spam package

Subpackages

• spam.DIC package
  • Submodules
  • spam.DIC.deform module
    • applyPhi()
    • applyPhiPython()
    • applyPhiField()
    • binning()
    • applyMeshTransformation()
  • spam.DIC.globalDVC module
    • surfaceLabels()
    • projectionMatrices()
    • isochoricField()
    • regularisationMatrix()
    • regularisationParameters()
    • globalCorrelation()
  • spam.DIC.grid module
    • makeGrid()
    • getImagettes()
  • spam.DIC.kinematics module
    • estimateLocalQuadraticCoherency()
    • estimateDisplacementFromQuadraticFit()
    • interpolatePhiField()
    • mergeRegularGridAndDiscrete()
    • getDisplacementFromNeighbours()
    • applyRegistrationToPoints()
    • mergeRegistrationAndDiscreteFields()
  • spam.DIC.multimodal module
    • multimodalRegistration()
    • gaussianMixtureParameters()
    • phaseDiagram()
  • spam.DIC.pixelSearch module
    • pixelSearch()
  • spam.DIC.registration module
    • register()
    • registerMultiscale()
  • Module contents
    • pixelSearch()
• spam.deformation package
  • Submodules
  • spam.deformation.deformationField module
    • FfieldRegularQ8()
    • FfieldRegularGeers()
    • FfieldBagi()
    • decomposeFfield()
    • decomposePhiField()
  • spam.deformation.deformationFunction module
    • computePhi()
    • decomposeF()
    • decomposePhi()
    • computeRigidPhi()
  • Module contents
• spam.excursions package
  • Submodules
  • spam.excursions.elkc module
    • expectedMesures()
    • gaussianMinkowskiFunctionals()
    • secondSpectralMoment()
    • flag()
    • hermitePolynomial()
    • ballVolume()
    • lkcCuboid()
    • getThresholdFromVolume()
    • getCorrelationLengthFormArea()
  • spam.excursions.randomFields module
    • simulateRandomField()
    • parametersLogToGauss()
    • fieldGaussToUniform()
    • fieldUniformToGauss()
  • Module contents
• spam.filters package
  • Submodules
  • spam.filters.distanceField module
    • distanceField()
  • spam.filters.morphologicalOperations module
    • greyDilation()
    • greyErosion()
    • greyMorphologicalGradient()
    • binaryDilation()
    • binaryErosion()
    • binaryMorphologicalGradient()
    • binaryGeodesicReconstruction()
    • directionalErosion()
    • morphologicalReconstruction()
  • spam.filters.movingFilters module
    • average()
    • variance()
    • hessian()
  • Module contents
    • distanceField()
• spam.helpers package
  • Submodules
  • spam.helpers.histogramTools module
    • findHistogramPeaks()
    • histogramNorm()
  • spam.helpers.imageManipulation module
    • stackToArray()
    • crop()
    • rescale()
    • rescaleToInteger()
    • convertUnsignedIntegers()
    • singleShift()
    • multipleShifts()
    • slicePadded()
    • splitImage()
    • rebuildImage()
    • checkerBoard()
  • spam.helpers.optionsParser module
    • str2bool()
    • isTwoDtiff()
    • pixelSearch()
    • pixelSearchPropagate()
    • ldicParser()
    • ddicParser()
    • multiModalRegistrationParser()
    • gdicParser()
    • regularStrainParser()
    • discreteStrainsCalcParser()
    • eregDiscreteParser()
    • moveLabelsParser()
    • ITKwatershedParser()
    • BCFromDVCParser()
    • deformImageParser()
    • register()
    • passPhiField()
    • filterPhiField()
    • mesh()
    • meshSubdomains()
    • hdfReader()
    • eregParser()
    • displaySettings()
  • spam.helpers.test module
    • TestSpam
      • TestSpam.DEBUG
      • TestSpam.setUp()
      • TestSpam.tearDown()
  • spam.helpers.tsvio module
    • writeRegistrationTSV()
    • writeStrainTSV()
    • readCorrelationTSV()
    • readStrainTSV()
    • TSVtoTIFF()
    • TSVtoVTK()
  • spam.helpers.vtkio module
    • readStructuredVTK()
    • writeStructuredVTK()
    • writeGlyphsVTK()
    • writeUnstructuredVTK()
    • readUnstructuredVTK()
    • TIFFtoVTK()
  • Module contents
• spam.kalisphera package
  • Submodules
  • spam.kalisphera.kalisphera module
    • makeSphere()
    • makeBlurryNoisySphere()
  • spam.kalisphera.spheroid module
    • makeBlurryNoisySpheroid()
  • Module contents
• spam.label package
  • Submodules
  • spam.label.ITKwatershed module
    • watershed()
  • spam.label.contacts module
    • contactingLabels()
    • contactPoints()
    • labelledContacts()
    • fetchTwoGrains()
    • localDetection()
    • contactOrientations()
    • localDetectionAssembly()
    • contactOrientationsAssembly()
  • spam.label.label module
    • boundingBoxes()
    • centresOfMass()
    • volumes()
    • equivalentRadii()
    • momentOfInertia()
    • ellipseAxes()
    • convertLabelToFloat()
    • makeLabelsSequential()
    • getLabel()
    • getImagettesLabelled()
    • labelsOnEdges()
    • removeLabels()
    • setVoronoi()
    • labelTetrahedra()
    • labelTetrahedraForScipyDelaunay()
    • filterIsolatedCells()
    • trueSphericity()
    • convexVolume()
    • moveLabels()
    • erodeLabels()
    • convexFillHoles()
    • getNeighbours()
    • detectUnderSegmentation()
    • detectOverSegmentation()
    • fixUndersegmentation()
    • fixOversegmentation()
    • shuffleLabels()
  • Module contents
• spam.measurements package
  • Submodules
  • spam.measurements.covariance module
    • How to import
    • covarianceAlongAxis()
    • covarianceSubPixel()
    • betaCovariance()
    • gaussianCovariance()
    • fitCovariance()
  • spam.measurements.globalDescriptors module
    • volume()
    • eulerCharacteristic()
    • surfaceArea()
    • totalCurvature()
    • perimeter()
    • generic()
  • spam.measurements.porosityField module
    • porosityField()
  • Module contents
• spam.mesh package
  • Submodules
  • spam.mesh.objects module
    • packSpheres()
    • packObjectsFromList()
  • spam.mesh.projection module
    • projectObjects()
    • projectField()
  • spam.mesh.structured module
    • createCylindricalMask()
    • structuringElement()
    • createLexicoCoordinates()
  • spam.mesh.tetrahedra module
    • tetCentroid()
    • tetVolume()
    • shapeFunctions()
    • elementaryStiffnessMatrix()
    • globalStiffnessMatrix()
  • spam.mesh.unstructured module
    • gmshToSpam()
    • getMeshCharacteristicLength()
    • createCuboid()
    • createCylinder()
    • triangulate()
    • projectTetFieldToGrains()
    • BCFieldFromDVCField()
    • tetVolumes()
    • rankPoints()
  • Module contents
• spam.orientations package
  • Submodules
  • spam.orientations.analyse module
    • fitVonMisesFisher()
    • meanOrientation()
    • fabricTensor()
    • projectOrientation()
  • spam.orientations.generate module
    • generateIsotropic()
    • generateIcosphere()
    • generateVonMisesFisher()
  • Module contents
• spam.plotting package
  • Submodules
  • spam.plotting.greyLevelHistogram module
    • plotGreyLevelHistogram()
  • spam.plotting.multivariateGaussians module
    • plotMultivariateGaussians()
  • spam.plotting.orientationPlotter module
    • plotOrientations()
    • distributionDensity()
    • plotSphericalHistogram()
  • spam.plotting.particleSizeDistribution module
    • plotParticleSizeDistribution()
  • spam.plotting.tetrahedraPlotter module
    • plotDelaunay3D()
  • Module contents
• spam.tests package
  • Module contents
• spam.visual package
  • Submodules
  • spam.visual.QtImageViewer module
    • QtImageViewer
      • QtImageViewer.leftMouseButtonPressed
      • QtImageViewer.rightMouseButtonPressed
      • QtImageViewer.leftMouseButtonReleased
      • QtImageViewer.rightMouseButtonReleased
      • QtImageViewer.leftMouseButtonDoubleClicked
      • QtImageViewer.rightMouseButtonDoubleClicked
      • QtImageViewer.hasImage()
      • QtImageViewer.clearImage()
      • QtImageViewer.pixmap()
      • QtImageViewer.image()
      • QtImageViewer.setImage()
      • QtImageViewer.loadImageFromFile()
      • QtImageViewer.updateViewer()
      • QtImageViewer.resizeEvent()
      • QtImageViewer.mousePressEvent()
      • QtImageViewer.mouseReleaseEvent()
      • QtImageViewer.mouseDoubleClickEvent()
  • spam.visual.visualClass module
    • ereg
      • ereg.slideIm1()
      • ereg.slideIm2()
      • ereg.showImages()
      • ereg.changeAxis()
      • ereg.checkSlave()
      • ereg.changeComp()
      • ereg.changeCB()
      • ereg.changeColorF()
      • ereg.modifyPhi()
      • ereg.saveTSV()
      • ereg.validate()
      • ereg.resetTSV()
      • ereg.resetIdentity()
      • ereg.output()
      • ereg.equalize()
    • QtCropWidget
      • QtCropWidget.showImages()
      • QtCropWidget.slideZMin()
      • QtCropWidget.slideZMax()
      • QtCropWidget.slideYMin()
      • QtCropWidget.slideYMax()
      • QtCropWidget.slideXMin()
      • QtCropWidget.slideXMax()
      • QtCropWidget.slideZView()
      • QtCropWidget.slideYView()
      • QtCropWidget.slideXView()
      • QtCropWidget.saveTSVCrop()
      • QtCropWidget.output()
      • QtCropWidget.changeImage()
    • JHist
      • JHist.slideIm1Max()
      • JHist.slideIm2Max()
      • JHist.slideIm1Min()
      • JHist.slideIm2Min()
      • JHist.changeBins()
      • JHist.changeDistance()
      • JHist.plusOrMinusDist()
      • JHist.changeNBP()
      • JHist.plusOrMinusNBP()
      • JHist.computeHistogram()
      • JHist.fitEllipsoid()
      • JHist.showHistogram()
      • JHist.slideIndexedValChange()
      • JHist.reFit()
    • PhaseDiagram
      • PhaseDiagram.distanceMax()
      • PhaseDiagram.changeDistanceType()
      • PhaseDiagram.changeSigma()
      • PhaseDiagram.findFullCoverage()
      • PhaseDiagram.computePhaseDiagram()
      • PhaseDiagram.showPhaseDiagram()
    • FinalStep
      • FinalStep.starCorrelation()
  • Module contents

Submodules

spam.datasets module

spam.datasets.loadtiff(filepath)

spam.datasets.load(filepath)

spam.datasets.loadPickle(filepath)

spam.datasets.loadSnow()

spam.datasets.loadStructuredMesh()

spam.datasets.loadUnstructuredMesh()

spam.datasets.loadConcreteXr()

spam.datasets.loadConcreteNe()

spam.datasets.loadDEMboxsizeCentreRadius()

spam.datasets.loadUniformDEMboxsizeCentreRadius()

spam.datasets.loadDEMtouchingGrainsAndBranchVector()

spam.datasets.loadDEMspheresMMR()

spam.errors module

exception spam.errors.Error

Bases: Exception

Base class for exceptions in this module.

exception spam.errors.InputError(variable, explanation=None)

Bases: Error

Exception raised for errors in the input.

Attributes:

variable – variable name which caused the error explanation – explanation of the error

Module contents