def test_mosflm_refine_cell(dials_regression, tmpdir):
tmpdir.chdir()
templ, directory = get_template_and_directory(dials_regression)
matrix = ''' -0.00728371 -0.00173706 -0.00994261
0.01008485 -0.00175152 -0.00708190
-0.00041078 -0.01220000 0.00243238
0.000 0.000 0.000
-0.5851825 -0.1395579 -0.7988023
0.8102298 -0.1407195 -0.5689691
-0.0330029 -0.9801641 0.1954206
78.6541 78.6541 78.6542 90.0000 90.0000 90.0000
0.000 0.000 0.000
SYMM I23 \n'''
tmpdir.join('xiaindex.mat').write(matrix)
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(two_images_indexing['beam_centre'])
refiner.set_mosaic(two_images_indexing['mosaicity'])
refiner.run()
output = ''.join(refiner.get_all_output())
print(output)
background_residual = refiner.get_background_residual()
rms_values = refiner.get_rms_values()
ref_residual = {
1: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1},
2: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1},
3: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1}
}
for cycle in background_residual:
for frame in background_residual[cycle]:
assert background_residual[cycle][frame] == \
pytest.approx(ref_residual[cycle][frame], abs=0.1)
ref_values = {
1: [0.027, 0.029, 0.027, 0.025, 0.027, 0.025, 0.024, 0.022, 0.025],
2: [0.02, 0.021, 0.023, 0.021, 0.02, 0.017, 0.018, 0.019, 0.022],
3: [0.02, 0.021, 0.025, 0.022, 0.021, 0.019, 0.018, 0.019, 0.021]
}
for cycle in rms_values:
for frame, value in enumerate(rms_values[cycle]):
assert value == \
pytest.approx(ref_values[cycle][frame], abs=0.05)
def exercise_mosflm_refine_cell():
if not have_dials_regression:
print "Skipping exercise_mosflm_refine_cell(): 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
# 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
background_residual = refiner.get_background_residual()
rms_values = refiner.get_rms_values()
ref_residual = {
1: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1},
2: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1},
3: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1}
}
for cycle in background_residual:
for frame in background_residual[cycle]:
assert abs(background_residual[cycle][frame] -
ref_residual[cycle][frame]) <= 0.1, (cycle, frame)
ref_values = {
1: [0.027, 0.029, 0.027, 0.025, 0.027, 0.025, 0.024, 0.022, 0.025],
2: [0.02, 0.021, 0.023, 0.021, 0.02, 0.017, 0.018, 0.019, 0.022],
3: [0.02, 0.021, 0.025, 0.022, 0.021, 0.019, 0.018, 0.019, 0.021]
}
for cycle in rms_values:
for frame in range(len(rms_values[cycle])):
assert abs(rms_values[cycle][frame] - ref_values[cycle][frame]) <= 0.05
