de.unihalle.informatik.MiToBo.visualization.colormappings

Class GrayscaleToGrayscaleMapping

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping

All Implemented Interfaces:

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

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

This operator transforms the intensity values of a gray-scale image according to a given intensity mapping.

The map must be provided in a file where each line contains a pair of tab-separated values. The first value is the value in the given image and the second value is the new value to which the first one is to be mapped in the output image.

Image values not being present in the map will be ignored, i.e. either mapped to zero or left untouched depending on the value of the parameter ignoredValuesMode.

Note that in single image mode the map file has to be specified explicitly while in directory mode it is assumed that the map files are located in the directory which is to be processed. For each image named 'X.tif' the corresponding map file should be named 'X-map.txt'.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode Available modes how to handle ignored values.
static class	GrayscaleToGrayscaleMapping.OperationMode Operation mode of the operator.

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 static String	classID Class identifier.
protected de.unihalle.informatik.Alida.datatypes.ALDFileString	filePath Textfile with mapping.
protected GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode	ignoredValuesMode Mode how to handle ignored values.
protected MTBImageByte	ignoreMask Optional binary mask of additional pixels to ignore.
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	inDir Input directory.
protected MTBImage	inputImg Input image.
private HashMap<Double,Double>	map Map for value mappings.
GrayscaleToGrayscaleMapping.OperationMode	opMode Mode of operation of the operator.
private MTBImage	resultImg Generated result image.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
GrayscaleToGrayscaleMapping() Default constructor.

Method Summary

Modifier and Type	Method and Description
MTBImage	getResultImage() Returns the result image.
protected void	operate() This method does the actual work.
protected MTBImage	processImage(MTBImage img) Convert a single image.
void	setIgnoreMask(MTBImageByte bImg) Specfiy additional mask of pixels to ignore.
void	setInputImage(MTBImage inimg) Set input image.
void	setMappingFile(String s) Specify mapping file.
private void	switchOpModeParameters() Callback routine to change operator mode parameters.
void	validateCustom()

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, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

classID

private static final String classID

Class identifier.

See Also:

Constant Field Values

opMode

@Parameter(label="Operation Mode",
           required=true,
           direction=IN,
           dataIOOrder=-5,
           description="Operation mode of the operator.",
           callback="switchOpModeParameters",
           paramModificationMode=MODIFIES_INTERFACE)
public GrayscaleToGrayscaleMapping.OperationMode opMode

Mode of operation of the operator.

inputImg

@Parameter(label="Input Image",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Input image.")
protected MTBImage inputImg

Input image.

inDir

@Parameter(label="Input Directory",
           required=true,
           direction=IN,
           description="Input directory.",
           dataIOOrder=1)
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString inDir

Input directory.

filePath

@Parameter(label="Map file",
           required=true,
           dataIOOrder=2,
           direction=IN,
           description="File with mapping information.")
protected de.unihalle.informatik.Alida.datatypes.ALDFileString filePath

Textfile with mapping.

ignoreMask

@Parameter(label="Ignore mask?",
           required=false,
           dataIOOrder=5,
           direction=IN,
           description="Ignore mask, pixels with values > 0 are ignored.")
protected MTBImageByte ignoreMask

Optional binary mask of additional pixels to ignore.

Pixels marked white are ignored, i.e. mapped to black or left untouched.

ignoredValuesMode

@Parameter(label="How to handle ignored values?",
           required=false,
           dataIOOrder=6,
           direction=IN,
           description="Mode how ignored values are treated.")
protected GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode ignoredValuesMode

Mode how to handle ignored values.

resultImg

@Parameter(label="Result Image",
           dataIOOrder=0,
           direction=OUT,
           description="Resulting image.")
private transient MTBImage resultImg

Generated result image.

map

private HashMap<Double,Double> map

Map for value mappings.

Constructor Detail

GrayscaleToGrayscaleMapping

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

Method Detail

switchOpModeParameters

private void switchOpModeParameters()

Callback routine to change operator mode parameters.

getResultImage

public MTBImage getResultImage()

Returns the result image.

Returns:

Result image.

setInputImage

public void setInputImage(MTBImage inimg)

Set input image.

Parameters:

inimg - Input grayscale image.

setMappingFile

public void setMappingFile(String s)

Specify mapping file.

Parameters:

s - File path.

setIgnoreMask

public void setIgnoreMask(MTBImageByte bImg)

Specfiy additional mask of pixels to ignore.

Parameters:

bImg - Binary mask.

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

operate

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

This method does the actual work.

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

processImage

protected MTBImage processImage(MTBImage img)

Convert a single image.

Parameters:

img - Image to convert.

Returns:

Result image.