field.py 21.8 KB
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# 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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#
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# Copyright(C) 2013-2018 Max-Planck-Society
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#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
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from __future__ import absolute_import, division, print_function
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import numpy as np
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from . import dobj, utilities
from .compat import *
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from .domain_tuple import DomainTuple
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class Field(object):
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    """ The discrete representation of a continuous field over multiple spaces.

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    In NIFTy, Fields are used to store data arrays and carry all the needed
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    metainformation (i.e. the domain) for operators to be able to work on them.
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    Parameters
    ----------
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    domain : DomainTuple
        the domain of the new Field
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    val : data_object
        This object's global shape must match the domain shape
        After construction, the object will no longer be writeable!
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    Notes
    -----
    If possible, do not invoke the constructor directly, but use one of the
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    many convenience functions for Field construction!
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    """
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    def __init__(self, domain, val):
        if not isinstance(domain, DomainTuple):
            raise TypeError("domain must be of type DomainTuple")
        if not isinstance(val, dobj.data_object):
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            if np.isscalar(val):
                val = dobj.from_local_data((), np.full((), val))
            else:
                raise TypeError("val must be of type dobj.data_object")
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        if domain.shape != val.shape:
            raise ValueError("mismatch between the shapes of val and domain")
        self._domain = domain
        self._val = val
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        dobj.lock(self._val)
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    # prevent implicit conversion to bool
    def __nonzero__(self):
        raise TypeError("Field does not support implicit conversion to bool")

    def __bool__(self):
        raise TypeError("Field does not support implicit conversion to bool")

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    @staticmethod
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    def full(domain, val):
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        """Creates a Field with a given domain, filled with a constant value.

        Parameters
        ----------
        domain : Domain, tuple of Domain, or DomainTuple
            domain of the new Field
        val : float/complex/int scalar
            fill value. Data type of the field is inferred from val.

        Returns
        -------
        Field
            the newly created field
        """
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        if not np.isscalar(val):
            raise TypeError("val must be a scalar")
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        if not (np.isreal(val) or np.iscomplex(val)):
            raise TypeError("need arithmetic scalar")
        domain = DomainTuple.make(domain)
        return Field(domain, dobj.full(domain.shape, fill_value=val))
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    @staticmethod
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    def from_global_data(domain, arr, sum_up=False):
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        """Returns a Field constructed from `domain` and `arr`.

        Parameters
        ----------
        domain : DomainTuple, tuple of Domain, or Domain
            the domain of the new Field
        arr : numpy.ndarray
            The data content to be used for the new Field.
            Its shape must match the shape of `domain`.
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        sum_up : bool, optional
            If True, the contents of `arr` are summed up over all MPI tasks
            (if any), and the sum is used as data content.
            If False, the contens of `arr` are used directly, and must be
            identical on all MPI tasks.
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        """
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        return Field(DomainTuple.make(domain),
                     dobj.from_global_data(arr, sum_up))
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    @staticmethod
    def from_local_data(domain, arr):
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        return Field(DomainTuple.make(domain),
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                     dobj.from_local_data(domain.shape, arr))
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    def to_global_data(self):
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        """Returns an array containing the full data of the field.

        Returns
        -------
        numpy.ndarray : array containing all field entries.
            Its shape is identical to `self.shape`.

        Notes
        -----
        Do not write to the returned array! Depending on whether MPI is
        active or not, this may or may not change the field's data content.
        """
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        return dobj.to_global_data(self._val)

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    @property
    def local_data(self):
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        """numpy.ndarray : locally residing field data

        Returns a handle to the part of the array data residing on the local
        task (or to the entore array if MPI is not active).
        """
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        return dobj.local_data(self._val)

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    def cast_domain(self, new_domain):
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        """Returns a field with the same data, but a different domain

        Parameters
        ----------
        new_domain : Domain, tuple of Domain, or DomainTuple
            The domain for the returned field. Must be shape-compatible to
            `self`.

        Returns
        -------
        Field
            Field living on `new_domain`, but with the same data as `self`.

        Notes
        -----
        No copy is made. If needed, use an additional copy() invocation.
        """
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        return Field(DomainTuple.make(new_domain), self._val)
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    @staticmethod
    def from_random(random_type, domain, dtype=np.float64, **kwargs):
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        """ Draws a random field with the given parameters.

        Parameters
        ----------
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        random_type : 'pm1', 'normal', or 'uniform'
            The random distribution to use.
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        domain : DomainTuple
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            The domain of the output random field
        dtype : type
            The datatype of the output random field
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        Returns
        -------
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        Field
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            The newly created Field.
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        """
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        domain = DomainTuple.make(domain)
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        return Field(domain=domain,
                     val=dobj.from_random(random_type, dtype=dtype,
                                          shape=domain.shape, **kwargs))
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    @property
    def val(self):
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        """dobj.data_object : the data object storing the field's entries

        Notes
        -----
        This property is intended for low-level, internal use only. Do not use
        from outside of NIFTy's core; there should be better alternatives.
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        """
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        return self._val
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    @property
    def dtype(self):
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        """type : the data type of the field's entries"""
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        return self._val.dtype

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    @property
    def domain(self):
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        """DomainTuple : the field's domain"""
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        return self._domain

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    @property
    def shape(self):
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        """tuple of int : the concatenated shapes of all sub-domains"""
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        return self._domain.shape
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    @property
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    def size(self):
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        """int : total number of pixels in the field"""
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        return self._domain.size
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    @property
    def real(self):
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        """Field : The real part of the field"""
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        if not np.issubdtype(self.dtype, np.complexfloating):
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            return self
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        return Field(self._domain, self._val.real)
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    @property
    def imag(self):
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        """Field : The imaginary part of the field"""
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        if not np.issubdtype(self.dtype, np.complexfloating):
            raise ValueError(".imag called on a non-complex Field")
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        return Field(self._domain, self._val.imag)
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    def scalar_weight(self, spaces=None):
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        """Returns the uniform volume element for a sub-domain of `self`.

        Parameters
        ----------
        spaces : int, tuple of int or None
            indices of the sub-domains of the field's domain to be considered.
            If `None`, the entire domain is used.

        Returns
        -------
        float or None
            if the requested sub-domain has a uniform volume element, it is
            returned. Otherwise, `None` is returned.
        """
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        if np.isscalar(spaces):
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            return self._domain[spaces].scalar_dvol
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        if spaces is None:
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            spaces = range(len(self._domain))
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        res = 1.
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        for i in spaces:
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            tmp = self._domain[i].scalar_dvol
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            if tmp is None:
                return None
            res *= tmp
        return res

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    def total_volume(self, spaces=None):
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        """Returns the total volume of a sub-domain of `self`.

        Parameters
        ----------
        spaces : int, tuple of int or None
            indices of the sub-domains of the field's domain to be considered.
            If `None`, the entire domain is used.

        Returns
        -------
        float
            the total volume of the requested sub-domain.
        """
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        if np.isscalar(spaces):
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            return self._domain[spaces].total_volume
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        if spaces is None:
            spaces = range(len(self._domain))
        res = 1.
        for i in spaces:
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            res *= self._domain[i].total_volume
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        return res

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    def weight(self, power=1, spaces=None):
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        """ Weights the pixels of `self` with their invidual pixel-volume.
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        Parameters
        ----------
        power : number
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            The pixels get weighted with the volume-factor**power.
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        spaces : None, int or tuple of int
            Determines on which sub-domain the operation takes place.
            If None, the entire domain is used.
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        Returns
        -------
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        Field
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            The weighted field.
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        """
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        aout = self.local_data.copy()
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        spaces = utilities.parse_spaces(spaces, len(self._domain))
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        fct = 1.
        for ind in spaces:
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            wgt = self._domain[ind].dvol
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            if np.isscalar(wgt):
                fct *= wgt
            else:
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                new_shape = np.ones(len(self.shape), dtype=np.int)
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                new_shape[self._domain.axes[ind][0]:
                          self._domain.axes[ind][-1]+1] = wgt.shape
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                wgt = wgt.reshape(new_shape)
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                if dobj.distaxis(self._val) >= 0 and ind == 0:
                    # we need to distribute the weights along axis 0
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                    wgt = dobj.local_data(dobj.from_global_data(wgt))
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                aout *= wgt**power
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        fct = fct**power
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        if fct != 1.:
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            aout *= fct
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        return Field.from_local_data(self._domain, aout)
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    def vdot(self, x=None, spaces=None):
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        """ Computes the dot product of 'self' with x.
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        Parameters
        ----------
        x : Field
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            x must live on the same domain as `self`.
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        spaces : None, int or tuple of int (default: None)
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            The dot product is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.
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        Returns
        -------
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        float, complex, either scalar (for full dot products)
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                              or Field (for partial dot products)
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        """
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        if not isinstance(x, Field):
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            raise TypeError("The dot-partner must be an instance of " +
                            "the NIFTy field class")
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        if x._domain is not self._domain:
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            raise ValueError("Domain mismatch")
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        ndom = len(self._domain)
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        spaces = utilities.parse_spaces(spaces, ndom)

        if len(spaces) == ndom:
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            return dobj.vdot(self._val, x._val)
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        # If we arrive here, we have to do a partial dot product.
        # For the moment, do this the explicit, non-optimized way
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        return (self.conjugate()*x).sum(spaces=spaces)
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    def norm(self):
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        """ Computes the L2-norm of the field values.
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        Returns
        -------
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        float
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            The L2-norm of the field values.
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        """
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        return np.sqrt(abs(self.vdot(x=self)))
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    def squared_norm(self):
        """ Computes the square of the L2-norm of the field values.

        Returns
        -------
        float
            The square of the L2-norm of the field values.
        """
        return abs(self.vdot(x=self))

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    def conjugate(self):
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        """ Returns the complex conjugate of the field.
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        Returns
        -------
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        Field
            The complex conjugated field.
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        """
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        if np.issubdtype(self._val.dtype, np.complexfloating):
            return Field(self._domain, self._val.conjugate())
        return self
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    # ---General unary/contraction methods---
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    def __pos__(self):
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        return self
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    def __neg__(self):
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        return Field(self._domain, -self._val)
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    def __abs__(self):
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        return Field(self._domain, abs(self._val))
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    def _contraction_helper(self, op, spaces):
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        if spaces is None:
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            return getattr(self._val, op)()
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        spaces = utilities.parse_spaces(spaces, len(self._domain))
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        axes_list = tuple(self._domain.axes[sp_index] for sp_index in spaces)
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        if len(axes_list) > 0:
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            axes_list = reduce(lambda x, y: x+y, axes_list)
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        # perform the contraction on the data
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        data = getattr(self._val, op)(axis=axes_list)
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        # check if the result is scalar or if a result_field must be constr.
        if np.isscalar(data):
            return data
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        else:
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            return_domain = tuple(dom
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                                  for i, dom in enumerate(self._domain)
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                                  if i not in spaces)
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            return Field(DomainTuple.make(return_domain), data)
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    def sum(self, spaces=None):
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        """Sums up over the sub-domains given by `spaces`.

        Parameters
        ----------
        spaces : None, int or tuple of int (default: None)
            The summation is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.

        Returns
        -------
        Field or scalar
            The result of the summation. If it is carried out over the entire
            domain, this is a scalar, otherwise a Field.
        """
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        return self._contraction_helper('sum', spaces)
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    def integrate(self, spaces=None):
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        """Integrates over the sub-domains given by `spaces`.

        Integration is performed by summing over `self` multiplied by its
        volume factors.

        Parameters
        ----------
        spaces : None, int or tuple of int (default: None)
            The summation is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.

        Returns
        -------
        Field or scalar
            The result of the integration. If it is carried out over the
            entire domain, this is a scalar, otherwise a Field.
        """
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        swgt = self.scalar_weight(spaces)
        if swgt is not None:
            res = self.sum(spaces)
            res *= swgt
            return res
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        tmp = self.weight(1, spaces=spaces)
        return tmp.sum(spaces)

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    def prod(self, spaces=None):
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        """Computes the product over the sub-domains given by `spaces`.

        Parameters
        ----------
        spaces : None, int or tuple of int (default: None)
            The operation is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.

        Returns
        -------
        Field or scalar
            The result of the product. If it is carried out over the entire
            domain, this is a scalar, otherwise a Field.
        """
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        return self._contraction_helper('prod', spaces)
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    def all(self, spaces=None):
        return self._contraction_helper('all', spaces)
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    def any(self, spaces=None):
        return self._contraction_helper('any', spaces)
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#     def min(self, spaces=None):
#         """Determines the minimum over the sub-domains given by `spaces`.
#
#         Parameters
#         ----------
#         spaces : None, int or tuple of int (default: None)
#             The operation is only carried out over the sub-domains in this
#             tuple. If None, it is carried out over all sub-domains.
#
#         Returns
#         -------
#         Field or scalar
#             The result of the operation. If it is carried out over the entire
#             domain, this is a scalar, otherwise a Field.
#         """
#         return self._contraction_helper('min', spaces)
#
#     def max(self, spaces=None):
#         """Determines the maximum over the sub-domains given by `spaces`.
#
#         Parameters
#         ----------
#         spaces : None, int or tuple of int (default: None)
#             The operation is only carried out over the sub-domains in this
#             tuple. If None, it is carried out over all sub-domains.
#
#         Returns
#         -------
#         Field or scalar
#             The result of the operation. If it is carried out over the entire
#             domain, this is a scalar, otherwise a Field.
#         """
#         return self._contraction_helper('max', spaces)
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    def mean(self, spaces=None):
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        """Determines the mean over the sub-domains given by `spaces`.

        ``x.mean(spaces)`` is equivalent to
        ``x.integrate(spaces)/x.total_volume(spaces)``.

        Parameters
        ----------
        spaces : None, int or tuple of int (default: None)
            The operation is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.

        Returns
        -------
        Field or scalar
            The result of the operation. If it is carried out over the entire
            domain, this is a scalar, otherwise a Field.
        """
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        if self.scalar_weight(spaces) is not None:
            return self._contraction_helper('mean', spaces)
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        # MR FIXME: not very efficient
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        # MR FIXME: do we need "spaces" here?
        tmp = self.weight(1, spaces)
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        return tmp.sum(spaces)*(1./tmp.total_volume(spaces))
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    def var(self, spaces=None):
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        """Determines the variance over the sub-domains given by `spaces`.

        Parameters
        ----------
        spaces : None, int or tuple of int (default: None)
            The operation is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.

        Returns
        -------
        Field or scalar
            The result of the operation. If it is carried out over the entire
            domain, this is a scalar, otherwise a Field.
        """
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        if self.scalar_weight(spaces) is not None:
            return self._contraction_helper('var', spaces)
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        # MR FIXME: not very efficient or accurate
        m1 = self.mean(spaces)
        if np.issubdtype(self.dtype, np.complexfloating):
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            sq = abs(self-m1)**2
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        else:
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            sq = (self-m1)**2
        return sq.mean(spaces)
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    def std(self, spaces=None):
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        """Determines the standard deviation over the sub-domains given by
        `spaces`.

        ``x.std(spaces)`` is equivalent to ``sqrt(x.var(spaces))``.

        Parameters
        ----------
        spaces : None, int or tuple of int (default: None)
            The operation is only carried out over the sub-domains in this
            tuple. If None, it is carried out over all sub-domains.

        Returns
        -------
        Field or scalar
            The result of the operation. If it is carried out over the entire
            domain, this is a scalar, otherwise a Field.
        """
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        from .sugar import sqrt
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        if self.scalar_weight(spaces) is not None:
            return self._contraction_helper('std', spaces)
        return sqrt(self.var(spaces))
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    def __repr__(self):
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        return "<nifty5.Field>"
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    def __str__(self):
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        return "nifty5.Field instance\n- domain      = " + \
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               self._domain.__str__() + \
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               "\n- val         = " + repr(self._val)
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    def isEquivalentTo(self, other):
        """Determines (as quickly as possible) whether `self`'s content is
        identical to `other`'s content."""
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        if self is other:
            return True
        if not isinstance(other, Field):
            return False
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        if self._domain is not other._domain:
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            return False
        return (self._val == other._val).all()

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    def extract(self, dom):
        if dom is not self._domain:
            raise ValueError("domain mismatch")
        return self

    def unite(self, other):
        return self + other
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    def positive_tanh(self):
        return 0.5*(1.+self.tanh())

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for op in ["__add__", "__radd__",
           "__sub__", "__rsub__",
           "__mul__", "__rmul__",
           "__div__", "__rdiv__",
           "__truediv__", "__rtruediv__",
           "__floordiv__", "__rfloordiv__",
           "__pow__", "__rpow__",
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           "__lt__", "__le__", "__gt__", "__ge__", "__eq__", "__ne__"]:
    def func(op):
        def func2(self, other):
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            # if other is a field, make sure that the domains match
            if isinstance(other, Field):
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                if other._domain is not self._domain:
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                    raise ValueError("domains are incompatible.")
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                tval = getattr(self._val, op)(other._val)
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                return Field(self._domain, tval)
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            if (np.isscalar(other) or
                    isinstance(other, (dobj.data_object, np.ndarray))):
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                tval = getattr(self._val, op)(other)
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                return Field(self._domain, tval)
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            return NotImplemented
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        return func2
    setattr(Field, op, func(op))
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for op in ["__iadd__", "__isub__", "__imul__", "__idiv__",
           "__itruediv__", "__ifloordiv__", "__ipow__"]:
    def func(op):
        def func2(self, other):
            raise TypeError(
                "In-place operations are deliberately not supported")
        return func2
    setattr(Field, op, func(op))
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for f in ["sqrt", "exp", "log", "tanh"]:
    def func(f):
        def func2(self):
            fu = getattr(dobj, f)
            return Field(domain=self._domain, val=fu(self.val))
        return func2
    setattr(Field, f, func(f))