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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
@ALDAOperator(genericExecutionMode=ALL, level=STANDARD, allowBatchMode=false) public class ActinFeatureExtractorEigenStructures
Operator for extracting Eigen structures as features for the
ActinAnalyzer2D
.
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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protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
imageDir
Input image directory. |
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
maskDir
Directory with (cell) masks. |
protected ActinAnalyzer2D.CellMaskFormat |
maskFormat
Format of provided cell masks. |
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
outDir
Output and working directory. |
protected int |
tileShiftX
Tile shift in x-direction. |
protected int |
tileShiftY
Tile size in y-direction. |
protected int |
tileSizeX
Tile size in x-direction. |
protected int |
tileSizeY
Tile size in y-direction. |
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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ActinFeatureExtractorEigenStructures()
Default constructor. |
Method Summary | |
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protected void |
operate()
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void |
setImageDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString iDir)
Specify input image directory. |
void |
setMaskDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString mDir)
Specify input mask directory. |
void |
setMaskFormat(ActinAnalyzer2D.CellMaskFormat mFormat)
Specify input mask format. |
void |
setOutputDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString oDir)
Specify output directory. |
void |
setTileShiftX(int tShiftX)
Specify shift of tiles in x-direction. |
void |
setTileShiftY(int tShiftY)
Specify shift of tiles in y-direction. |
void |
setTileSizeX(int tSizeX)
Specify size of tiles in x-direction. |
void |
setTileSizeY(int tSizeY)
Specify size of tiles in y-direction. |
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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@Parameter(label="Image directory", required=true, dataIOOrder=-10, direction=IN, description="Input image directory.", mode=STANDARD) protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString imageDir
All files in the directory are considered. If a file cannot be opened (e.g. because it is not an image) it is skipped.
@Parameter(label="Mask directory", required=true, dataIOOrder=-9, direction=IN, description="Cell mask directory.", mode=STANDARD) protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString maskDir
@Parameter(label="Mask format", required=true, dataIOOrder=-8, direction=IN, description="Format of cell masks.", mode=STANDARD) protected ActinAnalyzer2D.CellMaskFormat maskFormat
@Parameter(label="Output and working directory", required=true, dataIOOrder=-7, direction=IN, description="Output and working directory.", mode=STANDARD) protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString outDir
@Parameter(label="Tile size x", required=true, dataIOOrder=3, direction=IN, mode=STANDARD, description="Tile size in x-direction.") protected int tileSizeX
@Parameter(label="Tile size y", required=true, dataIOOrder=4, direction=IN, mode=STANDARD, description="Tile size in y-direction.") protected int tileSizeY
@Parameter(label="Tile shift x", required=true, dataIOOrder=5, direction=IN, mode=ADVANCED, description="Tile shift in x-direction.") protected int tileShiftX
@Parameter(label="Tile shift y", required=true, dataIOOrder=6, direction=IN, mode=ADVANCED, description="Tile shift in y-direction.") protected int tileShiftY
Constructor Detail |
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public ActinFeatureExtractorEigenStructures() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public void setImageDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString iDir)
iDir
- Directory with images.public void setMaskDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString mDir)
mDir
- Directory with masks.public void setMaskFormat(ActinAnalyzer2D.CellMaskFormat mFormat)
mFormat
- Format of mask files, i.e. label images or ImageJ ROI files.public void setOutputDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString oDir)
oDir
- Output directory for feature files.public void setTileSizeX(int tSizeX)
tSizeX
- Tile size in x.public void setTileSizeY(int tSizeY)
tSizeY
- Tile size in y.public void setTileShiftX(int tShiftX)
tShiftX
- Tile shift in x.public void setTileShiftY(int tShiftY)
tShiftY
- Tile shift in y.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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