de.unihalle.informatik.MiToBo.apps.cellMorphology.paceQuant

Class FeatureColorMapper

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.apps.cellMorphology.paceQuant.FeatureColorMapper

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false)
public class FeatureColorMapper
extends MTBOperator

This operator maps numerical feature values to objects in an indexed image.

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.

All images ending with the given suffix are considered as potential candidates to be matched to found table files. The default suffix "grayscale-result.tif" has been set to allow for maximmal compatibility with PaCeQuant. It is assumed that corresponding table and image files share the same file prefix, i.e., the operator seeks to find matching files by searching for the largest common prefix between table and image file name.

Author:

moeller

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private static String	classID Class identifier.
private PaCeQuant_FeatureColorMapperInputData	inData Input data.
protected String	inputImgSuffix Input image suffix.
private int	maxB Blue color value [0,255] of color for maximal value in range.
protected Color	maxColor Color for maximal value.
private int	maxG Green color value [0,255] of color for maximal value in range.
private int	maxR Red color value [0,255] of color for maximal value in range.
protected double	maxSizeValue Maximal value threshold.
private int	minB Blue color value [0,255] of color for minimal value in range.
protected Color	minColor Color for minimal value.
private int	minG Green color value [0,255] of color for minimal value in range.
private int	minR Red color value [0,255] of color for minimal value in range.
protected double	minSizeValue Minimal size threshold.

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
FeatureColorMapper() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	operate() This method does the actual work.
private void	saveColorLegend(String subfolder, MTBTableModel tm, int col, double[] vMins, double[] vMaxs, double[] ranges) Function to generate and save color legends to sub-directories.
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()

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

classID

private static final String classID

Class identifier.

See Also:

Constant Field Values

inData

@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

Input data.

inputImgSuffix

@Parameter(label="Input image suffix",
           required=true,
           dataIOOrder=2,
           direction=IN,
           description="Only images matching this suffix are processed.")
protected String inputImgSuffix

Input image suffix.

minColor

@Parameter(label="Color of Range Minimum",
           required=true,
           dataIOOrder=7,
           direction=IN,
           description="Color of small values.")
protected Color minColor

Color for minimal value.

maxColor

@Parameter(label="Color of Range Maximum",
           required=true,
           dataIOOrder=9,
           direction=IN,
           description="Color of large values.")
protected Color maxColor

Color for maximal value.

minSizeValue

@Parameter(label="Minimal size threshold",
           required=true,
           dataIOOrder=10,
           direction=IN,
           description="Values smaller than this one are ignored.")
protected double minSizeValue

Minimal size threshold.

maxSizeValue

@Parameter(label="Maximal size threshold",
           required=true,
           dataIOOrder=11,
           direction=IN,
           description="Values larger than this one are ignored.")
protected double maxSizeValue

Maximal value threshold.

minR

private transient int minR

Red color value [0,255] of color for minimal value in range.

minG

private transient int minG

Green color value [0,255] of color for minimal value in range.

minB

private transient int minB

Blue color value [0,255] of color for minimal value in range.

maxR

private transient int maxR

Red color value [0,255] of color for maximal value in range.

maxG

private transient int maxG

Green color value [0,255] of color for maximal value in range.

maxB

private transient int maxB

Blue color value [0,255] of color for maximal value in range.

Constructor Detail

FeatureColorMapper

public FeatureColorMapper()
                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

Method Detail

setInputData

public void setInputData(String indir,
                         int[] ids)

Set input data.

Parameters:

indir - Input experiment folder.

ids - Selected columns.

setColorRangeMinimum

public void setColorRangeMinimum(Color c)

Color for range minimum.

Parameters:

c - Color to use.

setColorRangeMaximum

public void setColorRangeMaximum(Color c)

Color for range maximum.

Parameters:

c - Color to use.

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

This method does the actual work.

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

saveColorLegend

private void saveColorLegend(String subfolder,
                             MTBTableModel tm,
                             int col,
                             double[] vMins,
                             double[] vMaxs,
                             double[] ranges)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Function to generate and save color legends to sub-directories.

Parameters:

subfolder - Folder where result feature maps are stored.

tm - Table model with data (currently unused).

col - Columns of data for which legend should be generated.

vMins - Minimal values of data per column.

vMaxs - Maximal values of data per column.

ranges - Ranges of data per column.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case that images cannot be generated/written.