1 #!/usr/bin/env python
   2 # Author: Stephen Murray (scmurray@bcm.edu), 2/14/11
   3 # Copyright (c) 2000-2011 Baylor Colelge of Medicine
   4 
   5 # Official copyright notice. EMAN2 is distributed under a joint GPL/BSD license. Please copy
   6 # this statement from one of the other programs. You must agree to use this license if your
   7 # code is distributed with EMAN2. While you may use your own institution for the copyright notice
   8 # the terms of the GPL/BSD license permit us to redistribute it.
   9 
  10 # import block
  11 import os
  12 import sys
  13 from EMAN2 import *
  14 
  15 if len(sys.argv) != 1:
  16 	print "Please use e2runfrealign.py"
  17 	exit(-1)
  18 
  19 E2n=E2init(sys.argv)
  20 
  21 os.system('clear')
  22 os.system('cp 3DMapInOut.mrc 3DMapInOut.mrc.old')
  23 os.system('cp ptcl_meta_data ptcl_meta_data.old')
  24 dir_list = os.listdir('.')
  25 dir_list.sort()
  26 high = 0
  27 for item in dir_list:
  28 	if len(item) > 6:
  29 		if item[:4] == 'card':
  30 			item = item.replace(".txt",'')
  31 			item = item.replace("card",'')
  32 			if int(item) > high:
  33 				high = int(item)
  34 
  35 if high == 0:
  36 	high = high + 1
  37 for i in range(high):
  38 	os.system('frealign_v8.exe < card' + str(i) + '.txt')
  39 	if i < 10:
  40 		k = '0' + str(i)
  41 	else:
  42 		k = str(i)
  43 	s = "cp 3DMapInOut.mrc OutputMap_" + k +".mrc"
  44 	os.system(s)
  45 	s = "cp OutParam OutParam_" + k
  46 	os.system(s)
  47 	os.system('mv OutParam ptcl_meta_data')
  48 	s = "cp OutParamShift OutParamShift_" + k
  49 	os.system(s)
  50 	os.system('cp 3DMapInOut.mrc.old 3DMapInOut.mrc')
  51 
  52 os.system('mv 3DMapInOut.mrc.old 3DMapInOut.mrc')
  53 os.system('mv ptcl_meta_data.old ptcl_meta_data')
  54 
  55 print "e2runfrealign.py finished"
  56 
  57 E2end(E2n)