def helical2( ref_data ):
from utilities import print_msg
from filter import fit_tanh, filt_tanl
from morphology import threshold
# Prepare the reference in helical refinement, i.e., low-pass filter.
# Input: list ref_data
# 2 - raw volume
# Output: filtered, and masked reference image
global ref_ali2d_counter
ref_ali2d_counter += 1
print_msg("helical2 #%6d\n"%(ref_ali2d_counter))
stat = Util.infomask(ref_data[2], None, True)
volf = ref_data[2] - stat[0]
volf = threshold(volf)
fl = 0.25#0.17
aa = 0.1
msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n"%(fl, aa)
print_msg(msg)
volf = filt_tanl(volf, fl, aa)
from utilities import read_text_file
dipr=read_text_file('symdoc.txt',-1)
#here pixel size, fract, rmax and rmin will have to be read from external text file
from alignment import helios
volf, dp, dphi = helios(volf, 2.175, dipr[0][-1], dipr[1][-1], 0.7, 30,3)
print_msg("New delta z and delta phi : %s, %s\n\n"%(dp,dphi))
fofo = open('symdoc.txt','a')
fofo.write(' %12.4f %12.4f\n'%(dp,dphi))
fofo.close()
return volf,[0.0,0.0,0.0]
def findHsym(vol,hfile,apix,isearch,osearch,vert=None): """ use helical search program to find helical symmetry """ import sys,shutil,subprocess from alignment import helios rot,rise,vrot,vrise = readHsym(hfile) orad=osearch/apix irad=isearch/apix v,newrise,newrot=helios(vol,apix,rise,rot,0.5,orad,irad) savepar = "%.6f\t%.6f"%(newrot,newrise) newvrise,newvrot=None,None # if applying vertical symmetry, determine here if vert is not None: v,newvrise,newvrot=helios(vol,apix,vrise,vrot,0.5,orad,irad) savepar += "\t%.6f\t%.6f"%(newvrot,newvrise) # store helical parameters f=open(hfile,'a') f.write(savepar+"\n") f.close() return newrot,newrise,newvrot,newvrise
def findHsym(vol, hfile, apix, isearch, osearch, vert=None):
"""
use helical search program to find helical symmetry
"""
import sys, shutil, subprocess
from alignment import helios
rot, rise, vrot, vrise = readHsym(hfile)
orad = osearch / apix
irad = isearch / apix
v, newrise, newrot = helios(vol, apix, rise, rot, 0.5, orad, irad)
savepar = "%.6f\t%.6f" % (newrot, newrise)
newvrise, newvrot = None, None
# if applying vertical symmetry, determine here
if vert is not None:
v, newvrise, newvrot = helios(vol, apix, vrise, vrot, 0.5, orad, irad)
savepar += "\t%.6f\t%.6f" % (newvrot, newvrise)
# store helical parameters
f = open(hfile, 'a')
f.write(savepar + "\n")
f.close()
return newrot, newrise, newvrot, newvrise
