def exercise_mosflm_integrater(dials_regression, tmp_dir, nproc):
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
# otherwise if this test is running multiple times simultaneously two mosflm
# processes try to write to the same genfile
os.environ['CCP4_SCR'] = tmp_dir
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from dxtbx.datablock import DataBlockTemplateImporter
indexer = MosflmIndexer()
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, indexer.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.MosflmRefiner import MosflmRefiner
refiner = MosflmRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
nref_error = 500
integrater = MosflmIntegrater()
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() - 81116) < nref_error, \
mtz_object.n_reflections()
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'I', 'SIGI', 'IPR', 'SIGIPR',
'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART', 'FLAG',
'BGPKRATIOS']
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.014, 78.014, 78.014, 90.0, 90.0, 90.0), eps=1e-2)
# test serialization of integrater
json_str = integrater.as_json()
#print json_str
integrater2 = MosflmIntegrater.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() - 81116) < nref_error, \
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() - 81116) < nref_error, \
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() - 81116) < nref_error, \
mtz_object.n_reflections()
def exercise_mosflm_integrater(nproc=None):
if not have_dials_regression:
print "Skipping exercise_mosflm_integrater(): dials_regression not configured"
return
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = 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)
# otherwise if this test is running multiple times simultaneously two mosflm
# processes try to write to the same genfile
os.environ['CCP4_SCR'] = tmp_dir
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from dxtbx.datablock import DataBlockTemplateImporter
indexer = MosflmIndexer()
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, indexer.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.MosflmRefiner import MosflmRefiner
refiner = MosflmRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
nref_error = 500
integrater = MosflmIntegrater()
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() - 81116) < nref_error, \
mtz_object.n_reflections()
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'I', 'SIGI', 'IPR', 'SIGIPR',
'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART', 'FLAG',
'BGPKRATIOS']
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.014, 78.014, 78.014, 90.0, 90.0, 90.0), eps=1e-2)
# test serialization of integrater
json_str = integrater.as_json()
#print json_str
integrater2 = MosflmIntegrater.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() - 81116) < nref_error, \
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() - 81116) < nref_error, \
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() - 81116) < nref_error, \
mtz_object.n_reflections()
if not integrater and \
(not preselection or preselection == 'dials'):
try:
integrater = DialsIntegrater()
Debug.write('Using Dials Integrater')
except NotAvailableError, e:
if preselection == 'dials':
raise RuntimeError, \
'preselected integrater dials not available: ' + \
'dials not installed?'
pass
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, e:
if preselection == 'mosflmr':
raise RuntimeError, \
'preselected integrater mosflmr not available'
pass
if not integrater and \
(not preselection or preselection == 'xdsr'):
try:
integrater = XDSIntegrater()
Debug.write('Using XDS Integrater in new resolution mode')
except NotAvailableError, e:
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 exercise_mosflm_integrate(nproc):
if not have_dials_regression:
raise RuntimeError, 'dials_regression not available'
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
from xia2.Handlers.Flags import Flags
Flags.set_parallel(nproc)
cwd = os.path.abspath(os.curdir)
tmp_dir1 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir1)
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
indexer = MosflmIndexer()
indexer.set_working_directory(tmp_dir1)
indexer.setup_from_image(template % 1)
refiner = MosflmRefiner()
refiner.add_refiner_indexer(1, indexer)
m1 = MosflmIntegrater()
m1.set_working_directory(tmp_dir1)
m1.setup_from_image(template % 1)
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, m1.get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(template %1)
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
m1.set_integrater_sweep(sweep)
m1.set_integrater_refiner(refiner)
m1.set_frame_wedge(1, 45)
m1.set_integrater_wedge(1, 45)
m1.integrate()
os.chdir(cwd)
tmp_dir2 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir2)
from Original import Mosflm
m2 = Mosflm()
m2.set_working_directory(tmp_dir2)
m2.setup_from_image(template % 1)
m2.set_integrater_indexer(m2)
m2.set_integrater_sweep(sweep)
m2.set_frame_wedge(1, 45)
m2.set_integrater_wedge(1, 45)
m2.integrate()
from libtbx.test_utils import approx_equal
assert approx_equal(m1.get_integrater_cell(), m2.get_integrater_cell(),
eps=0.02)
assert approx_equal(indexer.get_indexer_distance(), m2.get_indexer_distance(),
eps=0.2)
assert approx_equal(m1.get_integrater_cell(),
m2.get_integrater_cell(), eps=0.02)
assert indexer.get_indexer_lattice() == m2.get_indexer_lattice()
assert approx_equal(indexer.get_indexer_mosaic(), m2.get_indexer_mosaic(),
eps=0.01)
m1_mtz = m1.get_integrater_intensities()
m2_mtz = m2.get_integrater_intensities()
from iotbx.reflection_file_reader import any_reflection_file
mas_1 = any_reflection_file(m1_mtz).as_miller_arrays()
mas_2 = any_reflection_file(m2_mtz).as_miller_arrays()
assert len(mas_1) == len(mas_2)
for ma1, ma2 in zip(mas_1, mas_2):
assert ma1.size() == ma2.size()
assert ma1.space_group() == ma2.space_group()
assert ma1.unit_cell().parameters() == ma2.unit_cell().parameters()
assert ma1.indices() == ma2.indices()
assert ma1.data() == ma2.data()
assert ma1.sigmas() == ma2.sigmas()
return
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 exercise_mosflm_integrater(dials_data, tmp_dir, nproc):
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
# otherwise if this test is running multiple times simultaneously two mosflm
# processes try to write to the same genfile
os.environ["CCP4_SCR"] = tmp_dir
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
indexer = MosflmIndexer()
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, indexer.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.MosflmRefiner import MosflmRefiner
refiner = MosflmRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
nref_error = 500
integrater = MosflmIntegrater()
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() - 81116) <
nref_error), mtz_object.n_reflections()
assert mtz_object.column_labels() == [
"H",
"K",
"L",
"M_ISYM",
"BATCH",
"I",
"SIGI",
"IPR",
"SIGIPR",
"FRACTIONCALC",
"XDET",
"YDET",
"ROT",
"WIDTH",
"LP",
"MPART",
"FLAG",
"BGPKRATIOS",
]
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(
integrater.get_integrater_cell(),
(78.014, 78.014, 78.014, 90.0, 90.0, 90.0),
eps=1e-2,
)
# test serialization of integrater
json_str = integrater.as_json()
# print json_str
integrater2 = MosflmIntegrater.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() - 81116) <
nref_error), 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() - 81116) <
nref_error), 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() - 81116) <
nref_error), mtz_object.n_reflections()