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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
@ALDAOperator(genericExecutionMode=NONE, level=STANDARD, allowBatchMode=false) public class NeuriteExtractor2D
The Neurite Extractor 2D application offers advanced functionality to extract
neurite regions in 2D binary neuron images of neurons. The neurites are
separated from the soma. In addition, the borderlines between the soma and
the neurite shafts, as well as between the neurite shaft and their growth
cone is extracted.
The exact localization of neurites without the soma (cell body) region is
calculated via a wavelet based detection approach from the R script
"MTBNeuriteFeatureDetection.R". Neurites are returned as MTBNeurite2D
objects.
Note: Don't know why operator cannot run twice without restart of MiToBo.
Maybe a threading problem of the R engine.
MTBNeuriteSkelGraph
,
MTBNeurite2DSet
Nested Class Summary | |
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static class |
NeuriteExtractor2D.NeuronColor
Color of binary neuron image foreground. |
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary |
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Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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NeuriteExtractor2D()
Standard constructor. |
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NeuriteExtractor2D(MTBImageByte _neuronImage,
NeuriteExtractor2D.NeuronColor _neuronColor,
int _neuriteMaskSize,
int _maxSpineLength,
org.rosuda.JRI.Rengine _rEngine,
String _outputDir)
Constructor to create a new neurite extraction object. |
Method Summary | |
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void |
cleanNeurites(MTBNeurite2DSet tmpNeuriteSet)
Method to clean up the extracted neurites, due to multiple features along a NSG path or feature shifts at the start point due to different NSG lengths. |
MTBImageByte |
drawLine2D(Line2D.Double line,
Point2D.Double point)
Draws a 2D line into the neuron image. |
MTBNeurite2DSet |
getExtractedNeurites()
Get extracted neurites as result of the NeuriteExtraction2D operator. |
int |
getMaxSpineLength()
Get maximum length of a spine (filopodia-like protrusion) in pixel. |
int |
getNeuriteMaskSize()
Get neurite mask size in pixel. |
NeuriteExtractor2D.NeuronColor |
getNeuronColor()
Get binary neuron color. |
MTBImageByte |
getNeuronImage()
Get input image of the binary neuron. |
org.rosuda.JRI.Rengine |
getREngine()
Get R engine. |
protected void |
operate()
|
void |
setMaxSpineLength(int _maxSpineLength)
Set maximum length of a spine (filopodia-like protrusion) in pixel. |
void |
setNeuronColor(NeuriteExtractor2D.NeuronColor _neuronColor)
Set binary neuron color. |
void |
setNeuronImage(MTBImageByte _neuronImage)
Set input image of the binary neuron. |
void |
setNuriteMaskSize(int _neuriteMaskSize)
Set neurite mask size in pixel. |
void |
setREngine(org.rosuda.JRI.Rengine _rEngine)
Set R engine. |
void |
validateCustom()
Custom validation of some input parameters. |
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator |
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readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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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, validateGeneric, writeHistory, writeHistory, writeHistory |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public NeuriteExtractor2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NeuriteExtractor2D(MTBImageByte _neuronImage, NeuriteExtractor2D.NeuronColor _neuronColor, int _neuriteMaskSize, int _maxSpineLength, org.rosuda.JRI.Rengine _rEngine, String _outputDir) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_neuronImage
- binary neuron image_neuronColor
- binary neuron color, e.g. 0 (black) or 255 (white)_neuriteMaskSize
- mask size of average neurite width, in pixel_maxSpineLength
- maximum length of a branch to define it as spine, in pixel_rEngine
- engine to call R scripts_outputFile
- file path for feature output
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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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
public MTBImageByte getNeuronImage()
public void setNeuronImage(MTBImageByte _neuronImage)
public NeuriteExtractor2D.NeuronColor getNeuronColor()
public void setNeuronColor(NeuriteExtractor2D.NeuronColor _neuronColor)
public int getNeuriteMaskSize()
public void setNuriteMaskSize(int _neuriteMaskSize)
public org.rosuda.JRI.Rengine getREngine()
public void setREngine(org.rosuda.JRI.Rengine _rEngine)
public int getMaxSpineLength()
public void setMaxSpineLength(int _maxSpineLength)
public MTBNeurite2DSet getExtractedNeurites()
MTBNeurite2D
objects.protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
public MTBImageByte drawLine2D(Line2D.Double line, Point2D.Double point)
This function implements the Bresenham algorithm. Code was 'stolen' from
Wikipedia, http://de.wikipedia.org/wiki/Bresenham-Algorithmus
, and
then translated into Java (German comments where kept).
xstart
- x-coordinate of start point.ystart
- y-coordinate of start point.xend
- x-coordinate of end point.yend
- y-coordinate of end point.value
- Color/gray-scale value of the polygon.public void cleanNeurites(MTBNeurite2DSet tmpNeuriteSet)
tmpNeuriteSet
- current temporary neurite set
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