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#!/usr/bin/env python
# Create solution file for '--indexing=file' from a stream
#
# Copyright © 2020-2021 Max-Planck-Gesellschaft
# zur Förderung der Wissenschaften e.V.
# Copyright © 2021 Deutsches Elektronen-Synchrotron DESY,
# a research centre of the Helmholtz Association.
#
# Authors:
# 2020 Robert Bücker <robert.buecker@cssb-hamburg.de>
# 2021 Thomas White <thomas.white@desy.de>
from io import StringIO
import re
from warnings import warn
from copy import deepcopy
BEGIN_GEOM = '----- Begin geometry file -----'
END_GEOM = '----- End geometry file -----'
BEGIN_CELL = '----- Begin unit cell -----'
END_CELL = '----- End unit cell -----'
BEGIN_CHUNK = '----- Begin chunk -----'
END_CHUNK = '----- End chunk -----'
BEGIN_CRYSTAL = '--- Begin crystal'
END_CRYSTAL = '--- End crystal'
BEGIN_PEAKS = 'Peaks from peak search'
END_PEAKS = 'End of peak list'
BEGIN_REFLECTIONS = 'Reflections measured after indexing'
END_REFLECTIONS = 'End of reflections'
args = None
class Crystal:
def __init__(self, line):
self.astar = (None, None, None)
self.bstar = (None, None, None)
self.cstar = (None, None, None)
self.lattice_type = None
self.centering = None
self.unique_axis = None
self.det_shift = (None, None)
self.start_line = line
@property
def initialized(self):
return all([x is not None
for x in [*self.astar, *self.bstar, *self.cstar,
*self.det_shift, self.lattice_type,
self.centering]])
@property
def lattice_type_sym(self):
if self.lattice_type == 'triclinic':
return 'a' + self.centering
elif self.lattice_type == 'monoclinic':
return 'm' + self.centering + self.unique_axis
elif self.lattice_type == 'orthorhombic':
return 'o' + self.centering
elif self.lattice_type == 'tetragonal':
return 't' + self.centering + self.unique_axis
elif self.lattice_type == 'cubic':
return 'c' + self.centering
elif self.lattice_type == 'hexagonal':
return 'h' + self.centering + self.unique_axis
elif self.lattice_type == 'rhombohedral':
return 'r' + self.centering
else:
warn('Invalid lattice type {}'.format(self.lattice_type))
return 'invalid'
def __str__(self):
if not self.initialized:
warn('Trying to get string from non-initialized crystal from line {}.'.format(self.start_line))
return None
else:
cs = ' '.join(['{0[0]} {0[1]} {0[2]}'.format(vec)
for vec in [self.astar, self.bstar, self.cstar]])
cs += ' {0[0]} {0[1]}'.format(self.det_shift)
cs += ' ' + self.lattice_type_sym
return cs
class Chunk:
def __init__(self, line):
self.file = None
self.Event = None
self.crystals = []
self.start_line = line
self.x_shift = 0
self.y_shift = 0
@property
def n_cryst(self):
return len(self.crystals)
@property
def initialized(self):
return (self.file is not None) and (self.Event is not None)
def add_crystal(self, crystal):
if (not crystal.initialized) or (crystal is None):
raise RuntimeError('Trying to add non-initialied crystal to chunk from line {}.'.format(self.start_line))
self.crystals.append(deepcopy(crystal))
# print(crystal)
def __str__(self):
if not self.initialized:
warn('Trying to get string from non-initialized chunk from line {}.'.format(self.start_line))
return None
else:
# return '\n'.join([' '.join([self.file, *self.Event.split('//'), str(cryst)])
# for ii, cryst in enumerate(self.crystals)])
# new-style (not working yet)
return '\n'.join([' '.join([self.file, self.Event, str(cryst)])
for ii, cryst in enumerate(self.crystals)])
def parse_stream(stream, sol=None, return_meta=True,
file_label='Image filename', event_label='Event',
x_shift_label=None, y_shift_label=None, shift_factor=1):
curr_chunk = None
curr_cryst = None
geom = ''
cell = ''
command = ''
parsing_geom = False
parsing_cell = False
parsing_peaks = False
have_cell = False
have_geom = False
have_command = False
parsing_reflections = False
parse_vec = lambda l: tuple(float(k) for k in re.findall(r'[+-]?\d*\.\d*', l))
with open(stream, 'r') as fh_in, (StringIO() if sol is None else open(sol,'w')) as fh_out:
for ln, l in enumerate(fh_in):
if parsing_reflections:
if l.startswith(END_REFLECTIONS):
parsing_reflections = False
else:
# here, any reflection parsing would go
pass
elif parsing_peaks:
if l.startswith(END_PEAKS):
parsing_peaks = False
else:
# here, any peak parsing would go
pass
elif l.startswith(BEGIN_CHUNK):
curr_chunk = Chunk(ln)
elif (curr_chunk is not None) and (curr_cryst is None):
# parsing chunks (= events = shots) _outside_ crystals
if l.startswith(END_CHUNK):
if not curr_chunk.initialized:
raise RuntimeError('Incomplete chunk found before line ' + str(ln))
if curr_chunk.n_cryst:
fh_out.write(str(curr_chunk) + '\n')
# print(str(curr_chunk))
curr_chunk = None
elif l.startswith(file_label):
curr_chunk.file = l.split(' ', 2)[-1].strip()
elif l.startswith(event_label):
curr_chunk.Event = l.split(' ')[-1].strip()
elif x_shift_label and l.startswith(x_shift_label):
curr_chunk.x_shift = float(l.split(' ')[-1].strip())
elif y_shift_label and l.startswith(y_shift_label):
curr_chunk.y_shift = float(l.split(' ')[-1].strip())
elif l.startswith(BEGIN_CRYSTAL):
if not curr_chunk.initialized:
raise RuntimeError('Crystal for incomplete chunk in ' + str(ln))
curr_cryst = Crystal(ln)
elif curr_cryst is not None:
# parsing a (single) crystal
if l.startswith(END_CRYSTAL):
curr_chunk.add_crystal(curr_cryst)
curr_cryst = None
elif l.startswith('astar'):
curr_cryst.astar = parse_vec(l)
elif l.startswith('bstar'):
curr_cryst.bstar = parse_vec(l)
elif l.startswith('cstar'):
curr_cryst.cstar = parse_vec(l)
elif l.startswith('lattice_type'):
curr_cryst.lattice_type = l.split(' ')[2].strip()
elif l.startswith('centering'):
curr_cryst.centering = l.split(' ')[2].strip()
elif l.startswith('unique_axis'):
curr_cryst.unique_axis = l.split(' ')[2].strip()
elif l.startswith('predict_refine/det_shift'):
curr_cryst.det_shift = parse_vec(l)
curr_cryst.det_shift = (curr_cryst.det_shift[0] + curr_chunk.x_shift,
curr_cryst.det_shift[1] + curr_chunk.y_shift)
elif l.startswith(BEGIN_GEOM) and not have_geom:
parsing_geom = True
elif parsing_geom:
if not l.startswith(END_GEOM):
geom += l
else:
parsing_geom = False
have_geom = True
elif l.startswith(BEGIN_CELL) and not have_cell:
parsing_cell = True
elif parsing_cell:
if not l.startswith(END_CELL):
cell += l
else:
parsing_cell = False
have_cell = True
elif ('indexamajig' in l) and not have_command:
command = l
have_command = True
elif l.startswith(BEGIN_PEAKS):
parsing_peaks = True
elif l.startswith(BEGIN_REFLECTIONS):
parsing_reflections = True
if sol is None:
out = fh_out.getvalue()
if return_meta:
return out, (command, geom, cell)
else:
return out
else:
if return_meta:
return command, geom, cell
def main():
global args
from argparse import ArgumentParser
parser = ArgumentParser(description='Conversion tool from stream to solution file(s) for re-integration/-refinement.')
parser.add_argument('-i', '--input', type=str, help='Input stream file', required=True)
parser.add_argument('-o', '--output', type=str, help='Output solution file', required=True)
parser.add_argument('-g', '--geometry-out', type=str, help='Output geometry file (optional)')
parser.add_argument('-p', '--cell-out', type=str, help='Output cell file (optional)')
parser.add_argument('--file-field', type=str, help='Field in chunks for image filename', default='Image filename')
parser.add_argument('--event-field', type=str, help='Field in chunk for event identifier', default='Event')
parser.add_argument('--x-shift-field', type=str, help='Field in chunk for x-shift identifier', default='')
parser.add_argument('--y-shift-field', type=str, help='Field in chunk for y-shift identifier', default='')
parser.add_argument('--shift-factor', type=float,
help='Pre-factor for shifts, typically the pixel size in mm if the shifts are in pixel', default=1)
args = parser.parse_args()
meta = parse_stream(args.input, args.output, return_meta=True,
file_label=args.file_field, event_label=args.event_field,
x_shift_label=args.x_shift_field, y_shift_label=args.y_shift_field)
# print('Original indexamajig call was: \n' + meta[0])
if args.geometry_out:
with open(args.geometry_out, 'w') as fh:
fh.write(meta[1])
if args.cell_out:
if not meta[1]:
print('No cell found in stream file. Not writing cell file.')
else:
with open(args.cell_out, 'w') as fh:
fh.write(meta[2])
if __name__ == '__main__':
main()
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