def reference4(ref_data):
from utilities import print_msg
from filter import fit_tanh, filt_tanl, filt_gaussl
from fundamentals import fshift, fft
from morphology import threshold
# Prepare the reference in 3D alignment, i.e., low-pass filter and center.
# Input: list ref_data
# 0 - mask
# 1 - center flag
# 2 - raw average
# 3 - fsc result
# Output: filtered, centered, and masked reference image
# apply filtration (FSC) to reference image:
#print_msg("reference4\n")
cs = [0.0] * 3
stat = Util.infomask(ref_data[2], ref_data[0], False)
volf = ref_data[2] - stat[0]
Util.mul_scalar(volf, 1.0 / stat[1])
volf = threshold(volf)
#Util.mul_img(volf, ref_data[0])
#fl, aa = fit_tanh(ref_data[3])
fl = 0.25
aa = 0.1
#msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n"%(fl, aa)
#print_msg(msg)
volf = fft(filt_gaussl(filt_tanl(fft(volf), 0.35, 0.2), 0.3))
if ref_data[1] == 1:
cs = volf.phase_cog()
msg = "Center x = %10.3f Center y = %10.3f Center z = %10.3f\n" % (
cs[0], cs[1], cs[2])
print_msg(msg)
volf = fshift(volf, -cs[0], -cs[1], -cs[2])
return volf, cs
def reference4( ref_data ):
from utilities import print_msg
from filter import fit_tanh, filt_tanl, filt_gaussl
from fundamentals import fshift, fft
from morphology import threshold
# Prepare the reference in 3D alignment, i.e., low-pass filter and center.
# Input: list ref_data
# 0 - mask
# 1 - center flag
# 2 - raw average
# 3 - fsc result
# Output: filtered, centered, and masked reference image
# apply filtration (FSC) to reference image:
#print_msg("reference4\n")
cs = [0.0]*3
stat = Util.infomask(ref_data[2], ref_data[0], False)
volf = ref_data[2] - stat[0]
Util.mul_scalar(volf, 1.0/stat[1])
volf = threshold(volf)
#Util.mul_img(volf, ref_data[0])
#fl, aa = fit_tanh(ref_data[3])
fl = 0.25
aa = 0.1
#msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n"%(fl, aa)
#print_msg(msg)
volf = fft(filt_gaussl(filt_tanl(fft(volf),0.35,0.2),0.3))
if ref_data[1] == 1:
cs = volf.phase_cog()
msg = "Center x = %10.3f Center y = %10.3f Center z = %10.3f\n"%(cs[0], cs[1], cs[2])
print_msg(msg)
volf = fshift(volf, -cs[0], -cs[1], -cs[2])
return volf, cs
def spruce_up_var_m( refdata ): from utilities import print_msg from utilities import model_circle, get_im from filter import filt_tanl, filt_gaussl from morphology import threshold import os numref = refdata[0] outdir = refdata[1] fscc = refdata[2] total_iter = refdata[3] varf = refdata[4] mask = refdata[5] ali50S = refdata[6] if ali50S: mask_50S = get_im( "mask-50S.spi" ) if fscc is None: flmin = 0.4 aamin = 0.1 else: flmin,aamin,idmin=minfilt( fscc ) aamin = aamin msg = "Minimum tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n"%(fflmin, aamin) print_msg(msg) for i in xrange(numref): volf = get_im( os.path.join(outdir, "vol%04d.hdf"% total_iter) , i ) if(not (varf is None) ): volf = volf.filter_by_image( varf ) volf = filt_tanl(volf, flmin, aamin) stat = Util.infomask(volf, mask, True) volf -= stat[0] Util.mul_scalar(volf, 1.0/stat[1]) nx = volf.get_xsize() stat = Util.infomask(volf,model_circle(nx//2-2,nx,nx,nx)-model_circle(nx//2-6,nx,nx,nx), True) volf -= stat[0] Util.mul_img( volf, mask ) volf = threshold(volf) volf = filt_gaussl( volf, 0.4) if ali50S: if i==0: v50S_0 = volf.copy() v50S_0 *= mask_50S else: from applications import ali_vol_3 from fundamentals import rot_shift3D v50S_i = volf.copy() v50S_i *= mask_50S params = ali_vol_3(v50S_i, v50S_0, 10.0, 0.5, mask=mask_50S) volf = rot_shift3D( volf, params[0], params[1], params[2], params[3], params[4], params[5], 1.0) volf.write_image( os.path.join(outdir, "volf%04d.hdf"%total_iter), i )
def generate_helimic(refvol, outdir, pixel, CTF=False, Cs=2.0,voltage = 200.0, ampcont = 10.0, nonoise = False, rand_seed=14567):
from utilities import model_blank, model_gauss, model_gauss_noise, pad, get_im
from random import random
from projection import prgs, prep_vol
from 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', "sxhelical_demo", 1)
os.mkdir(outdir)
seed(rand_seed)
Util.set_randnum_seed(rand_seed)
angles =[]
for i in xrange(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 xrange(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 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 xrange(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 spruce_up_variance(ref_data):
from utilities import print_msg
from filter import filt_tanl, fit_tanh, filt_gaussl
from morphology import threshold
# Prepare the reference in 3D alignment, i.e., low-pass filter and center.
# Input: list ref_data
# 0 - mask
# 1 - center flag
# 2 - raw average
# 3 - fsc result
# 4 1.0/variance
# Output: filtered, centered, and masked reference image
# apply filtration (FSC) to reference image:
mask = ref_data[0]
center = ref_data[1]
vol = ref_data[2]
fscc = ref_data[3]
varf = ref_data[4]
print_msg("spruce_up with variance\n")
cs = [0.0] * 3
if not (varf is None):
volf = vol.filter_by_image(varf)
#fl, aa = fit_tanh(ref_data[3])
fl = 0.22
aa = 0.15
msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n" % (
fl, aa)
print_msg(msg)
volf = filt_tanl(volf, fl, aa)
stat = Util.infomask(volf, None, True)
volf = volf - stat[0]
Util.mul_scalar(volf, 1.0 / stat[1])
from utilities import model_circle
nx = volf.get_xsize()
stat = Util.infomask(
volf,
model_circle(nx // 2 - 2, nx, nx, nx) -
model_circle(nx // 2 - 6, nx, nx, nx), True)
volf -= stat[0]
Util.mul_img(volf, mask)
volf = threshold(volf)
volf = filt_gaussl(volf, 0.4)
return volf, cs
def spruce_up_variance( ref_data ):
from utilities import print_msg
from filter import filt_tanl, fit_tanh, filt_gaussl
from morphology import threshold
# Prepare the reference in 3D alignment, i.e., low-pass filter and center.
# Input: list ref_data
# 0 - mask
# 1 - center flag
# 2 - raw average
# 3 - fsc result
# 4 1.0/variance
# Output: filtered, centered, and masked reference image
# apply filtration (FSC) to reference image:
mask = ref_data[0]
center = ref_data[1]
vol = ref_data[2]
fscc = ref_data[3]
varf = ref_data[4]
print_msg("spruce_up with variance\n")
cs = [0.0]*3
if not(varf is None):
volf = vol.filter_by_image(varf)
#fl, aa = fit_tanh(ref_data[3])
fl = 0.22
aa = 0.15
msg = "Tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n"%(fl, aa)
print_msg(msg)
volf = filt_tanl(volf, fl, aa)
stat = Util.infomask(volf, None, True)
volf = volf - stat[0]
Util.mul_scalar(volf, 1.0/stat[1])
from utilities import model_circle
nx = volf.get_xsize()
stat = Util.infomask(volf, model_circle(nx//2-2,nx,nx,nx)-model_circle(nx//2-6,nx,nx,nx), True)
volf -= stat[0]
Util.mul_img(volf, mask)
volf = threshold(volf)
volf = filt_gaussl(volf, 0.4)
return volf, cs
def generate_helimic(refvol,
outdir,
pixel,
CTF=False,
Cs=2.0,
voltage=200.0,
ampcont=10.0,
nonoise=False,
rand_seed=14567):
from utilities import model_blank, model_gauss, model_gauss_noise, pad, get_im
from random import random
from projection import prgs, prep_vol
from 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',
"sxhelical_demo", 1)
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 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 spruce_up_var_m(refdata):
from utilities import print_msg
from utilities import model_circle, get_im
from filter import filt_tanl, filt_gaussl
from morphology import threshold
import os
numref = refdata[0]
outdir = refdata[1]
fscc = refdata[2]
total_iter = refdata[3]
varf = refdata[4]
mask = refdata[5]
ali50S = refdata[6]
if ali50S:
mask_50S = get_im("mask-50S.spi")
if fscc is None:
flmin = 0.4
aamin = 0.1
else:
flmin, aamin, idmin = minfilt(fscc)
aamin = aamin
msg = "Minimum tangent filter: cut-off frequency = %10.3f fall-off = %10.3f\n" % (
fflmin, aamin)
print_msg(msg)
for i in xrange(numref):
volf = get_im(os.path.join(outdir, "vol%04d.hdf" % total_iter), i)
if (not (varf is None)): volf = volf.filter_by_image(varf)
volf = filt_tanl(volf, flmin, aamin)
stat = Util.infomask(volf, mask, True)
volf -= stat[0]
Util.mul_scalar(volf, 1.0 / stat[1])
nx = volf.get_xsize()
stat = Util.infomask(
volf,
model_circle(nx // 2 - 2, nx, nx, nx) -
model_circle(nx // 2 - 6, nx, nx, nx), True)
volf -= stat[0]
Util.mul_img(volf, mask)
volf = threshold(volf)
volf = filt_gaussl(volf, 0.4)
if ali50S:
if i == 0:
v50S_0 = volf.copy()
v50S_0 *= mask_50S
else:
from applications import ali_vol_3
from fundamentals import rot_shift3D
v50S_i = volf.copy()
v50S_i *= mask_50S
params = ali_vol_3(v50S_i, v50S_0, 10.0, 0.5, mask=mask_50S)
volf = rot_shift3D(volf, params[0], params[1], params[2],
params[3], params[4], params[5], 1.0)
volf.write_image(os.path.join(outdir, "volf%04d.hdf" % total_iter), i)
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Generic 2-D image processing programs.
Functionality:
1. Phase flip a stack of images and write output to new file:
sxprocess.py input_stack.hdf output_stack.hdf --phase_flip
2. Resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.
The window size will change accordingly.
sxprocess input.hdf output.hdf --changesize --ratio=0.5
3. Compute average power spectrum of a stack of 2D images with optional padding (option wn) with zeroes or a 3-D volume.
sxprocess.py input_stack.hdf powerspectrum.hdf --pw [--wn=1024]
4. Generate a stack of projections bdb:data and micrographs with prefix mic (i.e., mic0.hdf, mic1.hdf etc) from structure input_structure.hdf, with CTF applied to both projections and micrographs:
sxprocess.py input_structure.hdf data mic --generate_projections format="bdb":apix=5.2:CTF=True:boxsize=64
5. Retrieve original image numbers in the selected ISAC group (here group 12 from generation 3):
sxprocess.py bdb:test3 class_averages_generation_3.hdf list3_12.txt --isacgroup=12 --params=originalid
6. Retrieve original image numbers of images listed in ISAC output stack of averages:
sxprocess.py select1.hdf ohk.txt
7. Adjust rotationally averaged power spectrum of an image to that of a reference image or a reference 1D power spectrum stored in an ASCII file.
Optionally use a tangent low-pass filter. Also works for a stack of images, in which case the output is also a stack.
sxprocess.py vol.hdf ref.hdf avol.hdf < 0.25 0.2> --adjpw
sxprocess.py vol.hdf pw.txt avol.hdf < 0.25 0.2> --adjpw
8. Generate a 1D rotationally averaged power spectrum of an image.
sxprocess.py vol.hdf --rotwp=rotpw.txt
# Output will contain three columns:
(1) rotationally averaged power spectrum
(2) logarithm of the rotationally averaged power spectrum
(3) integer line number (from zero to approximately to half the image size)
9. Apply 3D transformation (rotation and/or shift) to a set of orientation parameters associated with projection data.
sxprocess.py --transfromparams=phi,theta,psi,tx,ty,tz input.txt output.txt
The output file is then imported and 3D transformed volume computed:
sxheader.py bdb:p --params=xform.projection --import=output.txt
mpirun -np 2 sxrecons3d_n.py bdb:p tvol.hdf --MPI
The reconstructed volume is in the position of the volume computed using the input.txt parameters and then
transformed with rot_shift3D(vol, phi,theta,psi,tx,ty,tz)
10. Import ctf parameters from the output of sxcter into windowed particle headers.
There are three possible input files formats: (1) all particles are in one stack, (2 aor 3) particles are in stacks, each stack corresponds to a single micrograph.
In each case the particles should contain a name of the micrograph of origin stores using attribute name 'ptcl_source_image'.
Normally this is done by e2boxer.py during windowing.
Particles whose defocus or astigmatism error exceed set thresholds will be skipped, otherwise, virtual stacks with the original way preceded by G will be created.
sxprocess.py --input=bdb:data --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
# Output will be a vritual stack bdb:Gdata
sxprocess.py --input="bdb:directory/stacks*" --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
To concatenate output files:
cd directory
e2bdb.py . --makevstack=bdb:allparticles --filt=G
IMPORTANT: Please do not move (or remove!) any input/intermediate EMAN2DB files as the information is linked between them.
11. Scale 3D shifts. The shifts in the input five columns text file with 3D orientation parameters will be DIVIDED by the scale factor
sxprocess.py orientationparams.txt scaledparams.txt scale=0.5
12. Generate 3D mask from a given 3-D volume automatically or using threshold provided by user.
13. Postprocess 3-D or 2-D images:
for 3-D volumes: calculate FSC with provided mask; weight summed volume with FSC; estimate B-factor from FSC weighted summed two volumes; apply negative B-factor to the weighted volume.
for 2-D images: calculate B-factor and apply negative B-factor to 2-D images.
14. Winow stack file -reduce size of images without changing the pixel size.
"""
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--order", action="store_true", help="Two arguments are required: name of input stack and desired name of output stack. The output stack is the input stack sorted by similarity in terms of cross-correlation coefficent.", default=False)
parser.add_option("--order_lookup", action="store_true", help="Test/Debug.", default=False)
parser.add_option("--order_metropolis", action="store_true", help="Test/Debug.", default=False)
parser.add_option("--order_pca", action="store_true", help="Test/Debug.", default=False)
parser.add_option("--initial", type="int", default=-1, help="Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)")
parser.add_option("--circular", action="store_true", help="Select circular ordering (fisr image has to be similar to the last", default=False)
parser.add_option("--radius", type="int", default=-1, help="Radius of a circular mask for similarity based ordering")
parser.add_option("--changesize", action="store_true", help="resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.", default=False)
parser.add_option("--ratio", type="float", default=1.0, help="The ratio of new to old image size (if <1 the pixel size will increase and image size decrease, if>1, the other way round")
parser.add_option("--pw", action="store_true", help="compute average power spectrum of a stack of 2-D images with optional padding (option wn) with zeroes", default=False)
parser.add_option("--wn", type="int", default=-1, help="Size of window to use (should be larger/equal than particle box size, default padding to max(nx,ny))")
parser.add_option("--phase_flip", action="store_true", help="Phase flip the input stack", default=False)
parser.add_option("--makedb", metavar="param1=value1:param2=value2", type="string",
action="append", help="One argument is required: name of key with which the database will be created. Fill in database with parameters specified as follows: --makedb param1=value1:param2=value2, e.g. 'gauss_width'=1.0:'pixel_input'=5.2:'pixel_output'=5.2:'thr_low'=1.0")
parser.add_option("--generate_projections", metavar="param1=value1:param2=value2", type="string",
action="append", help="Three arguments are required: name of input structure from which to generate projections, desired name of output projection stack, and desired prefix for micrographs (e.g. if prefix is 'mic', then micrographs mic0.hdf, mic1.hdf etc will be generated). Optional arguments specifying format, apix, box size and whether to add CTF effects can be entered as follows after --generate_projections: format='bdb':apix=5.2:CTF=True:boxsize=100, or format='hdf', etc., where format is bdb or hdf, apix (pixel size) is a float, CTF is True or False, and boxsize denotes the dimension of the box (assumed to be a square). If an optional parameter is not specified, it will default as follows: format='bdb', apix=2.5, CTF=False, boxsize=64.")
parser.add_option("--isacgroup", type="int", help="Retrieve original image numbers in the selected ISAC group. See ISAC documentation for details.", default=-1)
parser.add_option("--isacselect", action="store_true", help="Retrieve original image numbers of images listed in ISAC output stack of averages. See ISAC documentation for details.", default=False)
parser.add_option("--params", type="string", default=None, help="Name of header of parameter, which one depends on specific option")
parser.add_option("--adjpw", action="store_true", help="Adjust rotationally averaged power spectrum of an image", default=False)
parser.add_option("--rotpw", type="string", default=None, help="Name of the text file to contain rotationally averaged power spectrum of the input image.")
parser.add_option("--transformparams", type="string", default=None, help="Transform 3D projection orientation parameters using six 3D parameters (phi, theta,psi,sx,sy,sz). Input: --transformparams=45.,66.,12.,-2,3,-5.5 desired six transformation of the reconstructed structure. Output: file with modified orientation parameters.")
# import ctf estimates done using cter
parser.add_option("--input", type="string", default= None, help="Input particles.")
parser.add_option("--importctf", type="string", default= None, help="Name of the file containing CTF parameters produced by sxcter.")
parser.add_option("--defocuserror", type="float", default=1000000.0, help="Exclude micrographs whose relative defocus error as estimated by sxcter is larger than defocuserror percent. The error is computed as (std dev defocus)/defocus*100%")
parser.add_option("--astigmatismerror", type="float", default=360.0, help="Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sxcter is larger than astigmatismerror degrees.")
# import ctf estimates done using cter
parser.add_option("--scale", type="float", default=-1.0, help="Divide shifts in the input 3D orientation parameters text file by the scale factor.")
# generate adaptive mask from an given 3-D volume
parser.add_option("--adaptive_mask", action="store_true", help="create adavptive 3-D mask from a given volume", default=False)
parser.add_option("--nsigma", type="float", default= 1., help="number of times of sigma of the input volume to obtain the the large density cluster")
parser.add_option("--ndilation", type="int", default= 3, help="number of times of dilation applied to the largest cluster of density")
parser.add_option("--kernel_size", type="int", default= 11, help="convolution kernel for smoothing the edge of the mask")
parser.add_option("--gauss_standard_dev", type="int", default= 9, help="stanadard deviation value to generate Gaussian edge")
parser.add_option("--threshold", type="float", default= 9999., help="threshold provided by user to binarize input volume")
parser.add_option("--ne", type="int", default= 0, help="number of times to erode the binarized input image")
parser.add_option("--nd", type="int", default= 0, help="number of times to dilate the binarized input image")
parser.add_option("--postprocess", action="store_true", help="postprocess unfiltered odd, even 3-D volumes",default=False)
parser.add_option("--fsc_weighted", action="store_true", help="postprocess unfiltered odd, even 3-D volumes")
parser.add_option("--low_pass_filter", action="store_true", default=False, help="postprocess unfiltered odd, even 3-D volumes")
parser.add_option("--ff", type="float", default=.25, help="low pass filter stop band frequency in absolute unit")
parser.add_option("--aa", type="float", default=.1, help="low pass filter falloff" )
parser.add_option("--mask", type="string", help="input mask file", default=None)
parser.add_option("--output", type="string", help="output file name", default="postprocessed.hdf")
parser.add_option("--pixel_size", type="float", help="pixel size of the data", default=1.0)
parser.add_option("--B_start", type="float", help="starting frequency in Angstrom for B-factor estimation", default=10.)
parser.add_option("--FSC_cutoff", type="float", help="stop frequency in Angstrom for B-factor estimation", default=0.143)
parser.add_option("--2d", action="store_true", help="postprocess isac 2-D averaged images",default=False)
parser.add_option("--window_stack", action="store_true", help="window stack images using a smaller window size", default=False)
parser.add_option("--box", type="int", default= 0, help="the new window size ")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.phase_flip:
nargs = len(args)
if nargs != 2:
print "must provide name of input and output file!"
return
from EMAN2 import Processor
instack = args[0]
outstack = args[1]
nima = EMUtil.get_image_count(instack)
from filter import filt_ctf
for i in xrange(nima):
img = EMData()
img.read_image(instack, i)
try:
ctf = img.get_attr('ctf')
except:
print "no ctf information in input stack! Exiting..."
return
dopad = True
sign = 1
binary = 1 # phase flip
assert img.get_ysize() > 1
dict = ctf.to_dict()
dz = dict["defocus"]
cs = dict["cs"]
voltage = dict["voltage"]
pixel_size = dict["apix"]
b_factor = dict["bfactor"]
ampcont = dict["ampcont"]
dza = dict["dfdiff"]
azz = dict["dfang"]
if dopad and not img.is_complex(): ip = 1
else: ip = 0
params = {"filter_type": Processor.fourier_filter_types.CTF_,
"defocus" : dz,
"Cs": cs,
"voltage": voltage,
"Pixel_size": pixel_size,
"B_factor": b_factor,
"amp_contrast": ampcont,
"dopad": ip,
"binary": binary,
"sign": sign,
"dza": dza,
"azz":azz}
tmp = Processor.EMFourierFilter(img, params)
tmp.set_attr_dict({"ctf": ctf})
tmp.write_image(outstack, i)
elif options.changesize:
nargs = len(args)
if nargs != 2:
ERROR("must provide name of input and output file!", "change size", 1)
return
from utilities import get_im
instack = args[0]
outstack = args[1]
sub_rate = float(options.ratio)
nima = EMUtil.get_image_count(instack)
from fundamentals import resample
for i in xrange(nima):
resample(get_im(instack, i), sub_rate).write_image(outstack, i)
elif options.isacgroup>-1:
nargs = len(args)
if nargs != 3:
ERROR("Three files needed on input!", "isacgroup", 1)
return
from utilities import get_im
instack = args[0]
m=get_im(args[1],int(options.isacgroup)).get_attr("members")
l = []
for k in m:
l.append(int(get_im(args[0],k).get_attr(options.params)))
from utilities import write_text_file
write_text_file(l, args[2])
elif options.isacselect:
nargs = len(args)
if nargs != 2:
ERROR("Two files needed on input!", "isacgroup", 1)
return
from utilities import get_im
nima = EMUtil.get_image_count(args[0])
m = []
for k in xrange(nima):
m += get_im(args[0],k).get_attr("members")
m.sort()
from utilities import write_text_file
write_text_file(m, args[1])
elif options.pw:
nargs = len(args)
if nargs < 2:
ERROR("must provide name of input and output file!", "pw", 1)
return
from utilities import get_im, write_text_file
from fundamentals import rops_table
d = get_im(args[0])
ndim = d.get_ndim()
if ndim ==3:
pw = rops_table(d)
write_text_file(pw, args[1])
else:
nx = d.get_xsize()
ny = d.get_ysize()
if nargs ==3: mask = get_im(args[2])
wn = int(options.wn)
if wn == -1:
wn = max(nx, ny)
else:
if( (wn<nx) or (wn<ny) ): ERROR("window size cannot be smaller than the image size","pw",1)
n = EMUtil.get_image_count(args[0])
from utilities import model_blank, model_circle, pad
from EMAN2 import periodogram
p = model_blank(wn,wn)
for i in xrange(n):
d = get_im(args[0], i)
if nargs==3:
d *=mask
st = Util.infomask(d, None, True)
d -= st[0]
p += periodogram(pad(d, wn, wn, 1, 0.))
p /= n
p.write_image(args[1])
elif options.adjpw:
if len(args) < 3:
ERROR("filt_by_rops input target output fl aa (the last two are optional parameters of a low-pass filter)","adjpw",1)
return
img_stack = args[0]
from math import sqrt
from fundamentals import rops_table, fft
from utilities import read_text_file, get_im
from filter import filt_tanl, filt_table
if( args[1][-3:] == 'txt'):
rops_dst = read_text_file( args[1] )
else:
rops_dst = rops_table(get_im( args[1] ))
out_stack = args[2]
if(len(args) >4):
fl = float(args[3])
aa = float(args[4])
else:
fl = -1.0
aa = 0.0
nimage = EMUtil.get_image_count( img_stack )
for i in xrange(nimage):
img = fft(get_im(img_stack, i) )
rops_src = rops_table(img)
assert len(rops_dst) == len(rops_src)
table = [0.0]*len(rops_dst)
for j in xrange( len(rops_dst) ):
table[j] = sqrt( rops_dst[j]/rops_src[j] )
if( fl > 0.0):
img = filt_tanl(img, fl, aa)
img = fft(filt_table(img, table))
img.write_image(out_stack, i)
elif options.rotpw != None:
if len(args) != 1:
ERROR("Only one input permitted","rotpw",1)
return
from utilities import write_text_file, get_im
from fundamentals import rops_table
from math import log10
t = rops_table(get_im(args[0]))
x = range(len(t))
r = [0.0]*len(x)
for i in x: r[i] = log10(t[i])
write_text_file([t,r,x],options.rotpw)
elif options.transformparams != None:
if len(args) != 2:
ERROR("Please provide names of input and output files with orientation parameters","transformparams",1)
return
from utilities import read_text_row, write_text_row
transf = [0.0]*6
spl=options.transformparams.split(',')
for i in xrange(len(spl)): transf[i] = float(spl[i])
write_text_row( rotate_shift_params(read_text_row(args[0]), transf) , args[1])
elif options.makedb != None:
nargs = len(args)
if nargs != 1:
print "must provide exactly one argument denoting database key under which the input params will be stored"
return
dbkey = args[0]
print "database key under which params will be stored: ", dbkey
gbdb = js_open_dict("e2boxercache/gauss_box_DB.json")
parmstr = 'dummy:'+options.makedb[0]
(processorname, param_dict) = parsemodopt(parmstr)
dbdict = {}
for pkey in param_dict:
if (pkey == 'invert_contrast') or (pkey == 'use_variance'):
if param_dict[pkey] == 'True':
dbdict[pkey] = True
else:
dbdict[pkey] = False
else:
dbdict[pkey] = param_dict[pkey]
gbdb[dbkey] = dbdict
elif options.generate_projections:
nargs = len(args)
if nargs != 3:
ERROR("Must provide name of input structure(s) from which to generate projections, name of output projection stack, and prefix for output micrographs."\
"sxprocess - generate projections",1)
return
inpstr = args[0]
outstk = args[1]
micpref = args[2]
parmstr = 'dummy:'+options.generate_projections[0]
(processorname, param_dict) = parsemodopt(parmstr)
parm_CTF = False
parm_format = 'bdb'
parm_apix = 2.5
if 'CTF' in param_dict:
if param_dict['CTF'] == 'True':
parm_CTF = True
if 'format' in param_dict:
parm_format = param_dict['format']
if 'apix' in param_dict:
parm_apix = float(param_dict['apix'])
boxsize = 64
if 'boxsize' in param_dict:
boxsize = int(param_dict['boxsize'])
print "pixel size: ", parm_apix, " format: ", parm_format, " add CTF: ", parm_CTF, " box size: ", boxsize
scale_mult = 2500
sigma_add = 1.5
sigma_proj = 30.0
sigma2_proj = 17.5
sigma_gauss = 0.3
sigma_mic = 30.0
sigma2_mic = 17.5
sigma_gauss_mic = 0.3
if 'scale_mult' in param_dict:
scale_mult = float(param_dict['scale_mult'])
if 'sigma_add' in param_dict:
sigma_add = float(param_dict['sigma_add'])
if 'sigma_proj' in param_dict:
sigma_proj = float(param_dict['sigma_proj'])
if 'sigma2_proj' in param_dict:
sigma2_proj = float(param_dict['sigma2_proj'])
if 'sigma_gauss' in param_dict:
sigma_gauss = float(param_dict['sigma_gauss'])
if 'sigma_mic' in param_dict:
sigma_mic = float(param_dict['sigma_mic'])
if 'sigma2_mic' in param_dict:
sigma2_mic = float(param_dict['sigma2_mic'])
if 'sigma_gauss_mic' in param_dict:
sigma_gauss_mic = float(param_dict['sigma_gauss_mic'])
from filter import filt_gaussl, filt_ctf
from utilities import drop_spider_doc, even_angles, model_gauss, delete_bdb, model_blank,pad,model_gauss_noise,set_params2D, set_params_proj
from projection import prep_vol,prgs
seed(14567)
delta = 29
angles = even_angles(delta, 0.0, 89.9, 0.0, 359.9, "S")
nangle = len(angles)
modelvol = []
nvlms = EMUtil.get_image_count(inpstr)
from utilities import get_im
for k in xrange(nvlms): modelvol.append(get_im(inpstr,k))
nx = modelvol[0].get_xsize()
if nx != boxsize:
ERROR("Requested box dimension does not match dimension of the input model.", \
"sxprocess - generate projections",1)
nvol = 10
volfts = [[] for k in xrange(nvlms)]
for k in xrange(nvlms):
for i in xrange(nvol):
sigma = sigma_add + random() # 1.5-2.5
addon = model_gauss(sigma, boxsize, boxsize, boxsize, sigma, sigma, 38, 38, 40 )
scale = scale_mult * (0.5+random())
vf, kb = prep_vol(modelvol[k] + scale*addon)
volfts[k].append(vf)
del vf, modelvol
if parm_format == "bdb":
stack_data = "bdb:"+outstk
delete_bdb(stack_data)
else:
stack_data = outstk + ".hdf"
Cs = 2.0
pixel = parm_apix
voltage = 120.0
ampcont = 10.0
ibd = 4096/2-boxsize
iprj = 0
width = 240
xstart = 8 + boxsize/2
ystart = 8 + boxsize/2
rowlen = 17
from random import randint
params = []
for idef in xrange(3, 8):
irow = 0
icol = 0
mic = model_blank(4096, 4096)
defocus = idef * 0.5#0.2
if parm_CTF:
astampl=defocus*0.15
astangl=50.0
ctf = generate_ctf([defocus, Cs, voltage, pixel, ampcont, 0.0, astampl, astangl])
for i in xrange(nangle):
for k in xrange(12):
dphi = 8.0*(random()-0.5)
dtht = 8.0*(random()-0.5)
psi = 360.0*random()
phi = angles[i][0]+dphi
tht = angles[i][1]+dtht
s2x = 4.0*(random()-0.5)
s2y = 4.0*(random()-0.5)
params.append([phi, tht, psi, s2x, s2y])
ivol = iprj % nvol
#imgsrc = randint(0,nvlms-1)
imgsrc = iprj % nvlms
proj = prgs(volfts[imgsrc][ivol], kb, [phi, tht, psi, -s2x, -s2y])
x = xstart + irow * width
y = ystart + icol * width
mic += pad(proj, 4096, 4096, 1, 0.0, x-2048, y-2048, 0)
proj = proj + model_gauss_noise( sigma_proj, nx, nx )
if parm_CTF:
proj = filt_ctf(proj, ctf)
proj.set_attr_dict({"ctf":ctf, "ctf_applied":0})
proj = proj + filt_gaussl(model_gauss_noise(sigma2_proj, nx, nx), sigma_gauss)
proj.set_attr("origimgsrc",imgsrc)
proj.set_attr("test_id", iprj)
# flags describing the status of the image (1 = true, 0 = false)
set_params2D(proj, [0.0, 0.0, 0.0, 0, 1.0])
set_params_proj(proj, [phi, tht, psi, s2x, s2y])
proj.write_image(stack_data, iprj)
icol += 1
if icol == rowlen:
icol = 0
irow += 1
iprj += 1
mic += model_gauss_noise(sigma_mic,4096,4096)
if parm_CTF:
#apply CTF
mic = filt_ctf(mic, ctf)
mic += filt_gaussl(model_gauss_noise(sigma2_mic, 4096, 4096), sigma_gauss_mic)
mic.write_image(micpref + "%1d.hdf" % (idef-3), 0)
drop_spider_doc("params.txt", params)
elif options.importctf != None:
print ' IMPORTCTF '
from utilities import read_text_row,write_text_row
from random import randint
import subprocess
grpfile = 'groupid%04d'%randint(1000,9999)
ctfpfile = 'ctfpfile%04d'%randint(1000,9999)
cterr = [options.defocuserror/100.0, options.astigmatismerror]
ctfs = read_text_row(options.importctf)
for kk in xrange(len(ctfs)):
root,name = os.path.split(ctfs[kk][-1])
ctfs[kk][-1] = name[:-4]
if(options.input[:4] != 'bdb:'):
ERROR('Sorry, only bdb files implemented','importctf',1)
d = options.input[4:]
#try: str = d.index('*')
#except: str = -1
from string import split
import glob
uu = os.path.split(d)
uu = os.path.join(uu[0],'EMAN2DB',uu[1]+'.bdb')
flist = glob.glob(uu)
for i in xrange(len(flist)):
root,name = os.path.split(flist[i])
root = root[:-7]
name = name[:-4]
fil = 'bdb:'+os.path.join(root,name)
sourcemic = EMUtil.get_all_attributes(fil,'ptcl_source_image')
nn = len(sourcemic)
gctfp = []
groupid = []
for kk in xrange(nn):
junk,name2 = os.path.split(sourcemic[kk])
name2 = name2[:-4]
ctfp = [-1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]
for ll in xrange(len(ctfs)):
if(name2 == ctfs[ll][-1]):
# found correct
if(ctfs[ll][8]/ctfs[ll][0] <= cterr[0]):
# acceptable defocus error
ctfp = ctfs[ll][:8]
if(ctfs[ll][10] > cterr[1] ):
# error of astigmatism exceed the threshold, set astigmatism to zero.
ctfp[6] = 0.0
ctfp[7] = 0.0
gctfp.append(ctfp)
groupid.append(kk)
break
if(len(groupid) > 0):
write_text_row(groupid, grpfile)
write_text_row(gctfp, ctfpfile)
cmd = "{} {} {} {}".format('e2bdb.py',fil,'--makevstack=bdb:'+root+'G'+name,'--list='+grpfile)
#print cmd
subprocess.call(cmd, shell=True)
cmd = "{} {} {} {}".format('sxheader.py','bdb:'+root+'G'+name,'--params=ctf','--import='+ctfpfile)
#print cmd
subprocess.call(cmd, shell=True)
else:
print ' >>> Group ',name,' skipped.'
cmd = "{} {} {}".format("rm -f",grpfile,ctfpfile)
subprocess.call(cmd, shell=True)
elif options.scale > 0.0:
from utilities import read_text_row,write_text_row
scale = options.scale
nargs = len(args)
if nargs != 2:
print "Please provide names of input and output file!"
return
p = read_text_row(args[0])
for i in xrange(len(p)):
p[i][3] /= scale
p[i][4] /= scale
write_text_row(p, args[1])
elif options.adaptive_mask:
from utilities import get_im
from morphology import adaptive_mask, binarize, erosion, dilation
nsigma = options.nsigma
ndilation = options.ndilation
kernel_size = options.kernel_size
gauss_standard_dev = options.gauss_standard_dev
nargs = len(args)
if nargs ==0:
print " Create 3D mask from a given volume, either automatically or from the user provided threshold."
elif nargs > 2:
print "Too many inputs are given, try again!"
return
else:
inputvol = get_im(args[0])
input_path, input_file_name = os.path.split(args[0])
input_file_name_root,ext=os.path.splitext(input_file_name)
if nargs == 2: mask_file_name = args[1]
else: mask_file_name = "adaptive_mask_for_"+input_file_name_root+".hdf" # Only hdf file is output.
if options.threshold !=9999.:
mask3d = binarize(inputvol, options.threshold)
for i in xrange(options.ne): mask3d = erosion(mask3d)
for i in xrange(options.nd): mask3d = dilation(mask3d)
else:
mask3d = adaptive_mask(inputvol, nsigma, ndilation, kernel_size, gauss_standard_dev)
mask3d.write_image(mask_file_name)
elif options.postprocess:
from utilities import get_im
from fundamentals import rot_avg_table
from morphology import compute_bfactor,power
from statistics import fsc
from filter import filt_table, filt_gaussinv
from EMAN2 import periodogram
e1 = get_im(args[0],0)
if e1.get_zsize()==1:
nimage = EMUtil.get_image_count(args[0])
if options.mask !=None: m = get_im(options.mask)
else: m = None
for i in xrange(nimage):
e1 = get_im(args[0],i)
if m: e1 *=m
guinerline = rot_avg_table(power(periodogram(e1),.5))
freq_max = 1/(2.*pixel_size)
freq_min = 1./options.B_start
b,junk=compute_bfactor(guinerline, freq_min, freq_max, pixel_size)
tmp = b/pixel_size**2
sigma_of_inverse=sqrt(2./tmp)
e1 = filt_gaussinv(e1,sigma_of_inverse)
if options.low_pass_filter:
from filter import filt_tanl
e1 =filt_tanl(e1,options.ff, options.aa)
e1.write_image(options.output)
else:
nargs = len(args)
e1 = get_im(args[0])
if nargs >1: e2 = get_im(args[1])
if options.mask !=None: m = get_im(options.mask)
else: m =None
pixel_size = options.pixel_size
from math import sqrt
if m !=None:
e1 *=m
if nargs >1 :e2 *=m
if options.fsc_weighted:
frc = fsc(e1,e2,1)
## FSC is done on masked two images
#### FSC weighting sqrt((2.*fsc)/(1+fsc));
fil = len(frc[1])*[None]
for i in xrange(len(fil)):
if frc[1][i]>=options.FSC_cutoff: tmp = frc[1][i]
else: tmp = 0.0
fil[i] = sqrt(2.*tmp/(1.+tmp))
if nargs>1: e1 +=e2
if options.fsc_weighted: e1=filt_table(e1,fil)
guinerline = rot_avg_table(power(periodogram(e1),.5))
freq_max = 1/(2.*pixel_size)
freq_min = 1./options.B_start
b,junk = compute_bfactor(guinerline, freq_min, freq_max, pixel_size)
tmp = b/pixel_size**2
sigma_of_inverse=sqrt(2./tmp)
e1 = filt_gaussinv(e1,sigma_of_inverse)
if options.low_pass_filter:
from filter import filt_tanl
e1 =filt_tanl(e1,options.ff, options.aa)
e1.write_image(options.output)
elif options.window_stack:
nargs = len(args)
if nargs ==0:
print " Reduce image size of a stack"
return
else:
output_stack_name = None
inputstack = args[0]
if nargs ==2:output_stack_name = args[1]
input_path,input_file_name=os.path.split(inputstack)
input_file_name_root,ext=os.path.splitext(input_file_name)
if input_file_name_root[0:3]=="bdb":stack_is_bdb= True
else: stack_is_bdb= False
if output_stack_name is None:
if stack_is_bdb: output_stack_name ="bdb:reduced_"+input_file_name_root[4:]
else:output_stack_name = "reduced_"+input_file_name_root+".hdf" # Only hdf file is output.
nimage = EMUtil.get_image_count(inputstack)
from fundamentals import window2d
for i in xrange(nimage):
image = EMData()
image.read_image(inputstack,i)
w = window2d(image,options.box,options.box)
w.write_image(output_stack_name,i)
else: ERROR("Please provide option name","sxprocess.py",1)
def main():
import sys
import os
import math
import random
import pyemtbx.options
import time
from random import random, seed, randint
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <inputfile> <outputfile>
Generic 2-D image processing programs.
Functionality:
1. Phase flip a stack of images and write output to new file:
sxprocess.py input_stack.hdf output_stack.hdf --phase_flip
2. Resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.
The window size will change accordingly.
sxprocess input.hdf output.hdf --changesize --ratio=0.5
3. Compute average power spectrum of a stack of 2D images with optional padding (option wn) with zeroes.
sxprocess.py input_stack.hdf powerspectrum.hdf --pw [--wn=1024]
4. Generate a stack of projections bdb:data and micrographs with prefix mic (i.e., mic0.hdf, mic1.hdf etc) from structure input_structure.hdf, with CTF applied to both projections and micrographs:
sxprocess.py input_structure.hdf data mic --generate_projections format="bdb":apix=5.2:CTF=True:boxsize=64
5. Retrieve original image numbers in the selected ISAC group (here group 12 from generation 3):
sxprocess.py bdb:test3 class_averages_generation_3.hdf list3_12.txt --isacgroup=12 --params=originalid
6. Retrieve original image numbers of images listed in ISAC output stack of averages:
sxprocess.py select1.hdf ohk.txt
7. Adjust rotationally averaged power spectrum of an image to that of a reference image or a reference 1D power spectrum stored in an ASCII file.
Optionally use a tangent low-pass filter. Also works for a stack of images, in which case the output is also a stack.
sxprocess.py vol.hdf ref.hdf avol.hdf < 0.25 0.2> --adjpw
sxprocess.py vol.hdf pw.txt avol.hdf < 0.25 0.2> --adjpw
8. Generate a 1D rotationally averaged power spectrum of an image.
sxprocess.py vol.hdf --rotwp=rotpw.txt
# Output will contain three columns:
(1) rotationally averaged power spectrum
(2) logarithm of the rotationally averaged power spectrum
(3) integer line number (from zero to approximately to half the image size)
9. Apply 3D transformation (rotation and/or shift) to a set of orientation parameters associated with projection data.
sxprocess.py --transfromparams=phi,theta,psi,tx,ty,tz input.txt output.txt
The output file is then imported and 3D transformed volume computed:
sxheader.py bdb:p --params=xform.projection --import=output.txt
mpirun -np 2 sxrecons3d_n.py bdb:p tvol.hdf --MPI
The reconstructed volume is in the position of the volume computed using the input.txt parameters and then
transformed with rot_shift3D(vol, phi,theta,psi,tx,ty,tz)
10. Import ctf parameters from the output of sxcter into windowed particle headers.
There are three possible input files formats: (1) all particles are in one stack, (2 aor 3) particles are in stacks, each stack corresponds to a single micrograph.
In each case the particles should contain a name of the micrograph of origin stores using attribute name 'ptcl_source_image'.
Normally this is done by e2boxer.py during windowing.
Particles whose defocus or astigmatism error exceed set thresholds will be skipped, otherwise, virtual stacks with the original way preceded by G will be created.
sxprocess.py --input=bdb:data --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
# Output will be a vritual stack bdb:Gdata
sxprocess.py --input="bdb:directory/stacks*" --importctf=outdir/partres --defocuserror=10.0 --astigmatismerror=5.0
To concatenate output files:
cd directory
e2bdb.py . --makevstack=bdb:allparticles --filt=G
IMPORTANT: Please do not move (or remove!) any input/intermediate EMAN2DB files as the information is linked between them.
11. Scale 3D shifts. The shifts in the input five columns text file with 3D orientation parameters will be DIVIDED by the scale factor
sxprocess.py orientationparams.txt scaledparams.txt scale=0.5
12. Generate adaptive mask from a given 3-D volume.
"""
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--order",
action="store_true",
help=
"Two arguments are required: name of input stack and desired name of output stack. The output stack is the input stack sorted by similarity in terms of cross-correlation coefficent.",
default=False)
parser.add_option("--order_lookup",
action="store_true",
help="Test/Debug.",
default=False)
parser.add_option("--order_metropolis",
action="store_true",
help="Test/Debug.",
default=False)
parser.add_option("--order_pca",
action="store_true",
help="Test/Debug.",
default=False)
parser.add_option(
"--initial",
type="int",
default=-1,
help=
"Specifies which image will be used as an initial seed to form the chain. (default = 0, means the first image)"
)
parser.add_option(
"--circular",
action="store_true",
help=
"Select circular ordering (fisr image has to be similar to the last",
default=False)
parser.add_option(
"--radius",
type="int",
default=-1,
help="Radius of a circular mask for similarity based ordering")
parser.add_option(
"--changesize",
action="store_true",
help=
"resample (decimate or interpolate up) images (2D or 3D) in a stack to change the pixel size.",
default=False)
parser.add_option(
"--ratio",
type="float",
default=1.0,
help=
"The ratio of new to old image size (if <1 the pixel size will increase and image size decrease, if>1, the other way round"
)
parser.add_option(
"--pw",
action="store_true",
help=
"compute average power spectrum of a stack of 2-D images with optional padding (option wn) with zeroes",
default=False)
parser.add_option(
"--wn",
type="int",
default=-1,
help=
"Size of window to use (should be larger/equal than particle box size, default padding to max(nx,ny))"
)
parser.add_option("--phase_flip",
action="store_true",
help="Phase flip the input stack",
default=False)
parser.add_option(
"--makedb",
metavar="param1=value1:param2=value2",
type="string",
action="append",
help=
"One argument is required: name of key with which the database will be created. Fill in database with parameters specified as follows: --makedb param1=value1:param2=value2, e.g. 'gauss_width'=1.0:'pixel_input'=5.2:'pixel_output'=5.2:'thr_low'=1.0"
)
parser.add_option(
"--generate_projections",
metavar="param1=value1:param2=value2",
type="string",
action="append",
help=
"Three arguments are required: name of input structure from which to generate projections, desired name of output projection stack, and desired prefix for micrographs (e.g. if prefix is 'mic', then micrographs mic0.hdf, mic1.hdf etc will be generated). Optional arguments specifying format, apix, box size and whether to add CTF effects can be entered as follows after --generate_projections: format='bdb':apix=5.2:CTF=True:boxsize=100, or format='hdf', etc., where format is bdb or hdf, apix (pixel size) is a float, CTF is True or False, and boxsize denotes the dimension of the box (assumed to be a square). If an optional parameter is not specified, it will default as follows: format='bdb', apix=2.5, CTF=False, boxsize=64."
)
parser.add_option(
"--isacgroup",
type="int",
help=
"Retrieve original image numbers in the selected ISAC group. See ISAC documentation for details.",
default=-1)
parser.add_option(
"--isacselect",
action="store_true",
help=
"Retrieve original image numbers of images listed in ISAC output stack of averages. See ISAC documentation for details.",
default=False)
parser.add_option(
"--params",
type="string",
default=None,
help="Name of header of parameter, which one depends on specific option"
)
parser.add_option(
"--adjpw",
action="store_true",
help="Adjust rotationally averaged power spectrum of an image",
default=False)
parser.add_option(
"--rotpw",
type="string",
default=None,
help=
"Name of the text file to contain rotationally averaged power spectrum of the input image."
)
parser.add_option(
"--transformparams",
type="string",
default=None,
help=
"Transform 3D projection orientation parameters using six 3D parameters (phi, theta,psi,sx,sy,sz). Input: --transformparams=45.,66.,12.,-2,3,-5.5 desired six transformation of the reconstructed structure. Output: file with modified orientation parameters."
)
# import ctf estimates done using cter
parser.add_option("--input",
type="string",
default=None,
help="Input particles.")
parser.add_option(
"--importctf",
type="string",
default=None,
help="Name of the file containing CTF parameters produced by sxcter.")
parser.add_option(
"--defocuserror",
type="float",
default=1000000.0,
help=
"Exclude micrographs whose relative defocus error as estimated by sxcter is larger than defocuserror percent. The error is computed as (std dev defocus)/defocus*100%"
)
parser.add_option(
"--astigmatismerror",
type="float",
default=360.0,
help=
"Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sxcter is larger than astigmatismerror degrees."
)
# import ctf estimates done using cter
parser.add_option(
"--scale",
type="float",
default=-1.0,
help=
"Divide shifts in the input 3D orientation parameters text file by the scale factor."
)
# generate adaptive mask from an given 3-Db volue
parser.add_option("--adaptive_mask",
action="store_true",
help="create adavptive 3-D mask from a given volume",
default=False)
parser.add_option(
"--nsigma",
type="float",
default=1.,
help=
"number of times of sigma of the input volume to obtain the the large density cluster"
)
parser.add_option(
"--ndilation",
type="int",
default=3,
help=
"number of times of dilation applied to the largest cluster of density"
)
parser.add_option(
"--kernel_size",
type="int",
default=11,
help="convolution kernel for smoothing the edge of the mask")
parser.add_option(
"--gauss_standard_dev",
type="int",
default=9,
help="stanadard deviation value to generate Gaussian edge")
(options, args) = parser.parse_args()
global_def.BATCH = True
if options.phase_flip:
nargs = len(args)
if nargs != 2:
print "must provide name of input and output file!"
return
from EMAN2 import Processor
instack = args[0]
outstack = args[1]
nima = EMUtil.get_image_count(instack)
from filter import filt_ctf
for i in xrange(nima):
img = EMData()
img.read_image(instack, i)
try:
ctf = img.get_attr('ctf')
except:
print "no ctf information in input stack! Exiting..."
return
dopad = True
sign = 1
binary = 1 # phase flip
assert img.get_ysize() > 1
dict = ctf.to_dict()
dz = dict["defocus"]
cs = dict["cs"]
voltage = dict["voltage"]
pixel_size = dict["apix"]
b_factor = dict["bfactor"]
ampcont = dict["ampcont"]
dza = dict["dfdiff"]
azz = dict["dfang"]
if dopad and not img.is_complex(): ip = 1
else: ip = 0
params = {
"filter_type": Processor.fourier_filter_types.CTF_,
"defocus": dz,
"Cs": cs,
"voltage": voltage,
"Pixel_size": pixel_size,
"B_factor": b_factor,
"amp_contrast": ampcont,
"dopad": ip,
"binary": binary,
"sign": sign,
"dza": dza,
"azz": azz
}
tmp = Processor.EMFourierFilter(img, params)
tmp.set_attr_dict({"ctf": ctf})
tmp.write_image(outstack, i)
elif options.changesize:
nargs = len(args)
if nargs != 2:
ERROR("must provide name of input and output file!", "change size",
1)
return
from utilities import get_im
instack = args[0]
outstack = args[1]
sub_rate = float(options.ratio)
nima = EMUtil.get_image_count(instack)
from fundamentals import resample
for i in xrange(nima):
resample(get_im(instack, i), sub_rate).write_image(outstack, i)
elif options.isacgroup > -1:
nargs = len(args)
if nargs != 3:
ERROR("Three files needed on input!", "isacgroup", 1)
return
from utilities import get_im
instack = args[0]
m = get_im(args[1], int(options.isacgroup)).get_attr("members")
l = []
for k in m:
l.append(int(get_im(args[0], k).get_attr(options.params)))
from utilities import write_text_file
write_text_file(l, args[2])
elif options.isacselect:
nargs = len(args)
if nargs != 2:
ERROR("Two files needed on input!", "isacgroup", 1)
return
from utilities import get_im
nima = EMUtil.get_image_count(args[0])
m = []
for k in xrange(nima):
m += get_im(args[0], k).get_attr("members")
m.sort()
from utilities import write_text_file
write_text_file(m, args[1])
elif options.pw:
nargs = len(args)
if nargs < 2:
ERROR("must provide name of input and output file!", "pw", 1)
return
from utilities import get_im
d = get_im(args[0])
nx = d.get_xsize()
ny = d.get_ysize()
if nargs == 3: mask = get_im(args[2])
wn = int(options.wn)
if wn == -1:
wn = max(nx, ny)
else:
if ((wn < nx) or (wn < ny)):
ERROR("window size cannot be smaller than the image size",
"pw", 1)
n = EMUtil.get_image_count(args[0])
from utilities import model_blank, model_circle, pad
from EMAN2 import periodogram
p = model_blank(wn, wn)
for i in xrange(n):
d = get_im(args[0], i)
if nargs == 3:
d *= mask
st = Util.infomask(d, None, True)
d -= st[0]
p += periodogram(pad(d, wn, wn, 1, 0.))
p /= n
p.write_image(args[1])
elif options.adjpw:
if len(args) < 3:
ERROR(
"filt_by_rops input target output fl aa (the last two are optional parameters of a low-pass filter)",
"adjpw", 1)
return
img_stack = args[0]
from math import sqrt
from fundamentals import rops_table, fft
from utilities import read_text_file, get_im
from filter import filt_tanl, filt_table
if (args[1][-3:] == 'txt'):
rops_dst = read_text_file(args[1])
else:
rops_dst = rops_table(get_im(args[1]))
out_stack = args[2]
if (len(args) > 4):
fl = float(args[3])
aa = float(args[4])
else:
fl = -1.0
aa = 0.0
nimage = EMUtil.get_image_count(img_stack)
for i in xrange(nimage):
img = fft(get_im(img_stack, i))
rops_src = rops_table(img)
assert len(rops_dst) == len(rops_src)
table = [0.0] * len(rops_dst)
for j in xrange(len(rops_dst)):
table[j] = sqrt(rops_dst[j] / rops_src[j])
if (fl > 0.0):
img = filt_tanl(img, fl, aa)
img = fft(filt_table(img, table))
img.write_image(out_stack, i)
elif options.rotpw != None:
if len(args) != 1:
ERROR("Only one input permitted", "rotpw", 1)
return
from utilities import write_text_file, get_im
from fundamentals import rops_table
from math import log10
t = rops_table(get_im(args[0]))
x = range(len(t))
r = [0.0] * len(x)
for i in x:
r[i] = log10(t[i])
write_text_file([t, r, x], options.rotpw)
elif options.transformparams != None:
if len(args) != 2:
ERROR(
"Please provide names of input and output files with orientation parameters",
"transformparams", 1)
return
from utilities import read_text_row, write_text_row
transf = [0.0] * 6
spl = options.transformparams.split(',')
for i in xrange(len(spl)):
transf[i] = float(spl[i])
write_text_row(rotate_shift_params(read_text_row(args[0]), transf),
args[1])
elif options.makedb != None:
nargs = len(args)
if nargs != 1:
print "must provide exactly one argument denoting database key under which the input params will be stored"
return
dbkey = args[0]
print "database key under which params will be stored: ", dbkey
gbdb = js_open_dict("e2boxercache/gauss_box_DB.json")
parmstr = 'dummy:' + options.makedb[0]
(processorname, param_dict) = parsemodopt(parmstr)
dbdict = {}
for pkey in param_dict:
if (pkey == 'invert_contrast') or (pkey == 'use_variance'):
if param_dict[pkey] == 'True':
dbdict[pkey] = True
else:
dbdict[pkey] = False
else:
dbdict[pkey] = param_dict[pkey]
gbdb[dbkey] = dbdict
elif options.generate_projections:
nargs = len(args)
if nargs != 3:
ERROR("Must provide name of input structure(s) from which to generate projections, name of output projection stack, and prefix for output micrographs."\
"sxprocess - generate projections",1)
return
inpstr = args[0]
outstk = args[1]
micpref = args[2]
parmstr = 'dummy:' + options.generate_projections[0]
(processorname, param_dict) = parsemodopt(parmstr)
parm_CTF = False
parm_format = 'bdb'
parm_apix = 2.5
if 'CTF' in param_dict:
if param_dict['CTF'] == 'True':
parm_CTF = True
if 'format' in param_dict:
parm_format = param_dict['format']
if 'apix' in param_dict:
parm_apix = float(param_dict['apix'])
boxsize = 64
if 'boxsize' in param_dict:
boxsize = int(param_dict['boxsize'])
print "pixel size: ", parm_apix, " format: ", parm_format, " add CTF: ", parm_CTF, " box size: ", boxsize
scale_mult = 2500
sigma_add = 1.5
sigma_proj = 30.0
sigma2_proj = 17.5
sigma_gauss = 0.3
sigma_mic = 30.0
sigma2_mic = 17.5
sigma_gauss_mic = 0.3
if 'scale_mult' in param_dict:
scale_mult = float(param_dict['scale_mult'])
if 'sigma_add' in param_dict:
sigma_add = float(param_dict['sigma_add'])
if 'sigma_proj' in param_dict:
sigma_proj = float(param_dict['sigma_proj'])
if 'sigma2_proj' in param_dict:
sigma2_proj = float(param_dict['sigma2_proj'])
if 'sigma_gauss' in param_dict:
sigma_gauss = float(param_dict['sigma_gauss'])
if 'sigma_mic' in param_dict:
sigma_mic = float(param_dict['sigma_mic'])
if 'sigma2_mic' in param_dict:
sigma2_mic = float(param_dict['sigma2_mic'])
if 'sigma_gauss_mic' in param_dict:
sigma_gauss_mic = float(param_dict['sigma_gauss_mic'])
from filter import filt_gaussl, filt_ctf
from utilities import drop_spider_doc, even_angles, model_gauss, delete_bdb, model_blank, pad, model_gauss_noise, set_params2D, set_params_proj
from projection import prep_vol, prgs
seed(14567)
delta = 29
angles = even_angles(delta, 0.0, 89.9, 0.0, 359.9, "S")
nangle = len(angles)
modelvol = []
nvlms = EMUtil.get_image_count(inpstr)
from utilities import get_im
for k in xrange(nvlms):
modelvol.append(get_im(inpstr, k))
nx = modelvol[0].get_xsize()
if nx != boxsize:
ERROR("Requested box dimension does not match dimension of the input model.", \
"sxprocess - generate projections",1)
nvol = 10
volfts = [[] for k in xrange(nvlms)]
for k in xrange(nvlms):
for i in xrange(nvol):
sigma = sigma_add + random() # 1.5-2.5
addon = model_gauss(sigma, boxsize, boxsize, boxsize, sigma,
sigma, 38, 38, 40)
scale = scale_mult * (0.5 + random())
vf, kb = prep_vol(modelvol[k] + scale * addon)
volfts[k].append(vf)
del vf, modelvol
if parm_format == "bdb":
stack_data = "bdb:" + outstk
delete_bdb(stack_data)
else:
stack_data = outstk + ".hdf"
Cs = 2.0
pixel = parm_apix
voltage = 120.0
ampcont = 10.0
ibd = 4096 / 2 - boxsize
iprj = 0
width = 240
xstart = 8 + boxsize / 2
ystart = 8 + boxsize / 2
rowlen = 17
from random import randint
params = []
for idef in xrange(3, 8):
irow = 0
icol = 0
mic = model_blank(4096, 4096)
defocus = idef * 0.5 #0.2
if parm_CTF:
astampl = defocus * 0.15
astangl = 50.0
ctf = generate_ctf([
defocus, Cs, voltage, pixel, ampcont, 0.0, astampl, astangl
])
for i in xrange(nangle):
for k in xrange(12):
dphi = 8.0 * (random() - 0.5)
dtht = 8.0 * (random() - 0.5)
psi = 360.0 * random()
phi = angles[i][0] + dphi
tht = angles[i][1] + dtht
s2x = 4.0 * (random() - 0.5)
s2y = 4.0 * (random() - 0.5)
params.append([phi, tht, psi, s2x, s2y])
ivol = iprj % nvol
#imgsrc = randint(0,nvlms-1)
imgsrc = iprj % nvlms
proj = prgs(volfts[imgsrc][ivol], kb,
[phi, tht, psi, -s2x, -s2y])
x = xstart + irow * width
y = ystart + icol * width
mic += pad(proj, 4096, 4096, 1, 0.0, x - 2048, y - 2048, 0)
proj = proj + model_gauss_noise(sigma_proj, nx, nx)
if parm_CTF:
proj = filt_ctf(proj, ctf)
proj.set_attr_dict({"ctf": ctf, "ctf_applied": 0})
proj = proj + filt_gaussl(
model_gauss_noise(sigma2_proj, nx, nx), sigma_gauss)
proj.set_attr("origimgsrc", imgsrc)
proj.set_attr("test_id", iprj)
# flags describing the status of the image (1 = true, 0 = false)
set_params2D(proj, [0.0, 0.0, 0.0, 0, 1.0])
set_params_proj(proj, [phi, tht, psi, s2x, s2y])
proj.write_image(stack_data, iprj)
icol += 1
if icol == rowlen:
icol = 0
irow += 1
iprj += 1
mic += model_gauss_noise(sigma_mic, 4096, 4096)
if parm_CTF:
#apply CTF
mic = filt_ctf(mic, ctf)
mic += filt_gaussl(model_gauss_noise(sigma2_mic, 4096, 4096),
sigma_gauss_mic)
mic.write_image(micpref + "%1d.hdf" % (idef - 3), 0)
drop_spider_doc("params.txt", params)
elif options.importctf != None:
print ' IMPORTCTF '
from utilities import read_text_row, write_text_row
from random import randint
import subprocess
grpfile = 'groupid%04d' % randint(1000, 9999)
ctfpfile = 'ctfpfile%04d' % randint(1000, 9999)
cterr = [options.defocuserror / 100.0, options.astigmatismerror]
ctfs = read_text_row(options.importctf)
for kk in xrange(len(ctfs)):
root, name = os.path.split(ctfs[kk][-1])
ctfs[kk][-1] = name[:-4]
if (options.input[:4] != 'bdb:'):
ERROR('Sorry, only bdb files implemented', 'importctf', 1)
d = options.input[4:]
#try: str = d.index('*')
#except: str = -1
from string import split
import glob
uu = os.path.split(d)
uu = os.path.join(uu[0], 'EMAN2DB', uu[1] + '.bdb')
flist = glob.glob(uu)
for i in xrange(len(flist)):
root, name = os.path.split(flist[i])
root = root[:-7]
name = name[:-4]
fil = 'bdb:' + os.path.join(root, name)
sourcemic = EMUtil.get_all_attributes(fil, 'ptcl_source_image')
nn = len(sourcemic)
gctfp = []
groupid = []
for kk in xrange(nn):
junk, name2 = os.path.split(sourcemic[kk])
name2 = name2[:-4]
ctfp = [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
for ll in xrange(len(ctfs)):
if (name2 == ctfs[ll][-1]):
# found correct
if (ctfs[ll][8] / ctfs[ll][0] <= cterr[0]):
# acceptable defocus error
ctfp = ctfs[ll][:8]
if (ctfs[ll][10] > cterr[1]):
# error of astigmatism exceed the threshold, set astigmatism to zero.
ctfp[6] = 0.0
ctfp[7] = 0.0
gctfp.append(ctfp)
groupid.append(kk)
break
if (len(groupid) > 0):
write_text_row(groupid, grpfile)
write_text_row(gctfp, ctfpfile)
cmd = "{} {} {} {}".format(
'e2bdb.py', fil, '--makevstack=bdb:' + root + 'G' + name,
'--list=' + grpfile)
#print cmd
subprocess.call(cmd, shell=True)
cmd = "{} {} {} {}".format('sxheader.py',
'bdb:' + root + 'G' + name,
'--params=ctf',
'--import=' + ctfpfile)
#print cmd
subprocess.call(cmd, shell=True)
else:
print ' >>> Group ', name, ' skipped.'
cmd = "{} {} {}".format("rm -f", grpfile, ctfpfile)
subprocess.call(cmd, shell=True)
elif options.scale > 0.0:
from utilities import read_text_row, write_text_row
scale = options.scale
nargs = len(args)
if nargs != 2:
print "Please provide names of input and output file!"
return
p = read_text_row(args[0])
for i in xrange(len(p)):
p[i][3] /= scale
p[i][4] /= scale
write_text_row(p, args[1])
elif options.adaptive_mask:
from utilities import get_im
from morphology import adaptive_mask
nsigma = options.nsigma
ndilation = options.ndilation
kernel_size = options.kernel_size
gauss_standard_dev = options.gauss_standard_dev
nargs = len(args)
if nargs > 2:
print "Too many inputs are given, try again!"
return
else:
inputvol = get_im(args[0])
input_path, input_file_name = os.path.split(args[0])
input_file_name_root, ext = os.path.splitext(input_file_name)
if nargs == 2: mask_file_name = args[1]
else:
mask_file_name = "adaptive_mask_for" + input_file_name_root + ".hdf" # Only hdf file is output.
mask3d = adaptive_mask(inputvol, nsigma, ndilation, kernel_size,
gauss_standard_dev)
mask3d.write_image(mask_file_name)
else:
ERROR("Please provide option name", "sxprocess.py", 1)
