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 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_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)