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. Please copy
  10 # this statement from one of the other programs. You must agree to use this license if your
  11 # code is distributed with EMAN2. While you may use your own institution for the copyright notice
  12 # the terms of the GPL/BSD license permit us to redistribute it.
  13 
  14 # import block, any necessary import statements
  15 from EMAN2 import *
  16 from optparse import OptionParser
  17 import math
  18 
  19 # main() block. Each program will have a single function called main() which is executed when the
  20 # program is used from the command-line. Programs must also be 'import'able themselves, so you
  21 # must have main()
  22 def main():
  23 
  24   progname = os.path.basename(sys.argv[0])
  25   usage = """%prog <output> [options]
  26 
  27   This is the main documentation string for the program, which should define what it does an how to use it.
  28   """  
  29 
  30   # You MUST use OptionParser to parse command-line options
  31   parser = OptionParser(usage=usage,version=EMANVERSION)
  32         
  33   parser.add_option("--input", type="string", help="The name of the input particle stack", default=None)
  34   parser.add_option("--oneclass", type="int", help="Create only a single class-average. Specify the number.",default=None)
  35   parser.add_option("--verbose", "-v", dest="verbose", action="store", metavar="n",type="int", default=0, help='verbose level [0-9], hig
  36 ner number means higher level of verboseness')
  37 
  38   (options, args) = parser.parse_args()
  39 
  40   # Now we have a call to the function which actually implements the functionality of the program
  41   # main() is really just for parsing command-line arguments, etc.  The actual program algorithms 
  42   # must be implemented in additional functions so this program could be imported as a module and
  43   # the functionality used in another context
  44   data=EMData.read_images(args[1])
  45 
  46   results=myfunction(data,options.mine1,options.mine2)
  47 
  48   for im in results: im.write_image(args[2],-1)
  49 
  50 def myfunction(data,mine1,mine2):
  51   # do some stuff
  52   ret = [i*5.0 for i in data]
  53 
  54   return ret
  55 
  56 # This block must always be the last thing in the program and calls main()
  57 # if the program is executed, but not if it's imported
  58 if __name__ == "__main__":
  59     main()