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EMAN_to_FREALIGN.py
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EMAN_to_FREALIGN.py
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#!/usr/bin/env python
import optparse
from sys import *
import os,sys,re
from optparse import OptionParser
import glob
import subprocess
from os import system
import linecache
def setupParserOptions():
parser = optparse.OptionParser()
parser.set_usage("%prog -f <stack> -p <parameter> -c <ctf> --num=<float> --mag=<float>")
parser.add_option("-f",dest="stack",type="string",metavar="FILE",
help="raw, IMAGIC particle stack (black particles)")
parser.add_option("-p",dest="param",type="string",metavar="FILE",
help="EMAN2 output parameter file")
parser.add_option("-c",dest="ctf",type="string",metavar="FILE",
help="per-particle CTF information file from APPION")
parser.add_option("--num",dest="num",type="int", metavar="INT",
help="number of models used in refinement")
parser.add_option("--mag",dest="mag",type="float", metavar="FLOAT",
help="actual magnification of images")
parser.add_option("-s", action="store_true",dest="spider",default=False,
help="Flag if your original stack before converting to HDF format was a SPIDER stack OR if you used XMIPP normalization during APPION processing")
parser.add_option("-d", action="store_true",dest="debug",default=False,
help="debug")
options,args = parser.parse_args()
if len(args) > 0:
parser.error("Unknown commandline options: " +str(args))
if len(sys.argv) < 5:
parser.print_help()
params={}
for i in parser.option_list:
if isinstance(i.dest,str):
params[i.dest] = getattr(options,i.dest)
return params
def getIMAGICPath():
### get the imagicroot directory
impath = subprocess.Popen("env | grep IMAGIC_ROOT", shell=True, stdout=subprocess.PIPE).stdout.read().strip()
imagicpath = impath.replace("IMAGIC_ROOT=","")
if imagicpath != '/opt/qb3/imagic-070813':
print "imagic/070813 was not found, make sure it is in your path"
sys.exit()
def getEMANPath():
### get the imagicroot directory
emanpath = subprocess.Popen("env | grep EMAN2DIR", shell=True, stdout=subprocess.PIPE).stdout.read().strip()
if emanpath:
emanpath = emanpath.replace("EMAN2DIR=","")
if os.path.exists(emanpath):
return emanpath
print "EMAN2 was not found, make sure it is in your path"
sys.exit()
def getImagicVersion(imagicroot):
### get IMAGIC version from the "version_######S" file in
### the imagicroot directory, return as an int
versionstr=glob.glob(os.path.join(imagicroot,"version_*"))
if versionstr:
v = re.search('\d\d\d\d\d\d',versionstr[0]).group(0)
return int(v)
else:
print "Could not get version number from imagic root directory"
sys.exit()
def Eman2Freali(az,alt,phi):
t1 = Transform({"type":"eman","az":az,"alt":alt,"phi":phi,"mirror":False})
#t_conv = Transform({"type":"eman","alt":31.717474411458415,"az":90,"phi":-90,"mirror":False})
#t2 = t1*t_conv.inverse()
d = t1.get_params("eman")
psi = d["phi"]+90
if psi >360:
psi = psi-360
theta= d["alt"]
phi = d["az"]-90
return psi,theta,phi
def main(params):
parm=params['param']
numMods = params['num']
mag = params['mag']
stack = params['stack']
debug = params['debug']
if numMods == 1:
f=open(parm,'r')
out = open("%s_01_frealign"%(parm),'w')
count=1
text2='%s_%02d.txt' %(parm,1)
text=open(text2,'w')
count2=1
print "\n"
print "Calculating euler angle conversion..."
print "\n"
for line in f:
l = line.split()
parmPSI = float(l[0])
parmTHETA = float(l[1])
parmPHI = float(l[2])
sx =(float(l[3]))
sy =(float(l[4]))
model = float(l[5])
psi,theta,phi = Eman2Freali(parmPSI,parmTHETA,parmPHI)
if model == 999:
if debug is True:
print 'Particle %s is included' %(count-1)
text.write("%s\n" %(count-1))
ctf = linecache.getline(params['ctf'],count)
if debug is True:
print 'Reading line %s in ctf file' %(count)
print ctf
c = ctf.split()
micro = float(c[7])
df1 = float(c[8])
df2 = float(c[9])
astig = float(c[10])
out.write("%7d%8.3f%8.3f%8.3f%8.3f%8.3f%9.1f%6d%9.1f%9.1f%8.2f%7.2f%6.2f\n" %(count2,psi,theta,phi,sx,sy,mag,micro,df1,df2,astig,0,0))
count2 = count2 + 1
count = count + 1
f.close()
out.close()
text.close()
new = stack[:-4]
print "\n"
print "Selecting particles..."
print "\n"
cmd="e2proc2d.py --list=%s %s %s_model1.img" %(text2,stack,new)
subprocess.Popen(cmd,shell=True).wait()
print "\n"
print "Normalizing selected particles..."
print "\n"
cmd="proc2d %s_model1.img %s_model1_norm.img norm=0,1" %(new,new)
subprocess.Popen(cmd,shell=True).wait()
if params['spider'] is True:
print "\n"
print "Flipping particle coordinates..."
print "\n"
cmd="proc2d %s_model1_norm.img %s_model1_norm.img inplace flip" %(new,new)
subprocess.Popen(cmd,shell=True).wait()
print "\n"
print "Converting IMAGIC stack into FREALIGN particle stack..."
print "\n"
cmd="~michael/bin/imagic_to_frealign.b %s_model1_norm.img" %(new)
subprocess.Popen(cmd,shell=True).wait()
if numMods == 2:
f=open(parm,'r')
out0 = open("%s_00_frealign"%(parm),'w')
out1= open("%s_01_frealign"%(parm),'w')
count=1
text2='%s_%02d.txt' %(parm,0)
text3='%s_%02d.txt' %(parm,1)
text=open(text2,'w')
text1=open(text3,'w')
count2=1
count3=1
print "\n"
print "Calculating euler angle conversion..."
print "\n"
for line in f:
l = line.split()
parmPSI = float(l[0])
parmTHETA = float(l[1])
parmPHI = float(l[2])
sx =(float(l[3]))
sy =(float(l[4]))
model = float(l[5])
psi,theta,phi = Eman2Freali(parmPSI,parmTHETA,parmPHI)
if model == 0:
if debug is True:
print 'Particle %s is included' %(count-1)
text.write("%s\n" %(count-1))
ctf = linecache.getline(params['ctf'],count)
if debug is True:
print 'Reading line %s in ctf file' %(count)
print ctf
c = ctf.split()
micro = float(c[7])
df1 = float(c[8])
df2 = float(c[9])
astig = float(c[10])
out0.write("%7d%8.3f%8.3f%8.3f%8.3f%8.3f%8.1f%6d%9.1f%9.1f%8.2f%7.2f%6.2f\n" %(count2,psi,theta,phi,sx,sy,mag,micro,df1,df2,astig,0,0))
count2 = count2 + 1
if model == 1:
if debug is True:
print 'Particle %s is included' %(count-1)
text1.write("%s\n" %(count-1))
ctf = linecache.getline(params['ctf'],count)
if debug is True:
print 'Reading line %s in ctf file' %(count)
print ctf
c = ctf.split()
micro = float(c[7])
df1 = float(c[8])
df2 = float(c[9])
astig = float(c[10])
out1.write("%7d%8.3f%8.3f%8.3f%8.3f%8.3f%8.1f%6d%9.1f%9.1f%8.2f%7.2f%6.2f\n" %(count3,psi,theta,phi,sx,sy,mag,micro,df1,df2,astig,0,0))
count3 = count3 + 1
count = count + 1
f.close()
out1.close()
out0.close()
text.close()
text1.close()
new = stack[:-4]
print "\n"
print "Selecting particles..."
print "\n"
cmd="e2proc2d.py --list=%s %s %s_model00.img" %(text2,stack,new)
subprocess.Popen(cmd,shell=True).wait()
cmd="e2proc2d.py --list=%s %s %s_model01.img" %(text3,stack,new)
subprocess.Popen(cmd,shell=True).wait()
print "\n"
print "Normalizing selected particles..."
print "\n"
cmd="proc2d %s_model00.img %s_model00_norm.img norm=0,1" %(new,new)
subprocess.Popen(cmd,shell=True).wait()
cmd="proc2d %s_model01.img %s_model01_norm.img norm=0,1" %(new,new)
subprocess.Popen(cmd,shell=True).wait()
if params['spider'] is True:
print "\n"
print "Flipping particle coordinates..."
print "\n"
cmd="proc2d %s_model00_norm.img %s_model00_norm.img inplace flip" %(new,new)
subprocess.Popen(cmd,shell=True).wait()
cmd="proc2d %s_model01_norm.img %s_model01_norm.img inplace flip" %(new,new)
subprocess.Popen(cmd,shell=True).wait()
print "\n"
print "Converting IMAGIC stack into FREALIGN particle stack..."
print "\n"
cmd="~michael/bin/imagic_to_frealign.b %s_model00_norm.img" %(new)
subprocess.Popen(cmd,shell=True).wait()
cmd="~michael/bin/imagic_to_frealign.b %s_model01_norm.img" %(new)
subprocess.Popen(cmd,shell=True).wait()
if __name__ == "__main__":
imagicroot = getIMAGICPath()
getEMANPath()
from EMAN2 import *
from sparx import *
params=setupParserOptions()
main(params)