def test_dials_integrater_high_pressure_set(monkeypatch):
"""Check that the appropriate PHIL parameter triggers high-pressure mode."""
# Without the relevant PHIL parameter set, check everything is normal.
integrater = DialsIntegrater()
assert not integrater.high_pressure
# Check we can trigger high-pressure mode with the relevant PHIL parameter.
monkeypatch.setattr(PhilIndex.params.dials.high_pressure, "correction",
True)
integrater = DialsIntegrater()
assert integrater.high_pressure
def Integrater():
"""Return an Integrater implementation."""
# FIXME this should take an indexer as an argument...
integrater = None
preselection = get_preferences().get("integrater")
if not integrater and (not preselection or preselection == "dials"):
try:
integrater = DialsIntegrater()
logger.debug("Using Dials Integrater")
if PhilIndex.params.xia2.settings.scaler == "dials":
integrater.set_output_format("pickle")
except NotAvailableError:
if preselection == "dials":
raise RuntimeError(
"preselected integrater dials not available: "
+ "dials not installed?"
)
if not integrater and (not preselection or preselection == "xdsr"):
try:
integrater = XDSIntegrater()
logger.debug("Using XDS Integrater in new resolution mode")
except NotAvailableError:
if preselection == "xdsr":
raise RuntimeError(
"preselected integrater xdsr not available: " + "xds not installed?"
)
if not integrater:
raise RuntimeError("no integrater implementations found")
# check to see if resolution limits were passed in through the
# command line...
dmin = PhilIndex.params.xia2.settings.resolution.d_min
dmax = PhilIndex.params.xia2.settings.resolution.d_max
if dmin:
logger.debug("Adding user-assigned resolution limits:")
if dmax:
logger.debug(f"dmin: {dmin:.3f} dmax: {dmax:.2f}")
integrater.set_integrater_resolution(dmin, dmax, user=True)
else:
logger.debug("dmin: %.3f" % dmin)
integrater.set_integrater_high_resolution(dmin, user=True)
return integrater
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_dials_integrater(nproc=None):
if not have_dials_regression:
print "Skipping exercise_dials_integrater(): dials_regression not configured"
return
if nproc is not None:
from xia2.Handlers.Flags import Flags
Flags.set_parallel(nproc)
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.Integrater.DialsIntegrater import DialsIntegrater
from dxtbx.datablock import DataBlockTemplateImporter
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
#refiner.refine()
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.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
from iotbx.reflection_file_reader import any_reflection_file
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 48117) < 100, mtz_object.n_reflections()
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'IPR', 'SIGIPR', 'I', 'SIGI',
'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'LP', 'DQE']
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.14, 78.14, 78.14, 90, 90, 90), eps=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
#print json_str
integrater2 = DialsIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 48117) < 100, mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 48117) < 100, mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 48117) < 100, mtz_object.n_reflections()
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
def Integrater():
'''Return an Integrater implementation.'''
# FIXME this should take an indexer as an argument...
integrater = None
preselection = get_preferences().get('integrater')
if not integrater and \
(not preselection or preselection == 'dials'):
try:
integrater = DialsIntegrater()
Debug.write('Using Dials Integrater')
except NotAvailableError:
if preselection == 'dials':
raise RuntimeError( \
'preselected integrater dials not available: ' + \
'dials not installed?')
if not integrater and (not preselection or preselection == 'mosflmr'):
try:
integrater = MosflmIntegrater()
Debug.write('Using MosflmR Integrater')
if not get_preferences().get('scaler'):
add_preference('scaler', 'ccp4a')
except NotAvailableError:
if preselection == 'mosflmr':
raise RuntimeError('preselected integrater mosflmr not available')
if not integrater and \
(not preselection or preselection == 'xdsr'):
try:
integrater = XDSIntegrater()
Debug.write('Using XDS Integrater in new resolution mode')
except NotAvailableError:
if preselection == 'xdsr':
raise RuntimeError( \
'preselected integrater xdsr not available: ' + \
'xds not installed?')
if not integrater:
raise RuntimeError('no integrater implementations found')
# check to see if resolution limits were passed in through the
# command line...
dmin = PhilIndex.params.xia2.settings.resolution.d_min
dmax = PhilIndex.params.xia2.settings.resolution.d_max
if dmin:
Debug.write('Adding user-assigned resolution limits:')
if dmax:
Debug.write('dmin: %.3f dmax: %.2f' % (dmin, dmax))
integrater.set_integrater_resolution(dmin, dmax, user=True)
else:
Debug.write('dmin: %.3f' % dmin)
integrater.set_integrater_high_resolution(dmin, user=True)
return integrater
def test_ccp4_scalerA(dials_regression, tmpdir, nproc):
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = os.path.join(dials_regression, "xia2_demo_data", "insulin_1_###.img")
tmpdir.chdir()
tmpdir = tmpdir.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
indexer = DialsIndexer()
indexer.set_working_directory(tmpdir)
from dxtbx.datablock import DataBlockTemplateImporter
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
with mock.patch.object(sys, 'argv', []):
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
refiner = DialsRefiner()
refiner.set_working_directory(tmpdir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
integrater = DialsIntegrater()
integrater.set_working_directory(tmpdir)
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_sweep_name('SWEEP1')
integrater.set_integrater_project_info('CRYST1', 'WAVE1', 'SWEEP1')
scaler = CCP4ScalerA()
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info('CRYST1', 'WAVE1')
check_scaler_files_exist(scaler)
# test serialization of scaler
json_str = scaler.as_json()
#print json_str
scaler2 = CCP4ScalerA.from_json(string=json_str)
scaler2.set_scaler_xcrystal(cryst)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_finish_done(False)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_done(False)
check_scaler_files_exist(scaler2)
scaler2._scalr_integraters = {} # XXX
scaler2.add_scaler_integrater(integrater)
scaler2.set_scaler_prepare_done(False)
check_scaler_files_exist(scaler2)
def exercise_dials_integrater(dials_data, tmp_dir, nproc=None):
if nproc:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
# refiner.refine()
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.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
from iotbx.reflection_file_reader import any_reflection_file
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
expected_reflections = 47623
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
assert mtz_object.column_labels() == [
"H",
"K",
"L",
"M_ISYM",
"BATCH",
"IPR",
"SIGIPR",
"I",
"SIGI",
"BG",
"SIGBG",
"FRACTIONCALC",
"XDET",
"YDET",
"ROT",
"LP",
"QE",
]
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.14, 78.14, 78.14, 90, 90, 90),
eps=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
# print(json_str)
integrater2 = DialsIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
def test_ccp4_scalerA(regression_test, ccp4, dials_data, run_in_tmpdir, nproc):
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
tmpdir = run_in_tmpdir.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
indexer = DialsIndexer()
indexer.set_working_directory(tmpdir)
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
with mock.patch.object(sys, "argv", []):
sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
refiner = DialsRefiner()
refiner.set_working_directory(tmpdir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
integrater = DialsIntegrater()
integrater.set_working_directory(tmpdir)
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_sweep_name("SWEEP1")
integrater.set_integrater_project_info("CRYST1", "WAVE1", "SWEEP1")
scaler = CCP4ScalerA()
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info("CRYST1", "WAVE1")
check_scaler_files_exist(scaler)
# test serialization of scaler
json_str = scaler.as_json()
# print json_str
scaler2 = CCP4ScalerA.from_json(string=json_str)
scaler2.set_scaler_xcrystal(cryst)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_finish_done(False)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_done(False)
check_scaler_files_exist(scaler2)
scaler2._scalr_integraters = {} # XXX
scaler2.add_scaler_integrater(integrater)
scaler2.set_scaler_prepare_done(False)
check_scaler_files_exist(scaler2)
def exercise_dials_integrater(xia2_regression_build, tmp_dir, nproc=None):
if nproc:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(xia2_regression_build, "test_data",
"insulin")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
from dxtbx.datablock import DataBlockTemplateImporter
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
#refiner.refine()
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.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
from iotbx.reflection_file_reader import any_reflection_file
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
expected_reflections = 48456
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'IPR', 'SIGIPR', 'I', 'SIGI', 'BG',
'SIGBG', 'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'LP', 'QE'
]
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.14, 78.14, 78.14, 90, 90, 90),
eps=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
#print(json_str)
integrater2 = DialsIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
def exercise_ccp4_scaler(nproc=None):
if not have_dials_regression:
print "Skipping exercise_ccp4_scaler(): dials_regression not configured"
return
if nproc is not None:
from xia2.Handlers.Flags import Flags
Flags.set_parallel(nproc)
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
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
from dxtbx.datablock import DataBlockTemplateImporter
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
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_sweep_name('SWEEP1')
integrater.set_integrater_project_info('CRYST1', 'WAVE1', 'SWEEP1')
scaler = CCP4ScalerA()
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info('CRYST1', 'WAVE1')
check_scaler_files_exist(scaler)
# test serialization of scaler
json_str = scaler.as_json()
#print json_str
scaler2 = CCP4ScalerA.from_json(string=json_str)
scaler2.set_scaler_xcrystal(cryst)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_finish_done(False)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_done(False)
check_scaler_files_exist(scaler2)
scaler2._scalr_integraters = {} # XXX
scaler2.add_scaler_integrater(integrater)
scaler2.set_scaler_prepare_done(False)
check_scaler_files_exist(scaler2)
def exercise_dials_integrater(dials_data, tmp_dir, nproc=None):
if nproc:
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
# refiner.refine()
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.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz", repr(integrater_intensities)
mtz_object = reader.file_content()
expected_reflections = 47623
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
assert mtz_object.column_labels() == [
"H",
"K",
"L",
"M_ISYM",
"BATCH",
"IPR",
"SIGIPR",
"I",
"SIGI",
"BG",
"SIGBG",
"FRACTIONCALC",
"XDET",
"YDET",
"ROT",
"LP",
"QE",
]
assert integrater.get_integrater_wedge() == (1, 45)
assert integrater.get_integrater_cell() == pytest.approx(
(78.14, 78.14, 78.14, 90, 90, 90), abs=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
# print(json_str)
integrater2 = DialsIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
# Test that diamond anvil cell attenuation correction does something.
# That it does the right thing is left as a matter for the DIALS tests.
integrater3 = DialsIntegrater.from_json(string=json_str)
integrater3.set_integrater_sweep(sweep, reset=False)
integrater3.set_integrater_done(False)
integrater3.high_pressure = True
# Don't get .hkl output because we're applying the attenuation correction to data
# that weren't actually collected with a diamond anvil cell and some integrated
# intensities will be rather nonsensical, which causes an error
# 'cctbx Error: Inconsistent observation/sigma pair in columns: IPR, SIGIPR',
# when some internal .hkl consistency checks are run, which is not meaningful here.
integrater3.set_output_format("pickle")
# Compare the first ten profile-fitted integrated intensities without correction.
control_reflections = flex.reflection_table.from_file(
integrater2.get_integrated_reflections())
valid = control_reflections.get_flags(
control_reflections.flags.integrated_prf)
valid = valid.iselection()[:10]
control_reflections = control_reflections.select(valid)
# Get the first ten profile-fitted integrated intensities with DAC correction.
corrected_reflections = flex.reflection_table.from_file(
integrater3.get_integrated_reflections())
valid = corrected_reflections.get_flags(
corrected_reflections.flags.integrated_prf)
valid = valid.iselection()[:10]
corrected_reflections = corrected_reflections.select(valid)
# Check that we're comparing equivalent reflections.
assert control_reflections["miller_index"] == corrected_reflections[
"miller_index"]
control_intensities = control_reflections["intensity.prf.value"]
corrected_intensities = corrected_reflections["intensity.prf.value"]
# Check that the reflection intensities are not the same.
assert pytest.approx(control_intensities) != corrected_intensities
def Integrater():
"""Return an Integrater implementation."""
# FIXME this should take an indexer as an argument...
integrater = None
preselection = get_preferences().get("integrater")
if not integrater and (not preselection or preselection == "dials"):
try:
integrater = DialsIntegrater()
Debug.write("Using Dials Integrater")
except NotAvailableError:
if preselection == "dials":
raise RuntimeError(
"preselected integrater dials not available: " +
"dials not installed?")
if not integrater and (not preselection or preselection == "mosflmr"):
try:
integrater = MosflmIntegrater()
Debug.write("Using MosflmR Integrater")
if not get_preferences().get("scaler"):
add_preference("scaler", "ccp4a")
except NotAvailableError:
if preselection == "mosflmr":
raise RuntimeError(
"preselected integrater mosflmr not available")
if not integrater and (not preselection or preselection == "xdsr"):
try:
integrater = XDSIntegrater()
Debug.write("Using XDS Integrater in new resolution mode")
except NotAvailableError:
if preselection == "xdsr":
raise RuntimeError(
"preselected integrater xdsr not available: " +
"xds not installed?")
if not integrater:
raise RuntimeError("no integrater implementations found")
# check to see if resolution limits were passed in through the
# command line...
dmin = PhilIndex.params.xia2.settings.resolution.d_min
dmax = PhilIndex.params.xia2.settings.resolution.d_max
if dmin:
Debug.write("Adding user-assigned resolution limits:")
if dmax:
Debug.write("dmin: %.3f dmax: %.2f" % (dmin, dmax))
integrater.set_integrater_resolution(dmin, dmax, user=True)
else:
Debug.write("dmin: %.3f" % dmin)
integrater.set_integrater_high_resolution(dmin, user=True)
return integrater