def filterlocal(ui, vi, m, falloff, myid, main_node, number_of_proc):
if myid == main_node:
nx = vi.get_xsize()
ny = vi.get_ysize()
nz = vi.get_zsize()
# Round all resolution numbers to two digits
for x in range(nx):
for y in range(ny):
for z in range(nz):
ui.set_value_at_fast(x, y, z, round(ui.get_value_at(x, y, z), 2))
dis = [nx, ny, nz]
else:
falloff = 0.0
radius = 0
dis = [0, 0, 0]
falloff = sp_utilities.bcast_number_to_all(falloff, main_node)
dis = sp_utilities.bcast_list_to_all(dis, myid, source_node=main_node)
if myid != main_node:
nx = int(dis[0])
ny = int(dis[1])
nz = int(dis[2])
vi = sp_utilities.model_blank(nx, ny, nz)
ui = sp_utilities.model_blank(nx, ny, nz)
sp_utilities.bcast_EMData_to_all(vi, myid, main_node)
sp_utilities.bcast_EMData_to_all(ui, myid, main_node)
sp_fundamentals.fftip(vi) # volume to be filtered
st = EMAN2_cppwrap.Util.infomask(ui, m, True)
filteredvol = sp_utilities.model_blank(nx, ny, nz)
cutoff = max(st[2] - 0.01, 0.0)
while cutoff < st[3]:
cutoff = round(cutoff + 0.01, 2)
# if(myid == main_node): print cutoff,st
pt = EMAN2_cppwrap.Util.infomask(
sp_morphology.threshold_outside(ui, cutoff - 0.00501, cutoff + 0.005),
m,
True,
) # Ideally, one would want to check only slices in question...
if pt[0] != 0.0:
# print cutoff,pt[0]
vovo = sp_fundamentals.fft(filt_tanl(vi, cutoff, falloff))
for z in range(myid, nz, number_of_proc):
for x in range(nx):
for y in range(ny):
if m.get_value_at(x, y, z) > 0.5:
if round(ui.get_value_at(x, y, z), 2) == cutoff:
filteredvol.set_value_at_fast(
x, y, z, vovo.get_value_at(x, y, z)
)
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
sp_utilities.reduce_EMData_to_root(filteredvol, myid, main_node, mpi.MPI_COMM_WORLD)
return filteredvol
def prgq(volft, kb, nx, delta, ref_a, sym, MPI=False):
"""
Generate set of projections based on even angles
The command returns list of ffts of projections
"""
from sp_projection import prep_vol, prgs
from sp_applications import MPI_start_end
from sp_utilities import even_angles, model_blank
from sp_fundamentals import fft
# generate list of Eulerian angles for reference projections
# phi, theta, psi
mode = "F"
ref_angles = even_angles(delta,
symmetry=sym,
method=ref_a,
phiEqpsi="Minus")
cnx = nx // 2 + 1
cny = nx // 2 + 1
num_ref = len(ref_angles)
if MPI:
from mpi import mpi_comm_rank, mpi_comm_size, MPI_COMM_WORLD
myid = mpi_comm_rank(MPI_COMM_WORLD)
ncpu = mpi_comm_size(MPI_COMM_WORLD)
else:
ncpu = 1
myid = 0
from sp_applications import MPI_start_end
ref_start, ref_end = MPI_start_end(num_ref, ncpu, myid)
prjref = [
] # list of (image objects) reference projections in Fourier representation
for i in range(num_ref):
prjref.append(model_blank(
nx,
nx)) # I am not sure why is that necessary, why not put None's??
for i in range(ref_start, ref_end):
prjref[i] = prgs(
volft, kb,
[ref_angles[i][0], ref_angles[i][1], ref_angles[i][2], 0.0, 0.0])
if MPI:
from sp_utilities import bcast_EMData_to_all
for i in range(num_ref):
for j in range(ncpu):
ref_start, ref_end = MPI_start_end(num_ref, ncpu, j)
if i >= ref_start and i < ref_end: rootid = j
bcast_EMData_to_all(prjref[i], myid, rootid)
for i in range(len(ref_angles)):
prjref[i].set_attr_dict({
"phi": ref_angles[i][0],
"theta": ref_angles[i][1],
"psi": ref_angles[i][2]
})
return prjref
def plot_angles(agls, nx=256):
from math import cos, sin, fmod, pi, radians
from sp_utilities import model_blank
# var
im = model_blank(nx, nx)
"""
c = 2
kc = 10
# draw reperes
for i in xrange(nx):
im.set_value_at(i, int(nx / 2.0), 0.006)
im.set_value_at(int(nx / 2.0), i, 0.006)
# draw the circles
lth = range(0, 90, kc)
lth.append(90)
for th in lth:
if th == 90: color = 0.03
else: color = 0.006
rc = sin((float(th) / 180.0) * pi)
rc *= (nx - 1)
for n in xrange(3600):
a = (n / 1800.0) * pi
px = nx / 2.0 + (rc - 1) / 2.0 * cos(a)
py = nx / 2.0 + (rc - 1) / 2.0 * sin(a)
im.set_value_at(int(px), int(py), color)
"""
# for each angles plot on circle area
# agsl: [phi, theta, psi]
ri = nx // 2
rr = ri - 1
conv = pi / 180.0
for i in range(len(agls)):
if agls[i][1] > 90.0:
agls[i][0] = agls[i][0] + 180.0
agls[i][1] = 180.0 - float(agls[i][1])
rc = rr * sin(radians(agls[i][1]))
rd = radians(agls[i][0])
px = ri + rc * cos(rd)
py = ri + rc * sin(rd)
px = min(max(int(px + 0.5), 0), nx - 1)
py = min(max(int(py + 0.5), 0), nx - 1)
im.set_value_at(px, py, 1.0 + im.get_value_at(px, py))
return im
def makeAngRes(freqvol, nx, ny, nz, pxSize, freq_to_real=True):
outAngResVol = sp_utilities.model_blank(nx, ny, nz)
data_in = freqvol.get_3dview()
data_out = outAngResVol.get_3dview()
if freq_to_real:
mask = data_in > 0.0
else:
mask = data_in > 0.0
data_out[mask] = pxSize / data_in[mask]
return outAngResVol
def montage2(inputstack, ncol, marginwidth=0, bkgd=0, outfile=None):
"""
Generates montage of images into one image.
Adapted from sxmontage.py
Arguments:
inputstack : Stack of input images to merge into montage
ncol : Number of images per row
marginwidth : Margin width, pixels
bkgd : Background value of montage
outfile : Optional output file with montage output
Returns:
montage : EMData object of image montage
"""
if isinstance(inputstack, str): inputstack = EMData.read_images(inputstack)
# Get single-image dimensions
nx = inputstack[0].get_xsize()
ny = inputstack[0].get_ysize()
# Get number of images and calculate montage dimensions
numimgs = len(inputstack)
numrows = (numimgs - 1) / ncol + 1
# Create blank image
montage_xdim = (nx + marginwidth) * ncol
montage_ydim = (ny + marginwidth) * numrows
montage = model_blank(montage_xdim, montage_ydim, 1, bkgd)
# Loop through images
for imgnum in range(numimgs):
# Horizontal grid position is image# modulo NCOL
colnum = imgnum % ncol
# Montage is numbered from the top down
rownum = numrows - 1 - imgnum / ncol
xoffset = colnum * (nx + marginwidth)
yoffset = rownum * (ny + marginwidth)
insert_image(inputstack[imgnum], montage, xoffset, yoffset)
if outfile: montage.write_image(outfile)
return montage
def test_input_image_returns_values_freq_to_real(self):
nx = 10
ny = 10
nz = 10
apix = 2
test_data = numpy.arange(nx * ny * nz, dtype=numpy.float32).reshape(
nx, ny, nz
) / (2 * nx * ny * nz)
mask = test_data > 0
blank_data = sp_utilities.model_blank(nx, ny, nz)
data_in = blank_data.get_3dview()
data_in[...] = copy.deepcopy(test_data)
returned_data = sp_locres.makeAngRes(blank_data, nx, ny, nz, apix)
expected_data = copy.deepcopy(test_data)
expected_data[mask] = apix / test_data[mask]
assert numpy.array_equal(expected_data, returned_data.get_3dview())
def test_input_image_returns_values_real_to_freq(self):
nx = 10
ny = 10
nz = 10
apix = 2
test_data = numpy.arange(nx * ny * nz, dtype=numpy.float32).reshape(nx, ny, nz)
mask = test_data >= 2 * apix
blank_data = sp_utilities.model_blank(nx, ny, nz)
data_in = blank_data.get_3dview()
data_in[...] = copy.deepcopy(test_data)
returned_data = sp_locres.makeAngRes(blank_data, nx, ny, nz, apix, False)
expected_data = copy.deepcopy(test_data)
expected_data[mask] = apix / expected_data[mask]
expected_data[~mask] = 0
print("EXP", expected_data)
print("RET", returned_data.get_3dview())
assert numpy.array_equal(expected_data, returned_data.get_3dview())
def filterlocal(ui, vi, m, falloff, myid, main_node, number_of_proc): from mpi import mpi_init, mpi_comm_size, mpi_comm_rank, MPI_COMM_WORLD from mpi import mpi_reduce, mpi_bcast, mpi_barrier, mpi_gatherv, mpi_send, mpi_recv from mpi import MPI_SUM, MPI_FLOAT, MPI_INT from sp_utilities import bcast_number_to_all, bcast_list_to_all, model_blank, bcast_EMData_to_all, reduce_EMData_to_root from sp_morphology import threshold_outside from sp_filter import filt_tanl from sp_fundamentals import fft, fftip if(myid == main_node): nx = vi.get_xsize() ny = vi.get_ysize() nz = vi.get_zsize() # Round all resolution numbers to two digits for x in range(nx): for y in range(ny): for z in range(nz): ui.set_value_at_fast( x,y,z, round(ui.get_value_at(x,y,z), 2) ) dis = [nx,ny,nz] else: falloff = 0.0 radius = 0 dis = [0,0,0] falloff = bcast_number_to_all(falloff, main_node) dis = bcast_list_to_all(dis, myid, source_node = main_node) if(myid != main_node): nx = int(dis[0]) ny = int(dis[1]) nz = int(dis[2]) vi = model_blank(nx,ny,nz) ui = model_blank(nx,ny,nz) bcast_EMData_to_all(vi, myid, main_node) bcast_EMData_to_all(ui, myid, main_node) fftip(vi) # volume to be filtered st = Util.infomask(ui, m, True) filteredvol = model_blank(nx,ny,nz) cutoff = max(st[2] - 0.01,0.0) while(cutoff < st[3] ): cutoff = round(cutoff + 0.01, 2) #if(myid == main_node): print cutoff,st pt = Util.infomask( threshold_outside(ui, cutoff - 0.00501, cutoff + 0.005), m, True) # Ideally, one would want to check only slices in question... if(pt[0] != 0.0): #print cutoff,pt[0] vovo = fft( filt_tanl(vi, cutoff, falloff) ) for z in range(myid, nz, number_of_proc): for x in range(nx): for y in range(ny): if(m.get_value_at(x,y,z) > 0.5): if(round(ui.get_value_at(x,y,z),2) == cutoff): filteredvol.set_value_at_fast(x,y,z,vovo.get_value_at(x,y,z)) mpi_barrier(MPI_COMM_WORLD) reduce_EMData_to_root(filteredvol, myid, main_node, MPI_COMM_WORLD) return filteredvol
def write_montage_file(stack, montage_file, N, gx, gy, bg, scale, number,
begin_zero):
from sp_utilities import model_blank
font = [
"0011100010001010000011000001100000110000011000001100000101000100011100",
"0001000001100001010001001000000100000010000001000000100000010001111111",
"0111110100000110000010000001000001000001000011000010000001000001111111",
"1111111000000100000100000100000111000000010000001000000110000010111110",
"0000010000011000010100010010010001010000101111111000001000000100000010",
"1111111100000010000001011110110000100000010000001000000110000010111110",
"0011110010000010000001000000101111101100000110000011000001100000101111",
"1111111000000100000010000010000010000100000100000010000010000010000000",
"0011100010001010000010100010001110001000101000001100000101000010011100",
"0111110100000011000001100000110000110111101000000100000010000010011110"
]
if gy == -1: gy = gx
data = EMData.read_images(stack)
if scale:
for im in data:
st = Util.infomask(im, None, True)
im -= st[0]
im /= st[1]
nx = data[0].get_xsize()
ny = data[0].get_ysize()
K = len(data)
M = (K - 1) / N + 1
NX = (nx + gx) * N
NY = (ny + gy) * M
maxn = -1.e-20
minn = 1.e+20
avgn = 0
for im in data:
st = Util.infomask(im, None, True)
avgn += st[0]
if st[3] > maxn: maxn = st[3]
if st[2] < minn: minn = st[2]
avgn /= K
if bg == 0:
bk = minn
elif bg == 1:
bk = maxn
elif bg == 2:
bk = 0
else:
bk = avgn
montage = model_blank(NX, NY, 1, bk)
for i in range(K):
col = i % N
row = M - 1 - i / N
for s in range(nx):
for t in range(ny):
v = data[i].get_value_at(s, t)
montage.set_value_at(col * (nx + gx) + s,
row * (ny + gy) + t, v)
if number:
for s in range(10):
for t in range(7):
if font[i % 10][s * 7 + t] == '1':
montage.set_value_at(col * (nx + gx) + 2 + t,
row * (ny + gy) + 2 + 10 - s,
maxn)
montage.write_image(montage_file)
def align2d_direct3(input_images,
refim,
xrng=1,
yrng=1,
psimax=180,
psistep=1,
ou=-1,
CTF=None):
nx = input_images[0].get_xsize()
if ou < 0:
ou = old_div(nx, 2) - 1
mask = sp_utilities.model_circle(ou, nx, nx)
nk = int(old_div(psimax, psistep))
nm = 2 * nk + 1
nc = nk + 1
refs = [None] * nm * 2
for i in range(nm):
temp = sp_fundamentals.rot_shift2D(refim, (i - nc) * psistep) * mask
refs[2 * i] = [
sp_fundamentals.fft(temp),
sp_fundamentals.fft(sp_fundamentals.mirror(temp)),
]
temp = sp_fundamentals.rot_shift2D(refim,
(i - nc) * psistep + 180.0) * mask
refs[2 * i + 1] = [
sp_fundamentals.fft(temp),
sp_fundamentals.fft(sp_fundamentals.mirror(temp)),
]
del temp
results = []
mir = 0
for image in input_images:
if CTF:
ims = sp_filter.filt_ctf(sp_fundamentals.fft(image),
image.get_attr("ctf"))
else:
ims = sp_fundamentals.fft(image)
ama = -1.0e23
bang = 0.0
bsx = 0.0
bsy = 0.0
for i in range(nm * 2):
for mirror_flag in [0, 1]:
c = sp_fundamentals.ccf(ims, refs[i][mirror_flag])
w = EMAN2_cppwrap.Util.window(c, 2 * xrng + 1, 2 * yrng + 1)
pp = sp_utilities.peak_search(w)[0]
px = int(pp[4])
py = int(pp[5])
if pp[0] == 1.0 and px == 0 and py == 0:
pass # XSH, YSH, PEAKV = 0.,0.,0.
else:
ww = sp_utilities.model_blank(3, 3)
ux = int(pp[1])
uy = int(pp[2])
for k in range(3):
for l in range(3):
ww[k, l] = w[k + ux - 1, l + uy - 1]
XSH, YSH, PEAKV = parabl(ww)
# print i,pp[-1],XSH, YSH,px+XSH, py+YSH, PEAKV
if PEAKV > ama:
ama = PEAKV
bsx = px + round(XSH, 2)
bsy = py + round(YSH, 2)
bang = i
mir = mirror_flag
# returned parameters have to be inverted
bang = (old_div(bang, 2) - nc) * psistep + 180.0 * (bang % 2)
bang, bsx, bsy, _ = sp_utilities.inverse_transform2(
bang, (1 - 2 * mir) * bsx, bsy, mir)
results.append([bang, bsx, bsy, mir, ama])
return results
def main():
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = optparse.os.path.basename(arglist[0])
usage = progname + """ inputvolume locresvolume maskfile outputfile --radius --falloff --MPI
Locally filer a volume based on local resolution volume (sxlocres.py) within area outlined by the maskfile
"""
parser = optparse.OptionParser(usage, version=sp_global_def.SPARXVERSION)
parser.add_option(
"--radius",
type="int",
default=-1,
help=
"if there is no maskfile, sphere with r=radius will be used, by default the radius is nx/2-1"
)
parser.add_option("--falloff",
type="float",
default=0.1,
help="falloff of tanl filter (default 0.1)")
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version")
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 3 or len(args) > 4:
sp_global_def.sxprint("See usage " + usage)
sp_global_def.ERROR(
"Wrong number of parameters. Please see usage information above.")
return
if sp_global_def.CACHE_DISABLE:
pass #IMPORTIMPORTIMPORT from sp_utilities import disable_bdb_cache
sp_utilities.disable_bdb_cache()
if options.MPI:
number_of_proc = mpi.mpi_comm_size(mpi.MPI_COMM_WORLD)
myid = mpi.mpi_comm_rank(mpi.MPI_COMM_WORLD)
main_node = 0
if (myid == main_node):
#print sys.argv
vi = sp_utilities.get_im(sys.argv[1])
ui = sp_utilities.get_im(sys.argv[2])
#print Util.infomask(ui, None, True)
radius = options.radius
nx = vi.get_xsize()
ny = vi.get_ysize()
nz = vi.get_zsize()
dis = [nx, ny, nz]
else:
falloff = 0.0
radius = 0
dis = [0, 0, 0]
vi = None
ui = None
dis = sp_utilities.bcast_list_to_all(dis, myid, source_node=main_node)
if (myid != main_node):
nx = int(dis[0])
ny = int(dis[1])
nz = int(dis[2])
radius = sp_utilities.bcast_number_to_all(radius, main_node)
if len(args) == 3:
if (radius == -1):
radius = min(nx, ny, nz) // 2 - 1
m = sp_utilities.model_circle(radius, nx, ny, nz)
outvol = args[2]
elif len(args) == 4:
if (myid == main_node):
m = sp_morphology.binarize(sp_utilities.get_im(args[2]), 0.5)
else:
m = sp_utilities.model_blank(nx, ny, nz)
outvol = args[3]
sp_utilities.bcast_EMData_to_all(m, myid, main_node)
pass #IMPORTIMPORTIMPORT from sp_filter import filterlocal
filteredvol = sp_filter.filterlocal(ui, vi, m, options.falloff, myid,
main_node, number_of_proc)
if (myid == 0):
filteredvol.write_image(outvol)
else:
vi = sp_utilities.get_im(args[0])
ui = sp_utilities.get_im(
args[1]
) # resolution volume, values are assumed to be from 0 to 0.5
nn = vi.get_xsize()
falloff = options.falloff
if len(args) == 3:
radius = options.radius
if (radius == -1):
radius = nn // 2 - 1
m = sp_utilities.model_circle(radius, nn, nn, nn)
outvol = args[2]
elif len(args) == 4:
m = sp_morphology.binarize(sp_utilities.get_im(args[2]), 0.5)
outvol = args[3]
sp_fundamentals.fftip(vi) # this is the volume to be filtered
# Round all resolution numbers to two digits
for x in range(nn):
for y in range(nn):
for z in range(nn):
ui.set_value_at_fast(x, y, z,
round(ui.get_value_at(x, y, z), 2))
st = EMAN2_cppwrap.Util.infomask(ui, m, True)
filteredvol = sp_utilities.model_blank(nn, nn, nn)
cutoff = max(st[2] - 0.01, 0.0)
while (cutoff < st[3]):
cutoff = round(cutoff + 0.01, 2)
pt = EMAN2_cppwrap.Util.infomask(
sp_morphology.threshold_outside(ui, cutoff - 0.00501,
cutoff + 0.005), m, True)
if (pt[0] != 0.0):
vovo = sp_fundamentals.fft(
sp_filter.filt_tanl(vi, cutoff, falloff))
for x in range(nn):
for y in range(nn):
for z in range(nn):
if (m.get_value_at(x, y, z) > 0.5):
if (round(ui.get_value_at(x, y, z),
2) == cutoff):
filteredvol.set_value_at_fast(
x, y, z, vovo.get_value_at(x, y, z))
sp_global_def.write_command(optparse.os.path.dirname(outvol))
filteredvol.write_image(outvol)
def main():
"""
Main function.
Arguments:
None
Returns:
None
"""
command_args = parse_command_line()
# Import volume
sp_global_def.sxprint("Import volume.")
input_vol = sp_utilities.get_im(command_args.input_volume)
# Sanity checks
sanity_checks(command_args, input_vol)
try:
os.makedirs(command_args.output_dir)
except OSError:
sp_global_def.sxprint(
"Output directory already exists. No need to create it.")
else:
sp_global_def.sxprint("Created output directory.")
sp_global_def.write_command(command_args.output_dir)
output_prefix = os.path.join(command_args.output_dir, command_args.prefix)
# Filter volume if specified
if command_args.low_pass_filter_resolution is not None:
sp_global_def.sxprint("Filter volume to {0}A.".format(
command_args.low_pass_filter_resolution))
input_vol = sp_filter.filt_tanl(
input_vol,
old_div(command_args.pixel_size,
command_args.low_pass_filter_resolution),
command_args.low_pass_filter_falloff,
)
input_vol.write_image(output_prefix + "_filtered_volume.hdf")
else:
sp_global_def.sxprint("Skip filter volume.")
# Create a mask based on the filtered volume
sp_global_def.sxprint("Create mask")
density_threshold = -9999.0
nsigma = 1.0
if command_args.mol_mass:
density_threshold = input_vol.find_3d_threshold(
command_args.mol_mass, command_args.pixel_size)
sp_global_def.sxprint(
"Mask molecular mass translated into binary threshold: ",
density_threshold)
elif command_args.threshold:
density_threshold = command_args.threshold
elif command_args.nsigma:
nsigma = command_args.nsigma
else:
assert False
if command_args.edge_type == "cosine":
mode = "C"
elif command_args.edge_type == "gaussian":
mode = "G"
else:
assert False
mask_first = sp_morphology.adaptive_mask_scipy(
input_vol,
nsigma=nsigma,
threshold=density_threshold,
ndilation=command_args.ndilation,
nerosion=command_args.nerosion,
edge_width=command_args.edge_width,
allow_disconnected=command_args.allow_disconnected,
mode=mode,
do_approx=command_args.do_old,
do_fill=command_args.fill_mask,
do_print=True,
)
# Create a second mask based on the filtered volume
s_mask = None
s_density_threshold = 1
s_nsigma = 1.0
if command_args.second_mask is not None:
sp_global_def.sxprint("Prepare second mask")
s_mask = sp_utilities.get_im(command_args.second_mask)
s_density_threshold = -9999.0
s_nsigma = 1.0
if command_args.s_mol_mass:
s_density_threshold = input_vol.find_3d_threshold(
command_args.s_mol_mass, command_args.s_pixel_size)
sp_global_def.sxprint(
"Second mask molecular mass translated into binary threshold: ",
s_density_threshold,
)
elif command_args.s_threshold:
s_density_threshold = command_args.s_threshold
elif command_args.s_nsigma:
s_nsigma = command_args.s_nsigma
else:
assert False
elif command_args.second_mask_shape is not None:
sp_global_def.sxprint("Prepare second mask")
nx = mask_first.get_xsize()
ny = mask_first.get_ysize()
nz = mask_first.get_zsize()
if command_args.second_mask_shape == "cube":
s_nx = command_args.s_nx
s_ny = command_args.s_ny
s_nz = command_args.s_nz
s_mask = sp_utilities.model_blank(s_nx, s_ny, s_nz, 1)
elif command_args.second_mask_shape == "cylinder":
s_radius = command_args.s_radius
s_nx = command_args.s_nx
s_ny = command_args.s_ny
s_nz = command_args.s_nz
try:
s_mask = sp_utilities.model_cylinder(s_radius, s_nx, s_ny,
s_nz)
except RuntimeError as e:
sp_global_def.sxprint(
"An error occured! Please check the error log")
raise
elif command_args.second_mask_shape == "sphere":
s_radius = command_args.s_radius
s_nx = command_args.s_nx
s_ny = command_args.s_ny
s_nz = command_args.s_nz
try:
s_mask = sp_utilities.model_circle(s_radius, s_nx, s_ny, s_nz)
except RuntimeError as e:
sp_global_def.sxprint(
"An error occured! Please check the error log")
raise
else:
assert False
s_mask = sp_utilities.pad(s_mask, nx, ny, nz, 0)
if s_mask is not None:
sp_global_def.sxprint("Create second mask")
if command_args.s_edge_type == "cosine":
mode = "C"
elif command_args.s_edge_type == "gaussian":
mode = "G"
else:
assert False
s_mask = sp_morphology.adaptive_mask_scipy(
s_mask,
nsigma=s_nsigma,
threshold=s_density_threshold,
ndilation=command_args.s_ndilation,
nerosion=command_args.s_nerosion,
edge_width=command_args.s_edge_width,
allow_disconnected=command_args.s_allow_disconnected,
mode=mode,
do_approx=command_args.s_do_old,
do_fill=command_args.s_fill_mask,
do_print=True,
)
if command_args.s_invert:
s_mask = 1 - s_mask
sp_global_def.sxprint("Write outputs.")
mask_first.write_image(output_prefix + "_mask_first.hdf")
s_mask.write_image(output_prefix + "_mask_second.hdf")
masked_combined = mask_first * s_mask
masked_combined.write_image(output_prefix + "_mask.hdf")
else:
sp_global_def.sxprint("Write outputs.")
mask_first.write_image(output_prefix + "_mask.hdf")
def recons3d_4nn_ctf_MPI(
myid,
prjlist,
snr=1.0,
sign=1,
symmetry="c1",
finfo=None,
npad=2,
xysize=-1,
zsize=-1,
mpi_comm=None,
smearstep=0.0,
):
"""
recons3d_4nn_ctf - calculate CTF-corrected 3-D reconstruction from a set of projections using three Eulerian angles, two shifts, and CTF settings for each projeciton image
Input
stack: name of the stack file containing projection data, projections have to be squares
list_proj: list of projections to be included in the reconstruction or image iterator
snr: Signal-to-Noise Ratio of the data
sign: sign of the CTF
symmetry: point-group symmetry to be enforced, each projection will enter the reconstruction in all symmetry-related directions.
"""
if mpi_comm == None:
mpi_comm = mpi.MPI_COMM_WORLD
if type(prjlist) == list:
prjlist = sp_utilities.iterImagesList(prjlist)
if not prjlist.goToNext():
sp_global_def.ERROR("empty input list", "recons3d_4nn_ctf_MPI", 1)
imgsize = prjlist.image().get_xsize()
if prjlist.image().get_ysize() != imgsize:
imgsize = max(imgsize, prjlist.image().get_ysize())
dopad = True
else:
dopad = False
prjlist.goToPrev()
fftvol = EMAN2_cppwrap.EMData()
if smearstep > 0.0:
# if myid == 0: print " Setting smear in prepare_recons_ctf"
ns = 1
smear = []
for j in range(-ns, ns + 1):
if j != 0:
for i in range(-ns, ns + 1):
for k in range(-ns, ns + 1):
smear += [
i * smearstep, j * smearstep, k * smearstep, 1.0
]
# Deal with theta = 0.0 cases
prj = []
for i in range(-ns, ns + 1):
for k in range(-ns, ns + 1):
prj.append(i + k)
for i in range(-2 * ns, 2 * ns + 1, 1):
smear += [i * smearstep, 0.0, 0.0, float(prj.count(i))]
# if myid == 0: print " Smear ",smear
fftvol.set_attr("smear", smear)
weight = EMAN2_cppwrap.EMData()
if xysize == -1 and zsize == -1:
params = {
"size": imgsize,
"npad": npad,
"snr": snr,
"sign": sign,
"symmetry": symmetry,
"fftvol": fftvol,
"weight": weight,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctf", params)
else:
if xysize != -1 and zsize != -1:
rx = old_div(float(xysize), imgsize)
ry = old_div(float(xysize), imgsize)
rz = old_div(float(zsize), imgsize)
elif xysize != -1:
rx = old_div(float(xysize), imgsize)
ry = old_div(float(xysize), imgsize)
rz = 1.0
else:
rx = 1.0
ry = 1.0
rz = old_div(float(zsize), imgsize)
# There is an error here with sizeprojection PAP 10/22/2014
params = {
"size": sizeprojection,
"npad": npad,
"snr": snr,
"sign": sign,
"symmetry": symmetry,
"fftvol": fftvol,
"weight": weight,
"xratio": rx,
"yratio": ry,
"zratio": rz,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctf_rect", params)
r.setup()
# if not (finfo is None):
nimg = 0
while prjlist.goToNext():
prj = prjlist.image()
if dopad:
prj = sp_utilities.pad(prj, imgsize, imgsize, 1, "circumference")
# if params:
insert_slices(r, prj)
if not (finfo is None):
nimg += 1
finfo.write(" %4d inserted\n" % (nimg))
finfo.flush()
del sp_utilities.pad
if not (finfo is None):
finfo.write("begin reduce\n")
finfo.flush()
sp_utilities.reduce_EMData_to_root(fftvol, myid, comm=mpi_comm)
sp_utilities.reduce_EMData_to_root(weight, myid, comm=mpi_comm)
if not (finfo is None):
finfo.write("after reduce\n")
finfo.flush()
if myid == 0:
dummy = r.finish(True)
else:
if xysize == -1 and zsize == -1:
fftvol = sp_utilities.model_blank(imgsize, imgsize, imgsize)
else:
if zsize == -1:
fftvol = sp_utilities.model_blank(xysize, xysize, imgsize)
elif xysize == -1:
fftvol = sp_utilities.model_blank(imgsize, imgsize, zsize)
else:
fftvol = sp_utilities.model_blank(xysize, xysize, zsize)
return fftvol
def recons3d_trl_struct_MPI(
myid,
main_node,
prjlist,
paramstructure,
refang,
rshifts_shrank,
delta,
upweighted=True,
mpi_comm=None,
CTF=True,
target_size=-1,
avgnorm=1.0,
norm_per_particle=None,
):
"""
recons3d_4nn_ctf - calculate CTF-corrected 3-D reconstruction from a set of projections using three Eulerian angles, two shifts, and CTF settings for each projeciton image
Input
list_of_prjlist: list of lists of projections to be included in the reconstruction
"""
if mpi_comm == None:
mpi_comm = mpi.MPI_COMM_WORLD
refvol = sp_utilities.model_blank(target_size)
refvol.set_attr("fudge", 1.0)
if CTF:
do_ctf = 1
else:
do_ctf = 0
fftvol = EMAN2_cppwrap.EMData()
weight = EMAN2_cppwrap.EMData()
params = {
"size": target_size,
"npad": 2,
"snr": 1.0,
"sign": 1,
"symmetry": "c1",
"refvol": refvol,
"fftvol": fftvol,
"weight": weight,
"do_ctf": do_ctf,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctfw", params)
r.setup()
if prjlist:
if norm_per_particle == None:
norm_per_particle = len(prjlist) * [1.0]
nnx = prjlist[0].get_xsize()
nny = prjlist[0].get_ysize()
nshifts = len(rshifts_shrank)
for im in range(len(prjlist)):
# parse projection structure, generate three lists:
# [ipsi+iang], [ishift], [probability]
# Number of orientations for a given image
numbor = len(paramstructure[im][2])
ipsiandiang = [
old_div(paramstructure[im][2][i][0], 1000)
for i in range(numbor)
]
allshifts = [
paramstructure[im][2][i][0] % 1000 for i in range(numbor)
]
probs = [paramstructure[im][2][i][1] for i in range(numbor)]
# Find unique projection directions
tdir = list(set(ipsiandiang))
bckgn = prjlist[im].get_attr("bckgnoise")
ct = prjlist[im].get_attr("ctf")
# For each unique projection direction:
data = [None] * nshifts
for ii in range(len(tdir)):
# Find the number of times given projection direction appears on the list, it is the number of different shifts associated with it.
lshifts = sp_utilities.findall(tdir[ii], ipsiandiang)
toprab = 0.0
for ki in range(len(lshifts)):
toprab += probs[lshifts[ki]]
recdata = EMAN2_cppwrap.EMData(nny, nny, 1, False)
recdata.set_attr("is_complex", 0)
for ki in range(len(lshifts)):
lpt = allshifts[lshifts[ki]]
if data[lpt] == None:
data[lpt] = sp_fundamentals.fshift(
prjlist[im], rshifts_shrank[lpt][0],
rshifts_shrank[lpt][1])
data[lpt].set_attr("is_complex", 0)
EMAN2_cppwrap.Util.add_img(
recdata,
EMAN2_cppwrap.Util.mult_scalar(
data[lpt], old_div(probs[lshifts[ki]], toprab)),
)
recdata.set_attr_dict({
"padffted": 1,
"is_fftpad": 1,
"is_fftodd": 0,
"is_complex_ri": 1,
"is_complex": 1,
})
if not upweighted:
recdata = sp_filter.filt_table(recdata, bckgn)
recdata.set_attr_dict({"bckgnoise": bckgn, "ctf": ct})
ipsi = tdir[ii] % 100000
iang = old_div(tdir[ii], 100000)
r.insert_slice(
recdata,
EMAN2_cppwrap.Transform({
"type":
"spider",
"phi":
refang[iang][0],
"theta":
refang[iang][1],
"psi":
refang[iang][2] + ipsi * delta,
}),
old_div(toprab * avgnorm, norm_per_particle[im]),
)
# clean stuff
del bckgn, recdata, tdir, ipsiandiang, allshifts, probs
sp_utilities.reduce_EMData_to_root(fftvol, myid, main_node, comm=mpi_comm)
sp_utilities.reduce_EMData_to_root(weight, myid, main_node, comm=mpi_comm)
if myid == main_node:
dummy = r.finish(True)
mpi.mpi_barrier(mpi_comm)
if myid == main_node:
return fftvol, weight, refvol
else:
return None, None, None
def recons3d_4nnw_MPI(
myid,
prjlist,
bckgdata,
snr=1.0,
sign=1,
symmetry="c1",
finfo=None,
npad=2,
xysize=-1,
zsize=-1,
mpi_comm=None,
smearstep=0.0,
fsc=None,
):
"""
recons3d_4nn_ctf - calculate CTF-corrected 3-D reconstruction from a set of projections using three Eulerian angles, two shifts, and CTF settings for each projeciton image
Input
stack: name of the stack file containing projection data, projections have to be squares
prjlist: list of projections to be included in the reconstruction or image iterator
bckgdata = [get_im("tsd.hdf"),read_text_file("data_stamp.txt")]
snr: Signal-to-Noise Ratio of the data
sign: sign of the CTF
symmetry: point-group symmetry to be enforced, each projection will enter the reconstruction in all symmetry-related directions.
"""
pass # IMPORTIMPORTIMPORT from sp_utilities import reduce_EMData_to_root, pad
pass # IMPORTIMPORTIMPORT from EMAN2 import Reconstructors
pass # IMPORTIMPORTIMPORT from sp_utilities import iterImagesList, set_params_proj, model_blank
pass # IMPORTIMPORTIMPORT from mpi import MPI_COMM_WORLD
pass # IMPORTIMPORTIMPORT import types
if mpi_comm == None:
mpi_comm = mpi.MPI_COMM_WORLD
if type(prjlist) == list:
prjlist = sp_utilities.iterImagesList(prjlist)
if not prjlist.goToNext():
sp_global_def.ERROR("empty input list", "recons3d_4nnw_MPI", 1)
imgsize = prjlist.image().get_xsize()
if prjlist.image().get_ysize() != imgsize:
imgsize = max(imgsize, prjlist.image().get_ysize())
dopad = True
else:
dopad = False
prjlist.goToPrev()
# Do the FSC shtick.
bnx = old_div(imgsize * npad, 2) + 1
if fsc:
pass # IMPORTIMPORTIMPORT from math import sqrt
pass # IMPORTIMPORTIMPORT from sp_utilities import reshape_1d
t = [0.0] * len(fsc)
for i in range(len(fsc)):
t[i] = min(max(fsc[i], 0.0), 0.999)
t = sp_utilities.reshape_1d(t, len(t), npad * len(t))
refvol = sp_utilities.model_blank(bnx, 1, 1, 0.0)
for i in range(len(fsc)):
refvol.set_value_at(i, t[i])
else:
refvol = sp_utilities.model_blank(bnx, 1, 1, 1.0)
refvol.set_attr("fudge", 1.0)
fftvol = EMAN2_cppwrap.EMData()
weight = EMAN2_cppwrap.EMData()
if smearstep > 0.0:
# if myid == 0: print " Setting smear in prepare_recons_ctf"
ns = 1
smear = []
for j in range(-ns, ns + 1):
if j != 0:
for i in range(-ns, ns + 1):
for k in range(-ns, ns + 1):
smear += [
i * smearstep, j * smearstep, k * smearstep, 1.0
]
# Deal with theta = 0.0 cases
prj = []
for i in range(-ns, ns + 1):
for k in range(-ns, ns + 1):
prj.append(i + k)
for i in range(-2 * ns, 2 * ns + 1, 1):
smear += [i * smearstep, 0.0, 0.0, float(prj.count(i))]
# if myid == 0: print " Smear ",smear
fftvol.set_attr("smear", smear)
if xysize == -1 and zsize == -1:
params = {
"size": imgsize,
"npad": npad,
"snr": snr,
"sign": sign,
"symmetry": symmetry,
"refvol": refvol,
"fftvol": fftvol,
"weight": weight,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctfw", params)
else:
if xysize != -1 and zsize != -1:
rx = old_div(float(xysize), imgsize)
ry = old_div(float(xysize), imgsize)
rz = old_div(float(zsize), imgsize)
elif xysize != -1:
rx = old_div(float(xysize), imgsize)
ry = old_div(float(xysize), imgsize)
rz = 1.0
else:
rx = 1.0
ry = 1.0
rz = old_div(float(zsize), imgsize)
# There is an error here with sizeprojection PAP 10/22/2014
params = {
"size": sizeprojection,
"npad": npad,
"snr": snr,
"sign": sign,
"symmetry": symmetry,
"fftvol": fftvol,
"weight": weight,
"xratio": rx,
"yratio": ry,
"zratio": rz,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctf_rect", params)
r.setup()
# from utilities import model_blank, get_im, read_text_file
# bckgdata = [get_im("tsd.hdf"),read_text_file("data_stamp.txt")]
nnx = bckgdata[0].get_xsize()
nny = bckgdata[0].get_ysize()
bckgnoise = []
for i in range(nny):
prj = sp_utilities.model_blank(nnx)
for k in range(nnx):
prj[k] = bckgdata[0].get_value_at(k, i)
bckgnoise.append(prj)
datastamp = bckgdata[1]
if not (finfo is None):
nimg = 0
while prjlist.goToNext():
prj = prjlist.image()
try:
stmp = old_div(nnx, 0)
stmp = prj.get_attr("ptcl_source_image")
except:
try:
stmp = prj.get_attr("ctf")
stmp = round(stmp.defocus, 4)
except:
sp_global_def.ERROR(
"Either ptcl_source_image or ctf has to be present in the header.",
"recons3d_4nnw_MPI",
1,
myid,
)
try:
indx = datastamp.index(stmp)
except:
sp_global_def.ERROR("Problem with indexing ptcl_source_image.",
"recons3d_4nnw_MPI", 1, myid)
if dopad:
prj = sp_utilities.pad(prj, imgsize, imgsize, 1, "circumference")
prj.set_attr("bckgnoise", bckgnoise[indx])
insert_slices(r, prj)
if not (finfo is None):
nimg += 1
finfo.write(" %4d inserted\n" % (nimg))
finfo.flush()
del sp_utilities.pad
if not (finfo is None):
finfo.write("begin reduce\n")
finfo.flush()
sp_utilities.reduce_EMData_to_root(fftvol, myid, comm=mpi_comm)
sp_utilities.reduce_EMData_to_root(weight, myid, comm=mpi_comm)
if not (finfo is None):
finfo.write("after reduce\n")
finfo.flush()
if myid == 0:
dummy = r.finish(True)
else:
pass # IMPORTIMPORTIMPORT from sp_utilities import model_blank
if xysize == -1 and zsize == -1:
fftvol = sp_utilities.model_blank(imgsize, imgsize, imgsize)
else:
if zsize == -1:
fftvol = sp_utilities.model_blank(xysize, xysize, imgsize)
elif xysize == -1:
fftvol = sp_utilities.model_blank(imgsize, imgsize, zsize)
else:
fftvol = sp_utilities.model_blank(xysize, xysize, zsize)
return fftvol
def recons3d_4nn_MPI(
myid,
prjlist,
symmetry="c1",
finfo=None,
snr=1.0,
npad=2,
xysize=-1,
zsize=-1,
mpi_comm=None,
):
if mpi_comm == None:
mpi_comm = mpi.MPI_COMM_WORLD
if type(prjlist) == list:
prjlist = sp_utilities.iterImagesList(prjlist)
if not prjlist.goToNext():
sp_global_def.ERROR("empty input list", "recons3d_4nn_MPI", 1)
imgsize = prjlist.image().get_xsize()
if prjlist.image().get_ysize() != imgsize:
imgsize = max(imgsize, prjlist.image().get_ysize())
dopad = True
else:
dopad = False
prjlist.goToPrev()
fftvol = EMAN2_cppwrap.EMData()
weight = EMAN2_cppwrap.EMData()
if xysize == -1 and zsize == -1:
params = {
"size": imgsize,
"npad": npad,
"symmetry": symmetry,
"fftvol": fftvol,
"weight": weight,
"snr": snr,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4", params)
else:
if xysize != -1 and zsize != -1:
rx = old_div(float(xysize), imgsize)
ry = old_div(float(xysize), imgsize)
rz = old_div(float(zsize), imgsize)
elif xysize != -1:
rx = old_div(float(xysize), imgsize)
ry = old_div(float(xysize), imgsize)
rz = 1.0
else:
rx = 1.0
ry = 1.0
rz = old_div(float(zsize), imgsize)
params = {
"sizeprojection": imgsize,
"npad": npad,
"symmetry": symmetry,
"fftvol": fftvol,
"weight": weight,
"xratio": rx,
"yratio": ry,
"zratio": rz,
}
r = EMAN2_cppwrap.Reconstructors.get("nn4_rect", params)
r.setup()
if not (finfo is None):
nimg = 0
while prjlist.goToNext():
prj = prjlist.image()
if dopad:
prj = sp_utilities.pad(prj, imgsize, imgsize, 1, "circumference")
insert_slices(r, prj)
if not (finfo is None):
nimg += 1
finfo.write("Image %4d inserted.\n" % (nimg))
finfo.flush()
if not (finfo is None):
finfo.write("Begin reducing ...\n")
finfo.flush()
sp_utilities.reduce_EMData_to_root(fftvol, myid, comm=mpi_comm)
sp_utilities.reduce_EMData_to_root(weight, myid, comm=mpi_comm)
if myid == 0:
dummy = r.finish(True)
else:
if xysize == -1 and zsize == -1:
fftvol = sp_utilities.model_blank(imgsize, imgsize, imgsize)
else:
if zsize == -1:
fftvol = sp_utilities.model_blank(xysize, xysize, imgsize)
elif xysize == -1:
fftvol = sp_utilities.model_blank(imgsize, imgsize, zsize)
else:
fftvol = sp_utilities.model_blank(xysize, xysize, zsize)
return fftvol
def multalign2d_scf(image, refrings, frotim, numr, xrng=-1, yrng=-1, ou=-1):
nx = image.get_xsize()
ny = image.get_xsize()
if ou < 0:
ou = min(old_div(nx, 2) - 1, old_div(ny, 2) - 1)
if yrng < 0:
yrng = xrng
if ou < 2:
sp_global_def.ERROR("Radius of the object (ou) has to be given",
"align2d_scf", 1)
sci = sp_fundamentals.scf(image)
first_ring = 1
# center in SPIDER convention
cnx = old_div(nx, 2) + 1
cny = old_div(ny, 2) + 1
cimage = EMAN2_cppwrap.Util.Polar2Dm(sci, cnx, cny, numr, "H")
EMAN2_cppwrap.Util.Frngs(cimage, numr)
mimage = EMAN2_cppwrap.Util.Polar2Dm(sp_fundamentals.mirror(sci), cnx, cny,
numr, "H")
EMAN2_cppwrap.Util.Frngs(mimage, numr)
nrx = min(2 * (xrng + 1) + 1, ((old_div((nx - 2), 2)) * 2 + 1))
nry = min(2 * (yrng + 1) + 1, ((old_div((ny - 2), 2)) * 2 + 1))
totpeak = -1.0e23
for iki in range(len(refrings)):
# print "TEMPLATE ",iki
# Find angle
retvals = EMAN2_cppwrap.Util.Crosrng_e(refrings[iki], cimage, numr, 0,
0.0)
alpha1 = ang_n(retvals["tot"], "H", numr[-1])
peak1 = retvals["qn"]
retvals = EMAN2_cppwrap.Util.Crosrng_e(refrings[iki], mimage, numr, 0,
0.0)
alpha2 = ang_n(retvals["tot"], "H", numr[-1])
peak2 = retvals["qn"]
# print alpha1, peak1
# print alpha2, peak2
if peak1 > peak2:
mirr = 0
alpha = alpha1
else:
mirr = 1
alpha = -alpha2
ccf1 = EMAN2_cppwrap.Util.window(
sp_fundamentals.ccf(
sp_fundamentals.rot_shift2D(image, alpha, 0.0, 0.0, mirr),
frotim[iki]),
nrx,
nry,
)
p1 = sp_utilities.peak_search(ccf1)
ccf2 = EMAN2_cppwrap.Util.window(
sp_fundamentals.ccf(
sp_fundamentals.rot_shift2D(image, alpha + 180.0, 0.0, 0.0,
mirr),
frotim[iki],
),
nrx,
nry,
)
p2 = sp_utilities.peak_search(ccf2)
# print p1
# print p2
peak_val1 = p1[0][0]
peak_val2 = p2[0][0]
if peak_val1 > peak_val2:
sxs = -p1[0][4]
sys = -p1[0][5]
cx = int(p1[0][1])
cy = int(p1[0][2])
peak = peak_val1
else:
alpha += 180.0
sxs = -p2[0][4]
sys = -p2[0][5]
peak = peak_val2
cx = int(p2[0][1])
cy = int(p2[0][2])
ccf1 = ccf2
# print cx,cy
z = sp_utilities.model_blank(3, 3)
for i in range(3):
for j in range(3):
z[i, j] = ccf1[i + cx - 1, j + cy - 1]
# print ccf1[cx,cy],z[1,1]
XSH, YSH, PEAKV = parabl(z)
# print PEAKV
if PEAKV > totpeak:
totpeak = PEAKV
iref = iki
if mirr == 1:
sx = -sxs + XSH
else:
sx = sxs - XSH
sy = sys - YSH
talpha = alpha
tmirr = mirr
# print "BETTER",sx,sy,iref,talpha,tmirr,totpeak
# return alpha, sx, sys-YSH, mirr, PEAKV
return sx, sy, iref, talpha, tmirr, totpeak
def align2d_scf(image, refim, xrng=-1, yrng=-1, ou=-1):
nx = image.get_xsize()
ny = image.get_xsize()
if ou < 0:
ou = min(old_div(nx, 2) - 1, old_div(ny, 2) - 1)
if yrng < 0:
yrng = xrng
if ou < 2:
sp_global_def.ERROR("Radius of the object (ou) has to be given",
"align2d_scf", 1)
sci = sp_fundamentals.scf(image)
scr = sp_fundamentals.scf(refim)
first_ring = 1
# alpha1, sxs, sys, mirr, peak1 = align2d_no_mirror(scf(image), scr, last_ring=ou, mode="H")
# alpha2, sxs, sys, mirr, peak2 = align2d_no_mirror(scf(mirror(image)), scr, last_ring=ou, mode="H")
# alpha1, sxs, sys, mirr, peak1 = align2d_no_mirror(sci, scr, first_ring = 1, last_ring=ou, mode="H")
# alpha2, sxs, sys, mirr, peak2 = align2d_no_mirror(mirror(sci), scr, first_ring = 1, last_ring=ou, mode="H")
# center in SPIDER convention
cnx = old_div(nx, 2) + 1
cny = old_div(ny, 2) + 1
# precalculate rings
numr = Numrinit(first_ring, ou, 1, "H")
wr = ringwe(numr, "H")
crefim = EMAN2_cppwrap.Util.Polar2Dm(scr, cnx, cny, numr, "H")
EMAN2_cppwrap.Util.Frngs(crefim, numr)
EMAN2_cppwrap.Util.Applyws(crefim, numr, wr)
alpha1, sxs, sys, mirr, peak1 = ornq(sci, crefim, [0.0], [0.0], 1.0, "H",
numr, cnx, cny)
alpha2, sxs, sys, mirr, peak2 = ornq(sp_fundamentals.mirror(sci), crefim,
[0.0], [0.0], 1.0, "H", numr, cnx,
cny)
if peak1 > peak2:
mirr = 0
alpha = alpha1
else:
mirr = 1
alpha = -alpha2
nrx = min(2 * (xrng + 1) + 1, ((old_div((nx - 2), 2)) * 2 + 1))
nry = min(2 * (yrng + 1) + 1, ((old_div((ny - 2), 2)) * 2 + 1))
frotim = sp_fundamentals.fft(refim)
ccf1 = EMAN2_cppwrap.Util.window(
sp_fundamentals.ccf(
sp_fundamentals.rot_shift2D(image, alpha, 0.0, 0.0, mirr), frotim),
nrx,
nry,
)
p1 = sp_utilities.peak_search(ccf1)
ccf2 = EMAN2_cppwrap.Util.window(
sp_fundamentals.ccf(
sp_fundamentals.rot_shift2D(image, alpha + 180.0, 0.0, 0.0, mirr),
frotim),
nrx,
nry,
)
p2 = sp_utilities.peak_search(ccf2)
# print p1
# print p2
peak_val1 = p1[0][0]
peak_val2 = p2[0][0]
if peak_val1 > peak_val2:
sxs = -p1[0][4]
sys = -p1[0][5]
cx = int(p1[0][1])
cy = int(p1[0][2])
peak = peak_val1
else:
alpha += 180.0
sxs = -p2[0][4]
sys = -p2[0][5]
peak = peak_val2
cx = int(p2[0][1])
cy = int(p2[0][2])
ccf1 = ccf2
# print cx,cy
z = sp_utilities.model_blank(3, 3)
for i in range(3):
for j in range(3):
z[i, j] = ccf1[i + cx - 1, j + cy - 1]
# print ccf1[cx,cy],z[1,1]
XSH, YSH, PEAKV = parabl(z)
# print sxs, sys, XSH, YSH, PEAKV, peak
if mirr == 1:
sx = -sxs + XSH
else:
sx = sxs - XSH
return alpha, sx, sys - YSH, mirr, PEAKV
def generate_helimic(refvol,
outdir,
pixel,
CTF=False,
Cs=2.0,
voltage=200.0,
ampcont=10.0,
nonoise=False,
rand_seed=14567):
from sp_utilities import model_blank, model_gauss, model_gauss_noise, pad, get_im
from random import random
from sp_projection import prgs, prep_vol
from sp_filter import filt_gaussl, filt_ctf
from EMAN2 import EMAN2Ctf
if os.path.exists(outdir):
ERROR(
"Output directory exists, please change the name and restart the program"
)
return
os.mkdir(outdir)
seed(rand_seed)
Util.set_randnum_seed(rand_seed)
angles = []
for i in range(3):
angles.append([0.0 + 60.0 * i, 90.0 - i * 5, 0.0, 0.0, 0.0])
nangle = len(angles)
volfts = get_im(refvol)
nx = volfts.get_xsize()
ny = volfts.get_ysize()
nz = volfts.get_zsize()
volfts, kbx, kby, kbz = prep_vol(volfts)
iprj = 0
width = 500
xstart = 0
ystart = 0
for idef in range(3, 6):
mic = model_blank(2048, 2048)
#defocus = idef*0.2
defocus = idef * 0.6 ##@ming
if CTF:
#ctf = EMAN2Ctf()
#ctf.from_dict( {"defocus":defocus, "cs":Cs, "voltage":voltage, "apix":pixel, "ampcont":ampcont, "bfactor":0.0} )
from sp_utilities import generate_ctf
ctf = generate_ctf(
[defocus, 2, 200, 1.84, 0.0, ampcont, defocus * 0.2, 80]
) ##@ming the range of astigmatism amplitude is between 10 percent and 22 percent. 20 percent is a good choice.
i = idef - 4
for k in range(1):
psi = 90 + 10 * i
proj = prgs(
volfts, kbz,
[angles[idef - 3][0], angles[idef - 3][1], psi, 0.0, 0.0], kbx,
kby)
proj = Util.window(proj, 320, nz)
mic += pad(proj, 2048, 2048, 1, 0.0, 750 * i, 20 * i, 0)
if not nonoise: mic += model_gauss_noise(30.0, 2048, 2048)
if CTF:
#apply CTF
mic = filt_ctf(mic, ctf)
if not nonoise:
mic += filt_gaussl(model_gauss_noise(17.5, 2048, 2048), 0.3)
mic.write_image("%s/mic%1d.hdf" % (outdir, idef - 3), 0)
def main():
progname = os.path.basename(sys.argv[0])
usage = progname + """ Input Output [options]
Generate three micrographs, each micrograph contains one projection of a long filament.
Input: Reference Volume, output directory
Output: Three micrographs stored in output directory
sxhelical_demo.py tmp.hdf mic --generate_micrograph --CTF --apix=1.84
Generate noisy cylinder ini.hdf with radius 35 pixels and box size 100 by 100 by 200
sxhelical_demo.py ini.hdf --generate_noisycyl --boxsize="100,100,200" --rad=35
Generate rectangular 2D mask mask2d.hdf with width 60 pixels and image size 200 by 200 pixels
sxhelical_demo.py mask2d.hdf --generate_mask --masksize="200,200" --maskwidth=60
Apply the centering parameters to bdb:adata, normalize using average and standard deviation outside the mask, and output the new images to bdb:data
sxhelical_demo.py bdb:adata bdb:data mask2d.hdf --applyparams
Generate run through example script for helicon
sxhelical_demo.py --generate_script --filename=run --seg_ny=180 --ptcl_dist=15 --fract=0.35
"""
parser = OptionParser(usage, version=SPARXVERSION)
# helicise the Atom coordinates
# generate micrographs of helical filament
parser.add_option(
"--generate_micrograph",
action="store_true",
default=False,
help=
"Generate three micrographs where each micrograph contains one projection of a long filament. \n Input: Reference Volume, output directory \n Output: Three micrographs containing helical filament projections stored in output directory"
)
parser.add_option("--CTF",
action="store_true",
default=False,
help="Use CTF correction")
parser.add_option("--apix",
type="float",
default=-1,
help="pixel size in Angstroms")
parser.add_option(
"--rand_seed",
type="int",
default=14567,
help=
"the seed used for generating random numbers (default 14567) for adding noise to the generated micrographs."
)
parser.add_option("--Cs",
type="float",
default=2.0,
help="Microscope Cs (spherical aberation)")
parser.add_option("--voltage",
type="float",
default=200.0,
help="Microscope voltage in KV")
parser.add_option("--ac",
type="float",
default=10.0,
help="Amplitude contrast (percentage, default=10)")
parser.add_option("--nonoise",
action="store_true",
default=False,
help="Do not add noise to the micrograph.")
# generate initial volume
parser.add_option("--generate_noisycyl",
action="store_true",
default=False,
help="Generate initial volume of noisy cylinder.")
parser.add_option(
"--boxsize",
type="string",
default="100,100,200",
help=
"String containing x , y, z dimensions (separated by comma) in pixels")
parser.add_option("--rad",
type="int",
default=35,
help="Radius of initial volume in pixels")
# generate 2D mask
parser.add_option("--generate_mask",
action="store_true",
default=False,
help="Generate 2D rectangular mask.")
parser.add_option(
"--masksize",
type="string",
default="200,200",
help=
"String containing x and y dimensions (separated by comma) in pixels")
parser.add_option("--maskwidth",
type="int",
default=60,
help="Width of rectangular mask")
# Apply 2D alignment parameters to input stack and output new images to output stack
parser.add_option(
"--applyparams",
action="store_true",
default=False,
help=
"Apply the centering parameters to input stack, normalize using average and standard deviation outside the mask, and output the new images to output stack"
)
# Generate run script
parser.add_option("--generate_script",
action="store_true",
default=False,
help="Generate script for helicon run through example")
parser.add_option("--filename",
type="string",
default="runhelicon",
help="Name of run script to generate")
parser.add_option("--seg_ny",
type="int",
default=180,
help="y-dimension of segment used for refinement")
parser.add_option(
"--ptcl_dist",
type="int",
default=15,
help=
"Distance in pixels between adjacent segments windowed from same filament"
)
parser.add_option(
"--fract",
type="float",
default=0.35,
help="Fraction of the volume used for applying helical symmetry.")
(options, args) = parser.parse_args()
if len(args) > 3:
sxprint("usage: " + usage)
sxprint("Please run '" + progname + " -h' for detailed options")
ERROR(
"Invalid number of parameters. Please see usage information above."
)
return
else:
if options.generate_script:
generate_runscript(options.filename, options.seg_ny,
options.ptcl_dist, options.fract)
if options.generate_micrograph:
if options.apix <= 0:
ERROR("Please enter pixel size.")
return
generate_helimic(args[0], args[1], options.apix, options.CTF,
options.Cs, options.voltage, options.ac,
options.nonoise, options.rand_seed)
if options.generate_noisycyl:
from sp_utilities import model_cylinder, model_gauss_noise
outvol = args[0]
boxdims = options.boxsize.split(',')
if len(boxdims) < 1 or len(boxdims) > 3:
ERROR(
"Enter box size as string containing x , y, z dimensions (separated by comma) in pixels. E.g.: --boxsize=\'100,100,200\'"
)
return
nx = int(boxdims[0])
if len(boxdims) == 1:
ny = nx
nz = nx
else:
ny = int(boxdims[1])
if len(boxdims) == 3:
nz = int(boxdims[2])
(model_cylinder(options.rad, nx, ny, nz) *
model_gauss_noise(1.0, nx, ny, nz)).write_image(outvol)
if options.generate_mask:
from sp_utilities import model_blank, pad
outvol = args[0]
maskdims = options.masksize.split(',')
if len(maskdims) < 1 or len(maskdims) > 2:
ERROR(
"Enter box size as string containing x , y dimensions (separated by comma) in pixels. E.g.: --boxsize=\'200,200\'"
)
return
nx = int(maskdims[0])
if len(maskdims) == 1:
ny = nx
else:
ny = int(maskdims[1])
mask = pad(model_blank(options.maskwidth, ny, 1, 1.0), nx, ny, 1,
0.0)
mask.write_image(outvol)
if options.applyparams:
from sp_utilities import get_im, get_params2D, set_params2D
from sp_fundamentals import cyclic_shift
stack = args[0]
newstack = args[1]
mask = get_im(args[2])
nima = EMUtil.get_image_count(stack)
for im in range(nima):
prj = get_im(stack, im)
alpha, sx, sy, mirror, scale = get_params2D(prj)
prj = cyclic_shift(prj, int(sx))
set_params2D(prj, [0.0, 0., 0.0, 0, 1])
stat = Util.infomask(prj, mask, False)
prj = (prj - stat[0]) / stat[1]
ctf_params = prj.get_attr("ctf")
prj.set_attr('ctf_applied', 0)
prj.write_image(newstack, im)
emnumpy2 = EMNumPy()
bigbuffer = emnumpy2.register_numpy_to_emdata(buffer)
# bigbuffer = EMNumPy.numpy2em(buffer)
if (Blockdata["myid_on_node"] == 0):
# read data on process 0 of each node
#print " READING DATA FIRST :",Blockdata["myid"],Blockdata["stack_ali2d"],len(plist)
for i in range(nimastack):
bigbuffer.insert_clip(data[i], (0, 0, i))
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
alldata = [None] * nimastack
emnumpy3 = [None] * nimastack
msk = sp_utilities.model_blank(target_nx, target_nx, 1, 1)
# for i in range(nimastack):
# pointer_location = base_ptr + i*size_of_one_image*disp_unit
# img_buffer = np.frombuffer(np.core.multiarray.int_asbuffer(pointer_location, size_of_one_image*disp_unit), dtype = 'f4')
# img_buffer = img_buffer.reshape(target_nx, target_nx)
# emnumpy3[i] = EMNumPy()
# alldata[i] = emnumpy3[i].register_numpy_to_emdata(img_buffer)
for i in range(nimastack):
newpoint = base_ptr + i * size_of_one_image * disp_unit
pointer_location = ctypes.cast(
newpoint, ctypes.POINTER(ctypes.c_int * size_of_one_image))
img_buffer = numpy.frombuffer(pointer_location.contents, dtype="f4")
img_buffer = img_buffer.reshape(target_nx, target_nx)
emnumpy3[i] = EMNumPy()
alldata[i] = emnumpy3[i].register_numpy_to_emdata(img_buffer)
def main():
progname = os.path.basename(sys.argv[0])
usage = progname + " proj_stack output_averages --MPI"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--img_per_group",
type="int",
default=100,
help="number of images per group")
parser.add_option("--radius",
type="int",
default=-1,
help="radius for alignment")
parser.add_option(
"--xr",
type="string",
default="2 1",
help="range for translation search in x direction, search is +/xr")
parser.add_option(
"--yr",
type="string",
default="-1",
help=
"range for translation search in y direction, search is +/yr (default = same as xr)"
)
parser.add_option(
"--ts",
type="string",
default="1 0.5",
help=
"step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional"
)
parser.add_option(
"--iter",
type="int",
default=30,
help="number of iterations within alignment (default = 30)")
parser.add_option(
"--num_ali",
type="int",
default=5,
help="number of alignments performed for stability (default = 5)")
parser.add_option("--thld_err",
type="float",
default=1.0,
help="threshold of pixel error (default = 1.732)")
parser.add_option(
"--grouping",
type="string",
default="GRP",
help=
"do grouping of projections: PPR - per projection, GRP - different size groups, exclusive (default), GEV - grouping equal size"
)
parser.add_option(
"--delta",
type="float",
default=-1.0,
help="angular step for reference projections (required for GEV method)"
)
parser.add_option(
"--fl",
type="float",
default=0.3,
help="cut-off frequency of hyperbolic tangent low-pass Fourier filter")
parser.add_option(
"--aa",
type="float",
default=0.2,
help="fall-off of hyperbolic tangent low-pass Fourier filter")
parser.add_option("--CTF",
action="store_true",
default=False,
help="Consider CTF correction during the alignment ")
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version")
(options, args) = parser.parse_args()
myid = mpi.mpi_comm_rank(MPI_COMM_WORLD)
number_of_proc = mpi.mpi_comm_size(MPI_COMM_WORLD)
main_node = 0
if len(args) == 2:
stack = args[0]
outdir = args[1]
else:
sp_global_def.ERROR("Incomplete list of arguments",
"sxproj_stability.main",
1,
myid=myid)
return
if not options.MPI:
sp_global_def.ERROR("Non-MPI not supported!",
"sxproj_stability.main",
1,
myid=myid)
return
if sp_global_def.CACHE_DISABLE:
from sp_utilities import disable_bdb_cache
disable_bdb_cache()
sp_global_def.BATCH = True
img_per_grp = options.img_per_group
radius = options.radius
ite = options.iter
num_ali = options.num_ali
thld_err = options.thld_err
xrng = get_input_from_string(options.xr)
if options.yr == "-1":
yrng = xrng
else:
yrng = get_input_from_string(options.yr)
step = get_input_from_string(options.ts)
if myid == main_node:
nima = EMUtil.get_image_count(stack)
img = get_image(stack)
nx = img.get_xsize()
ny = img.get_ysize()
else:
nima = 0
nx = 0
ny = 0
nima = bcast_number_to_all(nima)
nx = bcast_number_to_all(nx)
ny = bcast_number_to_all(ny)
if radius == -1: radius = nx / 2 - 2
mask = model_circle(radius, nx, nx)
st = time()
if options.grouping == "GRP":
if myid == main_node:
sxprint(" A ", myid, " ", time() - st)
proj_attr = EMUtil.get_all_attributes(stack, "xform.projection")
proj_params = []
for i in range(nima):
dp = proj_attr[i].get_params("spider")
phi, theta, psi, s2x, s2y = dp["phi"], dp["theta"], dp[
"psi"], -dp["tx"], -dp["ty"]
proj_params.append([phi, theta, psi, s2x, s2y])
# Here is where the grouping is done, I didn't put enough annotation in the group_proj_by_phitheta,
# So I will briefly explain it here
# proj_list : Returns a list of list of particle numbers, each list contains img_per_grp particle numbers
# except for the last one. Depending on the number of particles left, they will either form a
# group or append themselves to the last group
# angle_list : Also returns a list of list, each list contains three numbers (phi, theta, delta), (phi,
# theta) is the projection angle of the center of the group, delta is the range of this group
# mirror_list: Also returns a list of list, each list contains img_per_grp True or False, which indicates
# whether it should take mirror position.
# In this program angle_list and mirror list are not of interest.
proj_list_all, angle_list, mirror_list = group_proj_by_phitheta(
proj_params, img_per_grp=img_per_grp)
del proj_params
sxprint(" B number of groups ", myid, " ", len(proj_list_all),
time() - st)
mpi_barrier(MPI_COMM_WORLD)
# Number of groups, actually there could be one or two more groups, since the size of the remaining group varies
# we will simply assign them to main node.
n_grp = nima / img_per_grp - 1
# Divide proj_list_all equally to all nodes, and becomes proj_list
proj_list = []
for i in range(n_grp):
proc_to_stay = i % number_of_proc
if proc_to_stay == main_node:
if myid == main_node: proj_list.append(proj_list_all[i])
elif myid == main_node:
mpi_send(len(proj_list_all[i]), 1, MPI_INT, proc_to_stay,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
mpi_send(proj_list_all[i], len(proj_list_all[i]), MPI_INT,
proc_to_stay, SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
elif myid == proc_to_stay:
img_per_grp = mpi_recv(1, MPI_INT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
img_per_grp = int(img_per_grp[0])
temp = mpi_recv(img_per_grp, MPI_INT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
proj_list.append(list(map(int, temp)))
del temp
mpi_barrier(MPI_COMM_WORLD)
sxprint(" C ", myid, " ", time() - st)
if myid == main_node:
# Assign the remaining groups to main_node
for i in range(n_grp, len(proj_list_all)):
proj_list.append(proj_list_all[i])
del proj_list_all, angle_list, mirror_list
# Compute stability per projection projection direction, equal number assigned, thus overlaps
elif options.grouping == "GEV":
if options.delta == -1.0:
ERROR(
"Angular step for reference projections is required for GEV method"
)
return
from sp_utilities import even_angles, nearestk_to_refdir, getvec
refproj = even_angles(options.delta)
img_begin, img_end = MPI_start_end(len(refproj), number_of_proc, myid)
# Now each processor keeps its own share of reference projections
refprojdir = refproj[img_begin:img_end]
del refproj
ref_ang = [0.0] * (len(refprojdir) * 2)
for i in range(len(refprojdir)):
ref_ang[i * 2] = refprojdir[0][0]
ref_ang[i * 2 + 1] = refprojdir[0][1] + i * 0.1
sxprint(" A ", myid, " ", time() - st)
proj_attr = EMUtil.get_all_attributes(stack, "xform.projection")
# the solution below is very slow, do not use it unless there is a problem with the i/O
"""
for i in xrange(number_of_proc):
if myid == i:
proj_attr = EMUtil.get_all_attributes(stack, "xform.projection")
mpi_barrier(MPI_COMM_WORLD)
"""
sxprint(" B ", myid, " ", time() - st)
proj_ang = [0.0] * (nima * 2)
for i in range(nima):
dp = proj_attr[i].get_params("spider")
proj_ang[i * 2] = dp["phi"]
proj_ang[i * 2 + 1] = dp["theta"]
sxprint(" C ", myid, " ", time() - st)
asi = Util.nearestk_to_refdir(proj_ang, ref_ang, img_per_grp)
del proj_ang, ref_ang
proj_list = []
for i in range(len(refprojdir)):
proj_list.append(asi[i * img_per_grp:(i + 1) * img_per_grp])
del asi
sxprint(" D ", myid, " ", time() - st)
#from sys import exit
#exit()
# Compute stability per projection
elif options.grouping == "PPR":
sxprint(" A ", myid, " ", time() - st)
proj_attr = EMUtil.get_all_attributes(stack, "xform.projection")
sxprint(" B ", myid, " ", time() - st)
proj_params = []
for i in range(nima):
dp = proj_attr[i].get_params("spider")
phi, theta, psi, s2x, s2y = dp["phi"], dp["theta"], dp[
"psi"], -dp["tx"], -dp["ty"]
proj_params.append([phi, theta, psi, s2x, s2y])
img_begin, img_end = MPI_start_end(nima, number_of_proc, myid)
sxprint(" C ", myid, " ", time() - st)
from sp_utilities import nearest_proj
proj_list, mirror_list = nearest_proj(
proj_params, img_per_grp,
list(range(img_begin, img_begin + 1))) #range(img_begin, img_end))
refprojdir = proj_params[img_begin:img_end]
del proj_params, mirror_list
sxprint(" D ", myid, " ", time() - st)
else:
ERROR("Incorrect projection grouping option")
return
###########################################################################################################
# Begin stability test
from sp_utilities import get_params_proj, read_text_file
#if myid == 0:
# from utilities import read_text_file
# proj_list[0] = map(int, read_text_file("lggrpp0.txt"))
from sp_utilities import model_blank
aveList = [model_blank(nx, ny)] * len(proj_list)
if options.grouping == "GRP":
refprojdir = [[0.0, 0.0, -1.0]] * len(proj_list)
for i in range(len(proj_list)):
sxprint(" E ", myid, " ", time() - st)
class_data = EMData.read_images(stack, proj_list[i])
#print " R ",myid," ",time()-st
if options.CTF:
from sp_filter import filt_ctf
for im in range(len(class_data)): # MEM LEAK!!
atemp = class_data[im].copy()
btemp = filt_ctf(atemp, atemp.get_attr("ctf"), binary=1)
class_data[im] = btemp
#class_data[im] = filt_ctf(class_data[im], class_data[im].get_attr("ctf"), binary=1)
for im in class_data:
try:
t = im.get_attr(
"xform.align2d") # if they are there, no need to set them!
except:
try:
t = im.get_attr("xform.projection")
d = t.get_params("spider")
set_params2D(im, [0.0, -d["tx"], -d["ty"], 0, 1.0])
except:
set_params2D(im, [0.0, 0.0, 0.0, 0, 1.0])
#print " F ",myid," ",time()-st
# Here, we perform realignment num_ali times
all_ali_params = []
for j in range(num_ali):
if (xrng[0] == 0.0 and yrng[0] == 0.0):
avet = ali2d_ras(class_data,
randomize=True,
ir=1,
ou=radius,
rs=1,
step=1.0,
dst=90.0,
maxit=ite,
check_mirror=True,
FH=options.fl,
FF=options.aa)
else:
avet = within_group_refinement(class_data, mask, True, 1,
radius, 1, xrng, yrng, step,
90.0, ite, options.fl,
options.aa)
ali_params = []
for im in range(len(class_data)):
alpha, sx, sy, mirror, scale = get_params2D(class_data[im])
ali_params.extend([alpha, sx, sy, mirror])
all_ali_params.append(ali_params)
#aveList[i] = avet
#print " G ",myid," ",time()-st
del ali_params
# We determine the stability of this group here.
# stable_set contains all particles deemed stable, it is a list of list
# each list has two elements, the first is the pixel error, the second is the image number
# stable_set is sorted based on pixel error
#from utilities import write_text_file
#write_text_file(all_ali_params, "all_ali_params%03d.txt"%myid)
stable_set, mir_stab_rate, average_pix_err = multi_align_stability(
all_ali_params, 0.0, 10000.0, thld_err, False, 2 * radius + 1)
#print " H ",myid," ",time()-st
if (len(stable_set) > 5):
stable_set_id = []
members = []
pix_err = []
# First put the stable members into attr 'members' and 'pix_err'
for s in stable_set:
# s[1] - number in this subset
stable_set_id.append(s[1])
# the original image number
members.append(proj_list[i][s[1]])
pix_err.append(s[0])
# Then put the unstable members into attr 'members' and 'pix_err'
from sp_fundamentals import rot_shift2D
avet.to_zero()
if options.grouping == "GRP":
aphi = 0.0
atht = 0.0
vphi = 0.0
vtht = 0.0
l = -1
for j in range(len(proj_list[i])):
# Here it will only work if stable_set_id is sorted in the increasing number, see how l progresses
if j in stable_set_id:
l += 1
avet += rot_shift2D(class_data[j], stable_set[l][2][0],
stable_set[l][2][1],
stable_set[l][2][2],
stable_set[l][2][3])
if options.grouping == "GRP":
phi, theta, psi, sxs, sy_s = get_params_proj(
class_data[j])
if (theta > 90.0):
phi = (phi + 540.0) % 360.0
theta = 180.0 - theta
aphi += phi
atht += theta
vphi += phi * phi
vtht += theta * theta
else:
members.append(proj_list[i][j])
pix_err.append(99999.99)
aveList[i] = avet.copy()
if l > 1:
l += 1
aveList[i] /= l
if options.grouping == "GRP":
aphi /= l
atht /= l
vphi = (vphi - l * aphi * aphi) / l
vtht = (vtht - l * atht * atht) / l
from math import sqrt
refprojdir[i] = [
aphi, atht,
(sqrt(max(vphi, 0.0)) + sqrt(max(vtht, 0.0))) / 2.0
]
# Here more information has to be stored, PARTICULARLY WHAT IS THE REFERENCE DIRECTION
aveList[i].set_attr('members', members)
aveList[i].set_attr('refprojdir', refprojdir[i])
aveList[i].set_attr('pixerr', pix_err)
else:
sxprint(" empty group ", i, refprojdir[i])
aveList[i].set_attr('members', [-1])
aveList[i].set_attr('refprojdir', refprojdir[i])
aveList[i].set_attr('pixerr', [99999.])
del class_data
if myid == main_node:
km = 0
for i in range(number_of_proc):
if i == main_node:
for im in range(len(aveList)):
aveList[im].write_image(args[1], km)
km += 1
else:
nl = mpi_recv(1, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL,
MPI_COMM_WORLD)
nl = int(nl[0])
for im in range(nl):
ave = recv_EMData(i, im + i + 70000)
nm = mpi_recv(1, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL,
MPI_COMM_WORLD)
nm = int(nm[0])
members = mpi_recv(nm, MPI_INT, i, SPARX_MPI_TAG_UNIVERSAL,
MPI_COMM_WORLD)
ave.set_attr('members', list(map(int, members)))
members = mpi_recv(nm, MPI_FLOAT, i,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
ave.set_attr('pixerr', list(map(float, members)))
members = mpi_recv(3, MPI_FLOAT, i,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
ave.set_attr('refprojdir', list(map(float, members)))
ave.write_image(args[1], km)
km += 1
else:
mpi_send(len(aveList), 1, MPI_INT, main_node, SPARX_MPI_TAG_UNIVERSAL,
MPI_COMM_WORLD)
for im in range(len(aveList)):
send_EMData(aveList[im], main_node, im + myid + 70000)
members = aveList[im].get_attr('members')
mpi_send(len(members), 1, MPI_INT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
mpi_send(members, len(members), MPI_INT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
members = aveList[im].get_attr('pixerr')
mpi_send(members, len(members), MPI_FLOAT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
try:
members = aveList[im].get_attr('refprojdir')
mpi_send(members, 3, MPI_FLOAT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
except:
mpi_send([-999.0, -999.0, -999.0], 3, MPI_FLOAT, main_node,
SPARX_MPI_TAG_UNIVERSAL, MPI_COMM_WORLD)
sp_global_def.BATCH = False
mpi_barrier(MPI_COMM_WORLD)
def cml_open_proj(stack, ir, ou, lf, hf, dpsi=1):
from sp_projection import cml_sinogram
from sp_utilities import model_circle, get_params_proj, model_blank, get_im
from sp_fundamentals import fftip
from sp_filter import filt_tanh
# number of projections
if type(stack) == type(""): nprj = EMUtil.get_image_count(stack)
else: nprj = len(stack)
Prj = [] # list of projections
Ori = [
-1
] * 4 * nprj # orientation intial (phi, theta, psi, index) for each projection
for i in range(nprj):
image = get_im(stack, i)
# read initial angles if given
try:
Ori[4 * i], Ori[4 * i +
1], Ori[4 * i +
2], s2x, s2y = get_params_proj(image)
except:
pass
if (i == 0):
nx = image.get_xsize()
if (ou < 1): ou = nx // 2 - 1
diameter = int(2 * ou)
mask2D = model_circle(ou, nx, nx)
if ir > 0: mask2D -= model_circle(ir, nx, nx)
# normalize under the mask
[mean_a, sigma, imin, imax] = Util.infomask(image, mask2D, True)
image -= mean_a
Util.mul_scalar(image, 1.0 / sigma)
Util.mul_img(image, mask2D)
# sinogram
sino = cml_sinogram(image, diameter, dpsi)
# prepare the cut positions in order to filter (lf: low freq; hf: high freq)
ihf = min(int(2 * hf * diameter), diameter + (diameter + 1) % 2)
ihf = ihf + (ihf + 1) % 2 # index ihf must be odd to take the img part
ilf = max(int(2 * lf * diameter), 0)
ilf = ilf + ilf % 2 # index ilf must be even to fall in the real part
bdf = ihf - ilf + 1
# process lines
nxe = sino.get_xsize()
nye = sino.get_ysize()
prj = model_blank(bdf, 2 * nye)
pp = model_blank(nxe, 2 * nye)
for li in range(nye):
# get the line li
line = Util.window(sino, nxe, 1, 1, 0, li - nye // 2, 0)
# u2 (not improve the results)
#line = filt_tanh(line, ou / float(nx), ou / float(nx))
# normalize this line
[mean_l, sigma_l, imin, imax] = Util.infomask(line, None, True)
line = (line - mean_l) / sigma_l
# fft
fftip(line)
# filter (cut part of coef) and create mirror line
Util.cml_prepare_line(prj, line, ilf, ihf, li, nye)
# store the projection
Prj.append(prj)
return Prj, Ori
def helicalshiftali_MPI(stack,
maskfile=None,
maxit=100,
CTF=False,
snr=1.0,
Fourvar=False,
search_rng=-1):
nproc = mpi.mpi_comm_size(mpi.MPI_COMM_WORLD)
myid = mpi.mpi_comm_rank(mpi.MPI_COMM_WORLD)
main_node = 0
ftp = file_type(stack)
if myid == main_node:
print_begin_msg("helical-shiftali_MPI")
max_iter = int(maxit)
if (myid == main_node):
infils = EMUtil.get_all_attributes(stack, "filament")
ptlcoords = EMUtil.get_all_attributes(stack, 'ptcl_source_coord')
filaments = ordersegments(infils, ptlcoords)
total_nfils = len(filaments)
inidl = [0] * total_nfils
for i in range(total_nfils):
inidl[i] = len(filaments[i])
linidl = sum(inidl)
nima = linidl
tfilaments = []
for i in range(total_nfils):
tfilaments += filaments[i]
del filaments
else:
total_nfils = 0
linidl = 0
total_nfils = bcast_number_to_all(total_nfils, source_node=main_node)
if myid != main_node:
inidl = [-1] * total_nfils
inidl = bcast_list_to_all(inidl, myid, source_node=main_node)
linidl = bcast_number_to_all(linidl, source_node=main_node)
if myid != main_node:
tfilaments = [-1] * linidl
tfilaments = bcast_list_to_all(tfilaments, myid, source_node=main_node)
filaments = []
iendi = 0
for i in range(total_nfils):
isti = iendi
iendi = isti + inidl[i]
filaments.append(tfilaments[isti:iendi])
del tfilaments, inidl
if myid == main_node:
print_msg("total number of filaments: %d" % total_nfils)
if total_nfils < nproc:
ERROR(
'number of CPUs (%i) is larger than the number of filaments (%i), please reduce the number of CPUs used'
% (nproc, total_nfils),
myid=myid)
# balanced load
temp = chunks_distribution([[len(filaments[i]), i]
for i in range(len(filaments))],
nproc)[myid:myid + 1][0]
filaments = [filaments[temp[i][1]] for i in range(len(temp))]
nfils = len(filaments)
#filaments = [[0,1]]
#print "filaments",filaments
list_of_particles = []
indcs = []
k = 0
for i in range(nfils):
list_of_particles += filaments[i]
k1 = k + len(filaments[i])
indcs.append([k, k1])
k = k1
data = EMData.read_images(stack, list_of_particles)
ldata = len(data)
sxprint("ldata=", ldata)
nx = data[0].get_xsize()
ny = data[0].get_ysize()
if maskfile == None:
mrad = min(nx, ny) // 2 - 2
mask = pad(model_blank(2 * mrad + 1, ny, 1, 1.0), nx, ny, 1, 0.0)
else:
mask = get_im(maskfile)
# apply initial xform.align2d parameters stored in header
init_params = []
for im in range(ldata):
t = data[im].get_attr('xform.align2d')
init_params.append(t)
p = t.get_params("2d")
data[im] = rot_shift2D(data[im], p['alpha'], p['tx'], p['ty'],
p['mirror'], p['scale'])
if CTF:
from sp_filter import filt_ctf
from sp_morphology import ctf_img
ctf_abs_sum = EMData(nx, ny, 1, False)
ctf_2_sum = EMData(nx, ny, 1, False)
else:
ctf_2_sum = None
ctf_abs_sum = None
from sp_utilities import info
for im in range(ldata):
data[im].set_attr('ID', list_of_particles[im])
st = Util.infomask(data[im], mask, False)
data[im] -= st[0]
if CTF:
ctf_params = data[im].get_attr("ctf")
qctf = data[im].get_attr("ctf_applied")
if qctf == 0:
data[im] = filt_ctf(fft(data[im]), ctf_params)
data[im].set_attr('ctf_applied', 1)
elif qctf != 1:
ERROR('Incorrectly set qctf flag', myid=myid)
ctfimg = ctf_img(nx, ctf_params, ny=ny)
Util.add_img2(ctf_2_sum, ctfimg)
Util.add_img_abs(ctf_abs_sum, ctfimg)
else:
data[im] = fft(data[im])
del list_of_particles
if CTF:
reduce_EMData_to_root(ctf_2_sum, myid, main_node)
reduce_EMData_to_root(ctf_abs_sum, myid, main_node)
if CTF:
if myid != main_node:
del ctf_2_sum
del ctf_abs_sum
else:
temp = EMData(nx, ny, 1, False)
tsnr = 1. / snr
for i in range(0, nx + 2, 2):
for j in range(ny):
temp.set_value_at(i, j, tsnr)
temp.set_value_at(i + 1, j, 0.0)
#info(ctf_2_sum)
Util.add_img(ctf_2_sum, temp)
#info(ctf_2_sum)
del temp
total_iter = 0
shift_x = [0.0] * ldata
for Iter in range(max_iter):
if myid == main_node:
start_time = time()
print_msg("Iteration #%4d\n" % (total_iter))
total_iter += 1
avg = EMData(nx, ny, 1, False)
for im in range(ldata):
Util.add_img(avg, fshift(data[im], shift_x[im]))
reduce_EMData_to_root(avg, myid, main_node)
if myid == main_node:
if CTF: tavg = Util.divn_filter(avg, ctf_2_sum)
else: tavg = Util.mult_scalar(avg, 1.0 / float(nima))
else:
tavg = model_blank(nx, ny)
if Fourvar:
bcast_EMData_to_all(tavg, myid, main_node)
vav, rvar = varf2d_MPI(myid, data, tavg, mask, "a", CTF)
if myid == main_node:
if Fourvar:
tavg = fft(Util.divn_img(fft(tavg), vav))
vav_r = Util.pack_complex_to_real(vav)
# normalize and mask tavg in real space
tavg = fft(tavg)
stat = Util.infomask(tavg, mask, False)
tavg -= stat[0]
Util.mul_img(tavg, mask)
tavg.write_image("tavg.hdf", Iter)
# For testing purposes: shift tavg to some random place and see if the centering is still correct
#tavg = rot_shift3D(tavg,sx=3,sy=-4)
if Fourvar: del vav
bcast_EMData_to_all(tavg, myid, main_node)
tavg = fft(tavg)
sx_sum = 0.0
nxc = nx // 2
for ifil in range(nfils):
"""
# Calculate filament average
avg = EMData(nx, ny, 1, False)
filnima = 0
for im in xrange(indcs[ifil][0], indcs[ifil][1]):
Util.add_img(avg, data[im])
filnima += 1
tavg = Util.mult_scalar(avg, 1.0/float(filnima))
"""
# Calculate 1D ccf between each segment and filament average
nsegms = indcs[ifil][1] - indcs[ifil][0]
ctx = [None] * nsegms
pcoords = [None] * nsegms
for im in range(indcs[ifil][0], indcs[ifil][1]):
ctx[im - indcs[ifil][0]] = Util.window(ccf(tavg, data[im]), nx,
1)
pcoords[im - indcs[ifil][0]] = data[im].get_attr(
'ptcl_source_coord')
#ctx[im-indcs[ifil][0]].write_image("ctx.hdf",im-indcs[ifil][0])
#print " CTX ",myid,im,Util.infomask(ctx[im-indcs[ifil][0]], None, True)
# search for best x-shift
cents = nsegms // 2
dst = sqrt(
max((pcoords[cents][0] - pcoords[0][0])**2 +
(pcoords[cents][1] - pcoords[0][1])**2,
(pcoords[cents][0] - pcoords[-1][0])**2 +
(pcoords[cents][1] - pcoords[-1][1])**2))
maxincline = atan2(ny // 2 - 2 - float(search_rng), dst)
kang = int(dst * tan(maxincline) + 0.5)
#print " settings ",nsegms,cents,dst,search_rng,maxincline,kang
# ## C code for alignment. @ming
results = [0.0] * 3
results = Util.helixshiftali(ctx, pcoords, nsegms, maxincline,
kang, search_rng, nxc)
sib = int(results[0])
bang = results[1]
qm = results[2]
#print qm, sib, bang
# qm = -1.e23
#
# for six in xrange(-search_rng, search_rng+1,1):
# q0 = ctx[cents].get_value_at(six+nxc)
# for incline in xrange(kang+1):
# qt = q0
# qu = q0
# if(kang>0): tang = tan(maxincline/kang*incline)
# else: tang = 0.0
# for kim in xrange(cents+1,nsegms):
# dst = sqrt((pcoords[cents][0] - pcoords[kim][0])**2 + (pcoords[cents][1] - pcoords[kim][1])**2)
# xl = dst*tang+six+nxc
# ixl = int(xl)
# dxl = xl - ixl
# #print " A ", ifil,six,incline,kim,xl,ixl,dxl
# qt += (1.0-dxl)*ctx[kim].get_value_at(ixl) + dxl*ctx[kim].get_value_at(ixl+1)
# xl = -dst*tang+six+nxc
# ixl = int(xl)
# dxl = xl - ixl
# qu += (1.0-dxl)*ctx[kim].get_value_at(ixl) + dxl*ctx[kim].get_value_at(ixl+1)
# for kim in xrange(cents):
# dst = sqrt((pcoords[cents][0] - pcoords[kim][0])**2 + (pcoords[cents][1] - pcoords[kim][1])**2)
# xl = -dst*tang+six+nxc
# ixl = int(xl)
# dxl = xl - ixl
# qt += (1.0-dxl)*ctx[kim].get_value_at(ixl) + dxl*ctx[kim].get_value_at(ixl+1)
# xl = dst*tang+six+nxc
# ixl = int(xl)
# dxl = xl - ixl
# qu += (1.0-dxl)*ctx[kim].get_value_at(ixl) + dxl*ctx[kim].get_value_at(ixl+1)
# if( qt > qm ):
# qm = qt
# sib = six
# bang = tang
# if( qu > qm ):
# qm = qu
# sib = six
# bang = -tang
#if incline == 0: print "incline = 0 ",six,tang,qt,qu
#print qm,six,sib,bang
#print " got results ",indcs[ifil][0], indcs[ifil][1], ifil,myid,qm,sib,tang,bang,len(ctx),Util.infomask(ctx[0], None, True)
for im in range(indcs[ifil][0], indcs[ifil][1]):
kim = im - indcs[ifil][0]
dst = sqrt((pcoords[cents][0] - pcoords[kim][0])**2 +
(pcoords[cents][1] - pcoords[kim][1])**2)
if (kim < cents): xl = -dst * bang + sib
else: xl = dst * bang + sib
shift_x[im] = xl
# Average shift
sx_sum += shift_x[indcs[ifil][0] + cents]
# #print myid,sx_sum,total_nfils
sx_sum = mpi.mpi_reduce(sx_sum, 1, mpi.MPI_FLOAT, mpi.MPI_SUM,
main_node, mpi.MPI_COMM_WORLD)
if myid == main_node:
sx_sum = float(sx_sum[0]) / total_nfils
print_msg("Average shift %6.2f\n" % (sx_sum))
else:
sx_sum = 0.0
sx_sum = 0.0
sx_sum = bcast_number_to_all(sx_sum, source_node=main_node)
for im in range(ldata):
shift_x[im] -= sx_sum
#print " %3d %6.3f"%(im,shift_x[im])
#exit()
# combine shifts found with the original parameters
for im in range(ldata):
t1 = Transform()
##import random
##shix=random.randint(-10, 10)
##t1.set_params({"type":"2D","tx":shix})
t1.set_params({"type": "2D", "tx": shift_x[im]})
# combine t0 and t1
tt = t1 * init_params[im]
data[im].set_attr("xform.align2d", tt)
# write out headers and STOP, under MPI writing has to be done sequentially
mpi.mpi_barrier(mpi.MPI_COMM_WORLD)
par_str = ["xform.align2d", "ID"]
if myid == main_node:
from sp_utilities import file_type
if (file_type(stack) == "bdb"):
from sp_utilities import recv_attr_dict_bdb
recv_attr_dict_bdb(main_node, stack, data, par_str, 0, ldata,
nproc)
else:
from sp_utilities import recv_attr_dict
recv_attr_dict(main_node, stack, data, par_str, 0, ldata, nproc)
else:
send_attr_dict(main_node, data, par_str, 0, ldata)
if myid == main_node: print_end_msg("helical-shiftali_MPI")
def main():
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage = progname + """ firstvolume secondvolume maskfile directory --prefix --wn --step --cutoff --radius --fsc --res_overall --out_ang_res --apix --MPI
Compute local resolution in real space within area outlined by the maskfile and within regions wn x wn x wn
"""
parser = optparse.OptionParser(usage, version=sp_global_def.SPARXVERSION)
parser.add_option("--prefix",
type="str",
default='localres',
help="Prefix for the output files. (default localres)")
parser.add_option(
"--wn",
type="int",
default=7,
help=
"Size of window within which local real-space FSC is computed. (default 7)"
)
parser.add_option(
"--step",
type="float",
default=1.0,
help="Shell step in Fourier size in pixels. (default 1.0)")
parser.add_option("--cutoff",
type="float",
default=0.143,
help="Resolution cut-off for FSC. (default 0.143)")
parser.add_option(
"--radius",
type="int",
default=-1,
help=
"If there is no maskfile, sphere with r=radius will be used. By default, the radius is nx/2-wn (default -1)"
)
parser.add_option(
"--fsc",
type="string",
default=None,
help=
"Save overall FSC curve (might be truncated). By default, the program does not save the FSC curve. (default none)"
)
parser.add_option(
"--res_overall",
type="float",
default=-1.0,
help=
"Overall resolution at the cutoff level estimated by the user [abs units]. (default None)"
)
parser.add_option(
"--out_ang_res",
action="store_true",
default=False,
help=
"Additionally creates a local resolution file in Angstroms. (default False)"
)
parser.add_option(
"--apix",
type="float",
default=1.0,
help=
"Pixel size in Angstrom. Effective only with --out_ang_res options. (default 1.0)"
)
parser.add_option("--MPI",
action="store_true",
default=False,
help="Use MPI version.")
(options, args) = parser.parse_args(arglist[1:])
if len(args) < 3 or len(args) > 4:
sxprint("Usage: " + usage)
ERROR(
"Invalid number of parameters used. Please see usage information above."
)
return
if sp_global_def.CACHE_DISABLE:
sp_utilities.disable_bdb_cache()
res_overall = options.res_overall
if options.MPI:
number_of_proc = mpi.mpi_comm_size(mpi.MPI_COMM_WORLD)
myid = mpi.mpi_comm_rank(mpi.MPI_COMM_WORLD)
main_node = 0
sp_global_def.MPI = True
cutoff = options.cutoff
nk = int(options.wn)
if (myid == main_node):
#print sys.argv
vi = sp_utilities.get_im(sys.argv[1])
ui = sp_utilities.get_im(sys.argv[2])
nx = vi.get_xsize()
ny = vi.get_ysize()
nz = vi.get_zsize()
dis = [nx, ny, nz]
else:
dis = [0, 0, 0, 0]
sp_global_def.BATCH = True
dis = sp_utilities.bcast_list_to_all(dis, myid, source_node=main_node)
if (myid != main_node):
nx = int(dis[0])
ny = int(dis[1])
nz = int(dis[2])
vi = sp_utilities.model_blank(nx, ny, nz)
ui = sp_utilities.model_blank(nx, ny, nz)
if len(args) == 3:
m = sp_utilities.model_circle((min(nx, ny, nz) - nk) // 2, nx, ny,
nz)
outdir = args[2]
elif len(args) == 4:
if (myid == main_node):
m = sp_morphology.binarize(sp_utilities.get_im(args[2]), 0.5)
else:
m = sp_utilities.model_blank(nx, ny, nz)
outdir = args[3]
if os.path.exists(outdir) and myid == 0:
sp_global_def.ERROR('Output directory already exists!')
elif myid == 0:
os.makedirs(outdir)
sp_global_def.write_command(outdir)
sp_utilities.bcast_EMData_to_all(m, myid, main_node)
"""Multiline Comment0"""
freqvol, resolut = sp_statistics.locres(vi, ui, m, nk, cutoff,
options.step, myid, main_node,
number_of_proc)
if (myid == 0):
# Remove outliers based on the Interquartile range
output_volume(freqvol, resolut, options.apix, outdir,
options.prefix, options.fsc, options.out_ang_res, nx,
ny, nz, res_overall)
else:
cutoff = options.cutoff
vi = sp_utilities.get_im(args[0])
ui = sp_utilities.get_im(args[1])
nn = vi.get_xsize()
nx = nn
ny = nn
nz = nn
nk = int(options.wn)
if len(args) == 3:
m = sp_utilities.model_circle((nn - nk) // 2, nn, nn, nn)
outdir = args[2]
elif len(args) == 4:
m = sp_morphology.binarize(sp_utilities.get_im(args[2]), 0.5)
outdir = args[3]
if os.path.exists(outdir):
sp_global_def.ERROR('Output directory already exists!')
else:
os.makedirs(outdir)
sp_global_def.write_command(outdir)
mc = sp_utilities.model_blank(nn, nn, nn, 1.0) - m
vf = sp_fundamentals.fft(vi)
uf = sp_fundamentals.fft(ui)
"""Multiline Comment1"""
lp = int(nn / 2 / options.step + 0.5)
step = 0.5 / lp
freqvol = sp_utilities.model_blank(nn, nn, nn)
resolut = []
for i in range(1, lp):
fl = step * i
fh = fl + step
#print(lp,i,step,fl,fh)
v = sp_fundamentals.fft(sp_filter.filt_tophatb(vf, fl, fh))
u = sp_fundamentals.fft(sp_filter.filt_tophatb(uf, fl, fh))
tmp1 = EMAN2_cppwrap.Util.muln_img(v, v)
tmp2 = EMAN2_cppwrap.Util.muln_img(u, u)
do = EMAN2_cppwrap.Util.infomask(
sp_morphology.square_root(
sp_morphology.threshold(
EMAN2_cppwrap.Util.muln_img(tmp1, tmp2))), m, True)[0]
tmp3 = EMAN2_cppwrap.Util.muln_img(u, v)
dp = EMAN2_cppwrap.Util.infomask(tmp3, m, True)[0]
resolut.append([i, (fl + fh) / 2.0, dp / do])
tmp1 = EMAN2_cppwrap.Util.box_convolution(tmp1, nk)
tmp2 = EMAN2_cppwrap.Util.box_convolution(tmp2, nk)
tmp3 = EMAN2_cppwrap.Util.box_convolution(tmp3, nk)
EMAN2_cppwrap.Util.mul_img(tmp1, tmp2)
tmp1 = sp_morphology.square_root(sp_morphology.threshold(tmp1))
EMAN2_cppwrap.Util.mul_img(tmp1, m)
EMAN2_cppwrap.Util.add_img(tmp1, mc)
EMAN2_cppwrap.Util.mul_img(tmp3, m)
EMAN2_cppwrap.Util.add_img(tmp3, mc)
EMAN2_cppwrap.Util.div_img(tmp3, tmp1)
EMAN2_cppwrap.Util.mul_img(tmp3, m)
freq = (fl + fh) / 2.0
bailout = True
for x in range(nn):
for y in range(nn):
for z in range(nn):
if (m.get_value_at(x, y, z) > 0.5):
if (freqvol.get_value_at(x, y, z) == 0.0):
if (tmp3.get_value_at(x, y, z) < cutoff):
freqvol.set_value_at(x, y, z, freq)
bailout = False
else:
bailout = False
if (bailout): break
#print(len(resolut))
# remove outliers
output_volume(freqvol, resolut, options.apix, outdir, options.prefix,
options.fsc, options.out_ang_res, nx, ny, nz,
res_overall)