# Path: pyem/mrc.py
# MODE = {0: np.dtype(np.int8), 1: np.dtype(np.int16), 2: np.dtype(np.float32), 6: np.dtype(np.uint16),
#         np.dtype(np.int8): 0, np.dtype(np.int16): 1, np.dtype(np.float32): 2, np.dtype(np.uint16): 6}
# HEADER_LEN = int(1024)  # Bytes.
# def mrc_header(shape, dtype=np.float32, psz=1.0):
# def mrc_header_complete(data, psz=1.0, origin=None):
# def _read_header(f):
# def read_header(fname):
# def read(fname, inc_header=False, compat="mrc2014"):
# def write(fname, data, psz=1, origin=None, fast=False):
# def append(fname, data):
# def write_imgs(fname, idx, data):
# def read_imgs(fname, idx, num=1, compat="mrc2014"):
# def read_zslices(fname):
#     def __init__(self, fname):
#     def read(self, i):
#     def close(self):
#     def __iter__(self):
#     def next(self):
#     def __enter__(self):
#     def __exit__(self, exc_type, exc_val, exc_tb):
#     def __init__(self, fname, shape=None, dtype=np.float32, psz=1.0, mode="w"):
#     def set_dtype(self, dtype):
#     def set_shape(self, shape):
#     def write(self, arr):
#     def close(self):
#     def __enter__(self):
#     def __exit__(self, exc_type, exc_val, exc_tb):
# class ZSliceReader:
# class ZSliceWriter:


import numpy as np
import sys
    import argparse
from pyem import mrc
#
# Simple program for computing mean and variance of maps.
# See help text and README file for more information.
#
# 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/>.


def main(args):
    x = mrc.read(args.input[0])
    m2 = np.zeros(x.shape)
    mu = x.copy()
    for i, f in enumerate(args.input[1:]):
        x = mrc.read(f)
        olddif = x - mu
        mu += (x - mu) / (i + 1)
        m2 += olddif * (x - mu)
    var = m2 / len(args.input)
    mrc.write(args.output, var)
    if args.mean is not None:

# Path: pyem/mrc.py
# MODE = {0: np.dtype(np.int8), 1: np.dtype(np.int16), 2: np.dtype(np.float32), 6: np.dtype(np.uint16),
#         np.dtype(np.int8): 0, np.dtype(np.int16): 1, np.dtype(np.float32): 2, np.dtype(np.uint16): 6}
# HEADER_LEN = int(1024)  # Bytes.
# def mrc_header(shape, dtype=np.float32, psz=1.0):
# def mrc_header_complete(data, psz=1.0, origin=None):
# def _read_header(f):
# def read_header(fname):
# def read(fname, inc_header=False, compat="mrc2014"):
# def write(fname, data, psz=1, origin=None, fast=False):
# def append(fname, data):
# def write_imgs(fname, idx, data):
# def read_imgs(fname, idx, num=1, compat="mrc2014"):
# def read_zslices(fname):
#     def __init__(self, fname):
#     def read(self, i):
#     def close(self):
#     def __iter__(self):
#     def next(self):
#     def __enter__(self):
#     def __exit__(self, exc_type, exc_val, exc_tb):
#     def __init__(self, fname, shape=None, dtype=np.float32, psz=1.0, mode="w"):
#     def set_dtype(self, dtype):
#     def set_shape(self, shape):
#     def write(self, arr):
#     def close(self):
#     def __enter__(self):
#     def __exit__(self, exc_type, exc_val, exc_tb):
# class ZSliceReader:
# class ZSliceWriter:


# Path: varmap.py
import numpy as np
import sys
    import argparse
from pyem import mrc

#
# Simple program for computing mean and variance of maps.
# See help text and README file for more information.
#
# 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/>.


def main(args):
    x = mrc.read(args.input[0])
    m2 = np.zeros(x.shape)
    mu = x.copy()
    for i, f in enumerate(args.input[1:]):
        x = mrc.read(f)
        olddif = x - mu
        mu += (x - mu) / (i + 1)
        m2 += olddif * (x - mu)
    var = m2 / len(args.input)
    mrc.write(args.output, var)
    if args.mean is not None:

        mrc.write(args.mean, mu)