def test_stack_substack(self):
# img = EMAN2db.EMData()
# EMAN2db.db_read_image(img, "bdb:/home/adnan/DemoResults/06_SUBSTACK_ANO#isac_substack",0 )
# img1 = EMAN2db.db_read_images("bdb:/home/adnan/DemoResults/06_SUBSTACK_ANO#isac_substack")
# print(img1[0].get_2dview())
e = EMAN2_cppwrap.EMData()
e.read_image("bdb:/home/adnan/DemoResults/04_ISAC#stack_ali2d", 5)
d = EMAN2_cppwrap.EMData()
d.read_image("bdb:/home/adnan/DemoResults/04_ISAC#case4stack", 5)
img = EMAN2db.EMData.read_images(
"bdb:/home/adnan/DemoResults/04_ISAC#case4stack")
self.assertTrue(numpy.array_equal(e.get_2dview(), d.get_2dview()))
self.assertTrue(numpy.array_equal(img[5].get_2dview(), d.get_2dview()))
def max_3D_pixel_error(t1, t2, r=1.0):
"""
Compute maximum pixel error between two sets of orientation parameters
assuming object has radius r, t1 is the projection transformation
of the first projection and t2 of the second one, respectively:
t = Transform({"type":"spider","phi":phi,"theta":theta,"psi":psi})
t.set_trans(Vec2f(-tx, -ty))
Note the function is symmetric in t1, t2.
"""
pass #IMPORTIMPORTIMPORT from EMAN2 import Vec2f
pass #IMPORTIMPORTIMPORT import types
dummy = EMAN2_cppwrap.Transform()
if (type(dummy) != type(t1)):
t = EMAN2_cppwrap.Transform({
"type": "spider",
"phi": t1[0],
"theta": t1[1],
"psi": t1[2]
})
t.set_trans(EMAN2_cppwrap.Vec2f(-t1[3], -t1[4]))
else:
t = t1
if (type(dummy) != type(t2)):
u = EMAN2_cppwrap.Transform({
"type": "spider",
"phi": t2[0],
"theta": t2[1],
"psi": t2[2]
})
u.set_trans(EMAN2_cppwrap.Vec2f(-t2[3], -t2[4]))
else:
u = t2
return EMAN2_cppwrap.EMData().max_3D_pixel_error(t, u, r)
def import_particle_stack(particle_stack, output_dir):
"""
Import the particle stack.
Arguments:
particle_stack - Path to the particle stack
Returns:
Particle array
"""
particle_header = EMAN2_cppwrap.EMData()
particle_header.read_image(
particle_stack,
0,
True
)
dtype_list, name_list = create_stack_dtype(particle_header.get_attr_dict())
header_dict = {}
for name in name_list:
header_dict[name] = np.array(EMAN2_cppwrap.EMUtil.get_all_attributes(particle_stack, name))
stack_array, create_stack = create_stack_array(dtype_list, header_dict, output_dir)
return stack_array, create_stack
def create_particle_stack(particle_stack, output_dir, particle_data):
"""
Create a mrcs particle stack based on the bdb/hdf input stack.
Arguments:
particle_stack - Particle stack name
output_dir - Output directory
particle_data - Particle_data array
Returns:
None
"""
print('|_Get particle ID and particle names')
ptcl_ids = [int(entry.split('@')[0]) for entry in particle_data['_rlnImageName']]
ptcl_names = [entry.split('@')[1] for entry in particle_data['_rlnImageName']]
print('|_Write images')
for particle_idx in range(particle_data.shape[0]):
if particle_idx % 10000 == 0:
print(particle_idx, ' of ', particle_data.shape[0])
emdata = EMAN2_cppwrap.EMData(particle_stack, particle_idx)
output_name = os.path.join(output_dir, ptcl_names[particle_idx])
try:
os.makedirs(os.path.dirname(output_name))
except OSError:
pass
emdata.write_image(output_name, -1)
def create_particle_stack(particle_stack, output_dir, particle_data):
"""
Create a mrcs particle stack based on the bdb/hdf input stack.
Arguments:
particle_stack - Particle stack name
output_dir - Output directory
particle_data - Particle_data array
Returns:
None
"""
sp_global_def.sxprint("|_Get particle ID and particle names")
ptcl_names = [entry.split("@")[1] for entry in particle_data["_rlnImageName"]]
sp_global_def.sxprint("|_Write images")
for particle_idx in range(particle_data.shape[0]):
if particle_idx % 10000 == 0:
sp_global_def.sxprint(particle_idx, " of ", particle_data.shape[0])
emdata = EMAN2_cppwrap.EMData(particle_stack, particle_idx)
output_name = os.path.join(output_dir, "Particles", os.path.basename(ptcl_names[particle_idx]))
try:
os.makedirs(os.path.dirname(output_name))
except OSError:
pass
emdata.write_image(output_name, -1)
def import_particle_stack(particle_stack, output_dir, project_dir):
"""
Import the particle stack.
Arguments:
particle_stack - Path to the particle stack
Returns:
Particle array
"""
particle_header = EMAN2_cppwrap.EMData()
particle_header.read_image(particle_stack, 0, True)
dtype_list, name_list = create_stack_dtype(particle_header.get_attr_dict())
new_header = sp_utilities.make_v_stack_header(particle_stack, project_dir)
header_dict = {}
for name in name_list:
for entry in new_header:
header_dict.setdefault(name, []).append(entry[name])
for key in header_dict:
header_dict[key] = np.array(header_dict[key])
stack_array, create_stack = create_stack_array(dtype_list, header_dict,
output_dir, project_dir)
return stack_array, create_stack
def prepare_refrings(
volft,
kb,
nz=-1,
delta=2.0,
ref_a="P",
sym="c1",
numr=None,
MPI=False,
phiEqpsi="Zero",
kbx=None,
kby=None,
initial_theta=None,
delta_theta=None,
initial_phi=None,
):
"""
Generate quasi-evenly distributed reference projections converted to rings
ref_a can be a list of angles, in which case it is used instead of being generated
"""
# mpi communicator can be sent by the MPI parameter
if type(MPI) is bool:
if MPI:
mpi_comm = mpi.MPI_COMM_WORLD
else:
mpi_comm = MPI
MPI = True
mode = "F"
if type(ref_a) is list:
# if ref_a is list, it has to be a list of projection directions, use it
ref_angles = ref_a
else:
# generate list of Eulerian angles for reference projections
# phi, theta, psi
if initial_theta and initial_phi:
ref_angles = sp_utilities.even_angles(
delta,
theta1=initial_theta,
phi1=initial_phi,
symmetry=sym,
method=ref_a,
phiEqpsi=phiEqpsi,
)
else:
if initial_theta is None:
if sym[:1] == "c" or sym[:1] == "d":
ref_angles = sp_utilities.even_angles(
delta, symmetry=sym, method=ref_a, phiEqpsi=phiEqpsi
)
else:
psp = sp_fundamentals.symclass(sym)
ref_angles = psp.even_angles(delta)
del psp
else:
if delta_theta is None:
delta_theta = 1.0
ref_angles = sp_utilities.even_angles(
delta,
theta1=initial_theta,
theta2=delta_theta,
symmetry=sym,
method=ref_a,
phiEqpsi=phiEqpsi,
)
wr_four = ringwe(numr, mode)
cnx = old_div(nz, 2) + 1
cny = old_div(nz, 2) + 1
num_ref = len(ref_angles)
if MPI:
myid = mpi.mpi_comm_rank(mpi_comm)
ncpu = mpi.mpi_comm_size(mpi_comm)
else:
ncpu = 1
myid = 0
if nz < 1:
sp_global_def.ERROR(
"Data size has to be given (nz)", "prepare_refrings", 1, myid
)
ref_start, ref_end = sp_applications.MPI_start_end(num_ref, ncpu, myid)
refrings = (
[]
) # list of (image objects) reference projections in Fourier representation
sizex = numr[len(numr) - 2] + numr[len(numr) - 1] - 1
for i in range(num_ref):
prjref = EMAN2_cppwrap.EMData()
prjref.set_size(sizex, 1, 1)
refrings.append(prjref)
if kbx is None:
for i in range(ref_start, ref_end):
prjref = sp_projection.prgs(
volft,
kb,
[ref_angles[i][0], ref_angles[i][1], ref_angles[i][2], 0.0, 0.0],
)
cimage = EMAN2_cppwrap.Util.Polar2Dm(
prjref, cnx, cny, numr, mode
) # currently set to quadratic....
EMAN2_cppwrap.Util.Normalize_ring(cimage, numr, 0)
EMAN2_cppwrap.Util.Frngs(cimage, numr)
EMAN2_cppwrap.Util.Applyws(cimage, numr, wr_four)
refrings[i] = cimage
else:
for i in range(ref_start, ref_end):
prjref = sp_projection.prgs(
volft,
kb,
[ref_angles[i][0], ref_angles[i][1], ref_angles[i][2], 0.0, 0.0],
kbx,
kby,
)
cimage = EMAN2_cppwrap.Util.Polar2Dm(
prjref, cnx, cny, numr, mode
) # currently set to quadratic....
EMAN2_cppwrap.Util.Normalize_ring(cimage, numr, 0)
EMAN2_cppwrap.Util.Frngs(cimage, numr)
EMAN2_cppwrap.Util.Applyws(cimage, numr, wr_four)
refrings[i] = cimage
if MPI:
sp_utilities.bcast_compacted_EMData_all_to_all(refrings, myid, comm=mpi_comm)
for i in range(len(ref_angles)):
n1, n2, n3 = sp_utilities.getfvec(ref_angles[i][0], ref_angles[i][1])
refrings[i].set_attr_dict(
{
"phi": ref_angles[i][0],
"theta": ref_angles[i][1],
"psi": ref_angles[i][2],
"n1": n1,
"n2": n2,
"n3": n3,
}
)
return refrings
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(
stack_name,
list_proj=[],
symmetry="c1",
npad=4,
snr=None,
weighting=1,
varsnr=False,
xysize=-1,
zsize=-1,
):
"""
Perform a 3-D reconstruction using Pawel's FFT Back Projection algorithm.
Input:
stack_name - name of the file with projection data.
list_proj - list of projections to be used in the reconstruction
symmetry - Point group of the target molecule (defaults to "C1")
npad -
Angles and shifts are passed in the file header as set_attr. Keywords are phi, theta, psi, sx, sy
Return: 3D reconstructed volume image
Usage:
vol = recons3d_4nn(filepattern, list_proj, symmetry)
"""
if list_proj == []:
if type(stack_name) == bytes:
nima = EMAN2_cppwrap.EMUtil.get_image_count(stack_name)
else:
nima = len(stack_name)
list_proj = list(range(nima))
# read first image to determine the size to use
if type(stack_name) == bytes:
proj = EMAN2_cppwrap.EMData()
proj.read_image(stack_name, list_proj[0])
else:
proj = stack_name[list_proj[0]].copy()
size = proj.get_xsize()
# sanity check -- image must be square
if size != proj.get_ysize():
sp_global_def.ERROR("input data has to be square", "recons3d_4nn", 1)
# reconstructor
fftvol = EMAN2_cppwrap.EMData()
weight = EMAN2_cppwrap.EMData()
params = {
"npad": npad,
"symmetry": symmetry,
"weighting": weighting,
"fftvol": fftvol,
"weight": weight,
}
if xysize == -1 and zsize == -1:
params["size"] = size
if snr != None:
params["snr"] = snr
# params["varsnr"] = int(varsnr)
r = EMAN2_cppwrap.Reconstructors.get("nn4", params)
else:
if xysize != -1 and zsize != -1:
rx = old_div(float(xysize), size)
ry = old_div(float(xysize), size)
rz = old_div(float(zsize), size)
elif xysize != -1:
rx = old_div(float(xysize), size)
ry = old_div(float(xysize), size)
rz = 1.0
else:
rx = 1.0
ry = 1.0
rz = old_div(float(zsize), size)
if snr is None:
params["sizeprojection"] = size
params["xratio"] = rx
params["yratio"] = ry
params["zratio"] = rz
else:
params["sizeprojection"] = size
params["snr"] = snr
params["varsnr"] = int(varsnr)
params["xratio"] = rx
params["yratio"] = ry
params["zratio"] = rz
r = EMAN2_cppwrap.Reconstructors.get("nn4_rect", params)
r.setup()
if type(stack_name) == bytes:
for i in range(len(list_proj)):
proj.read_image(stack_name, list_proj[i])
# horatio active_refactoring Jy51i1EwmLD4tWZ9_00000_1
# active = proj.get_attr_default('active', 1)
# if active == 1:
# insert_slices(r, proj)
insert_slices(r, proj)
else:
for i in list_proj:
# horatio active_refactoring Jy51i1EwmLD4tWZ9_00000_1
# active = stack_name[i].get_attr_default('active', 1)
# if active == 1:
# insert_slices(r, stack_name[i])
insert_slices(r, stack_name[i])
dummy = r.finish(True)
return fftvol
def recons3d_4nn_ctf(
stack_name,
list_proj=[],
snr=1.0,
sign=1,
symmetry="c1",
verbose=0,
npad=2,
xysize=-1,
zsize=-1,
):
"""Perform a 3-D reconstruction using Pawel's FFT Back Projection algoritm.
Input:
stack_name - name of the stack file on a disk,
each image has to have the following attributes set:
psi, theta, phi, sx, sy, defocus,
list_proj - list of images from stack_name to be included in the reconstruction
symmetry -- Point group of the target molecule (defaults to "C1")
Return: 3d reconstructed volume image
Usage:
anglelist = getAngles("myangles.txt") # not yet written
vol = do_reconstruction(filepattern, start, end, anglelist, symmetry)
"""
# read first image to determine the size to use
if list_proj == []:
if type(stack_name) == bytes:
nima = EMAN2_cppwrap.EMUtil.get_image_count(stack_name)
else:
nima = len(stack_name)
list_proj = list(range(nima))
# read first image to determine the size to use
if type(stack_name) == bytes:
proj = EMAN2_cppwrap.EMData()
proj.read_image(stack_name, list_proj[0])
else:
proj = stack_name[list_proj[0]].copy()
# convert angles to transform (rotation) objects
# horatio active_refactoring Jy51i1EwmLD4tWZ9_00000_1
# active = proj.get_attr_default('active', 1)
size = proj.get_xsize()
if proj.get_ysize() != size:
size = max(size, proj.get_ysize())
dopad = True
else:
dopad = False
# reconstructor
fftvol = EMAN2_cppwrap.EMData()
weight = EMAN2_cppwrap.EMData()
params = {
"npad": npad,
"symmetry": symmetry,
"snr": snr,
"sign": sign,
"fftvol": fftvol,
"weight": weight,
}
if xysize == -1 and zsize == -1:
params["size"] = size
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctf", params)
else:
if xysize != -1 and zsize != -1:
rx = old_div(float(xysize), size)
ry = old_div(float(xysize), size)
rz = old_div(float(zsize), size)
elif xysize != -1:
rx = old_div(float(xysize), size)
ry = old_div(float(xysize), size)
rz = 1.0
else:
rx = 1.0
ry = 1.0
rz = old_div(float(zsize), size)
params["sizeprojection"] = size
params["xratio"] = rx
params["yratio"] = ry
params["zratio"] = rz
r = EMAN2_cppwrap.Reconstructors.get("nn4_ctf_rect", params)
r.setup()
if type(stack_name) == bytes:
for i in range(len(list_proj)):
proj.read_image(stack_name, list_proj[i])
if dopad:
proj = sp_utilities.pad(proj, size, size, 1, "circumference")
insert_slices(r, proj)
else:
for i in range(len(list_proj)):
insert_slices(r, stack_name[list_proj[i]])
dummy = r.finish(True)
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 run():
progname = optparse.os.path.basename(sys.argv[0])
usage = """%prog [options] input.pdb output.hdf
Converts a pdb file into an electron density map. 0,0,0 in PDB space will
map to the center of the volume."""
parser = optparse.OptionParser(usage=usage, version=EMAN2_meta.EMANVERSION)
parser.add_option("--apix",
"-A",
type="float",
help="Angstrom/voxel",
default=1.0)
parser.add_option("--box",
"-B",
type="string",
help="Box size in pixels, <xyz> or <x,y,z>")
parser.add_option("--het",
action="store_true",
help="Include HET atoms in the map",
default=False)
parser.add_option(
"--chains",
type="string",
help=
"String list of chain identifiers to include, e.g. 'ABEFG'; default: include all chains",
default="",
)
parser.add_option(
"--center",
type="string",
default="a",
help=
"center: c - coordinates; a (default) - center of gravity; <x,y,z> - vector (in Angstrom) to subtract from all coordinates; n - none",
)
parser.add_option("--O",
action="store_true",
default=False,
help="use O system of coordinates")
parser.add_option("--quiet",
action="store_true",
default=False,
help="Verbose is the default")
parser.add_option(
"--tr0",
type="string",
default="none",
help="Filename of initial 3x4 transformation matrix",
)
parser.add_option(
"--set_apix_value",
action="store_true",
help="Set apix value in header of the ouput map",
default=False,
)
(options, args) = parser.parse_args() #
if len(args) < 2:
sp_global_def.ERROR("Input and output files required")
return
if sp_global_def.CACHE_DISABLE:
sp_utilities.disable_bdb_cache()
chains = options.chains
if chains == "":
chains = None
try:
infile = open(args[0], "r")
except:
sp_global_def.ERROR("Cannot open input file")
return
aavg = [0, 0, 0] # calculate atomic center
asig = [0, 0, 0] # to compute radius of gyration
natm = 0
atoms = [] # we store a list of atoms to process to avoid multiple passes
nelec = 0
mass = 0
# read in initial-transformation file:
if options.tr0 != "none":
cols = sp_utilities.read_text_file(options.tr0, -1)
txlist = []
for i in range(3):
txlist.append(cols[0][i])
txlist.append(cols[1][i])
txlist.append(cols[2][i])
txlist.append(cols[3][i])
tr0 = EMAN2_cppwrap.Transform(txlist)
# parse the pdb file and pull out relevant atoms
for line in infile:
if line[:4] == "ATOM" or (line[:6] == "HETATM" and options.het):
if chains and (line[21] not in chains):
continue
try:
a = line[12:14].strip()
aseq = int(line[6:11].strip())
res = int(line[22:26].strip())
if options.O:
x = float(line[38:46])
y = float(line[30:38])
z = -float(line[46:54])
else:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
except:
sp_global_def.sxprint(
"PDB Parse error:\n%s\n'%s','%s','%s' '%s','%s','%s'\n" %
(
line,
line[12:14],
line[6:11],
line[22:26],
line[30:38],
line[38:46],
line[46:54],
))
sp_global_def.sxprint(a, aseq, res, x, y, z)
try:
nelec += atomdefs[a.upper()][0]
mass += atomdefs[a.upper()][1]
except:
sp_global_def.sxprint((
"Unknown atom %s ignored at %d. You can modify the atomdefs info at the top of this file with the atomic number and atomic weight."
% (a, aseq)))
continue
atoms.append([a, x, y, z])
natm += 1
if options.center == "a":
aavg[0] += x * atomdefs[a.upper()][1]
aavg[1] += y * atomdefs[a.upper()][1]
aavg[2] += z * atomdefs[a.upper()][1]
asig[0] += x**2 * atomdefs[a.upper()][1]
asig[1] += y**2 * atomdefs[a.upper()][1]
asig[2] += z**2 * atomdefs[a.upper()][1]
else:
aavg[0] += x
aavg[1] += y
aavg[2] += z
asig[0] += x**2
asig[1] += y**2
asig[2] += z**2
infile.close()
if options.center == "a":
rad_gyr = math.sqrt(
old_div((asig[0] + asig[1] + asig[2]), mass) -
(old_div(aavg[0], mass))**2 - (old_div(aavg[1], mass))**2 -
(old_div(aavg[2], mass))**2)
else:
rad_gyr = math.sqrt(
old_div((asig[0] + asig[1] + asig[2]), natm) -
(old_div(aavg[0], natm))**2 - (old_div(aavg[1], natm))**2 -
(old_div(aavg[2], natm))**2)
if not options.quiet:
sp_global_def.sxprint(
"%d atoms; total charge = %d e-; mol mass = %.2f kDa; radius of gyration = %.2f A"
% (natm, nelec, old_div(mass, 1000.0), rad_gyr))
# center PDB according to option:
if options.center == "a":
if not options.quiet:
sp_global_def.sxprint(
"center of gravity at %1.1f,%1.1f,%1.1f (center of volume at 0,0,0)"
% (
old_div(aavg[0], mass),
old_div(aavg[1], mass),
old_div(aavg[2], mass),
))
for i in range(len(atoms)):
atoms[i][1] -= old_div(aavg[0], mass)
atoms[i][2] -= old_div(aavg[1], mass)
atoms[i][3] -= old_div(aavg[2], mass)
if options.center == "c":
if not options.quiet:
sp_global_def.sxprint(
"atomic center at %1.1f,%1.1f,%1.1f (center of volume at 0,0,0)"
% (
old_div(aavg[0], natm),
old_div(aavg[1], natm),
old_div(aavg[2], natm),
))
for i in range(len(atoms)):
atoms[i][1] -= old_div(aavg[0], natm)
atoms[i][2] -= old_div(aavg[1], natm)
atoms[i][3] -= old_div(aavg[2], natm)
spl = options.center.split(",")
if len(spl) == 3: # substract the given vector from all coordinates
if not options.quiet:
sp_global_def.sxprint(
"vector to substract: %1.1f,%1.1f,%1.1f (center of volume at 0,0,0)"
% (float(spl[0]), float(spl[1]), float(spl[2])))
for i in range(len(atoms)):
atoms[i][1] -= float(spl[0])
atoms[i][2] -= float(spl[1])
atoms[i][3] -= float(spl[2])
# apply given initial transformation (this used to be done before centering,
# thereby loosing the translation. This is the right place to apply tr0):
if options.tr0 != "none":
if not options.quiet:
sp_global_def.sxprint(
"Applying initial transformation to PDB coordinates... ")
for i in range(len(atoms)):
atom_coords = EMAN2_cppwrap.Vec3f(atoms[i][1], atoms[i][2],
atoms[i][3])
new_atom_coords = tr0 * atom_coords
atoms[i][1] = new_atom_coords[0]
atoms[i][2] = new_atom_coords[1]
atoms[i][3] = new_atom_coords[2]
if not options.quiet:
sp_global_def.sxprint("done.\n")
# bounding box:
amin = [atoms[0][1], atoms[0][2], atoms[0][3]]
amax = [atoms[0][1], atoms[0][2], atoms[0][3]]
for i in range(1, len(atoms)):
for k in range(3):
amin[k] = min(atoms[i][k + 1], amin[k])
amax[k] = max(atoms[i][k + 1], amax[k])
if not options.quiet:
sp_global_def.sxprint("Range of coordinates [A]: x: %7.2f - %7.2f" %
(amin[0], amax[0]))
sp_global_def.sxprint(" y: %7.2f - %7.2f" %
(amin[1], amax[1]))
sp_global_def.sxprint(" z: %7.2f - %7.2f" %
(amin[2], amax[2]))
# find the output box size, either user specified or from bounding box
box = [0, 0, 0]
try:
spl = options.box.split(",")
if len(spl) == 1:
box[0] = box[1] = box[2] = int(spl[0])
else:
box[0] = int(spl[0])
box[1] = int(spl[1])
box[2] = int(spl[2])
except:
for i in range(3):
box[i] = int(
old_div(2 * max(math.fabs(amax[i]), math.fabs(amin[i])),
options.apix))
# Increase the box size by 1/4.
box[i] += old_div(box[i], 4)
if not options.quiet:
sp_global_def.sxprint("Bounding box [pixels]: x: %5d " % box[0])
sp_global_def.sxprint(" y: %5d " % box[1])
sp_global_def.sxprint(" z: %5d " % box[2])
# figure oversampled box size
# bigb = max(box[0],box[1],box[2])
fcbig = 1
"""Multiline Comment0"""
if not options.quiet:
sp_global_def.sxprint(
"Box size: %d x %d x %d" % (box[0], box[1], box[2]),
", oversampling ",
fcbig,
)
# Calculate working dimensions
pixelbig = old_div(options.apix, fcbig)
bigbox = []
for i in range(3):
bigbox.append(box[i] * fcbig)
# initialize the final output volume
outmap = EMAN2_cppwrap.EMData(bigbox[0], bigbox[1], bigbox[2], True)
nc = []
for i in range(3):
nc.append(old_div(bigbox[i], 2))
# fill in the atoms
for i in range(len(atoms)):
# print "Adding %d '%s'"%(i,atoms[i][0])
if not options.quiet and i % 1000 == 0:
sp_global_def.sxprint("\r %d" % i, end=" ")
sys.stdout.flush()
try:
elec = atomdefs[atoms[i][0].upper()][0]
# outmap[int(atoms[i][1]/pixelbig+bigbox[0]//2),int(atoms[i][2]/pixelbig+bigbox[1]//2),int(atoms[i][3]/pixelbig+bigbox[2]//2)] += elec
for k in range(2):
pz = old_div(atoms[i][3], pixelbig) + nc[2]
dz = pz - int(pz)
uz = ((1 - k) + (2 * k - 1) * dz) * elec
for l in range(2):
py = old_div(atoms[i][2], pixelbig) + nc[1]
dy = py - int(py)
uy = ((1 - l) + (2 * l - 1) * dy) * uz
for m in range(2):
px = old_div(atoms[i][1], pixelbig) + nc[0]
dx = px - int(px)
outmap[int(px) + m,
int(py) + l,
int(pz) + k] += ((1 - m) +
(2 * m - 1) * dx) * uy
except:
sp_global_def.sxprint("Skipping %d '%s'" % (i, atoms[i][0]))
if not options.quiet:
sp_global_def.sxprint("\r %d\nConversion complete." %
len(atoms)) # ," Now shape atoms."
"""Multiline Comment1"""
(filename_path, filextension) = optparse.os.path.splitext(args[1])
if filextension == ".hdf":
if options.set_apix_value:
outmap.set_attr("apix_x", options.apix)
outmap.set_attr("apix_y", options.apix)
outmap.set_attr("apix_z", options.apix)
outmap.set_attr("pixel_size", options.apix)
else:
sp_global_def.sxprint("Pixel_size is not set in the header!")
outmap.write_image(args[1], 0,
EMAN2_cppwrap.EMUtil.ImageType.IMAGE_HDF)
elif filextension == ".spi":
outmap.write_image(args[1], 0,
EMAN2_cppwrap.EMUtil.ImageType.IMAGE_SINGLE_SPIDER)
else:
sp_global_def.ERROR("Unknown image type")
return
def runcheck(classavgstack, reconfile, outdir, inangles=None, selectdoc=None, prjmethod='trilinear', displayYN=False,
projstack='proj.hdf', outangles='angles.txt', outstack='comp-proj-reproj.hdf', normstack='comp-proj-reproj-norm.hdf'):
print("\n%s, Modified 2018-12-07\n" % __file__)
# Check if inputs exist
check(classavgstack)
check(reconfile)
# Create directory if it doesn't exist
if not os.path.isdir(outdir):
os.makedirs(outdir) # os.mkdir() can only operate one directory deep
print("mkdir -p %s" % outdir)
# Expand path for outputs
projstack = os.path.join(outdir, projstack)
outangles = os.path.join(outdir, outangles)
outstack = os.path.join(outdir, outstack)
normstack = os.path.join(outdir, normstack)
# Get number of images
nimg0 = EMAN2_cppwrap.EMUtil.get_image_count(classavgstack)
recon = EMAN2_cppwrap.EMData(reconfile)
nx = recon.get_xsize()
# In case class averages include discarded images, apply selection file
if selectdoc:
goodavgs, extension = os.path.splitext(classavgstack)
newclasses = goodavgs + "_kept" + extension
# e2proc2d appends to existing files, so rename existing output
if os.path.exists(newclasses):
renamefile = newclasses + '.bak'
os.rename(newclasses, renamefile)
print("mv %s %s" % (newclasses, renamefile))
cmd7="e2proc2d.py %s %s --list=%s" % (classavgstack, newclasses, selectdoc)
print(cmd7)
os.system(cmd7)
# Update class-averages
classavgstack = newclasses
# Import Euler angles
if inangles:
cmd6 = "sxheader.py %s --params=xform.projection --import=%s" % (classavgstack, inangles)
print(cmd6)
header(classavgstack, 'xform.projection', fimport=inangles)
try:
header(classavgstack, 'xform.projection', fexport=outangles)
cmd1 = "sxheader.py %s --params=xform.projection --export=%s" % (classavgstack, outangles)
print(cmd1)
except RuntimeError:
print("\nERROR!! No projection angles found in class-average stack header!\n")
print('Usage:', USAGE)
exit()
#cmd2="sxproject3d.py %s %s --angles=%s" % (recon, projstack, outangles)
#print(cmd2)
#os.system(cmd2)
# Here if you want to be fancy, there should be an option to chose the projection method,
# the mechanism can be copied from sxproject3d.py PAP
if prjmethod=='trilinear':
method_num = 1
elif prjmethod=='gridding':
method_num = -1
elif prjmethod=='nn':
method_num = 0
else:
print("\nERROR!! Valid projection methods are: trilinear (default), gridding, and nn (nearest neighbor).")
print('Usage:', USAGE)
exit()
#project3d(recon, stack=projstack, listagls=outangles)
recon = prep_vol(recon, npad = 2, interpolation_method = 1)
result=[]
# Here you need actual radius to compute proper ccc's, but if you do, you have to deal with translations, PAP
mask = model_circle(nx//2-2,nx,nx)
# Number of images may have changed
nimg1 = EMAN2_cppwrap.EMUtil.get_image_count(classavgstack)
outangles = read_text_row(outangles)
for imgnum in range(nimg1):
# get class average
classimg = get_im(classavgstack, imgnum)
# compute re-projection
prjimg = prgl(recon, outangles[imgnum], 1, False)
# calculate 1D power spectra
rops_dst = rops_table(classimg*mask)
rops_src = rops_table(prjimg)
# Set power spectrum of reprojection to the data.
# Since data has an envelope, it would make more sense to set data to reconstruction,
# but to do it one would have to know the actual resolution of the data.
# you can check sxprocess.py --adjpw to see how this is done properly PAP
table = [0.0]*len(rops_dst) # initialize table
for j in range( len(rops_dst) ):
table[j] = sqrt( old_div(rops_dst[j],rops_src[j]) )
prjimg = fft(filt_table(prjimg, table)) # match FFT amplitdes of re-projection and class average
cccoeff = ccc(prjimg, classimg, mask)
#print(imgnum, cccoeff)
classimg.set_attr_dict({'cross-corr':cccoeff})
prjimg.set_attr_dict({'cross-corr':cccoeff})
prjimg.write_image(outstack,2*imgnum)
classimg.write_image(outstack, 2*imgnum+1)
result.append(cccoeff)
del outangles
meanccc = old_div(sum(result),nimg1)
print("Average CCC is %s" % meanccc)
nimg2 = EMAN2_cppwrap.EMUtil.get_image_count(outstack)
for imgnum in xrange(nimg2):
if (imgnum % 2 ==0):
prjimg = get_im(outstack,imgnum)
meanccc1 = prjimg.get_attr_default('mean-cross-corr', -1.0)
prjimg.set_attr_dict({'mean-cross-corr':meanccc})
write_header(outstack,prjimg,imgnum)
if (imgnum % 100) == 0:
print(imgnum)
# e2proc2d appends to existing files, so delete existing output
if os.path.exists(normstack):
os.remove(normstack)
print("rm %s" % normstack)
# Why would you want to do it? If you do, it should have been done during ccc calculations,
# otherwise what is see is not corresponding to actual data, thus misleading. PAP
#cmd5="e2proc2d.py %s %s --process=normalize" % (outstack, normstack)
#print(cmd5)
#os.system(cmd5)
# Optionally pop up e2display
if displayYN:
cmd8 = "e2display.py %s" % outstack
print(cmd8)
os.system(cmd8)
print("Done!")