Label Analysis 2d

Connected component 2d analysis and measurement algorithm. More...

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr	ipsdk::imaproc::shape::analysis::labelAnalysis2d (const ipsdk::image::ImageConstPtr &pInGreyMsrImg, const ipsdk::image::ImageConstPtr &pInLabelImg, const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet2d)
	wrapper function for Connected component 2d analysis and measurement algorithm More...
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr	ipsdk::imaproc::shape::analysis::labelAnalysis2d (const ipsdk::image::ImageConstPtr &pInGreyMsrImg, const ipsdk::image::ImageConstPtr &pInLabelImg, const ipsdk::imaproc::attr::ContourExtractionSettingsConstPtr &pInOptContourExtractionSettings, const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet2d)
	wrapper function for Connected component 2d analysis and measurement algorithm More...
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr	ipsdk::imaproc::shape::analysis::multiSlice_labelAnalysis2d (const ipsdk::image::ImageConstPtr &pInGreyMsrImg, const ipsdk::image::ImageConstPtr &pInLabelImg, const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet2d)
	wrapper function for Connected component 2d analysis and measurement algorithm More...
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr	ipsdk::imaproc::shape::analysis::multiSlice_labelAnalysis2d (const ipsdk::image::ImageConstPtr &pInGreyMsrImg, const ipsdk::image::ImageConstPtr &pInLabelImg, const ipsdk::imaproc::attr::ContourExtractionSettingsConstPtr &pInOptContourExtractionSettings, const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet2d)
	wrapper function for Connected component 2d analysis and measurement algorithm More...

Detailed Description

Connected component 2d analysis and measurement algorithm.

This algorithm is a simple version of Shape Analysis 2d algorithm. It allows to process measurements and analysis using a label (connected components) image as input which will be proceeded to extract associated 2d shapes (see Label shape extraction 2d).

Note

Note that boundary approximation will only be computed on extracted shapes if the input measure set requests it (ie if at least one mesure among measure set requests it, see Measure requirements).

For more information on shape analysis and measurement framework, please refers to Shape Analysis and Measurement.

Here is an example of shape 2d measurement and analysis :

Attributes description

Attribute description for algorithm :

Name	ToolTip	Default Initializer
ipsdk::imaproc::attr::InGreyMsrImg	[Input] grey image used for intensity measurements	X
ipsdk::imaproc::attr::InLabelImg	[Input] label image for processing operation	X
ipsdk::imaproc::attr::InOptContourExtractionSettings	[Input Optional] Settings used for contours extraction	X
ipsdk::imaproc::attr::InMeasureInfoSet2d	[Input] shape analysis 2d measure information set	X
ipsdk::imaproc::attr::OutPIMeasureSet	[Output] Plan indexed collection of shape analysis measure set	fromImageButColor (_pOutPIMeasureSet, _pInGreyMsrImg, boost::function<OutPIMeasureSet::PlanStorageType()>(boost::bind(&ipsdk::imaproc::createMeasureSetFromInfo,_pInMeasureInfoSet2d)))

Global Rule description

Global rule description for algorithm :
ipsdk::imaproc::matchSize (ipsdk::imaproc::eMatchImageSizeType::eMIST_XYZT,_pInGreyMsrImg,_pInLabelImg) && 
ipsdk::imaproc::matchImagePlansButColor (_pOutPIMeasureSet,_pInGreyMsrImg) && 
matchLabelAnalysis (_pInMeasureInfoSet2d)

Example of Python code :

Example imports

import PyIPSDK
import PyIPSDK.IPSDKIPLAdvancedMorphology as advmorpho
import PyIPSDK.IPSDKIPLShapeAnalysis as shapeanalysis

Code Example

    # opening of input images
    inGreyImg = PyIPSDK.loadTiffImageFile(inputGreyImgPath)
    inBinImg = PyIPSDK.loadTiffImageFile(inputBinImgPath)
    
    # connected components analysis of binary image
    inLabelImg2d = advmorpho.connectedComponent2dImg(inBinImg)
    
    # definition of proceeded measure
    inMeasureInfoSet2d1 = PyIPSDK.createMeasureInfoSet2d()
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d1, "AreaMinusHoles", "Area2dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(True))
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d1, "AreaWithHoles", "Area2dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(False))
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d1, "EquivalentRay", "EquivalentRayMsr")
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d1, "SumMsr")
    
    # shape analysis computation
    # in this case area measure request boundary approximation of shapes so it will
    # be automatically computed
    outMeasureSet1 = shapeanalysis.labelAnalysis2d(inGreyImg,  inLabelImg2d,  inMeasureInfoSet2d1)
    
    # save results to csv format
    PyIPSDK.saveCsvMeasureFile(os.path.join(utTmpPath,  "shape_analysis_results.csv"), outMeasureSet1)
    
    # retrieve measure results
    outAreaMinusHolesMsr = outMeasureSet1.getMeasure("AreaMinusHoles")
    outAreaWithHolesMsr = outMeasureSet1.getMeasure("AreaWithHoles")
    outEquivalentRayMsr = outMeasureSet1.getMeasure("EquivalentRay")
    outSumMsr = outMeasureSet1.getMeasure("SumMsr")
    
    # retrieve measure valus for area with holes measurement
    outAreaWithHolesValues = outAreaWithHolesMsr.getMeasureResult().getColl(0)
    print("First label area with holes measurement equal " + str(outAreaWithHolesValues[1]))
    
    # define a second measure info set which do not implies boundary approximation of shapes 
    inMeasureInfoSet2d2 = PyIPSDK.createMeasureInfoSet2d()
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d2, "HistogramQuantileMsr", shapeanalysis.createHistogramQuantileMsrParamsBinWidth(1.0, 25.0))
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d2, "NbPixels2dMsr")
    PyIPSDK.createMeasureInfo(inMeasureInfoSet2d2, "MeanMsr")
    
    # in this case area measure request only row intersections of shapes with image so it will
    # be automatically computed (boundary approximation are not)
    outMeasureSet2 = shapeanalysis.labelAnalysis2d(inGreyImg,  inLabelImg2d,  inMeasureInfoSet2d2)
    
    # retrieve associated results
    outHistogramQuantileMsr = outMeasureSet2.getMeasure("HistogramQuantileMsr")
    outNbPixels2dMsr = outMeasureSet2.getMeasure("NbPixels2dMsr")
    outMeanMsr = outMeasureSet2.getMeasure("MeanMsr")

Example of C++ code :

Example informations

Associated library

IPSDKIPLShapeAnalysis

Header file

#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Processor/LabelAnalysis2d/LabelAnalysis2d.h>

Code Example

    // opening grey level input image
    ImagePtr pInGreyImg2d = loadTiffImageFile(inputGreyImgPath);

    // opening binary input image
    ImagePtr pInBinImg2d = loadTiffImageFile(inputBinImgPath);

    // connected components analysis
    ImagePtr pInLabelImg2d = connectedComponent2dImg(pInBinImg2d);

    // define a measure info set
    MeasureInfoSetPtr pMeasureInfoSet1 = MeasureInfoSet::create2dInstance();
    createMeasureInfo(pMeasureInfoSet1, "AreaMinusHoles", "Area2dMsr", createHolesBasicPolicyMsrParams(true));
    createMeasureInfo(pMeasureInfoSet1, "AreaWithHoles", "Area2dMsr", createHolesBasicPolicyMsrParams(false));
    createMeasureInfo(pMeasureInfoSet1, "EquivalentRay", "EquivalentRayMsr");
    createMeasureInfo(pMeasureInfoSet1, "SumMsr");
    
    // compute measure on extracted data
    // in this case area measure request boundary approximation of shapes so it will
    // be automatically computed
    MeasureSetPtr pOutMeasureSet1 = labelAnalysis2d(pInGreyImg2d, pInLabelImg2d, pMeasureInfoSet1);

    // complete csv dump of results
    saveCsvMeasureFile(csvOutputPath, *pOutMeasureSet1);

    // retrieve associated results
    const MeasureConstPtr& pAreaMinusHolesOutMsr = pOutMeasureSet1->getMeasure("AreaMinusHoles");
    const MeasureConstPtr& pAreaWithHolesOutMsr = pOutMeasureSet1->getMeasure("AreaWithHoles");
    const MeasureConstPtr& pEquivalentRayOutMsr = pOutMeasureSet1->getMeasure("EquivalentRay");
    const MeasureConstPtr& pSumOutMsr = pOutMeasureSet1->getMeasure("SumMsr");

    // define a second measure info set which do not implies boundary approximation of shapes 
    MeasureInfoSetPtr pMeasureInfoSet2 = MeasureInfoSet::create2dInstance();
    createMeasureInfo(pMeasureInfoSet2, "HistogramQuantileMsr", createHistogramQuantileMsrParamsBinWidth(1.0, 25.0));
    createMeasureInfo(pMeasureInfoSet2, "NbPixels2dMsr");
    createMeasureInfo(pMeasureInfoSet2, "MeanMsr");
    
    // compute measure on extracted data
    // in this case area measure request only row intersections of shapes with image so it will
    // be automatically computed (boundary approximation are not)
    MeasureSetPtr pOutMeasureSet2 = labelAnalysis2d(pInGreyImg2d, pInLabelImg2d, pMeasureInfoSet2);

    // retrieve associated results
    const MeasureConstPtr& pHistogramQuantileOutMsr = pOutMeasureSet2->getMeasure("HistogramQuantileMsr");
    const MeasureConstPtr& pNbPixels2dOutMsr = pOutMeasureSet2->getMeasure("NbPixels2dMsr");
    const MeasureConstPtr& pMeanOutMsr = pOutMeasureSet2->getMeasure("MeanMsr");

See also

LabelAnalysis2dLvl1

Function Documentation

labelAnalysis2d() [1/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr ipsdk::imaproc::shape::analysis::labelAnalysis2d	(	const ipsdk::image::ImageConstPtr &	pInGreyMsrImg,
		const ipsdk::image::ImageConstPtr &	pInLabelImg,
		const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet2d
	)

wrapper function for Connected component 2d analysis and measurement algorithm

Note

This wrapper must be used with mono slice (sizeZ=sizeC=sizeT=1) input images

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure

multiSlice_labelAnalysis2d() [1/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr ipsdk::imaproc::shape::analysis::multiSlice_labelAnalysis2d	(	const ipsdk::image::ImageConstPtr &	pInGreyMsrImg,
		const ipsdk::image::ImageConstPtr &	pInLabelImg,
		const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet2d
	)

wrapper function for Connected component 2d analysis and measurement algorithm

Note

This wrapper can be used with multi slice input images

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure

labelAnalysis2d() [2/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr ipsdk::imaproc::shape::analysis::labelAnalysis2d	(	const ipsdk::image::ImageConstPtr &	pInGreyMsrImg,
		const ipsdk::image::ImageConstPtr &	pInLabelImg,
		const ipsdk::imaproc::attr::ContourExtractionSettingsConstPtr &	pInOptContourExtractionSettings,
		const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet2d
	)

wrapper function for Connected component 2d analysis and measurement algorithm

Note

This wrapper must be used with mono slice (sizeZ=sizeC=sizeT=1) input images

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure

multiSlice_labelAnalysis2d() [2/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr ipsdk::imaproc::shape::analysis::multiSlice_labelAnalysis2d	(	const ipsdk::image::ImageConstPtr &	pInGreyMsrImg,
		const ipsdk::image::ImageConstPtr &	pInLabelImg,
		const ipsdk::imaproc::attr::ContourExtractionSettingsConstPtr &	pInOptContourExtractionSettings,
		const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet2d
	)

wrapper function for Connected component 2d analysis and measurement algorithm

Note

This wrapper can be used with multi slice input images

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure