def exercise_mosflm_index():
if not have_dials_regression:
print 'SKIP: dials_regression not configured'
exit(0)
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
cwd = os.path.abspath(os.curdir)
tmp_dir1 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir1)
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
m1 = MosflmIndexer()
m1.set_working_directory(tmp_dir1)
m1.setup_from_image(template % 1)
m1.index()
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.index()
assert m1.get_indexer_beam_centre() == m2.get_indexer_beam_centre()
assert m1.get_indexer_distance() == m2.get_indexer_distance()
assert m1.get_indexer_cell() == m2.get_indexer_cell()
assert m1.get_indexer_lattice() == m2.get_indexer_lattice()
assert m1.get_indexer_mosaic() == m2.get_indexer_mosaic()
os.chdir(cwd)
return
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