1 #!/usr/bin/env python
   2 # The first line is critical, and must be exactly this
   3 
   4 # Example Author block:
   5 # Author: Steven Ludtke (sludtke@bcm.edu), 10/27/2010 - rewritten almost from scratch
   6 # Author: David Woolford (woolford@bcm.edu), 9/7/2007 (woolford@bcm.edu)
   7 # Copyright (c) 2000-2010 Baylor College of Medicine
   8 
   9 # Official copyright notice. EMAN2 is distributed under a joint GPL/BSD license. 
  10 # Please copy the actual notice from the top of one of the other EMAN2 programs. 
  11 #
  12 # You must agree to use this license if your
  13 # code is distributed with EMAN2. While you may use your own institution for the copyright notice
  14 # the terms of the GPL/BSD license permit us to redistribute it.
  15 
  16 # import block, any necessary import statements
  17 from EMAN2 import *
  18 import math
  19 
  20 # main() block. Each program will have a single function called main() which is executed when the
  21 # program is used from the command-line. Programs must also be 'import'able themselves, so you
  22 # must have main()
  23 def main():
  24 
  25   progname = os.path.basename(sys.argv[0])
  26   usage = """prog [options]
  27 
  28   This is the main documentation string for the program, which should define what it does and how to use it.
  29   """  
  30 
  31   # You MUST use EMArgumentParser to parse command-line options
  32   parser = EMArgumentParser(usage=usage,version=EMANVERSION)
  33         
  34   parser.add_argument("--input", type=str, help="The name of the input particle stack", default=None)
  35   parser.add_argument("--output", type=str, help="The name of the output particle stack", default=None)
  36   parser.add_argument("--oneclass", type=int, help="Create only a single class-average. Specify the number.",default=None)
  37   parser.add_argument("--verbose", "-v", dest="verbose", action="store", metavar="n",type=int, default=0, help='verbose level [0-9], higher number means higher level of verboseness')
  38 
  39   (options, args) = parser.parse_args()
  40 
  41   # Now we have a call to the function which actually implements the functionality of the program
  42   # main() is really just for parsing command-line arguments, etc.  The actual program algorithms 
  43   # must be implemented in additional functions so this program could be imported as a module and
  44   # the functionality used in another context
  45 
  46   E2n=E2init(sys.argv)
  47 
  48   data=EMData.read_images(options.input)
  49 
  50   results=myfunction(data,options.oneclass)
  51 
  52   for im in results: im.write_image(options.output,-1)
  53 
  54   E2end(E2n)
  55 
  56 def myfunction(data,oneclass):
  57   # do some stuff
  58   ret = [i*5.0 for i in data]
  59 
  60   return ret
  61 
  62 # This block must always be the last thing in the program and calls main()
  63 # if the program is executed, but not if it's imported
  64 if __name__ == "__main__":
  65     main()