LandmarkTableModel (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- javax.swing.table.AbstractTableModel
- - bigwarp.landmarks.LandmarkTableModel

All Implemented Interfaces:

TransformListener<InvertibleRealTransform>, Serializable, TableModel
```
public class LandmarkTableModel
extends AbstractTableModel
implements TransformListener<InvertibleRealTransform>
```
Author:

John Bogovic <bogovicj@janelia.hhmi.org>

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ACTIVECOLUMN`
`protected ArrayList<Boolean>`	`activeList`
`static Color`	`DEFAULTBGCOLOR`
`protected ArrayList<Boolean>`	`doesPointHaveAndNeedWarp`
`protected boolean`	`elementDeleted`
`protected ThinPlateR2LogRSplineKernelTransform`	`estimatedXfm`
`protected ArrayList<Integer>`	`indicesOfChangedPoints`
`protected double`	`inverseThreshold`
`protected double[]`	`lastPoint`
`org.apache.log4j.Logger`	`logger`
`protected int`	`maxInverseIterations`
`protected BigWarpMessageAnimator`	`message`
`protected boolean`	`modifiedSinceLastSave`
`protected ArrayList<Boolean>`	`movingDisplayPointUnreliable`
`protected ArrayList<Double[]>`	`movingPts`
`static int`	`NAMECOLUMN`
`protected ArrayList<String>`	`names`
`protected int`	`ndims`
`protected ArrayList<Boolean>`	`needsInverse`
`protected int`	`nextRowP`
`protected int`	`nextRowQ`
`protected int`	`numActive`
`protected int`	`numCols`
`protected int`	`numRows`
`protected Double[]`	`pointToOverride`
`protected boolean`	`pointUpdatePending`
`protected boolean`	`pointUpdatePendingMoving`
`protected ArrayList<Integer>`	`tableIndexToActiveIndex`
`protected ArrayList<Double[]>`	`targetPts`
`protected double[]`	`tmp`
`protected LandmarkUndoManager`	`undoRedoManager`
`static Color`	`WARNINGBGCOLOR`
`protected ArrayList<Double[]>`	`warpedPoints`

Fields inherited from class javax.swing.table.AbstractTableModel
listenerList

Constructor Summary

Constructors
Constructor and Description

LandmarkTableModel(int ndims)

Constructors
Constructor and Description
`LandmarkTableModel(int ndims)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`activateRow(int index)`
`boolean`	`add(double[] pt, boolean isMoving)`
`boolean`	`add(double[] pt, boolean isMoving, RealTransform xfm)`
`void`	`clear()`
`void`	`clearPt(int row, boolean isMoving)`
`void`	`computeWarpedPoint(int i, InvertibleRealTransform xfm)` Given an row in this table, updates the warped point position if necessary.
`static double[]`	`copy(double[] in)`
`void`	`copyLandmarks(double[][] movingLandmarks, double[][] targetLandmarks)`
`void`	`copyLandmarks(int tableIndex, double[][] movingLandmarks, double[][] targetLandmarks)`
`void`	`deleteRow(int i)`
`void`	`deleteRowHelper(int i)`
`protected void`	`exportTransformation(File ffwd, File finv)`
`protected void`	`firePointUpdated(int row, boolean isMoving)`
`int`	`getActiveIndex(int tableIndex)`
`int`	`getActiveRowCount()`
`ArrayList<Boolean>`	`getChangedSinceWarp()`
`Class<?>`	`getColumnClass(int col)`
`int`	`getColumnCount()`
`String`	`getColumnName(int col)`
`Double[]`	`getFixedPoint(int index)`
`int`	`getIndexNearestTo(double[] pt, boolean isMoving)`
`int`	`getIndexNearestTo(RealLocalizable pt, boolean isMoving)`
`boolean`	`getIsActive(int row)`
`Double[]`	`getMovingPoint(int index)`
`ArrayList<String>`	`getNames()`
`int`	`getNextRow(boolean isMoving)` Returns the next row to be updated for the moving or target columns.
`int`	`getNumdims()`
`double[]`	`getPendingPoint()`
`Double[]`	`getPoint(boolean isMoving, int index)`
`ArrayList<Double[]>`	`getPoints(boolean moving)`
`int`	`getRowCount()`
`ThinPlateR2LogRSplineKernelTransform`	`getTransform()`
`LandmarkUndoManager`	`getUndoManager()`
`Object`	`getValueAt(int rowIndex, int columnIndex)`
`ArrayList<Double[]>`	`getWarpedPoints()`
`protected void`	`importTransformation(File ffwd, File finv)`
`void`	`initTransformation()`
`LandmarkTableModel`	`invert()` Returns a new LandmarkTableModel but makes the moving points fixed and vice versa.
`boolean`	`isActive(int i)`
`boolean`	`isCellEditable(int row, int col)` Only allow editing of the first ("Name") and second ("Active") column
`boolean`	`isFixedPoint(int index)`
`boolean`	`isFixedPoint(int index, boolean isMoving)`
`boolean`	`isModifiedSinceSave()`
`boolean`	`isMovingPoint(int index)`
`boolean`	`isPointUpdatePending()`
`boolean`	`isPointUpdatePendingMoving()`
`boolean`	`isRowUnpaired(int i)` Returns true if the ith row is unpaired - i.e., if either of the moving or target points are unset.
`boolean`	`isUpdatePending()` Returns true if any row is unpaired.
`Boolean`	`isWarped(int i)`
`void`	`load(File f)`
`void`	`load(File f, boolean invert)` Loads this table from a file
`int`	`numActive()`
`boolean`	`pointEdit(int index, double[] pt, boolean forceAdd, boolean isMoving, boolean isWarped, boolean isUndoable, RealTransform xfm)`
`boolean`	`pointEdit(int index, double[] pt, boolean forceAdd, boolean isMoving, double[] warpedPt, boolean isUndoable)` Changes a point's position, or adds a new point.
`static String`	`print(Double[] d)`
`void`	`printDistances()`
`void`	`printState()`
`void`	`printWarpedPoints()`
`void`	`resetLastPoint()`
`void`	`resetNeedsInverse()`
`void`	`resetUpdated()`
`void`	`resetWarpedPoint(int i)`
`void`	`resetWarpedPoints()`
`void`	`restorePendingUpdate()`
`boolean`	`rowNeedsWarning(int row)`
`void`	`save(File f)` Saves the table to a file
`void`	`setColumnName(int row, String name)`
`void`	`setInverseThreshold(double inverseThreshold)`
`void`	`setIsActive(int row, boolean isActive)`
`void`	`setLastPoint(int i, boolean isMoving)`
`void`	`setMaxInverseIterations(int maxIters)`
`void`	`setMessage(BigWarpMessageAnimator message)`
`void`	`setNeedsInverse(int i)`
`void`	`setNextRow(boolean isMoving, int row)`
`void`	`setPoint(int row, boolean isMoving, double[] pt, boolean isUndoable, RealTransform xfm)`
`void`	`setPoint(int row, boolean isMoving, double[] pt, RealTransform xfm)`
`void`	`setTableListener()`
`void`	`setValueAt(Object value, int row, int col)`
`double`	`squaredDistance(Double[] p, double[] q)`
`double`	`squaredDistance(Double[] p, RealLocalizable q)`
`static double[]`	`toPrimitive(Double[] in)`
`String`	`toString()`
`void`	`transferUpdatesToModel()`
`void`	`transformChanged(InvertibleRealTransform transform)`
`void`	`updateAllWarpedPoints(InvertibleRealTransform xfm)` Looks through the table for points where there is a point in moving space but not fixed space.
`void`	`updateNextRows(int lastAddedIndex)`
`void`	`updateWarpedPoint(int i, double[] pt)`
`boolean`	`validateTransformPoints()`

Methods inherited from class javax.swing.table.AbstractTableModel
addTableModelListener, findColumn, fireTableCellUpdated, fireTableChanged, fireTableDataChanged, fireTableRowsDeleted, fireTableRowsInserted, fireTableRowsUpdated, fireTableStructureChanged, getListeners, getTableModelListeners, removeTableModelListener

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

Field Detail

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

Constant Field Values

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

Constant Field Values

WARNINGBGCOLOR
```
public static Color WARNINGBGCOLOR
```

DEFAULTBGCOLOR
```
public static Color DEFAULTBGCOLOR
```

ndims
```
protected int ndims
```

numCols
```
protected int numCols
```

numRows
```
protected int numRows
```

nextRowP
```
protected int nextRowP
```

nextRowQ
```
protected int nextRowQ
```

numActive
```
protected int numActive
```

names
```
protected ArrayList<String> names
```

activeList

protected ArrayList<Boolean> activeList

movingPts

protected ArrayList<Double[]> movingPts

targetPts

protected ArrayList<Double[]> targetPts

tableIndexToActiveIndex

protected ArrayList<Integer> tableIndexToActiveIndex

pointUpdatePending
```
protected boolean pointUpdatePending
```

pointUpdatePendingMoving

protected boolean pointUpdatePendingMoving

pointToOverride
```
protected Double[] pointToOverride
```

doesPointHaveAndNeedWarp

protected ArrayList<Boolean> doesPointHaveAndNeedWarp

indicesOfChangedPoints

protected ArrayList<Integer> indicesOfChangedPoints

elementDeleted
```
protected boolean elementDeleted
```

needsInverse

protected ArrayList<Boolean> needsInverse

movingDisplayPointUnreliable

protected ArrayList<Boolean> movingDisplayPointUnreliable

estimatedXfm

protected ThinPlateR2LogRSplineKernelTransform estimatedXfm

warpedPoints

protected ArrayList<Double[]> warpedPoints

maxInverseIterations
```
protected int maxInverseIterations
```

inverseThreshold
```
protected double inverseThreshold
```

lastPoint
```
protected double[] lastPoint
```

tmp
```
protected double[] tmp
```

undoRedoManager

protected LandmarkUndoManager undoRedoManager

message

protected BigWarpMessageAnimator message

modifiedSinceLastSave

protected boolean modifiedSinceLastSave

logger

public final org.apache.log4j.Logger logger

Constructor Detail
- LandmarkTableModel
```
public LandmarkTableModel(int ndims)
```

Method Detail

setMessage

public void setMessage(BigWarpMessageAnimator message)

getNumdims
```
public int getNumdims()
```

getPendingPoint
```
public double[] getPendingPoint()
```

getTransform

public ThinPlateR2LogRSplineKernelTransform getTransform()

printDistances
```
public void printDistances()
```

printState
```
public void printState()
```

toString
```
public String toString()
```
Overrides:

toString in class Object

validateTransformPoints

public boolean validateTransformPoints()

setTableListener
```
public void setTableListener()
```

isModifiedSinceSave
```
public boolean isModifiedSinceSave()
```

importTransformation

protected void importTransformation(File ffwd,
                                    File finv)
                             throws IOException

Throws:: IOException

exportTransformation

protected void exportTransformation(File ffwd,
                                    File finv)
                             throws IOException

Throws:: IOException

isPointUpdatePending
```
public boolean isPointUpdatePending()
```

isPointUpdatePendingMoving

public boolean isPointUpdatePendingMoving()

restorePendingUpdate
```
public void restorePendingUpdate()
```

getColumnCount
```
public int getColumnCount()
```
Specified by:

getColumnCount in interface TableModel

getRowCount
```
public int getRowCount()
```
Specified by:

getRowCount in interface TableModel

getActiveRowCount
```
public int getActiveRowCount()
```

getColumnName
```
public String getColumnName(int col)
```
Specified by:

getColumnName in interface TableModel

Overrides:

getColumnName in class AbstractTableModel

getPoints

public ArrayList<Double[]> getPoints(boolean moving)

getNames
```
public ArrayList<String> getNames()
```

setColumnName

public void setColumnName(int row,
                          String name)

getIsActive
```
public boolean getIsActive(int row)
```

setIsActive

public void setIsActive(int row,
                        boolean isActive)

getActiveIndex

public int getActiveIndex(int tableIndex)

getColumnClass
```
public Class<?> getColumnClass(int col)
```
Specified by:

getColumnClass in interface TableModel

Overrides:

getColumnClass in class AbstractTableModel

isActive
```
public boolean isActive(int i)
```

clear
```
public void clear()
```

deleteRow
```
public void deleteRow(int i)
```

deleteRowHelper
```
public void deleteRowHelper(int i)
```

isRowUnpaired
```
public boolean isRowUnpaired(int i)
```
Returns true if the ith row is unpaired - i.e., if either of the moving or target points are unset.

Parameters:

i - row index

Returns:

true of the

isUpdatePending
```
public boolean isUpdatePending()
```
Returns true if any row is unpaired.

Returns:

is update pending

setNextRow

public void setNextRow(boolean isMoving,
                       int row)

updateNextRows

public void updateNextRows(int lastAddedIndex)

getNextRow
```
public int getNextRow(boolean isMoving)
```
Returns the next row to be updated for the moving or target columns.

Parameters:

isMoving - isMoving

Returns:

index of the next row

isWarped
```
public Boolean isWarped(int i)
```

updateWarpedPoint

public void updateWarpedPoint(int i,
                              double[] pt)

printWarpedPoints
```
public void printWarpedPoints()
```

getWarpedPoints

public ArrayList<Double[]> getWarpedPoints()

getChangedSinceWarp

public ArrayList<Boolean> getChangedSinceWarp()

resetWarpedPoint
```
public void resetWarpedPoint(int i)
```

resetWarpedPoints
```
public void resetWarpedPoints()
```

resetNeedsInverse
```
public void resetNeedsInverse()
```

setNeedsInverse
```
public void setNeedsInverse(int i)
```

rowNeedsWarning

public boolean rowNeedsWarning(int row)

firePointUpdated

protected void firePointUpdated(int row,
                                boolean isMoving)

clearPt

public void clearPt(int row,
                    boolean isMoving)

add

public boolean add(double[] pt,
                   boolean isMoving)

add

public boolean add(double[] pt,
                   boolean isMoving,
                   RealTransform xfm)

setPoint

public void setPoint(int row,
                     boolean isMoving,
                     double[] pt,
                     RealTransform xfm)

setPoint

public void setPoint(int row,
                     boolean isMoving,
                     double[] pt,
                     boolean isUndoable,
                     RealTransform xfm)

pointEdit

public boolean pointEdit(int index,
                         double[] pt,
                         boolean forceAdd,
                         boolean isMoving,
                         boolean isWarped,
                         boolean isUndoable,
                         RealTransform xfm)

pointEdit
```
public boolean pointEdit(int index,
                         double[] pt,
                         boolean forceAdd,
                         boolean isMoving,
                         double[] warpedPt,
                         boolean isUndoable)
```
Changes a point's position, or adds a new point.

Parameters:

index - The index into this table that this edit will affect ( a value of -1 will add a new point )

pt - the point position

forceAdd - force addition of a new point at the specified index

isMoving - is this point in the moving image space

warpedPt - position of the warped point

isUndoable - is this action undo-able

Returns:

true if a new row was added

setLastPoint

public void setLastPoint(int i,
                         boolean isMoving)

resetLastPoint
```
public void resetLastPoint()
```

updateAllWarpedPoints
```
public void updateAllWarpedPoints(InvertibleRealTransform xfm)
```
Looks through the table for points where there is a point in moving space but not fixed space. For any such landmarks that are found, compute the inverse transform and add the result to the fixed points line.

Parameters:

xfm - the new transformation

computeWarpedPoint
```
public void computeWarpedPoint(int i,
                               InvertibleRealTransform xfm)
```
Given an row in this table, updates the warped point position if necessary.
An action is taken if, for the input row if:
- 1) There is a point in moving space, and
- 2) There is not a point in target space, and
- 3) A transformation has been estimated.
If these conditions are satisfied, the position of the moving point in target space by iteratively estimating the inverse of the thin plate spline transformation.
Parameters:

i - the row in the table

xfm - the invertible transformation

setMaxInverseIterations

public void setMaxInverseIterations(int maxIters)

setInverseThreshold

public void setInverseThreshold(double inverseThreshold)

getIndexNearestTo

public int getIndexNearestTo(double[] pt,
                             boolean isMoving)

squaredDistance

public double squaredDistance(Double[] p,
                              double[] q)

getIndexNearestTo

public int getIndexNearestTo(RealLocalizable pt,
                             boolean isMoving)

squaredDistance

public double squaredDistance(Double[] p,
                              RealLocalizable q)

getPoint

public Double[] getPoint(boolean isMoving,
                         int index)

getMovingPoint

public Double[] getMovingPoint(int index)

getFixedPoint

public Double[] getFixedPoint(int index)

isMovingPoint

public boolean isMovingPoint(int index)

isFixedPoint

public boolean isFixedPoint(int index)

isFixedPoint

public boolean isFixedPoint(int index,
                            boolean isMoving)

activateRow
```
public void activateRow(int index)
```

resetUpdated
```
public void resetUpdated()
```

transferUpdatesToModel
```
public void transferUpdatesToModel()
```

load

public void load(File f)
          throws IOException

Throws:: IOException

load
```
public void load(File f,
                 boolean invert)
          throws IOException
```
Loads this table from a file

Parameters:

f - the file

invert - invert the moving and target point sets

Throws:

IOException - an exception

numActive
```
public int numActive()
```

copyLandmarks

public void copyLandmarks(int tableIndex,
                          double[][] movingLandmarks,
                          double[][] targetLandmarks)

copyLandmarks

public void copyLandmarks(double[][] movingLandmarks,
                          double[][] targetLandmarks)

initTransformation
```
public void initTransformation()
```

save
```
public void save(File f)
          throws IOException
```
Saves the table to a file

Parameters:

f - the file

Throws:

IOException - an exception

print

public static String print(Double[] d)

setValueAt

public void setValueAt(Object value,
                       int row,
                       int col)

Specified by:: setValueAt in interface TableModel
Overrides:: setValueAt in class AbstractTableModel

getValueAt

public Object getValueAt(int rowIndex,
                         int columnIndex)

Specified by:: getValueAt in interface TableModel

isCellEditable
```
public boolean isCellEditable(int row,
                              int col)
```
Only allow editing of the first ("Name") and second ("Active") column

Specified by:

isCellEditable in interface TableModel

Overrides:

isCellEditable in class AbstractTableModel

invert
```
public LandmarkTableModel invert()
```
Returns a new LandmarkTableModel but makes the moving points fixed and vice versa.

Returns:

the LandmarkTableModel

getUndoManager

public LandmarkUndoManager getUndoManager()

copy

public static double[] copy(double[] in)

toPrimitive

public static double[] toPrimitive(Double[] in)

transformChanged
```
public void transformChanged(InvertibleRealTransform transform)
```
Specified by:

transformChanged in interface TransformListener<InvertibleRealTransform>

Class LandmarkTableModel

Field Summary

Fields inherited from class javax.swing.table.AbstractTableModel

Constructor Summary

Method Summary

Methods inherited from class javax.swing.table.AbstractTableModel

Methods inherited from class java.lang.Object

Field Detail

NAMECOLUMN

ACTIVECOLUMN

WARNINGBGCOLOR

DEFAULTBGCOLOR

ndims

numCols

numRows

nextRowP

nextRowQ

numActive

names

activeList

movingPts

targetPts

tableIndexToActiveIndex

pointUpdatePending

pointUpdatePendingMoving

pointToOverride

doesPointHaveAndNeedWarp

indicesOfChangedPoints

elementDeleted

needsInverse

movingDisplayPointUnreliable

estimatedXfm

warpedPoints

maxInverseIterations

inverseThreshold

lastPoint

tmp

undoRedoManager

message

modifiedSinceLastSave

logger

Constructor Detail

LandmarkTableModel

Method Detail

setMessage

getNumdims

getPendingPoint

getTransform

printDistances

printState

toString

validateTransformPoints

setTableListener

isModifiedSinceSave

importTransformation

exportTransformation

isPointUpdatePending

isPointUpdatePendingMoving

restorePendingUpdate

getColumnCount

getRowCount

getActiveRowCount

getColumnName

getPoints

getNames

setColumnName

getIsActive

setIsActive

getActiveIndex

getColumnClass

isActive

clear

deleteRow

deleteRowHelper

isRowUnpaired

isUpdatePending

setNextRow

updateNextRows

getNextRow

isWarped