|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION, allowBatchMode=false) public class ActinAnalyzer2D
Operator for analyzing actin filament structures in 2D images.
Nested Class Summary | |
---|---|
static class |
ActinAnalyzer2D.CellMaskFormat
Format of cell segmentation data. |
static class |
ActinAnalyzer2D.FeatureType
Type of features to characterize local structure. |
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
---|
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary | |
---|---|
protected Vector<org.jfree.chart.JFreeChart> |
boxWhiskerCharts
Box-whisker plot of the group-wise cluster distributions. |
protected int |
clusterNum
Number of clusters to be used in feature clustering. |
protected Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> |
directions
Set of directions. |
protected int |
distance
Distance. |
protected boolean |
doFeatureCalculation
Flag for calculating features. |
protected boolean |
doPCA
Perform PCA in second stage? |
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
featureDir
Feature directory. |
protected ActinAnalyzer2D.FeatureType |
featureType
Type of features to apply. |
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString |
imageDir
Input image directory. |
protected boolean |
isotropicCalcs
Flag for isotropic calculations. |
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 Vector<org.jfree.chart.JFreeChart> |
stackedBarCharts
Resulting stacked bar plot of cluster distributions. |
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 |
---|
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
---|---|
ActinAnalyzer2D()
Default constructor. |
Method Summary | |
---|---|
protected void |
operate()
|
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator |
---|
readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
---|
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 |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
@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="Calculate features?", required=true, dataIOOrder=0, direction=IN, description="Flag to enable/disable feature calculation.", mode=STANDARD) protected boolean doFeatureCalculation
If set to false, the name of a directory containing the features must be provided.
@Parameter(label="Type of features", required=true, dataIOOrder=1, direction=IN, description="Select type of features to apply.", mode=STANDARD) protected ActinAnalyzer2D.FeatureType featureType
@Parameter(label="Feature directory", required=true, dataIOOrder=2, direction=IN, mode=STANDARD, description="Feature directory, may be the same as output directory.") protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString featureDir
@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
@Parameter(label="Haralick distance", required=true, direction=IN, dataIOOrder=7, mode=STANDARD, description="Desired distance.") protected int distance
@Parameter(label="Set of directions", required=true, direction=IN, dataIOOrder=8, mode=STANDARD, description="Desired directions.") protected Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> directions
@Parameter(label="Isotropic calculations", required=true, direction=IN, dataIOOrder=9, description="Flag to enable isotropic calculations.", mode=ADVANCED) protected boolean isotropicCalcs
If flag is true the average of each feature for the four directions EAST, NORTH_EAST, NORTH and NORTH_WEST is taken as result. But, note that this causes the computation time to be increased by a factor of four as well.
@Parameter(label="Number of feature clusters", required=true, dataIOOrder=10, direction=IN, mode=ADVANCED, description="Number of feature clusters.") protected int clusterNum
@Parameter(label="Do PCA in stage II?", required=true, dataIOOrder=11, direction=IN, mode=ADVANCED, description="Enable/disable PCA prior to hierarchical clustering.") protected boolean doPCA
@Parameter(label="Resulting chart plots for each group", dataIOOrder=1, direction=OUT, description="Resulting chart plots.", mode=STANDARD) protected Vector<org.jfree.chart.JFreeChart> stackedBarCharts
@Parameter(label="Resulting box-whisker plot", dataIOOrder=1, direction=OUT, description="Resulting box-whisker plot.", mode=STANDARD) protected Vector<org.jfree.chart.JFreeChart> boxWhiskerCharts
Constructor Detail |
---|
public ActinAnalyzer2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
---|
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
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |