def find_hdf5_lib(template=None):
global __hdf5_lib
from xia2.Applications.xia2setup import is_hdf5_name
if template and not is_hdf5_name(template):
return ""
if __hdf5_lib:
return __hdf5_lib
from xia2.Handlers.Phil import PhilIndex
from dials.util import Sorry
plugin_name = PhilIndex.get_python_object().xds.hdf5_plugin
if os.path.isabs(plugin_name):
if not os.path.exists(plugin_name):
raise Sorry("Cannot find plugin %s" % plugin_name)
__hdf5_lib = "LIB=%s\n" % plugin_name
return __hdf5_lib
for d in os.environ["PATH"].split(os.pathsep):
if os.path.exists(os.path.join(d, plugin_name)):
__hdf5_lib = "LIB=%s\n" % os.path.join(d, plugin_name)
return __hdf5_lib
return ""
def update(self):
"""Check to see if any more frames have appeared - if they
have update myself and reset."""
from xia2.Applications.xia2setup import is_hdf5_name
if is_hdf5_name(os.path.join(self._directory, self._template)):
return
images = find_matching_images(self._template, self._directory)
if len(images) > len(self._images):
self._images = images
from xia2.Schema import load_imagesets
imagesets = load_imagesets(
self._template,
self._directory,
id_image=self._id_image,
use_cache=False,
reversephi=PhilIndex.params.xia2.settings.input.reverse_phi,
)
max_images = 0
best_sweep = None
for imageset in imagesets:
scan = imageset.get_scan()
if scan is None:
continue
if imageset.get_scan().get_num_images() > max_images:
best_sweep = imageset
self._imageset = best_sweep
def image2template_directory(filename):
"""Separate out the template and directory from an image name."""
directory, image = os.path.split(os.path.abspath(filename))
from xia2.Applications.xia2setup import is_hdf5_name
if is_hdf5_name(filename):
return image, directory
template = image2template(image)
return template, directory
def template_to_xds(template):
from xia2.Applications.xia2setup import is_hdf5_name
if is_hdf5_name(template):
# Given (e.g.) XYZ_master.h5 and data files XYZ_data_00000[0-9].h5
# XDS expects the template XYZ_??????.h5
assert template.endswith("master.h5"), template
# FIXME for #401 - should look into the master file for references
# either explicitly to child data sets or via the VDS - meantimes,
# remove the check
# master_file = template
# g = glob.glob(master_file.split("master.h5")[0] + "data_*[0-9].h5")
# g.extend(glob.glob(master_file.split("master.h5")[0] + "*[0-9].h5"))
# assert len(g), "No associated data files found for %s" % master_file
# we don't know what is in the master file but we know at this point
# that the word master is in there, so... otherwise can get complicated
# side-effects when people have a folder named e.g. data_200.
return template.replace("master.h5", "??????.h5")
return template.replace("#", "?")
def setup(self):
"""Set everything up..."""
# check arguments are all ascii
logger.debug("Start parsing command line: " + str(sys.argv))
for token in sys.argv:
try:
token.encode("ascii")
except UnicodeDecodeError:
raise RuntimeError("non-ascii characters in input")
self._argv = copy.deepcopy(sys.argv)
# first of all try to interpret arguments as phil parameters/files
from xia2.Handlers.Phil import master_phil
from libtbx.phil import command_line
cmd_line = command_line.argument_interpreter(master_phil=master_phil)
working_phil, self._argv = cmd_line.process_and_fetch(
args=self._argv, custom_processor="collect_remaining")
PhilIndex.merge_phil(working_phil)
try:
params = PhilIndex.get_python_object()
except RuntimeError as e:
raise Sorry(e)
# sanity check / interpret Auto in input
from libtbx import Auto
if params.xia2.settings.input.atom is None:
if params.xia2.settings.input.anomalous is Auto:
PhilIndex.update("xia2.settings.input.anomalous=false")
else:
if params.xia2.settings.input.anomalous is False:
raise Sorry(
"Setting anomalous=false and atom type inconsistent")
params.xia2.settings.input.anomalous = True
PhilIndex.update("xia2.settings.input.anomalous=true")
if params.xia2.settings.resolution.keep_all_reflections is Auto:
if (params.xia2.settings.small_molecule is True
and params.xia2.settings.resolution.d_min is None
and params.xia2.settings.resolution.d_max is None):
PhilIndex.update(
"xia2.settings.resolution.keep_all_reflections=true")
else:
PhilIndex.update(
"xia2.settings.resolution.keep_all_reflections=false")
if params.xia2.settings.small_molecule is True:
logger.debug("Small molecule selected")
if params.xia2.settings.symmetry.chirality is None:
PhilIndex.update("xia2.settings.symmetry.chirality=nonchiral")
params = PhilIndex.get_python_object()
# pipeline options
self._read_pipeline()
for (parameter, value) in (
("project", params.xia2.settings.project),
("crystal", params.xia2.settings.crystal),
):
validate_project_crystal_name(parameter, value)
logger.debug("Project: %s" % params.xia2.settings.project)
logger.debug("Crystal: %s" % params.xia2.settings.crystal)
# FIXME add some consistency checks in here e.g. that there are
# images assigned, there is a lattice assigned if cell constants
# are given and so on
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
from xia2.Handlers.Environment import get_number_cpus
if mp_params.mode == "parallel":
if mp_params.type == "qsub":
if which("qsub") is None:
raise Sorry("qsub not available")
if mp_params.njob is Auto:
mp_params.njob = get_number_cpus()
if mp_params.nproc is Auto:
mp_params.nproc = 1
elif mp_params.nproc is Auto:
mp_params.nproc = get_number_cpus()
elif mp_params.mode == "serial":
if mp_params.type == "qsub":
if which("qsub") is None:
raise Sorry("qsub not available")
if mp_params.njob is Auto:
mp_params.njob = 1
if mp_params.nproc is Auto:
mp_params.nproc = get_number_cpus()
PhilIndex.update("xia2.settings.multiprocessing.njob=%d" %
mp_params.njob)
PhilIndex.update("xia2.settings.multiprocessing.nproc=%d" %
mp_params.nproc)
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
if mp_params.nproc > 1 and os.name == "nt":
raise Sorry("nproc > 1 is not supported on Windows.") # #191
if params.xia2.settings.indexer is not None:
add_preference("indexer", params.xia2.settings.indexer)
if params.xia2.settings.refiner is not None:
add_preference("refiner", params.xia2.settings.refiner)
if params.xia2.settings.integrater is not None:
add_preference("integrater", params.xia2.settings.integrater)
if params.xia2.settings.scaler is not None:
add_preference("scaler", params.xia2.settings.scaler)
if params.xia2.settings.multi_sweep_indexing is Auto:
if (params.xia2.settings.small_molecule is True
and "dials" == params.xia2.settings.indexer):
PhilIndex.update("xia2.settings.multi_sweep_indexing=True")
else:
PhilIndex.update("xia2.settings.multi_sweep_indexing=False")
if (params.xia2.settings.multi_sweep_indexing is True
and params.xia2.settings.multiprocessing.mode == "parallel"):
logger.info(
"Multi sweep indexing disabled:\nMSI is not available for parallel processing."
)
PhilIndex.update("xia2.settings.multi_sweep_indexing=False")
input_json = params.xia2.settings.input.json
if input_json is not None and len(input_json):
for json_file in input_json:
assert os.path.isfile(json_file)
load_experiments(json_file)
reference_geometry = params.xia2.settings.input.reference_geometry
if reference_geometry is not None and len(reference_geometry) > 0:
reference_geometries = "\n".join([
"xia2.settings.input.reference_geometry=%s" %
os.path.abspath(g)
for g in params.xia2.settings.input.reference_geometry
])
logger.debug(reference_geometries)
PhilIndex.update(reference_geometries)
logger.debug("xia2.settings.trust_beam_centre=true")
PhilIndex.update("xia2.settings.trust_beam_centre=true")
params = PhilIndex.get_python_object()
params = PhilIndex.get_python_object()
if params.xia2.settings.input.xinfo is not None:
xinfo_file = os.path.abspath(params.xia2.settings.input.xinfo)
PhilIndex.update("xia2.settings.input.xinfo=%s" % xinfo_file)
params = PhilIndex.get_python_object()
self.set_xinfo(xinfo_file)
# issue #55 if not set ATOM in xinfo but anomalous=true or atom= set
# on commandline, set here, should be idempotent
if params.xia2.settings.input.anomalous is True:
crystals = self._xinfo.get_crystals()
for xname in crystals:
xtal = crystals[xname]
logger.debug("Setting anomalous for crystal %s" % xname)
xtal.set_anomalous(True)
else:
xinfo_file = "%s/automatic.xinfo" % os.path.abspath(os.curdir)
PhilIndex.update("xia2.settings.input.xinfo=%s" % xinfo_file)
params = PhilIndex.get_python_object()
if params.dials.find_spots.phil_file is not None:
PhilIndex.update(
"dials.find_spots.phil_file=%s" %
os.path.abspath(params.dials.find_spots.phil_file))
if params.dials.index.phil_file is not None:
PhilIndex.update("dials.index.phil_file=%s" %
os.path.abspath(params.dials.index.phil_file))
if params.dials.refine.phil_file is not None:
PhilIndex.update("dials.refine.phil_file=%s" %
os.path.abspath(params.dials.refine.phil_file))
if params.dials.integrate.phil_file is not None:
PhilIndex.update("dials.integrate.phil_file=%s" %
os.path.abspath(params.dials.integrate.phil_file))
if params.xds.index.xparm is not None:
Flags.set_xparm(params.xds.index.xparm)
if params.xds.index.xparm_ub is not None:
Flags.set_xparm_ub(params.xds.index.xparm_ub)
if params.xia2.settings.scale.freer_file is not None:
freer_file = os.path.abspath(params.xia2.settings.scale.freer_file)
if not os.path.exists(freer_file):
raise RuntimeError("%s does not exist" % freer_file)
from xia2.Modules.FindFreeFlag import FindFreeFlag
column = FindFreeFlag(freer_file)
logger.debug("FreeR_flag column in %s found: %s" %
(freer_file, column))
PhilIndex.update("xia2.settings.scale.freer_file=%s" % freer_file)
if params.xia2.settings.scale.reference_reflection_file is not None:
reference_reflection_file = os.path.abspath(
params.xia2.settings.scale.reference_reflection_file)
if not os.path.exists(reference_reflection_file):
raise RuntimeError("%s does not exist" %
reference_reflection_file)
PhilIndex.update(
"xia2.settings.scale.reference_reflection_file=%s" %
reference_reflection_file)
params = PhilIndex.get_python_object()
datasets = unroll_datasets(PhilIndex.params.xia2.settings.input.image)
for dataset in datasets:
start_end = None
# here we only care about ':' which are later than C:\
if ":" in dataset[3:]:
tokens = dataset.split(":")
# cope with windows drives i.e. C:\data\blah\thing_0001.cbf:1:100
if len(tokens[0]) == 1:
tokens = ["%s:%s" % (tokens[0], tokens[1])] + tokens[2:]
if len(tokens) != 3:
raise RuntimeError("/path/to/image_0001.cbf:start:end")
dataset = tokens[0]
start_end = int(tokens[1]), int(tokens[2])
from xia2.Applications.xia2setup import is_hdf5_name
if os.path.exists(os.path.abspath(dataset)):
dataset = os.path.abspath(dataset)
else:
directories = [os.getcwd()] + self._argv[1:]
found = False
for d in directories:
if os.path.exists(os.path.join(d, dataset)):
dataset = os.path.join(d, dataset)
found = True
break
if not found:
raise Sorry("Could not find %s in %s" %
(dataset, " ".join(directories)))
if is_hdf5_name(dataset):
self._hdf5_master_files.append(dataset)
if start_end:
logger.debug("Image range: %d %d" % start_end)
if dataset not in self._default_start_end:
self._default_start_end[dataset] = []
self._default_start_end[dataset].append(start_end)
else:
logger.debug("No image range specified")
else:
template, directory = image2template_directory(
os.path.abspath(dataset))
self._default_template.append(os.path.join(
directory, template))
self._default_directory.append(directory)
logger.debug("Interpreted from image %s:" % dataset)
logger.debug("Template %s" % template)
logger.debug("Directory %s" % directory)
if start_end:
logger.debug("Image range: %d %d" % start_end)
key = os.path.join(directory, template)
if key not in self._default_start_end:
self._default_start_end[key] = []
self._default_start_end[key].append(start_end)
else:
logger.debug("No image range specified")
# finally, check that all arguments were read and raise an exception
# if any of them were nonsense.
with open("xia2-working.phil", "w") as f:
f.write(PhilIndex.working_phil.as_str())
f.write(
os.linesep
) # temporarily required for https://github.com/dials/dials/issues/522
with open("xia2-diff.phil", "w") as f:
f.write(PhilIndex.get_diff().as_str())
f.write(
os.linesep
) # temporarily required for https://github.com/dials/dials/issues/522
logger.debug("\nDifference PHIL:")
logger.debug(PhilIndex.get_diff().as_str())
logger.debug("Working PHIL:")
logger.debug(PhilIndex.working_phil.as_str())
nonsense = "Unknown command-line options:"
was_nonsense = False
for j, argv in enumerate(self._argv):
if j == 0:
continue
if argv[0] != "-" and "=" not in argv:
continue
if j not in self._understood:
nonsense += " %s" % argv
was_nonsense = True
if was_nonsense:
raise RuntimeError(nonsense)