smoothing_operator.py 13.3 KB
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# NIFTy
# Copyright (C) 2017  Theo Steininger
#
# Author: Theo Steininger
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

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import numpy as np

import nifty.nifty_utilities as utilities
from nifty.operators.endomorphic_operator import EndomorphicOperator
from nifty.operators.fft_operator import FFTOperator
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#from nifty.operators.smoothing_operator import smooth_util as su
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from d2o import STRATEGIES
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class SmoothingOperator(EndomorphicOperator):
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    # ---Overwritten properties and methods---
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    def __init__(self, domain, sigma, log_distances=False,
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                 default_spaces=None):
        super(SmoothingOperator, self).__init__(default_spaces)
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        self._domain = self._parse_domain(domain)
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        if len(self.domain) != 1:
            raise ValueError(
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                'ERROR: SmoothOperator accepts only exactly one '
                'space as input domain.'
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            )
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        self.sigma = sigma
        self.log_distances = log_distances

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        self._direct_smoothing_width = 3.
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    def _inverse_times(self, x, spaces):
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        return self._smoothing_helper(x, spaces, inverse=True)
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    def _times(self, x, spaces):
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        return self._smoothing_helper(x, spaces, inverse=False)
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    # ---Mandatory properties and methods---
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    @property
    def domain(self):
        return self._domain

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    @property
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    def self_adjoint(self):
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        return True
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    @property
    def unitary(self):
        return False
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    # ---Added properties and methods---
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    @property
    def sigma(self):
        return self._sigma

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    @sigma.setter
    def sigma(self, sigma):
        self._sigma = np.float(sigma)

    @property
    def log_distances(self):
        return self._log_distances

    @log_distances.setter
    def log_distances(self, log_distances):
        self._log_distances = bool(log_distances)

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    @staticmethod
    def smoothingHelper (x,sigma,dxmax=None):
        """ Performs the precomputations for Gaussian smoothing on a 1D irregular grid.

        Parameters
        ----------
        x: 1D floating point array or list containing the individual grid positions.
            Points must be given in ascending order.

        sigma: The sigma of the Gaussian with which the function living on x should
            be smoothed, in the same units as x.
        dxmax: (optional) The maximum distance up to which smoothing is performed,
            in the same units as x. Default is 3.01*sigma.

        Returns
        -------
        ibegin: integer array of the same size as x
            ibegin[i] is the minimum grid index to consider when computing the
            smoothed value at grid index i
        nval: integer array of the same size as x
            nval[i] is the number of indices to consider when computing the
            smoothed value at grid index i.
        wgt: list with the same number of entries as x
            wgt[i] is an array with nval[i] entries containing the
            normalized smoothing weights.
        """

        if dxmax==None:
            dxmax=3.01*sigma

        x=np.asarray(x)

        ibegin=np.searchsorted(x,x-dxmax)
        nval=np.searchsorted(x,x+dxmax)-ibegin

        wgt=[]
        expfac=1./(2.*sigma*sigma)
        for i in range(x.size):
            t=x[ibegin[i]:ibegin[i]+nval[i]]-x[i]
            t=np.exp(-t*t*expfac)
            t*=1./np.sum(t)
            wgt.append(t)

        return ibegin,nval,wgt

    @staticmethod
    def apply_kernel_along_array(power, startindex, endindex, distances,
        smooth_length, smoothing_width,ibegin,nval,wgt):

        if smooth_length == 0.0:
            return power[startindex:endindex]

        p_smooth = np.empty(endindex-startindex, dtype=np.float64)

        for i in xrange(startindex, endindex):
            p_smooth[i-startindex]=np.sum(power[ibegin[i]:ibegin[i]+nval[i]]*wgt[i])

        return p_smooth

    @staticmethod
    def getShape(a):
        return tuple(a.shape)

    @staticmethod
    def apply_along_axis(axis, arr, startindex, endindex, distances,
        smooth_length, smoothing_width):

        nd = arr.ndim
        if axis < 0:
            axis += nd
        if (axis >= nd):
            raise ValueError("axis must be less than arr.ndim; axis=%d, rank=%d."
                % (axis, nd))
        ibegin,nval,wgt=SmoothingOperator.smoothingHelper(distances,smooth_length,smooth_length*smoothing_width)

        ind = np.zeros(nd-1, dtype=np.int)
        i = np.zeros(nd, dtype=object)
        shape = SmoothingOperator.getShape(arr)
        indlist = np.asarray(range(nd))
        indlist = np.delete(indlist,axis)
        i[axis] = slice(None, None)
        outshape = np.asarray(shape).take(indlist)

        i.put(indlist, ind)

        Ntot =np.product(outshape)
        holdshape = outshape
        slicedArr = arr[tuple(i.tolist())]

        res = SmoothingOperator.apply_kernel_along_array(slicedArr,
                                       startindex,
                                       endindex,
                                       distances,
                                       smooth_length,
                                       smoothing_width, ibegin,nval,wgt)

        outshape = np.asarray(SmoothingOperator.getShape(arr))
        outshape[axis] = endindex - startindex
        outarr = np.zeros(outshape, dtype=np.float64)
        outarr[tuple(i.tolist())] = res
        k = 1
        while k < Ntot:
            # increment the index
            ind[nd-1] += 1
            n = -1
            while (ind[n] >= holdshape[n]) and (n > (1-nd)):
                ind[n-1] += 1
                ind[n] = 0
                n -= 1
            i.put(indlist, ind)
            slicedArr = arr[tuple(i.tolist())]
            res = SmoothingOperator.apply_kernel_along_array(slicedArr,
                                           startindex,
                                           endindex,
                                           distances,
                                           smooth_length,
                                           smoothing_width,ibegin,nval,wgt)
            outarr[tuple(i.tolist())] = res
            k += 1

        return outarr

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    def _smoothing_helper(self, x, spaces, inverse):
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        if self.sigma == 0:
            return x.copy()

        # the domain of the smoothing operator contains exactly one space.
        # Hence, if spaces is None, but we passed LinearOperator's
        # _check_input_compatibility, we know that x is also solely defined
        # on that space
        if spaces is None:
            spaces = (0,)
        else:
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            spaces = utilities.cast_axis_to_tuple(spaces, len(x.domain))

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        try:
            result = self._fft_smoothing(x, spaces, inverse)
        except ValueError:
            result = self._direct_smoothing(x, spaces, inverse)
        return result

    def _fft_smoothing(self, x, spaces, inverse):
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        Transformator = FFTOperator(x.domain[spaces[0]])
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        # transform to the (global-)default codomain and perform all remaining
        # steps therein
        transformed_x = Transformator(x, spaces=spaces)
        codomain = transformed_x.domain[spaces[0]]
        coaxes = transformed_x.domain_axes[spaces[0]]
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        # create the kernel using the knowledge of codomain about itself
        axes_local_distribution_strategy = \
            transformed_x.val.get_axes_local_distribution_strategy(axes=coaxes)
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        kernel = codomain.get_distance_array(
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            distribution_strategy=axes_local_distribution_strategy)

        if self.log_distances:
            kernel.apply_scalar_function(np.log, inplace=True)

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        kernel.apply_scalar_function(
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            codomain.get_fft_smoothing_kernel_function(self.sigma),
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            inplace=True)
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        # now, apply the kernel to transformed_x
        # this is done node-locally utilizing numpys reshaping in order to
        # apply the kernel to the correct axes
        local_transformed_x = transformed_x.val.get_local_data(copy=False)
        local_kernel = kernel.get_local_data(copy=False)
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        reshaper = [transformed_x.shape[i] if i in coaxes else 1
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                    for i in xrange(len(transformed_x.shape))]
        local_kernel = np.reshape(local_kernel, reshaper)
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        # apply the kernel
        if inverse:
            local_transformed_x /= local_kernel
        else:
            local_transformed_x *= local_kernel
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        transformed_x.val.set_local_data(local_transformed_x, copy=False)
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        smoothed_x = Transformator.inverse_times(transformed_x, spaces=spaces)

        result = x.copy_empty()
        result.set_val(smoothed_x, copy=False)
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        return result
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    def _direct_smoothing(self, x, spaces, inverse):
        # infer affected axes
        # we rely on the knowledge, that `spaces` is a tuple with length 1.
        affected_axes = x.domain_axes[spaces[0]]

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        if len(affected_axes) > 1:
            raise ValueError("By this implementation only one-dimensional "
                             "spaces can be smoothed directly.")

        affected_axis = affected_axes[0]
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        distance_array = x.domain[spaces[0]].get_distance_array(
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            distribution_strategy='not')
        distance_array = distance_array.get_local_data(copy=False)
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        if self.log_distances:
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            np.log(distance_array, out=distance_array)
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        # collect the local data + ghost cells
        local_data_Q = False

        if x.distribution_strategy == 'not':
            local_data_Q = True
        elif x.distribution_strategy in STRATEGIES['slicing']:
            # infer the local start/end based on the slicing information of
            # x's d2o. Only gets non-trivial for axis==0.
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            if 0 != affected_axis:
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                local_data_Q = True
            else:
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                start_index = x.val.distributor.local_start
                start_distance = distance_array[start_index]
                augmented_start_distance = \
                    (start_distance - self._direct_smoothing_width*self.sigma)
                augmented_start_index = \
                    np.searchsorted(distance_array, augmented_start_distance)
                true_start = start_index - augmented_start_index
                end_index = x.val.distributor.local_end
                end_distance = distance_array[end_index-1]
                augmented_end_distance = \
                    (end_distance + self._direct_smoothing_width*self.sigma)
                augmented_end_index = \
                    np.searchsorted(distance_array, augmented_end_distance)
                true_end = true_start + x.val.distributor.local_length
                augmented_slice = slice(augmented_start_index,
                                        augmented_end_index)

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                augmented_data = x.val.get_data(augmented_slice,
                                                local_keys=True,
                                                copy=False)
                augmented_data = augmented_data.get_local_data(copy=False)

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                augmented_distance_array = distance_array[augmented_slice]
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        else:
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            raise ValueError("Direct smoothing not implemented for given"
                             "distribution strategy.")
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        if local_data_Q:
            # if the needed data resides on the nodes already, the necessary
            # are the same; no matter what the distribution strategy was.
            augmented_data = x.val.get_local_data(copy=False)
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            augmented_distance_array = distance_array
            true_start = 0
            true_end = x.shape[affected_axis]
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        # perform the convolution along the affected axes
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        # currently only one axis is supported
        data_axis = affected_axes[0]
        local_result = self._direct_smoothing_single_axis(
                                                    augmented_data,
                                                    data_axis,
                                                    augmented_distance_array,
                                                    true_start,
                                                    true_end,
                                                    inverse)
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        result = x.copy_empty()
        result.val.set_local_data(local_result, copy=False)
        return result

    def _direct_smoothing_single_axis(self, data, data_axis, distances,
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                                      true_start, true_end, inverse):
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        if inverse:
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            true_sigma = 1. / self.sigma
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        else:
            true_sigma = self.sigma

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        distances = distances.astype(np.float64, copy=False)
        smoothed_data = SmoothingOperator.apply_along_axis(
                              data_axis, data,
                              startindex=true_start,
                              endindex=true_end,
                              distances=distances,
                              smooth_length=true_sigma,
                              smoothing_width=self._direct_smoothing_width)
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        return smoothed_data