if to_write:
timer = py_utils.my_timer()
pm = read_config.get_detector_config(args.config_file, show=args.vb)
q_pm = read_config.compute_q_params(pm['detd'], pm['dets_x'], pm['dets_y'], pm['pixsize'], pm['wavelength'], show=args.vb)
timer.reset_and_report("Reading experiment parameters") if args.vb else timer.reset()
fov_len = int(np.ceil(q_pm['fov_in_A']/q_pm['half_p_res']) + 1)
eV = process_pdb.wavelength_in_A_to_eV(pm['wavelength'])
if pdb_code is not None:
process_pdb.fetch_pdb(pdb_code)
atom_types = process_pdb.find_atom_types(pdb_file)
scatt_list = process_pdb.make_scatt_list(atom_types, aux_dir, eV)
atoms = process_pdb.get_atom_coords(pdb_file, scatt_list)
(s_l, t_l) = process_pdb.read_symmetry(pdb_file)
if len(s_l)*len(t_l)>0:
all_atoms = process_pdb.apply_symmetry(atoms, s_l, t_l)
else:
all_atoms = atoms
timer.reset_and_report("Reading PDB") if args.vb else timer.reset()
# all_atoms=[.nff['f1'],x,y,z,mass]
den = process_pdb.atoms_to_density_map(all_atoms, q_pm['half_p_res'])
lp_den = process_pdb.low_pass_filter_density_map(den)
timer.reset_and_report("Creating density map") if args.vb else timer.reset()
py_utils.write_density(den_file, lp_den, binary=True)
timer.reset_and_report("Writing densities to file") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
def main():
'''Parses command line arguments to create 3D intensity file using config file parameters'''
logging.basicConfig(filename="recon.log",
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description="make intensities")
args = parser.special_parse_args()
den_file = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_intensities',
'in_density_file'))
intens_file = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_intensities',
'out_intensity_file'))
try:
num_threads = int(
read_config.get_param(args.config_file, 'make_intensities',
'num_threads'))
except read_config.configparser.NoOptionError:
num_threads = 4
if args.yes:
to_write = True
else:
to_write = py_utils.check_to_overwrite(intens_file)
logging.info("\n\nStarting.... make_intensities")
logging.info(' '.join(sys.argv))
if to_write:
timer = py_utils.MyTimer()
pm = read_config.get_detector_config(args.config_file, show=args.vb) #pylint: disable=C0103
q_pm = read_config.compute_q_params(pm['detd'],
pm['dets_x'],
pm['dets_y'],
pm['pixsize'],
pm['wavelength'],
pm['ewald_rad'],
show=args.vb)
timer.reset_and_report(
"Reading experiment parameters") if args.vb else timer.reset()
fov_len = 2 * int(np.ceil(
q_pm['fov_in_A'] / q_pm['half_p_res'] / 2.)) + 3
logging.info('Volume size: %d', fov_len)
den = py_utils.read_density(den_file)
min_over = float(fov_len) / den.shape[0]
if min_over > 12:
if py_utils.confirm_oversampling(min_over) is False:
sys.exit(0)
timer.reset_and_report(
"Reading densities") if args.vb else timer.reset()
pad_den = np.zeros(3 * (fov_len, ))
den_sh = den.shape
pad_den[:den_sh[0], :den_sh[1], :den_sh[2]] = den.copy()
if WITH_PYFFTW:
intens = np.abs(
np.fft.fftshift(
pyfftw.interfaces.numpy_fft.fftn(
pad_den,
threads=num_threads,
planner_effort='FFTW_ESTIMATE')))**2
else:
intens = np.abs(np.fft.fftshift(np.fft.fftn(pad_den)))**2
timer.reset_and_report(
"Computing intensities") if args.vb else timer.reset()
py_utils.write_density(intens_file, intens, binary=True)
timer.reset_and_report(
"Writing intensities") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
else:
pass
timer = py_utils.my_timer()
pm = read_config.get_detector_config(args.config_file, show=args.vb)
q_pm = read_config.compute_q_params(pm['detd'],
pm['detsize'],
pm['pixsize'],
pm['wavelength'],
show=args.vb)
timer.reset_and_report(
"Reading experiment parameters") if args.vb else timer.reset()
fov_len = int(np.ceil(q_pm['fov_in_A'] / q_pm['half_p_res']) + 1)
den = py_utils.read_density(den_file, binary=True)
timer.reset_and_report(
"Reading densities") if args.vb else timer.reset()
pad_den = np.zeros(3 * (fov_len, ))
den_sh = den.shape
pad_den[:den_sh[0], :den_sh[1], :den_sh[2]] = den.copy()
ft = np.abs(np.fft.fftshift(np.fft.fftn(pad_den)))
intens = ft * ft
timer.reset_and_report(
"Computing intensities") if args.vb else timer.reset()
py_utils.write_density(intens_file, intens, binary=True)
timer.reset_and_report(
"Writing intensities") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
else:
pass
def main():
'''Parses command line arguments to create 3D intensity file using config file parameters'''
logging.basicConfig(filename="recon.log", level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description="make intensities")
args = parser.special_parse_args()
den_file = os.path.join(args.main_dir,
read_config.get_filename(args.config_file,
'make_intensities',
'in_density_file'))
intens_file = os.path.join(args.main_dir,
read_config.get_filename(args.config_file,
'make_intensities',
'out_intensity_file'))
try:
num_threads = int(read_config.get_param(args.config_file,
'make_intensities',
'num_threads'))
except read_config.configparser.NoOptionError:
num_threads = 4
if args.yes:
to_write = True
else:
to_write = py_utils.check_to_overwrite(intens_file)
logging.info("\n\nStarting.... make_intensities")
logging.info(' '.join(sys.argv))
if to_write:
timer = py_utils.MyTimer()
pm = read_config.get_detector_config(args.config_file, show=args.vb) #pylint: disable=C0103
q_pm = read_config.compute_q_params(pm['detd'], pm['dets_x'],
pm['dets_y'], pm['pixsize'],
pm['wavelength'], pm['ewald_rad'], show=args.vb)
timer.reset_and_report("Reading experiment parameters") if args.vb else timer.reset()
fov_len = 2 * int(np.ceil(q_pm['fov_in_A']/q_pm['half_p_res']/2.)) + 3
logging.info('Volume size: %d', fov_len)
den = py_utils.read_density(den_file)
min_over = float(fov_len)/den.shape[0]
if min_over > 12:
if py_utils.confirm_oversampling(min_over) is False:
sys.exit(0)
timer.reset_and_report("Reading densities") if args.vb else timer.reset()
pad_den = np.zeros(3*(fov_len,))
den_sh = den.shape
pad_den[:den_sh[0], :den_sh[1], :den_sh[2]] = den.copy()
if WITH_PYFFTW:
intens = np.abs(np.fft.fftshift(pyfftw.interfaces.numpy_fft.fftn(
pad_den, threads=num_threads, planner_effort='FFTW_ESTIMATE')))**2
else:
intens = np.abs(np.fft.fftshift(np.fft.fftn(pad_den)))**2
timer.reset_and_report("Computing intensities") if args.vb else timer.reset()
py_utils.write_density(intens_file, intens, binary=True)
timer.reset_and_report("Writing intensities") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
else:
pass
def main():
'''Parse command line arguments and generate electron density volume with config file'''
logging.basicConfig(filename="recon.log",
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description="make electron density")
args = parser.special_parse_args()
logging.info("\n\nStarting.... make_densities")
logging.info(' '.join(sys.argv))
try:
pdb_file = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_densities',
'in_pdb_file'))
pdb_code = None
except read_config.configparser.NoOptionError:
pdb_code = read_config.get_filename(args.config_file, 'make_densities',
'pdb_code')
pdb_file = 'aux/%s.pdb' % pdb_code.upper()
try:
num_threads = int(
read_config.get_param(args.config_file, 'make_densities',
'num_threads'))
except read_config.configparser.NoOptionError:
num_threads = 4
aux_dir = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_densities',
'scatt_dir'))
den_file = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_densities',
'out_density_file'))
if args.yes:
to_write = True
else:
to_write = py_utils.check_to_overwrite(den_file)
if to_write:
timer = py_utils.MyTimer()
pm = read_config.get_detector_config(args.config_file, show=args.vb) # pylint: disable=C0103
q_pm = read_config.compute_q_params(pm['detd'],
pm['dets_x'],
pm['dets_y'],
pm['pixsize'],
pm['wavelength'],
pm['ewald_rad'],
show=args.vb)
timer.reset_and_report(
"Reading experiment parameters") if args.vb else timer.reset()
if pdb_code is not None:
process_pdb.fetch_pdb(pdb_code)
all_atoms = process_pdb.process(pdb_file, aux_dir, pm['wavelength'])
timer.reset_and_report("Reading PDB") if args.vb else timer.reset()
den = process_pdb.atoms_to_density_map(all_atoms, q_pm['half_p_res'])
lp_den = process_pdb.low_pass_filter_density_map(den,
threads=num_threads)
timer.reset_and_report(
"Creating density map") if args.vb else timer.reset()
py_utils.write_density(den_file, lp_den, binary=True)
timer.reset_and_report(
"Writing densities to file") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()