#!/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 05/27/2009 (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
#
#

from builtins import range
from ..libpy import sp_global_def
from ..libpy.sp_global_def import sxprint, ERROR
from ..libpy.sp_global_def import *
from optparse import OptionParser

import os
import sys

      
def run():
    progname = os.path.basename(sys.argv[0])
    usage = progname + " input_stack start end output_stack  <mask> --rad=mask_radius"
    parser = OptionParser(usage, version=SPARXVERSION)
    parser.add_option("--rad",     type="int", default=-1, help="radius of mask")
    parser.add_option("--verbose", type="int", default=0,  help="verbose level (0|1)")

    (options, args) = parser.parse_args()

    if len(args) < 4:
        sxprint("Usage: " + usage)
        sxprint("Please run \'" + progname + " -h\' for details")
        ERROR( "Invalid number of parameters used. Please see usage information above." )
        return
    else:
        from string import atoi
        input_stack  = args[0]
        imgstart     = atoi( args[1] )
        imgend       = atoi( args[2] ) +1
        output_stack = args[3]
        if(len(args) == 5): 
            mask = args[4]
        else:
            mask = None

    if sp_global_def.CACHE_DISABLE:
        from ..libpy.sp_utilities import disable_bdb_cache
        disable_bdb_cache()
    from ..libpy.sp_applications import varimax
    sp_global_def.BATCH = True
    varimax(input_stack, list(range(imgstart, imgend)), output_stack, mask, options.rad, options.verbose)
    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" )

if __name__ == "__main__":
    main()
