#!/usr/bin/env python # XInfo.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 handler for .xinfo files, an example of which can be found in: # # os.path.join(os.environ['XIA2_ROOT'], 'Data', 'Test', 'Xinfo', '1vr9.xinfo') # # This file should record some metadata about the experiment, and contain # enough information to solve the structure. A similar .xinfo file # will be needed & generated in xia2dc. # # FIXME 25/AUG/06 Something similar will be needed by xia2dc, and will # need to be populated by that program based on # flourescence scans and so on. xia2dc will, however, # require a minimally populated .xinfo file for input. # Comment 27/OCT/06 something like this will also be # needed for the xia2ss phase as well... # # FIXME 25/AUG/06 I need to implement a "wizard" for generating the .xinfo # file because it's not particularly helpful or friendly # in the amount of information it contains. # # FIXME 25/AUG/06 Need to implement a system to ensure that the datasets # point at different sweeps, not two of them pointing # a the same sweep. Will allow two very similar looking # wavelength definitions (i.e. with the same lambda) for # one crystal because these could pertain to RIP, and may # correspond to different f', f'' values (although, will # these change as a function of radiation damage? unlikely) # FIXME I need to find this out to get a proper structure! # # FIXED 30/AUG/06 Probably should redefine DATASET as SWEEP to get a more # accurate mapping to the MTZ hierarchy. For the interim # I could allow either. So, for the moment, we have: # # WAVELENGTH -> MTZ dataset # PROJECT -> MTZ project # CRYSTAL -> MTZ dataset # # Fix this... later! # # FIXED 05/SEP/06 Need to kill current definition of DATASET so I can use # it when going to xia2ss as a dataset. => sed /dataset/sweep/ # for xia2dpa. Done, and documentation, examples are # updated. # # FIXED 05/SEP/06 Need to produce an object hierarchy based on Schema/Object # to give object versioning which will represent the contents # of the .xinfo+ file, that is, the representation of this # information during the data reduction process, to make the # join from the input-to-dpa .xinfo file and the xia2ss # .xinfo input file. This will be: # # XProject # XCrystal # XWavelength # XSweep # XDataset # # A slightly poor naming convention, but it will do the # job. So - the properties of these are defined in # /Schema. Note well that these have subproperties # (e.g. sweep resolution) which will also have to be # defined as classes... # # FIXED 19/SEP/06 also allow the DISTANCE to be provided in the .xinfo # file in the same way as the beam - unfortunately this # is sometimes wrong and very hard to find right ;o(. # See NaI/Lysozyme data collected on 14.1 in /data1/graeme. # # FIXED 26/SEP/06 allow for INTEGRATED_REFLECTION_FILE in sweep record in place # of or in addition to the DIRECTORY, TEMPLATE to allow for # development of the scaling independently of the scaling # &c. The same could be applied to the scaled reflections # belonging to a wavelength etc. # # FIXED 27/OCT/06 need to be able to override or provide the epoch # information in the .xinfo file to cope with cases # where this information is not in the image headers. # # FIXED 15/NOV/06 allow for a role for wavelengths, for example in shelxc/d/e # it would help matters to define peak, inflection, low and # high remote. This should be done automatically in a perfect # world. In fact, this is best done by assigning one of these # names to the wavelength name - job done! # # FIXME 04/DEC/06 need to also allow for starting from post-scaled data - # this will make debugging easier and also provide a # xia2ha like functionality. # class XInfo: '''A class to represent all of the input to the xia2dpa system, with enough information to allow structure solution, as parsed from a .xinfo file, an example of which is in the source code.''' def __init__(self, xinfo_file): '''Initialise myself from an input .xinfo file.''' # first initialise all of the data structures which will hold the # information... self._project = None self._crystals = { } # read the contents of the xinfo file self._parse_project(xinfo_file) self._validate() return def __repr__(self): '''Generate a string representation of the project.''' repr = 'Project %s\n' % self._project for crystal in self._crystals.keys(): repr += 'Crystal %s\n' % crystal repr += '%s\n' % str(self._crystals[crystal]) # remove a trailing newline... return repr[:-1] def get_project(self): return self._project def get_crystals(self): return self._crystals def _validate(self): '''Validate the structure of this object, ensuring that everything looks right... raise exception if I find something wrong.''' return True def _parse_project(self, xinfo_file): '''Parse & validate the contents of the .xinfo file. This parses the project element (i.e. the whole thing..)''' project_records = [] for r in open(xinfo_file, 'r').readlines(): record = r.strip() if len(record) == 0: pass elif record[0] == '!' or record[0] == '#': pass else : # then it may contain something useful... project_records.append(record) # so now we have loaded the whole file into memory stripping # out the crud... let's look for something useful for i in range(len(project_records)): record = project_records[i] if 'BEGIN PROJECT' in record: self._project = record.replace('BEGIN PROJECT', '').strip() if 'END PROJECT' in record: if not self._project == record.replace( 'END PROJECT', '').strip(): raise RuntimeError, 'error parsing END PROJECT record' # next look for crystals if 'BEGIN CRYSTAL ' in record: crystal_records = [record] while True: i += 1 record = project_records[i] crystal_records.append(record) if 'END CRYSTAL ' in record: break self._parse_crystal(crystal_records) # that's everything, because parse_crystal handles # the rest... return def _parse_crystal(self, crystal_records): '''Parse the interesting information out of the crystal description.''' crystal = '' for i in range(len(crystal_records)): record = crystal_records[i] if 'BEGIN CRYSTAL ' in record: # we should only ever have one of these records in # a call to this method if crystal != '': raise RuntimeError, 'error in BEGIN CRYSTAL record' crystal = record.replace('BEGIN CRYSTAL ', '').strip() if self._crystals.has_key(crystal): raise RuntimeError, 'crystal %s already exists' % \ crystal # cardinality: # # sequence - exactly one, a long string # wavelengths - a dictionary of data structures keyed by the # wavelength id # sweeps - a dictionary of data structures keyed by the # sweep id # ha_info - exactly one dictionary containing the heavy atom # information self._crystals[crystal] = { 'sequence':'', 'wavelengths':{}, 'sweeps':{}, 'ha_info':{}, 'crystal_data':{} } # next look for interesting stuff in the data structure... # starting with the sequence if 'BEGIN AA_SEQUENCE' in record: sequence = '' i += 1 record = crystal_records[i] while record != 'END AA_SEQUENCE': if not '#' in record or '!' in record: sequence += record.strip() i += 1 record = crystal_records[i] if self._crystals[crystal]['sequence'] != '': raise RuntimeError, 'error two SEQUENCE records found' self._crystals[crystal]['sequence'] = sequence # look for heavy atom information if 'BEGIN HA_INFO' in record: i += 1 record = crystal_records[i] while record != 'END HA_INFO': key = record.split()[0].lower() value = record.split()[1] # things which are numbers are integers... if 'number' in key: value = int(value) self._crystals[crystal]['ha_info'][key] = value i += 1 record = crystal_records[i] # look for wavelength definitions # FIXME need to check that there are not two wavelength # definitions with the same numerical value for the wavelength - # unless this is some way of handling RIP? maybe a NOFIXME. # look for data blocks if 'BEGIN CRYSTAL_DATA' in record: i += 1 record = crystal_records[i] while not 'END CRYSTAL_DATA' in record: key = record.split()[0].lower() value = record.replace(record.split()[0], '').strip() self._crystals[crystal]['crystal_data'][key] = value i += 1 record = crystal_records[i] if 'BEGIN WAVELENGTH ' in record: wavelength = record.replace('BEGIN WAVELENGTH ', '').strip() # check that this is a new wavelength definition if self._crystals[crystal]['wavelengths'].has_key(wavelength): raise RuntimeError, \ 'wavelength %s already exists for crystal %s' % \ (wavelength, crystal) self._crystals[crystal]['wavelengths'][wavelength] = { } i += 1 record = crystal_records[i] # populate this with interesting things while not 'END WAVELENGTH' in record: # deal with a nested WAVELENGTH_STATISTICS block if 'BEGIN WAVELENGTH_STATISTICS' in record: self._crystals[crystal]['wavelengths'][ wavelength]['statistics'] = { } i += 1 record = crystal_records[i] while not 'END WAVELENGTH_STATISTICS' in record: key, value = tuple(record.split()) self._crystals[crystal]['wavelengths'][ wavelength]['statistics'][ key.lower()] = float(value) i += 1 record = crystal_records[i] # else deal with the usual tokens key = record.split()[0].lower() if key == 'resolution': lst = record.split() if len(lst) < 2 or len(lst) > 3: raise RuntimeError, 'resolution dmin [dmax]' if len(lst) == 2: dmin = float(lst[1]) self._crystals[crystal]['wavelengths'][ wavelength]['dmin'] = dmin else: dmin = min(map(float, lst[1:])) dmax = max(map(float, lst[1:])) self._crystals[crystal]['wavelengths'][ wavelength]['dmin'] = dmin self._crystals[crystal]['wavelengths'][ wavelength]['dmax'] = dmax i += 1 record = crystal_records[i] continue if len(record.split()) == 1: raise RuntimeError, 'missing value for token %s' % \ record.split()[0] try: value = float(record.split()[1]) except ValueError, e: value = record.replace(record.split()[0], '').strip() self._crystals[crystal]['wavelengths'][ wavelength][key] = value i += 1 record = crystal_records[i] # next look for sweeps, checking that the wavelength # definitions match up... if 'BEGIN SWEEP' in record: sweep = record.replace('BEGIN SWEEP', '').strip() if self._crystals[crystal]['sweeps'].has_key(sweep): raise RuntimeError, \ 'sweep %s already exists for crystal %s' % \ (sweep, crystal) self._crystals[crystal]['sweeps'][sweep] = { } self._crystals[crystal]['sweeps'][sweep][ 'excluded_regions'] = [] # in here I expect to find IMAGE, DIRECTORY, WAVELENGTH # and optionally BEAM # FIXME 30/OCT/06 this may not be the case, for instance # if an INTEGRATED_REFLECTION_FILE record is in there... # c/f XProject.py, XSweep.py i += 1 record = crystal_records[i] # populate this with interesting things while not 'END SWEEP' in record: # allow for WAVELENGTH_ID (bug # 2358) if 'WAVELENGTH_ID' == record.split()[0]: record = record.replace('WAVELENGTH_ID', 'WAVELENGTH') if 'WAVELENGTH' == record.split()[0]: wavelength = record.replace('WAVELENGTH', '').strip() if not wavelength in self._crystals[crystal][ 'wavelengths'].keys(): raise RuntimeError, \ 'wavelength %s unknown for crystal %s' % \ (wavelength, crystal) self._crystals[crystal]['sweeps'][sweep][ 'wavelength'] = wavelength elif 'BEAM' == record.split()[0]: beam = map(float, record.split()[1:]) self._crystals[crystal]['sweeps'][sweep][ 'beam'] = beam elif 'DISTANCE' == record.split()[0]: distance = float(record.split()[1]) self._crystals[crystal]['sweeps'][sweep][ 'distance'] = distance elif 'EPOCH' == record.split()[0]: epoch = int(record.split()[1]) self._crystals[crystal]['sweeps'][sweep][ 'epoch'] = epoch elif 'REVERSEPHI' == record.split()[0]: self._crystals[crystal]['sweeps'][sweep][ 'reversephi'] = True elif 'START_END' == record.split()[0]: start_end = map(int, record.split()[1:]) if len(start_end) != 2: raise RuntimeError, \ 'START_END start end, not "%s"' % record self._crystals[crystal]['sweeps'][sweep][ 'start_end'] = start_end elif 'EXCLUDE' == record.split()[0]: if record.split()[1].upper() == 'ICE': self._crystals[crystal]['sweeps'][sweep][ 'ice'] = True else: excluded_region = map(float, record.split()[1:]) if len(excluded_region) != 2: raise RuntimeError, \ 'EXCLUDE upper lower, not "%s". \ eg. EXCLUDE 2.28 2.22' % record if excluded_region[0] <= excluded_region[1]: raise RuntimeError, \ 'EXCLUDE upper lower, where upper \ must be greater than lower (not "%s").\n\ eg. EXCLUDE 2.28 2.22' % record self._crystals[crystal]['sweeps'][sweep][ 'excluded_regions'].append(excluded_region) else: key = record.split()[0] value = record.replace(key, '').strip() self._crystals[crystal]['sweeps'][sweep][ key] = value i += 1 record = crystal_records[i] # now look for one-record things if 'SCALED_MERGED_REFLECTION_FILE' in record: self._crystals[crystal][ 'scaled_merged_reflection_file'] = \ record.replace('SCALED_MERGED_REFLECTION_FILE', '').strip() if 'REFERENCE_REFLECTION_FILE' in record: self._crystals[crystal][ 'reference_reflection_file'] = \ record.replace('REFERENCE_REFLECTION_FILE', '').strip() if 'FREER_FILE' in record: # free file also needs to be used for indexing reference to # make any sense at all... self._crystals[crystal][ 'freer_file'] = record.replace('FREER_FILE', '').strip() self._crystals[crystal][ 'reference_reflection_file'] = \ record.replace('FREER_FILE', '').strip() # user assigned spacegroup and cell constants if 'USER_SPACEGROUP' in record: self._crystals[crystal][ 'user_spacegroup'] = record.replace( 'USER_SPACEGROUP', '').strip() if 'USER_CELL' in record: self._crystals[crystal][ 'user_cell'] = tuple(map(float, record.split()[1:])) if __name__ == '__main__': import os xi = XInfo(os.path.join(os.environ['XIA2_ROOT'], 'Data', 'Test', 'Xinfo', '1vrm-post-scale.xinfo')) print xi