def run(xds_inp, xparm=None, integrate_lp=None, integrate_hkl=None, spot_xds=None,
space_group=None, reindex_op=None, out_prefix=None, out_dir="."):
out_prefix = out_prefix+"_" if out_prefix else ""
if integrate_lp is not None:
xparm_objs = prep_xparm_objects_from_integrate_lp(integrate_lp, xparm_ref=xparm)
rr, xp = xparm_objs[0]
xparm = os.path.join(os.path.dirname(xds_inp), "XPARM.XDS_%.6d-%.6d"%rr)
open(xparm, "w").write(xp.xparm_str())
# FIXME template of experiment.imageset could be wrong when relative path
# and ######.h5 may need to be replaced with master.h5
experiments = ExperimentListFactory.from_xds(xds_inp, xparm) # XDS.INP needed for sweep info
assert len(experiments) == 1
experiment = experiments[0]
# I don't know what invalid X/Y/ZOBS values should be when multi-panel detector
assert len(experiment.detector) == 1
if None not in (space_group, reindex_op):
cryst_orig = copy.deepcopy(experiment.crystal)
cryst_reindexed = cryst_orig.change_basis(reindex_op)
a, b, c = cryst_reindexed.get_real_space_vectors()
cryst_reindexed = Crystal(a, b, c, space_group=space_group)
experiment.crystal.update(cryst_reindexed)
# Very dirty fix.. but no way to change template after object creation??
json_str = ExperimentListDumper(experiments).as_json().replace("_######.h5", "_master.h5")
ret = [os.path.join(out_dir, out_prefix+"experiments.json")]
open(ret[-1], "w").write(json_str)
if integrate_hkl is not None:
table = import_integrated(integrate_hkl)
px_to_mm(experiment, table)
if None not in (space_group, reindex_op): table["miller_index"] = reindex_op.apply(table["miller_index"])
ret.append(os.path.join(out_dir, out_prefix+"integrate_hkl.pickle"))
table.as_pickle(ret[-1])
if spot_xds is not None:
table = import_spot_xds(spot_xds)
px_to_mm(experiment, table)
if None not in (space_group, reindex_op): table["miller_index"] = reindex_op.apply(table["miller_index"])
ret.append(os.path.join(out_dir, out_prefix+"spot_xds.pickle"))
table.as_pickle(ret[-1])
return ret
def __call__(self, params, options):
# Get the XDS.INP file
xds_inp = os.path.join(self.args[0], "XDS.INP")
if params.input.xds_file is None:
xds_file = XDSFileImporter.find_best_xds_file(self.args[0])
else:
xds_file = os.path.join(self.args[0], params.input.xds_file)
# Check a file is given
if xds_file is None:
raise RuntimeError("No XDS file found")
# Load the experiment list
unhandled = []
experiments = ExperimentListFactory.from_xds(xds_inp, xds_file)
# Print out any unhandled files
if len(unhandled) > 0:
print("-" * 80)
print("The following command line arguments were not handled:")
for filename in unhandled:
print(f" {filename}")
# Print some general info
print("-" * 80)
print(f"Read {len(experiments)} experiments from {xds_file}")
# Attempt to create scan-varying crystal model if requested
if params.read_varying_crystal:
integrate_lp = os.path.join(self.args[0], "INTEGRATE.LP")
if os.path.isfile(integrate_lp):
self.extract_varying_crystal(integrate_lp, experiments)
else:
print("No INTEGRATE.LP to extract varying crystal model. Skipping")
# Loop through the data blocks
for i, exp in enumerate(experiments):
# Print some experiment info
print("-" * 80)
print("Experiment %d" % i)
print(f" format: {exp.imageset.get_format_class()}")
print(f" type: {type(exp.imageset)}")
print(f" num images: {len(exp.imageset)}")
# Print some model info
if options.verbose > 1:
print("")
if exp.beam:
print(exp.beam)
else:
print("no beam!")
if exp.detector:
print(exp.detector)
else:
print("no detector!")
if exp.goniometer:
print(exp.goniometer)
else:
print("no goniometer!")
if exp.scan:
print(exp.scan)
else:
print("no scan!")
if exp.crystal:
print(exp.crystal)
else:
print("no crystal!")
# Write the experiment list to a JSON or pickle file
if params.output.filename is None:
params.output.filename = "xds_models.expt"
print("-" * 80)
print(f"Writing experiments to {params.output.filename}")
experiments.as_file(params.output.filename)
# Optionally save as a data block
if params.output.xds_experiments:
print("-" * 80)
print(f"Writing data block to {params.output.xds_experiments}")
experiments.as_file(params.output.xds_experiments)
def __call__(self, params, options):
from dxtbx.model.experiment_list import ExperimentListFactory
from dxtbx.model.experiment_list import ExperimentListDumper
import os
# Get the XDS.INP file
xds_inp = os.path.join(self.args[0], 'XDS.INP')
if params.input.xds_file is None:
xds_file = XDSFileImporter.find_best_xds_file(self.args[0])
else:
xds_file = os.path.join(self.args[0], params.input.xds_file)
# Check a file is given
if xds_file is None:
raise RuntimeError('No XDS file found')
# Load the experiment list
unhandled = []
experiments = ExperimentListFactory.from_xds(xds_inp, xds_file)
# Print out any unhandled files
if len(unhandled) > 0:
print('-' * 80)
print('The following command line arguments were not handled:')
for filename in unhandled:
print(' %s' % filename)
# Print some general info
print('-' * 80)
print('Read %d experiments from %s' % (len(experiments), xds_file))
# Attempt to create scan-varying crystal model if requested
if params.read_varying_crystal:
integrate_lp = os.path.join(self.args[0], 'INTEGRATE.LP')
if os.path.isfile(integrate_lp):
self.extract_varying_crystal(integrate_lp, experiments)
else:
print(
"No INTEGRATE.LP to extract varying crystal model. Skipping"
)
# Loop through the data blocks
for i, exp in enumerate(experiments):
# Print some experiment info
print("-" * 80)
print("Experiment %d" % i)
print(" format: %s" % str(exp.imageset.get_format_class()))
print(" type: %s" % type(exp.imageset))
print(" num images: %d" % len(exp.imageset))
# Print some model info
if options.verbose > 1:
print("")
if exp.beam: print(exp.beam)
else: print("no beam!")
if exp.detector: print(exp.detector)
else: print("no detector!")
if exp.goniometer: print(exp.goniometer)
else: print("no goniometer!")
if exp.scan: print(exp.scan)
else: print("no scan!")
if exp.crystal: print(exp.crystal)
else: print("no crystal!")
# Write the experiment list to a JSON or pickle file
if params.output.filename is None:
params.output.filename = 'experiments.json'
print("-" * 80)
print('Writing experiments to %s' % params.output.filename)
dump = ExperimentListDumper(experiments)
dump.as_file(params.output.filename)
# Optionally save as a data block
if params.output.xds_datablock:
print("-" * 80)
print("Writing data block to %s" % params.output.xds_datablock)
dump = DataBlockDumper(experiments.to_datablocks())
dump.as_file(params.output.xds_datablock)
def __call__(self, params, options):
from dxtbx.model.experiment_list import ExperimentListFactory
from dxtbx.model.experiment_list import ExperimentListDumper
import os
# Get the XDS.INP file
xds_inp = os.path.join(self.args[0], 'XDS.INP')
if params.input.xds_file is None:
xds_file = XDSFileImporter.find_best_xds_file(self.args[0])
else:
xds_file = os.path.join(self.args[0], params.input.xds_file)
# Check a file is given
if xds_file is None:
raise RuntimeError('No XDS file found')
# Load the experiment list
unhandled = []
experiments = ExperimentListFactory.from_xds(xds_inp, xds_file)
# Print out any unhandled files
if len(unhandled) > 0:
print '-' * 80
print 'The following command line arguments were not handled:'
for filename in unhandled:
print ' %s' % filename
# Print some general info
print '-' * 80
print 'Read %d experiments from %s' % (len(experiments), xds_file)
# Attempt to create scan-varying crystal model if requested
if params.read_varying_crystal:
integrate_lp = os.path.join(self.args[0], 'INTEGRATE.LP')
if os.path.isfile(integrate_lp):
self.extract_varying_crystal(integrate_lp, experiments)
else:
print "No INTEGRATE.LP to extract varying crystal model. Skipping"
# Loop through the data blocks
for i, exp in enumerate(experiments):
# Print some experiment info
print "-" * 80
print "Experiment %d" % i
print " format: %s" % str(
exp.imageset.reader().get_format_class())
print " type: %s" % type(exp.imageset)
print " num images: %d" % len(exp.imageset)
# Print some model info
if options.verbose > 1:
print ""
if exp.beam: print exp.beam
else: print "no beam!"
if exp.detector: print exp.detector
else: print "no detector!"
if exp.goniometer: print exp.goniometer
else: print "no goniometer!"
if exp.scan: print exp.scan
else: print "no scan!"
if exp.crystal: print exp.crystal
else: print "no crystal!"
