__author__ = 'matt' from . import ch import numpy as np from .utils import row, col import scipy.sparse as sp import scipy.special class Interp3D(ch.Ch): dterms = 'locations' terms = 'image' def on_changed(self, which): if 'image' in which: self.gx, self.gy, self.gz = np.gradient(self.image) def compute_r(self): locations = self.locations.r.copy() for i in range(3): locations[:,i] = np.clip(locations[:,i], 0, self.image.shape[i]-1) locs = np.floor(locations).astype(np.uint32) result = self.image[locs[:,0], locs[:,1], locs[:,2]] offset = (locations - locs) dr = self.dr_wrt(self.locations).dot(offset.ravel()) return result + dr def compute_dr_wrt(self, wrt): if wrt is self.locations: locations = self.locations.r.copy() for i in range(3): locations[:,i] = np.clip(locations[:,i], 0, self.image.shape[i]-1) locations = locations.astype(np.uint32) xc = col(self.gx[locations[:,0], locations[:,1], locations[:,2]]) yc = col(self.gy[locations[:,0], locations[:,1], locations[:,2]]) zc = col(self.gz[locations[:,0], locations[:,1], locations[:,2]]) data = np.vstack([xc.ravel(), yc.ravel(), zc.ravel()]).T.copy() JS = np.arange(locations.size) IS = JS // 3 return sp.csc_matrix((data.ravel(), (IS, JS))) class gamma(ch.Ch): dterms = 'x', def compute_r(self): return scipy.special.gamma(self.x.r) def compute_dr_wrt(self, wrt): if wrt is self.x: d = scipy.special.polygamma(0, self.x.r)*self.r return sp.diags([d.ravel()], [0]) # This function is based directly on the "moment" function # in scipy, specifically in mstats_basic.py. def moment(a, moment=1, axis=0): if moment == 1: # By definition the first moment about the mean is 0. shape = list(a.shape) del shape[axis] if shape: # return an actual array of the appropriate shape return ch.zeros(shape, dtype=float) else: # the input was 1D, so return a scalar instead of a rank-0 array return np.float64(0.0) else: mn = ch.expand_dims(a.mean(axis=axis), axis) s = ch.power((a-mn), moment) return s.mean(axis=axis)