Shape Analysis 3d

Shape 3d analysis and measurement algorithm. More...

Typedefs
typedef ShapeAnalysisOptParams< ipsdk::shape::segmentation::Shape3dColl >	ipsdk::imaproc::shape::analysis::ShapeAnalysis3dOptParams
	optional parameter type for mono slice shape analysis
typedef ShapeAnalysisOptParams< ipsdk::shape::segmentation::PlanIndexedShape3dColl >	ipsdk::imaproc::shape::analysis::ShapeAnalysis3dPIOptParams
	optional parameter type for mono slice shape analysis
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr	ipsdk::imaproc::shape::analysis::shapeAnalysis3d (const ipsdk::image::ImageConstPtr &pInOptGreyMsrImg3d1, const ipsdk::shape::segmentation::Shape3dCollConstPtr &pInLabelsShape3d, const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet3d)
	wrapper function for Shape 3d analysis and measurement algorithm More...
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr	ipsdk::imaproc::shape::analysis::shapeAnalysis3d (const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet3d, const ipsdk::shape::segmentation::Shape3dCollConstPtr &pInLabelsShape3d, const ipsdk::imaproc::shape::analysis::ShapeAnalysis3dOptParams &shapeAnalysis3dOptParams)
	wrapper function for Shape 3d analysis and measurement algorithm More...
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr	ipsdk::imaproc::shape::analysis::multiSlice_shapeAnalysis3d (const ipsdk::image::ImageConstPtr &pInOptGreyMsrImg3d1, const ipsdk::shape::segmentation::PlanIndexedShape3dCollConstPtr &pInPILabelsShape3d, const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet3d)
	wrapper function for Shape 3d analysis and measurement algorithm More...
IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr	ipsdk::imaproc::shape::analysis::multiSlice_shapeAnalysis3d (const ipsdk::shape::analysis::MeasureInfoSetConstPtr &pInMeasureInfoSet3d, const ipsdk::shape::segmentation::PlanIndexedShape3dCollConstPtr &pInPILabelsShape3d, const ipsdk::imaproc::shape::analysis::ShapeAnalysis3dPIOptParams &shapeAnalysis3dPIOptParams)
	wrapper function for Shape 3d analysis and measurement algorithm More...

Detailed Description

Shape 3d analysis and measurement algorithm.

This algorithm allows to process measurements and analysis on shape 3d connected components.

User should first extract surface on a connected component label image (see Label shape extraction 3d).

Shape 3d measurements and analysis can be decomposed in three main groups :

• Intensity measurement which allows to analyse intensity data covered by each shape. This kind of measure aggregates for example : mean, variance, grey moments, ... analysis of particules.
• Geometry measurements which use polyhedral approximation of shape contours. This kind of measure aggregates for example : area, axis aligned bounding box computation (min by axis, size by axis), ...
• Generic measurements which allows to combinate other measurements to obtain new values. This kind of measure aggregates for example : EquivalentRay which is defined using Volume3d measurement (in 3d case).

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

Here is an example of shape 3d measurement and analysis :

Attributes description

Attribute description for algorithm :

Name	ToolTip	Default Initializer
ipsdk::imaproc::attr::InMeasureInfoSet3d	[Input] shape analysis 3d measure information set	X
ipsdk::imaproc::attr::InPILabelsShape3d	[Input] Plan indexed collection of shape 3d associated to labels	X
ipsdk::imaproc::shape::analysis::InOptPILabelsShape3d2	[Input Optional] second plan indexed collection of shape 3d associated to labels	X
ipsdk::imaproc::shape::analysis::InOptPILabelsShape3d3	[Input Optional] third plan indexed collection of shape 3d associated to labels	X
ipsdk::imaproc::shape::analysis::InOptPILabelsShape3d4	[Input Optional] fourth plan indexed collection of shape 3d associated to labels	X
ipsdk::imaproc::shape::analysis::InOptGreyMsrImg3d1	[Input Optional] first grey image3d used for intensity measurements	X
ipsdk::imaproc::shape::analysis::InOptGreyMsrImg3d2	[Input Optional] second grey image3d used for intensity measurements	X
ipsdk::imaproc::shape::analysis::InOptGreyMsrImg3d3	[Input Optional] third grey image3d used for intensity measurements	X
ipsdk::imaproc::shape::analysis::InOptGreyMsrImg3d4	[Input Optional] fourth grey image3d used for intensity measurements	X
ipsdk::imaproc::attr::OutPIMeasureSet	[Output] Plan indexed collection of shape analysis measure set	fromOther (_pOutPIMeasureSet, _pInPILabelsShape3d, boost::function<OutPIMeasureSet::PlanStorageType()>(boost::bind(&ipsdk::imaproc::createMeasureSetFromInfo,_pInMeasureInfoSet3d)))

Global Rule description

Global rule description for algorithm :
ipsdk::imaproc::matchOther (_pInPILabelsShape3d,_pOutPIMeasureSet) && 
validateMeasureRequirements (_pInMeasureInfoSet3d,_pInPILabelsShape3d,_pInOptPILabelsShape3d2,_pInOptPILabelsShape3d3,_pInOptPILabelsShape3d4,_pInOptGreyMsrImg3d1,_pInOptGreyMsrImg3d2,_pInOptGreyMsrImg3d3,_pInOptGreyMsrImg3d4)

Example of Python code :

Example imports

import PyIPSDK
import PyIPSDK.IPSDKIPLAdvancedMorphology as advmorpho
import PyIPSDK.IPSDKIPLShapeSegmentation as shapesegmentation
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
    inLabelImg3d = advmorpho.connectedComponent3dImg(inBinImg)
    
    # label contour extraction computation
    inShape3dColl = shapesegmentation.labelShapeExtraction3d(inLabelImg3d, PyIPSDK.createSubSampledSurfaceExtractionSettings(0))
    
    # definition of proceeded measure
    inMeasureInfoSet3d = PyIPSDK.createMeasureInfoSet3d();
    PyIPSDK.createMeasureInfo(inMeasureInfoSet3d, "VolumeMinusHoles", "MeshVolume3dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(True));
    PyIPSDK.createMeasureInfo(inMeasureInfoSet3d, "VolumeWithHoles", "MeshVolume3dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(False));
    PyIPSDK.createMeasureInfo(inMeasureInfoSet3d, "AreaMinusHoles", "Area3dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(True));
    PyIPSDK.createMeasureInfo(inMeasureInfoSet3d, "AreaWithHoles", "Area3dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(False));
    PyIPSDK.createMeasureInfo(inMeasureInfoSet3d, "EquivalentRay", "EquivalentRayMsr");
    PyIPSDK.createMeasureInfo(inMeasureInfoSet3d, "SumMsr");
    
    # shape analysis computation
    outMeasureSet = shapeanalysis.shapeAnalysis3d(inGreyImg,  inShape3dColl, inMeasureInfoSet3d)
    
    # save results to csv format
    PyIPSDK.saveCsvMeasureFile(os.path.join(utTmpPath,  "shape_analysis_results.csv"), outMeasureSet)
    
    # retrieve measure results
    outVolumeMinusHolesMsr = outMeasureSet.getMeasure("VolumeMinusHoles")
    outVolumeWithHolesMsr = outMeasureSet.getMeasure("VolumeWithHoles")
    outAreaMinusHolesMsr = outMeasureSet.getMeasure("AreaMinusHoles")
    outAreaWithHolesMsr = outMeasureSet.getMeasure("AreaWithHoles")
    outEquivalentRayMsr = outMeasureSet.getMeasure("EquivalentRay")
    outSumMsr = outMeasureSet.getMeasure("SumMsr")
    
    # retrieve measure valus for area with holes measurement
    outVolumeWithHolesValues = outVolumeWithHolesMsr.getMeasureResult().getColl(0)
    print("First label volume with holes measurement equal " + str(outVolumeWithHolesValues[1]))

Example of C++ code :

Example informations

Associated library

IPSDKIPLShapeAnalysis

Header file

#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Processor/ShapeAnalysis3d/ShapeAnalysis3d.h>

Code Example

    // opening grey level input image
    ImagePtr pInGreyImg3d = loadTiffImageFile(inputGreyImgPath, eTiffDirectoryMode::eTDM_Volume);

    // opening binary input image
    ImagePtr pInBinImg3d = loadTiffImageFile(inputBinImgPath, eTiffDirectoryMode::eTDM_Volume);

    // connected components analysis
    ImagePtr pInLabelImg3d = connectedComponent3dImg(pInBinImg3d);

    // extract contours from connected component (label) image
    Shape3dCollPtr pShape3dColl = labelShapeExtraction3d(pInLabelImg3d);

    // define a measure info set
    MeasureInfoSetPtr pMeasureInfoSet = MeasureInfoSet::create3dInstance();
    createMeasureInfo(pMeasureInfoSet, "VolumeMinusHoles", "Volume3dMsr", createHolesBasicPolicyMsrParams(true));
    createMeasureInfo(pMeasureInfoSet, "VolumeWithHoles", "Volume3dMsr", createHolesBasicPolicyMsrParams(false));
    createMeasureInfo(pMeasureInfoSet, "EquivalentRay", "EquivalentRayMsr");
    createMeasureInfo(pMeasureInfoSet, "SumMsr");
    
    // compute measure on extracted data
    MeasureSetPtr pOutMeasureSet = shapeAnalysis3d(pInGreyImg3d, pShape3dColl, pMeasureInfoSet);

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

    // retrieve associated results
    const MeasureConstPtr& pAreaMinusHolesOutMsr = pOutMeasureSet->getMeasure("VolumeMinusHoles");
    const MeasureConstPtr& pAreaWithHolesOutMsr = pOutMeasureSet->getMeasure("VolumeWithHoles");
    const MeasureConstPtr& pEquivalentRayOutMsr = pOutMeasureSet->getMeasure("EquivalentRay");
    const MeasureConstPtr& pSumOutMsr = pOutMeasureSet->getMeasure("SumMsr");

See also

ShapeAnalysis3dLvl1

ShapeAnalysis3dLvl2

Function Documentation

shapeAnalysis3d() [1/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr ipsdk::imaproc::shape::analysis::shapeAnalysis3d	(	const ipsdk::image::ImageConstPtr &	pInOptGreyMsrImg3d1,
		const ipsdk::shape::segmentation::Shape3dCollConstPtr &	pInLabelsShape3d,
		const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet3d
	)

wrapper function for Shape 3d analysis and measurement algorithm

Note

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

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure

multiSlice_shapeAnalysis3d() [1/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr ipsdk::imaproc::shape::analysis::multiSlice_shapeAnalysis3d	(	const ipsdk::image::ImageConstPtr &	pInOptGreyMsrImg3d1,
		const ipsdk::shape::segmentation::PlanIndexedShape3dCollConstPtr &	pInPILabelsShape3d,
		const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet3d
	)

wrapper function for Shape 3d analysis and measurement algorithm

Note

This wrapper can be used with multi slice input images

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure

shapeAnalysis3d() [2/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::MeasureSetPtr ipsdk::imaproc::shape::analysis::shapeAnalysis3d	(	const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet3d,
		const ipsdk::shape::segmentation::Shape3dCollConstPtr &	pInLabelsShape3d,
		const ipsdk::imaproc::shape::analysis::ShapeAnalysis3dOptParams &	shapeAnalysis3dOptParams
	)

wrapper function for Shape 3d analysis and measurement algorithm

Note

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

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure

multiSlice_shapeAnalysis3d() [2/2]

IPSDKIPLSHAPEANALYSIS_API ipsdk::shape::analysis::PlanIndexedMeasureSetPtr ipsdk::imaproc::shape::analysis::multiSlice_shapeAnalysis3d	(	const ipsdk::shape::analysis::MeasureInfoSetConstPtr &	pInMeasureInfoSet3d,
		const ipsdk::shape::segmentation::PlanIndexedShape3dCollConstPtr &	pInPILabelsShape3d,
		const ipsdk::imaproc::shape::analysis::ShapeAnalysis3dPIOptParams &	shapeAnalysis3dPIOptParams
	)

wrapper function for Shape 3d analysis and measurement algorithm

Note

This wrapper can be used with multi slice input images

Exceptions

ipsdk::processor::IPSDKBaseProcessingException

on failure