de.unihalle.informatik.MiToBo.apps.actinAnalysis
Class ActinFeatureExtractorHaralickMeasures

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperator
          extended by de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              allowBatchMode=false)
public class ActinFeatureExtractorHaralickMeasures
extends MTBOperator

Operator for extracting Haralick texture measures from cooccurrence matrices as features for the ActinAnalyzer2D.

Author:
moeller

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
protected  Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> directions
          Directions for calculating cooccurrence matrices.
protected  int distance
          Distance.
protected  de.unihalle.informatik.Alida.datatypes.ALDDirectoryString imageDir
          Input image directory.
protected  boolean isotropicCalcs
          Flag for isotropic calculations.
protected  de.unihalle.informatik.Alida.datatypes.ALDDirectoryString maskDir
          Directory with (cell) masks.
protected  ActinAnalyzer2D.CellMaskFormat maskFormat
          Format of provided cell masks.
protected  de.unihalle.informatik.Alida.datatypes.ALDDirectoryString outDir
          Output and working directory.
protected  int tileShiftX
          Tile shift in x-direction.
protected  int tileShiftY
          Tile size in y-direction.
protected  int tileSizeX
          Tile size in x-direction.
protected  int tileSizeY
          Tile size in y-direction.
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider
 
Constructor Summary
ActinFeatureExtractorHaralickMeasures()
          Default constructor.
 
Method Summary
protected  void operate()
           
 void setDistance(int d)
          Specify distance for calculating cooccurrence matrices.
 void setFlagIsotropicCalculations(boolean flag)
          Enable/disable isotropic calculations.
 void setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> dirs)
          Set directions for which to calculate cooccurence matrices.
 void setImageDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString iDir)
          Specify input image directory.
 void setMaskDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString mDir)
          Specify input mask directory.
 void setMaskFormat(ActinAnalyzer2D.CellMaskFormat mFormat)
          Specify input mask format.
 void setOutputDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString oDir)
          Specify output directory.
 void setTileShiftX(int tShiftX)
          Specify shift of tiles in x-direction.
 void setTileShiftY(int tShiftY)
          Specify shift of tiles in y-direction.
 void setTileSizeX(int tSizeX)
          Specify size of tiles in x-direction.
 void setTileSizeY(int tSizeY)
          Specify size of tiles in y-direction.
 
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
readResolve
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
addOperatorExecutionProgressEventListener, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, 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

imageDir

@Parameter(label="Image directory",
           required=true,
           dataIOOrder=-10,
           direction=IN,
           description="Input image directory.",
           mode=STANDARD)
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString imageDir
Input image directory.

All files in the directory are considered. If a file cannot be opened (e.g. because it is not an image) it is skipped.


maskDir

@Parameter(label="Mask directory",
           required=true,
           dataIOOrder=-9,
           direction=IN,
           description="Cell mask directory.",
           mode=STANDARD)
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString maskDir
Directory with (cell) masks.


maskFormat

@Parameter(label="Mask format",
           required=true,
           dataIOOrder=-8,
           direction=IN,
           description="Format of cell masks.",
           mode=STANDARD)
protected ActinAnalyzer2D.CellMaskFormat maskFormat
Format of provided cell masks.


outDir

@Parameter(label="Output and working directory",
           required=true,
           dataIOOrder=-7,
           direction=IN,
           description="Output and working directory.",
           mode=STANDARD)
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString outDir
Output and working directory.


tileSizeX

@Parameter(label="Tile size x",
           required=true,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="Tile size in x-direction.")
protected int tileSizeX
Tile size in x-direction.


tileSizeY

@Parameter(label="Tile size y",
           required=true,
           dataIOOrder=4,
           direction=IN,
           mode=STANDARD,
           description="Tile size in y-direction.")
protected int tileSizeY
Tile size in y-direction.


tileShiftX

@Parameter(label="Tile shift x",
           required=true,
           dataIOOrder=5,
           direction=IN,
           mode=ADVANCED,
           description="Tile shift in x-direction.")
protected int tileShiftX
Tile shift in x-direction.


tileShiftY

@Parameter(label="Tile shift y",
           required=true,
           dataIOOrder=6,
           direction=IN,
           mode=ADVANCED,
           description="Tile shift in y-direction.")
protected int tileShiftY
Tile size in y-direction.


distance

@Parameter(label="Haralick distance",
           required=true,
           direction=IN,
           dataIOOrder=7,
           mode=STANDARD,
           description="Desired distance.")
protected int distance
Distance.


directions

@Parameter(label="Haralick directions",
           required=true,
           dataIOOrder=8,
           direction=IN,
           mode=STANDARD,
           description="Directions for matrices.")
protected Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> directions
Directions for calculating cooccurrence matrices.


isotropicCalcs

@Parameter(label="Isotropic calculations",
           required=true,
           direction=IN,
           dataIOOrder=9,
           description="Flag to enable isotropic calculations.",
           mode=ADVANCED)
protected boolean isotropicCalcs
Flag for isotropic calculations.

If flag is true the average of each feature for the four directions EAST, NORTH_EAST, NORTH and NORTH_WEST is taken as result. But, note that this causes the computation time to be increased by a factor of four as well.

Constructor Detail

ActinFeatureExtractorHaralickMeasures

public ActinFeatureExtractorHaralickMeasures()
                                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Default constructor.

Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

setImageDir

public void setImageDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString iDir)
Specify input image directory.

Parameters:
iDir - Directory with images.

setMaskDir

public void setMaskDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString mDir)
Specify input mask directory.

Parameters:
mDir - Directory with masks.

setMaskFormat

public void setMaskFormat(ActinAnalyzer2D.CellMaskFormat mFormat)
Specify input mask format.

Parameters:
mFormat - Format of mask files, i.e. label images or ImageJ ROI files.

setOutputDir

public void setOutputDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString oDir)
Specify output directory.

Parameters:
oDir - Output directory for feature files.

setTileSizeX

public void setTileSizeX(int tSizeX)
Specify size of tiles in x-direction.

Parameters:
tSizeX - Tile size in x.

setTileSizeY

public void setTileSizeY(int tSizeY)
Specify size of tiles in y-direction.

Parameters:
tSizeY - Tile size in y.

setTileShiftX

public void setTileShiftX(int tShiftX)
Specify shift of tiles in x-direction.

Parameters:
tShiftX - Tile shift in x.

setTileShiftY

public void setTileShiftY(int tShiftY)
Specify shift of tiles in y-direction.

Parameters:
tShiftY - Tile shift in y.

setDistance

public void setDistance(int d)
Specify distance for calculating cooccurrence matrices.

Parameters:
d - Pixel distance to apply.

setHaralickDirections

public void setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> dirs)
Set directions for which to calculate cooccurence matrices.

Parameters:
dirs - List of directions.

setFlagIsotropicCalculations

public void setFlagIsotropicCalculations(boolean flag)
Enable/disable isotropic calculations.

Parameters:
flag - If true, isotropic calculations are enabled.

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


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