de.unihalle.informatik.MiToBo.apps.neurites2D

Class NeuriteMolProfExtractor2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

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

All Implemented Interfaces:

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

@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, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private static int	color_blue
private static int	color_red
private int	height
private Integer[]	moleculeChannels
private MTBImage	moleculeImage
private MTBNeurite2DSet	neuriteSet
private Vector<MTBNeurite2DProfileSet>	profileVector
private int	sizeC
private int	width

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NeuriteMolProfExtractor2D() Standard constructor
NeuriteMolProfExtractor2D(MTBImage _moleculeImage, Integer[] _moleculeChannels, MTBNeurite2DSet _neuriteSet, Boolean _verbose) Constructor to create a new neurite profile extraction operator.

Method Summary

Modifier and Type	Method and Description
private 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.
Integer[]	getMoleculeChannles() Get molecule channels, used for extraction.
MTBNeurite2DSet	getNeuriteSet() Get the input set of neurites.
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

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

color_blue

private static transient int color_blue

color_red

private static transient int color_red

width

private transient int width

height

private transient int height

sizeC

private transient int sizeC

moleculeImage

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

moleculeChannels

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

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 Vector<MTBNeurite2DProfileSet> profileVector

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,
                                 Integer[] _moleculeChannels,
                                 MTBNeurite2DSet _neuriteSet,
                                 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

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

getMoelculeImg

public MTBImage getMoelculeImg()

Get the input image with the fluorescence labeled molecules.

Returns:

Gray value molecule image.

getMoleculeChannles

public Integer[] getMoleculeChannles()

Get molecule channels, used for extraction.

getNeuriteSet

public MTBNeurite2DSet getNeuriteSet()

Get the input set of neurites.

Returns:

Neurite set.

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.

getProfiles

public 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

calcProfile

private Vector<MTBNeurite2DProfileSet> calcProfile()