de.unihalle.informatik.MiToBo.apps.actinAnalysis
Class ActinAnalyzer2D

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.ActinAnalyzer2D
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false)
public class ActinAnalyzer2D
extends MTBOperator

Operator for analyzing actin filament structures in 2D images.

Author:
moeller

Nested Class Summary
static class ActinAnalyzer2D.CellMaskFormat
          Format of cell segmentation data.
static class ActinAnalyzer2D.FeatureType
          Type of features to characterize local structure.
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
protected  Vector<org.jfree.chart.JFreeChart> boxWhiskerCharts
          Box-whisker plot of the group-wise cluster distributions.
protected  int clusterNum
          Number of clusters to be used in feature clustering.
protected  Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> directions
          Set of directions.
protected  int distance
          Distance.
protected  boolean doFeatureCalculation
          Flag for calculating features.
protected  boolean doPCA
          Perform PCA in second stage?
protected  de.unihalle.informatik.Alida.datatypes.ALDDirectoryString featureDir
          Feature directory.
protected  ActinAnalyzer2D.FeatureType featureType
          Type of features to apply.
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  Vector<org.jfree.chart.JFreeChart> stackedBarCharts
          Resulting stacked bar plot of cluster distributions.
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
ActinAnalyzer2D()
          Default constructor.
 
Method Summary
protected  void operate()
           
 
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.


doFeatureCalculation

@Parameter(label="Calculate features?",
           required=true,
           dataIOOrder=0,
           direction=IN,
           description="Flag to enable/disable feature calculation.",
           mode=STANDARD)
protected boolean doFeatureCalculation
Flag for calculating features.

If set to false, the name of a directory containing the features must be provided.


featureType

@Parameter(label="Type of features",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Select type of features to apply.",
           mode=STANDARD)
protected ActinAnalyzer2D.FeatureType featureType
Type of features to apply.


featureDir

@Parameter(label="Feature directory",
           required=true,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Feature directory, may be the same as output directory.")
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString featureDir
Feature 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="Set of directions",
           required=true,
           direction=IN,
           dataIOOrder=8,
           mode=STANDARD,
           description="Desired directions.")
protected Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> directions
Set of directions.


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.


clusterNum

@Parameter(label="Number of feature clusters",
           required=true,
           dataIOOrder=10,
           direction=IN,
           mode=ADVANCED,
           description="Number of feature clusters.")
protected int clusterNum
Number of clusters to be used in feature clustering.


doPCA

@Parameter(label="Do PCA in stage II?",
           required=true,
           dataIOOrder=11,
           direction=IN,
           mode=ADVANCED,
           description="Enable/disable PCA prior to hierarchical clustering.")
protected boolean doPCA
Perform PCA in second stage?


stackedBarCharts

@Parameter(label="Resulting chart plots for each group",
           dataIOOrder=1,
           direction=OUT,
           description="Resulting chart plots.",
           mode=STANDARD)
protected Vector<org.jfree.chart.JFreeChart> stackedBarCharts
Resulting stacked bar plot of cluster distributions.


boxWhiskerCharts

@Parameter(label="Resulting box-whisker plot",
           dataIOOrder=1,
           direction=OUT,
           description="Resulting box-whisker plot.",
           mode=STANDARD)
protected Vector<org.jfree.chart.JFreeChart> boxWhiskerCharts
Box-whisker plot of the group-wise cluster distributions.

Constructor Detail

ActinAnalyzer2D

public ActinAnalyzer2D()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Default constructor.

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

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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