#!/usr/bin/env python # XProject.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. # # A versioning object representation of a complete project - this # represents the "top level" of the .xinfo hierarchy, and should # exactly correspond to the contents of the .xinfo file. # # Thoughts: # Scaling will fix radiation damage issues, so I don't need epochs # in the post-scaling universe. import os import sys import math import exceptions if not os.environ.has_key('XIA2_ROOT'): raise RuntimeError, 'XIA2_ROOT not defined' if not os.environ['XIA2_ROOT'] in sys.path: sys.path.append(os.environ['XIA2_ROOT']) # hooks to all of the child objects from Schema.XCrystal import XCrystal from Schema.XWavelength import XWavelength # .xinfo parser from Handlers.XInfo import XInfo from Handlers.Flags import Flags from Handlers.Syminfo import Syminfo # output stream from Handlers.Streams import Chatter, Debug class XProject(): '''A representation of a complete project. This will contain a dictionary of crystals.''' def __init__(self, xinfo_file = None): self._crystals = { } if xinfo_file: self.setup_from_xinfo_file(xinfo_file) else: self._name = None return def __repr__(self): result = 'Project: %s\n' % self._name for crystal in self._crystals.keys(): result += str(self._crystals[crystal]) return result[:-1] def __str__(self): return self.__repr__() def summarise(self): '''Produce summary information.''' summary = ['Project: %s' % self._name] for crystal in self._crystals.keys(): for record in self._crystals[crystal].summarise(): summary.append(record) return summary def get_name(self): return self._name def add_crystal(self, xcrystal): '''Add a new xcrystal to the project.''' if not xcrystal.__class__.__name__ == 'XCrystal': raise RuntimeError, 'crystal must be class XCrystal.' if xcrystal.get_name() in self._crystals.keys(): raise RuntimeError, 'XCrystal with name %s already exists' % \ xcrystal.get_name() self._crystals[xcrystal.get_name()] = xcrystal return def get_crystals(self): return self._crystals def setup_from_xinfo_file(self, xinfo_file): '''Set up this object & all subobjects based on the .xinfo file contents.''' xinfo = XInfo(xinfo_file) self._name = xinfo.get_project() crystals = xinfo.get_crystals() for crystal in crystals.keys(): xc = XCrystal(crystal, self) if crystals[crystal].has_key('sequence'): xc.set_aa_sequence(crystals[crystal]['sequence']) if crystals[crystal].has_key('ha_info'): if crystals[crystal]['ha_info'] != { }: xc.set_ha_info(crystals[crystal]['ha_info']) if crystals[crystal].has_key('scaled_merged_reflection_file'): xc.set_scaled_merged_reflections( crystals[crystal]['scaled_merged_reflections']) if crystals[crystal].has_key('reference_reflection_file'): xc.set_reference_reflection_file( crystals[crystal]['reference_reflection_file']) if crystals[crystal].has_key('freer_file'): xc.set_freer_file(crystals[crystal]['freer_file']) # user assigned spacegroup if crystals[crystal].has_key('user_spacegroup'): xc.set_user_spacegroup(crystals[crystal]['user_spacegroup']) elif Flags.get_spacegroup(): xc.set_user_spacegroup(Flags.get_spacegroup()) for wavelength in crystals[crystal]['wavelengths'].keys(): # FIXME 29/NOV/06 in here need to be able to cope with # no wavelength information - this should default to the # information in the image header (John Cowan pointed # out that this was untidy - requiring that it agrees # with the value in the header makes this almost # useless.) wave_info = crystals[crystal]['wavelengths'][wavelength] if not wave_info.has_key('wavelength'): Debug.write( 'No wavelength value given for wavelength %s' % wavelength) else: Debug.write( 'Overriding value for wavelength %s to %8.6f' % \ (wavelength, float(wave_info['wavelength']))) # handle case where user writes f" in place of f'' if wave_info.has_key('f"') and not \ wave_info.has_key('f\'\''): wave_info['f\'\''] = wave_info['f"'] xw = XWavelength(wavelength, xc, wavelength = wave_info.get('wavelength', 0.0), f_pr = wave_info.get('f\'', 0.0), f_prpr = wave_info.get('f\'\'', 0.0), dmin = wave_info.get('dmin', 0.0), dmax = wave_info.get('dmax', 0.0)) # in here I also need to look and see if we have # been given any scaled reflection files... # check to see if we have a user supplied lattice... if crystals[crystal].has_key('user_spacegroup'): lattice = Syminfo.get_lattice( crystals[crystal]['user_spacegroup']) elif Flags.get_spacegroup(): lattice = Syminfo.get_lattice(Flags.get_spacegroup()) elif Flags.get_lattice(): lattice = Flags.get_lattice() else: lattice = None # and also user supplied cell constants - from either # the xinfo file (the first port of call) or the # command-line. if crystals[crystal].has_key('user_cell'): cell = crystals[crystal]['user_cell'] elif Flags.get_cell(): cell = Flags.get_cell() else: cell = None dmin = wave_info.get('dmin', 0.0) dmax = wave_info.get('dmax', 0.0) if dmin == 0.0 and dmax == 0.0: dmin = Flags.get_resolution_high() dmax = Flags.get_resolution_low() # want to be able to locally override the resolution limits # for this sweep while leaving the rest for the data set # intact... for sweep_name in crystals[crystal]['sweeps'].keys(): sweep_info = crystals[crystal]['sweeps'][sweep_name] dmin_old = dmin dmax_old = dmax replace = False if 'RESOLUTION' in sweep_info: values = map(float, sweep_info['RESOLUTION'].split()) if len(values) == 1: dmin = values[0] elif len(values) == 2: dmin = min(values) dmax = max(values) else: raise RuntimeError, \ 'bad resolution for sweep %s' % sweep_name replace = True # FIXME: AJP to implement if 'ice' in sweep_info: pass if 'excluded_regions' in sweep_info: pass if sweep_info['wavelength'] == wavelength: frames_to_process = sweep_info.get('start_end') if not frames_to_process and Flags.get_start_end(): frames_to_process = Flags.get_start_end() xw.add_sweep( sweep_name, directory = sweep_info.get('DIRECTORY'), image = sweep_info.get('IMAGE'), beam = sweep_info.get('beam'), reversephi = sweep_info.get('reversephi', False), distance = sweep_info.get('distance'), gain = float(sweep_info.get('GAIN', 0.0)), dmin = dmin, dmax = dmax, polarization = float(sweep_info.get( 'POLARIZATION', 0.0)), frames_to_process = frames_to_process, user_lattice = lattice, user_cell = cell, epoch = sweep_info.get('epoch', 0), ice = sweep_info.get('ice', False), excluded_regions = sweep_info.get( 'excluded_regions', []), ) dmin = dmin_old dmax = dmax_old xc.add_wavelength(xw) self.add_crystal(xc) return def write_xifo(self): '''Write an updated .xinfo file which takes into account the input provided by the user on the command line and any input xinfo file: this is what xia2 understood to be the problem.''' raise RuntimeError, 'FIXME this method must be implemented' if __name__ == '__main__': import os xi_file = os.path.join(os.environ['XIA2_ROOT'], 'Data', 'Test', 'Xinfo', '1vpj.xinfo') xp = XProject(xi_file) Chatter.write(str(xp))