#!/usr/bin/env python # -*- coding: utf-8 -*- # Copyright (C) 2018 Daniel Asarnow # University of California, San Francisco # # Program for sorting particles in electron microscopy. # See help text and README file for more information. # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. import numpy as np import pyfftw import sys from numpy.fft import fftshift from numpy.fft import fftfreq from numpy.fft import rfftfreq from pyem import ctf from pyem import mrc from pyem import star from pyem import util from pyem import vop from pyfftw.interfaces.numpy_fft import rfft2 from pyfftw.interfaces.numpy_fft import irfft2 def main(args): pyfftw.interfaces.cache.enable() refmap = mrc.read(args.key, compat="relion") df = star.parse_star(args.input, keep_index=False) star.augment_star_ucsf(df) refmap_ft = vop.vol_ft(refmap, threads=args.threads) apix = star.calculate_apix(df) sz = refmap_ft.shape[0] // 2 - 1 sx, sy = np.meshgrid(rfftfreq(sz), fftfreq(sz)) s = np.sqrt(sx ** 2 + sy ** 2) r = s * sz r = np.round(r).astype(np.int64) r[r > sz // 2] = sz // 2 + 1 a = np.arctan2(sy, sx) def1 = df["rlnDefocusU"].values def2 = df["rlnDefocusV"].values angast = df["rlnDefocusAngle"].values phase = df["rlnPhaseShift"].values kv = df["rlnVoltage"].values ac = df["rlnAmplitudeContrast"].values cs = df["rlnSphericalAberration"].values xshift = df["rlnOriginX"].values yshift = df["rlnOriginY"].values score = np.zeros(df.shape[0]) # TODO parallelize for i, row in df.iterrows(): xcor = particle_xcorr(row, refmap_ft) if args.top is None: args.top = df.shape[0] top = df.iloc[np.argsort(score)][:args.top] star.simplify_star_ucsf(top) star.write_star(args.output, top) return 0 def particle_xcorr(ptcl, refmap_ft): r = util.euler2rot(*np.deg2rad(ptcl[star.Relion.ANGLES])) proj = vop.interpolate_slice_numba(refmap_ft, r) c = ctf.eval_ctf(s / apix, a, def1[i], def2[i], angast[i], phase[i], kv[i], ac[i], cs[i], bf=0, lp=2 * apix) pshift = np.exp(-2 * np.pi * 1j * (-xshift[i] * sx + -yshift * sy)) proj_ctf = proj * pshift * c with mrc.ZSliceReader(ptcl[star.Relion.IMAGE_NAME]) as f: exp_image_fft = rfft2(fftshift(f.read(i))) xcor_fft = exp_image_fft * proj_ctf xcor = fftshift(irfft2(xcor_fft)) return xcor if __name__ == "__main__": import argparse parser = argparse.ArgumentParser() parser.add_argument("input") parser.add_argument("output") parser.add_argument("--key") parser.add_argument("--highpass") parser.add_argument("--lowpass") parser.add_argument("--top", help="Write top N particles", metavar="N", type=int) parser.add_argument("--threads", "-j", help="Number of parallel threads", type=int) sys.exit(main(parser.parse_args()))