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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION) public class MultiChannelParticleAnalyzer2D
Operator for detecting sub-cellular structures in a given image.
This operator allows to configure a particle detector for each channel of the image separately. If a proper nucleus channel is given that one is skipped. The first detector in the vector of detectors is applied to the first non-nucleus channel, the second to the second, etc. It is important that for all channels to be processed detectors are provided.
Nested Class Summary | |
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static class |
MultiChannelParticleAnalyzer2D.ResultImageMode
Display mode of the result image. |
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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private MTBImageByte |
excludeMask
Optional mask to exclude particles in certain regions. |
private int |
height
Height of the processed image. |
private MTBImage |
inImg
Multi-channel input image to be processed. |
private SegResultEnums.MeasureUnit |
measureUnits
Units for measurements. |
private ParticleDetector |
particleDetector_1
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private ParticleDetector |
particleDetector_2
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private ParticleDetector |
particleDetector_3
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private ParticleDetector |
particleDetector_4
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private ParticleDetector |
particleDetector_5
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private SegResult_ParticlesMultiChannel |
resultData
Vector of result data objects. |
private MultiChannelParticleAnalyzer2D.ResultImageMode |
resultDisplayMode
Mode of how to display result image. |
private MTBImageRGB |
resultImg
Stack with result overlays corresponding to channels. |
private int |
stackSize
Number of channels in image. |
private int |
width
Width of the processed image. |
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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MultiChannelParticleAnalyzer2D()
Empty constructor. |
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MultiChannelParticleAnalyzer2D(MTBImage image,
java.util.Vector<ParticleDetector> pOps)
Default constructor. |
Method Summary | |
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java.util.Vector<ParticleDetector> |
getDetectors()
Get a reference to configured detectors' vector. |
SegResult_ParticlesMultiChannel |
getResultDataArray()
Returns extracted result data. |
MTBImageRGB |
getResultImage()
Returns result image, i.e. the segmentation mask. |
protected void |
operate()
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private void |
prepareResultImage()
Prepare visualization of result data by overlay on input image. |
private MTBImageRGB |
prepareResultImageStack(java.util.Vector<MTBImage> imgvec)
Initialize result image stack. |
void |
setInputImage(MTBImage img)
Specify input image. |
void |
setMeasureUnits(SegResultEnums.MeasureUnit mu)
Specify units in which to measure areas. |
void |
setNucleiMask(MTBImageByte mask)
Specify nuclei mask. |
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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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, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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@Parameter(label="Region exclude mask", direction=IN, mode=ADVANCED, required=false, description="Region exclude mask.") private transient MTBImageByte excludeMask
Particles in exclude regions are ignored if mask is non-null.
private transient int height
@Parameter(label="Input image", required=true, mode=STANDARD, direction=IN, description="Input image.", dataIOOrder=-20) private transient MTBImage inImg
@Parameter(label="Measure units", required=false, dataIOOrder=20, mode=ADVANCED, direction=IN, description="Units for area measurements.") private SegResultEnums.MeasureUnit measureUnits
@Parameter(label="Particle detector channel 1", required=false, direction=IN, dataIOOrder=-15, mode=STANDARD, description="Particle detector operator(s) for channels.") private ParticleDetector particleDetector_1
@Parameter(label="Particle detector channel 2", required=false, direction=IN, dataIOOrder=-14, mode=STANDARD, description="Particle detector operator(s) for channels.") private ParticleDetector particleDetector_2
@Parameter(label="Particle detector channel 3", required=false, direction=IN, dataIOOrder=-13, mode=STANDARD, description="Particle detector operator(s) for channels.") private ParticleDetector particleDetector_3
@Parameter(label="Particle detector channel 4", required=false, direction=IN, dataIOOrder=-12, mode=STANDARD, description="Particle detector operator(s) for channels.") private ParticleDetector particleDetector_4
@Parameter(label="Particle detector channel 5", required=false, direction=IN, dataIOOrder=-11, mode=STANDARD, description="Particle detector operator(s) for channels.") private ParticleDetector particleDetector_5
@Parameter(label="Result statistics", direction=OUT, description="Result data.") private transient SegResult_ParticlesMultiChannel resultData
@Parameter(label="Result image display mode", required=false, mode=ADVANCED, direction=IN, supplemental=true, description="Mode how result image is displayed.") private MultiChannelParticleAnalyzer2D.ResultImageMode resultDisplayMode
@Parameter(label="Result image", direction=OUT, description="Result image", supplemental=true) private transient MTBImageRGB resultImg
private transient int stackSize
private transient int width
Constructor Detail |
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public MultiChannelParticleAnalyzer2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public MultiChannelParticleAnalyzer2D(MTBImage image, java.util.Vector<ParticleDetector> pOps) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
image
- Image to be processed.pOps
- List of detectors.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public java.util.Vector<ParticleDetector> getDetectors()
public SegResult_ParticlesMultiChannel getResultDataArray()
public MTBImageRGB getResultImage()
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
private void prepareResultImage()
private MTBImageRGB prepareResultImageStack(java.util.Vector<MTBImage> imgvec)
Transfers result images to a multi-channel RGB image.
public void setInputImage(MTBImage img)
public void setMeasureUnits(SegResultEnums.MeasureUnit mu)
public void setNucleiMask(MTBImageByte mask)
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