def from_dict(cls, obj):
assert obj['__id__'] == 'XProject'
return_obj = cls()
for k, v in obj.iteritems():
if k == '_crystals':
v_ = {}
for cname, cdict in v.iteritems():
cryst = XCrystal.from_dict(cdict)
cryst._project = return_obj
v_[cname] = cryst
v = v_
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj):
assert obj["__id__"] == "XProject"
return_obj = cls()
for k, v in obj.iteritems():
if k == "_crystals":
v_ = {}
for cname, cdict in v.iteritems():
cryst = XCrystal.from_dict(cdict)
cryst._project = return_obj
v_[cname] = cryst
v = v_
setattr(return_obj, k, v)
return return_obj
def from_dict(cls, obj, base_path=None):
assert obj["__id__"] == "XProject"
return_obj = cls()
for k, v in obj.items():
if k == "_crystals":
v_ = {}
for cname, cdict in v.items():
cryst = XCrystal.from_dict(cdict)
cryst._project = return_obj
v_[cname] = cryst
v = v_
setattr(return_obj, k, v)
if hasattr(return_obj, "path"):
return_obj.path = pathlib.Path(return_obj.path).absolute()
else:
return_obj.path = pathlib.Path(base_path or os.getcwd()).absolute()
return return_obj
def exercise_serialization(dials_regression, tmp_dir):
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
os.chdir(tmp_dir)
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
from xia2.Modules.Scaler.CCP4ScalerA import CCP4ScalerA
from dxtbx.datablock import DataBlockTemplateImporter
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
from xia2.Schema.XProject import XProject
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
proj = XProject()
proj._name = "PROJ1"
cryst = XCrystal("CRYST1", proj)
proj.add_crystal(cryst)
wav = XWavelength("WAVE1", cryst, wavelength=0.98)
samp = XSample("X1", cryst)
cryst.add_wavelength(wav)
cryst.set_ha_info({'atom': 'S'})
directory, image = os.path.split(imageset.get_path(1))
wav.add_sweep(name='SWEEP1', sample=samp, directory=directory, image=image)
import json
from dxtbx.serialize.load import _decode_dict
sweep = wav.get_sweeps()[0]
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
indexer.add_indexer_imageset(imageset)
indexer.set_indexer_sweep(sweep)
sweep._indexer = indexer
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
sweep._refiner = refiner
integrater = DialsIntegrater()
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
#integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.set_integrater_epoch(sweep.get_epoch(1))
integrater.set_integrater_sweep_name(sweep.get_name())
integrater.set_integrater_project_info(cryst.get_name(), wav.get_name(),
sweep.get_name())
sweep._integrater = integrater
scaler = CCP4ScalerA()
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info(cryst.get_name(), wav.get_name())
scaler._scalr_xcrystal = cryst
cryst._scaler = scaler
s_dict = sweep.to_dict()
s_str = json.dumps(s_dict, ensure_ascii=True)
s_dict = json.loads(s_str, object_hook=_decode_dict)
xsweep = XSweep.from_dict(s_dict)
w_dict = wav.to_dict()
w_str = json.dumps(w_dict, ensure_ascii=True)
w_dict = json.loads(w_str, object_hook=_decode_dict)
xwav = XWavelength.from_dict(w_dict)
assert xwav.get_sweeps()[0].get_wavelength() is xwav
c_dict = cryst.to_dict()
c_str = json.dumps(c_dict, ensure_ascii=True)
c_dict = json.loads(c_str, object_hook=_decode_dict)
xcryst = XCrystal.from_dict(c_dict)
assert xcryst.get_xwavelength(
xcryst.get_wavelength_names()[0]).get_crystal() is xcryst
p_dict = proj.to_dict()
p_str = json.dumps(p_dict, ensure_ascii=True)
p_dict = json.loads(p_str, object_hook=_decode_dict)
xproj = XProject.from_dict(p_dict)
assert xproj.get_crystals().values()[0].get_project() is xproj
json_str = proj.as_json()
xproj = XProject.from_json(string=json_str)
assert xproj.get_crystals().values()[0].get_project() is xproj
print(xproj.get_output())
print("\n".join(xproj.summarise()))
json_str = xproj.as_json()
xproj = XProject.from_json(string=json_str)
assert xproj.get_crystals().values()[0].get_project() is xproj
xcryst = xproj.get_crystals().values()[0]
intgr = xcryst._get_integraters()[0]
assert intgr.get_integrater_finish_done()
assert xcryst._get_scaler()._sweep_handler.get_sweep_information(
intgr.get_integrater_epoch()).get_integrater() is intgr
print(xproj.get_output())
print("\n".join(xproj.summarise()))
def exercise_serialization(dials_data, tmp_dir):
base_path = pathlib.Path(tmp_dir)
template = dials_data("insulin").join("insulin_1_###.img").strpath
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
from xia2.Modules.Scaler.CCP4ScalerA import CCP4ScalerA
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
from xia2.Schema.XProject import XProject
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
proj = XProject(base_path=base_path)
proj._name = "PROJ1"
cryst = XCrystal("CRYST1", proj)
wav = XWavelength("WAVE1", cryst, wavelength=0.98)
samp = XSample("X1", cryst)
cryst.add_wavelength(wav)
cryst.set_ha_info({"atom": "S"})
cryst.add_sample(samp)
directory, image = os.path.split(imageset.get_path(1))
sweep = wav.add_sweep(name="SWEEP1", sample=samp, directory=directory, image=image)
samp.add_sweep(sweep)
from dxtbx.serialize.load import _decode_dict
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
indexer.add_indexer_imageset(imageset)
indexer.set_indexer_sweep(sweep)
sweep._indexer = indexer
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
refiner.add_refiner_sweep(sweep)
sweep._refiner = refiner
integrater = DialsIntegrater()
integrater.set_output_format("hkl")
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
# integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.set_integrater_epoch(sweep.get_epoch(1))
integrater.set_integrater_sweep_name(sweep.get_name())
integrater.set_integrater_project_info(
cryst.get_name(), wav.get_name(), sweep.get_name()
)
sweep._integrater = integrater
scaler = CCP4ScalerA(base_path=base_path)
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info(cryst.get_name(), wav.get_name())
scaler._scalr_xcrystal = cryst
cryst._scaler = scaler
proj.add_crystal(cryst)
s_dict = sweep.to_dict()
s_str = json.dumps(s_dict, ensure_ascii=True)
s_dict = json.loads(s_str, object_hook=_decode_dict)
xsweep = XSweep.from_dict(s_dict)
assert xsweep
w_dict = wav.to_dict()
w_str = json.dumps(w_dict, ensure_ascii=True)
w_dict = json.loads(w_str, object_hook=_decode_dict)
xwav = XWavelength.from_dict(w_dict)
assert xwav.get_sweeps()[0].get_wavelength() is xwav
c_dict = cryst.to_dict()
c_str = json.dumps(c_dict, ensure_ascii=True)
c_dict = json.loads(c_str, object_hook=_decode_dict)
xcryst = XCrystal.from_dict(c_dict)
assert (
xcryst.get_xwavelength(xcryst.get_wavelength_names()[0]).get_crystal() is xcryst
)
p_dict = proj.to_dict()
p_str = json.dumps(p_dict, ensure_ascii=True)
p_dict = json.loads(p_str, object_hook=_decode_dict)
xproj = XProject.from_dict(p_dict)
assert xproj.path == base_path
assert list(xproj.get_crystals().values())[0].get_project() is xproj
assert list(xproj.get_crystals().values())[0]._scaler._base_path == base_path
json_str = proj.as_json()
xproj = XProject.from_json(string=json_str)
assert xproj.path == base_path
assert list(xproj.get_crystals().values())[0].get_project() is xproj
print(xproj.get_output())
print("\n".join(xproj.summarise()))
json_str = xproj.as_json()
xproj = XProject.from_json(string=json_str)
assert xproj.path == base_path
# Test that we can serialize to json and back again
xproj = XProject.from_json(string=xproj.as_json())
assert xproj.path == base_path
xcryst = list(xproj.get_crystals().values())[0]
assert xcryst.get_project() is xproj
intgr = xcryst._get_integraters()[0]
assert intgr.get_integrater_finish_done()
assert (
xcryst._get_scaler()
._sweep_handler.get_sweep_information(intgr.get_integrater_epoch())
.get_integrater()
is intgr
)
print(xproj.get_output())
print("\n".join(xproj.summarise()))
def exercise_serialization():
if not have_dials_regression:
print "Skipping exercise_serialization(): dials_regression not configured"
return
from xia2.Handlers.CommandLine import CommandLine
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
cwd = os.path.abspath(os.curdir)
tmp_dir = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir)
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
from xia2.Modules.Scaler.CCP4ScalerA import CCP4ScalerA
from dxtbx.datablock import DataBlockTemplateImporter
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
from xia2.Schema.XProject import XProject
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
proj = XProject()
proj._name = "PROJ1"
cryst = XCrystal("CRYST1", proj)
proj.add_crystal(cryst)
wav = XWavelength("WAVE1", cryst, wavelength=0.98)
samp = XSample("X1", cryst)
cryst.add_wavelength(wav)
cryst.set_ha_info({'atom': 'S'})
directory, image = os.path.split(imageset.get_path(1))
wav.add_sweep(name='SWEEP1', sample=samp, directory=directory, image=image)
import json
from dxtbx.serialize.load import _decode_dict
sweep = wav.get_sweeps()[0]
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
indexer.add_indexer_imageset(imageset)
indexer.set_indexer_sweep(sweep)
sweep._indexer = indexer
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
sweep._refiner = refiner
integrater = DialsIntegrater()
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
#integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.set_integrater_epoch(sweep.get_epoch(1))
integrater.set_integrater_sweep_name(sweep.get_name())
integrater.set_integrater_project_info(
cryst.get_name(), wav.get_name(), sweep.get_name())
sweep._integrater = integrater
scaler = CCP4ScalerA()
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info(cryst.get_name(), wav.get_name())
scaler._scalr_xcrystal = cryst
cryst._scaler = scaler
s_dict = sweep.to_dict()
s_str = json.dumps(s_dict, ensure_ascii=True)
s_dict = json.loads(s_str, object_hook=_decode_dict)
xsweep = XSweep.from_dict(s_dict)
w_dict = wav.to_dict()
w_str = json.dumps(w_dict, ensure_ascii=True)
w_dict = json.loads(w_str, object_hook=_decode_dict)
xwav = XWavelength.from_dict(w_dict)
assert xwav.get_sweeps()[0].get_wavelength() is xwav
c_dict = cryst.to_dict()
c_str = json.dumps(c_dict, ensure_ascii=True)
c_dict = json.loads(c_str, object_hook=_decode_dict)
xcryst = XCrystal.from_dict(c_dict)
assert xcryst.get_xwavelength(xcryst.get_wavelength_names()[0]).get_crystal() is xcryst
p_dict = proj.to_dict()
p_str = json.dumps(p_dict, ensure_ascii=True)
p_dict = json.loads(p_str, object_hook=_decode_dict)
xproj = XProject.from_dict(p_dict)
assert xproj.get_crystals().values()[0].get_project() is xproj
json_str = proj.as_json()
xproj = XProject.from_json(string=json_str)
assert xproj.get_crystals().values()[0].get_project() is xproj
print xproj.get_output()
print "\n".join(xproj.summarise())
json_str = xproj.as_json()
xproj = XProject.from_json(string=json_str)
assert xproj.get_crystals().values()[0].get_project() is xproj
xcryst = xproj.get_crystals().values()[0]
intgr = xcryst._get_integraters()[0]
assert intgr.get_integrater_finish_done()
assert xcryst._get_scaler()._sweep_handler.get_sweep_information(
intgr.get_integrater_epoch()).get_integrater() is intgr
print xproj.get_output()
print "\n".join(xproj.summarise())
print