@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION, allowBatchMode=false) public class FeatureColorMapper extends MTBOperator
The input images are assumed to be label images with the label corresponding
to an object ID in the given feature table file. The IDs are assumend to be
larger than zero.
For each image the range of feature values in the selected column of the
feature table is determined, and the values are linearly mapped to the color
range defined by the given minimal and maximal color.
Finally, each pixel an image with a value larger than zero gets the color
value corresponding to the color of its feature value as derived from the
feature value in the corresponding row of the feature table.
The minimal and maximal size threshold can be used to exclude too small or too large cells from mapping. The thresholds are always applied to the cell areas and sizes below the minimal or above the maximal threshold are ignored.
Modifier and Type | Field and Description |
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private static String |
classID
Class identifier.
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private PaCeQuant_FeatureColorMapperInputData |
inData
Input data.
|
protected Color |
maxColor
Color for maximal value.
|
protected double |
maxSizeValue
Maximal value threshold.
|
protected Color |
minColor
Color for minimal value.
|
protected double |
minSizeValue
Minimal size threshold.
|
Constructor and Description |
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FeatureColorMapper()
Default constructor.
|
Modifier and Type | Method and Description |
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protected void |
operate()
This method does the actual work.
|
void |
setColorRangeMaximum(Color c)
Color for range maximum.
|
void |
setColorRangeMinimum(Color c)
Color for range minimum.
|
void |
setInputData(String indir,
int[] ids)
Set input data.
|
void |
validateCustom() |
readResolve
addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory
private static final String classID
@Parameter(label="Input Data", required=true, dataIOOrder=1, direction=IN, description="Input experiment directory and column selection, all sub-folders named \'results\' will be considered") private PaCeQuant_FeatureColorMapperInputData inData
@Parameter(label="Color of Range Minimum", required=true, dataIOOrder=7, direction=IN, description="Color of small values.") protected Color minColor
@Parameter(label="Color of Range Maximum", required=true, dataIOOrder=9, direction=IN, description="Color of large values.") protected Color maxColor
@Parameter(label="Minimal size threshold", required=true, dataIOOrder=10, direction=IN, description="Values smaller than this one are ignored.") protected double minSizeValue
@Parameter(label="Maximal size threshold", required=true, dataIOOrder=11, direction=IN, description="Values larger than this one are ignored.") protected double maxSizeValue
public FeatureColorMapper() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Thrown in case of failure.public void setInputData(String indir, int[] ids)
indir
- Input experiment folder.ids
- Selected columns.public void setColorRangeMinimum(Color c)
c
- Color to use.public void setColorRangeMaximum(Color c)
c
- Color to use.public void validateCustom() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
validateCustom
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
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
- Thrown in case of failure.de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- Thrown in case of failure.Copyright © 2010–2020 Martin Luther University Halle-Wittenberg, Institute of Computer Science, Pattern Recognition and Bioinformatics. All rights reserved.