isUpdateWarpOnChange()`
`protected void`	`loadLandmarks()`
`void`	`loadLandmarks(String filename)`
`protected void`	`loadSettings()`
`protected void`	`loadSettings(String xmlFilename)`
`static void`	`main(String[] args)`
`void`	`matchActiveViewerPanelToOther()`
`void`	`matchOtherViewerPanelToActive()`
`protected void`	`matchWindowTransforms(BigWarpViewerPanel panelToChange, BigWarpViewerPanel panelToMatch)` Changes the view transformation of 'panelToChange' to match that of 'panelToMatch'
`int`	`numDimensions()`
`void`	`quickSaveLandmarks()` Saves landmarks to either the last File the user saved landmarks to, or a unique location in the user's bigwarp folder.
`void`	`removeKeyEventPostProcessor(KeyEventPostProcessor ke)`
`void`	`resetView()`
`boolean`	`restimateTransformation()`
`protected void`	`saveLandmarks()`
`protected void`	`saveLandmarks(String filename)`
`void`	`saveMovingImageToFile()` Deprecated.
`File`	`saveMovingImageXml()`
`File`	`saveMovingImageXml(String proposedFilePath)`
`protected void`	`saveSettings()`
`protected void`	`saveSettings(String xmlFilename)`
`protected int`	`selectedLandmark(double[] pt, boolean isMoving)`
`protected int`	`selectedLandmark(double[] pt, boolean isMoving, boolean selectInTable)` Returns the index of the landmark closest to the input point, if it is within a certain distance threshold.
`void`	`setAutosaveFolder(File autoSaveFolder)` Set the folder where the results of auto-saving will be stored.
`void`	`setGridType(GridSource.GRID_TYPE method)`
`void`	`setInLandmarkMode(boolean inLmMode)`
`void`	`setIsMovingDisplayTransformed(boolean isTransformed)`
`void`	`setLastDirectory(File dir)`
`void`	`setMovingSpimData(SpimData movingSpimData, File movingImageXml)`
`void`	`setSpotColor(Color c)`
`void`	`setTransformType(String type)`
`void`	`setUpdateWarpOnChange(boolean updateWarpOnPtChange)`
`protected void`	`setupImageJExportOption()`
`void`	`setupKeyListener()`
`protected void`	`setUpLandmarkMenus()`
`protected void`	`setUpViewerMenu(BigWarpViewerFrame vframe)`
`protected void`	`setupWarpMagBaselineOptions(CoordinateTransform[] xfm, int ndim)`
`void`	`setWarpGridSpacing(double spacing)`
`void`	`setWarpGridWidth(double width)`
`void`	`setWarpMagBaselineIndex(int index)`
`void`	`setWarpVisGridType(GridSource.GRID_TYPE type)`
`void`	`setWarpVisMode(BigWarp.WarpVisType type, BigWarpViewerFrame viewerFrame, boolean both)`
`void`	`stopAutosave()`
`void`	`toggleInLandmarkMode()`
`boolean`	`toggleMovingImageDisplay()` Toggles whether the moving image is displayed after warping (in the same space as the fixed image), or in its native space.
`void`	`toggleNameVisibility()`
`void`	`togglePointVisibility()`
`void`	`toggleUpdateWarpOnChange()`
`void`	`toggleWarpVisMode(BigWarpViewerFrame viewerFrame)`
`void`	`updatePointLocation(double[] ptarray, boolean isMoving, int selectedPointIndex)`
`void`	`updatePointLocation(double[] ptarray, boolean isMoving, int selectedPointIndex, BigWarpViewerPanel viewer)`
`void`	`updateRowSelection(boolean isMoving, int lastRowEdited)`
`static void`	`updateRowSelection(LandmarkTableModel landmarkModel, JTable table, boolean isMoving, int lastRowEdited)`
`int`	`updateWarpedPoint(double[] ptarray, boolean isMoving)`
`void`	`warpToLandmark(int row, BigWarpViewerPanel viewer)`
`void`	`warpToNearest(BigWarpViewerPanel viewer)`
`static <T> List<SourceAndConverter<T>>`	`wrapSourcesAsTransformed(List<SourceAndConverter<T>> sources, int ndims, BigWarp.BigWarpData<?> data)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_WIDTH
```
protected static final int DEFAULT_WIDTH
```
See Also:

Constant Field Values

DEFAULT_HEIGHT
```
protected static final int DEFAULT_HEIGHT
```
See Also:

Constant Field Values

GRID_SOURCE_ID
```
public static final int GRID_SOURCE_ID
```
See Also:

Constant Field Values

WARPMAG_SOURCE_ID
```
public static final int WARPMAG_SOURCE_ID
```
See Also:

Constant Field Values

JACDET_SOURCE_ID
```
public static final int JACDET_SOURCE_ID
```
See Also:

Constant Field Values

options
```
protected BigWarpViewerOptions options
```

data
```
protected BigWarp.BigWarpData<T> data
```

movingSourceIndexList
```
protected int[] movingSourceIndexList
```

targetSourceIndexList
```
protected int[] targetSourceIndexList
```

sources

protected List<SourceAndConverter<T>> sources

setupAssignments

protected final SetupAssignments setupAssignments

brightnessDialog

protected final BrightnessDialog brightnessDialog

warpVisDialog

protected final WarpVisFrame warpVisDialog

helpDialog
```
protected final HelpDialog helpDialog
```

sourceInfoDialog

protected final SourceInfoDialog sourceInfoDialog

activeSourcesDialogP

protected final VisibilityAndGroupingDialog activeSourcesDialogP

activeSourcesDialogQ

protected final VisibilityAndGroupingDialog activeSourcesDialogQ

bookmarkEditorP

protected final BookmarksEditor bookmarkEditorP

bookmarkEditorQ

protected final BookmarksEditor bookmarkEditorQ

viewerP

protected final BigWarpViewerPanel viewerP

viewerQ

protected final BigWarpViewerPanel viewerQ

initialViewP

protected final AffineTransform3D initialViewP

initialViewQ

protected final AffineTransform3D initialViewQ

landmarkPanel

protected BigWarpLandmarkPanel landmarkPanel

landmarkPopupMenu

protected final LandmarkPointMenu landmarkPopupMenu

landmarkFrame

protected final BigWarpLandmarkFrame landmarkFrame

viewerSettings

protected final BigWarpViewerSettings viewerSettings

overlayP

protected final BigWarpOverlay overlayP

overlayQ

protected final BigWarpOverlay overlayQ

dragOverlayP

protected final BigWarpDragOverlay dragOverlayP

dragOverlayQ

protected final BigWarpDragOverlay dragOverlayQ

currentLandmark
```
protected RealPoint currentLandmark
```

landmarkModel

protected LandmarkTableModel landmarkModel

currentTransform

protected InvertibleRealTransform currentTransform

landmarkTable
```
protected JTable landmarkTable
```

landmarkModellistener

protected BigWarp.LandmarkTableListener landmarkModellistener

landmarkClickListenerP

protected BigWarp.MouseLandmarkListener landmarkClickListenerP

landmarkClickListenerQ

protected BigWarp.MouseLandmarkListener landmarkClickListenerQ

landmarkTableListener

protected BigWarp.MouseLandmarkTableListener landmarkTableListener

message

protected BigWarpMessageAnimator message

keyEventPostProcessorSet

protected final Set<KeyEventPostProcessor> keyEventPostProcessorSet

gridSource

protected final SourceAndConverter<FloatType> gridSource

warpMagSource

protected final SourceAndConverter<FloatType> warpMagSource

jacDetSource

protected final SourceAndConverter<FloatType> jacDetSource

baseXfmList

protected final AbstractModel<?>[] baseXfmList

transformSelector

protected TransformTypeSelectDialog transformSelector

tmpTransform

protected AffineTransform3D tmpTransform

inLandmarkMode
```
protected boolean inLandmarkMode
```

baselineModelIndex
```
protected int baselineModelIndex
```

autoSaveDirectory
```
protected File autoSaveDirectory
```

lastDirectory
```
protected File lastDirectory
```

lastLandmarks
```
protected File lastLandmarks
```

autoSaver
```
protected BigWarpAutoSaver autoSaver
```

updateWarpOnPtChange
```
protected boolean updateWarpOnPtChange
```

firstWarpEstimation
```
protected boolean firstWarpEstimation
```

logger

protected static org.apache.log4j.Logger logger

Constructor Detail

BigWarp

public BigWarp(BigWarp.BigWarpData<T> data,
               String windowTitle,
               ProgressWriter progressWriter)
        throws SpimDataException

Throws:: SpimDataException

BigWarp

public BigWarp(BigWarp.BigWarpData<T> data,
               String windowTitle,
               BigWarpViewerOptions options,
               ProgressWriter progressWriter)
        throws SpimDataException

Throws:: SpimDataException

Method Detail

numDimensions
```
public int numDimensions()
```

initBrightness

@Deprecated
public static void initBrightness(double cumulativeMinCutoff,
                                              double cumulativeMaxCutoff,
                                              ViewerState state,
                                              ConverterSetups converterSetups)

Deprecated. Use InitializeViewerState method instead.

TODO Make a PR that updates this method in InitializeViewerState in bdv-core

Parameters:: cumulativeMinCutoff - the min image intensity; cumulativeMaxCutoff - the max image intensity; state - the viewer state; converterSetups - the converter setups

addKeyEventPostProcessor

public void addKeyEventPostProcessor(KeyEventPostProcessor ke)

removeKeyEventPostProcessor

public void removeKeyEventPostProcessor(KeyEventPostProcessor ke)

closeAll
```
public void closeAll()
```

setUpdateWarpOnChange

public void setUpdateWarpOnChange(boolean updateWarpOnPtChange)

toggleUpdateWarpOnChange

public void toggleUpdateWarpOnChange()

isInLandmarkMode
```
public boolean isInLandmarkMode()
```

toggleInLandmarkMode
```
public void toggleInLandmarkMode()
```

isUpdateWarpOnChange
```
public boolean isUpdateWarpOnChange()
```

invertPointCorrespondences

public void invertPointCorrespondences()

getLastDirectory
```
public File getLastDirectory()
```

setLastDirectory

public void setLastDirectory(File dir)

setSpotColor
```
public void setSpotColor(Color c)
```

setUpViewerMenu

protected void setUpViewerMenu(BigWarpViewerFrame vframe)

setupImageJExportOption

protected void setupImageJExportOption()

exportAsImagePlus

public void exportAsImagePlus(boolean virtual)

saveMovingImageToFile

@Deprecated
public void saveMovingImageToFile()

Deprecated.

saveMovingImageXml
```
public File saveMovingImageXml()
```

saveMovingImageXml

public File saveMovingImageXml(String proposedFilePath)

getMovingToFixedTransformAsAffineTransform3D

public AffineTransform3D getMovingToFixedTransformAsAffineTransform3D()

exportAsImagePlus

public void exportAsImagePlus(boolean virtual,
                              String path)

exportWarpField
```
public void exportWarpField()
```

setUpLandmarkMenus
```
protected void setUpLandmarkMenus()
```

getBookmarks
```
public Bookmarks getBookmarks()
```

getViewerFrameP

public BigWarpViewerFrame getViewerFrameP()

getViewerFrameQ

public BigWarpViewerFrame getViewerFrameQ()

getOverlayP
```
public BigWarpOverlay getOverlayP()
```

getOverlayQ
```
public BigWarpOverlay getOverlayQ()
```

getSetupAssignments

public SetupAssignments getSetupAssignments()

getData

public BigWarp.BigWarpData<T> getData()

getSources

public List<SourceAndConverter<T>> getSources()

getLandmarkFrame

public BigWarpLandmarkFrame getLandmarkFrame()

getLandmarkPanel

public BigWarpLandmarkPanel getLandmarkPanel()

setInLandmarkMode

public void setInLandmarkMode(boolean inLmMode)

updatePointLocation

public void updatePointLocation(double[] ptarray,
                                boolean isMoving,
                                int selectedPointIndex,
                                BigWarpViewerPanel viewer)

Parameters:: ptarray - location of the clicked point; isMoving - is the viewer in moving space; selectedPointIndex - the index of the selected point; viewer - the BigWarpViewerPanel clicked on

updatePointLocation

public void updatePointLocation(double[] ptarray,
                                boolean isMoving,
                                int selectedPointIndex)

updateWarpedPoint

public int updateWarpedPoint(double[] ptarray,
                             boolean isMoving)

updateRowSelection

public void updateRowSelection(boolean isMoving,
                               int lastRowEdited)

updateRowSelection

public static void updateRowSelection(LandmarkTableModel landmarkModel,
                                      JTable table,
                                      boolean isMoving,
                                      int lastRowEdited)

getSelectedUnpairedRow
```
public int getSelectedUnpairedRow(boolean isMoving)
```
Returns the index of the selected row, if it is unpaired, -1 otherwise

Parameters:

isMoving - isMoving

Returns:

index of the selected row

addPoint
```
public String addPoint(double[] ptarray,
                       boolean isMoving,
                       BigWarpViewerPanel viewer)
```
Updates the global variable ptBack

Parameters:

ptarray - the point location

isMoving - is the point location in moving image space

viewer - the viewer panel

Returns:

an error string if an error occurred, empty string otherwise

addPoint
```
public boolean addPoint(double[] ptarray,
                        boolean isMoving)
```
Updates the global variable ptBack

Parameters:

ptarray - the point location

isMoving - is the point location in moving image space

Returns:

true if a new row was created

selectedLandmark

protected int selectedLandmark(double[] pt,
                               boolean isMoving)

selectedLandmark
```
protected int selectedLandmark(double[] pt,
                               boolean isMoving,
                               boolean selectInTable)
```
Returns the index of the landmark closest to the input point, if it is within a certain distance threshold. Updates the global variable ptBack

Parameters:

pt - the point location

isMoving - is the point location in moving image space

selectInTable - also select the landmark in the table

Returns:

the index of the selected landmark

computeScaleAssumeRigid

public static double computeScaleAssumeRigid(AffineTransform3D xfm)

disableTransformHandlers

protected void disableTransformHandlers()

enableTransformHandlers

protected void enableTransformHandlers()

matchWindowTransforms
```
protected void matchWindowTransforms(BigWarpViewerPanel panelToChange,
                                     BigWarpViewerPanel panelToMatch)
```
Changes the view transformation of 'panelToChange' to match that of 'panelToMatch'

Parameters:

panelToChange - the viewer panel whose transform will change

panelToMatch - the viewer panel the transform will come from

matchOtherViewerPanelToActive

public void matchOtherViewerPanelToActive()

matchActiveViewerPanelToOther

public void matchActiveViewerPanelToOther()

warpToNearest

public void warpToNearest(BigWarpViewerPanel viewer)

warpToLandmark

public void warpToLandmark(int row,
                           BigWarpViewerPanel viewer)

goToBookmark
```
public void goToBookmark()
```

resetView
```
public void resetView()
```

toggleNameVisibility
```
public void toggleNameVisibility()
```

togglePointVisibility
```
public void togglePointVisibility()
```

toggleMovingImageDisplay
```
public boolean toggleMovingImageDisplay()
```
Toggles whether the moving image is displayed after warping (in the same space as the fixed image), or in its native space.

Returns:

true of the display mode changed

addDefaultTableMouseListener

protected void addDefaultTableMouseListener()

setGridType

public void setGridType(GridSource.GRID_TYPE method)

wrapSourcesAsTransformed

public static <T> List<SourceAndConverter<T>> wrapSourcesAsTransformed(List<SourceAndConverter<T>> sources,
                                                                       int ndims,
                                                                       BigWarp.BigWarpData<?> data)

setupKeyListener
```
public void setupKeyListener()
```

setWarpVisGridType

public void setWarpVisGridType(GridSource.GRID_TYPE type)

setWarpGridWidth

public void setWarpGridWidth(double width)

setWarpGridSpacing

public void setWarpGridSpacing(double spacing)

setupWarpMagBaselineOptions

protected void setupWarpMagBaselineOptions(CoordinateTransform[] xfm,
                                           int ndim)

setWarpMagBaselineIndex

public void setWarpMagBaselineIndex(int index)

fitBaselineWarpMagModel

protected void fitBaselineWarpMagModel()

setMovingSpimData

public void setMovingSpimData(SpimData movingSpimData,
                              File movingImageXml)

setWarpVisMode

public void setWarpVisMode(BigWarp.WarpVisType type,
                           BigWarpViewerFrame viewerFrame,
                           boolean both)

toggleWarpVisMode

public void toggleWarpVisMode(BigWarpViewerFrame viewerFrame)

restimateTransformation

public boolean restimateTransformation()

setIsMovingDisplayTransformed

public void setIsMovingDisplayTransformed(boolean isTransformed)

isRowIncomplete
```
public boolean isRowIncomplete()
```
Returns true if the currently selected row in the landmark table is missing on the the landmarks

Returns:

true if there is a missing value

isMovingDisplayTransformed

public boolean isMovingDisplayTransformed()

detectNumDims
```
protected int detectNumDims()
```
The display will be in 3d if any of the input sources are 3d.

Returns:

dimension of the input sources

detectNumDims
```
public static <T> int detectNumDims(List<SourceAndConverter<T>> sources)
```
The display will be in 3d if any of the input sources are 3d.

Type Parameters:

T - the type

Parameters:

sources - the sources

Returns:

dimension of the input sources

main

public static void main(String[] args)

checkBoxInputMaps
```
public void checkBoxInputMaps()
```

setTransformType

public void setTransformType(String type)

getTransformType
```
public String getTransformType()
```

getBwTransform

public BigWarpTransform getBwTransform()

getTransform
```
@Deprecated
public ThinPlateR2LogRSplineKernelTransform getTransform()
```
Deprecated.

Use getTps, getTpsBase, or getTransformation instead

Returns:

addTransformListener

public void addTransformListener(TransformListener<InvertibleRealTransform> listener)

setAutosaveFolder
```
public void setAutosaveFolder(File autoSaveFolder)
```
Set the folder where the results of auto-saving will be stored.

Parameters:

autoSaveFolder - the destination folder

autoSaveLandmarks
```
public void autoSaveLandmarks()
```
Saves landmarks to a new File in the user's bigwarp folder.

quickSaveLandmarks
```
public void quickSaveLandmarks()
```
Saves landmarks to either the last File the user saved landmarks to, or a unique location in the user's bigwarp folder.

getBigwarpSettingsFolder
```
public File getBigwarpSettingsFolder()
```
Returns the default location for bigwarp settings / auto saved files: ~/.bigwarp

Returns:

the folder

getAutoSaver
```
public BigWarpAutoSaver getAutoSaver()
```
Returns the BigWarpAutoSaver.

Returns:

stopAutosave
```
public void stopAutosave()
```

saveLandmarks
```
protected void saveLandmarks()
```

saveLandmarks

protected void saveLandmarks(String filename)
                      throws IOException

Throws:: IOException

loadLandmarks
```
protected void loadLandmarks()
```

loadLandmarks

public void loadLandmarks(String filename)

saveSettings
```
protected void saveSettings()
```

saveSettings

protected void saveSettings(String xmlFilename)
                     throws IOException

Throws:: IOException

loadSettings
```
protected void loadSettings()
```

loadSettings

protected void loadSettings(String xmlFilename)
                     throws IOException,
                            org.jdom2.JDOMException

Throws:: IOException; org.jdom2.JDOMException

Class BigWarp<T>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_WIDTH

DEFAULT_HEIGHT

GRID_SOURCE_ID

WARPMAG_SOURCE_ID

JACDET_SOURCE_ID

options

data

movingSourceIndexList

targetSourceIndexList

sources

setupAssignments

brightnessDialog

warpVisDialog

helpDialog

sourceInfoDialog

activeSourcesDialogP

activeSourcesDialogQ

bookmarkEditorP

bookmarkEditorQ

viewerP

viewerQ

initialViewP

initialViewQ

landmarkPanel

landmarkPopupMenu

landmarkFrame

viewerSettings

overlayP

overlayQ

dragOverlayP

dragOverlayQ

currentLandmark

landmarkModel

currentTransform

landmarkTable

landmarkModellistener

landmarkClickListenerP

landmarkClickListenerQ

landmarkTableListener

message

keyEventPostProcessorSet

gridSource

warpMagSource

jacDetSource

baseXfmList

transformSelector

tmpTransform

inLandmarkMode

baselineModelIndex

autoSaveDirectory

lastDirectory

lastLandmarks

autoSaver

updateWarpOnPtChange

firstWarpEstimation

logger

Constructor Detail

BigWarp

BigWarp

Method Detail

numDimensions

initBrightness

addKeyEventPostProcessor

removeKeyEventPostProcessor

closeAll

setUpdateWarpOnChange

toggleUpdateWarpOnChange

isInLandmarkMode

toggleInLandmarkMode

isUpdateWarpOnChange

invertPointCorrespondences

getLastDirectory

setLastDirectory