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EMAN2 Python Programming Style Guide
This document describes the structure of programs distributed with EMAN2. If you plan to write a program for inclusion with EMAN2 in the 'bin' directory, you must follow the following general guidelines.
Program naming and options
All programs must be e2<program>.py This helps distinguish them from non-eman2 programs and from SPARX programs which are sx<program>.py
Where possible, the same options should be used across programs. For example, the '--verbose' option is required for all programs. See StandardParms for details.
Program sample code
This little example shows how all EMAN2 programs are expected to be structured.
Each program should include:
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()