#/usr/bin/env python # Flags.py # Copyright (C) 2006 CCLRC, Graeme Winter # # This code is distributed under the BSD license, a copy of which is # included in the root directory of this package. # # 4th May 2007 # # A singleton to handle flags, which can be imported more easily # as it will not suffer the problems with circular references that # the CommandLine singleton suffers from. import os import sys if not os.environ.has_key('XIA2_ROOT'): raise RuntimeError, 'XIA2_ROOT not defined' if not os.environ.has_key('XIA2CORE_ROOT'): raise RuntimeError, 'XIA2CORE_ROOT not defined' if not os.environ['XIA2_ROOT'] in sys.path: sys.path.append(os.path.join(os.environ['XIA2_ROOT'])) from Handlers.Environment import get_number_cpus from Toolkit.BackstopMask import BackstopMask class _Flags: '''A singleton to manage boolean flags.''' # by default now switch on smart scaling and chef - after the smart # scaling has been reset in the XDS Scaler to be "everything" def __init__(self): self._quick = False self._interactive = False self._ice = False self._egg = False self._uniform_sd = True self._chef = False self._mask = None self._reversephi = False self._no_lattice_test = False self._migrate_data = False self._trust_timestaps = False # XDS specific things - to help with handling tricky data sets self._xparm = None self._xparm_beam_vector = None self._xparm_rotation_axis = None self._xparm_origin = None self._xparm_a = None self._xparm_b = None self._xparm_c = None try: self._parallel = get_number_cpus() except: self._parallel = 0 self._xparallel = 0 self._min_images = 10 self._start_end = None self._batch_scale = False # File from which to copy the FreeR_flag column self._freer_file = None # or alternatively the fraction, or total number of free # reflections self._free_fraction = None self._free_total = None # reference reflection file self._reference_reflection_file = None # these are development parameters for the XDS implementation self._z_min = 0.0 self._refine = True self._remove = True self._zero_dose = False self._relax = True self._profile = True # and these for the Mosflm / Scala and perhaps XDS implementation self._scale_model = False self._scale_model_decay = False self._scale_model_modulation = False self._scale_model_absorption = False self._scale_model_partiality = False self._rmerge_target = 'low' # options to support the -spacegroup flag - the spacegroup is # set from this, the lattice and pointgroup derived from such self._spacegroup = None self._pointgroup = None self._lattice = None # scala secondary correction self._scala_secondary = 6 # options to support the -cell option self._cell = None # resolution limit flags self._resolution_low = None self._resolution_high = None # and these are general rejection criteria self._rejection_threshold = 1.5 self._isigma = 1.0 self._misigma = 2.0 self._completeness = 0.0 self._rmerge = 0.0 self._microcrystal = False self._failover = False self._blend = False # are we working with small molecule data? self._small_molecule = False # flags relating to fixing specific bugs self._fixed_628 = False # ISPyB things self._ispyb_xml_out = None # header cache / json things self._hdr_in = None self._hdr_out = None return def set_batch_scale(self, batch_scale): self._batch_scale = batch_scale return def get_batch_scale(self): return self._batch_scale def set_rmerge_target(self, rmerge_target): assert(rmerge_target in ['low', 'high', 'overall']) self._rmerge_target = rmerge_target return def get_rmerge_target(self): return self._rmerge_target # matters relating to the manual definition of a scaling model def set_scale_model(self, scale_model): self._scale_model = scale_model # now unpack this self.set_scale_model_decay('decay' in scale_model) self.set_scale_model_modulation('modulation' in scale_model) self.set_scale_model_absorption('absorption' in scale_model) self.set_scale_model_partiality('partiality' in scale_model) return def get_scale_model(self): return self._scale_model def set_scale_model_decay(self, scale_model_decay = True): self._scale_model_decay = scale_model_decay return def get_scale_model_decay(self): return self._scale_model_decay def set_scale_model_modulation(self, scale_model_modulation = True): self._scale_model_modulation = scale_model_modulation return def get_scale_model_modulation(self): return self._scale_model_modulation def set_scale_model_absorption(self, scale_model_absorption = True): self._scale_model_absorption = scale_model_absorption return def get_scale_model_absorption(self): return self._scale_model_absorption def set_scale_model_partiality(self, scale_model_partiality = True): self._scale_model_partiality = scale_model_partiality return def get_scale_model_partiality(self): return self._scale_model_partiality # the end of such matters ### SETTING OF RESOLUTION LIMITS #### bug # 3183 def set_resolution_high(self, resolution): self._resolution_high = resolution return def set_resolution_low(self, resolution): self._resolution_low = resolution return def get_resolution_high(self): return self._resolution_high def get_resolution_low(self): return self._resolution_low def set_spacegroup(self, spacegroup): '''A handler for the command-line option -spacegroup - this will set the spacegroup and derive from this the pointgroup and lattice appropriate for such...''' from Handlers.Syminfo import Syminfo spacegroup = spacegroup.upper() # validate by deriving the pointgroup and lattice... pointgroup = Syminfo.get_pointgroup(spacegroup) lattice = Syminfo.get_lattice(spacegroup) # assign self._spacegroup = spacegroup self._pointgroup = pointgroup self._lattice = lattice # debug print from Handlers.Streams import Debug Debug.write('Derived information from spacegroup flag: %s' % \ spacegroup) Debug.write('Pointgroup: %s Lattice: %s' % (pointgroup, lattice)) # indicate that since this has been assigned, we do not wish to # test it! self.set_no_lattice_test(True) return def get_spacegroup(self): return self._spacegroup def get_pointgroup(self): return self._pointgroup def get_lattice(self): return self._lattice def set_cell(self, cell): self._cell = cell return def get_cell(self): return self._cell def set_quick(self, quick): self._quick = quick return def get_quick(self): return self._quick def set_interactive(self, interactive): self._interactive = interactive return def get_interactive(self): return self._interactive def set_ice(self, ice): self._ice = ice return def get_ice(self): return self._ice def set_egg(self, egg): self._egg = egg return def get_egg(self): return self._egg def set_uniform_sd(self, uniform_sd): self._uniform_sd = uniform_sd return def get_uniform_sd(self): return self._uniform_sd def set_chef(self, chef): self._chef = chef return def get_chef(self): return self._chef def set_reversephi(self, reversephi): self._reversephi = reversephi return def get_reversephi(self): return self._reversephi def set_no_lattice_test(self, no_lattice_test): self._no_lattice_test = no_lattice_test return def get_no_lattice_test(self): return self._no_lattice_test def set_relax(self, relax): self._relax = relax return def get_relax(self): return self._relax def set_profile(self, profile): self._profile = profile return def get_profile(self): return self._profile def set_migrate_data(self, migrate_data): self._migrate_data = migrate_data return def get_migrate_data(self): return self._migrate_data def set_trust_timestamps(self, trust_timestamps): self._trust_timestamps = trust_timestamps return def get_trust_timestamps(self): return self._trust_timestamps def set_small_molecule(self, small_molecule): self._small_molecule = small_molecule return def get_small_molecule(self): return self._small_molecule def set_parallel(self, parallel): self._parallel = parallel return def get_parallel(self): return self._parallel def set_xparm(self, xparm): self._xparm = xparm tokens = map(float, open(xparm, 'r').read().split()) rotation_axis = tuple(tokens[3:6]) beam_vector = tuple(tokens[7:10]) origin = tuple(tokens[15:17]) self._xparm_origin = origin self._xparm_beam_vector = beam_vector self._xparm_rotation_axis = rotation_axis return def get_xparm(self): return self._xparm def get_xparm_origin(self): return self._xparm_origin def get_xparm_rotation_axis(self): return self._xparm_rotation_axis def get_xparm_beam_vector(self): return self._xparm_beam_vector def set_xparm_ub(self, xparm): self._xparm_ub = xparm tokens = map(float, open(xparm, 'r').read().split()) self._xparm_a = tokens[-9:-6] self._xparm_b = tokens[-6:-3] self._xparm_c = tokens[-3:] return def get_xparm_a(self): return self._xparm_a def get_xparm_b(self): return self._xparm_b def get_xparm_c(self): return self._xparm_c def set_min_images(self, min_images): self._min_images = min_images return def get_min_images(self): return self._min_images def set_start_end(self, start, end): assert(end > start) self._start_end = start, end return def get_start_end(self): return self._start_end def set_xparallel(self, xparallel): self._xparallel = xparallel return def get_xparallel(self): return self._xparallel def set_z_min(self, z_min): self._z_min = z_min return def get_z_min(self): return self._z_min def set_scala_secondary(self, scala_secondary): self._scala_secondary = scala_secondary return def get_scala_secondary(self): return self._scala_secondary def set_freer_file(self, freer_file): # mtzdump this file to make sure that there is a FreeR_flag # column therein... freer_file = os.path.abspath(freer_file) if not os.path.exists(freer_file): raise RuntimeError, '%s does not exist' % freer_file from Modules.FindFreeFlag import FindFreeFlag from Handlers.Streams import Debug column = FindFreeFlag(freer_file) Debug.write('FreeR_flag column in %s found: %s' % \ (freer_file, column)) self._freer_file = freer_file return def get_freer_file(self): return self._freer_file def set_free_fraction(self, free_fraction): self._free_fraction = free_fraction return def get_free_fraction(self): return self._free_fraction def set_free_total(self, free_total): self._free_total = free_total return def get_free_total(self): return self._free_total def set_mask(self, mask): self._mask = BackstopMask(mask) return def get_mask(self): return self._mask def set_ispyb_xml_out(self, ispyb_xml_out): self._ispyb_xml_out = ispyb_xml_out return def get_ispyb_xml_out(self): return self._ispyb_xml_out def set_hdr_in(self, hdr_in): self._hdr_in = hdr_in from Wrappers.XIA.Diffdump import HeaderCache from Handlers.Streams import Debug Debug.write('Read %d headers from %s' % (HeaderCache.read(hdr_in), hdr_in)) return def get_hdr_in(self): return self._hdr_in def set_hdr_out(self, hdr_out): self._hdr_out = hdr_out return def get_hdr_out(self): return self._hdr_out def set_fixed_628(self): self._fixed_628 = True return def get_fixed_628(self): return self._fixed_628 def set_reference_reflection_file(self, reference_reflection_file): '''Set a new reference reflection file.''' reference_reflection_file = os.path.abspath(reference_reflection_file) if not os.path.exists(reference_reflection_file): raise RuntimeError, '%s does not exist' % reference_reflection_file self._reference_reflection_file = reference_reflection_file return def get_reference_reflection_file(self): return self._reference_reflection_file def set_rejection_threshold(self, rejection_threshold): self._rejection_threshold = rejection_threshold return def get_rejection_threshold(self): return self._rejection_threshold def set_isigma(self, isigma): self._isigma = isigma return def get_isigma(self): return self._isigma def set_misigma(self, misigma): self._misigma = misigma return def get_misigma(self): return self._misigma def set_completeness(self, completeness): self._completeness = completeness return def get_completeness(self): return self._completeness def set_rmerge(self, rmerge): self._rmerge = rmerge return def get_rmerge(self): return self._rmerge def set_microcrystal(self, microcrystal = True): self._microcrystal = microcrystal return def get_microcrystal(self): return self._microcrystal def set_failover(self, failover = True): self._failover = failover return def get_failover(self): return self._failover def set_blend(self, blend = True): self._blend = blend return def get_blend(self): return self._blend def set_refine(self, refine): self._refine = refine return def get_refine(self): return self._refine def set_remove(self, remove): self._remove = remove return def get_remove(self): return self._remove def set_zero_dose(self, zero_dose): self._zero_dose = zero_dose return def get_zero_dose(self): return self._zero_dose Flags = _Flags()