if(len(sys.argv) != 4):

raise Exception("Usage: paramfile, jobid, npix for center positions of spots")

paramfile = sys.argv[1]

jobid = sys.argv[2]

npix = int(sys.argv[3])

#types = ['mgrid','ft_onespot1','ft_onespot2']

types = ['mgrid']

with open(paramfile) as f:

params = f.readlines()

params = [x.strip() for x in params]

modelfile = params[0]

stop = int(params[1])

for i in range(0,stop):

j = i*7 +2

for t in types:

prefix = params[j] + t + '_' + jobid

file = prefix + '.gfx'

lines_to_3d_wave(file, prefix + '.txt')

if(t == 'mgrid'):

p = subprocess.Popen(['/home/maldonis/3dft/stdev',file,jobid], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

for nextline in iter(p.stdout.readline, ""):

sys.stdout.write(nextline)

sys.stdout.flush()

poutput = p.stdout.read()

perr = p.stderr.read()

preturncode = p.wait()

if(preturncode != 0):

print("stdev exit status: "+str(preturncode))

raise Exception("stdev failed on file {0}!".format(file)+perr)

new_model_file_base_name = params[j] + jobid

worked = atom_selection(modelfile, 'stdev_'+jobid+'.gfx', 256, new_model_file_base_name)

x0,y0,z0 = tuple([float(x) for x in params[j+1].split()])

sx,sy,sz = tuple([float(x) for x in params[j+2].split()])

cxy,cxz,cyz = tuple([float(x) for x in params[j+3].split()])

xc = eval(params[j+4].split()[2])

yc = eval(params[j+5].split()[2])

zc = eval(params[j+6].split()[2])

gvec = float(params[j+6].split()[3])

print("g-vector length = {0}".format(gvec))

print("The more correct g-vector length == {0}".format(sqrt((npix/4.0-x0+1)**2 + (npix/4.0-y0+1)**2 + (npix/4.0-z0)**2+1)*3.0/(npix/2)))

if(worked == 0):

m = Model(new_model_file_base_name+'.xyz')

rot_arr = calc_rot_array_from_hkl(npix/2-xc,npix/2-yc,npix/2-zc)

rot(m, rot_arr)

m.write(new_model_file_base_name+'.rotated.xyz')

m.write(new_model_file_base_name+'.rotated.cif')