de.unihalle.informatik.MiToBo.segmentation.evaluation

Class CalcStructureStatistics

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics

All Implemented Interfaces:

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

public class CalcStructureStatistics
extends MTBOperator

Extracts statistics from cell and structure segmentation results.

For each structure region a corresponding region in the given cell segmentation result is detected and the structure region assigned to it. Note that structure regions along image borders are ignored. In addition, optionally also regions in given nuclei regions might be excluded if a mask with detected nuclei regions is available.

In parts the code of this file has been copied from Oliver's tool 'EvalParticleDetection'. However, this class is more generic in the sense that only a single cell segmentation result and a single structure segmentation result are processed on call of this tool.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CalcStructureStatistics.StructureCountMode Mode how to assign structures to cell regions.

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 MTBImageByte	cellLabelImg Label image of cell areas.
private CalcStructureStatistics.StructureCountMode	countMode Mode for assigning structures to regions.
private HashMap<Integer,MTBRegion2DSet>	cparticles
private int	height
private boolean	ignoreStructsAtBorder Flag to ignore structures along border.
private boolean	ignoreStructsInNuclei
private int	minStructureSize Minimal size of structure regions to be considered.
private MTBImageByte	nucleiMask Nuclei mask.
private HashMap<Integer,Double>	resultDataAreaFractions Result data: area fractions.
private HashMap<Integer,Double>	resultDataAvgSize Result data: average size.
private HashMap<Integer,Integer>	resultDataCellSizes Result data: cell sizes.
private HashMap<Integer,Integer>	resultDataCounts Result data: counts.
private HashMap<Integer,Integer>	resultDataTotalSize Result data: total structure size per cell.
private MTBImageByte	structureMask Structure mask.
private int	width

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CalcStructureStatistics() Default constructor.
	CalcStructureStatistics(MTBImageByte sMask, MTBImageByte nMask, MTBImageByte labelImg) Default constructor.
	CalcStructureStatistics(MTBImageByte sMask, MTBImageByte nMask, MTBImageByte labelImg, boolean ignoreNuclei) Deprecated.

Method Summary

Modifier and Type	Method and Description
private void	assignStructsToCell_com(MTBRegion2DSet regs) Assigns the given set of structure regions to individual cells.
private void	assignStructsToCell_overlap(MTBRegion2DSet regions) Assigns the given set of structure regions to individual cells.
HashMap<Integer,Double>	getResultDataAreaFractions() Returns result data object with area fractions per cell.
HashMap<Integer,Double>	getResultDataAvgSize() Returns result data object with average size per cell.
HashMap<Integer,Integer>	getResultDataCellSizes() Returns result data object with areas per cell.
HashMap<Integer,Integer>	getResultDataCounts() Returns result data object with counts per cell.
HashMap<Integer,Integer>	getResultDataTotalSize() Returns result data object with total structure size per cell.
protected void	operate()
void	setCountMode(CalcStructureStatistics.StructureCountMode m) Specify mode how to assign structures to cells.
void	setIgnoreBorderFlag(boolean f) Set flag to include/ignore structures along image border.
void	setMinimalRegionSize(int minsize) Specify minimal size of regions considered.

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, 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

structureMask

@Parameter(label="structureMask",
           required=true,
           direction=IN,
           description="Binary mask of structures.")
private MTBImageByte structureMask

Structure mask.

nucleiMask

@Parameter(label="nucleiMask",
           required=false,
           direction=IN,
           description="Binary mask of nuclei.")
private MTBImageByte nucleiMask

Nuclei mask.

cellLabelImg

@Parameter(label="cellLabelImg",
           required=true,
           direction=IN,
           description="Label image of cell areas.")
private MTBImageByte cellLabelImg

Label image of cell areas.

countMode

@Parameter(label="countMode",
           required=false,
           direction=IN,
           description="Mode for assigning structures to regions.")
private CalcStructureStatistics.StructureCountMode countMode

Mode for assigning structures to regions.

minStructureSize

@Parameter(label="minStructureSize",
           required=false,
           direction=IN,
           description="Minimal size of structure regions to be considered.")
private int minStructureSize

Minimal size of structure regions to be considered.

ignoreStructsAtBorder

@Parameter(label="ignoreStructsAtBorder",
           required=false,
           direction=IN,
           description="Flag for ignoring structures along image border.")
private boolean ignoreStructsAtBorder

Flag to ignore structures along border.

resultDataCounts

@Parameter(label="resultDataCounts",
           required=true,
           direction=OUT,
           description="Result data for counts per cell.")
private HashMap<Integer,Integer> resultDataCounts

Result data: counts.

resultDataTotalSize

@Parameter(label="resultDataTotalSize",
           required=true,
           direction=OUT,
           description="Result data for total structure size per cell.")
private HashMap<Integer,Integer> resultDataTotalSize

Result data: total structure size per cell.

resultDataAvgSize

@Parameter(label="resultDataAvgSize",
           required=true,
           direction=OUT,
           description="Result data for average size per cell.")
private HashMap<Integer,Double> resultDataAvgSize

Result data: average size.

resultDataAreaFractions

@Parameter(label="resultDataAreaFractions",
           required=true,
           direction=OUT,
           description="Result data for area fraction per cell.")
private HashMap<Integer,Double> resultDataAreaFractions

Result data: area fractions.

resultDataCellSizes

@Parameter(label="resultDataCellSizes",
           required=true,
           direction=OUT,
           description="Result data for size per cell.")
private HashMap<Integer,Integer> resultDataCellSizes

Result data: cell sizes.

width

private int width

height

private int height

cparticles

private HashMap<Integer,MTBRegion2DSet> cparticles

ignoreStructsInNuclei

private boolean ignoreStructsInNuclei

Constructor Detail

CalcStructureStatistics

protected CalcStructureStatistics()
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CalcStructureStatistics

@Deprecated
public CalcStructureStatistics(MTBImageByte sMask,
                                           MTBImageByte nMask,
                                           MTBImageByte labelImg,
                                           boolean ignoreNuclei)
                                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Deprecated.

Default constructor.

Parameters:

sMask - Binary mask of detected structures.

nMask - Binary mask of detected nuclei.

labelImg - Label image of detected cell areas.

ignoreNuclei - Flag for ignoring nuclei regions.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CalcStructureStatistics

public CalcStructureStatistics(MTBImageByte sMask,
                               MTBImageByte nMask,
                               MTBImageByte labelImg)
                        throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

sMask - Binary mask of detected structures.

nMask - Binary mask of detected nuclei.

labelImg - Label image of detected cell areas.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setCountMode

public void setCountMode(CalcStructureStatistics.StructureCountMode m)

Specify mode how to assign structures to cells.

setMinimalRegionSize

public void setMinimalRegionSize(int minsize)

Specify minimal size of regions considered.

setIgnoreBorderFlag

public void setIgnoreBorderFlag(boolean f)

Set flag to include/ignore structures along image border.

getResultDataCounts

public HashMap<Integer,Integer> getResultDataCounts()

Returns result data object with counts per cell.

getResultDataTotalSize

public HashMap<Integer,Integer> getResultDataTotalSize()

Returns result data object with total structure size per cell.

getResultDataAreaFractions

public HashMap<Integer,Double> getResultDataAreaFractions()

Returns result data object with area fractions per cell.

getResultDataCellSizes

public HashMap<Integer,Integer> getResultDataCellSizes()

Returns result data object with areas per cell.

getResultDataAvgSize

public HashMap<Integer,Double> getResultDataAvgSize()

Returns result data object with average size per cell.

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

assignStructsToCell_com

private void assignStructsToCell_com(MTBRegion2DSet regs)

Assigns the given set of structure regions to individual cells.

For the assignment the center of mass of each region is calculated and the corresponding cell region chosen according to its location.

assignStructsToCell_overlap

private void assignStructsToCell_overlap(MTBRegion2DSet regions)

Assigns the given set of structure regions to individual cells.

For the assignment the overlap of each region to all cell regions is calculated and the cell with largest overlap is chosen as corresponding cell region.