de.unihalle.informatik.MiToBo.apps.neurites2D
Class NeuriteMolProfExtractor2D

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.neurites2D.NeuriteMolProfExtractor2D
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator

@ALDAOperator(genericExecutionMode=NONE,
              level=STANDARD,
              allowBatchMode=false)
public class NeuriteMolProfExtractor2D
extends MTBOperator

The Neurite Molecular Profile Extractor 2D application offers advanced functionality to extract molecular intensity profiles of multichannel fluorescence images along detected neurite regions. The profiles are stored in a vector of profile sets. Each set includes the profiles for one neurite region over all protein stains (image channels).

Author:
Birgit Moeller, Danny Misiak

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
private static int color_blue
           
private static int color_red
           
private  int height
           
private  java.lang.Integer[] moleculeChannels
           
private  MTBImage moleculeImage
           
private  MTBNeurite2DSet neuriteSet
           
private  java.util.Vector<MTBNeurite2DProfileSet> profileVector
           
private  int sizeC
           
private  int width
           
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, portHashAccess, verbose, versionProvider
 
Constructor Summary
NeuriteMolProfExtractor2D()
          Standard constructor
NeuriteMolProfExtractor2D(MTBImage _moleculeImage, java.lang.Integer[] _moleculeChannels, MTBNeurite2DSet _neuriteSet, java.lang.Boolean _verbose)
          Constructor to create a new neurite profile extraction operator.
 
Method Summary
private  java.util.Vector<MTBNeurite2DProfileSet> calcProfile()
           
 int getImageSizeX()
          Get the image size in x-direction.
 int getImageSizeY()
          Get the image size in y-direction.
 MTBImage getMoelculeImg()
          Get the input image with the fluorescence labeled molecules.
 java.lang.Integer[] getMoleculeChannles()
          Get molecule channels, used for extraction.
 MTBNeurite2DSet getNeuriteSet()
          Get the input set of neurites.
 java.util.Vector<MTBNeurite2DProfileSet> getProfiles()
          Get the resulting set of neurite profiles.
protected  void operate()
          This method does the actual work.
 void validateCustom()
          Custom validation of some input parameters.
 
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
readResolve
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
deserializeFromXmlFile, fieldContained, getALDPortHashAccessKey, getConstructionMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, isConfigured, parametersToXmlObject, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, runOp, runOp, runOp, serializeToXmlFile, setConstructionMode, setName, setParameter, setParametersFromXml, setParametersFromXml, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

color_blue

private static transient int color_blue

color_red

private static transient int color_red

height

private transient int height

moleculeChannels

@Parameter(label="Profile Molecule Channels",
           direction=IN,
           required=true,
           description="Channels of molecules for profile extraction.",
           mode=STANDARD,
           dataIOOrder=1)
private java.lang.Integer[] moleculeChannels

moleculeImage

@Parameter(label="Molecule Image",
           required=true,
           direction=IN,
           description="Multichannel image with fluorescence labeled molecules.",
           mode=STANDARD,
           dataIOOrder=0)
private transient MTBImage moleculeImage

neuriteSet

@Parameter(label="Neurite Set",
           required=true,
           direction=IN,
           description="Set of 2D neurites.",
           mode=STANDARD,
           dataIOOrder=2)
private transient MTBNeurite2DSet neuriteSet

profileVector

@Parameter(label="Profile Vector",
           required=false,
           direction=OUT,
           description="Result vector of protein profile set.")
private transient java.util.Vector<MTBNeurite2DProfileSet> profileVector

sizeC

private transient int sizeC

width

private transient int width
Constructor Detail

NeuriteMolProfExtractor2D

public NeuriteMolProfExtractor2D()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Standard constructor

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

NeuriteMolProfExtractor2D

public NeuriteMolProfExtractor2D(MTBImage _moleculeImage,
                                 java.lang.Integer[] _moleculeChannels,
                                 MTBNeurite2DSet _neuriteSet,
                                 java.lang.Boolean _verbose)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor to create a new neurite profile extraction operator.

Parameters:
_moleculeImage - multichannel fluorescence image with stained molecules
_moleculeChannels - channles including molecule stains
_neuriteSet - set of MTBNeurite2D objects
_molecules -
_verbose - flag for standard console outputs
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

calcProfile

private java.util.Vector<MTBNeurite2DProfileSet> calcProfile()

getImageSizeX

public int getImageSizeX()
Get the image size in x-direction.

Returns:
Image size in x.

getImageSizeY

public int getImageSizeY()
Get the image size in y-direction.

Returns:
Image size in y.

getMoelculeImg

public MTBImage getMoelculeImg()
Get the input image with the fluorescence labeled molecules.

Returns:
Gray value molecule image.

getMoleculeChannles

public java.lang.Integer[] getMoleculeChannles()
Get molecule channels, used for extraction.


getNeuriteSet

public MTBNeurite2DSet getNeuriteSet()
Get the input set of neurites.

Returns:
Neurite set.

getProfiles

public java.util.Vector<MTBNeurite2DProfileSet> getProfiles()
Get the resulting set of neurite profiles.

Returns:
Neurite profiles.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
This method does the actual work.

Specified by:
operate in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Custom validation of some input parameters.

Overrides:
validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException