#! /usr/bin/env python
#
# Author: Markus Stabrin 2019 (markus.stabrin@mpi-dortmund.mpg.de)
# Author: Fabian Schoenfeld 2019 (fabian.schoenfeld@mpi-dortmund.mpg.de)
# Author: Thorsten Wagner 2019 (thorsten.wagner@mpi-dortmund.mpg.de)
# Author: Tapu Shaikh 2019 (tapu.shaikh@mpi-dortmund.mpg.de)
# Author: Adnan Ali 2019 (adnan.ali@mpi-dortmund.mpg.de)
# Author: Luca Lusnig 2019 (luca.lusnig@mpi-dortmund.mpg.de)
# Author: Toshio Moriya 2019 (toshio.moriya@kek.jp)
# Author: Pawel A.Penczek, 09/09/2006 (Pawel.A.Penczek@uth.tmc.edu)
#
# Copyright (c) 2019 Max Planck Institute of Molecular Physiology
# Copyright (c) 2000-2006 The University of Texas - Houston Medical School
#
# This software is issued under a joint BSD/GNU license. You may use the
# source code in this file under either license. However, note that the
# complete EMAN2 and SPARX software packages have some GPL dependencies,
# so you are responsible for compliance with the licenses of these packages
# if you opt to use BSD licensing. The warranty disclaimer below holds
# in either instance.
#
# This complete copyright notice must be included in any revised version of the
# source code. Additional authorship citations may be added, but existing
# author citations must be preserved.
#
# 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 2 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, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
#
#


import os
from ..libpy import sp_global_def
from ..libpy.sp_global_def import sxprint, ERROR
from ..libpy.sp_global_def     import *
from ..libpy.sp_user_functions import *
from   optparse       import OptionParser
import sys

import mpi

mpi.mpi_init( 0, [] )


def run():
	progname = os.path.basename(sys.argv[0])
	usage = progname + " stack outdir <maskfile> --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translation_step --dst=delta --center=center --maxit=max_iteration --CTF --snr=SNR --Fourvar=Fourier_variance --Ng=group_number --Function=user_function_name --CUDA --GPUID --MPI"
	parser = OptionParser(usage,version=SPARXVERSION)
	parser.add_option("--ir",       type="float",  default=1,             help="inner radius for rotational correlation > 0 (set to 1)")
	parser.add_option("--ou",       type="float",  default=-1,            help="outer radius for rotational correlation < nx/2-1 (set to the radius of the particle)")
	parser.add_option("--rs",       type="float",  default=1,             help="step between rings in rotational correlation > 0 (set to 1)" ) 
	parser.add_option("--xr",       type="string", default="4 2 1 1",     help="range for translation search in x direction, search is +/xr ")
	parser.add_option("--yr",       type="string", default="-1",          help="range for translation search in y direction, search is +/yr ")
	parser.add_option("--ts",       type="string", default="2 1 0.5 0.25",help="step of translation search in both directions")
	parser.add_option("--dst",      type="float",  default=0.0,           help="delta")
	parser.add_option("--center",   type="float",  default=-1,            help="-1.average center method; 0.not centered; 1.phase approximation; 2.cc with Gaussian function; 3.cc with donut-shaped image 4.cc with user-defined reference 5.cc with self-rotated average")
	parser.add_option("--maxit",    type="float",  default=0,             help="maximum number of iterations (0 means the maximum iterations is 10, but it will automatically stop should the criterion falls")
	parser.add_option("--CTF",      action="store_true", default=False,   help="use CTF correction during alignment ")
	parser.add_option("--snr",      type="float",  default=1.0,           help="signal-to-noise ratio of the data (set to 1.0)")
	parser.add_option("--Fourvar",  action="store_true", default=False,   help="compute Fourier variance")
	parser.add_option("--Ng",       type="int",    default=-1,            help="number of groups in the new CTF filtration")
	parser.add_option("--num_ali",  type="int",    default=3,             help="number of independent alignments to do")
	parser.add_option("--function", type="string", default="ref_ali2d",   help="name of the reference preparation function (default ref_ali2d)")
	parser.add_option("--CUDA",     action="store_true", default=False,   help="use CUDA program")
	parser.add_option("--GPUID",    type="string",    default="",         help="ID of GPUs available")
	parser.add_option("--MPI",      action="store_true", default=False,   help="use MPI version ")

	(options, args) = parser.parse_args()
	
	if len(args) < 2 or len(args) > 3:
    		sxprint( "Usage: " + usage )
    		sxprint( "Please run '" + progname + " -h' for detailed options" )
    		ERROR( "Invalid number of parameters used. Please see usage information above." )
    		return

	else:
		if args[1] == 'None':
			outdir = None
		else:
			outdir = args[1]

		if len(args) == 2:
			mask = None
		else:
			mask = args[2]
		
		from ..libpy.sp_development import multi_ali2d

		if sp_global_def.CACHE_DISABLE:
			from ..libpy.sp_utilities import disable_bdb_cache
			disable_bdb_cache()
		
		sp_global_def.BATCH = True
		multi_ali2d(args[0], outdir, mask, options.ir, options.ou, options.rs, options.xr, options.yr, options.ts, options.dst, options.center, \
			options.maxit, options.CTF, options.snr, options.Fourvar, options.Ng, options.num_ali, options.function, options.CUDA, options.GPUID, options.MPI)
		sp_global_def.BATCH = False

def main():
	sp_global_def.print_timestamp( "Start" )
	sp_global_def.write_command()
	run()
	sp_global_def.print_timestamp( "Finish" )
	mpi.mpi_finalize()

if __name__ == "__main__":
	main()
