def internal_test_image2(self, nx, ny=1, nz=1):
from EMAN2 import EMData, display
from fundamentals import cyclic_shift, mirror
e = EMData()
e.set_size(nx, ny, nz)
e.process_inplace("testimage.tomo.objects")
e = cyclic_shift(e, nx/2, ny/3, nz/5)
e = mirror(e)
return e
def shift2d(image, dx=0, dy=0): """Shift a 2-d image.""" # split shift into integer and fractional parts DOES NOT SEEM TO MAKE MUCH SENSE from filter import fshift from fundamentals import cyclic_shift idx = int(dx) fdx = dx - idx idy = int(dy) fdy = dy - idy # perform cyclic integer shift rimage=cyclic_shift(image, idx, idy) # perform fractional shift in Fourier space and return return fshift(image, fdx, fdy)
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:
print("usage: " + usage)
print("Please run '" + progname + " -h' for detailed options")
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:
print("Please enter pixel size.")
sys.exit()
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 utilities import model_cylinder, model_gauss_noise
outvol = args[0]
boxdims = options.boxsize.split(',')
if len(boxdims) < 1 or len(boxdims) > 3:
print(
"Enter box size as string containing x , y, z dimensions (separated by comma) in pixels. E.g.: --boxsize='100,100,200'"
)
sys.exit()
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 utilities import model_blank, pad
outvol = args[0]
maskdims = options.masksize.split(',')
if len(maskdims) < 1 or len(maskdims) > 2:
print(
"Enter box size as string containing x , y dimensions (separated by comma) in pixels. E.g.: --boxsize='200,200'"
)
sys.exit()
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 utilities import get_im, get_params2D, set_params2D
from 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 = old_div((prj - stat[0]), stat[1])
ctf_params = prj.get_attr("ctf")
prj.set_attr('ctf_applied', 0)
prj.write_image(newstack, im)
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:
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options"
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:
print "Please enter pixel size."
sys.exit()
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 utilities import model_cylinder, model_gauss_noise
outvol = args[0]
boxdims = options.boxsize.split(',')
if len(boxdims) < 1 or len(boxdims) > 3:
print "Enter box size as string containing x , y, z dimensions (separated by comma) in pixels. E.g.: --boxsize='100,100,200'"
sys.exit()
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 utilities import model_blank, pad
outvol = args[0]
maskdims = options.masksize.split(',')
if len(maskdims) < 1 or len(maskdims) > 2:
print "Enter box size as string containing x , y dimensions (separated by comma) in pixels. E.g.: --boxsize='200,200'"
sys.exit()
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 utilities import get_im, get_params2D, set_params2D
from fundamentals import cyclic_shift
stack = args[0]
newstack = args[1]
mask = get_im(args[2])
nima = EMUtil.get_image_count(stack)
for im in xrange(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)
def internal_correlation(self, A, B, center, circulant, normalized, lag_normalization): # A, B - images, circulant - bool (False - zero padded), center - bool, normalized - bool
from EMAN2 import EMData
from utilities import model_blank
from fundamentals import cyclic_shift
from math import sqrt
anx = A.get_xsize()
any = A.get_ysize()
anz = A.get_zsize()
self.assertEqual(anx, B.get_xsize())
self.assertEqual(any, B.get_ysize())
self.assertEqual(anz, B.get_zsize())
snx = 2*anx
sny = 2*any
snz = 2*anz
if normalized:
A = A.copy()
B = B.copy()
A.sub(A.get_attr("mean"))
B.sub(B.get_attr("mean"))
A.div(A.get_attr("sigma") * sqrt(anz) * sqrt(any) * sqrt(anx))
B.div(B.get_attr("sigma") * sqrt(anz) * sqrt(any) * sqrt(anx))
S = model_blank(snx, sny, snz)
if circulant:
tx = snx
ty = sny
tz = snz
else:
tx = anx
ty = any
tz = anz
for x in xrange(tx):
for y in xrange(ty):
for z in xrange(tz):
S.set_value_at(x, y, z, A.get_value_at( (x)%anx, (y)%any, (z)%anz ))
if center:
S = cyclic_shift(S, anx/2, any/2, anz/2)
R = model_blank(anx, any, anz)
for x in xrange(anx):
for y in xrange(any):
for z in xrange(anz):
s = 0.0
for x2 in xrange(anx):
for y2 in xrange(any):
for z2 in xrange(anz):
s += S.get_value_at(x+x2, y+y2, z+z2) * B.get_value_at(x2, y2, z2)
R.set_value_at(x, y, z, s)
if lag_normalization:
cx = anx/2
cy = any/2
cz = anz/2
for x in xrange(anx):
x_center = abs(x-cx)
x_lag = 1 + (x_center * 1.0) / (anx - x_center)
for y in xrange(any):
y_center = abs(y-cy)
y_lag = 1 + (y_center * 1.0) / (any - y_center)
for z in xrange(anz):
z_center = abs(z-cz)
z_lag = 1 + (z_center * 1.0) / (anz - z_center)
R.set_value_at(x, y, z, R.get_value_at(x,y,z) * x_lag * y_lag * z_lag )
return R