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_explore_completeness():
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 contains_substring
from libtbx import easy_run
def run(args):
cmd = " ".join(["rstbx.simage.explore_completeness"] + args)
print(cmd)
buf = easy_run.fully_buffered(
command=cmd,
stdout_splitlines=False).raise_if_errors().stdout_buffer
for key in [
"Complete with ", "Observations per reflection:", " Median: "
]:
assert contains_substring(buf, key)
return buf
run(["d_min=10"])
args = ["d_min=10", "intensity_symmetry=P4", "use_symmetry=True"]
from libtbx import easy_mp
if (easy_mp.detect_problem() is None):
args.append("multiprocessing=True")
buf = run(args)
assert contains_substring(buf, 'lattice_symmetry = "P 4 2 2"')
def exercise_explore_completeness():
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 contains_substring
from libtbx import easy_run
def run(args):
cmd = " ".join(["rstbx.simage.explore_completeness"] + args)
print cmd
buf = easy_run.fully_buffered(
command=cmd, stdout_splitlines=False).raise_if_errors().stdout_buffer
for key in [
"Complete with ",
"Observations per reflection:",
" Median: "]:
assert contains_substring(buf, key)
return buf
run(["d_min=10"])
args = ["d_min=10", "intensity_symmetry=P4", "use_symmetry=True"]
from libtbx import easy_mp
if (easy_mp.detect_problem() is None):
args.append("multiprocessing=True")
buf = run(args)
assert contains_substring(buf, 'lattice_symmetry = "P 4 2 2"')
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
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
def run(args):
cmd = " ".join(["rstbx.simage.explore_completeness"] + args)
print(cmd)
buf = easy_run.fully_buffered(
command=cmd,
stdout_splitlines=False).raise_if_errors().stdout_buffer
for key in [
"Complete with ", "Observations per reflection:", " Median: "
]:
assert contains_substring(buf, key)
return buf
def run(args):
cmd = " ".join(["rstbx.simage.explore_completeness"] + args)
print cmd
buf = easy_run.fully_buffered(
command=cmd, stdout_splitlines=False).raise_if_errors().stdout_buffer
for key in [
"Complete with ",
"Observations per reflection:",
" Median: "]:
assert contains_substring(buf, key)
return buf
def test_hklinfo_run(cifstr, filename, philstr, expectedstr):
with open(filename, "w") as fh:
fh.write(cifstr)
with open("philinput.txt", "w") as fh:
fh.write(philstr)
obj = subprocess.Popen("cctbx.HKLinfo %s philinput.txt" %filename,
shell=True,
stdin = subprocess.PIPE,
stdout = subprocess.PIPE,
stderr = subprocess.STDOUT)
out,err = obj.communicate()
fullstdout = out.decode().replace("\r\n", "\n") # omit \r\n line endings on Windows
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
assert (contains_substring( fullstdout, expectedstr ) )
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")