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
def run(self, ignore_errors = False):
'''Run idxref.'''
#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(),
refined_beam_vector=self._refined_beam_vector,
refined_rotation_axis=self._refined_rotation_axis,
refined_distance=self._refined_distance)
xds_inp = open(os.path.join(self.get_working_directory(),
'XDS.INP'), 'w')
# what are we doing?
xds_inp.write('JOB=IDXREF\n')
xds_inp.write('MAXIMUM_NUMBER_OF_PROCESSORS=%d\n' % \
self._parallel)
# FIXME this needs to be calculated from the beam centre...
if self._refined_origin:
xds_inp.write('ORGX=%f ORGY=%f\n' % \
tuple(self._refined_origin))
else:
xds_inp.write('ORGX=%f ORGY=%f\n' % \
tuple(self._org))
# FIXME in here make sure sweep is wider than 5 degrees
# before specifying AXIS: if <= 5 degrees replace AXIS with
# nothing - base this on the maximum possible angular separation
min_frame = self._spot_range[0][0]
max_frame = self._spot_range[-1][1]
refine_params = [p for p in self._params.refine]
phi_width = self.get_phi_width()
if ('AXIS' in refine_params
and (max_frame - min_frame) * phi_width < 5.0):
refine_params.remove('AXIS')
xds_inp.write('REFINE(IDXREF)=%s\n' %
' '.join(refine_params))
if self._starting_frame and self._starting_angle:
xds_inp.write('STARTING_FRAME=%d\n' % \
self._starting_frame)
xds_inp.write('STARTING_ANGLE=%f\n' % \
self._starting_angle)
# FIXME this looks like a potential bug - what will
# happen if the input lattice has not been set??
if self._indxr_input_cell:
self._cell = self._indxr_input_cell
if self._indxr_input_lattice:
self._symm = lattice_to_spacegroup_number(
self._indxr_input_lattice)
if self._cell:
xds_inp.write('SPACE_GROUP_NUMBER=%d\n' % self._symm)
cell_format = '%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f'
xds_inp.write('UNIT_CELL_CONSTANTS=%s\n' % \
cell_format % self._cell)
if self._a_axis:
xds_inp.write('UNIT_CELL_A-AXIS=%.2f %.2f %.2f\n' %
tuple(self._a_axis))
if self._b_axis:
xds_inp.write('UNIT_CELL_B-AXIS=%.2f %.2f %.2f\n' %
tuple(self._b_axis))
if self._c_axis:
xds_inp.write('UNIT_CELL_C-AXIS=%.2f %.2f %.2f\n' %
tuple(self._c_axis))
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)
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)
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_IDXREF.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())
if not ignore_errors:
xds_check_error(self.get_all_output())
# If xds_check_error detects any errors it will raise an exception
# The caller can then continue using the run_continue_from_error()
# function. If XDS does not throw any errors we just plow on.
return self.continue_from_error()
def run(self):
'''Run defpix.'''
#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=DEFPIX\n')
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)
# include the resolution range, perhaps
if self._resolution_high > 0.0 or self._resolution_low > 0.0:
xds_inp.write('INCLUDE_RESOLUTION_RANGE=%.2f %.2f\n' % \
(self._resolution_low, self._resolution_high))
if self._value_range_for_trusted_detector_pixels is not None:
xds_inp.write('VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=%i %i'
%self._value_range_for_trusted_detector_pixels)
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_DEFPIX.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())
# copy the LP file
shutil.copyfile(os.path.join(self.get_working_directory(),
'DEFPIX.LP'),
os.path.join(self.get_working_directory(),
'%d_DEFPIX.LP' % self.get_xpid()))
# check the resolution asked for is achievable (if set)
for record in open(os.path.join(self.get_working_directory(),
'DEFPIX.LP')):
if 'RESOLUTION RANGE RECORDED BY DETECTOR' in record:
real_high = float(record.split()[-1])
if self._resolution_high:
if real_high > self._resolution_high + 0.01:
Chatter.write(
'Warning: resolution limited to %.2f' % \
real_high)
# 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 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 = 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)
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 correct."""
# this is ok...
# if not self._cell:
# raise RuntimeError, 'cell not set'
# if not self._spacegroup_number:
# raise RuntimeError, 'spacegroup not set'
# 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=CORRECT\n")
xds_inp.write("MAXIMUM_NUMBER_OF_PROCESSORS=%d\n" % self._parallel)
# check to see if we are excluding ice rings
if self._ice != 0:
Debug.write("Excluding ice rings")
for record in open(
os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "Data", "ice-rings.dat"))
).readlines():
resol = tuple(map(float, record.split()[:2]))
xds_inp.write("EXCLUDE_RESOLUTION_RANGE= %.2f %.2f\n" % resol)
# exclude requested resolution ranges
if self._excluded_regions:
Debug.write("Excluding regions: %s" % ` self._excluded_regions `)
for upper, lower in self._excluded_regions:
xds_inp.write("EXCLUDE_RESOLUTION_RANGE= %.2f %.2f\n" % (upper, lower))
# postrefine everything to give better values to the
# next INTEGRATE run
xds_inp.write("REFINE(CORRECT)=%s\n" % " ".join(self._params.refine))
if self._polarization > 0.0:
xds_inp.write("FRACTION_OF_POLARIZATION=%.2f\n" % self._polarization)
if self._params.air is not None:
xds_inp.write("AIR=%f" % self._params.air)
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')
# include the resolution range, perhaps
if self._resolution_high or self._resolution_low:
xds_inp.write("INCLUDE_RESOLUTION_RANGE=%.2f %.2f\n" % (self._resolution_low, self._resolution_high))
if self._anomalous:
xds_inp.write("FRIEDEL'S_LAW=FALSE\n")
xds_inp.write("STRICT_ABSORPTION_CORRECTION=TRUE\n")
else:
xds_inp.write("FRIEDEL'S_LAW=TRUE\n")
if self._spacegroup_number:
if not self._cell:
raise RuntimeError, "cannot set spacegroup without unit cell"
xds_inp.write("SPACE_GROUP_NUMBER=%d\n" % self._spacegroup_number)
if self._cell:
xds_inp.write("UNIT_CELL_CONSTANTS=")
xds_inp.write("%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f\n" % tuple(self._cell))
if self._reindex_matrix:
xds_inp.write("REIDX=%d %d %d %d %d %d %d %d %d %d %d %d" % tuple(map(int, self._reindex_matrix)))
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_CORRECT.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
# !!! ERROR !!! ILLEGAL SPACE GROUP NUMBER OR UNIT CELL
# copy the LP file
shutil.copyfile(
os.path.join(self.get_working_directory(), "CORRECT.LP"),
os.path.join(self.get_working_directory(), "%d_CORRECT.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._xds_ascii_hkl = os.path.join(self.get_working_directory(), "XDS_ASCII.HKL")
# do some parsing of the correct output...
self._results = _parse_correct_lp(os.path.join(self.get_working_directory(), "CORRECT.LP"))
# check that the unit cell is comparable to what went in i.e.
# the volume is the same to within a factor of 10 (which is
# extremely generous and should only spot gross errors)
original = unit_cell(self._cell)
refined = unit_cell(self._results["cell"])
if original.volume() / refined.volume() > 10:
raise RuntimeError, "catastrophic change in unit cell volume"
if refined.volume() / original.volume() > 10:
raise RuntimeError, "catastrophic change in unit cell volume"
# record reindex operation used for future reference... this
# is to trap trac #419
if "reindex_op" in self._results:
format = "XDS applied reindex:" + 12 * " %d"
Debug.write(format % tuple(self._results["reindex_op"]))
self._reindex_used = self._results["reindex_op"]
# get the reflections to remove...
for line in open(os.path.join(self.get_working_directory(), "CORRECT.LP"), "r").readlines():
if '"alien"' in line:
h, k, l = tuple(map(int, line.split()[:3]))
z = float(line.split()[4])
if not (h, k, l, z) in self._remove:
self._remove.append((h, k, l, z))
return
def run(self):
'''Run colspot.'''
#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=COLSPOT\n')
xds_inp.write('MAXIMUM_NUMBER_OF_PROCESSORS=%d\n' % \
self._parallel)
#if image_header['detector'] in ('pilatus', 'dectris'):
if self.get_imageset().get_detector()[0].get_type() == 'SENSOR_PAD':
xds_inp.write('MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=%d\n' %
self._params.minimum_pixels_per_spot)
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)
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 PhilIndex.params.xia2.settings.small_molecule == True:
xds_inp.write('STRONG_PIXEL=5\n')
# FIXME should probably be moved to a phil parameter
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_COLSPOT.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())
# copy the LP file
shutil.copyfile(os.path.join(self.get_working_directory(),
'COLSPOT.LP'),
os.path.join(self.get_working_directory(),
'%d_COLSPOT.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
