|
||||||||||
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.segmentation.evaluation.CalcStructureStatistics
public class CalcStructureStatistics
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.
Nested Class Summary | |
---|---|
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 |
Field Summary |
---|
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
---|
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
---|---|
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 | |
---|---|
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, 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 |
Constructor Detail |
---|
protected CalcStructureStatistics() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
@Deprecated public CalcStructureStatistics(MTBImageByte sMask, MTBImageByte nMask, MTBImageByte labelImg, boolean ignoreNuclei) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
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.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public CalcStructureStatistics(MTBImageByte sMask, MTBImageByte nMask, MTBImageByte labelImg) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
sMask
- Binary mask of detected structures.nMask
- Binary mask of detected nuclei.labelImg
- Label image of detected cell areas.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
---|
public void setCountMode(CalcStructureStatistics.StructureCountMode m)
public void setMinimalRegionSize(int minsize)
public void setIgnoreBorderFlag(boolean f)
public HashMap<Integer,Integer> getResultDataCounts()
public HashMap<Integer,Integer> getResultDataTotalSize()
public HashMap<Integer,Double> getResultDataAreaFractions()
public HashMap<Integer,Integer> getResultDataCellSizes()
public HashMap<Integer,Double> getResultDataAvgSize()
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 |