def make_crystal(fnam):
from crappy_crystals import symmetry_operations
import disorder
# read the h5 file
kwargs = read_input_output_h5(fnam)
config = kwargs['config_file']
if 'solid_unit_retrieved' in kwargs.keys():
print '\nsolid_unit = solid_unit_retrieved'
solid_unit = kwargs['solid_unit_retrieved']
elif 'solid_unit_init' in kwargs.keys():
print '\nsolid_unit = solid_unit_init'
solid_unit = kwargs['solid_unit_init']
elif 'solid_unit' in kwargs.keys():
print '\nsolid_unit = solid_unit'
solid_unit = kwargs['solid_unit']
if config['crystal']['space_group'] == 'P1':
sym_ops = symmetry_operations
sym_ops_obj = sym_ops.P1(config['crystal']['unit_cell'], config['detector']['shape'])
elif config['crystal']['space_group'] == 'P212121':
sym_ops = symmetry_operations
sym_ops_obj = sym_ops.P212121(config['crystal']['unit_cell'], config['detector']['shape'])
Solid_unit = np.fft.fftn(solid_unit, config['detector']['shape'])
solid_unit_expanded = np.fft.ifftn(Solid_unit)
modes = sym_ops_obj.solid_syms_Fourier(Solid_unit)
#N = config['disorder']['n']
#exp = disorder.make_exp(config['disorder']['sigma'], config['detector']['shape'])
lattice = sym_ops.lattice(config['crystal']['unit_cell'], config['detector']['shape'])
#diff = N * exp * np.abs(lattice * np.sum(modes, axis=0)**2)
#diff += (1. - exp) * np.sum(np.abs(modes)**2, axis=0)
fourier_space_crystal = np.sum(modes, axis=0) * lattice
real_space_crystal = np.fft.ifftn(fourier_space_crystal)
real_space_crystal = np.fft.fftshift(real_space_crystal)
return real_space_crystal
def parse_cmdline_args():
import argparse
import os
parser = argparse.ArgumentParser(prog = 'display.py', description='display the contents of output.h5 in a GUI')
parser.add_argument('path', type=str, \
help="path to output.h5 file")
parser.add_argument('-i', '--isosurface', action='store_true', \
help="display the crystal in the field of view as an iso surface")
args = parser.parse_args()
# check that args.ini exists
if not os.path.exists(args.path):
raise NameError('output h5 file does not exist: ' + args.path)
return args
if __name__ == '__main__':
args = parse_cmdline_args()
if args.isosurface :
show_crystal(args.path)
else :
# read the h5 file
kwargs = read_input_output_h5(args.path)
signal.signal(signal.SIGINT, signal.SIG_DFL) # allow Control-C
#app = QtGui.QApplication(sys.argv)
ex = Application(fnam = args.path, **kwargs)
