def parse_args(
self, args, verbose=False, return_unhandled=False, quick_parse=False
):
"""
Parse the command line arguments.
:param args: The input arguments
:param verbose: Print verbose output
:param return_unhandled: True/False also return unhandled arguments
:param quick_parse: Return as fast as possible and without reading any data,
ignoring class constructor options.
:return: The options and parameters and (optionally) unhandled arguments
"""
from dxtbx.model.experiment_list import (
BeamComparison,
DetectorComparison,
GoniometerComparison,
)
from dials.util.phil import parse
# Parse the command line phil parameters
user_phils = []
unhandled = []
interpretor = self.system_phil.command_line_argument_interpreter()
def _is_a_phil_file(filename):
return any(
filename.endswith(phil_ext)
for phil_ext in (".phil", ".param", ".params", ".eff", ".def")
)
for arg in args:
if (
_is_a_phil_file(arg)
and os.path.isfile(arg)
and os.path.getsize(arg) > 0
):
try:
user_phils.append(parse(file_name=arg))
except Exception:
if return_unhandled:
unhandled.append(arg)
else:
raise
# Treat "has a schema" as "looks like a URL (not phil)
elif "=" in arg and not get_url_scheme(arg):
try:
user_phils.append(interpretor.process_arg(arg=arg))
except Exception:
if return_unhandled:
unhandled.append(arg)
else:
raise
else:
unhandled.append(arg)
# Fetch the phil parameters
self._phil, unused = self.system_phil.fetch(
sources=user_phils, track_unused_definitions=True
)
# Print if bad definitions
if len(unused) > 0:
msg = [item.object.as_str().strip() for item in unused]
msg = "\n".join([" %s" % line for line in msg])
raise RuntimeError(f"The following definitions were not recognised\n{msg}")
# Extract the parameters
params = self._phil.extract()
# Stop at this point if quick_parse is set. A second pass may be needed.
if quick_parse:
return params, unhandled
# Create some comparison functions
if self._read_experiments_from_images:
compare_beam = BeamComparison(
wavelength_tolerance=params.input.tolerance.beam.wavelength,
direction_tolerance=params.input.tolerance.beam.direction,
polarization_normal_tolerance=params.input.tolerance.beam.polarization_normal,
polarization_fraction_tolerance=params.input.tolerance.beam.polarization_fraction,
)
compare_detector = DetectorComparison(
fast_axis_tolerance=params.input.tolerance.detector.fast_axis,
slow_axis_tolerance=params.input.tolerance.detector.slow_axis,
origin_tolerance=params.input.tolerance.detector.origin,
)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=params.input.tolerance.goniometer.rotation_axis,
fixed_rotation_tolerance=params.input.tolerance.goniometer.fixed_rotation,
setting_rotation_tolerance=params.input.tolerance.goniometer.setting_rotation,
)
scan_tolerance = params.input.tolerance.scan.oscillation
# FIXME Should probably make this smarter since it requires editing here
# and in dials.import phil scope
try:
format_kwargs = {
"dynamic_shadowing": params.format.dynamic_shadowing,
"multi_panel": params.format.multi_panel,
}
except AttributeError:
format_kwargs = None
else:
compare_beam = None
compare_detector = None
compare_goniometer = None
scan_tolerance = None
format_kwargs = None
try:
load_models = params.load_models
except AttributeError:
load_models = True
# Try to import everything
importer = Importer(
unhandled,
read_experiments=self._read_experiments,
read_reflections=self._read_reflections,
read_experiments_from_images=self._read_experiments_from_images,
check_format=self._check_format,
verbose=verbose,
compare_beam=compare_beam,
compare_detector=compare_detector,
compare_goniometer=compare_goniometer,
scan_tolerance=scan_tolerance,
format_kwargs=format_kwargs,
load_models=load_models,
)
# Grab a copy of the errors that occurred in case the caller wants them
self.handling_errors = importer.handling_errors
# Add the cached arguments
for obj in importer.experiments:
params.input.experiments.append(obj)
for obj in importer.reflections:
params.input.reflections.append(obj)
# Convert to phil
self._phil = self.system_phil.format(python_object=params)
return params, importer.unhandled
def __call__(self, experiment):
if self.tolerance:
compare_beam = BeamComparison(
wavelength_tolerance=self.tolerance.beam.wavelength,
direction_tolerance=self.tolerance.beam.direction,
polarization_normal_tolerance=self.tolerance.beam.
polarization_normal,
polarization_fraction_tolerance=self.tolerance.beam.
polarization_fraction,
)
compare_detector = DetectorComparison(
fast_axis_tolerance=self.tolerance.detector.fast_axis,
slow_axis_tolerance=self.tolerance.detector.slow_axis,
origin_tolerance=self.tolerance.detector.origin,
)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=self.tolerance.goniometer.
rotation_axis,
fixed_rotation_tolerance=self.tolerance.goniometer.
fixed_rotation,
setting_rotation_tolerance=self.tolerance.goniometer.
setting_rotation,
)
else:
compare_beam = None
compare_detector = None
compare_goniometer = None
if self.ref_beam:
if compare_beam:
if not compare_beam(self.ref_beam, experiment.beam):
raise ComparisonError(
compare.beam_diff(
self.ref_beam,
experiment.beam,
wavelength_tolerance=self.tolerance.beam.
wavelength,
direction_tolerance=self.tolerance.beam.direction,
polarization_normal_tolerance=self.tolerance.beam.
polarization_normal,
polarization_fraction_tolerance=self.tolerance.
beam.polarization_fraction,
))
beam = self.ref_beam
else:
beam = experiment.beam
if self.ref_detector and self.average_detector:
detector = self.ref_detector
elif self.ref_detector and not self.average_detector:
if compare_detector:
if not compare_detector(self.ref_detector,
experiment.detector):
raise ComparisonError(
compare.detector_diff(
self.ref_detector,
experiment.detector,
fast_axis_tolerance=self.tolerance.detector.
fast_axis,
slow_axis_tolerance=self.tolerance.detector.
slow_axis,
origin_tolerance=self.tolerance.detector.origin,
))
detector = self.ref_detector
else:
detector = experiment.detector
if self.ref_goniometer:
if compare_goniometer:
if not compare_goniometer(self.ref_goniometer,
experiment.goniometer):
raise ComparisonError(
compare.goniometer_diff(
self.ref_goniometer,
experiment.goniometer,
rotation_axis_tolerance=self.tolerance.goniometer.
rotation_axis,
fixed_rotation_tolerance=self.tolerance.goniometer.
fixed_rotation,
setting_rotation_tolerance=self.tolerance.
goniometer.setting_rotation,
))
goniometer = self.ref_goniometer
else:
goniometer = experiment.goniometer
if self.ref_scan:
scan = self.ref_scan
else:
scan = experiment.scan
if self.ref_crystal:
crystal = self.ref_crystal
else:
crystal = experiment.crystal
if self._last_imageset == experiment.imageset:
imageset = self._last_imageset
else:
imageset = experiment.imageset
self._last_imageset = imageset
return Experiment(
identifier=experiment.identifier,
beam=beam,
detector=detector,
scan=scan,
goniometer=goniometer,
crystal=crystal,
imageset=imageset,
)
def load_imagesets(
template,
directory,
id_image=None,
image_range=None,
use_cache=True,
reversephi=False,
):
global imageset_cache
from dxtbx.model.experiment_list import ExperimentListFactory
from xia2.Applications.xia2setup import known_hdf5_extensions
from dxtbx.imageset import ImageSweep
full_template_path = os.path.join(directory, template)
if full_template_path not in imageset_cache or not use_cache:
from dxtbx.model.experiment_list import BeamComparison
from dxtbx.model.experiment_list import DetectorComparison
from dxtbx.model.experiment_list import GoniometerComparison
params = PhilIndex.params.xia2.settings
compare_beam = BeamComparison(
wavelength_tolerance=params.input.tolerance.beam.wavelength,
direction_tolerance=params.input.tolerance.beam.direction,
polarization_normal_tolerance=params.input.tolerance.beam.polarization_normal,
polarization_fraction_tolerance=params.input.tolerance.beam.polarization_fraction,
)
compare_detector = DetectorComparison(
fast_axis_tolerance=params.input.tolerance.detector.fast_axis,
slow_axis_tolerance=params.input.tolerance.detector.slow_axis,
origin_tolerance=params.input.tolerance.detector.origin,
)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=params.input.tolerance.goniometer.rotation_axis,
fixed_rotation_tolerance=params.input.tolerance.goniometer.fixed_rotation,
setting_rotation_tolerance=params.input.tolerance.goniometer.setting_rotation,
)
scan_tolerance = params.input.tolerance.scan.oscillation
format_kwargs = {
"dynamic_shadowing": params.input.format.dynamic_shadowing,
"multi_panel": params.input.format.multi_panel,
}
if os.path.splitext(full_template_path)[-1] in known_hdf5_extensions:
# if we are passed the correct file, use this, else look for a master
# file (i.e. something_master.h5)
if os.path.exists(full_template_path) and os.path.isfile(
full_template_path
):
master_file = full_template_path
else:
import glob
g = glob.glob(os.path.join(directory, "*_master.h5"))
master_file = None
for p in g:
substr = longest_common_substring(template, p)
if substr:
if master_file is None or (
len(substr)
> len(longest_common_substring(template, master_file))
):
master_file = p
if master_file is None:
raise RuntimeError("Can't find master file for %s" % full_template_path)
unhandled = []
experiments = ExperimentListFactory.from_filenames(
[master_file],
verbose=False,
unhandled=unhandled,
compare_beam=compare_beam,
compare_detector=compare_detector,
compare_goniometer=compare_goniometer,
scan_tolerance=scan_tolerance,
format_kwargs=format_kwargs,
)
assert len(unhandled) == 0, (
"unhandled image files identified: %s" % unhandled
)
else:
from dxtbx.sweep_filenames import locate_files_matching_template_string
params = PhilIndex.get_python_object()
read_all_image_headers = params.xia2.settings.read_all_image_headers
if read_all_image_headers:
paths = sorted(
locate_files_matching_template_string(full_template_path)
)
unhandled = []
experiments = ExperimentListFactory.from_filenames(
paths,
verbose=False,
unhandled=unhandled,
compare_beam=compare_beam,
compare_detector=compare_detector,
compare_goniometer=compare_goniometer,
scan_tolerance=scan_tolerance,
format_kwargs=format_kwargs,
)
assert len(unhandled) == 0, (
"unhandled image files identified: %s" % unhandled
)
else:
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
importer = ExperimentListTemplateImporter(
[full_template_path], format_kwargs=format_kwargs
)
experiments = importer.experiments
imagesets = [
iset for iset in experiments.imagesets() if isinstance(iset, ImageSweep)
]
assert len(imagesets) > 0, "no imageset found"
imageset_cache[full_template_path] = collections.OrderedDict()
if reversephi:
for imageset in imagesets:
goniometer = imageset.get_goniometer()
goniometer.set_rotation_axis(
tuple(-g for g in goniometer.get_rotation_axis())
)
reference_geometry = PhilIndex.params.xia2.settings.input.reference_geometry
if reference_geometry is not None and len(reference_geometry) > 0:
update_with_reference_geometry(imagesets, reference_geometry)
# Update the geometry
params = PhilIndex.params.xia2.settings
update_geometry = []
from dials.command_line.dials_import import ManualGeometryUpdater
from dials.util.options import geometry_phil_scope
# Then add manual geometry
work_phil = geometry_phil_scope.format(params.input)
diff_phil = geometry_phil_scope.fetch_diff(source=work_phil)
if diff_phil.as_str() != "":
update_geometry.append(ManualGeometryUpdater(params.input))
imageset_list = []
for imageset in imagesets:
for updater in update_geometry:
imageset = updater(imageset)
imageset_list.append(imageset)
imagesets = imageset_list
from scitbx.array_family import flex
for imageset in imagesets:
scan = imageset.get_scan()
exposure_times = scan.get_exposure_times()
epochs = scan.get_epochs()
if exposure_times.all_eq(0) or exposure_times[0] == 0:
exposure_times = flex.double(exposure_times.size(), 1)
scan.set_exposure_times(exposure_times)
elif not exposure_times.all_gt(0):
exposure_times = flex.double(exposure_times.size(), exposure_times[0])
scan.set_exposure_times(exposure_times)
if epochs.size() > 1 and not epochs.all_gt(0):
if epochs[0] == 0:
epochs[0] = 1
for i in range(1, epochs.size()):
epochs[i] = epochs[i - 1] + exposure_times[i - 1]
scan.set_epochs(epochs)
_id_image = scan.get_image_range()[0]
imageset_cache[full_template_path][_id_image] = imageset
if id_image is not None:
return [imageset_cache[full_template_path][id_image]]
elif image_range is not None:
for imageset in imageset_cache[full_template_path].values():
scan = imageset.get_scan()
scan_image_range = scan.get_image_range()
if (
image_range[0] >= scan_image_range[0]
and image_range[1] <= scan_image_range[1]
):
imagesets = [
imageset[
image_range[0]
- scan_image_range[0] : image_range[1]
+ 1
- scan_image_range[0]
]
]
assert len(imagesets[0]) == image_range[1] - image_range[0] + 1, len(
imagesets[0]
)
return imagesets
return imageset_cache[full_template_path].values()
def __call__(self, experiment):
from dxtbx.model.experiment_list import BeamComparison
from dxtbx.model.experiment_list import DetectorComparison
from dxtbx.model.experiment_list import GoniometerComparison
from dxtbx.datablock import BeamDiff
from dxtbx.datablock import DetectorDiff
from dxtbx.datablock import GoniometerDiff
if self.tolerance:
compare_beam = BeamComparison(
wavelength_tolerance=self.tolerance.beam.wavelength,
direction_tolerance=self.tolerance.beam.direction,
polarization_normal_tolerance=self.tolerance.beam.
polarization_normal,
polarization_fraction_tolerance=self.tolerance.beam.
polarization_fraction,
)
compare_detector = DetectorComparison(
fast_axis_tolerance=self.tolerance.detector.fast_axis,
slow_axis_tolerance=self.tolerance.detector.slow_axis,
origin_tolerance=self.tolerance.detector.origin,
)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=self.tolerance.goniometer.
rotation_axis,
fixed_rotation_tolerance=self.tolerance.goniometer.
fixed_rotation,
setting_rotation_tolerance=self.tolerance.goniometer.
setting_rotation,
)
else:
compare_beam = None
compare_detector = None
compare_goniometer = None
if self.ref_beam:
if compare_beam:
if not compare_beam(self.ref_beam, experiment.beam):
diff = BeamDiff(
wavelength_tolerance=self.tolerance.beam.wavelength,
direction_tolerance=self.tolerance.beam.direction,
polarization_normal_tolerance=self.tolerance.beam.
polarization_normal,
polarization_fraction_tolerance=self.tolerance.beam.
polarization_fraction,
)
raise ComparisonError("\n".join(
diff(self.ref_beam, experiment.beam)))
beam = self.ref_beam
else:
beam = experiment.beam
if self.ref_detector and self.average_detector:
detector = self.ref_detector
elif self.ref_detector and not self.average_detector:
if compare_detector:
if not compare_detector(self.ref_detector,
experiment.detector):
diff = DetectorDiff(
fast_axis_tolerance=self.tolerance.detector.fast_axis,
slow_axis_tolerance=self.tolerance.detector.slow_axis,
origin_tolerance=self.tolerance.detector.origin,
)
raise ComparisonError("\n".join(
diff(self.ref_detector, experiment.detector)))
detector = self.ref_detector
else:
detector = experiment.detector
if self.ref_goniometer:
if compare_goniometer:
if not compare_goniometer(self.ref_goniometer,
experiment.goniometer):
diff = GoniometerDiff(
rotation_axis_tolerance=self.tolerance.goniometer.
rotation_axis,
fixed_rotation_tolerance=self.tolerance.goniometer.
fixed_rotation,
setting_rotation_tolerance=self.tolerance.goniometer.
setting_rotation,
)
raise ComparisonError("\n".join(
diff(self.ref_goniometer, experiment.goniometer)))
goniometer = self.ref_goniometer
else:
goniometer = experiment.goniometer
if self.ref_scan:
scan = self.ref_scan
else:
scan = experiment.scan
if self.ref_crystal:
crystal = self.ref_crystal
else:
crystal = experiment.crystal
if self._last_imageset == experiment.imageset:
imageset = self._last_imageset
else:
imageset = experiment.imageset
self._last_imageset = imageset
from dxtbx.model.experiment_list import Experiment
return Experiment(
beam=beam,
detector=detector,
scan=scan,
goniometer=goniometer,
crystal=crystal,
imageset=imageset,
)
def _run_dials_import(self):
"""
Perform a minimal version of dials.import to get an experiment list.
Use some filleted bits of dials.import and dials.util.options.Importer.
"""
# Get some key data format arguments.
try:
format_kwargs = {
"dynamic_shadowing":
self.params.dials_import.format.dynamic_shadowing,
"multi_panel": self.params.dials_import.format.multi_panel,
}
except AttributeError:
format_kwargs = {}
# If filenames contain wildcards, expand
args = []
for arg in self.params.dials_import.input.experiments:
if "*" in arg:
args.extend(glob(arg))
else:
args.append(arg)
if args:
# Are compare{beam,detector,goniometer} and scan_tolerance necessary?
# They are cargo-culted from the DIALS option parser.
tol_params = self.params.dials_import.input.tolerance
compare_beam = BeamComparison(
wavelength_tolerance=tol_params.beam.wavelength,
direction_tolerance=tol_params.beam.direction,
polarization_normal_tolerance=tol_params.beam.
polarization_normal,
polarization_fraction_tolerance=tol_params.beam.
polarization_fraction,
)
compare_detector = DetectorComparison(
fast_axis_tolerance=tol_params.detector.fast_axis,
slow_axis_tolerance=tol_params.detector.slow_axis,
origin_tolerance=tol_params.detector.origin,
)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=tol_params.goniometer.rotation_axis,
fixed_rotation_tolerance=tol_params.goniometer.fixed_rotation,
setting_rotation_tolerance=tol_params.goniometer.
setting_rotation,
)
scan_tolerance = tol_params.scan.oscillation
# Import an experiment list from image data.
try:
experiments = ExperimentListFactory.from_filenames(
args,
compare_beam=compare_beam,
compare_detector=compare_detector,
compare_goniometer=compare_goniometer,
scan_tolerance=scan_tolerance,
format_kwargs=format_kwargs,
)
except IOError as e:
warning("%s '%s'", e.strerror, e.filename)
sys.exit(1)
# Record the imported experiments for use elsewhere.
# Quit if there aren't any.
self.expts.extend(experiments)
if not self.expts:
warning("No images found.")
sys.exit(1)
else:
# Use the template importer.
if len(self.params.dials_import.input.template) > 0:
importer = ExperimentListTemplateImporter(
self.params.dials_import.input.template,
format_kwargs=format_kwargs)
# Record the imported experiments for use elsewhere.
# Quit if there aren't any.
self.expts.extend(importer.experiments)
if not self.expts:
warning("No images found matching template %s" %
self.params.dials_import.input.template[0])
sys.exit(1)
# Setup the metadata updater
metadata_updater = MetaDataUpdater(self.params.dials_import)
# Extract the experiments and loop through
self.expts = metadata_updater(self.expts.imagesets())