def exercise_solver():
import libtbx.load_env
if (not libtbx.env.has_module("spotfinder")):
print "Skipping some tests due to missing module: spotfinder"
return
from libtbx.test_utils import block_show_diff, contains_substring
from libtbx import easy_run
def run(args):
cmd = " ".join(["rstbx.simage.solver"] + args)
print cmd
buf = easy_run.fully_buffered(
command=cmd, stdout_splitlines=False).raise_if_errors().stdout_buffer
for key in [
"Final:"]:
assert contains_substring(buf, key)
return buf
buf = run(["d_min=5"])
assert not block_show_diff(buf, """\
input_im0_i_perm: 0
Correlation of input and estimated I-obs:
i_perm=0: 1.00000 (r1: 0.00000)
""")
buf = run(["d_min=5", "lattice_symmetry=R32:R", "intensity_symmetry=R3:R"])
assert not block_show_diff(buf, """\
input_im0_i_perm: 1
Correlation of input and estimated I-obs:
i_perm=0: 0.06799 (r1: 0.37555)
i_perm=1: 1.00000 (r1: 0.00000)
""")
buf = run(["d_min=5", "lattice_symmetry=R32:R", "intensity_symmetry=P1"])
assert not block_show_diff(buf, """\
input_im0_i_perm: 5
Correlation of input and estimated I-obs:
i_perm=0: 0.07524 (r1: 0.38937)
i_perm=1: -0.02385 (r1: 0.40114)
i_perm=2: -0.04577 (r1: 0.41742)
i_perm=3: -0.00099 (r1: 0.40390)
i_perm=4: 0.00764 (r1: 0.39213)
i_perm=5: 1.00000 (r1: 0.00000)
""")
if (not libtbx.env.has_module("labelit")):
print "Skipping some tests due to missing module: labelit"
else:
from libtbx import easy_mp
mp_problem = easy_mp.detect_problem()
if (mp_problem is not None):
print "Skipping some tests:", mp_problem
else:
buf = run([
"d_min=5", "lattice_symmetry=P422", "intensity_symmetry=P4",
"index_and_integrate=True", "multiprocessing=True"])
assert contains_substring(buf, "Refined unit cell 9 (")
assert contains_substring(
buf, "Correlation of input and estimated I-obs:")
assert contains_substring(buf, " Best correlation: 0.999")
def exercise_solver():
import libtbx.load_env
if (not libtbx.env.has_module("spotfinder")):
print("Skipping some tests due to missing module: spotfinder")
return
from libtbx.test_utils import block_show_diff, contains_substring
from libtbx import easy_run
def run(args):
cmd = " ".join(["rstbx.simage.solver"] + args)
print(cmd)
buf = easy_run.fully_buffered(
command=cmd,
stdout_splitlines=False).raise_if_errors().stdout_buffer
for key in ["Final:"]:
assert contains_substring(buf, key)
return buf
buf = run(["d_min=5"])
assert not block_show_diff(
buf, """\
input_im0_i_perm: 0
Correlation of input and estimated I-obs:
i_perm=0: 1.00000 (r1: 0.00000)
""")
buf = run(["d_min=5", "lattice_symmetry=R32:R", "intensity_symmetry=R3:R"])
assert not block_show_diff(
buf, """\
input_im0_i_perm: 1
Correlation of input and estimated I-obs:
i_perm=0: 0.06799 (r1: 0.37555)
i_perm=1: 1.00000 (r1: 0.00000)
""")
buf = run(["d_min=5", "lattice_symmetry=R32:R", "intensity_symmetry=P1"])
assert not block_show_diff(
buf, """\
input_im0_i_perm: 5
Correlation of input and estimated I-obs:
i_perm=0: 0.07524 (r1: 0.38937)
i_perm=1: -0.02385 (r1: 0.40114)
i_perm=2: -0.04577 (r1: 0.41742)
i_perm=3: -0.00099 (r1: 0.40390)
i_perm=4: 0.00764 (r1: 0.39213)
i_perm=5: 1.00000 (r1: 0.00000)
""")
if (not libtbx.env.has_module("labelit")):
print("Skipping some tests due to missing module: labelit")
else:
from libtbx import easy_mp
mp_problem = easy_mp.detect_problem()
if (mp_problem is not None):
print("Skipping some tests:", mp_problem)
else:
buf = run([
"d_min=5", "lattice_symmetry=P422", "intensity_symmetry=P4",
"index_and_integrate=True", "multiprocessing=True"
])
assert contains_substring(buf, "Refined unit cell 9 (")
assert contains_substring(
buf, "Correlation of input and estimated I-obs:")
assert contains_substring(buf, " Best correlation: 0.999")
def check(args, expected_block):
sio = StringIO()
work_params = create.process_args(args=args, out=sio)
assert not block_show_diff(sio.getvalue(), expected_block)
pixels = create.compute_image(work_params)
assert pixels.all() == tuple(work_params.detector.pixels)
def check(args, expected_block): sio = StringIO() work_params = create.process_args(args=args, out=sio) assert not block_show_diff(sio.getvalue(), expected_block) pixels = create.compute_image(work_params) assert pixels.all() == tuple(work_params.detector.pixels)