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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
@ALDAOperator(genericExecutionMode=SWING, level=STANDARD) public class CellSegmentationPostprocessing
operator for doing common postprocessing tasks on already segmented cell images
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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private java.lang.Double |
fg_value
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private MTBImage |
inImg
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private java.lang.Integer |
minArea
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private java.lang.Boolean |
objects8Connected
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private java.lang.Boolean |
removeBorderObjects
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private MTBImage |
resultImg
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private int |
sizeC
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private int |
sizeT
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private int |
sizeX
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private int |
sizeY
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private int |
sizeZ
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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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CellSegmentationPostprocessing()
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CellSegmentationPostprocessing(MTBImage inImg)
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Method Summary | |
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private void |
drawRegions(MTBRegion2DSet keepRegions,
int z,
int t,
int c)
draw regions to the output image |
private MTBRegion2DSet |
excludeBorderRegions(MTBRegion2DSet regions)
exclude regions that are adjacent to the image borders |
private MTBRegion2DSet |
excludeSmallRegions(MTBRegion2DSet regions)
exclude regions that are smaller than the predefined (Parameter minArea) minimum |
MTBImage |
getResultImage()
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void |
operate()
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void |
setBorderExclusion(boolean excludeBorderObjects)
should border touching objects be excluded |
void |
setFG_Value(double val)
set the intensity value of the remaining foreground regions |
void |
setMinimumObjectArea(int minArea)
set the minimum area (number of pixels) a region must have in order to be kept |
void |
setObjectsEightConnected(boolean eightconnected)
are regions to be considered 8-connected (4-connected otherwise) |
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="foreground value", required=false, direction=IN, supplemental=false, description="intensity value for remaining foreground object pixel") private java.lang.Double fg_value
@Parameter(label="input image", required=true, direction=IN, supplemental=false, description="binary input image") private transient MTBImage inImg
@Parameter(label="minimum area (pixels)", required=false, direction=IN, supplemental=false, description="minimum area (number of pixels) an object should have") private java.lang.Integer minArea
@Parameter(label="are objects 8-connected", required=false, direction=IN, supplemental=false, description="are objects 8-connected (4-connected otherwise)") private java.lang.Boolean objects8Connected
@Parameter(label="remove border touching objects", required=false, direction=IN, supplemental=false, description="should border touching objects be removed") private java.lang.Boolean removeBorderObjects
@Parameter(label="result image", required=true, direction=OUT, supplemental=false, description="result image") private transient MTBImage resultImg
private int sizeC
private int sizeT
private int sizeX
private int sizeY
private int sizeZ
Constructor Detail |
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public CellSegmentationPostprocessing() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public CellSegmentationPostprocessing(MTBImage inImg) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
inImg
- input image
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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private void drawRegions(MTBRegion2DSet keepRegions, int z, int t, int c)
keepRegions
- 2D regions to drawz
- slice numbert
- frame numberc
- channel numberprivate MTBRegion2DSet excludeBorderRegions(MTBRegion2DSet regions)
regions
- image regions
private MTBRegion2DSet excludeSmallRegions(MTBRegion2DSet regions)
regions
- image regions
public MTBImage getResultImage()
public 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 void setBorderExclusion(boolean excludeBorderObjects)
excludeBorderObjects
- public void setFG_Value(double val)
val
- public void setMinimumObjectArea(int minArea)
minArea
- public void setObjectsEightConnected(boolean eightconnected)
eightconnected
-
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