Class to compute various metrics to evaluate segmentation results. More...

#include <animaSegPerfCAnalyzer.h>

Public Member Functions
bool	checkImagesMatrixAndVolumes ()
	Check if the 2 inputs images are compatible. More...

double	computeAverageSurfaceDistance ()
	Compute average surface distance. More...

double	computeHausdorffDist ()
	Compute Haussdorf distance. More...

void	computeITKMeasures ()
	Compute different measures with ITK to evaluate segmentation. More...

double	computeMeanDist ()
	Compute mean distance. More...

bool	getDetectionMarks (double &po_fPPVL, double &po_fSensL, double &po_fF1)
	Compute useful variables to get detection scores. More...

double	getDiceCoefficient ()
	Getter of Dice coefficient. More...

double	getJaccardCoefficient ()
	Getter of Jaccard coefficient. More...

double	getMeanOverlap ()
	Getter of Mean overlap. More...

double	getNPV ()
	Getter of Negative predictive value. More...

int	getNumberOfClusters ()
	Return the number of clusters. More...

double	getPPV ()
	Getter of Positive predictive value. More...

double	getRelativeVolumeError ()
	Getter of Relative volume error. More...

double	getSensitivity ()
	Getter of Sensibility. More...

double	getSpecificity ()
	Getter of Specificity. More...

double	getUnionOverlap ()
	Getter of Union overlap. More...

	SegPerfCAnalyzer (std::string &pi_pchImageTestName, std::string &pi_pchImageRefName, bool advancedEvaluation)
	Constructor. More...

void	selectCluster (unsigned int)
	Select the cluster we want to use to compute evaluation results. More...

void	setDetectionThresholdAlpha (double pi_fVal)

void	setDetectionThresholdBeta (double pi_fVal)

void	setDetectionThresholdGamma (double pi_fVal)

void	setMinLesionVolumeDetection (double pi_fVal)

void	setNbThreads (int pi_iNbThreads)
	Set the number of threads to use for the computation of ITK. More...

	~SegPerfCAnalyzer ()

Protected Member Functions
void	checkNumberOfLabels (int, int)
	Check if the number of labels is the same for both input images. More...

void	contourDectection ()
	Extract the contour of the image to evaluate and the ground truth. More...

bool	falsePositiveRatioTester (int pi_iLessionReference, int pi_iNbLabelsTest, int pi_iNbLabelsRef, int *pi_ppiOverlapTab, int pi_piTPRowSumTab, int *pi_piColumnSumTab, double pi_dfBeta, double pi_dfGamma)
	Compute if a lesion is detected or not with beta and gamma thresholds. More...

void	formatLabels ()
	Format labels values for the image to evaluate and the ground truth to obtain : background pixels values = 0, cluster 1 pixels values = 1 ...etc. More...

void	getOverlapTab (int &po_iNbLabelsRef, int &po_iNbLabelsTest, int **&po_ppiOverlapTab)
	Compute a table of lesion overlap between 2 images. More...

int	getTruePositiveLesions (int pi_iNbLabelsRef, int pi_iNbLabelsTest, int **pi_ppiOverlapTab)
	Getter of True positive lesions. More...

Detailed Description

Class to compute various metrics to evaluate segmentation results.

Definition at line 25 of file animaSegPerfCAnalyzer.h.

Constructor & Destructor Documentation

◆ SegPerfCAnalyzer()

anima::SegPerfCAnalyzer::SegPerfCAnalyzer	(	std::string &	pi_pchImageTestName,
		std::string &	pi_pchImageRefName,
		bool	bAdvancedEvaluation
	)

Constructor.

Read input images

Parameters

[in]	pi_pchImageTestName	Name of the image to evaluate
[in]	pi_pchImageRefName	Name of the ground truth image
[in]	bAdvancedEvaluation

Definition at line 23 of file animaSegPerfCAnalyzer.cxx.

References checkImagesMatrixAndVolumes(), and formatLabels().

◆ ~SegPerfCAnalyzer()

anima::SegPerfCAnalyzer::~SegPerfCAnalyzer ( )

Definition at line 160 of file animaSegPerfCAnalyzer.cxx.

Member Function Documentation

◆ checkImagesMatrixAndVolumes()

bool anima::SegPerfCAnalyzer::checkImagesMatrixAndVolumes ( )

Check if the 2 inputs images are compatible.

Returns: true if image are compatible else false.

Definition at line 97 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::play(), and SegPerfCAnalyzer().

◆ checkNumberOfLabels()

void anima::SegPerfCAnalyzer::checkNumberOfLabels	(	int	iNbLabelsImageTest,
		int	iNbLabelsImageRef
	)

protected

Check if the number of labels is the same for both input images.

Definition at line 391 of file animaSegPerfCAnalyzer.cxx.

Referenced by formatLabels(), and setMinLesionVolumeDetection().

◆ computeAverageSurfaceDistance()

double anima::SegPerfCAnalyzer::computeAverageSurfaceDistance ( )

Compute average surface distance.

Returns: average surface distance

Definition at line 662 of file animaSegPerfCAnalyzer.cxx.

References contourDectection().

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ computeHausdorffDist()

double anima::SegPerfCAnalyzer::computeHausdorffDist ( )

Compute Haussdorf distance.

Returns: hausdorffDistance in double

Definition at line 590 of file animaSegPerfCAnalyzer.cxx.

References anima::SegmentationMeasuresImageFilter< TLabelImage >::New().

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ computeITKMeasures()

void anima::SegPerfCAnalyzer::computeITKMeasures ( )

Compute different measures with ITK to evaluate segmentation.

Definition at line 288 of file animaSegPerfCAnalyzer.cxx.

References anima::SegmentationMeasuresImageFilter< TLabelImage >::New().

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ computeMeanDist()

double anima::SegPerfCAnalyzer::computeMeanDist ( )

Compute mean distance.

Returns: meanDistance

Definition at line 624 of file animaSegPerfCAnalyzer.cxx.

References contourDectection(), and anima::SegmentationMeasuresImageFilter< TLabelImage >::New().

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ contourDectection()

void anima::SegPerfCAnalyzer::contourDectection ( )

protected

Extract the contour of the image to evaluate and the ground truth.

Definition at line 232 of file animaSegPerfCAnalyzer.cxx.

References anima::SegmentationMeasuresImageFilter< TLabelImage >::New().

Referenced by computeAverageSurfaceDistance(), computeMeanDist(), and setMinLesionVolumeDetection().

◆ falsePositiveRatioTester()

bool anima::SegPerfCAnalyzer::falsePositiveRatioTester	(	int	pi_iLesionReference,
		int	pi_iNbLabelsTest,
		int	pi_iNbLabelsRef,
		int **	pi_ppiOverlapTab,
		int *	pi_piTPRowSumTab,
		int *	pi_piColumnSumTab,
		double	pi_dfBeta,
		double	pi_dfGamma
	)

protected

Compute if a lesion is detected or not with beta and gamma thresholds.

Parameters

[out]	pi_iLesionReference	the number of labels found by connected components into reference image (1 by connected component + 1 for the background).
[out]	pi_iNbLabelsTest	the number of labels found by connected components into tested image (1 by connected component + 1 for the background).
[out]	pi_iNbLabelsRef	the number of the label of the tested lesion.
[out]	pi_ppiOverlapTab	the mapping table.
[out]	pi_piTPRowSumTab	the table of sum of Rows.
[out]	pi_piColumnSumTab	the table of sum of Columns.
[out]	pi_dfBeta	the beta threshold.
[out]	pi_dfGamma	the beta threshold.

Returns: true if the lesion is detected, false in other cases.

Definition at line 965 of file animaSegPerfCAnalyzer.cxx.

References pair_decreasing_comparator.

Referenced by getTruePositiveLesions(), and setMinLesionVolumeDetection().

◆ formatLabels()

void anima::SegPerfCAnalyzer::formatLabels ( )

protected

Format labels values for the image to evaluate and the ground truth to obtain : background pixels values = 0, cluster 1 pixels values = 1 ...etc.

Definition at line 477 of file animaSegPerfCAnalyzer.cxx.

References checkNumberOfLabels().

Referenced by SegPerfCAnalyzer(), and setMinLesionVolumeDetection().

◆ getDetectionMarks()

bool anima::SegPerfCAnalyzer::getDetectionMarks	(	double &	po_fPPVL,
		double &	po_fSensL,
		double &	po_fF1
	)

Compute useful variables to get detection scores.

Parameters

[out]	po_fFNL	the output FNL (False Negative Lesions) ratio.
[out]	po_fFPL	the output FPL (False Positive Lesions) ratio.
[out]	po_fPPVL	the output PPVL (Positive Predictive Value for Lesions) ratio.
[out]	po_fSensL	the output SensL, Lesion detection sensitivity ratio.
[out]	po_fF1	the output F1_score.

Returns: true

Definition at line 755 of file animaSegPerfCAnalyzer.cxx.

References getOverlapTab(), and getTruePositiveLesions().

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getDiceCoefficient()

double anima::SegPerfCAnalyzer::getDiceCoefficient ( )

Getter of Dice coefficient.

Returns: Dice coefficient in double

Definition at line 365 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getJaccardCoefficient()

double anima::SegPerfCAnalyzer::getJaccardCoefficient ( )

Getter of Jaccard coefficient.

Returns: Jaccard coefficient in double

Definition at line 374 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getMeanOverlap()

double anima::SegPerfCAnalyzer::getMeanOverlap ( )

Getter of Mean overlap.

Returns: Mean overlap in double

Definition at line 320 of file animaSegPerfCAnalyzer.cxx.

Referenced by setMinLesionVolumeDetection().

◆ getNPV()

double anima::SegPerfCAnalyzer::getNPV ( )

Getter of Negative predictive value.

Returns: Negative predictive value in double

Definition at line 356 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getNumberOfClusters()

int anima::SegPerfCAnalyzer::getNumberOfClusters ( )

Return the number of clusters.

Returns: Number of clusters

Definition at line 168 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::play(), and setMinLesionVolumeDetection().

◆ getOverlapTab()

void anima::SegPerfCAnalyzer::getOverlapTab	(	int &	po_iNbLabelsRef,
		int &	po_iNbLabelsTest,
		int **&	po_ppiOverlapTab
	)

protected

Compute a table of lesion overlap between 2 images.

Parameters

[out]	po_iNbLabelsRef	the number of labels found by connected components into reference image (1 by connected component + 1 for the background).
[out]	po_iNbLabelsTest	the number of labels found by connected components into tested image (1 by connected component + 1 for the background).
[out]	po_ppiOverlapTab	the table allocated by this method. Dimensions are po_iNbLabelsTest*po_iNbLabelsRef. The first cell [0][0] is the number of True-Negative voxels (background in both images), first line (excepte first cell) are False-Posite voxels, first colomne are False-Negative voxels and the rest of cels are True positive voxels. In Other words: first line is the back ground into Ref-image, first column is the back ground into Tested-image and the element [i][j] (with i,j > 0) correspond to the number of voxel belonging to the label i, that overlap with a voxel of the label j.

Definition at line 801 of file animaSegPerfCAnalyzer.cxx.

Referenced by getDetectionMarks(), and setMinLesionVolumeDetection().

◆ getPPV()

double anima::SegPerfCAnalyzer::getPPV ( )

Getter of Positive predictive value.

Returns: Positive predictive value in double

Definition at line 347 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getRelativeVolumeError()

double anima::SegPerfCAnalyzer::getRelativeVolumeError ( )

Getter of Relative volume error.

Returns: Relative volume error in double

Definition at line 383 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getSensitivity()

double anima::SegPerfCAnalyzer::getSensitivity ( )

Getter of Sensibility.

Returns: Sensibility in double

Definition at line 329 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getSpecificity()

double anima::SegPerfCAnalyzer::getSpecificity ( )

Getter of Specificity.

Returns: Specificity in double

Definition at line 338 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze(), and setMinLesionVolumeDetection().

◆ getTruePositiveLesions()

int anima::SegPerfCAnalyzer::getTruePositiveLesions	(	int	pi_iNbLabelsRef,
		int	pi_iNbLabelsTest,
		int **	pi_ppiOverlapTab
	)

protected

Getter of True positive lesions.

Returns: True positive lesions

Definition at line 896 of file animaSegPerfCAnalyzer.cxx.

References falsePositiveRatioTester().

Referenced by getDetectionMarks(), and setMinLesionVolumeDetection().

◆ getUnionOverlap()

double anima::SegPerfCAnalyzer::getUnionOverlap ( )

Getter of Union overlap.

Returns: Union overlap in double

Definition at line 311 of file animaSegPerfCAnalyzer.cxx.

Referenced by setMinLesionVolumeDetection().

◆ selectCluster()

void anima::SegPerfCAnalyzer::selectCluster ( unsigned int iCluster )

Select the cluster we want to use to compute evaluation results.

Parameters

[in] iCluster

Definition at line 177 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::processAnalyze().

◆ setDetectionThresholdAlpha()

void anima::SegPerfCAnalyzer::setDetectionThresholdAlpha ( double pi_fVal )

inline

Definition at line 36 of file animaSegPerfCAnalyzer.h.

Referenced by anima::SegPerfApp::processAnalyze().

◆ setDetectionThresholdBeta()

void anima::SegPerfCAnalyzer::setDetectionThresholdBeta ( double pi_fVal )

inline

Definition at line 41 of file animaSegPerfCAnalyzer.h.

Referenced by anima::SegPerfApp::processAnalyze().

◆ setDetectionThresholdGamma()

void anima::SegPerfCAnalyzer::setDetectionThresholdGamma ( double pi_fVal )

inline

Definition at line 46 of file animaSegPerfCAnalyzer.h.

Referenced by anima::SegPerfApp::processAnalyze().

◆ setMinLesionVolumeDetection()

void anima::SegPerfCAnalyzer::setMinLesionVolumeDetection ( double pi_fVal )

inline

◆ setNbThreads()

void anima::SegPerfCAnalyzer::setNbThreads ( int pi_iNbThreads )

Set the number of threads to use for the computation of ITK.

Parameters

[in] pi_iNbThreads Number of threads.

Definition at line 790 of file animaSegPerfCAnalyzer.cxx.

Referenced by anima::SegPerfApp::play().

The documentation for this class was generated from the following files:

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SegPerfCAnalyzer()

◆ ~SegPerfCAnalyzer()

Member Function Documentation

◆ checkImagesMatrixAndVolumes()

◆ checkNumberOfLabels()

◆ computeAverageSurfaceDistance()

◆ computeHausdorffDist()

◆ computeITKMeasures()

◆ computeMeanDist()

◆ contourDectection()

◆ falsePositiveRatioTester()

◆ formatLabels()

◆ getDetectionMarks()

◆ getDiceCoefficient()

◆ getJaccardCoefficient()

◆ getMeanOverlap()

◆ getNPV()

◆ getNumberOfClusters()

◆ getOverlapTab()

◆ getPPV()

◆ getRelativeVolumeError()

◆ getSensitivity()

◆ getSpecificity()

◆ getTruePositiveLesions()

◆ getUnionOverlap()

◆ selectCluster()

◆ setDetectionThresholdAlpha()

◆ setDetectionThresholdBeta()

◆ setDetectionThresholdGamma()

◆ setMinLesionVolumeDetection()

◆ setNbThreads()