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_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_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