Yayi core python extensions

This page details the python bindings of Yayi. Since these are bindings, for each class or function described here, there exist the equivalent C++ class or function. The python modules are also consistent with their C++ counterparts.

• Common
  • Structures
    • Data types
    • Coordinates
    • Graphs
    • Color manipulation
    • Histograms
  • Examples
    • Coordinates
    • Graphs
  • Reference
• IO
  • Reference
• Pixel processing
  • Reference

Contents

• Yayi core python extensions
  • Reference
    • Core
    • Structuring Elements
    • Neighborhood Processing
    • Low level morphology
    • Labels
    • Reconstructions
    • Segmentation
  • Example
  • Reference
    • Measurements
    • Distances

Reference

Core

Structuring Elements

class YayiStructuringElementPython.ConstNeighborhood

Main const neighborhood class. This class does not allow any writing into the image

Center((ConstNeighborhood)arg1, (object)arg2) → object :

(coordinate): centers the structuring element at the specified coordinate

C++ signature :

yayi::s_return_code Center(yayi::se::IConstNeighborhood {lvalue},yayi::s_coordinate<0, int>)

Center( (ConstNeighborhood)arg1, (object)arg2) -> object :

(iterator): centers the structuring element at the specified iterator position

C++ signature :

yayi::s_return_code Center(yayi::se::IConstNeighborhood {lvalue},yayi::IConstIterator*)

Center( (ConstNeighborhood)arg1, (long)arg2) -> object :

(offset): centers the structuring element at the specified offset

C++ signature :

yayi::s_return_code Center(yayi::se::IConstNeighborhood {lvalue},long long)

SetShift((ConstNeighborhood)arg1, (object)arg2) → object :

specifies the shift that will be later applied to the center

C++ signature :

yayi::s_return_code SetShift(yayi::se::IConstNeighborhood {lvalue},yayi::s_coordinate<0, int>)

ShiftCenter((ConstNeighborhood)arg1) → object :

shifts the center by a shift previously defined

C++ signature :

yayi::s_return_code ShiftCenter(yayi::se::IConstNeighborhood {lvalue})

pixels

returns an iterator on the pixels in the neighborhood previously centered

YayiStructuringElementPython.NeighborhoodFactory((Image)arg1, (StructuringElement)arg2) → ConstNeighborhood :

(image, structuring element): factory for the neighborhood. Returns a neighborhood instance on the image based on the provided structuring element. Returns None on error.

C++ signature :

yayi::se::IConstNeighborhood* NeighborhoodFactory(yayi::IImage,yayi::se::IStructuringElement)

YayiStructuringElementPython.SECross2D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SECross2D()

YayiStructuringElementPython.SEFactory((structuring_element_type)arg1, (int)arg2, (HyperRectangle)arg3, (structuring_element_subtype)arg4) → StructuringElement :

(structuring element type, dimension, shape, structuring element subtype): factory for structuring elements

C++ signature :

yayi::se::IStructuringElement* SEFactory(yayi::se::e_structuring_element_type,unsigned char,yayi::s_any_type,yayi::se::e_structuring_element_subtype)

YayiStructuringElementPython.SEHex2D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SEHex2D()

YayiStructuringElementPython.SESegmentX2D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESegmentX2D()

YayiStructuringElementPython.SESegmentX3D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESegmentX3D()

YayiStructuringElementPython.SESegmentY2D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESegmentY2D()

YayiStructuringElementPython.SESegmentY3D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESegmentY3D()

YayiStructuringElementPython.SESegmentZ3D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESegmentZ3D()

YayiStructuringElementPython.SESquare2D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESquare2D()

YayiStructuringElementPython.SESquare3D() → StructuringElement :

C++ signature :

yayi::se::IStructuringElement const* SESquare3D()

class YayiStructuringElementPython.StructuringElement

Main structuring element class

GetSESubType((StructuringElement)arg1) → structuring_element_subtype :

returns the subtype of the structuring element

C++ signature :

yayi::se::e_structuring_element_subtype GetSESubType(yayi::se::IStructuringElement {lvalue})

GetSEType((StructuringElement)arg1) → structuring_element_type :

returns the type of the structuring element

C++ signature :

yayi::se::e_structuring_element_type GetSEType(yayi::se::IStructuringElement {lvalue})

IsEqualUnordered((StructuringElement)arg1, (StructuringElement)arg2) → bool :

returns true if the provided structuring element is equivalent to the current instance. Two structuring elements are equivalent if, for any position, they yield the same set of neighboring points.

C++ signature :

bool IsEqualUnordered(yayi::se::IStructuringElement {lvalue},yayi::se::IStructuringElement const*)

RemoveCenter((StructuringElement)arg1) → StructuringElement :

returns a new structuring element with the same shape, but without any center element

C++ signature :

yayi::se::IStructuringElement* RemoveCenter(yayi::se::IStructuringElement {lvalue})

Transpose((StructuringElement)arg1) → StructuringElement :

returns a new structuring element that is the transposed of this one

C++ signature :

yayi::se::IStructuringElement* Transpose(yayi::se::IStructuringElement {lvalue})

Neighborhood Processing

YayiNeighborhoodProcessingPython.local_circular_mean_and_concentration((Image)imin, (StructuringElement)se, (Image)imout) → object :

Computes the circular mean and concentration over each neighborhoods of imin defined by se (imout should be complex)

C++ signature :

yayi::s_return_code local_circular_mean_and_concentration(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiNeighborhoodProcessingPython.local_mean((Image)imin, (StructuringElement)se, (Image)imout) → object :

Computes the mean over each neighborhoods of imin defined by se

C++ signature :

yayi::s_return_code local_mean(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiNeighborhoodProcessingPython.local_median((Image)imin, (StructuringElement)se, (Image)imout) → object :

Computes the median on each neighborhood

C++ signature :

yayi::s_return_code local_median(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiNeighborhoodProcessingPython.local_weighted_circular_mean_and_concentration((Image)imin, (StructuringElement)se, (Image)imout) → object :

Computes the circular mean and concentration of channel 0 linearly weighted by channel 2 over each neighborhoods of imin defined by se (imout should be complex)

C++ signature :

yayi::s_return_code local_weighted_circular_mean_and_concentration(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

Low level morphology

YayiLowLevelMorphologyPython.Close((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the closing/closure of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code Close(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.Dilation((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the dilation of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code Dilation(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.Erosion((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the erosion of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code Erosion(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.GeodesicDilation((Image)im_source, (Image)im_mask, (StructuringElement)SE, (Image)im_destination) → object :

Performs the classical geodesic dilation of im_source under im_mask with the provided structuring element

C++ signature :

yayi::s_return_code GeodesicDilation(yayi::IImage const*,yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.GeodesicErosion((Image)im_source, (Image)im_mask, (StructuringElement)SE, (Image)im_destination) → object :

Performs the classical geodesic erosion of im_source over im_mask with the provided structuring element

C++ signature :

yayi::s_return_code GeodesicErosion(yayi::IImage const*,yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.Gradient((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the classical morphological gradient of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code Gradient(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.GradientInf((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the classical morphological half inferior gradient of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code GradientInf(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.GradientSup((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the classical morphological half superior gradient of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code GradientSup(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.MinkowskiAddition((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the Minkowski addition of one image into another with the specified structuring element (basically dilation with the implicitely transposed structuring element)

C++ signature :

yayi::s_return_code MinkowskiAddition(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.MinkowskiSubtraction((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the Minkowski subtraction of one image into another with the specified structuring element (basically erosion with the implicitely transposed structuring element)

C++ signature :

yayi::s_return_code MinkowskiSubtraction(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.Open((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_destination) : Performs the opening of one image into another with the specified structuring element

C++ signature :

yayi::s_return_code Open(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLowLevelMorphologyPython.SoillesHitOrMiss((Image)im_source, (StructuringElement)foreground_SE, (StructuringElement)background_SE, (Image)im_destination) → object :

Performs the hit-or_miss transform for gray level images based on Soilles definition.

C++ signature :

yayi::s_return_code SoillesHitOrMiss(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::se::IStructuringElement const*,yayi::IImage*)

Labels

YayiLabelPython.ImageLabelMaximas((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(imin, se, imout) : labels maximum plateaus of imin into imout with a single id per connected component

C++ signature :

yayi::s_return_code ImageLabelMaximas(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLabelPython.ImageLabelMinimas((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(imin, se, imout) : labels minimum plateaus of imin into imout with a single id per connected component

C++ signature :

yayi::s_return_code ImageLabelMinimas(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLabelPython.image_label((Image)imin, (StructuringElement)se, (Image)imout) → object :

Labels the connected components of imin in imout. Each connected component is identified in imout with a unique value. The connectivity used for the connected components is given by se.

Parameters:

• imin (image) – input image
• se (SE) – connectivity in imin for discovering the connection between two pixels
• imout (image) – output image

Returns:

None on success, throws an error otherwise

C++ signature :

yayi::s_return_code image_label(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLabelPython.image_label_binary_components_with_area((Image)imin, (StructuringElement)se, (Image)imout) → object :

Labels components formed of non “black” pixels and extracts their area

returns:a “dictionary” which key is the id of the connected component, and the value is its area.

C++ signature :

yayi::s_any_type image_label_binary_components_with_area(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiLabelPython.image_label_non_black_to_offset((Image)imin, (StructuringElement)se) → object :

returns a list of list containing the offsets of the points of each connected component

C++ signature :

yayi::s_any_type image_label_non_black_to_offset(yayi::IImage const*,yayi::se::IStructuringElement const*)

Reconstructions

YayiReconstructionPython.ClosingByReconstruction((Image)image_marker, (Image)image_mask, (StructuringElement)SE, (Image)reconstruction) → object :

Performs an algebraic closing by morphological reconstruction of image_marker over image_mask (successive geodesic erosions)

C++ signature :

yayi::s_return_code ClosingByReconstruction(yayi::IImage const*,yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiReconstructionPython.FillHoles((Image)imin, (StructuringElement)SE, (Image)imout) → object :

Fills the holes of imin using SE as neighboring graph. Stores the output in imout

C++ signature :

yayi::s_return_code FillHoles(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiReconstructionPython.HConcave((Image)im_source, (StructuringElement)SE, (HyperRectangle)variant, (Image)im_destination) → object :

Performs the h-concave transformation, abs(h-minima(im_source) - im_source).

C++ signature :

yayi::s_return_code HConcave(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*)

YayiReconstructionPython.HConvex((Image)im_source, (StructuringElement)SE, (HyperRectangle)variant, (Image)im_destination) → object :

Performs the h-convex transformation, abs(h-maxima(im_source) - im_source).

C++ signature :

yayi::s_return_code HConvex(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*)

YayiReconstructionPython.HMaxima((Image)im_source, (StructuringElement)SE, (HyperRectangle)variant, (Image)im_destination) → object :

Performs the h-maxima transformation, it suppresses all maxima whose depth is below a given level threshold (variant).

C++ signature :

yayi::s_return_code HMaxima(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*)

YayiReconstructionPython.HMinima((Image)im_source, (StructuringElement)SE, (HyperRectangle)variant, (Image)im_destination) → object :

Performs the h-minima transformation, it suppresses all minima whose depth is above a given level threshold (variant).

C++ signature :

yayi::s_return_code HMinima(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*)

YayiReconstructionPython.Levelings((Image)image_marker, (Image)image_mask, (StructuringElement)SE, (Image)levelings) → object :

Performs a leveling of image_marker with reference image_mask

C++ signature :

yayi::s_return_code Levelings(yayi::IImage const*,yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiReconstructionPython.OpeningByReconstruction((Image)image_marker, (Image)image_mask, (StructuringElement)SE, (Image)reconstruction) → object :

Performs an algebraic opening by morphological reconstruction of image_marker under image_mask (successive geodesic dilations)

C++ signature :

yayi::s_return_code OpeningByReconstruction(yayi::IImage const*,yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiReconstructionPython.PseudoDynamicClosing((Image)im_source, (StructuringElement)SE, (HyperRectangle)variant, (Image)im_destination) → object :

Performs the PseudoDynamiClosing transformation, similar to h-minima but restores the dynamic of remaining minima

C++ signature :

yayi::s_return_code PseudoDynamicClosing(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*)

YayiReconstructionPython.PseudoDynamicOpening((Image)im_source, (StructuringElement)SE, (HyperRectangle)variant, (Image)im_destination) → object :

Performs the PseudoDynamiOpening transformation, similar to h-maxima but restores the dynamic of remaining maxima

C++ signature :

yayi::s_return_code PseudoDynamicOpening(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*)

Segmentation

This module contains segmentation methods.

Example

Reference

YayiSegmentationPython.IsotropicSeededWatershed((Image)topographical_map, (Image)im_seeds, (StructuringElement)SE, (Image)watershed) → object :

Performs the isotropic watershed transform of topographical_map, and using im_seeds as seeds

C++ signature :

yayi::s_return_code IsotropicSeededWatershed(yayi::IImage const*,yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiSegmentationPython.IsotropicWatershed((Image)topographical_map, (StructuringElement)SE, (Image)watershed) → object :

Performs the isotropic watershed transform of topographical_map, and using local minima as seeds

C++ signature :

yayi::s_return_code IsotropicWatershed(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

Measurements

YayiMeasurementsPython.MeasCircularMeanAndConcentrationOnMask((Image)imin, (Image)immask, (HyperRectangle)mask_value) → object :

Returns the circular mean and concentration for each region of the image. The regions are non-overlapping and defined by immask. The return type is a map of complex elements

C++ signature :

yayi::s_any_type MeasCircularMeanAndConcentrationOnMask(yayi::IImage const*,yayi::IImage const*,yayi::s_any_type)

YayiMeasurementsPython.MeasCircularMeanAndConcentrationOnRegions((Image)imin, (Image)imregions) → object :

Returns the circular mean and concentration for each region of the image. The regions are non-overlapping and defined by imregions. The return type is a map of complex elements

C++ signature :

yayi::s_any_type MeasCircularMeanAndConcentrationOnRegions(yayi::IImage const*,yayi::IImage const*)

YayiMeasurementsPython.MeasHistogram((Image)imin) → object :

Returns the histogram of the image

C++ signature :

yayi::s_any_type MeasHistogram(yayi::IImage const*)

YayiMeasurementsPython.MeasHistogramOnRegions((Image)imin, (Image)imregions) → object :

Returns the histogram for each region of the image. The regions are non-overlapping and defined by imregions

C++ signature :

yayi::s_any_type MeasHistogramOnRegions(yayi::IImage const*,yayi::IImage const*)

YayiMeasurementsPython.MeasMean((Image)imin) → object :

Returns the mean of the image

C++ signature :

yayi::s_any_type MeasMean(yayi::IImage const*)

YayiMeasurementsPython.MeasMeanOnRegions((Image)imin, (Image)imregions) → object :

Returns the mean for each region of the image. The regions are non-overlapping and defined by imregions

C++ signature :

yayi::s_any_type MeasMeanOnRegions(yayi::IImage const*,yayi::IImage const*)

YayiMeasurementsPython.MeasMinMax((Image)arg1) → object :

C++ signature :

yayi::s_any_type MeasMinMax(yayi::IImage const*)

YayiMeasurementsPython.MeasWeightedCircularMeanAndConcentrationOnMask((Image)imin, (Image)immask, (HyperRectangle)mask_value) → object :

Returns the circular mean and concentration of channel 0 weighted by channel 2 for each region of the image. The regions are non-overlapping and defined by immask. The return type is a map of complex elements.

C++ signature :

yayi::s_any_type MeasWeightedCircularMeanAndConcentrationOnMask(yayi::IImage const*,yayi::IImage const*,yayi::s_any_type)

YayiMeasurementsPython.MeasWeightedCircularMeanAndConcentrationOnRegion((Image)imin, (Image)imregions) → object :

Returns the circular mean and concentration of channel 0 weighted by channel 2 for each region of the image. The regions are non-overlapping and defined by imregions. The return type is a map of complex elements.

C++ signature :

yayi::s_any_type MeasWeightedCircularMeanAndConcentrationOnRegion(yayi::IImage const*,yayi::IImage const*)

YayiMeasurementsPython.meas_median((Image)imin) → object :

Returns the median of the image

C++ signature :

yayi::s_any_type meas_median(yayi::IImage const*)

Distances

YayiDistancesPython.DistanceFromSetsBoundary((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_source, SE, im_distance) : Performs the morphological distance transform from the sets boundary

C++ signature :

yayi::s_return_code DistanceFromSetsBoundary(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiDistancesPython.DistanceRegularization((Image)arg1, (StructuringElement)arg2, (Image)arg3) → object :

(im_distance, SE, im_regular_distance) : forces the 1-Lipschitz property on the distance map returned by the QuasiDistance algorithm

C++ signature :

yayi::s_return_code DistanceRegularization(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*)

YayiDistancesPython.QuasiDistance((Image)arg1, (StructuringElement)arg2, (Image)arg3, (Image)arg4) → object :

(im_source, SE, im_distance, im_residuals) : Performs the unregularized quasi-distance morphological transform

C++ signature :

yayi::s_return_code QuasiDistance(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::IImage*,yayi::IImage*)

YayiDistancesPython.QuasiDistancesWeighted((Image)arg1, (StructuringElement)arg2, (HyperRectangle)arg3, (Image)arg4, (Image)arg5) → object :

(im_source, SE, weights, im_distance, im_residuals) : Performs the unregularized weighted quasi-distance morphological transform

C++ signature :

yayi::s_return_code QuasiDistancesWeighted(yayi::IImage const*,yayi::se::IStructuringElement const*,yayi::s_any_type,yayi::IImage*,yayi::IImage*)