def from_dict(cls, obj):
assert obj['__id__'] == 'XSweep'
return_obj = cls(name=None, sample=None, wavelength=None)
for k, v in obj.iteritems():
if k in ('_indexer', '_refiner', '_integrater') and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(import_path=".".join(
(v['__module__'], v['__name__'])),
error_prefix='',
target_must_be='',
where_str='').object
v = cls.from_dict(v)
if k == '_indexer':
v.add_indexer_sweep(return_obj)
elif k == '_refiner':
v.add_refiner_sweep(return_obj)
elif k == '_integrater':
v.set_integrater_sweep(return_obj, reset=False)
if isinstance(v, dict):
#if v.get('__id__') == 'ExperimentList':
#from dxtbx.model.experiment_list import ExperimentListFactory
#v = ExperimentListFactory.from_dict(v)
if v.get('__id__') == 'imageset':
from dxtbx.serialize.imageset import imageset_from_dict
v = imageset_from_dict(v, check_format=False)
setattr(return_obj, k, v)
if return_obj._indexer is not None and return_obj._integrater is not None:
return_obj._integrater._intgr_indexer = return_obj._indexer
if return_obj._integrater is not None and return_obj._refiner is not None:
return_obj._integrater._intgr_refiner = return_obj._refiner
if return_obj._indexer is not None and return_obj._refiner is not None:
return_obj._refiner._refinr_indexers[return_obj.get_epoch(1)] \
= return_obj._indexer
return return_obj
def get_module_tests (module_name, valgrind=False) :
dist_path = libtbx.env.dist_path(module_name)
if (dist_path is None) :
raise Sorry("'%s' is not a valid CCTBX module." % module_name)
elif (not os.path.isfile(os.path.join(dist_path, "run_tests.py"))) :
raise Sorry("%s/run_tests.py does not exist." % module_name)
tst_list = import_python_object(
import_path="%s.run_tests.tst_list" % module_name,
error_prefix="",
target_must_be="",
where_str="").object
assert (isinstance(tst_list, tuple) or isinstance(tst_list, list))
build_path = libtbx.env.under_build(module_name)
assert (build_path is not None) and (dist_path is not None)
commands = []
co = group_args(
verbose=False,
quick=True,
valgrind=valgrind)
for cmd in test_utils.iter_tests_cmd(
co=co,
build_dir=build_path,
dist_dir=dist_path,
tst_list=tst_list) :
commands.append(cmd)
return commands
def from_dict(cls, obj):
import json
assert obj['__id__'] == 'Scaler'
return_obj = cls()
for k, v in obj.iteritems():
if k == '_scalr_integraters':
for k_, v_ in v.iteritems():
from libtbx.utils import import_python_object
integrater_cls = import_python_object(import_path=".".join(
(v_['__module__'], v_['__name__'])),
error_prefix='',
target_must_be='',
where_str='').object
v[k_] = integrater_cls.from_dict(v_)
elif k == '_scalr_statistics' and v is not None:
d = {}
for k_, v_ in v.iteritems():
k_ = tuple(str(s) for s in json.loads(k_))
d[k_] = v_
v = d
elif k in ('_scalr_resolution_limits'):
d = {}
for k_, v_ in v.iteritems():
k_ = tuple(str(s) for s in json.loads(k_))
d[k_] = v_
v = d
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
assert obj['__id__'] == 'XSweep'
return_obj = cls(name=None, sample=None, wavelength=None)
for k, v in obj.iteritems():
if k in ('_indexer', '_refiner', '_integrater') and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(
import_path=".".join((v['__module__'], v['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v = cls.from_dict(v)
if k == '_indexer':
v.add_indexer_sweep(return_obj)
elif k == '_refiner':
v.add_refiner_sweep(return_obj)
elif k == '_integrater':
v.set_integrater_sweep(return_obj, reset=False)
if isinstance(v, dict):
#if v.get('__id__') == 'ExperimentList':
#from dxtbx.model.experiment.experiment_list import ExperimentListFactory
#v = ExperimentListFactory.from_dict(v)
if v.get('__id__') == 'imageset':
from dxtbx.serialize.imageset import imageset_from_dict
v = imageset_from_dict(v, check_format=False)
setattr(return_obj, k, v)
if return_obj._indexer is not None and return_obj._integrater is not None:
return_obj._integrater._intgr_indexer = return_obj._indexer
if return_obj._integrater is not None and return_obj._refiner is not None:
return_obj._integrater._intgr_refiner = return_obj._refiner
if return_obj._indexer is not None and return_obj._refiner is not None:
return_obj._refiner._refinr_indexers[return_obj.get_epoch(1)] \
= return_obj._indexer
return return_obj
def from_dict(cls, obj):
assert obj["__id__"] == "Integrater"
return_obj = cls()
for k, v in obj.iteritems():
if k in ("_intgr_indexer", "_intgr_refiner") and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(
import_path=".".join((v["__module__"], v["__name__"])),
error_prefix="",
target_must_be="",
where_str="",
).object
v = cls.from_dict(v)
if isinstance(v, dict):
if v.get("__id__") == "ExperimentList":
from dxtbx.model.experiment_list import ExperimentListFactory
v = ExperimentListFactory.from_dict(v)
elif v.get("__id__") == "imageset":
from dxtbx.serialize.imageset import imageset_from_dict
v = imageset_from_dict(v, check_format=False)
setattr(return_obj, k, v)
return return_obj
def get_module_tests (module_name, valgrind=False) :
dist_path = libtbx.env.dist_path(module_name)
if (dist_path is None) :
raise Sorry("'%s' is not a valid CCTBX module." % module_name)
# XXX don't check for file name, because import conventions differ among
# derived modules - dist_path can be either the sys.path entry or the actual
# module contents. If the file is missing the import below will fail, which
# is okay for testing purposes.
tst_list = import_python_object(
import_path="%s.run_tests.tst_list" % module_name,
error_prefix="",
target_must_be="",
where_str="").object
assert (isinstance(tst_list, tuple) or isinstance(tst_list, list))
build_path = libtbx.env.under_build(module_name)
assert (build_path is not None) and (dist_path is not None)
commands = []
co = group_args(
verbose=False,
quick=True,
valgrind=valgrind)
for cmd in test_utils.iter_tests_cmd(
co=co,
build_dir=build_path,
dist_dir=dist_path,
tst_list=tst_list) :
commands.append(cmd)
return commands
def from_dict(cls, obj):
import json
assert obj['__id__'] == 'Scaler'
return_obj = cls()
for k, v in obj.iteritems():
if k == '_scalr_integraters':
for k_, v_ in v.iteritems():
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join((v_['__module__'], v_['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v[k_] = integrater_cls.from_dict(v_)
elif k == '_scalr_statistics' and v is not None:
d = {}
for k_, v_ in v.iteritems():
k_ = tuple(str(s) for s in json.loads(k_))
d[k_] = v_
v = d
elif k == '_scalr_resolution_limits':
d = {}
for k_, v_ in v.iteritems():
k_ = tuple(str(s) for s in json.loads(k_))
d[k_] = v_
v = d
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSample import XSample
assert obj['__id__'] == 'XCrystal'
return_obj = cls(name=None, project=None)
for k, v in obj.iteritems():
if k == '_scaler' and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(import_path=".".join(
(v['__module__'], v['__name__'])),
error_prefix='',
target_must_be='',
where_str='').object
v = cls.from_dict(v)
v._scalr_xcrystal = return_obj
elif k == '_wavelengths':
v_ = {}
for wname, wdict in v.iteritems():
wav = XWavelength.from_dict(wdict)
wav._crystal = return_obj
v_[wname] = wav
v = v_
elif k == '_samples':
v_ = {}
for sname, sdict in v.iteritems():
sample = XSample.from_dict(sdict)
sample._crystal = return_obj
v_[sname] = sample
v = v_
elif k == '_aa_sequence' and v is not None:
v = _aa_sequence.from_dict(v)
elif k == '_ha_info' and v is not None:
for k_, v_ in v.iteritems():
v[k_] = _ha_info.from_dict(v_)
setattr(return_obj, k, v)
sweep_dict = {}
for sample in return_obj._samples.values():
for i, sname in enumerate(sample._sweeps):
found_sweep = False
for wav in return_obj._wavelengths.values():
if found_sweep: break
for sweep in wav._sweeps:
if sweep.get_name() == sname:
sample._sweeps[i] = sweep
sweep._sample = sample
found_sweep = True
break
for s in sample._sweeps:
assert not isinstance(s, basestring)
if return_obj._scaler is not None:
for intgr in return_obj._get_integraters():
return_obj._scaler._scalr_integraters[intgr.get_integrater_epoch()] \
= intgr
if (hasattr(return_obj._scaler, '_sweep_handler')
and return_obj._scaler._sweep_handler is not None):
if intgr.get_integrater_epoch() in \
return_obj._scaler._sweep_handler._sweep_information:
return_obj._scaler._sweep_handler._sweep_information[
intgr.get_integrater_epoch()]._integrater = intgr
return return_obj
def from_dict(cls, obj):
import json
assert obj['__id__'] == 'Refiner'
return_obj = cls()
for k, v in obj.iteritems():
if k == '_refinr_indexers':
v_new = {}
for k_, v_ in v.iteritems():
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join((v_['__module__'], v_['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v_new[float(k_)] = integrater_cls.from_dict(v_)
v = v_new
elif k == '_refinr_payload':
v_new = {}
for k_, v_ in v.iteritems():
try:
v_new[float(k_)] = v_
except ValueError, e:
v_new[k_] = v_
v = v_new
if isinstance(v, dict):
if v.get('__id__', None) == 'ExperimentList':
from dxtbx.model.experiment.experiment_list import ExperimentListFactory
v = ExperimentListFactory.from_dict(v, check_format=False)
setattr(return_obj, k, v)
def from_dict(cls, obj):
import json
assert obj['__id__'] == 'Refiner'
return_obj = cls()
for k, v in obj.iteritems():
if k == '_refinr_indexers':
v_new = {}
for k_, v_ in v.iteritems():
from libtbx.utils import import_python_object
integrater_cls = import_python_object(import_path=".".join(
(v_['__module__'], v_['__name__'])),
error_prefix='',
target_must_be='',
where_str='').object
v_new[float(k_)] = integrater_cls.from_dict(v_)
v = v_new
elif k == '_refinr_payload':
v_new = {}
for k_, v_ in v.iteritems():
try:
v_new[float(k_)] = v_
except ValueError:
v_new[k_] = v_
v = v_new
if isinstance(v, dict):
if v.get('__id__') == 'ExperimentList':
from dxtbx.model.experiment_list import ExperimentListFactory
v = ExperimentListFactory.from_dict(v, check_format=False)
setattr(return_obj, k, v)
return return_obj
def get_test_list(module_name,
test_type='tst_list',
valgrind=False,
python_keyword_text=None):
dist_path = libtbx.env.dist_path(module_name)
if dist_path is None:
raise Sorry("'%s' is not a valid CCTBX module." % module_name)
# XXX don't check for file name, because import conventions differ among
# derived modules - dist_path can be either the sys.path entry or the actual
# module contents. If the file is missing the import below will fail, which
# is okay for testing purposes.
try:
tst_list = list(
import_python_object(import_path="%s.run_tests.%s" %
(module_name, test_type),
error_prefix="",
target_must_be="",
where_str="").object)
except AttributeError:
tst_list = list()
build_path = libtbx.env.under_build(module_name)
assert (build_path is not None) and (dist_path is not None)
commands = []
co = group_args(verbose=False,
quick=True,
valgrind=valgrind,
python_keyword_text=python_keyword_text)
for cmd in test_utils.iter_tests_cmd(co=co,
build_dir=build_path,
dist_dir=dist_path,
tst_list=tst_list):
commands.append(cmd)
return commands
def from_dict(cls, obj):
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSample import XSample
assert obj['__id__'] == 'XCrystal'
return_obj = cls(name=None, project=None)
for k, v in obj.iteritems():
if k == '_scaler' and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(
import_path=".".join((v['__module__'], v['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v = cls.from_dict(v)
v._scalr_xcrystal = return_obj
elif k == '_wavelengths':
v_ = {}
for wname, wdict in v.iteritems():
wav = XWavelength.from_dict(wdict)
wav._crystal = return_obj
v_[wname] = wav
v = v_
elif k == '_samples':
v_ = {}
for sname, sdict in v.iteritems():
sample = XSample.from_dict(sdict)
sample._crystal = return_obj
v_[sname] = sample
v = v_
elif k == '_aa_sequence' and v is not None:
v = _aa_sequence.from_dict(v)
elif k == '_ha_info' and v is not None:
for k_, v_ in v.iteritems():
v[k_] = _ha_info.from_dict(v_)
setattr(return_obj, k, v)
sweep_dict = {}
for sample in return_obj._samples.values():
for i, sname in enumerate(sample._sweeps):
found_sweep = False
for wav in return_obj._wavelengths.values():
if found_sweep: break
for sweep in wav._sweeps:
if sweep.get_name() == sname:
sample._sweeps[i] = sweep
sweep._sample = sample
found_sweep = True
break
for s in sample._sweeps: assert not isinstance(s, basestring)
if return_obj._scaler is not None:
for intgr in return_obj._get_integraters():
return_obj._scaler._scalr_integraters[intgr.get_integrater_epoch()] \
= intgr
if (hasattr(return_obj._scaler, '_sweep_handler') and
return_obj._scaler._sweep_handler is not None):
if intgr.get_integrater_epoch() in \
return_obj._scaler._sweep_handler._sweep_information:
return_obj._scaler._sweep_handler._sweep_information[
intgr.get_integrater_epoch()]._integrater = intgr
return return_obj
def get_module_tests(module_name, valgrind=False, slow_tests=False):
dist_path = libtbx.env.dist_path(module_name)
if dist_path is None:
raise Sorry("'%s' is not a valid CCTBX module." % module_name)
# XXX don't check for file name, because import conventions differ among
# derived modules - dist_path can be either the sys.path entry or the actual
# module contents. If the file is missing the import below will fail, which
# is okay for testing purposes.
tst_list = import_python_object(import_path="%s.run_tests.tst_list" %
module_name,
error_prefix="",
target_must_be="",
where_str="").object
assert (isinstance(tst_list, tuple) or isinstance(tst_list, list))
if slow_tests:
try:
tst_list_slow = import_python_object(
import_path="%s.run_tests.tst_list_slow" % module_name,
error_prefix="",
target_must_be="",
where_str="").object
except AttributeError:
pass
else:
assert (isinstance(tst_list_slow, tuple)
or isinstance(tst_list_slow, list))
if isinstance(tst_list, tuple):
tst_list = list(tst_list)
tst.list.extend(tst_list_slow)
tst_list = tuple(tst_list)
else:
tst_list.extend(tst_list_slow)
build_path = libtbx.env.under_build(module_name)
assert (build_path is not None) and (dist_path is not None)
commands = []
co = group_args(verbose=False, quick=True, valgrind=valgrind)
for cmd in test_utils.iter_tests_cmd(co=co,
build_dir=build_path,
dist_dir=dist_path,
tst_list=tst_list):
commands.append(cmd)
return commands
def load_from_cache_if_possible(self, phil_path):
import libtbx.load_env
full_path = os.path.join(abs(libtbx.env.build_path), "phil_cache",
"%s.phil" % phil_path)
if (os.path.exists(full_path)):
return parse(file_name=full_path)
else:
return import_python_object(import_path=phil_path,
error_prefix="",
target_must_be="",
where_str="").object
def from_dict(cls, obj):
assert obj['__id__'] == 'SweepInformation'
return_obj = cls.__new__(cls)
for k, v in obj.iteritems():
if k == '_integrater':
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join((v['__module__'], v['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v = integrater_cls.from_dict(v)
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
assert obj['__id__'] == 'SweepInformation'
return_obj = cls.__new__(cls)
for k, v in obj.iteritems():
if k == '_integrater':
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join((v['__module__'], v['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v = integrater_cls.from_dict(v)
setattr(return_obj, k, v)
return return_obj
def load_from_cache_if_possible (phil_path) :
import libtbx.load_env
full_path = os.path.join(abs(libtbx.env.build_path), "phil_cache",
"%s.phil" % phil_path)
if (os.path.exists(full_path)) :
return parse(file_name=full_path)
else :
return import_python_object(
import_path=phil_path,
error_prefix="",
target_must_be="",
where_str="").object
def from_dict(cls, obj):
assert obj['__id__'] == 'XSample'
return_obj = cls(name=None, crystal=None)
for k, v in obj.iteritems():
if k == '_sweeps':
v = [s_dict['_name'] for s_dict in v]
elif k == '_multi_indexer' and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(
import_path=".".join((v['__module__'], v['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v = cls.from_dict(v)
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
return_obj = super(XDSScalerA, cls).from_dict(obj)
for i in return_obj._sweep_information.keys():
d = return_obj._sweep_information[i]['integrater']
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join((d['__module__'], d['__name__'])),
error_prefix='', target_must_be='', where_str='').object
return_obj._sweep_information[i]['integrater'] \
= integrater_cls.from_dict(d)
# expects epoch as number (or int?)
if isinstance(i, basestring):
return_obj._sweep_information[float(i)] = return_obj._sweep_information[i]
del return_obj._sweep_information[i]
return return_obj
def from_dict(cls, obj):
assert obj['__id__'] == 'XSample'
return_obj = cls(name=None, crystal=None)
for k, v in obj.iteritems():
if k == '_sweeps':
v = [s_dict['_name'] for s_dict in v]
elif k == '_multi_indexer' and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(import_path=".".join(
(v['__module__'], v['__name__'])),
error_prefix='',
target_must_be='',
where_str='').object
v = cls.from_dict(v)
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
assert obj["__id__"] == "SweepInformation"
return_obj = cls.__new__(cls)
for k, v in obj.items():
if k == "_integrater":
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join((v["__module__"], v["__name__"])),
error_prefix="",
target_must_be="",
where_str="",
).object
v = integrater_cls.from_dict(v)
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
assert obj["__id__"] == "XSample"
return_obj = cls(name=None, crystal=None)
for k, v in obj.items():
if k == "_sweeps":
v = [s_dict["_name"] for s_dict in v]
elif k in ["multi_indexer", "multi_refiner"] and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(
import_path=".".join((v["__module__"], v["__name__"])),
error_prefix="",
target_must_be="",
where_str="",
).object
v = cls.from_dict(v)
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
assert obj['__id__'] == 'Integrater'
return_obj = cls()
for k, v in obj.iteritems():
if k in ('_intgr_indexer', '_intgr_refiner') and v is not None:
from libtbx.utils import import_python_object
cls = import_python_object(
import_path=".".join((v['__module__'], v['__name__'])),
error_prefix='', target_must_be='', where_str='').object
v = cls.from_dict(v)
if isinstance(v, dict):
if v.get('__id__') == 'ExperimentList':
from dxtbx.model.experiment.experiment_list import ExperimentListFactory
v = ExperimentListFactory.from_dict(v)
elif v.get('__id__') == 'imageset':
from dxtbx.serialize.imageset import imageset_from_dict
v = imageset_from_dict(v, check_format=False)
setattr(return_obj, k, v)
return return_obj
def run(args):
phil_path = args[-1]
phil_inp = import_python_object(import_path=phil_path,
error_prefix="",
target_must_be="",
where_str="").object
if (isinstance(phil_inp, str)):
phil_object = phil.parse(phil_inp)
elif (hasattr(phil_inp, "__call__")):
phil_object = phil_inp()
else:
assert isinstance(phil_inp, phil.scope)
phil_object = phil_inp
cache_dir = os.path.join(libtbx.env.build_path, "phil_cache")
if (not os.path.isdir(cache_dir)):
os.mkdir(cache_dir)
full_path = os.path.join(cache_dir, phil_path)
f = open("%s.phil" % full_path, "w")
phil_object.show(out=f, attributes_level=3)
f.close()
print("Wrote master parameters to %s.phil" % full_path)
def run (args) :
phil_path = args[-1]
phil_inp = import_python_object(
import_path=phil_path,
error_prefix="",
target_must_be="",
where_str="").object
if (isinstance(phil_inp, str)) :
phil_object = phil.parse(phil_inp)
elif (hasattr(phil_inp, "__call__")) :
phil_object = phil_inp()
else :
assert isinstance(phil_inp, phil.scope)
phil_object = phil_inp
cache_dir = os.path.join(libtbx.env.build_path, "phil_cache")
if (not os.path.isdir(cache_dir)) :
os.mkdir(cache_dir)
full_path = os.path.join(cache_dir, phil_path)
f = open("%s.phil" % full_path, "w")
phil_object.show(out=f, attributes_level=3)
f.close()
print "Wrote master parameters to %s.phil" % full_path
def get_module_tests(module_name, valgrind=False):
dist_path = libtbx.env.dist_path(module_name)
if (dist_path is None):
raise Sorry("'%s' is not a valid CCTBX module." % module_name)
elif (not os.path.isfile(os.path.join(dist_path, "run_tests.py"))):
raise Sorry("%s/run_tests.py does not exist." % module_name)
tst_list = import_python_object(import_path="%s.run_tests.tst_list" %
module_name,
error_prefix="",
target_must_be="",
where_str="").object
assert (isinstance(tst_list, tuple) or isinstance(tst_list, list))
build_path = libtbx.env.under_build(module_name)
assert (build_path is not None) and (dist_path is not None)
commands = []
co = group_args(verbose=False, quick=True, valgrind=valgrind)
for cmd in test_utils.iter_tests_cmd(co=co,
build_dir=build_path,
dist_dir=dist_path,
tst_list=tst_list):
commands.append(cmd)
return commands
def from_dict(cls, obj):
assert obj["__id__"] == "Scaler"
base_path = obj.get("_base_path")
if base_path:
base_path = pathlib.Path(base_path)
else:
base_path = None
return_obj = cls(base_path=base_path)
for k, v in obj.items():
if k == "_scalr_integraters":
for k_, v_ in v.items():
from libtbx.utils import import_python_object
integrater_cls = import_python_object(
import_path=".".join(
(v_["__module__"], v_["__name__"])),
error_prefix="",
target_must_be="",
where_str="",
).object
v[k_] = integrater_cls.from_dict(v_)
elif k == "_scalr_statistics" and v is not None:
d = {}
for k_, v_ in v.items():
k_ = tuple(str(s) for s in json.loads(k_))
d[k_] = v_
v = d
elif k == "_scalr_resolution_limits":
d = {}
for k_, v_ in v.items():
k_ = tuple(str(s) for s in json.loads(k_))
d[k_] = v_
v = d
elif k == "_base_path":
continue
setattr(return_obj, k, v)
return return_obj