de.unihalle.informatik.MiToBo.enhance

Class IlluminationCorrection

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              allowBatchMode=true,
              shortDescription="Correction of uneven illumination.")
public class IlluminationCorrection
extends MTBOperator

 
 This class corrects the uneven illumination (e.g. background gradient) of
 especially gray value bright filed or DIC images.
 The original image is transformed by a morphological closing
 (or an other morphological transformation). The correction of the uneven
 illumination is obtained by dividing the original image by the transformed
 image. This approach works well for DIC images, maybe also for bright field
 or other illumination/contrast based images. Mask size of the structuring
 element should be large to remove the cells or objects but preserve the
 (uneven) illumination function.
 
 
 The approach is adapted from:
 
 author = {Soille, Pierre},
 title = {Morphological Image Analysis: Principles
 and Applications},
 year = {2010},
 isbn = {9783642076961},
 edition = {2},
 pages = {124 -- 126},
 publisher = {Springer Berlin Heidelberg}. 
 
 
 Also other morphological operations can be used instead of the closing
 followed with a division of the images. Approach maybe depends on the image
 data.
 
 Feel free to extend this class!

Author:

Danny Misiak

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 MTBImage	inputImage
private BasicMorphology	morphOp
private MTBImage	outputImage
private MTBImage.MTBImageType	outputType

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
IlluminationCorrection() Standard constructor.
IlluminationCorrection(MTBImage _inputImage, BasicMorphology _morphOp, MTBImage.MTBImageType _outputType) Constructor to create a new IlluminationCorrection object.

Method Summary

Modifier and Type	Method and Description
private MTBImage	div(MTBImage img1, MTBImage img2) Method to divide two images.
String	getDocumentation()
MTBImage.MTBImageType	getImageType() Get output image type.
MTBImage	getInputImage() Get uneven illuminated input image.
BasicMorphology	getMorphOp() Get morphological operation for illumination correction, default is closing.
MTBImage	getResultImage() Get illumination corrected result image.
protected void	operate()
void	setImageType(MTBImage.MTBImageType _outputType) Set output image type.
void	setInputImage(MTBImage _inputImage) Set uneven illuminated input image.
void	setMorphOp(BasicMorphology _morphOp) Set morphological operation for illumination correction, default is closing.

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, 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

inputImage

@Parameter(label="Input Image",
           required=true,
           direction=IN,
           description="Uneven illuminated input image.",
           mode=STANDARD,
           dataIOOrder=0)
private transient MTBImage inputImage

morphOp

@Parameter(label="Morphology",
           required=true,
           direction=IN,
           description="Morphological operator for correction.",
           mode=STANDARD,
           dataIOOrder=1)
private BasicMorphology morphOp

outputType

@Parameter(label="Output Image Type",
           required=true,
           direction=IN,
           description="Image type of illumination corrected output image.",
           mode=STANDARD,
           dataIOOrder=2)
private MTBImage.MTBImageType outputType

outputImage

@Parameter(label="Output Image",
           required=true,
           direction=OUT,
           description="Illumination corrected output image.")
private transient MTBImage outputImage

Constructor Detail

IlluminationCorrection

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

Standard constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

IlluminationCorrection

public IlluminationCorrection(MTBImage _inputImage,
                              BasicMorphology _morphOp,
                              MTBImage.MTBImageType _outputType)
                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor to create a new IlluminationCorrection object.

Parameters:

image - uneven illuminated input image

operator - morphological operator for correction, e.g. closing

type - MTBImageType of illumination corrected output image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

getInputImage

public MTBImage getInputImage()

Get uneven illuminated input image.

setInputImage

public void setInputImage(MTBImage _inputImage)

Set uneven illuminated input image.

getMorphOp

public BasicMorphology getMorphOp()

Get morphological operation for illumination correction, default is closing.

setMorphOp

public void setMorphOp(BasicMorphology _morphOp)

Set morphological operation for illumination correction, default is closing.

getImageType

public MTBImage.MTBImageType getImageType()

Get output image type.

setImageType

public void setImageType(MTBImage.MTBImageType _outputType)

Set output image type.

getResultImage

public MTBImage getResultImage()

Get illumination corrected result image.

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

div

private MTBImage div(MTBImage img1,
                     MTBImage img2)

Method to divide two images. Method is copied and modified from ImageArithmetics.

getDocumentation

public String getDocumentation()

Overrides:

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