import argparse
import datetime
import numpy as np
import dnstool
from pycompact import CompactScheme


program_description = '''\
Read all DNS data files and extract u, c and ddx(c) to single array.
New array dimension is (nx, time, ny, nz)
'''

# Commandline argument parser
parser = argparse.ArgumentParser(description=program_description)
parser.add_argument("-c", "--case", help="target case name", required=True)
args = parser.parse_args()
params = vars(args)

casename = params["case"]
u_idx = 0
y_idx = 4

cases = dnstool.case_library()

case = cases[casename]

nx, ny, nz = case.shape

cs = CompactScheme(nx, ny, nz, False, True, True, 4, 2, 2)

file1 = "u.dat"
file2 = "c.dat"
file3 = "ddxc.dat"

storage1 = np.memmap(file1, mode='w+', dtype=np.double, shape=(nx, len(case.data_files), ny, nz))
storage2 = np.memmap(file2, mode='w+', dtype=np.double, shape=(nx, len(case.data_files), ny, nz))
storage3 = np.memmap(file3, mode='w+', dtype=np.double, shape=(nx, len(case.data_files), ny, nz))

for i, fname in enumerate(case.data_files):
    print(datetime.datetime.now(), i, fname)
    time, u = case.read_single_field(fname, u_idx)
    time, y = case.read_single_field(fname, y_idx)
    c = (1. - y)
    storage1[:,i,:,:] = u.T
    storage2[:,i,:,:] = c.T
    storage3[:,i,:,:] = cs.ddx(c).T

storage.flush()