# This file is part of cfelpyutils.
#
# cfelpyutils 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.
#
# cfelpyutils 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 cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
"""
Utilities for interoperability with the CrystFEL software package.
This module contains reimplementation of Crystfel functions and utilities.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from collections import OrderedDict
from math import inf, sqrt
import re
def load_crystfel_geometry(filename):
def assplode_algebraic(v):
items = [item for item in re.split('([+-])', v.strip()) if item != '']
if len(items) != 0 and items[0] not in ('+', '-'):
items.insert(0, '+')
return [''.join((items[x], items[x + 1])) for x in range(0, len(items), 2)]
def dir_conv(direction_x, direction_y, direction_z):
direction = [direction_x, direction_y, direction_z]
items = assplode_algebraic(value)
if len(items) == 0:
raise RuntimeError('Invalid direction: {}.'.format(value))
for item in items:
axis = item[-1]
if axis != 'x' and axis != 'y' and axis != 'z':
raise RuntimeError('Invalid Symbol: {} (must be x, y or z).'.format(axis))
if item[:-1] == '+':
v = '1.0'
elif item[:-1] == '-':
v = '-1.0'
else:
v = item[-1]
if axis == 'x':
direction[0] = float(v)
elif axis == 'y':
direction[1] = float(v)
elif axis == 'z':
direction[2] = float(v)
return direction
def set_dim_structure_entry(k, v, pan):
if pan['dim_structure'] is not None:
dim = pan['dim_structure']
else:
dim = []
dim_index = int(k[3])
if dim_index > len(dim)-1:
for index in range(len(dim), dim_index + 1):
dim.append(None)
if v == 'ss' or v == 'fs' or v == '%':
dim[dim_index] = v
elif v.isdigit():
dim[dim_index] = int(v)
else:
raise RuntimeError('Invalid dim entry: {}.'.format(v))
def parse_field_for_panel(k, v, pan):
if k == 'min_fs':
pan['origin_min_fs'] = int(v)
pan['min_fs'] = int(v)
elif k == 'max_fs':
pan['origin_max_fs'] = int(v)
pan['max_fs'] = int(v)
elif k == 'min_ss':
pan['origin_min_ss'] = int(v)
pan['min_ss'] = int(v)
elif k == 'max_ss':
pan['origin_max_ss'] = int(v)
pan['max_ss'] = int(v)
elif k == 'corner_x':
pan['cnx'] = float(v)
elif k == 'corner_y':
pan['cny'] = float(v)
elif k == 'rail_direction':
try:
pan['rail_x'], pan['rail_y'], pan['rail_z'] = dir_conv(pan['rail_x'],
pan['rail_y'],
pan['rail_z'])
except RuntimeError as e:
raise RuntimeError('Invalid rail direction. ', e)
elif k == 'clen_for_centering':
pan['clen_for_centering'] = float(v)
elif k == 'adu_per_eV':
pan['adu_per_eV'] = float(v)
elif k == 'adu_per_photon':
pan['adu_per_photon'] = float(v)
elif k == 'rigid_group':
pan['rigid_group'] = v
elif k == 'clen':
try:
pan['clen'] = float(v)
pan['clen_from'] = None
except ValueError:
pan['clen'] = -1
pan['clen_from'] = v
elif k == 'data':
if not v.startswith('/'):
raise RuntimeError('Invalid data location: {}'.format(v))
pan['data'] = v
elif k == 'mask':
if not v.startswith('/'):
raise RuntimeError('Invalid data location: {}'.format(v))
pan['mask'] = v
elif k == 'mask_file':
pan['mask_file'] = v
elif k == 'saturation_map':
pan['saturation_map'] = v
elif k == 'saturation_map_file':
pan['saturation_map_file'] = v
elif k == 'coffset':
pan['coffset'] = float(v)
elif k == 'res':
pan['res'] = float(v)
elif k == 'max_adu':
pan['max_adu'] = v
elif k == 'badrow_direction':
if v == 'x':
pan['badrow'] = 'f'
elif v == 'y':
pan['badrow'] = 's'
elif v == 'f':
pan['badrow'] = 'f'
elif v == 's':
pan['badrow'] = 's'
elif v == '-':
pan['badrow'] = '-'
else:
print('badrow_direction must be x, t, f, s, or \'-\'')
print('Assuming \'-\'.')
pan['badrow'] = '-'
elif k == 'no_index':
pan['no_index'] = bool(v)
elif k == 'fs':
try:
pan['fsx'], pan['fsy'], pan['fsz'] = dir_conv(pan['fsx'], pan['fsy'],
pan['fsz'])
except RuntimeError as e:
raise RuntimeError('Invalid fast scan direction. ', e)
elif k == 'ss':
try:
pan['ssx'], pan['ssy'], pan['ssz'] = dir_conv(pan['ssx'], pan['ssy'],
pan['ssz'])
except RuntimeError as e:
raise RuntimeError('Invalid slow scan direction. ', e)
elif k.startswith('dim'):
set_dim_structure_entry(k, v, pan)
else:
raise RuntimeError('Unrecognised field: {}'.format(k))
def parse_top_level(k, v, det, b, pan):
if k == 'mask_bad':
try:
det['mask_bad'] = int(v)
except ValueError:
det['mask_bad'] = int(v, 16)
elif k == 'mask_good':
try:
det['mask_good'] = int(v)
except ValueError:
det['mask_good'] = int(v, 16)
elif k == 'coffset':
pan['coffset'] = float(v)
elif k == 'photon_energy':
if v.startswith('/'):
b['photon_energy'] = 0.0
b['photon_energy_from'] = v
else:
b['photon_energy'] = float(v)
b['photon_energy_from'] = None
elif k == 'photon_energy_scale':
b['photon_energy_scale'] = float(v)
elif k == 'peak_info_location':
det['peak_info_location'] = v
elif k.startswith('rigid_group') and not k.startswith('rigid_group_collection'):
det['rigid_groups'][k[12:]] = v.split(',')
elif k.startswith('rigid_group_collection'):
det['rigid_group_collections'][k[23:]] = v.split(',')
else:
parse_field_for_panel(k, v, pan)
def check_bad_fsss(bad, is_fsss):
if bad['is_fsss'] == 99:
bad['is_fsss'] = is_fsss
return
if is_fsss != bad['is_fsss']:
raise RuntimeError("You can't mix x/y and fs/ss in a bad region")
return
def parse_field_bad(k, v, bad):
if k == 'min_x':
bad['min_x'] = float(v)
check_bad_fsss(bad, False)
elif k == 'max_x':
bad['max_x'] = float(v)
check_bad_fsss(bad, False)
elif k == 'min_y':
bad['min_y'] = float(v)
check_bad_fsss(bad, False)
elif k == 'max_y':
bad['max_y'] = float(v)
check_bad_fsss(bad, False)
elif k == 'min_fs':
bad['min_fs'] = int(v)
check_bad_fsss(bad, True)
elif k == 'max_fs':
bad['max_fs'] = int(v)
check_bad_fsss(bad, True)
elif k == 'min_ss':
bad['min_ss'] = int(v)
check_bad_fsss(bad, True)
elif k == 'max_ss':
bad['max_ss'] = int(v)
check_bad_fsss(bad, True)
elif k == 'panel':
bad['panel'] = v
else:
raise RuntimeError('Unrecognised field: {}'.format(k))
return
def check_point(n, pan, fs, ss, min_d, max_d, det):
xs = fs * pan['fsx'] + ss * pan['ssx']
ys = fs * pan['fsy'] + ss * pan['ssy']
rx = (xs + pan['cnx']) / pan['res']
ry = (ys + pan['cny']) / pan['res']
dist = sqrt(rx * rx + ry * ry)
if dist > max_d:
det['furthest_out_panel'] = n
det['furthest_out_fs'] = fs
det['furthest_out_ss'] = ss
max_d = dist
elif dist < min_d:
det['furthest_in_panel'] = n
det['furthest_in_fs'] = fs
det['furthest_in_ss'] = ss
min_d = dist
return min_d, max_d
def find_min_max_d(det):
min_d = inf
max_d = 0.0
for n, pan in det['panels'].items():
min_d, max_d = check_point(n, pan, 0, 0, min_d, max_d, det)
min_d, max_d = check_point(n, pan, pan['w'], 0, min_d, max_d, det)
min_d, max_d = check_point(n, pan, 0, pan['h'], min_d, max_d, det)
min_d, max_d = check_point(n, pan, pan['w'], pan['h'], min_d, max_d, det)
fh = open(filename, 'r')
beam = {
'photon_energy': 0.0,
'photon_energy_from': None,
'photon_energy_scale': 1
}
detector = {
'panels': OrderedDict(),
'bad': OrderedDict(),
'mask_good': 0,
'mask_bad': 0,
'rigid_groups': {},
'rigid_group_collections': {}
}
default_panel = {
'cnx': None,
'cny': None,
'clen': None,
'coffset': 0.0,
'res': -1.0,
'badrow': '-',
'no_index': False,
'fsx': 1.0,
'fsy': 0.0,
'fsz': 0.0,
'ssx': 0.0,
'ssy': 1.0,
'ssz': 0.0,
'rail_x': None,
'rail_y': None,
'rail_z': None,
'clen_for_centering': None,
'adu_per_eV': None,
'adu_per_photon': None,
'max_adu': inf,
'mask': None,
'mask_file': None,
'satmap': None,
'satmap_file': None,
'data': None,
'dim_structure': None,
'name': ''
}
default_bad_region = {
'min_x': None,
'max_x': None,
'min_y': None,
'max_y': None,
'min_fs': 0,
'max_fs': 0,
'min_ss': 0,
'max_ss': 0,
'is_fsss': 99,
'name': ''
}
default_dim = ['ss', 'fs']
fhlines = fh.readlines()
for line in fhlines:
if line.startswith(';'):
continue
line_without_comments = line.strip().split(';')[0]
line_items = re.split('([ \t])', line_without_comments)
line_items = [item for item in line_items if item not in ('', ' ', '\t')]
if len(line_items) < 3:
continue
value = ''.join(line_items[2:])
if line_items[1] != '=':
continue
path = re.split('(/)', line_items[0])
path = [item for item in path if item not in '/']
if len(path) < 2:
parse_top_level(line_items[0], value, detector, beam, default_panel)
continue
curr_bad = None
curr_panel = None
if path[0].startswith('bad'):
if path[0] in detector['bad']:
curr_bad = detector['bad'][path[0]]
else:
curr_bad = default_bad_region.copy()
detector['bad'][path[0]] = curr_bad
else:
if path[0] in detector['panels']:
curr_panel = detector['panels'][path[0]]
else:
curr_panel = default_panel.copy()
detector['panels'][path[0]] = curr_panel
if curr_panel is not None:
parse_field_for_panel(path[1], value, curr_panel)
else:
parse_field_bad(path[1], value, curr_bad)
if len(detector['panels']) == 0:
raise RuntimeError("No panel descriptions in geometry file.")
num_placeholders_in_panels = None
for panel in detector['panels'].values():
if panel['dim_structure'] is not None:
curr_num_placeholders = panel['dim_structure'].values().count('%')
else:
curr_num_placeholders = 0
if num_placeholders_in_panels is None:
num_placeholders_in_panels = curr_num_placeholders
else:
if curr_num_placeholders != num_placeholders_in_panels:
raise RuntimeError('All panels\' data and mask entries must have the same number of placeholders.')
num_placeholders_in_masks = None
for panel in detector['panels'].values():
if panel['mask'] is not None:
curr_num_placeholders = panel['mask'].count('%')
else:
curr_num_placeholders = 0
if num_placeholders_in_masks is None:
num_placeholders_in_masks = curr_num_placeholders
else:
if curr_num_placeholders != num_placeholders_in_masks:
raise RuntimeError('All panels\' data and mask entries must have the same number of placeholders.')
if num_placeholders_in_masks > num_placeholders_in_panels:
raise RuntimeError('Number of placeholders in mask cannot be larget than for data.')
dim_length = None
for panel in detector['panels'].values():
if panel['dim_structure'] is None:
panel['dim_structure'] = default_dim.copy()
found_ss = False
found_fs = False
found_placeholder = False
for entry in panel['dim_structure']:
if entry is None:
raise RuntimeError('Not all dim entries are defined for all panels.')
elif entry == 'ss':
if found_ss is True:
raise RuntimeError('Only one slow scan dim coordinate is allowed.')
else:
found_ss = True
elif entry == 'fs':
if found_fs is True:
raise RuntimeError('Only one fast scan dim coordinate is allowed.')
else:
found_fs = True
elif entry == '%':
if found_placeholder is True:
raise RuntimeError('Only one placeholder dim coordinate is allowed.')
else:
found_placeholder = True
for panel in detector['panels'].values():
if panel['origin_min_fs'] < 0:
raise RuntimeError('Please specify the minimum fs coordinate for panel {}.'.format(panel['name']))
if panel['origin_max_fs'] < 0:
raise RuntimeError('Please specify the maximum fs coordinate for panel {}.'.format(panel['name']))
if panel['origin_min_ss'] < 0:
raise RuntimeError('Please specify the minimum ss coordinate for panel {}.'.format(panel['name']))
if panel['origin_max_ss'] < 0:
raise RuntimeError('Please specify the maximum ss coordinate for panel {}.'.format(panel['name']))
if panel['cnx'] is None:
raise RuntimeError('Please specify the corner X coordinate for panel {}.'.format(panel['name']))
if panel['clen'] is None and panel['clen_from'] is None:
raise RuntimeError('Please specify the camera length for panel {}.'.format(panel['name']))
if panel['res'] < 0:
raise RuntimeError('Please specify the resolution or panel {}.'.format(panel['name']))
if panel['adu_per_eV'] is None and panel['adu_per_photon'] is None:
raise RuntimeError('Please specify either adu_per_eV or adu_per_photon for '
'panel {}.'.format(panel['name']))
if panel['clen_for_centering'] is None and panel['rail_x'] is not None:
raise RuntimeError('You must specify clen_for_centering if you specify the rail direction '
'(panel {})'.format(panel['name']))
if panel['rail_x'] is None:
panel['rail_x'] = 0.0
panel['rail_y'] = 0.0
panel['rail_z'] = 1.0
if panel['clen_for_centering'] is None:
panel['clen_for_centering'] = 0.0
panel['w'] = panel['origin_max_fs'] - panel['origin_min_fs'] + 1
panel['h'] = panel['origin_max_ss'] - panel['origin_min_ss'] + 1
for bad_region in detector['bad']:
if bad_region['is_fsss'] == 99:
raise RuntimeError('Please specify the coordinate ranges for bad region {}.'.format(bad_region['name']))
for group in detector['rigid_groups'].keys():
for name in detector['rigid_groups'][group]:
if name not in detector['panels']:
raise RuntimeError('Cannot add panel to rigid_group. Panel not found: {}'.format(name))
for group_collection in detector['rigid_group_collections'].keys():
for name in detector['rigid_group_collections'][group_collection]:
if name not in detector['rigid_groups']:
raise RuntimeError('Cannot add rigid_group to collection. Rigid group not found: {}'.format(name))
for panel in detector['panels'].values():
d = panel['fsx'] * panel['ssy'] - panel['ssx'] * panel['fsy']
if d == 0.0:
raise RuntimeError('Panel {} transformation is singluar.')
panel['xfs'] = panel['ssy'] / d
panel['yfs'] = panel['ssx'] / d
panel['xss'] = panel['fsy'] / d
panel['yss'] = panel['fsx'] / d
find_min_max_d(detector)
fh.close()
return detector