Blob/Source API¶

These classes define image pixel data structure. Defined in src/imgproc/Pixel.h

class Caesar::Pixel : public TObject¶

Public Types

enum PixelType¶

Pixel type.

Values:

enumerator eNormal¶

enumerator eSeed¶

enumerator eHalo¶

Public Functions

Pixel()¶: Class constructor: initialize structures.

Pixel(long int _gbin, long int _ix, long int _iy, double _x, double _y, double _S)¶: Parametric constructor.

Pixel(const Pixel &pixel)¶: Copy constructor.

virtual ~Pixel()¶: Class destructor: free allocated memory.

Pixel &operator=(const Pixel &pixel)¶: Assignment Operator.

inline bool operator==(const Pixel &pixel) const¶: Equality Operator.

inline bool operator<(const Pixel &pixel) const¶: < Operator

inline int AddPixelFlux(Pixel *aPixel)¶: Sum pixel.

void Copy(TObject &pixel) const¶: Copy method.

inline void SetPhysCoords(double xx, double yy)¶: Set physical coordinates.

inline void SetCoords(long int i, long int j)¶: Set coordinates.

inline void SetBkg(double bkg, double noise)¶: Set bkg and rms value.

inline void SetCurv(double val)¶: Set curvature information.

inline void SetEdge(double val)¶: Set edgeness information.

inline std::pair<double, double> GetBkg()¶: Get bkg and noise.

inline double GetCurv()¶: Get curvature information.

inline double GetEdge()¶: Get edgeness information.

inline void Print()¶: Dump pixel info.

This class defines contour (point collection) data structure. Defined in src/imgproc/Contour.h

class Caesar::Contour : public TObject¶

Public Functions

Contour()¶: Class constructor: initialize structures.

Contour(const Contour &contour)¶: Copy constructor.

virtual ~Contour()¶: Class destructor: free allocated memory.

Contour &operator=(const Contour &contour)¶: Assignment Operator.

void Copy(TObject &contour) const¶: Copy method.

inline int GetN()¶: Get number of points.

inline bool HasPoints()¶: Check if contour has points.

inline void SetPoints(Points p)¶: Set contour points.

inline Points GetPoints()¶: Get contour points.

inline TVector2 *GetPoint(int i)¶: Get contour point with given index.

TVector2 *FindPoint(double x, double y, double tol = 0)¶: Find point (with tolerance)

bool IsPointInsideContour(double x, double y)¶: Check if point is inside contour.

int ApplyOffset(double offsetX, double offsetY)¶: Apply offset to points and centroid.

inline int GetPointXY(double &x, double &y, int i)¶: Get contour point x & y.

inline void AddPoint(TVector2 p)¶: Add contour points.

inline int SortPointsCounterClockWise()¶: Sort points counter-clockwise.

inline void Reset()¶: Reset contour.

TGraph *GetGraph(bool addLastPoint = true)¶: Return a graph object with contour points.

TPolyLine *GetBoundingBoxLine()¶: Return a polyline object with bounding box.

TPaveText *GetParamInfoBox()¶: Return a info box with parameter values.

int ComputeParameters()¶: Compute contour parameters.

void ComputeShapeParams(std::vector<cv::Point2f> const &points)¶: Compute shape parameters.

void ComputeMomentParams(std::vector<cv::Point2f> const &points)¶: Compute moments pars.

int ComputeFittedEllipse()¶: Compute fitted ellipse.

TEllipse *GetFittedEllipse()¶: Return an ellipse object fitted to contour.

void ComputeFourierDescriptors()¶: Compute Fourier descriptors.

void ComputeCentroidDistanceFD()¶: Compute centroid distance FD.

void ComputeBendingEnergy()¶: Compute bending energy.

inline void Dump()¶: Dump.

inline void Log(std::string level = "INFO")¶: Log.

inline std::string GetPrintable()¶: GetPrintable.

This class defines an image blob data structure. Defined in src/imgproc/Blob.h

class Caesar::Blob : public TNamed

Subclassed by Caesar::Region, Caesar::Source

Public Functions

Blob(): Class constructor: initialize structures.

Blob(std::string name): Parametric constructor.

Blob(std::vector<Pixel*> const &pixels, std::string name = ""): Parametric constructor.

Blob(const Blob &blob): Copy constructor.

virtual ~Blob(): Class destructor: free allocated memory.

Blob &operator=(const Blob &blob): Assignment Operator.

void Copy(TObject &blob) const: Copy method.

inline void SetId(int id): Set blob id.

inline void SetName(std::string name): Set blob name.

inline bool IsAtEdge(): Is blob at image edge.

inline void SetEdgeFlag(bool choice): Set edge flag.

inline int SetImageMetaData(ImgMetaData *data, double crpix1Offset = 0, double crpix2Offset = 0): Set image metadata.

inline ImgMetaData *GetImageMetaData(): get image metadata

inline bool HasImageMetaData(): Set image metadata.

inline long int GetNPixels(): Get number of pixels.

inline const PixelCollection &GetPixels() const: Get pixel collection.

inline void SetPixels(PixelCollection &pixels): Set pixel collection.

int AddPixel(Pixel *pixel, bool makeCopy = false): Add a pixel to collection.

inline bool HasPixels(): Has pixels stored?

inline Pixel *GetPixel(int index): Get access to pixel by index.

inline std::vector<int> GetSeedPixelIndexes(): Get access to seed pixel indexes.

inline Pixel *GetSeedPixel(): Find and return largest-significance seed pixel.

inline void MarkHaloPixels(double ZThr): Mark pixels with significance within given thresholds as halo pixels.

int ComputeStats(bool computeRobustStats = true, bool forceRecomputing = false, bool useParallelMedian = false): Compute stats.

inline bool HasStats(): Has stats?

inline void SetHasStats(bool value): Has stats?

int ComputeMorphologyParams(): Compute morphology parameters.

int ComputeZernikeMoments(int order = 6): Compute Zernike moments.

inline bool HasParameters(): Has morphology parameters computed.

inline void SetHasParameters(bool value): Set has morphology pars.

inline double GetM1(): Get 1st pixel moment (= mean)

inline void SetM1(double value): Set 1st pixel moment (= mean)

inline double GetM2(): Get 2nd pixel moment.

inline void SetM2(double value): Set 2nd pixel moment.

inline double GetM3(): Get 3rd pixel moment.

inline void SetM3(double value): Set 3rd pixel moment.

inline double GetM4(): Get 4th pixel moment.

inline void SetM4(double value): Set 4th pixel moment.

inline double GetM1Curv(): Get 1st pixel curvature moment (= mean)

inline void SetM1Curv(double value): Set 1st pixel curvature moment (= mean)

inline double GetM2Curv(): Get 2nd pixel curvature moment.

inline void SetM2Curv(double value): Set 2nd pixel curvature moment.

inline double GetS(): Get pixel flux sum.

inline void SetS(double value): Set pixel flux sum.

inline double GetSmax() const: Get pixel flux max.

inline void SetSmax(double value): Set pixel flux max.

inline double GetSmin() const: Get pixel flux min.

inline void SetSmin(double value): Set pixel flux min.

inline double GetSxx(): Get pixel flux XX correlation.

inline void SetSxx(double value): Set pixel flux XX correlation.

inline double GetSyy(): Get pixel flux YY correlation.

inline void SetSyy(double value): Get pixel flux YY correlation.

inline double GetSxy(): Get pixel flux XY correlation.

inline void SetSxy(double value): Set pixel flux XY correlation.

inline double GetSx(): Get pixel flux sum weighted by position x.

inline void SetSx(double value): Set pixel flux sum weighted by position x.

inline double GetSy(): Get pixel flux sum weighted by position y.

inline void SetSy(double value): Set pixel flux sum weighted by position y.

inline long int GetSmaxPixId(): Get id of maximum flux pixel.

inline void SetSmaxPixId(long int value): Set id of maximum flux pixel.

inline long int GetSminPixId(): Get id of minimum flux pixel.

inline void SetSminPixId(long int value): Set id of minimum flux pixel.

inline double GetScurv(): Get pixel sum of curvature.

inline void SetScurv(double value): Set pixel sum of curvature.

inline double GetSedge(): Get pixel sum of edgeness.

inline void SetSedge(double value): Set pixel sum of edgeness.

inline void GetSourceRange(float &xmin, float &xmax, float &ymin, float &ymax): Get source x-y range.

inline long int GetXmin(): Get source pixel x_min.

inline long int GetXmax(): Get source pixel x_max.

inline long int GetYmin(): Get source pixel y_min.

inline long int GetYmax(): Get source pixel y_max.

inline void SetSourceRange(float xmin, float xmax, float ymin, float ymax): Set source x-y range.

inline void GetSourcePixelRange(long int &ixmin, long int &ixmax, long int &iymin, long int &iymax): Get source pixel coordinate range.

inline long int GetIxMin(): Get source pixel ix_min.

inline long int GetIxMax(): Get source pixel ix_max.

inline long int GetIyMin(): Get source pixel iy_min.

inline long int GetIyMax(): Get source pixel iy_max.

inline void SetSourcePixelRange(long int ixmin, long int ixmax, long int iymin, long int iymax): Set source pixel coordinate range.

int GetSampleStdDev(double &sigmaX, double &sigmaY, double &covXY): Get sample source standard deviations.

inline void Print(): Dump blob info.

Image *GetImage(ImgType mode, int pixMargin = 1, bool includeHaloPixels = false): Generate an image from source pixel.

TH2D *GetWCSHisto(ImgType mode, int pixMargin = 1, int coordSyst = -1): Generate an image from source pixel.

Image *GetNestedBlobMask(Image *sourceImage = 0, int pixMargin = 1, double nestedBlobMinScale = 1, double nestedBlobMaxScale = 3, double nestedBlobScaleStep = 1, double nestedBlobPeakZThr = 5, double nestedBlobPeakZMergeThr = 2.5, int NMinPix = 5, double nestedBlobThrFactor = 0, double nestedBlobKernFactor = 6): Get blob mask.

inline bool HasContours(): Has contours.

inline std::vector<Contour*> GetContours()

Return contours.

NB: Do not delete pointers.

inline Contour *GetContour(int index): Return contour with index.

std::vector<Contour*> GetWCSContours(WCS *wcs = 0, int coordSystem = -1, double pixOffset = 0, bool computePars = false, bool castCoordsToInt = false): Return contours converted in WCS.

Contour *GetWCSContour(int index, WCS *wcs = 0, int coordSystem = -1, double pixOffset = 0, bool computePars = false, bool castCoordsToInt = false): Return contour with index and convert to WCS.

inline void AddContour(Contour *aContour): Add contour.

bool IsPointOnContour(double x, double y, double tol = 1): Is point on contour?

inline double GetBkgSum(): Get bkg sum.

inline double GetBkgRMSSum(): Get bkg rms sum.

inline void SetBkgSum(double bkg): Set bkg sum (USED BY SERIALIZER)

inline void SetBkgRMSSum(double rms): Set bkg rms sum (USED BY SERIALIZER)

inline bool HasBoxBkgInfo(): Check if bkg info in a box around the blob has ben set.

inline void SetHasBoxBkgInfo(bool flag): Set has box bkg info flag (USED BY SERIALIZER)

inline double GetBoxBkg(): Get bkg estimate in a box around the blob.

inline double GetBoxBkgRMS(): Get bkg rms estimate in a box around the blob.

inline void SetBoxBkgInfo(double bkg, double rms): Set bkg and rms estimate in a box around the blob.

inline WCS *GetWCS(int coordSystem = -1)

Get WCS from stored metadata (TO BE DEPRECATED)

Get WCS from stored metadata

This class defines a source data structure. Defined in src/imgproc/Source.h and inheriting from Blob class.

class Caesar::Source : public Caesar::Blob ¶

Public Functions

Source()¶: Class constructor: initialize structures.

Source(std::string name)¶: Parametric constructor.

Source(std::vector<Pixel*> const &pixels, std::string name = "")¶: Parametric constructor.

Source(const Source &source)¶: Copy constructor.

virtual ~Source()¶: Class destructor: free allocated memory.

Source &operator=(const Source &source)¶: Assignment Operator.

void Copy(TObject &source) const¶: Copy method.

inline void SetType(SourceType choice)¶: Set source type.

inline void SetFlag(SourceFlag choice)¶: Set source flag.

inline void SetSimType(SimSourceType choice)¶: Set source sim type.

inline void SetSimMaxScale(float val)¶: Set source sim max scale.

inline void SetBeamFluxIntegral(double val)¶: Set beam flux integral.

inline double GetBeamFluxIntegral()¶: Get beam flux integral.

inline bool IsGoodSource()¶: Is a “good” source.

inline void SetGoodSourceFlag(bool flag)¶: Set source as “good”.

inline void SetDepthLevel(int level)¶: Set source depth level (0=mother, 1=nested)

inline int GetDepthLevel()¶: Get source depth level (0=mother, 1=nested)

inline void AddNestedSource(Source *aNestedSource)¶: Add nested sources.

inline bool HasNestedSources()¶: Has nested sources?

inline void SetHasNestedSources(bool val)¶: Set has nested sources.

inline std::vector<Source*> &GetNestedSources()¶: Get nested sources.

inline int ClearNestedSources()¶: Clear nested sources.

inline int SetNestedSources(std::vector<Source*> &sources, bool clear_existing = true)¶: Set nested sources.

inline int GetNestedSourceNumber()¶: Get nested source number.

inline Source *GetNestedSource(int index)¶: Get nested source.

int FindNestedSources(std::vector<Source*> &nestedSources, double nestedBlobMinScale = 1, double nestedBlobMaxScale = 3, double nestedBlobScaleStep = 1, double nestedBlobPeakZThr = 5, double nestedBlobPeakZMergeThr = 2.5, int minPixels = 5, double nestedBlobThrFactor = 0, double nestedBlobKernFactor = 6, double minNestedMotherDist = 2, double maxMatchingPixFraction = 0.5)¶: Find nested sources.

void Draw(bool drawBoundingBox = false, bool drawFittedEllipse = false, bool drawNested = false, int lineColor = kBlack, int lineStyle = kSolid)¶: Draw contours.

int Draw(int pixMargin = 0, ImgType imgType = eFluxMap, bool drawImage = true, bool drawContours = true, bool drawNested = true, bool drawFitComponents = true, int lineColor = kBlack, int lineStyle = kSolid, bool useWCS = false, int coordSyst = 0)¶: Draw source.

const std::string GetDS9Region(bool dumpNestedSourceInfo = false, bool convertToWCS = false, WCS *wcs = 0, int coordSystem = -1)¶: Get DS9 region info.

const std::string GetDS9EllipseRegion(bool dumpNestedSourceInfo = false)¶: Get DS9 ellipse info.

const std::string GetDS9FittedEllipseRegion(bool useFWHM = true, bool dumpNestedSourceInfo = false, bool convertToWCS = false, WCS *wcs = 0, int coordSystem = -1, bool useWCSSimpleConversion = true)¶: Get DS9 fitted ellipse info.

inline std::string GetDS9RegionColor()¶: Get DS9 region color according to source type.

inline std::string GetDS9RegionTag()¶: Get DS9 region tag according to source type.

inline void Print()¶: Dump source info.

inline bool IsInsideSource(Source *aSource)¶: Is source inside given source.

inline bool IsAtBoxEdge(float xmin, float xmax, float ymin, float ymax)¶: Check if source share boundary with given box.

inline bool HasBoxOverlap(float xmin, float xmax, float ymin, float ymax)¶: Is source inside given box.

bool CheckBoxOverlapping(Source*)¶: Check if this source bounding box overlaps with another given source.

bool IsAdjacentSource(Source *aSource)¶: Check if this source is adjacent to another given source.

int MergeSource(Source *aSource, bool copyPixels = false, bool checkIfAdjacent = true, bool computeStatPars = true, bool computeMorphPars = true, bool sumMatchingPixels = false)¶: Merge this source with given source.

long int GetNMatchingPixels(std::vector<Pixel*> &matching_pixels, Source *aSource, bool sorted = false)¶: Get collection of matching pixels between this and another source.

inline long int GetNMatchingPixels(Source *aSource, bool sorted = false)¶: Get number of matching pixels between this and another source.

bool FindSourceMatchByOverlapArea(SourceOverlapMatchPars &pars, const std::vector<Source*> &sources, float overlapThr)¶: Find source match in a collection by overlapping area.

bool FindSourceMatchByPos(std::vector<SourcePosMatchPars> &pars, const std::vector<Source*> &sources, float posThr)¶: Find source match in a collection by position.

float GetCentroidDistance(Source *aSource)¶: Get distance in pixels between source centroids.

int Fit(SourceFitOptions &fitOptions)¶: Fit source with a multi-component gaussian model.

int Fit(SourceFitOptions &fitOptions, SourceFitPars &initfitPars)¶: Fit source with a multi-component gaussian model using provided start fit parameters.

inline void SetTrueInfo(double S_true, double X0_true, double Y0_true)¶: Set true source info.

inline bool HasTrueInfo()¶: Has true source info.

inline double GetTrueFlux()¶: Get true source flux.

inline void GetTruePos(double &x, double &y)¶: Get true source position.

inline bool HasFitInfo()¶: Has fit info.

inline void SetHasFitInfo(bool flag)¶: Set Has fit info (for serialization scopes)

inline SourceFitPars &GetFitPars()¶: Get fit pars.

inline void SetFitPars(SourceFitPars &fitPars)¶: Set fit pars (for serialization scopes)

inline int SetFitComponentFlag(int componentId, int flag)¶: Set fit component flag.

inline int GetFitComponentFlag(int &flag, int componentId)¶: Get fit component flag.

inline int GetFitStatus()¶: Get fit status.

inline void SetFitStatus(int fitStatus)¶: Set fit status (for serialization scopes)

inline int GetFluxDensity(double &fluxDensity)¶: Get integrated flux density.

inline int GetFluxDensityErr(double &fluxDensityErr)¶: Get integrated flux density error.

inline int GetFitQuality()¶: Get fit quality flag.

inline int GetCondonComponentFluxDensityErr(std::vector<double> &fluxDensityErrList)¶: Get integrated flux density error on components according to Condon (1997) formula 14.

int GetFitEllipses(std::vector<TEllipse*> &fitEllipses, bool useFWHM = true, bool convertToWCS = false, WCS *wcs = 0, int coordSystem = -1, double pixOffset = 0, bool useWCSSimpleConversion = true)¶: Get fit ellipses.

inline int GetNFitComponents()¶: Get number of fit components.

inline int GetNSelFitComponents()¶: Get number of selected fit components.

int FindComponentPeaks(std::vector<ImgPeak> &peaks, double peakZThr = 0, int maxPeaks = -1, int peakShiftTolerance = 2, std::vector<int> kernels = {3, 5, 7}, int peakKernelMultiplicityThr = 1, bool invertSearch = false)¶: Find component peaks.

int FindBlendedComponents(std::vector<Source*> &deblendedComponents, std::vector<ImgPeak> &deblendedPeaks, double peakZThr = 0, int maxPeaks = -1, double sigmaMin = 3, double sigmaMax = 3, double sigmaStep = 1, int minBlobSize = 5, double thrFactor = 0, int kernelFactor = 1, int pixMargin = 10)¶: Find blended source components.

inline int GetWCSPos(double &xwcs, double &ywcs, WCS *wcs = 0, int coordSystem = eJ2000)¶: Return source position in WCS coordinates.

inline int GetWCSWeightedPos(double &xwcs, double &ywcs, WCS *wcs = 0, int coordSystem = eJ2000)¶: Return signal-weighted source position in WCS coordinates.

inline int GetWCSSourceRange(double &xmin_wcs, double &xmax_wcs, double &ymin_wcs, double &ymax_wcs, WCS *wcs = 0, int coordSystem = eJ2000)¶: Return bounding box in WCS coordinates.

std::string GetIAUName(bool useWeightedPos = false, WCS *wcs = 0, int coordSystem = eJ2000)¶: Return source name following IAU convention.

int GetSpectralAxisInfo(double &val, double &dval, std::string &units)¶: Return spectral axis info.

inline bool HasSpectralIndexData()¶: Has spectral index data.

inline void SetHasSpectralIndexData(bool val)¶: Set has spectral index data flag.

inline SpectralIndexData &GetSpectralIndexData()¶: Get spectral index data.

inline void SetSpectralIndexData(SpectralIndexData &data)¶: Set spectral index data.

inline bool HasComponentSpectralIndexData()¶: Has component spectral index data.

inline void SetHasComponentSpectralIndexData(bool val)¶: Set has spectral index data flag.

inline std::vector<SpectralIndexData> &GetComponentSpectralIndexData()¶: Get component spectral index data.

inline void SetComponentSpectralIndexData(std::vector<SpectralIndexData> &data)¶: Set component spectral index data.

inline bool HasAstroObjects()¶: Has astro object data.

inline void SetHasAstroObjects(bool choice)¶: Has astro object data.

inline std::vector<AstroObject> &GetAstroObjects()¶: Get astro objects data.

inline void SetAstroObjects(std::vector<AstroObject> &data)¶: Set astro objects data.

int AddAstroObject(AstroObject &astroObject)¶: Add astro objects data.

inline bool HasComponentAstroObjects()¶: Has component astro object data.

inline void SetHasComponentAstroObjects(bool choice)¶: Has astro object data.

inline std::vector<std::vector<AstroObject>> &GetComponentAstroObjects()¶: Get astro objects data.

inline void SetComponentAstroObjects(std::vector<std::vector<AstroObject>> &data)¶: Set astro objects data.

int AddComponentAstroObject(int componentIndex, AstroObject &astroObject)¶: Add component astro objects data.

int ComputeObjClassId()¶: Compute object class id from astro object data (if available)

int ComputeComponentObjClassId()¶: Compute component object class id from astro object data (if available)

inline bool IsResolved_XXLSurveyMethod(double p0 = 1.08, double p1 = 2.03)¶: Compute if source island is resolved according to XXL survey criterion.

inline bool IsComponentResolved_XXLSurveyMethod(int componentId, double p0 = 1.08, double p1 = 2.03)¶: Compute if source fit component is resolved according to XXL survey criterion.

This class defines a source cube (source at different frequency channels) data structure. Defined in src/imgproc/SourceCube.h

class Caesar::SourceCube : public TNamed¶

Public Functions

SourceCube()¶: Class constructor: initialize structures.

SourceCube(std::string name)¶: Parametric constructor.

virtual ~SourceCube()¶: Class destructor: free allocated memory.

SourceCube(const SourceCube &scube)¶: Copy constructor.

SourceCube &operator=(const SourceCube &scube)¶: Assignment Operator.

void Copy(TObject &scube) const¶: Copy method.

inline int GetSize()¶: Get cube size.

inline int GetNMatches()¶: Get number of matches.

inline int AddSource(Source *aSource)¶: Add source to cube.

inline void AddComponentMatch()¶: Add component.

int AddIndexToComponent(int cubeComponentIndex, size_t sindex, size_t componentIndex)¶: Add index to existing component.

int DoSourceImagePlot(bool useWCS = true, int coordSyst = 0)¶: Draw source images.

int DoSourceSEDs()¶: Draw source SEDs.