def run(self):
'''Run init.'''
#image_header = self.get_header()
## crank through the header dictionary and replace incorrect
## information with updated values through the indexer
## interface if available...
## need to add distance, wavelength - that should be enough...
#if self.get_distance():
#image_header['distance'] = self.get_distance()
#if self.get_wavelength():
#image_header['wavelength'] = self.get_wavelength()
#if self.get_two_theta():
#image_header['two_theta'] = self.get_two_theta()
header = imageset_to_xds(self.get_imageset())
xds_inp = open(os.path.join(self.get_working_directory(),
'XDS.INP'), 'w')
# what are we doing?
xds_inp.write('JOB=INIT\n')
for record in header:
xds_inp.write('%s\n' % record)
name_template = os.path.join(self.get_directory(),
self.get_template().replace('#', '?'))
record = 'NAME_TEMPLATE_OF_DATA_FRAMES=%s\n' % \
name_template
xds_inp.write(record)
xds_inp.write('DATA_RANGE=%d %d\n' % self._data_range)
for spot_range in self._spot_range:
xds_inp.write('SPOT_RANGE=%d %d\n' % spot_range)
xds_inp.write('BACKGROUND_RANGE=%d %d\n' % \
self._background_range)
if self._params.fix_scale:
if _running_xds_version() >= 20130330:
xds_inp.write('DATA_RANGE_FIXED_SCALE_FACTOR= %d %d 1\n' %
self._data_range)
else:
xds_inp.write('FIXED_SCALE_FACTOR=TRUE\n')
xds_inp.close()
# copy the input file...
shutil.copyfile(os.path.join(self.get_working_directory(),
'XDS.INP'),
os.path.join(self.get_working_directory(),
'%d_INIT.INP' % self.get_xpid()))
# write the input data files...
for file_name in self._input_data_files_list:
src = self._input_data_files[file_name]
dst = os.path.join(
self.get_working_directory(), file_name)
if src != dst:
shutil.copyfile(src, dst)
self.start()
self.close_wait()
xds_check_version_supported(self.get_all_output())
# check the job status here
# copy the LP file
shutil.copyfile(os.path.join(self.get_working_directory(),
'INIT.LP'),
os.path.join(self.get_working_directory(),
'%d_INIT.LP' % self.get_xpid()))
# gather the output files
for file in self._output_data_files_list:
self._output_data_files[file] = os.path.join(
self.get_working_directory(), file)
return
def run(self):
'''Run integrate.'''
#image_header = self.get_header()
## crank through the header dictionary and replace incorrect
## information with updated values through the indexer
## interface if available...
## need to add distance, wavelength - that should be enough...
#if self.get_distance():
#image_header['distance'] = self.get_distance()
#if self.get_wavelength():
#image_header['wavelength'] = self.get_wavelength()
#if self.get_two_theta():
#image_header['two_theta'] = self.get_two_theta()
header = imageset_to_xds(self.get_imageset())
xds_inp = open(os.path.join(self.get_working_directory(),
'XDS.INP'), 'w')
# what are we doing?
xds_inp.write('JOB=INTEGRATE\n')
xds_inp.write('MAXIMUM_NUMBER_OF_PROCESSORS=%d\n' % \
self._parallel)
from xia2.Handlers.Phil import PhilIndex
xds_params = PhilIndex.params.xds
if xds_params.profile_grid_size:
ab, c = xds_params.profile_grid_size
assert(ab > 0 and ab < 22 and (ab % 2) == 1)
assert(c > 0 and c < 22 and (c % 2) == 1)
xds_inp.write(
'NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA= %d\n' % ab)
xds_inp.write(
'NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= %d\n' % c)
from libtbx import Auto
mp_params = PhilIndex.params.xia2.settings.multiprocessing
if mp_params.mode == 'serial' and mp_params.njob > 1:
xds_inp.write('MAXIMUM_NUMBER_OF_JOBS=%d\n' %mp_params.njob)
elif mp_params.mode == 'serial' and mp_params.njob == Auto:
chunk_width = 30.0
phi_width = self.get_phi_width()
nchunks = int(
(self._data_range[1] - self._data_range[0] + 1) * \
phi_width / chunk_width)
Debug.write('Xparallel: -1 using %d chunks' % nchunks)
xds_inp.write('MAXIMUM_NUMBER_OF_JOBS=%d\n' % nchunks)
profile_fitting = PhilIndex.params.xia2.settings.integration.profile_fitting
if not profile_fitting:
xds_inp.write('PROFILE_FITTING=FALSE\n')
# write out lots of output
xds_inp.write('TEST=2\n')
if self._params.delphi:
xds_inp.write('DELPHI=%.1f\n' % self._params.delphi)
elif PhilIndex.params.xia2.settings.small_molecule == True:
xds_inp.write('DELPHI=%.1f\n' % \
xds_params.delphi_small)
else:
xds_inp.write('DELPHI=%.1f\n' % \
xds_params.delphi)
if self._refined_xparm:
xds_inp.write('REFINE(INTEGRATE)=%s\n' %
' '.join(self._params.refine_final))
else:
xds_inp.write('REFINE(INTEGRATE)=%s\n' %
' '.join(self._params.refine))
if self._params.fix_scale:
if _running_xds_version() >= 20130330:
xds_inp.write('DATA_RANGE_FIXED_SCALE_FACTOR= %d %d 1\n' %
self._data_range)
else:
xds_inp.write('FIXED_SCALE_FACTOR=TRUE\n')
# check for updated input parameters or ones from phil
if 'BEAM_DIVERGENCE' in self._updates and \
'BEAM_DIVERGENCE_E.S.D.' in self._updates:
xds_inp.write(
'BEAM_DIVERGENCE=%f BEAM_DIVERGENCE_E.S.D.=%f\n' % \
(self._updates['BEAM_DIVERGENCE'],
self._updates['BEAM_DIVERGENCE_E.S.D.']))
elif self._params.beam_divergence and self._params.beam_divergence_esd:
xds_inp.write(
'BEAM_DIVERGENCE=%f BEAM_DIVERGENCE_E.S.D.=%f\n' % \
(self._params.beam_divergence,
self._params.beam_divergence_esd))
if 'REFLECTING_RANGE' in self._updates and \
'REFLECTING_RANGE_E.S.D.' in self._updates:
xds_inp.write(
'REFLECTING_RANGE=%f REFLECTING_RANGE_E.S.D.=%f\n' % \
(self._updates['REFLECTING_RANGE'],
self._updates['REFLECTING_RANGE_E.S.D.']))
elif self._params.reflecting_range and self._params.reflecting_range_esd:
xds_inp.write(
'REFLECTING_RANGE=%f REFLECTING_RANGE_E.S.D.=%f\n' % \
(self._params.reflecting_range,
self._params.reflecting_range_esd))
for record in header:
xds_inp.write('%s\n' % record)
name_template = template_to_xds(
os.path.join(self.get_directory(), self.get_template()))
record = 'NAME_TEMPLATE_OF_DATA_FRAMES=%s\n' % \
name_template
xds_inp.write(record)
xds_inp.write('DATA_RANGE=%d %d\n' % self._data_range)
# xds_inp.write('MINIMUM_ZETA=0.1\n')
xds_inp.close()
# copy the input file...
shutil.copyfile(os.path.join(self.get_working_directory(),
'XDS.INP'),
os.path.join(self.get_working_directory(),
'%d_INTEGRATE.INP' % self.get_xpid()))
# write the input data files...
for file_name in self._input_data_files_list:
src = self._input_data_files[file_name]
dst = os.path.join(
self.get_working_directory(), file_name)
if src != dst:
shutil.copyfile(src, dst)
self.start()
self.close_wait()
xds_check_version_supported(self.get_all_output())
xds_check_error(self.get_all_output())
# look for errors
# like this perhaps - what the hell does this mean?
# !!! ERROR !!! "STRONGHKL": ASSERT VIOLATION
# copy the LP file
shutil.copyfile(os.path.join(self.get_working_directory(),
'INTEGRATE.LP'),
os.path.join(self.get_working_directory(),
'%d_INTEGRATE.LP' % self.get_xpid()))
# gather the output files
for file in self._output_data_files_list:
self._output_data_files[file] = os.path.join(
self.get_working_directory(), file)
self._integrate_hkl = os.path.join(self.get_working_directory(),
'INTEGRATE.HKL')
# look through integrate.lp for some useful information
# to help with the analysis
space_group_number = 0
mosaics = []
for o in open(os.path.join(
self.get_working_directory(),
'INTEGRATE.LP')).readlines():
if 'SPACE_GROUP_NUMBER' in o:
space_group_number = int(o.split()[-1])
if 'CRYSTAL MOSAICITY (DEGREES)' in o:
mosaic = float(o.split()[-1])
mosaics.append(mosaic)
assert len(mosaics) > 0, "XDS refinement failed (no mosaic spread range reported)"
self._min_mosaic = min(mosaics)
self._max_mosaic = max(mosaics)
self._mean_mosaic = sum(mosaics) / len(mosaics)
Debug.write(
'Mosaic spread range: %.3f %.3f %.3f' % \
(self._min_mosaic, self._mean_mosaic, self._max_mosaic))
stats = _parse_integrate_lp(os.path.join(
self.get_working_directory(),
'INTEGRATE.LP'))
self._per_image_statistics = stats
self._updates = _parse_integrate_lp_updates(os.path.join(
self.get_working_directory(),
'INTEGRATE.LP'))
return