de.unihalle.informatik.MiToBo.segmentation.thresholds

Class ImgThresh

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD)
public class ImgThresh
extends MTBOperator

Image thresholding operator with lower threshold (threshold and upper threshold (upperThreshold.

All pixels with threshold < intensity <= upperThreshold are defined as foreground pixels.

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	actualSliceOnly
private double	bgValue
private MTBImage	destinationImage
private double	fgValue
private MTBImage	inputImage
private MTBImage	resultImage
private MTBDoubleData	threshold
private MTBDoubleData	upperThreshold

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ImgThresh()
ImgThresh(MTBImage img, double thres) Constructor for thresholding using 255 as foreground and 0 as background value.
ImgThresh(MTBImage img, double thres, double fg, double bg) Constructor for thresholding using 'fgValue' as foreground and 'bgValue' as background value.

Method Summary

Modifier and Type	Method and Description
boolean	getActualSliceOnly() Get flag for thresholding only the actual slice (true) or the whole image (false)
double	getBGValue() Get background value
MTBImage	getDestinationImage() Get value of Input argument DestinationImage.
double	getFGValue() Get foreground value
MTBImage	getInputImage() Get input image
MTBImage	getResultImage() Get the result image
Double	getThreshold() Get threshold.
boolean	isBGOriginalValue() Test if background pixels keep their original pixel values
boolean	isFGOriginalValue() Test if foreground pixels keep their original pixel values
protected void	operate()
void	setActualSliceOnly() Only actual slice is thresholded, this will force the output image type to be of the same type as the input image (or destination image type)
void	setBGOriginalValue() Tell the thresholder to use the original pixel value for background pixels
void	setBGValue(double value) Set value of Parameter argument BGValue.
void	setDestinationImage(MTBImage img) Set value of Input argument DestinationImage.
void	setFGOriginalValue() Tell the thresholder to use the original pixel value for foreground pixels
void	setFGValue(double value) Set value of Parameter argument FGValue.
void	setInputImage(MTBImage img) Set input image
protected void	setResultImage(MTBImage img) Set result image.
void	setThreshold(double thres) Set threshold
protected MTBImage	threshold(MTBImage img, double thresh, double upperThres, double _fgValue, double _bgValue, boolean _actualSliceOnly) Apply threshold to an MTBImage and create a new thresholded MTBImage.
protected void	threshold(MTBImage img, MTBImage threshImg, double thresh, double upperThresh, double fgValue, double bgValue, boolean actualSliceOnly) Apply threshold to an MTBImage and write results to a destination MTBImage.
void	unsetActualSliceOnly() The whole image is thresholded (default)

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

threshold

@Parameter(label="Lower Threshold",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="Lower threshold, all pixels with intensity less this lower threshold are background pixels")
private MTBDoubleData threshold

upperThreshold

@Parameter(label="Upper Threshold",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="Upper threshold, all pixels with intensity greater equal this upper threshold are background pixels")
private MTBDoubleData upperThreshold

actualSliceOnly

@Parameter(label="Current slice only",
           required=false,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=5,
           description="Threshold only the current slice")
private boolean actualSliceOnly

fgValue

@Parameter(label="FG-value",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=3,
           description="Gray value for foreground pixel). If value is INFINITY then the original pixel values are used.")
private double fgValue

bgValue

@Parameter(label="BG-value",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=4,
           description="Gray value for background pixels. If value is INFINITY then the original pixel values are used.")
private double bgValue

inputImage

@Parameter(label="Input image",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=1,
           description="Input image")
private transient MTBImage inputImage

destinationImage

@Parameter(label="Destination image",
           required=false,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=6,
           description="Optional destination image to draw to. If ommited a new image is created.")
private transient MTBImage destinationImage

resultImage

@Parameter(label="Result image",
           required=true,
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=1,
           description="Result image")
private transient MTBImage resultImage

Constructor Detail

ImgThresh

public ImgThresh(MTBImage img,
                 double thres)
          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor for thresholding using 255 as foreground and 0 as background value. The result image will be of type MTB_BYTE

Parameters:

img - input image

thres - values < threshold are set to 0, value >= threshold are set to 255

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ImgThresh

public ImgThresh(MTBImage img,
                 double thres,
                 double fg,
                 double bg)
          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor for thresholding using 'fgValue' as foreground and 'bgValue' as background value. The result image will have the same type as the input image.

Parameters:

img - input image

thres - values < threshold are set to 'fgValue', value >= threshold are set to 'bgValue'

fg - foreground value (POSITIVE_INFINITY is interpreted as use original value)

bg - background value (POSITIVE_INFINITY is interpreted as use original value)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ImgThresh

public ImgThresh()
          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

threshold

protected MTBImage threshold(MTBImage img,
                             double thresh,
                             double upperThres,
                             double _fgValue,
                             double _bgValue,
                             boolean _actualSliceOnly)

Apply threshold to an MTBImage and create a new thresholded MTBImage. Specify values for foreground and background value. If fgValue/bgValue is Double.POSITIVE_INFINITY the original image values are used for foreground/background pixels. If fgValue == 255 and bgValue == 0 and !actualSliceOnly, the result image will be of type MTB_BYTE

Parameters:

img - source MTBImage

thresh - Lower threshold.

upperThres - Uppper threshold.

_fgValue - Foreground pixel value. If set to Double.POSITIVE_INFINITY, pixels higher than/equal to the threshold are set to their original values.

_bgValue - Background pixel value. If set to Double.POSITIVE_INFINITY, pixels lower to the threshold are set to their original values.

_actualSliceOnly - flag for only thresholding actual slice (true) or whole image (false)

Returns:

new thresholded MTBImage object

threshold

protected void threshold(MTBImage img,
                         MTBImage threshImg,
                         double thresh,
                         double upperThresh,
                         double fgValue,
                         double bgValue,
                         boolean actualSliceOnly)
                  throws IllegalArgumentException

Apply threshold to an MTBImage and write results to a destination MTBImage. Specify values for foreground and background value. If fgValue/bgValue is Double.POSITIVE_INFINITY the original image values are used for foreground/background pixels.

Parameters:

img - source MTBImage

threshImg - destination image to write the thresholded result to

thresh - Threshold

fgValue - Foreground pixel value. If set to Double.POSITIVE_INFINITY, pixels higher than/equal to the threshold are set to their original values.

bgValue - Background pixel value. If set to Double.POSITIVE_INFINITY, pixels lower to the threshold are set to their original values.

actualSliceOnly - flag for only thresholding actual slice (true) or whole image (false)

Throws:

IllegalArgumentException

getInputImage

public MTBImage getInputImage()

Get input image

Returns:

input image

setInputImage

public void setInputImage(MTBImage img)

Set input image

getThreshold

public Double getThreshold()

Get threshold. Might be null if no threshold was specified, but this will cause an exception on runtime

Returns:

threshold

setThreshold

public void setThreshold(double thres)

Set threshold

getFGValue

public double getFGValue()

Get foreground value

Returns:

foreground value

getBGValue

public double getBGValue()

Get background value

Returns:

background value

isFGOriginalValue

public boolean isFGOriginalValue()

Test if foreground pixels keep their original pixel values

Returns:

true if foreground pixels keep their original pixel values

isBGOriginalValue

public boolean isBGOriginalValue()

Test if background pixels keep their original pixel values

Returns:

true if background pixels keep their original pixel values

setFGOriginalValue

public void setFGOriginalValue()

Tell the thresholder to use the original pixel value for foreground pixels

setBGOriginalValue

public void setBGOriginalValue()

Tell the thresholder to use the original pixel value for background pixels

getActualSliceOnly

public boolean getActualSliceOnly()

Get flag for thresholding only the actual slice (true) or the whole image (false)

setActualSliceOnly

public void setActualSliceOnly()

Only actual slice is thresholded, this will force the output image type to be of the same type as the input image (or destination image type)

unsetActualSliceOnly

public void unsetActualSliceOnly()

The whole image is thresholded (default)

getResultImage

public MTBImage getResultImage()

Get the result image

Returns:

result image

setResultImage

protected void setResultImage(MTBImage img)

Set result image. You may specify a destination image to which the thresholding results are written. Otherwise the operator sets a new resulting image.

Parameters:

img - result image

setFGValue

public void setFGValue(double value)

Set value of Parameter argument FGValue.

Parameters:

value - New value for FGValue

setBGValue

public void setBGValue(double value)

Set value of Parameter argument BGValue.

Parameters:

value - New value for BGValue

getDestinationImage

public MTBImage getDestinationImage()

Get value of Input argument DestinationImage.

Returns:

value of DestinationImage

setDestinationImage

public void setDestinationImage(MTBImage img)

Set value of Input argument DestinationImage.

Parameters:

img - destination image