def Distance(i1, i2, lccc): return max(1.0 - lccc[mono(i1,i2)][0], 0.0)
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Forms chains of 2D images based on their similarities.
Functionality:
4. Order a 2-D stack of image based on pair-wise similarity (computed as a cross-correlation coefficent).
Options 1-3 require image stack to be aligned. The program will apply orientation parameters if present in headers.
The ways to use the program:
4.1 Use option initial to specify which image will be used as an initial seed to form the chain.
sxprocess.py input_stack.hdf output_stack.hdf --initial=23 --radius=25
4.2 If options initial is omitted, the program will determine which image best serves as initial seed to form the chain
sxprocess.py input_stack.hdf output_stack.hdf --radius=25
4.3 Use option circular to form a circular chain.
sxprocess.py input_stack.hdf output_stack.hdf --circular--radius=25
4.4 New circular code based on pairwise alignments
sxprocess.py aclf.hdf chain.hdf circle.hdf --align --radius=25 --xr=2 --pairwiseccc=lcc.txt
4.5 Circular ordering based on pairwise alignments
sxprocess.py vols.hdf chain.hdf mask.hdf --dd --radius=25
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--dd", action="store_true", help="Circular ordering without adjustment of orientations", default=False)
parser.add_option("--circular", action="store_true", help="Select circular ordering (first image has to be similar to the last)", default=False)
parser.add_option("--align", action="store_true", help="Compute all pairwise alignments and for the table of their similarities find the best chain", default=False)
parser.add_option("--initial", type="int", default=-1, help="Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)")
parser.add_option("--radius", type="int", default=-1, help="Radius of a circular mask for similarity based ordering")
# import params for 2D alignment
parser.add_option("--ou", type="int", default=-1, help="outer radius for 2D alignment < nx/2-1 (set to the radius of the particle)")
parser.add_option("--xr", type="int", default=0, help="range for translation search in x direction, search is +/xr (0)")
parser.add_option("--yr", type="int", default=0, help="range for translation search in y direction, search is +/yr (0)")
#parser.add_option("--nomirror", action="store_true", default=False, help="Disable checking mirror orientations of images (default False)")
parser.add_option("--pairwiseccc", type="string", default= None, help="Input/output pairwise ccc file")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.dd:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
stack = args[0]
new_stack = args[1]
from utilities import model_circle
from statistics import ccc
from statistics import mono
lend = EMUtil.get_image_count(stack)
lccc = [None]*(lend*(lend-1)/2)
for i in xrange(lend-1):
v1 = get_im( stack, i )
if( i == 0 and nargs == 2):
nx = v1.get_xsize()
ny = v1.get_ysize()
nz = v1.get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny, nz)
else:
mask = get_im(args[2])
for j in xrange(i+1, lend):
lccc[mono(i,j)] = [ccc(v1, get_im( stack, j ), mask), 0]
order = tsp(lccc)
if(len(order) != lend):
print " problem with data length"
from sys import exit
exit()
print "Total sum of cccs :",TotalDistance(order, lccc)
print "ordering :",order
for i in xrange(lend): get_im(stack, order[i]).write_image( new_stack, i )
elif options.align:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
from utilities import get_params2D, model_circle
from fundamentals import rot_shift2D
from statistics import ccc
from time import time
from alignment import align2d, align2d_scf
from multi_shc import mult_transform
stack = args[0]
new_stack = args[1]
d = EMData.read_images(stack)
"""
# will align anyway
try:
ttt = d[0].get_attr('xform.params2d')
for i in xrange(len(d)):
alpha, sx, sy, mirror, scale = get_params2D(d[i])
d[i] = rot_shift2D(d[i], alpha, sx, sy, mirror)
except:
pass
"""
nx = d[0].get_xsize()
ny = d[0].get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny)
if(options.xr < 0): xrng = 0
else: xrng = options.xr
if(options.yr < 0): yrng = xrng
else: yrng = options.yr
initial = max(options.initial, 0)
from statistics import mono
lend = len(d)
lccc = [None]*(lend*(lend-1)/2)
from utilities import read_text_row
if options.pairwiseccc == None or not os.path.exists(options.pairwiseccc) :
st = time()
for i in xrange(lend-1):
for j in xrange(i+1, lend):
# j>i meaning mono entry (i,j) or (j,i) indicates T i->j (from smaller index to larger)
#alpha, sx, sy, mir, peak = align2d(d[i],d[j], xrng, yrng, step=options.ts, first_ring=options.ir, last_ring=radius, mode = "F")
alpha, sx, sy, mir, peak = align2d_scf(d[i],d[j], xrng, yrng, ou=radius)
lccc[mono(i,j)] = [ccc(d[j], rot_shift2D(d[i], alpha, sx, sy, mir, 1.0), mask), alpha, sx, sy, mir]
#print " %4d %10.1f"%(i,time()-st)
if(not os.path.exists(options.pairwiseccc)):
from utilities import write_text_row
write_text_row([[initial,0,0,0,0]]+lccc,options.pairwiseccc)
elif(os.path.exists(options.pairwiseccc)):
lccc = read_text_row(options.pairwiseccc)
initial = int(lccc[0][0] + 0.1)
del lccc[0]
for i in xrange(len(lccc)):
T = Transform({"type":"2D","alpha":lccc[i][1],"tx":lccc[i][2],"ty":lccc[i][3],"mirror":int(lccc[i][4]+0.1)})
lccc[i] = [lccc[i][0],T]
tdummy = Transform({"type":"2D"})
maxsum = -1.023
for m in xrange(0,lend):#initial, initial+1):
indc = range( lend )
lsnake = [[m, tdummy, 0.0]]
del indc[m]
lsum = 0.0
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = lccc[mono(indc[i], lsnake[-1][0])][0]
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
# Here we need transformation from the current to the previous,
# meaning indc[i] -> lsnake[-1][0]
T = lccc[mono(indc[i], lsnake[-1][0])][1]
# If direction is from larger to smaller index, the transformation has to be inverted
if( indc[i] > lsnake[-1][0] ): T = T.inverse()
lsnake.append([qi,T, maxcit])
lsum += maxcit
del indc[indc.index(qi)]
T = lccc[mono(indc[-1], lsnake[-1][0])][1]
if( indc[-1] > lsnake[-1][0]): T = T.inverse()
lsnake.append([indc[-1], T, lccc[mono(indc[-1], lsnake[-1][0])][0]])
print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(lend)]
print " Initial image selected : ",init,maxsum," ",TotalDistance([snake[m][0] for m in xrange(lend)], lccc)
#for q in snake: print q
from copy import deepcopy
trans=deepcopy([snake[i][1] for i in xrange(len(snake))])
print [snake[i][0] for i in xrange(len(snake))]
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Forms chains of 2D images based on their similarities.
Functionality:
4. Order a 2-D stack of image based on pair-wise similarity (computed as a cross-correlation coefficent).
Options 1-3 require image stack to be aligned. The program will apply orientation parameters if present in headers.
The ways to use the program:
4.1 Use option initial to specify which image will be used as an initial seed to form the chain.
sxprocess.py input_stack.hdf output_stack.hdf --initial=23 --radius=25
4.2 If options initial is omitted, the program will determine which image best serves as initial seed to form the chain
sxprocess.py input_stack.hdf output_stack.hdf --radius=25
4.3 Use option circular to form a circular chain.
sxprocess.py input_stack.hdf output_stack.hdf --circular--radius=25
4.4 New circular code based on pairwise alignments
sxprocess.py aclf.hdf chain.hdf circle.hdf --align --radius=25 --xr=2 --pairwiseccc=lcc.txt
4.5 Circular ordering based on pairwise alignments
sxprocess.py vols.hdf chain.hdf mask.hdf --dd --radius=25
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--dd", action="store_true", help="Circular ordering without adjustment of orientations", default=False)
parser.add_option("--circular", action="store_true", help="Select circular ordering (first image has to be similar to the last)", default=False)
parser.add_option("--align", action="store_true", help="Compute all pairwise alignments and for the table of their similarities find the best chain", default=False)
parser.add_option("--initial", type="int", default=-1, help="Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)")
parser.add_option("--radius", type="int", default=-1, help="Radius of a circular mask for similarity based ordering")
# import params for 2D alignment
parser.add_option("--ou", type="int", default=-1, help="outer radius for 2D alignment < nx/2-1 (set to the radius of the particle)")
parser.add_option("--xr", type="int", default=0, help="range for translation search in x direction, search is +/xr (0)")
parser.add_option("--yr", type="int", default=0, help="range for translation search in y direction, search is +/yr (0)")
#parser.add_option("--nomirror", action="store_true", default=False, help="Disable checking mirror orientations of images (default False)")
parser.add_option("--pairwiseccc", type="string", default= None, help="Input/output pairwise ccc file")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.dd:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
stack = args[0]
new_stack = args[1]
from utilities import model_circle
from statistics import ccc
from statistics import mono
lend = EMUtil.get_image_count(stack)
lccc = [None]*(lend*(lend-1)/2)
for i in xrange(lend-1):
v1 = get_im( stack, i )
if( i == 0 and nargs == 2):
nx = v1.get_xsize()
ny = v1.get_ysize()
nz = v1.get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny, nz)
else:
mask = get_im(args[2])
for j in xrange(i+1, lend):
lccc[mono(i,j)] = [ccc(v1, get_im( stack, j ), mask), 0]
order = tsp(lccc)
if(len(order) != lend):
print " problem with data length"
from sys import exit
exit()
print "Total sum of cccs :",TotalDistance(order, lccc)
print "ordering :",order
for i in xrange(lend): get_im(stack, order[i]).write_image( new_stack, i )
elif options.align:
nargs = len(args)
if nargs != 3:
print "must provide name of input and two output files!"
return
from utilities import get_params2D, model_circle
from fundamentals import rot_shift2D
from statistics import ccc
from time import time
from alignment import align2d, align2d_scf
from multi_shc import mult_transform
stack = args[0]
new_stack = args[1]
d = EMData.read_images(stack)
"""
# will align anyway
try:
ttt = d[0].get_attr('xform.params2d')
for i in xrange(len(d)):
alpha, sx, sy, mirror, scale = get_params2D(d[i])
d[i] = rot_shift2D(d[i], alpha, sx, sy, mirror)
except:
pass
"""
nx = d[0].get_xsize()
ny = d[0].get_ysize()
if options.ou < 1 : radius = nx//2-2
else: radius = options.ou
mask = model_circle(radius, nx, ny)
if(options.xr < 0): xrng = 0
else: xrng = options.xr
if(options.yr < 0): yrng = xrng
else: yrng = options.yr
initial = max(options.initial, 0)
from statistics import mono
lend = len(d)
lccc = [None]*(lend*(lend-1)/2)
from utilities import read_text_row
if options.pairwiseccc == None or not os.path.exists(options.pairwiseccc) :
st = time()
for i in xrange(lend-1):
for j in xrange(i+1, lend):
# j>i meaning mono entry (i,j) or (j,i) indicates T i->j (from smaller index to larger)
#alpha, sx, sy, mir, peak = align2d(d[i],d[j], xrng, yrng, step=options.ts, first_ring=options.ir, last_ring=radius, mode = "F")
alpha, sx, sy, mir, peak = align2d_scf(d[i],d[j], xrng, yrng, ou=radius)
lccc[mono(i,j)] = [ccc(d[j], rot_shift2D(d[i], alpha, sx, sy, mir, 1.0), mask), alpha, sx, sy, mir]
#print " %4d %10.1f"%(i,time()-st)
if(not os.path.exists(options.pairwiseccc)):
from utilities import write_text_row
write_text_row([[initial,0,0,0,0]]+lccc,options.pairwiseccc)
elif(os.path.exists(options.pairwiseccc)):
lccc = read_text_row(options.pairwiseccc)
initial = int(lccc[0][0] + 0.1)
del lccc[0]
for i in xrange(len(lccc)):
T = Transform({"type":"2D","alpha":lccc[i][1],"tx":lccc[i][2],"ty":lccc[i][3],"mirror":int(lccc[i][4]+0.1)})
lccc[i] = [lccc[i][0],T]
tdummy = Transform({"type":"2D"})
maxsum = -1.023
for m in xrange(0,lend):#initial, initial+1):
indc = range( lend )
lsnake = [[m, tdummy, 0.0]]
del indc[m]
lsum = 0.0
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = lccc[mono(indc[i], lsnake[-1][0])][0]
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
# Here we need transformation from the current to the previous,
# meaning indc[i] -> lsnake[-1][0]
T = lccc[mono(indc[i], lsnake[-1][0])][1]
# If direction is from larger to smaller index, the transformation has to be inverted
if( indc[i] > lsnake[-1][0] ): T = T.inverse()
lsnake.append([qi,T, maxcit])
lsum += maxcit
del indc[indc.index(qi)]
T = lccc[mono(indc[-1], lsnake[-1][0])][1]
if( indc[-1] > lsnake[-1][0]): T = T.inverse()
lsnake.append([indc[-1], T, lccc[mono(indc[-1], lsnake[-1][0])][0]])
print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(lend)]
print " Initial image selected : ",init,maxsum," ",TotalDistance([snake[m][0] for m in xrange(lend)], lccc)
#for q in snake: print q
from copy import deepcopy
trans=deepcopy([snake[i][1] for i in xrange(len(snake))])
print [snake[i][0] for i in xrange(len(snake))]
"""
for m in xrange(lend):
prms = trans[m].get_params("2D")
print " %3d %7.1f %7.1f %7.1f %2d %6.2f"%(snake[m][0], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"], snake[m][2])
"""
for k in xrange(lend-2,0,-1):
T = snake[k][1]
for i in xrange(k+1, lend):
trans[i] = T*trans[i]
# To add - apply all transformations and do the overall centering.
for m in xrange(lend):
prms = trans[m].get_params("2D")
#print " %3d %7.1f %7.1f %7.1f %2d %6.2f"%(snake[m][0], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"], snake[m][2])
#rot_shift2D(d[snake[m][0]], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"]).write_image(new_stack, m)
rot_shift2D(d[snake[m][0]], prms["alpha"], 0.0,0.0, prms["mirror"]).write_image(new_stack, m)
order = tsp(lccc)
if(len(order) != lend):
print " problem with data length"
from sys import exit
exit()
print TotalDistance(order, lccc)
print order
ibeg = order.index(init)
order = [order[(i+ibeg)%lend] for i in xrange(lend)]
print TotalDistance(order, lccc)
print order
snake = [tdummy]
for i in xrange(1,lend):
# Here we need transformation from the current to the previous,
# meaning order[i] -> order[i-1]]
T = lccc[mono(order[i], order[i-1])][1]
# If direction is from larger to smaller index, the transformation has to be inverted
if( order[i] > order[i-1] ): T = T.inverse()
snake.append(T)
assert(len(snake) == lend)
from copy import deepcopy
trans = deepcopy(snake)
for k in xrange(lend-2,0,-1):
T = snake[k]
for i in xrange(k+1, lend):
trans[i] = T*trans[i]
# Try to smooth the angles - complicated, I am afraid one would have to use angles forward and backwards
# and find their average??
# In addition, one would have to recenter them
"""
trms = []
for m in xrange(lend):
prms = trans[m].get_params("2D")
trms.append([prms["alpha"], prms["mirror"]])
for i in xrange(3):
for m in xrange(lend):
mb = (m-1)%lend
me = (m+1)%lend
# angles order mb,m,me
# calculate predicted angles mb->m
"""
for m in xrange(lend):
prms = trans[m].get_params("2D")
#rot_shift2D(d[order[m]], prms["alpha"], prms["tx"], prms["ty"], prms["mirror"]).write_image("metro.hdf", m)
rot_shift2D(d[order[m]], prms["alpha"], 0.0,0.0, prms["mirror"]).write_image(args[2], m)
"""
# This was an effort to get number of loops, inconclusive, to say the least
from numpy import outer, zeros, float32, sqrt
lend = len(d)
cor = zeros(lend,float32)
cor = outer(cor, cor)
for i in xrange(lend): cor[i][i] = 1.0
for i in xrange(lend-1):
for j in xrange(i+1, lend):
cor[i,j] = lccc[mono(i,j)][0]
cor[j,i] = cor[i,j]
lmbd, eigvec = pca(cor)
from utilities import write_text_file
nvec=20
print [lmbd[j] for j in xrange(nvec)]
print " G"
mm = [-1]*lend
for i in xrange(lend): # row
mi = -1.0e23
for j in xrange(nvec):
qt = eigvec[j][i]
if(abs(qt)>mi):
mi = abs(qt)
mm[i] = j
for j in xrange(nvec):
qt = eigvec[j][i]
print round(qt,3), # eigenvector
print mm[i]
print
for j in xrange(nvec):
qt = []
for i in xrange(lend):
if(mm[i] == j): qt.append(i)
if(len(qt)>0): write_text_file(qt,"loop%02d.txt"%j)
"""
"""
print [lmbd[j] for j in xrange(nvec)]
print " B"
mm = [-1]*lend
for i in xrange(lend): # row
mi = -1.0e23
for j in xrange(nvec):
qt = eigvec[j][i]/sqrt(lmbd[j])
if(abs(qt)>mi):
mi = abs(qt)
mm[i] = j
for j in xrange(nvec):
qt = eigvec[j][i]/sqrt(lmbd[j])
print round(qt,3), # eigenvector
print mm[i]
print
"""
"""
lend=3
cor = zeros(lend,float32)
cor = outer(cor, cor)
cor[0][0] =136.77
cor[0][1] = 79.15
cor[0][2] = 37.13
cor[1][0] = 79.15
cor[2][0] = 37.13
cor[1][1] = 50.04
cor[1][2] = 21.65
cor[2][1] = 21.65
cor[2][2] = 13.26
lmbd, eigvec = pca(cor)
print lmbd
print eigvec
for i in xrange(lend): # row
for j in xrange(lend): print eigvec[j][i], # eigenvector
print
print " B"
for i in xrange(lend): # row
for j in xrange(lend): print eigvec[j][i]/sqrt(lmbd[j]), # eigenvector
print
print " G"
for i in xrange(lend): # row
for j in xrange(lend): print eigvec[j][i]*sqrt(lmbd[j]), # eigenvector
print
"""
else:
nargs = len(args)
if nargs != 2:
print "must provide name of input and output file!"
return
from utilities import get_params2D, model_circle
from fundamentals import rot_shift2D
from statistics import ccc
from time import time
from alignment import align2d
from multi_shc import mult_transform
stack = args[0]
new_stack = args[1]
d = EMData.read_images(stack)
try:
ttt = d[0].get_attr('xform.params2d')
for i in xrange(len(d)):
alpha, sx, sy, mirror, scale = get_params2D(d[i])
d[i] = rot_shift2D(d[i], alpha, sx, sy, mirror)
except:
pass
nx = d[0].get_xsize()
ny = d[0].get_ysize()
if options.radius < 1 : radius = nx//2-2
else: radius = options.radius
mask = model_circle(radius, nx, ny)
init = options.initial
if init > -1 :
print " initial image: %d" % init
temp = d[init].copy()
temp.write_image(new_stack, 0)
del d[init]
k = 1
lsum = 0.0
while len(d) > 1:
maxcit = -111.
for i in xrange(len(d)):
cuc = ccc(d[i], temp, mask)
if cuc > maxcit:
maxcit = cuc
qi = i
# print k, maxcit
lsum += maxcit
temp = d[qi].copy()
del d[qi]
temp.write_image(new_stack, k)
k += 1
print lsum
d[0].write_image(new_stack, k)
else:
if options.circular :
print "Using options.circular"
# figure the "best circular" starting image
maxsum = -1.023
for m in xrange(len(d)):
indc = range(len(d) )
lsnake = [-1]*(len(d)+1)
lsnake[0] = m
lsnake[-1] = m
del indc[m]
temp = d[m].copy()
lsum = 0.0
direction = +1
k = 1
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = ccc(d[indc[i]], temp, mask)
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
lsnake[k] = qi
lsum += maxcit
del indc[indc.index(qi)]
direction = -direction
for i in xrange( 1,len(d) ):
if( direction > 0 ):
if(lsnake[i] == -1):
temp = d[lsnake[i-1]].copy()
#print " forw ",lsnake[i-1]
k = i
break
else:
if(lsnake[len(d) - i] == -1):
temp = d[lsnake[len(d) - i +1]].copy()
#print " back ",lsnake[len(d) - i +1]
k = len(d) - i
break
lsnake[lsnake.index(-1)] = indc[-1]
#print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(len(d))]
print " Initial image selected : ",init,maxsum
print lsnake
for m in xrange(len(d)): d[snake[m]].write_image(new_stack, m)
else:
# figure the "best" starting image
maxsum = -1.023
for m in xrange(len(d)):
indc = range(len(d) )
lsnake = [m]
del indc[m]
temp = d[m].copy()
lsum = 0.0
while len(indc) > 1:
maxcit = -111.
for i in xrange(len(indc)):
cuc = ccc(d[indc[i]], temp, mask)
if cuc > maxcit:
maxcit = cuc
qi = indc[i]
lsnake.append(qi)
lsum += maxcit
temp = d[qi].copy()
del indc[indc.index(qi)]
lsnake.append(indc[-1])
#print " initial image and lsum ",m,lsum
#print lsnake
if(lsum > maxsum):
maxsum = lsum
init = m
snake = [lsnake[i] for i in xrange(len(d))]
print " Initial image selected : ",init,maxsum
print lsnake
for m in xrange(len(d)): d[snake[m]].write_image(new_stack, m)
print " problem with data length" from sys import exit exit() print TotalDistance(order, lccc) print order ibeg = order.index(init) order = [order[(i+ibeg)%lend] for i in xrange(lend)] print TotalDistance(order, lccc) print order snake = [tdummy] for i in xrange(1,lend): # Here we need transformation from the current to the previous, # meaning order[i] -> order[i-1]] T = lccc[mono(order[i], order[i-1])][1] # If direction is from larger to smaller index, the transformation has to be inverted if( order[i] > order[i-1] ): T = T.inverse() snake.append(T) assert(len(snake) == lend) from copy import deepcopy trans = deepcopy(snake) for k in xrange(lend-2,0,-1): T = snake[k] for i in xrange(k+1, lend): trans[i] = T*trans[i] # Try to smooth the angles - complicated, I am afraid one would have to use angles forward and backwards # and find their average?? # In addition, one would have to recenter them """
