Shape integrals

GPy/kern/src/shapeintegrals.py

@@ -0,0 +1,77 @@
+# Written by Mike Smith michaeltsmith.org.uk
+
+from __future__ import division
+import numpy as np
+from .kern import Kern
+from ...core.parameterization import Param
+from paramz.transformations import Logexp
+import math
+from rbf import RBF
+
+class ShapeIntegral(Kern):
+    """
+    
+    """
+
+    def __init__(self, input_dim, active_dims=None, kernel=None, name='shapeintegral',Nperunit=100):
+        super(ShapeIntegral, self).__init__(input_dim, active_dims, name)
+        
+        if kernel is None:
+            kernel = RBF(2)
+        self.kernel = kernel
+        self.Nperunit = Nperunit
+        
+    def getarea(self,a,b,c):
+        B = b-a
+        C = c-a
+        area = np.abs(np.cross(B,C)/2.0)
+        return area
+
+    def placetrianglepoints(self,a,b,c,Nperunit=400):
+        x = b-a
+        y = c-a
+        N = Nperunit * self.getarea(a,b,c)
+        u = np.random.rand(N,1)**0.5
+        v = np.random.rand(N,1)*u
+        return a+(x*(1-u) + y*v)
+
+
+    def placepoints(self,shape,Nperunit=100):
+        a = np.mean(shape,0)
+        allps = []
+        for b,c in zip(np.r_[shape[0:-1,:],shape[-1:,:]],np.r_[shape[1:,:],shape[0:1,:]]):
+            allps.extend(self.placetrianglepoints(a,b,c,Nperunit))
+        return np.array(allps)
+        
+    def calc_K_xx_wo_variance(self,X):
+        """Calculates K_xx without the variance term"""
+
+        ps = []
+        qs = []
+        for i in range(0,X.shape[0],2):
+            s = X[i:i+2,:]
+            s = s[:,~np.isnan(s[0,:])]
+            ps.append(self.placepoints(s.T,self.Nperunit))
+            qs.append(self.placepoints(s.T,self.Nperunit))
+
+        K_xx = np.ones([len(ps),len(qs)])
+        
+        for i,p in enumerate(ps):
+            for j,q in enumerate(qs): 
+                cov = self.kernel.K(p,q)
+                v = np.sum(cov)/(self.Nperunit**2)
+                K_xx[i,j] = v
+        return K_xx, ps, qs 
+
+    def K(self, X, X2=None):
+        if X2 is None: #X vs X
+            K_xx = self.calc_K_xx_wo_variance(X)
+            return K_xx
+        else: #X vs X2
+            pass #TODO
+
+    def Kdiag(self, X):
+        """I've used the fact that we call this method for K_ff when finding the covariance as a hack so
+        I know if I should return K_ff or K_xx. In this case we're returning K_ff!!
+        $K_{ff}^{post} = K_{ff} - K_{fx} K_{xx}^{-1} K_{xf}$"""
+        pass #TODO