diff --git a/cfel_crystfel.py b/cfel_crystfel.py
new file mode 100644
index 0000000000000000000000000000000000000000..21951ef0ee7cc28a1f36111cc5390e1609ce8a6c
--- /dev/null
+++ b/cfel_crystfel.py
@@ -0,0 +1,578 @@
+# 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
+ 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