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 test_json(dials_data, tmpdir):
# Call dials.export
result = procrunner.run(
[
"dials.export",
"format=json",
dials_data("centroid_test_data").join("datablock.json").strpath,
dials_data("centroid_test_data").join("strong.pickle").strpath,
],
working_directory=tmpdir.strpath,
)
assert not result.returncode and not result.stderr
assert tmpdir.join("rlp.json").check(file=1)
from dxtbx.model.experiment_list import ExperimentListFactory
with tmpdir.join("rlp.json").open("rb") as f:
d = json.load(f, object_hook=_decode_dict)
assert set(d) == {"imageset_id", "experiments", "rlp", "experiment_id"}
assert d["rlp"][:3] == [0.123454, 0.57687, 0.186465], d["rlp"][:3]
assert d["imageset_id"][0] == 0
assert d["experiment_id"][0] == 0
experiments = ExperimentListFactory.from_dict(d["experiments"])
imgset = experiments.imagesets()
assert len(imgset) == 1
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 test_static_mask(dials_data):
master_h5 = (dials_data("image_examples").join(
"SACLA-MPCCD-Phase3-21528-5images.h5").strpath)
assert FormatHDF5SaclaMPCCD.understand(master_h5)
expts_from_filename = ExperimentListFactory.from_filenames([master_h5])
expts_from_dict = ExperimentListFactory.from_dict(
expts_from_filename.to_dict())
for expts in (expts_from_filename, expts_from_dict):
assert len(expts) == 5
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5SaclaMPCCD
mask = imageset.get_mask(0)
assert len(mask) == 8
assert [m.count(False) for m in mask] == [24296] * 8
def test_static_mask(dials_regression):
filename = os.path.join(
dials_regression,
"image_examples/LCLS_CXI/shot-s00-2011-12-02T21_07Z29.723_00569.pickle",
)
assert FormatPYunspecifiedStill.understand(filename)
expts_from_filename = ExperimentListFactory.from_filenames([filename])
expts_from_dict = ExperimentListFactory.from_dict(expts_from_filename.to_dict())
for expts in (expts_from_filename, expts_from_dict):
assert len(expts) == 1
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatPYunspecifiedStill
mask = imageset.get_mask(0)
assert len(mask) == 1
assert mask[0].count(False) == 867109
def from_dict(cls, obj):
assert obj['__id__'] == 'Indexer'
assert obj['__name__'] == cls.__name__
return_obj = cls()
for k, v in obj.iteritems():
if k == '_indxr_helper' and v is not None:
from xia2.Schema.Interfaces.Indexer import _IndexerHelper
v = _IndexerHelper(v)
if k == '_indxr_imagesets' and len(v):
assert v[0].get('__id__') == 'imageset'
from dxtbx.serialize.imageset import imageset_from_dict
v = [imageset_from_dict(v_, check_format=False) for v_ in v]
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 from_dict(cls, obj):
assert obj["__id__"] == "Indexer"
assert obj["__name__"] == cls.__name__
return_obj = cls()
for k, v in obj.items():
if k == "_indxr_helper" and v is not None:
v = _IndexerHelper(v)
if k == "_indxr_imagesets" and len(v):
assert v[0].get("__id__") == "imageset"
from dxtbx.serialize.imageset import imageset_from_dict
v = [imageset_from_dict(v_, check_format=False) for v_ in v]
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 test_combine_with_user_static_mask(dials_data, tmpdir):
master_h5 = (dials_data("image_examples").join(
"SACLA-MPCCD-Phase3-21528-5images.h5").strpath)
assert FormatHDF5SaclaMPCCD.understand(master_h5)
expts_from_filename = ExperimentListFactory.from_filenames([master_h5])
for i, expt in enumerate(expts_from_filename):
mask = []
for panel in expt.detector:
m = flex.bool(flex.grid(reversed(panel.get_image_size())), True)
mask_untrusted_resolution_range(m, expt.beam, panel, 0, 2.23)
mask.append(m)
mask = tuple(mask)
# exact number of masked pixels varies with wavelength between experiments
assert [_.count(False) for _ in mask
] == pytest.approx([50643, 0, 0, 48003, 48356, 0, 0, 52191],
abs=1e3)
mask_file = tmpdir.join("pixel_%i.mask" % i)
with mask_file.open("wb") as f:
pickle.dump(mask, f)
expt.imageset.external_lookup.mask.filename = mask_file.strpath
expt.imageset.external_lookup.mask.data = ImageBool(mask)
expts_from_dict = ExperimentListFactory.from_dict(
expts_from_filename.to_dict())
imageset = expts_from_dict[0].imageset
mask = imageset.get_mask(0)
assert len(mask) == 8
assert [_.count(False) for _ in mask] == [
65332,
24296,
24296,
63335,
63660,
24296,
24296,
66691,
]
imageset.reader().nullify_format_instance()
def test_json(dials_data, tmp_path):
# Call dials.export
result = procrunner.run(
[
"dials.export",
"format=json",
dials_data("centroid_test_data", pathlib=True)
/ "imported_experiments.json",
dials_data("centroid_test_data", pathlib=True) / "strong.pickle",
],
working_directory=tmp_path,
)
assert not result.returncode and not result.stderr
assert (tmp_path / "rlp.json").is_file()
d = json.load((tmp_path / "rlp.json").open("rb"))
assert set(d) == {"imageset_id", "experiments", "rlp", "experiment_id"}
assert d["rlp"][:3] == [0.123413, 0.576679, 0.186326], d["rlp"][:3]
assert d["imageset_id"][0] == 0
assert d["experiment_id"][0] == 0
experiments = ExperimentListFactory.from_dict(d["experiments"])
imgset = experiments.imagesets()
assert len(imgset) == 1
def test_partial_missing_model_serialization():
goniometer = Goniometer()
elist = ExperimentList([Experiment(), Experiment(goniometer=goniometer)])
elist_ = ExperimentListFactory.from_dict(elist.to_dict())
check(elist, elist_)
