def run(self):
"""Run init."""
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)
lib_str = find_hdf5_lib(
os.path.join(self.get_directory(), self.get_template()))
if lib_str:
xds_inp.write(lib_str)
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)
else:
xds_inp.write("MAXIMUM_NUMBER_OF_JOBS=1\n")
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:
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)
lib_str = find_hdf5_lib(
os.path.join(self.get_directory(), self.get_template())
)
if lib_str:
xds_inp.write(lib_str)
xds_inp.write("DATA_RANGE=%d %d\n" % self._data_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_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):
'''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)
xds_inp.write('MAXIMUM_NUMBER_OF_JOBS=1\n')
#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)
lib_str = find_hdf5_lib(
os.path.join(self.get_directory(), self.get_template()))
if lib_str:
xds_inp.write(lib_str)
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
def run(self):
"""Run colspot."""
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)
xds_inp.write("MAXIMUM_NUMBER_OF_JOBS=1\n")
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)
lib_str = find_hdf5_lib(
os.path.join(self.get_directory(), self.get_template())
)
if lib_str:
xds_inp.write(lib_str)
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:
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
)
