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| Deletions are marked like this. | Additions are marked like this. |
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| === Program outline | === Program sample code === This little example shows how all EMAN2 programs are expected to be structured. |
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| {{{ | {{{#!python |
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| # The first line is critical, and must be exactly this | |
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| # Official copyright notice. EMAN2 is distributed under a joint GPL/BSD license. Please copy # this statement from one of the other programs. You must agree to use this license if your |
# Official copyright notice. EMAN2 is distributed under a joint GPL/BSD license. # Please copy the actual notice from the top of one of the other EMAN2 programs. # # You must agree to use this license if your |
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| usage = """%prog <output> [options] | usage = """%prog [options] |
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| # You MUST use OptionParser to parse command-line options parser = OptionParser(usage=usage,version=EMANVERSION) |
# You MUST use EMArgumentParser to parse command-line options parser = EMArgumentParser(usage=usage,version=EMANVERSION) |
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| parser.add_option("--input", type="string", help="The name of the input particle stack", default=None) parser.add_option("--oneclass", type="int", help="Create only a single class-average. Specify the number.",default=None) parser.add_option("--verbose", "-v", dest="verbose", action="store", metavar="n",type="int", default=0, help="verbose level [0-9], hig ner number means higher level of verboseness") |
parser.add_argument("--input", type=str, help="The name of the input particle stack", default=None) parser.add_argument("--output", type=str, help="The name of the output particle stack", default=None) parser.add_argument("--oneclass", type=int, help="Create only a single class-average. Specify the number.",default=None) 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') |
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| data=EMData.read_images(args[1]) | |
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| results=myfunction(data,options.mine1,options.mine2) | E2n=E2init(sys.argv) |
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| for im in results: im.write_image(args[2],-1) | data=EMData.read_images(options.input) |
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| def myfunction(data,mine1,mine2): | results=myfunction(data,options.oneclass) for im in results: im.write_image(options.output,-1) E2end(E2n) def myfunction(data,oneclass): |
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 from optparse import OptionParser
19 import math
20
21 # main() block. Each program will have a single function called main() which is executed when the
22 # program is used from the command-line. Programs must also be 'import'able themselves, so you
23 # must have main()
24 def main():
25
26 progname = os.path.basename(sys.argv[0])
27 usage = """%prog [options]
28
29 This is the main documentation string for the program, which should define what it does an how to use it.
30 """
31
32 # You MUST use EMArgumentParser to parse command-line options
33 parser = EMArgumentParser(usage=usage,version=EMANVERSION)
34
35 parser.add_argument("--input", type=str, help="The name of the input particle stack", default=None)
36 parser.add_argument("--output", type=str, help="The name of the output particle stack", default=None)
37 parser.add_argument("--oneclass", type=int, help="Create only a single class-average. Specify the number.",default=None)
38 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')
39
40 (options, args) = parser.parse_args()
41
42 # Now we have a call to the function which actually implements the functionality of the program
43 # main() is really just for parsing command-line arguments, etc. The actual program algorithms
44 # must be implemented in additional functions so this program could be imported as a module and
45 # the functionality used in another context
46
47 E2n=E2init(sys.argv)
48
49 data=EMData.read_images(options.input)
50
51 results=myfunction(data,options.oneclass)
52
53 for im in results: im.write_image(options.output,-1)
54
55 E2end(E2n)
56
57 def myfunction(data,oneclass):
58 # do some stuff
59 ret = [i*5.0 for i in data]
60
61 return ret
62
63 # This block must always be the last thing in the program and calls main()
64 # if the program is executed, but not if it's imported
65 if __name__ == "__main__":
66 main()