Ngawari

Contents:

  • Installation Guide
    • Requirements
    • Installation Methods
      • From PyPI (Recommended)
      • From Source
      • Development Installation
    • Verifying Installation
      • Version Compatibility
  • Quick Start Guide
    • Basic Concepts
    • Getting Started
    • Creating Basic Geometry
    • Working with Arrays
    • Filtering Operations
    • Clipping and Cutting
    • File I/O
    • Mathematical Operations
    • Complete Example
    • Next Steps
  • API Reference
    • Core Modules
      • ftk - Mathematical and Utility Functions
        • getIDOfClosestFloat()
        • getClosestFloat()
        • getIDOfClosestPoint()
        • getClosestPoint()
        • distPointPoints()
        • squareDistPointPoints()
        • sortedIDsOfClosestPoints()
        • distTwoPoints()
        • getIDsOfClosestPoints()
        • getIDsOfFartherestPoints()
        • vectorMagnitudes()
        • normaliseArray()
        • angleBetween2Vec()
        • angleBetweenVecAndPlane()
        • areVecsMatching()
        • linearFit()
        • fitPlaneToPoints()
        • polyfit2d()
        • polyval2d()
        • projectPtsToPlane()
        • project3DPointsToPlanarCoordinateSystem()
        • project3DPointsToPlanarCoordinateSystem_OLD()
        • project3DPointsToPlanarCoordinateSystem2()
        • convert2DPointsTo3DCoordinateSystem()
        • fitCircle2D()
        • fitCircleRANSAC()
        • fitCircleRANSAC3D_xyz()
        • fit_ellipse_2d()
        • fit_ellipse_3d()
        • buildCircle3D()
        • fitPlaneToPointCloud_RANSAC()
        • linerFit_RANSAC()
        • deg2rad()
        • rad2deg()
        • rotateArray()
        • rotationMatrixFromThreeAngles()
        • getClosestInSortedList()
        • getIdOfClosestFloat()
        • polar2Cart()
        • polar2z()
        • z2Polar()
        • cart2Polar()
        • unit_vector()
        • vecFromPtToLine()
        • fcdot()
        • cosineDifferenceBetweenTwoMats()
        • getVectorComponentAlongRefVec()
        • getVectorComponentAlongRefVec_Mag()
        • getVectorComponentNormalToRefVec()
        • closeCurve()
        • splinePoints()
        • splineFunction()
        • splineXY()
        • splineCurve()
        • getMaxsMinsInflections()
        • sigmoidFunction()
        • extractContinuousSegFromPeriodic()
        • fitGaussianToData()
        • gaussianFunction()
        • calculate_signed_area_2d()
        • isClosedPolygonClockwise()
        • ensureClosedPolyIsClockwise()
        • setFirstPtOfPolygon()
        • reorderPointsStartClosestToX()
        • reorderPointsStatingAti()
        • sortPointsByClosest_RETURNIDs()
        • sortPointsByClosest()
        • cumulativeDistanceAlongLine()
        • getIdOfPointClosestToX()
        • getPolygonMeanRadius()
        • getPolygonMeanDiameter()
        • getPolygonCenterPoint()
        • lineMagnitude()
        • distancePointToLineSegPerpendicular()
        • ndarrayToListOfTuple3()
        • diff()
        • circleFit2DErr()
        • distanceToPlane()
        • residualPlane()
        • residualsCircle()
        • icp()
        • fitPlane3DOptimize()
        • fitCircle3D()
        • lagBetweenTwoCurves()
        • calculatePlaneThreePoints()
        • getPlaneConstantsFromPointAndVector()
        • calculateDerivativeOnLine_backwardDiff()
        • calculateSecondDerivativeOnLine()
        • calculateCurvature3Pts()
        • calculateCurvature_D()
        • setVectorDirection()
        • buildRotationMatrix()
        • adjustPointsCenterOfMassToOrigin()
        • areVecsConsistent()
        • setVecAConsitentWithVecB()
        • buildConvexHUll3D()
        • orderPointsConvexHull_IDs()
        • orderPointsConvexHull()
        • groupContinuousLinesByTol()
        • buildContinuousLineByClosestPt()
        • accumulatedAverage()
        • interpolateNANsFromSurroundingValues_cubic()
        • doesLineSegPierceTriangle()
        • doesLinePierceTriangle()
        • pluckerSideOperator()
        • pluckerLine()
        • doesVectorPierceAnyTriangle()
        • calculateBSA()
        • interpolateNANsFromSurroundingValues_linear()
        • convexHull()
        • Vector Operations
        • Matrix Operations
        • Geometric Calculations
        • Point and Line Utilities
        • Mathematical Transformations
      • fIO - File Input/Output
        • remove_symbols()
        • remove_not_allowed()
        • countFilesInDir()
        • getAllFilesUnderDir()
        • parseFileToTagsDictionary()
        • writeDictionaryToFile()
        • NumpyEncoder
        • writeDictionaryToJSON()
        • parseJsonToDictionary()
        • strListToFloatList()
        • xmlIndent()
        • findAndReplaceTextInFile()
        • readFileToListOfLines()
        • appendFiles()
        • pickleData()
        • unpickleData()
        • tarGZLocal_AndMove()
        • addSuffixToName()
        • checkIfExtnPresent()
        • readDataCSV()
        • writeCSVFile()
        • detectDelimiter()
        • writePlyFile()
        • writeVTKFile()
        • readVTKFile()
        • nii_to_niigz()
        • writeNifti()
        • readNifti()
        • readNRRD()
        • writeVTK_PVD_Dict()
        • pvdAddTimeToFieldData()
        • writeZipFromVTK_PVD_Dict()
        • deleteFilesByPVD()
        • readPVDFileName()
        • readImageFileToDict()
        • readPVD()
        • pvdGetDict()
        • pvdGetClosestTimeToT()
        • pvdGetTimes()
        • pvdGetIdOfT()
        • pvdGetFileAtT()
        • pvdGetNumberTimePoints()
        • pvdGetDataFileRoot_Prefix_and_Ext()
        • pvdGetDataClosestTo()
        • pvdMultiply()
        • pvdReverse()
        • pvdRestart_t()
        • pvdRestart()
        • pvdClip()
        • pvdResetTimes()
        • pvdResetStartPoint_Id()
        • pvdResetStartPoint()
        • pvdAddStartPointAtEndForPeriodicy()
        • buildPVD_WaterFallRestarts()
        • VTK File Formats
        • Other File Formats
        • PVD File Operations
        • Data Conversion
        • Batch Processing
      • vtkfilters - VTK Filtering and Processing
        • isVTI()
        • isVTP()
        • isVTS()
        • angleBetweenTwoVectors()
        • getArrayNames()
        • getArray()
        • getScalarsArrayName()
        • getVectorsArrayName()
        • getArrayId()
        • renameArray()
        • getArrayAsNumpy()
        • getScalarsAsNumpy()
        • setArrayFromNumpy()
        • addNpArray()
        • setArrayDtype()
        • setArrayAsScalars()
        • setArrayAsVectors()
        • ensureScalarsSet()
        • delArray()
        • delArraysExcept()
        • addFieldData()
        • getFieldData()
        • getFieldDataDict()
        • getFieldDataNames()
        • duplicateFieldData()
        • deleteFieldData()
        • getVtkPointsAsNumpy()
        • getPtsAsNumpy()
        • getCellCenters()
        • buildImplicitSphere()
        • buildSphereSource()
        • buildCylinderSource()
        • buildImplicitBox()
        • buildCubeSource()
        • buildPolyLineBetweenTwoPoints()
        • buildPolyTrianglesAtCp()
        • buildPlaneCentredOnRoi()
        • buildPlaneCentredOnSphere()
        • buildPlanePtAndNorm()
        • buildPlaneCentredOnO()
        • buildPlaneSource()
        • buildPolyLineFromXYZ_spline()
        • buildPolyLineFromXYZ()
        • buildPolydataFromXYZ()
        • clippedByCircle()
        • sliceByPlane()
        • getDataCutByPlane()
        • getPolyDataClippedByROI()
        • getPolyDataClippedByBox()
        • getPolyDataClippedBySphere()
        • clippedByPolyData()
        • doesLinePierceTri()
        • doesLinePiercePolygon()
        • clippedByPlane()
        • clipDataByPlane()
        • clippedByPlaneClosedSurface()
        • clippedBySphere()
        • clippedByScalar()
        • clipVolumeToEightPolydataBoxes()
        • roi_line_to_roi_plane()
        • clipPlaneToROI()
        • vtiToVts()
        • vtsToVti()
        • getVtsOrigin()
        • getVtsDirectionVectors()
        • getVtsResolution()
        • getResolution_VTI()
        • resetIndexing()
        • resetVTSIndexing()
        • resetVTIIndexing()
        • getDimsResOriginFromOutline()
        • buildRawImageDataFromPolyData()
        • buildRawImageDataFromOutline()
        • buildRawImageDataFromOutline_dims()
        • duplicateImageData()
        • buildRawImageData()
        • surf2ImageBW()
        • getVarValueAtI_ImageData()
        • getImageX()
        • imageX_ToStructuredCoords()
        • imageIndex_ToStructuredCoords()
        • getNeighbours26_fromImageIndex()
        • imageStrucCoords_toIndex()
        • imageStrucCoords_toX()
        • filterFlipImageData()
        • getPolyDataMeanFromCenter()
        • copyPolyData()
        • copyData()
        • contourFilter()
        • cleanData()
        • reduceNumberOfPoints()
        • filterBoolean()
        • tubeFilter()
        • filterVtpSpline()
        • filterTransformPolyData()
        • translatePoly_AxisA_To_AxisB()
        • transformPolydataA_to_B_ICP()
        • iterativeClosestPointsTransform()
        • filterWarpPolydataByVectors()
        • transformImageData()
        • pointToCellData()
        • cellToPointData()
        • getOutline()
        • getMaximumBounds()
        • appendPolyData()
        • appendPolyDataList()
        • appendImageList()
        • appendUnstructured()
        • mergeTwoImageData()
        • multiblockToList()
        • idListToVtkIDs()
        • extractCells()
        • extractSelection()
        • delCellsByEdgeLength()
        • delCellsByID()
        • getPolylineLength()
        • getLoopSubDivided()
        • decimateTris()
        • shrinkWrapData()
        • poissonRecon()
        • pointCloudRemoveOutliers()
        • smoothTris()
        • smoothTris_SINC()
        • filterExtractEdges()
        • isPolyDataWaterTight()
        • isPolyDataPolyLine()
        • calculatePolyDataArea()
        • getPolyDataCenterPtNormal()
        • addMagnitudeArray()
        • addNormalVelocities()
        • filterDilateErode()
        • filterExtractSurface()
        • filterExtractTri()
        • filterTriangulate()
        • getVolumeSurfaceAreaOfPolyData()
        • mergeSurfsByPointsInsideVti()
        • getTriangleAreaAndNormal()
        • addNormalsToPolyData()
        • getBoundaryEdges()
        • getEdges()
        • getConnectedCellIds()
        • extractStructuredSubGrid()
        • extractVOI()
        • extractVOI_fromFov()
        • filterNullOutsideSurface()
        • filterNullInsideSurface()
        • filterResampleToDataset()
        • filterResampleToImage()
        • getTransposeIDS_and_FlipIDs_VTS2VTI()
        • filterResampleToImage_BestAligned()
        • getAxesDirectionCosinesForNormal()
        • filterResliceImage()
        • filterGaussianSmooth()
        • filterVtiMedian()
        • filterImageGradient()
        • filterAnisotropicDiffusion()
        • filterSurfaceToImageStencil()
        • filterMaskImageBySurface()
        • filterGetPointsInsideSurface()
        • filterGetPointIDsInsideSurface()
        • filterGetPolydataInsideSurface()
        • filterGetEnclosedPts()
        • filterGetArrayValuesWithinSurface()
        • getDataWithThreshold()
        • countPointsInVti()
        • getConnectedRegionLargest()
        • getConnectedRegionContaining()
        • getConnectedRegionClosestToX()
        • getConnectedRegionClosestToX_UnStruct()
        • getConnectedRegionAll()
        • getConnectedRegionMinDistToX()
        • Data Type Checkers
        • Array Operations
        • Geometry Creation
        • Filtering Operations
        • Clipping and Cutting
        • Image Data Operations
        • Surface Operations
        • Data Conversion
        • Utility Functions
    • Module Overview
      • ftk - Mathematical and Utility Functions
      • fIO - File Input/Output
      • vtkfilters - VTK Filtering and Processing
    • Usage Examples
      • Basic Import
      • Common Patterns
  • Examples
    • Basic Geometry Example
    • Clipping Example
    • Image Data Example
    • Mathematical Operations Example
    • File I/O Example
  • Contributing to Ngawari
    • Getting Started
    • Development Setup
    • Code Style
    • Testing
    • Building Documentation
    • Pull Request Guidelines
    • Issue Reporting
    • Getting Help
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