<commit_before>""" Pyaccel tracking module

This module concentrates all tracking routines of the accelerator.
Most of them take a structure called 'positions' as an argument which
should store the initial coordinates of the particle, or the bunch of particles
to be tracked. Most of these routines generate tracked particle positions as
output, among other data. These input and ouput particle positions are stored
as native python lists or numpy arrays. Depending on the routine these position
objects may have one, two, three or four indices. These indices are used to
select particle's inices (p), coordinates(c), lattice element indices(e) or
turn number (n). For example, v = pos[p,c,e,n]. Routines in these module may
return particle positions structure missing one or more indices but the
PCEN ordering is preserved.
"""
import multiprocessing as _multiproc

import numpy as _np
import trackcpp as _trackcpp

import mathphys as _mp

from . import accelerator as _accelerator
from . import utils as _utils
from .utils import interactive as _interactive
from .optics.edwards_teng import EdwardsTeng


LOST_PLANES = (None, 'x', 'y', 'z')


class TrackingException(Exception):
    """."""


@_interactive
def generate_bunch(emit1, emit2, sigmae, sigmas, twi, n_part, cutoff=3):
    """
    Create centered bunch with the desired equilibrium and twiss params.

    Inputs:
        emit1 = first mode emittance, corresponds to horizontal emmitance at
         the limit of zero coupling;
        emit2 = second mode emittance, corresponds to vertical emmitance at
         the limit of zero coupling;
        sigmae = energy dispersion;
        sigmas = bunch length;
        twi = TwissObject at the desired location
        n_part = number of particles
        cutoff = number of sigmas to cut the distribution (in bunch size)

    Output:
        particles = numpy.array.shape == (6, n_part)
    """

    if isinstance(twi, EdwardsTeng):
        beta1 = twi.beta1
        beta2 = twi.beta2
        eta1 = twi.eta1
        eta2 = twi.eta2
        etap1 = twi.etap1
        etap2 = twi.etap2
        alpha1 = twi.alpha1
        alpha2 = twi.alpha2
    else:
        beta1 = twi.betax
        beta2 = twi.betay
        eta1 = twi.etax
        eta2 = twi.etay
        etap1 = twi.etapx
        etap2 = twi.etapy
        alpha1 = twi.alphax
        alpha2 = twi.alphay

    # generate longitudinal phase space<commit_msg>Nomeclature correction<commit_after>""" Pyaccel tracking module

This module concentrates all tracking routines of the accelerator.
Most of them take a structure called 'positions' as an argument which
should store the initial coordinates of the particle, or the bunch of particles
to be tracked. Most of these routines generate tracked particle positions as
output, among other data. These input and ouput particle positions are stored
as native python lists or numpy arrays. Depending on the routine these position
objects may have one, two, three or four indices. These indices are used to
select particle's inices (p), coordinates(c), lattice element indices(e) or
turn number (n). For example, v = pos[p,c,e,n]. Routines in these module may
return particle positions structure missing one or more indices but the
PCEN ordering is preserved.
"""
import multiprocessing as _multiproc

import numpy as _np
import trackcpp as _trackcpp

import mathphys as _mp

from . import accelerator as _accelerator
from . import utils as _utils
from .utils import interactive as _interactive
from .optics.twiss import Twiss


LOST_PLANES = (None, 'x', 'y', 'z')


class TrackingException(Exception):
    """."""


@_interactive
def generate_bunch(emit1, emit2, sigmae, sigmas, optics, n_part, cutoff=3):
    """
    Create centered bunch with the desired equilibrium and opticsss params.

    Inputs:
        emit1 = first mode emittance, corresponds to horizontal emmitance at
         the limit of zero coupling;
        emit2 = second mode emittance, corresponds to vertical emmitance at
         the limit of zero coupling;
        sigmae = energy dispersion;
        sigmas = bunch length;
        optics = Optical functions at desired location, it should be a Twiss
         or EdwardsTeng object;
        n_part = number of particles;
        cutoff = number of sigmas to cut the distribution (in bunch size).

    Output:
        particles = numpy.array.shape == (6, n_part)
    """

    if isinstance(optics, Twiss):
        beta1 = optics.betax
        beta2 = optics.betay
        eta1 = optics.etax
        eta2 = optics.etay
        etap1 = optics.etapx
        etap2 = optics.etapy
        alpha1 = optics.alphax
        alpha2 = optics.alphay
    else:
        beta1 = optics.beta1
        beta2 = optics.beta2
        eta1 = optics.eta1
        eta2 = optics.eta2
        etap1 = optics.etap1
        etap2 = optics.etap2
        alpha1 = optics.alpha1
        alpha2 = optics.alpha2

    # generate longitudinal phase space
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