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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
@ALDAOperator(genericExecutionMode=NONE) public class NucleusSeparator2DPeakSearch_RegionSeparator
Operator to analyze a given binary image or a set of nuclei regions.
The data will be transformed into a distance map in which the peaks are analyzed and compared to identify overlapping nuclei.
The result will be center-coordinates of all nuclei in the data. Furthermore the regions may be divided or initial regions for further analysis may be delivered.
This operator has been written as part of Jochen's project in WS 2011/12.
Nested Class Summary |
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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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boolean |
report
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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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NucleusSeparator2DPeakSearch_RegionSeparator()
Default constructor. |
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NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte image)
Constructor with input image. |
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NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet oset)
Constructor with region set. |
Method Summary | |
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MTBRegion2DSet |
getCandidates()
Returns set of detected candidate peaks. |
MTBImage |
getDistImg()
Returns calculated distance map. |
MTBPolygon2DSet |
getEllipsoidSnakePrimer()
Returns set of initial snake ellipses. |
MTBRegion2DSet |
getInputRegs()
Get set of input regions. |
MTBRegion2DSet[] |
getRegCenters()
Returns the centers of the nuclei sorted to their original regions. |
MTBRegion2DSet[] |
getResultAreas()
Returns separated regions sorted according to original regions. |
MTBRegion2DSet |
getResultCenters()
Returns centers of result regions. |
MTBPolygon2DSet |
getVoronoidSnakePrimer()
Returns set of snake polygons resulting from Voronoi tesselation. |
protected void |
operate()
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void |
setDistmet(DistanceTransform.DistanceMetric _distmet)
Specify the metric for the distance transformation. |
void |
setInImg(MTBImageByte _inImg)
Specify binary input image. |
void |
setInputRegs(MTBRegion2DSet _inputRegions)
Specify set of input regions. |
void |
setMad(double _mad)
Sets maximal allowed discrepancy of direct connection to actual profile between two peaks. |
void |
setMax_d2c(double _max_d2c)
Sets factor to adjust maximal allowed distance from lower to upper peak. |
void |
setSuppressor(int sup)
Sets threshold to suppress peak analysis close to scraggy contours. |
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, validateCustom, 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 |
Field Detail |
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public transient boolean report
Constructor Detail |
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public NucleusSeparator2DPeakSearch_RegionSeparator() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte image) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
image
- Binary input image.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet oset) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Note: the set needs correct referenced dimensions!
oset
- Set of input regions.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public void setInImg(MTBImageByte _inImg)
inImg
- Binary input image.public MTBRegion2DSet getInputRegs()
public void setInputRegs(MTBRegion2DSet _inputRegions)
inputRegions
- Set of input regions.public MTBImage getDistImg()
public MTBRegion2DSet getResultCenters()
public MTBRegion2DSet getCandidates()
public void setMax_d2c(double _max_d2c)
max_d2c
- Adjustment factor, default is 1.5.public void setMad(double _mad)
mad
- Max. discrepancy, default is 0.11.public void setDistmet(DistanceTransform.DistanceMetric _distmet)
distmet
- Distance metric, default is Chessboard-Distance.public void setSuppressor(int sup)
sup
- Threshold, should be >4.public MTBRegion2DSet[] getRegCenters()
public MTBRegion2DSet[] getResultAreas()
public MTBPolygon2DSet getVoronoidSnakePrimer() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
public MTBPolygon2DSet getEllipsoidSnakePrimer()
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
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