def exercise_mosflm_integrate():
if not have_dials_regression:
print "Skipping exercise_mosflm_integrate(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1,45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.39, 0.39, 0.39, 0.39, 0.39]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0, 'full': 507.0, 'dist': 158.6, 'ccx': -0.01, 'yscale': 1.0,
'sdrat': 7.5, 'tilt': 25.0, 'rsym': 0.027, 'bad': 0.0, 'i/sigi': 18.1,
'i/sigi_out': 1.6, 'twist': 13.0, 'resid': 0.021, 'wresid': 1.1,
'part': 1309.0, 'nsym': 18.0, 'neg': 158.0, 'ccy': -0.01, 'ccom': -0.01,
'toff': 0.0, 'roff': 0.0}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0, 1.0,
0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9, 0.8, 0.8,
0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9, 0.8, 0.9, 1.0]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'
def exercise_mosflm_integrate():
if not have_dials_regression:
print "Skipping exercise_mosflm_integrate(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1,45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.39, 0.39, 0.39, 0.39, 0.39]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0, 'full': 507.0, 'dist': 158.6, 'ccx': -0.01, 'yscale': 1.0,
'sdrat': 7.5, 'tilt': 25.0, 'rsym': 0.027, 'bad': 0.0, 'i/sigi': 18.1,
'i/sigi_out': 1.6, 'twist': 13.0, 'resid': 0.021, 'wresid': 1.1,
'part': 1309.0, 'nsym': 18.0, 'neg': 158.0, 'ccy': -0.01, 'ccom': -0.01,
'toff': 0.0, 'roff': 0.0}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0, 1.0,
0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9, 0.8, 0.8,
0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9, 0.8, 0.9, 1.0]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'
