import sys

import os

import argparse

import numpy as np

from scipy import constants

from cosy_output import CosyOutput

from coordinate_vector_3d import Cartesian3DVector

from phase_volume_6d import Phase6DVolume

from my_covariance_matrix import MyEditableCovarianceMatrix

parser = argparse.ArgumentParser(description='Write the columns for the emittance versus time.')

parser.add_argument('list_of_directories', type=str, help='The path to a where file containing the list of the directories to be used to calculated the stats..', default=None)

parser.add_argument('-s','--stepsize', type=int, help='The number by which *-x-*.txt were reported.', default=10)

parser.add_argument('-m','--number_of_electron_per_macroparticle', dest="number_of_electrons_per_macroparticle", type=int, help='The number of electrons per macroparticle for the simulation. This defaults to 100 unless specified.', default=100)

args = parser.parse_args()

mass_of_electron = constants.physical_constants["electron mass energy equivalent in MeV"][0]

mass_of_macroparticle = args.number_of_electrons_per_macroparticle*mass_of_electron

scaling_factor_for_x_mean = 1e8

scaling_factor_for_p_mean = 1e4

header = []

header.append("time")

header.append("det_ref_cov_matrix")

header.append("det_cov_matrix")

header.append("log_emittance")

print ",".join(header)

step = 100 #Only calculate once all particles are present.

in_loop = True

while in_loop is True:

output = []

sum_covariance_matrix = MyEditableCovarianceMatrix()

mean_phase_volume=Phase6DVolume(mass=mass_of_macroparticle)

with open(args.list_of_directories) as f:

initialized = False

for directory in f:

directory = directory.rstrip()

if not initialized:

cosy_output = CosyOutput()

cosy_output.injectFile(os.path.join(directory,"screen.txt"))

row_numbers = cosy_output.getRowNumbersWithKeyValuePair("step number",step,comparison = 'eq')

if row_numbers == []:

in_loop = False

break

time = float(cosy_output.returnTableValue("time",row_numbers[0]))

output.append(time)

initialized = True

phase_volume = Phase6DVolume()

for filename in os.listdir(directory):

if filename.startswith(str(step)+"-x-") and filename.endswith(".txt"):

phase_volume.injectFile(os.path.join(directory,filename),mass=mass_of_macroparticle)

sum_covariance_matrix.cov_matrix += phase_volume.getCovarianceMatrix().cov_matrix

x_mean = Cartesian3DVector(x=scaling_factor_for_x_mean*phase_volume.getMean(["x"]),y=scaling_factor_for_x_mean*phase_volume.getMean(["y"]),z=scaling_factor_for_x_mean*phase_volume.getMean(["z"]))

#print x_mean

p_mean = Cartesian3DVector(x=scaling_factor_for_p_mean*phase_volume.getMean(["px"]),y=scaling_factor_for_p_mean*phase_volume.getMean(["py"]),z=phase_volume.getMean(["pz"]))

#print p_mean

mean_phase_volume.addParticle(mean_phase_volume.mass,x=x_mean,p=p_mean)

sum_covariance_matrix.cov_matrix = sum_covariance_matrix.cov_matrix/len(mean_phase_volume)

#sum_covariance_matrix.printCovarianceMatrix()

det_cov_matrix = sum_covariance_matrix.getSubDeterminant()

ref_cov_matrix = mean_phase_volume.getCovarianceMatrix()

det_ref_cov_matrix = ref_cov_matrix.getSubDeterminant()/(scaling_factor_for_x_mean**6*scaling_factor_for_p_mean**4)

#ref_cov_matrix.printCovarianceMatrix()

log_emittance = np.log10(det_ref_cov_matrix) + (len(phase_volume)-1)*np.log10(det_cov_matrix)

output.append(det_ref_cov_matrix)

output.append(det_cov_matrix)

output.append(log_emittance)

print ",".join([str(o) for o in output])

step += args.stepsize