|
||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
@ALDAOperator(genericExecutionMode=NONE, level=STANDARD, allowBatchMode=false) public class NeuriteMolProfExtractor2D
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).
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 |
---|
private static transient int color_blue
private static transient int color_red
private transient int height
@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
@Parameter(label="Molecule Image", required=true, direction=IN, description="Multichannel image with fluorescence labeled molecules.", mode=STANDARD, dataIOOrder=0) private transient MTBImage moleculeImage
@Parameter(label="Neurite Set", required=true, direction=IN, description="Set of 2D neurites.", mode=STANDARD, dataIOOrder=2) private transient MTBNeurite2DSet neuriteSet
@Parameter(label="Profile Vector", required=false, direction=OUT, description="Result vector of protein profile set.") private transient java.util.Vector<MTBNeurite2DProfileSet> profileVector
private transient int sizeC
private transient int width
Constructor Detail |
---|
public NeuriteMolProfExtractor2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NeuriteMolProfExtractor2D(MTBImage _moleculeImage, java.lang.Integer[] _moleculeChannels, MTBNeurite2DSet _neuriteSet, java.lang.Boolean _verbose) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_moleculeImage
- multichannel fluorescence image with stained molecules_moleculeChannels
- channles including molecule stains_neuriteSet
- set of MTBNeurite2D objects_molecules
- _verbose
- flag for standard console outputs
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
---|
private java.util.Vector<MTBNeurite2DProfileSet> calcProfile()
public int getImageSizeX()
public int getImageSizeY()
public MTBImage getMoelculeImg()
public java.lang.Integer[] getMoleculeChannles()
public MTBNeurite2DSet getNeuriteSet()
public java.util.Vector<MTBNeurite2DProfileSet> getProfiles()
protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public void validateCustom() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
validateCustom
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
|
||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |