def resample( prjfile, outdir, bufprefix, nbufvol, nvol, seedbase,\
delta, d, snr, CTF, npad,\
MPI, myid, ncpu, verbose = 0 ):
from utilities import even_angles
from random import seed, jumpahead, shuffle
import os
from sys import exit
nprj = EMUtil.get_image_count(prjfile)
if MPI:
from mpi import mpi_barrier, MPI_COMM_WORLD
if myid == 0:
if os.path.exists(outdir): nx = 1
else: nx = 0
else: nx = 0
ny = bcast_number_to_all(nx, source_node=0)
if ny == 1:
ERROR(
'Output directory exists, please change the name and restart the program',
"resample", 1, myid)
mpi_barrier(MPI_COMM_WORLD)
if myid == 0:
os.mkdir(outdir)
mpi_barrier(MPI_COMM_WORLD)
else:
if os.path.exists(outdir):
ERROR(
'Output directory exists, please change the name and restart the program',
"resample", 1, 0)
os.mkdir(outdir)
if (verbose == 1):
finfo = open(os.path.join(outdir, "progress%04d.txt" % myid), "w")
else:
finfo = None
#print " before evenangles",myid
from utilities import getvec
from numpy import array, reshape
refa = even_angles(delta)
nrefa = len(refa)
refnormal = zeros((nrefa, 3), 'float32')
tetref = [0.0] * nrefa
for i in range(nrefa):
tr = getvec(refa[i][0], refa[i][1])
for j in range(3):
refnormal[i][j] = tr[j]
tetref[i] = refa[i][1]
del refa
vct = array([0.0] * (3 * nprj), 'float32')
if myid == 0:
print(" will read ", myid)
tr = EMUtil.get_all_attributes(prjfile, 'xform.projection')
tetprj = [0.0] * nprj
for i in range(nprj):
temp = tr[i].get_params("spider")
tetprj[i] = temp["theta"]
if (tetprj[i] > 90.0): tetprj[i] = 180.0 - tetprj[i]
vct[3 * i + 0] = tr[i].at(2, 0)
vct[3 * i + 1] = tr[i].at(2, 1)
vct[3 * i + 2] = tr[i].at(2, 2)
del tr
else:
tetprj = [0.0] * nprj
#print " READ ",myid
if MPI:
#print " will bcast",myid
from mpi import mpi_bcast, MPI_FLOAT, MPI_COMM_WORLD
vct = mpi_bcast(vct, len(vct), MPI_FLOAT, 0, MPI_COMM_WORLD)
from utilities import bcast_list_to_all
tetprj = bcast_list_to_all(tetprj, myid, 0)
#print " reshape ",myid
vct = reshape(vct, (nprj, 3))
assignments = [[] for i in range(nrefa)]
dspn = 1.25 * delta
for k in range(nprj):
best_s = -1.0
best_i = -1
for i in range(nrefa):
if (abs(tetprj[k] - tetref[i]) <= dspn):
s = abs(refnormal[i][0] * vct[k][0] +
refnormal[i][1] * vct[k][1] +
refnormal[i][2] * vct[k][2])
if s > best_s:
best_s = s
best_i = i
assignments[best_i].append(k)
am = len(assignments[0])
mufur = 1.0 / am
for i in range(1, len(assignments)):
ti = len(assignments[i])
am = min(am, ti)
if (ti > 0): mufur += 1.0 / ti
del tetprj, tetref
dp = 1.0 - d # keep that many in each direction
keep = int(am * dp + 0.5)
mufur = keep * nrefa / (1.0 - mufur * keep / float(nrefa))
if myid == 0:
print(" Number of projections ", nprj,
". Number of reference directions ", nrefa,
", multiplicative factor for the variance ", mufur)
print(" Minimum number of assignments ", am,
" Number of projections used per stratum ", keep,
" Number of projections in resampled structure ",
int(am * dp + 0.5) * nrefa)
if am < 2 or am == keep:
print("incorrect settings")
exit() # FIX
if (seedbase < 1):
seed()
jumpahead(17 * myid + 123)
else:
seed(seedbase)
jumpahead(17 * myid + 123)
volfile = os.path.join(outdir, "bsvol%04d.hdf" % myid)
from random import randint
niter = nvol / ncpu / nbufvol
for kiter in range(niter):
if (verbose == 1):
finfo.write("Iteration %d: \n" % kiter)
finfo.flush()
iter_start = time()
# the following has to be converted to resample mults=1 means take given projection., mults=0 means omit
mults = [[0] * nprj for i in range(nbufvol)]
for i in range(nbufvol):
for l in range(nrefa):
mass = assignments[l][:]
shuffle(mass)
mass = mass[:keep]
mass.sort()
#print l, " * ",mass
for k in range(keep):
mults[i][mass[k]] = 1
'''
lout = []
for l in xrange(len(mults[i])):
if mults[i][l] == 1: lout.append(l)
write_text_file(lout, os.path.join(outdir, "list%04d_%03d.txt" %(i, myid)))
del lout
'''
del mass
rectors, fftvols, wgtvols = resample_prepare(prjfile, nbufvol, snr,
CTF, npad)
resample_insert(bufprefix, fftvols, wgtvols, mults, CTF, npad, finfo)
del mults
resample_finish(rectors, fftvols, wgtvols, volfile, kiter, nprj, finfo)
rectors = None
fftvols = None
wgtvols = None
if (verbose == 1):
finfo.write("time for iteration: %10.3f\n" % (time() - iter_start))
finfo.flush()
def resample( prjfile, outdir, bufprefix, nbufvol, nvol, seedbase,\
delta, d, snr, CTF, npad,\
MPI, myid, ncpu, verbose = 0 ):
from utilities import even_angles
from random import seed, jumpahead, shuffle
import os
from sys import exit
nprj = EMUtil.get_image_count( prjfile )
if MPI:
from mpi import mpi_barrier, MPI_COMM_WORLD
if myid == 0:
if os.path.exists(outdir): nx = 1
else: nx = 0
else: nx = 0
ny = bcast_number_to_all(nx, source_node = 0)
if ny == 1: ERROR('Output directory exists, please change the name and restart the program', "resample", 1,myid)
mpi_barrier(MPI_COMM_WORLD)
if myid == 0:
os.mkdir(outdir)
mpi_barrier(MPI_COMM_WORLD)
else:
if os.path.exists(outdir):
ERROR('Output directory exists, please change the name and restart the program', "resample", 1,0)
os.mkdir(outdir)
if(verbose == 1): finfo=open( os.path.join(outdir, "progress%04d.txt" % myid), "w" )
else: finfo = None
#print " before evenangles",myid
from utilities import getvec
from numpy import array, reshape
refa = even_angles(delta)
nrefa = len(refa)
refnormal = zeros((nrefa,3),'float32')
tetref = [0.0]*nrefa
for i in xrange(nrefa):
tr = getvec( refa[i][0], refa[i][1] )
for j in xrange(3): refnormal[i][j] = tr[j]
tetref[i] = refa[i][1]
del refa
vct = array([0.0]*(3*nprj),'float32')
if myid == 0:
print " will read ",myid
tr = EMUtil.get_all_attributes(prjfile,'xform.projection')
tetprj = [0.0]*nprj
for i in xrange(nprj):
temp = tr[i].get_params("spider")
tetprj[i] = temp["theta"]
if(tetprj[i] > 90.0): tetprj[i] = 180.0 - tetprj[i]
vct[3*i+0] = tr[i].at(2,0)
vct[3*i+1] = tr[i].at(2,1)
vct[3*i+2] = tr[i].at(2,2)
del tr
else:
tetprj = [0.0]*nprj
#print " READ ",myid
if MPI:
#print " will bcast",myid
from mpi import mpi_bcast, MPI_FLOAT, MPI_COMM_WORLD
vct = mpi_bcast(vct,len(vct),MPI_FLOAT,0,MPI_COMM_WORLD)
from utilities import bcast_list_to_all
tetprj = bcast_list_to_all(tetprj, myid, 0)
#print " reshape ",myid
vct = reshape(vct,(nprj,3))
assignments = [[] for i in xrange(nrefa)]
dspn = 1.25*delta
for k in xrange(nprj):
best_s = -1.0
best_i = -1
for i in xrange( nrefa ):
if(abs(tetprj[k] - tetref[i]) <= dspn):
s = abs(refnormal[i][0]*vct[k][0] + refnormal[i][1]*vct[k][1] + refnormal[i][2]*vct[k][2])
if s > best_s:
best_s = s
best_i = i
assignments[best_i].append(k)
am = len(assignments[0])
mufur = 1.0/am
for i in xrange(1,len(assignments)):
ti = len(assignments[i])
am = min(am, ti)
if(ti>0): mufur += 1.0/ti
del tetprj,tetref
dp = 1.0 - d # keep that many in each direction
keep = int(am*dp +0.5)
mufur = keep*nrefa/(1.0 - mufur*keep/float(nrefa))
if myid == 0:
print " Number of projections ",nprj,". Number of reference directions ",nrefa,", multiplicative factor for the variance ",mufur
print " Minimum number of assignments ",am," Number of projections used per stratum ", keep," Number of projections in resampled structure ",int(am*dp +0.5)*nrefa
if am <2 or am == keep:
print "incorrect settings"
exit() # FIX
if(seedbase < 1):
seed()
jumpahead(17*myid+123)
else:
seed(seedbase)
jumpahead(17*myid+123)
volfile = os.path.join(outdir, "bsvol%04d.hdf" % myid)
from random import randint
niter = nvol/ncpu/nbufvol
for kiter in xrange(niter):
if(verbose == 1):
finfo.write( "Iteration %d: \n" % kiter )
finfo.flush()
iter_start = time()
# the following has to be converted to resample mults=1 means take given projection., mults=0 means omit
mults = [ [0]*nprj for i in xrange(nbufvol) ]
for i in xrange(nbufvol):
for l in xrange(nrefa):
mass = assignments[l][:]
shuffle(mass)
mass = mass[:keep]
mass.sort()
#print l, " * ",mass
for k in xrange(keep):
mults[i][mass[k]] = 1
'''
lout = []
for l in xrange(len(mults[i])):
if mults[i][l] == 1: lout.append(l)
write_text_file(lout, os.path.join(outdir, "list%04d_%03d.txt" %(i, myid)))
del lout
'''
del mass
rectors, fftvols, wgtvols = resample_prepare( prjfile, nbufvol, snr, CTF, npad )
resample_insert( bufprefix, fftvols, wgtvols, mults, CTF, npad, finfo )
del mults
resample_finish( rectors, fftvols, wgtvols, volfile, kiter, nprj, finfo )
rectors = None
fftvols = None
wgtvols = None
if(verbose == 1):
finfo.write( "time for iteration: %10.3f\n" % (time() - iter_start) )
finfo.flush()