Merge pull request #220 from JuliaRobotics/22Q4/refac/consolwmanicov

consolidation towards Manifolds.jl cov

src/CommonUtils.jl

@@ -60,21 +60,23 @@ function updateProductSample( dest::BallTreeDensity,
   manikde!(pts, manifolds)
 end
 
-# Returns the covariance (square), not deviation
-function calcCovarianceBasic(M::AbstractManifold, ptsArr::Vector{P}) where P
-  #TODO double check the maths,. it looks like its working at least for groups
-  μ = mean(M, ptsArr)
-  Xcs = vee.(Ref(M), Ref(μ), log.(Ref(M), Ref(μ), ptsArr))
-  Σ = mean(Xcs .* transpose.(Xcs))
-  @debug "calcCovarianceBasic" μ
-  @debug "calcCovarianceBasic" Σ
-  # TODO don't know what to do here so keeping as before, #FIXME it will break
-  # a change between this and previous is that a full covariance matrix is returned
-  msst = Σ
-  msst_ = 0 < sum(1e-10 .< msst) ? maximum(msst) : 1.0
-  return msst_
+function Statistics.cov(mkd::ManifoldKernelDensity, args...; kwargs...) 
+  cov(mkd.manifold, getPoints(mkd),  args...; kwargs...)
 end
 
+function Statistics.mean(mkd::ManifoldKernelDensity, args...; kwargs...)
+  return mean(mkd.manifold, getPoints(mkd), args...; kwargs...)
+end
+
+function Statistics.std(mkd::ManifoldKernelDensity, args...; kwargs...)
+  return std(mkd.manifold, getPoints(mkd), args...; kwargs...)
+end
+
+function Statistics.var(mkd::ManifoldKernelDensity, args...; kwargs...)
+  return var(mkd.manifold, getPoints(mkd), args...; kwargs...)
+end
+
+
 """
     $SIGNATURES
 

src/Deprecated.jl

@@ -7,6 +7,17 @@
 @deprecate R(th::Real) _Rot.RotMatrix2(th).mat # = [[cos(th);-sin(th)]';[sin(th);cos(th)]'];
 @deprecate R(;x::Real=0.0,y::Real=0.0,z::Real=0.0) (M=SpecialOrthogonal(3);exp(M,identity_element(M),hat(M,Identity(M),[x,y,z]))) # convert(SO3, so3([x,y,z]))
 
+export calcCovarianceBasic
+# Returns the covariance (square), not deviation
+function calcCovarianceBasic(M::AbstractManifold, ptsArr::Vector{P}) where P
+  @warn "`calcCovarianceBasic` is deprecated. Replace with IIF.calcSTDBasicSpread from IIF or `cov` or `var` from Manifolds. See issue AMP#150."
+  μ = mean(M, ptsArr)
+  Xcs = vee.(Ref(M), Ref(μ), log.(Ref(M), Ref(μ), ptsArr))
+  Σ = mean(Xcs .* transpose.(Xcs))
+  msst = Σ
+  msst_ = 0 < sum(1e-10 .< msst) ? maximum(msst) : 1.0
+  return msst_
+end
 
 ## ======================================================================================================
 ## Remove below before v0.7

src/ExportAPI.jl

@@ -19,7 +19,6 @@ export
   getKDEManifoldBandwidths,
   manifoldProduct,
   manikde!,
-  calcCovarianceBasic,
   isPartial,
   calcProductGaussians