"""
Module flow provides classes to compute and analyse positions to characterise
the structure of systems of ABPs.

(see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#ABP%20structure%20characteristics)
"""

import numpy as np

from active_work.read import Dat
from active_work.maths import g2Dto1D, g2Dto1Dgrid, wave_vectors_2D

class Positions(Dat):
    """
    Compute and analyse positions from simulation data.

    (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#Active%20Brownian%20particles)
    """

    def __init__(self, filename, skip=1):
        """
        Loads file.

        Parameters
        ----------
        filename : string
            Name of input data file.
        skip : int
            Skip the `skip' first computed frames in the following calculations.
            (default: 1)
            NOTE: This can be changed at any time by setting self.skip.
        """

        super().__init__(filename, loadWork=False) # initialise with super class

        self.skip = skip    # skip the `skip' first frames in the analysis

    def getParticleDensity(self, time, nBoxes=None):
        """
        Returns particle density at `time' as grid where each box is equal to
        the number of particles in the corresponding region of space divided by
        the surface of this region.

        Parameters
        ----------
        time : int
            Frame index.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then nBoxes = int(sqrt(self.N)).

        Returns
        -------
        rho : (nBoxes, nBoxes) float Numpy array
            Particle density grid.
        """

        time = int(time)

        if nBoxes == None: nBoxes = np.sqrt(self.N)
        nBoxes = int(nBoxes)

        return self.toGrid(time,
            np.full((self.N,), fill_value=1),
            nBoxes=nBoxes, box_size=self.L, centre=(0, 0), average=False)

    def nPositions(self, int_max=None):
        """
        Returns array of positions.

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.

        Returns
        -------
        positions : (*, self.N) float numpy array
            Array of computed positions.
        """

        return np.array(list(map(
            lambda time0: self.getPositions(time0),
            self._time0(int_max=int_max))))

    def nParticleDensity(self, int_max=None, nBoxes=None):
        """
        Returns array of particle density as grids.

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then None is passed to
                  self.getParticleDensity.

        Returns
        -------
        rho : (*, self.N) float numpy array
            Array of computed positions.
        """

        return np.array(list(map(
            lambda time0: self.getParticleDensity(time0, nBoxes=nBoxes),
            self._time0(int_max=int_max))))

    def structureFactor(self, int_max=None, nBoxes=None):
        """
        Returns static structure factor averaged along directions of space
        (assuming isotropy).

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then nBoxes = int(sqrt(self.N)).

        Returns
        -------
        S : (*, 2) float Numpy array
            Array of (k, S(k)) with S(k) the cylindrically averaged structure
            factor at wavevector k.
        """

        if nBoxes == None: nBoxes = np.sqrt(self.N)
        nBoxes = int(nBoxes)

        particleDensity = self.nParticleDensity(int_max=int_max, nBoxes=nBoxes)

        _S2D = np.array(list(map(
            lambda _rho:
                (lambda FFT: np.real(np.conj(FFT)*FFT))
                    (np.fft.fft2(_rho)),
            particleDensity)))/self.N

        k2D = np.sqrt(
            (wave_vectors_2D(nBoxes, nBoxes, self.L/nBoxes)**2).sum(axis=-1))

        return g2Dto1Dgrid(_S2D.mean(axis=0), k2D)

    def densityCorrelation(self, int_max=None, nBoxes=None):
        """
        Returns particle spacial density averaged along directions of space
        (assuming isotropy).

        NOTE: Correlations are computed with FFT.
              (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#Fourier%20transform%20field%20correlation)

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then None is passed to
                  self.getParticleDensity.

        Returns
        -------
        G : float Numpy array
            Array of (r, G(r)) with G(r) the averaged density correlation at
            radius r.
        """

        particleDensity = self.nParticleDensity(int_max=int_max, nBoxes=nBoxes)

        _G2D = np.array(list(map(
            lambda _rho:
                (lambda FFT: np.real(np.fft.ifft2(np.conj(FFT)*FFT)))
                    (np.fft.fft2(_rho - self.rho)),
            particleDensity)))/(nBoxes**2)

        return g2Dto1D(_G2D.mean(axis=0), self.L)

    def _time0(self, int_max=None):
        """
        Returns array of frames at which to compute positions.

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.

        Returns
        -------
        time0 : (*,) float numpy array
            Array of frames.
        """

        if int_max == None: return np.array(range(self.skip, self.frames - 1))
        return np.linspace(
            self.skip, self.frames - 1, int(int_max), endpoint=False, dtype=int)

"""
Module flow provides classes to compute and analyse positions to characterise
the structure of systems of ABPs.

(see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#ABP%20structure%20characteristics)
"""

import numpy as np

from active_work.read import Dat
from active_work.maths import g2Dto1D, g2Dto1Dgrid, wave_vectors_2D

class Positions(Dat):
    """
    Compute and analyse positions from simulation data.

    (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#Active%20Brownian%20particles)
    """

    def __init__(self, filename, skip=1):
        """
        Loads file.

        Parameters
        ----------
        filename : string
            Name of input data file.
        skip : int
            Skip the `skip' first computed frames in the following calculations.
            (default: 1)
            NOTE: This can be changed at any time by setting self.skip.
        """

        super().__init__(filename, loadWork=False) # initialise with super class

        self.skip = skip    # skip the `skip' first frames in the analysis

    def getParticleDensity(self, time, nBoxes=None):
        """
        Returns particle density at `time' as grid where each box is equal to
        the number of particles in the corresponding region of space divided by
        the surface of this region.

        Parameters
        ----------
        time : int
            Frame index.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then nBoxes = int(sqrt(self.N)).

        Returns
        -------
        rho : (nBoxes, nBoxes) float Numpy array
            Particle density grid.
        """

        time = int(time)

        if nBoxes == None: nBoxes = np.sqrt(self.N)
        nBoxes = int(nBoxes)

        return self.toGrid(time,
            np.full((self.N,), fill_value=1),
            nBoxes=nBoxes, box_size=self.L, centre=(0, 0), average=False)

    def nPositions(self, int_max=None):
        """
        Returns array of positions.

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.

        Returns
        -------
        positions : (*, self.N) float numpy array
            Array of computed positions.
        """

        return np.array(list(map(
            lambda time0: self.getPositions(time0),
            self._time0(int_max=int_max))))

    def nParticleDensity(self, int_max=None, nBoxes=None):
        """
        Returns array of particle density as grids.

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then None is passed to
                  self.getParticleDensity.

        Returns
        -------
        rho : (*, self.N) float numpy array
            Array of computed positions.
        """

        return np.array(list(map(
            lambda time0: self.getParticleDensity(time0, nBoxes=nBoxes),
            self._time0(int_max=int_max))))

    def structureFactor(self, int_max=None, nBoxes=None):
        """
        Returns static structure factor averaged along directions of space
        (assuming isotropy).

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then nBoxes = int(sqrt(self.N)).

        Returns
        -------
        S : (*, 2) float Numpy array
            Array of (k, S(k)) with S(k) the cylindrically averaged structure
            factor at wavevector k.
        """

        if nBoxes == None: nBoxes = np.sqrt(self.N)
        nBoxes = int(nBoxes)

        particleDensity = self.nParticleDensity(int_max=int_max, nBoxes=nBoxes)

        _S2D = np.array(list(map(
            lambda _rho:
                (lambda FFT: np.real(np.conj(FFT)*FFT))
                    (np.fft.fft2(_rho)),
            particleDensity)))/self.N

        k2D = np.sqrt(
            (wave_vectors_2D(nBoxes, nBoxes, self.L/nBoxes)**2).sum(axis=-1))

        return g2Dto1Dgrid(_S2D.mean(axis=0), k2D)

    def densityCorrelation(self, int_max=None, nBoxes=None):
        """
        Returns particle spacial density averaged along directions of space
        (assuming isotropy).

        NOTE: Correlations are computed with FFT.
              (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#Fourier%20transform%20field%20correlation)

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.
        nBoxes : int
            Number of grid boxes in each direction. (default: None)
            NOTE: if nBoxes==None, then None is passed to
                  self.getParticleDensity.

        Returns
        -------
        G : float Numpy array
            Array of (r, G(r)) with G(r) the averaged density correlation at
            radius r.
        """

        particleDensity = self.nParticleDensity(int_max=int_max, nBoxes=nBoxes)

        _G2D = np.array(list(map(
            lambda _rho:
                (lambda FFT: np.real(np.fft.ifft2(np.conj(FFT)*FFT)))
                    (np.fft.fft2(_rho - self.rho)),
            particleDensity)))/(nBoxes**2)

        return g2Dto1D(_G2D.mean(axis=0), self.L)

    def _time0(self, int_max=None):
        """
        Returns array of frames at which to compute positions.

        Parameters
        ----------
        int_max : int or None
            Maximum number of frames to consider. (default: None)
            NOTE: If int_max == None, then take the maximum number of frames.
                  WARNING: This can be very big.

        Returns
        -------
        time0 : (*,) float numpy array
            Array of frames.
        """

        if int_max == None: return np.array(range(self.skip, self.frames - 1))
        return np.linspace(
            self.skip, self.frames - 1, int(int_max), endpoint=False, dtype=int)

Module flow provides classes to compute and analyse positions to characterise the structure of systems of ABPs.  (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#ABP%20structure%20characteristics) Compute and analyse positions from simulation data.      (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#Active%20Brownian%20particles) Loads file.          Parameters         ----------         filename : string             Name of input data file.         skip : int             Skip the `skip' first computed frames in the following calculations.             (default: 1)             NOTE: This can be changed at any time by setting self.skip. # initialise with super class # skip the `skip' first frames in the analysis Returns particle density at `time' as grid where each box is equal to         the number of particles in the corresponding region of space divided by         the surface of this region.          Parameters         ----------         time : int             Frame index.         nBoxes : int             Number of grid boxes in each direction. (default: None)             NOTE: if nBoxes==None, then nBoxes = int(sqrt(self.N)).          Returns         -------         rho : (nBoxes, nBoxes) float Numpy array             Particle density grid. Returns array of positions.          Parameters         ----------         int_max : int or None             Maximum number of frames to consider. (default: None)             NOTE: If int_max == None, then take the maximum number of frames.                   WARNING: This can be very big.          Returns         -------         positions : (*, self.N) float numpy array             Array of computed positions. Returns array of particle density as grids.          Parameters         ----------         int_max : int or None             Maximum number of frames to consider. (default: None)             NOTE: If int_max == None, then take the maximum number of frames.                   WARNING: This can be very big.         nBoxes : int             Number of grid boxes in each direction. (default: None)             NOTE: if nBoxes==None, then None is passed to                   self.getParticleDensity.          Returns         -------         rho : (*, self.N) float numpy array             Array of computed positions. Returns static structure factor averaged along directions of space         (assuming isotropy).          Parameters         ----------         int_max : int or None             Maximum number of frames to consider. (default: None)             NOTE: If int_max == None, then take the maximum number of frames.                   WARNING: This can be very big.         nBoxes : int             Number of grid boxes in each direction. (default: None)             NOTE: if nBoxes==None, then nBoxes = int(sqrt(self.N)).          Returns         -------         S : (*, 2) float Numpy array             Array of (k, S(k)) with S(k) the cylindrically averaged structure             factor at wavevector k. Returns particle spacial density averaged along directions of space         (assuming isotropy).          NOTE: Correlations are computed with FFT.               (see https://yketa.github.io/DAMTP_MSC_2019_Wiki/#Fourier%20transform%20field%20correlation)          Parameters         ----------         int_max : int or None             Maximum number of frames to consider. (default: None)             NOTE: If int_max == None, then take the maximum number of frames.                   WARNING: This can be very big.         nBoxes : int             Number of grid boxes in each direction. (default: None)             NOTE: if nBoxes==None, then None is passed to                   self.getParticleDensity.          Returns         -------         G : float Numpy array             Array of (r, G(r)) with G(r) the averaged density correlation at             radius r. Returns array of frames at which to compute positions.          Parameters         ----------         int_max : int or None             Maximum number of frames to consider. (default: None)             NOTE: If int_max == None, then take the maximum number of frames.                   WARNING: This can be very big.          Returns         -------         time0 : (*,) float numpy array             Array of frames.