def rescale_with_specified_symm_worker(sym_wd_wdr,
topdir,
log_out,
reference_symm,
sgnum,
sgnum_laue,
prep_dials_files=False):
# XXX Unsafe if multiple processes run this function for the same target directory at the same time
sym, wd, wdr = sym_wd_wdr
out = StringIO()
print >> out, os.path.relpath(wd, topdir),
# Find appropriate data # XXX not works for DIALS data!!
xac_file = util.return_first_found_file(
("XDS_ASCII.HKL_noscale.org", "XDS_ASCII.HKL_noscale",
"XDS_ASCII_fullres.HKL.org", "XDS_ASCII_fullres.HKL",
"XDS_ASCII.HKL.org", "XDS_ASCII.HKL"),
wd=wd)
if xac_file is None:
print >> out, "Can't find XDS_ASCII file in %s" % wd
log_out.write(out.getvalue())
log_out.flush()
return (wd, None)
xac = XDS_ASCII(xac_file, read_data=False)
print >> out, "%s %s (%s)" % (os.path.basename(xac_file),
xac.symm.space_group_info(), ",".join(
map(lambda x: "%.2f" % x,
xac.symm.unit_cell().parameters())))
if xac.symm.reflection_intensity_symmetry(
False).space_group_info().type().number() == sgnum_laue:
if xac.symm.unit_cell().is_similar_to(reference_symm.unit_cell(), 0.1,
10):
print >> out, " Already scaled with specified symmetry"
log_out.write(out.getvalue())
log_out.flush()
if wd != wdr: shutil.copy2(xac_file, wdr)
if prep_dials_files: prepare_dials_files(wd, out, moveto=wdr)
return (wdr, (numpy.array(xac.symm.unit_cell().parameters()),
os.path.join(wdr, os.path.basename(xac_file))))
xdsinp = os.path.join(wd, "XDS.INP")
cosets = reindex.reindexing_operators(reference_symm, xac.symm, 0.2, 20)
if len(cosets.combined_cb_ops()) == 0:
print >> out, "Can't find operator:"
sym.show_summary(out, " ")
reference_symm.show_summary(out, " ")
log_out.write(out.getvalue())
log_out.flush()
return (wdr, None)
newcell = reference_symm.space_group().average_unit_cell(
xac.symm.change_basis(cosets.combined_cb_ops()[0]).unit_cell())
newcell = " ".join(map(lambda x: "%.3f" % x, newcell.parameters()))
print >> out, "Scaling with transformed cell:", newcell
#for f in xds_files.generated_by_CORRECT:
# util.rotate_file(os.path.join(wd, f))
bk_prefix = make_backup(xds_files.generated_by_CORRECT,
wdir=wd,
quiet=True)
modify_xdsinp(
xdsinp,
inp_params=[
("JOB", "CORRECT"),
("SPACE_GROUP_NUMBER", "%d" % sgnum),
("UNIT_CELL_CONSTANTS", newcell),
("INCLUDE_RESOLUTION_RANGE", "50 0"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", None), # use default
("REFINE(CORRECT)", None), # use default
])
run_xds(wd)
for f in ("XDS.INP", "CORRECT.LP", "XDS_ASCII.HKL", "GXPARM.XDS"):
if os.path.exists(os.path.join(wd, f)):
shutil.copyfile(os.path.join(wd, f),
os.path.join(wdr, f + "_rescale"))
revert_files(xds_files.generated_by_CORRECT,
bk_prefix,
wdir=wd,
quiet=True)
new_xac = os.path.join(wdr, "XDS_ASCII.HKL_rescale")
if prep_dials_files:
prepare_dials_files(wd,
out,
space_group=reference_symm.space_group(),
reindex_op=cosets.combined_cb_ops()[0],
moveto=wdr)
ret = None
if os.path.isfile(new_xac):
ret = (XDS_ASCII(new_xac,
read_data=False).symm.unit_cell().parameters(),
new_xac)
print >> out, " OK:", ret[0]
else:
print >> out, "Error: rescaling failed (Can't find XDS_ASCII.HKL)"
return (wd, ret)
def rescale_with_specified_symm(topdir,
dirs,
symms,
out,
sgnum=None,
reference_symm=None):
assert (sgnum, reference_symm).count(None) == 1
if sgnum is not None:
sgnum_laue = sgtbx.space_group_info(sgnum).group(
).build_derived_reflection_intensity_group(False).type().number()
matches = filter(
lambda x: x.reflection_intensity_symmetry(False).space_group_info(
).type().number() == sgnum_laue, symms)
matched_cells = numpy.array(
map(lambda x: x.unit_cell().parameters(), matches))
median_cell = map(lambda x: numpy.median(matched_cells[:, x]),
xrange(6))
reference_symm = crystal.symmetry(median_cell, sgnum)
else:
sgnum = reference_symm.space_group_info().type().number()
sgnum_laue = reference_symm.space_group(
).build_derived_reflection_intensity_group(False).type().number()
print >> out
print >> out, "Re-scaling with specified symmetry:", reference_symm.space_group_info(
).symbol_and_number()
print >> out, " reference cell:", reference_symm.unit_cell()
print >> out
print >> out
cells = {} # cell and file
for sym, wd in zip(symms, dirs):
print >> out, os.path.relpath(wd, topdir),
# Find appropriate data
xac_file = util.return_first_found_file(
("XDS_ASCII.HKL_noscale.org", "XDS_ASCII.HKL_noscale",
"XDS_ASCII_fullres.HKL.org", "XDS_ASCII_fullres.HKL",
"XDS_ASCII.HKL.org", "XDS_ASCII.HKL"),
wd=wd)
if xac_file is None:
print >> out, "Can't find XDS_ASCII file in %s" % wd
continue
xac = XDS_ASCII(xac_file, read_data=False)
print >> out, "%s %s (%s)" % (
os.path.basename(xac_file), xac.symm.space_group_info(), ",".join(
map(lambda x: "%.2f" % x,
xac.symm.unit_cell().parameters())))
if xac.symm.reflection_intensity_symmetry(
False).space_group_info().type().number() == sgnum_laue:
if xac.symm.unit_cell().is_similar_to(reference_symm.unit_cell(),
0.1, 10):
print >> out, " Already scaled with specified symmetry"
cells[wd] = (numpy.array(xac.symm.unit_cell().parameters()),
xac_file)
continue
xdsinp = os.path.join(wd, "XDS.INP")
cosets = reindex.reindexing_operators(reference_symm, xac.symm, 0.2,
20)
if len(cosets.combined_cb_ops()) == 0:
print >> out, "Can't find operator:"
sym.show_summary(out, " ")
reference_symm.show_summary(out, " ")
continue
newcell = reference_symm.space_group().average_unit_cell(
xac.symm.change_basis(cosets.combined_cb_ops()[0]).unit_cell())
newcell = " ".join(map(lambda x: "%.3f" % x, newcell.parameters()))
print >> out, "Scaling with transformed cell:", newcell
#for f in xds_files.generated_by_CORRECT:
# util.rotate_file(os.path.join(wd, f))
bk_prefix = make_backup(xds_files.generated_by_CORRECT,
wdir=wd,
quiet=True)
modify_xdsinp(
xdsinp,
inp_params=[
("JOB", "CORRECT"),
("SPACE_GROUP_NUMBER", "%d" % sgnum),
("UNIT_CELL_CONSTANTS", newcell),
("INCLUDE_RESOLUTION_RANGE", "50 0"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", None), # use default
("REFINE(CORRECT)", None), # use default
])
run_xds(wd)
for f in ("XDS.INP", "CORRECT.LP", "XDS_ASCII.HKL", "GXPARM.XDS"):
if os.path.exists(os.path.join(wd, f)):
shutil.copyfile(os.path.join(wd, f),
os.path.join(wd, f + "_rescale"))
revert_files(xds_files.generated_by_CORRECT,
bk_prefix,
wdir=wd,
quiet=True)
new_xac = os.path.join(wd, "XDS_ASCII.HKL_rescale")
new_gxparm = os.path.join(wd, "GXPARM.XDS_rescale")
if os.path.isfile(new_xac) and os.path.isfile(new_gxparm):
cells[wd] = (XPARM(new_gxparm).unit_cell, new_xac)
print "OK:", cells[wd][0]
else:
print >> out, "Error: rescaling failed (Can't find XDS_ASCII.HKL)"
continue
return cells, reference_symm
def xds_sequence(img_in, topdir, data_root_dir, params):
relpath = os.path.relpath(os.path.dirname(img_in), data_root_dir)
workdir = os.path.abspath(os.path.join(topdir, relpath, os.path.splitext(os.path.basename(img_in))[0]))
print workdir
frame_num = None
if not os.path.exists(img_in):
if "<>" in img_in:
img_in, num = img_in.split("<>")
frame_num = int(num)
if not os.path.exists(img_in):
print "Error: Not found!!", img_in
return
workdir += "_%.6d" % frame_num
assert img_in.endswith(".h5")
else:
for ext in (".bz2", ".gz", ".xz"):
if os.path.exists(img_in+ext):
img_in += ext
break
if params.tmpdir is not None:
tmpdir = tempfile.mkdtemp(prefix="xds", dir=params.tmpdir)
else:
tmpdir = workdir
if not os.path.exists(tmpdir): os.makedirs(tmpdir)
xparm = os.path.join(tmpdir, "XPARM.XDS")
xdsinp = os.path.join(tmpdir, "XDS.INP")
integrate_hkl = os.path.join(tmpdir, "INTEGRATE.HKL")
decilog = open(os.path.join(tmpdir, "decision.log"), "w")
try:
print >>decilog, "Paramters:"
libtbx.phil.parse(master_params_str).format(params).show(out=decilog, prefix=" ")
print >>decilog, "\nStarting at %s" % time.strftime("%Y-%m-%d %H:%M:%S")
# Prepare XDS.INP
if params.sfx.cheetah_mpccd:
xdsinp_str = sfx_xds_inp(img_in, xdsinp, params)
else:
if frame_num is not None: # Eiger
from yamtbx.dataproc import eiger
img_in_work = os.path.join(os.path.dirname(xdsinp), "data_10000.cbf")
eiger.extract_to_minicbf(img_in, frame_num, img_in_work)
else:
ext = os.path.splitext(img_in)[1]
img_in_work = os.path.join(os.path.dirname(xdsinp), "data_10000" + ext)
os.symlink(img_in, img_in_work)
xdsinp_str = xds_inp.generate_xds_inp(img_files=[img_in_work],
inp_dir=tmpdir,
reverse_phi=True, anomalous=params.anomalous,
spot_range=None, minimum=False,
crystal_symmetry=None,
integrate_nimages=None,
osc_range=params.osc_range,
orgx=params.orgx, orgy=params.orgy,
rotation_axis=params.rotation_axis,
distance=params.distance)
ofs = open(xdsinp, "w")
ofs.write(xdsinp_str)
ofs.close()
# Start processing
modify_xdsinp(xdsinp, inp_params=[("JOB", "XYCORR INIT COLSPOT IDXREF"),
("MAXIMUM_NUMBER_OF_PROCESSORS", "1"),
("MINPK", "%.2f"%params.minpk),
("PROFILE_FITTING", bool_to_str(params.profile_fitting)),
("STRONG_PIXEL", "%.2f"%params.strong_pixel),
("MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT", "%d"%params.minimum_number_of_pixels_in_a_spot),
("SEPMIN", "%.2f"%params.sepmin),
("CLUSTER_RADIUS", "%.2f"%params.cluster_radius),
("INDEX_ERROR", "%.4f"%params.index_error),
("INDEX_MAGNITUDE", "%d"%params.index_magnitude),
("INDEX_QUALITY", "%.2f"%params.index_quality),
("REFINE(IDXREF)", " ".join(params.refine_idxref)),
("INCLUDE_RESOLUTION_RANGE", "%.2f %.2f" % (params.d_max, params.idxref_d_min)),
("VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS", "%.1f %.1f" % tuple(params.value_range_for_trusted_detector_pixels))
])
if len(params.extra_inp_str) > 0:
ofs = open(xdsinp, "a")
ofs.write("\n%s\n" % "\n".join(params.extra_inp_str))
ofs.close()
run_xds(wdir=tmpdir, show_progress=False)
if params.tryhard:
try_indexing_hard(tmpdir, show_progress=True, decilog=decilog)
# If Cell hint exists, try to use it..
if params.sgnum > 0:
flag_try_cell_hint = False
if not os.path.isfile(xparm):
flag_try_cell_hint = True
else:
xsxds = XPARM(xparm).crystal_symmetry()
cosets = check_cell(params, xsxds)
if cosets.double_cosets is None: flag_try_cell_hint = True
if flag_try_cell_hint:
print >>decilog, " Worth trying to use prior cell for indexing."
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF"),
("UNIT_CELL_CONSTANTS",
" ".join(map(lambda x: "%.3f"%x, params.cell))),
("SPACE_GROUP_NUMBER", "%d"%params.sgnum),
])
run_xds(wdir=tmpdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[("SPACE_GROUP_NUMBER", "0"),
])
if not os.path.isfile(xparm):
raise ProcFailed("Indexing failed")
if params.checkcell.check and params.sgnum > 0:
xsxds = XPARM(xparm).crystal_symmetry()
cosets = check_cell(params, xsxds)
if cosets.double_cosets is None:
raise ProcFailed("Incompatible cell. Indexing failed.")
if not cosets.combined_cb_ops()[0].is_identity_op():
print >>decilog, "Re-idxref to match reference symmetry."
xsxds_cb = xsxds.change_basis(cosets.combined_cb_ops()[0]) # Really OK??
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF"),
("SPACE_GROUP_NUMBER", "%d"%params.sgnum),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f"%x, xsxds_cb.unit_cell().parameters())))
])
run_xds(wdir=tmpdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[("INCLUDE_RESOLUTION_RANGE", "%.2f %.2f" % (params.d_max, params.d_min)),
])
# To Integration
modify_xdsinp(xdsinp, inp_params=[("JOB", "DEFPIX INTEGRATE"),])
run_xds(wdir=tmpdir, show_progress=False)
if not os.path.isfile(integrate_hkl):
raise ProcFailed("Integration failed.")
# Determine unit cell in CORRECT
if params.refine_correct:
tmp = [("REFINE(CORRECT)", "ALL"),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f"%x, params.cell)))]
else:
# XXX What if CELL is refined in INTEGRATE?
xsxds = XPARM(xparm).crystal_symmetry()
cosets = check_cell(params, xsxds)
if cosets.double_cosets is None:
raise ProcFailed(" Incompatible cell. Failed before CORRECT.")
xsxds_cb = xsxds.change_basis(cosets.combined_cb_ops()[0]) # Really OK??
tmp = [("REFINE(CORRECT)", ""),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f"%x, xsxds_cb.unit_cell().parameters())))]
# PEAK-corrected INTEGRATE.HKL
ihk = os.path.join(tmpdir, "INTEGRATE.HKL")
ihk_full = os.path.join(tmpdir, "INTEGRATE_full.HKL")
ihk_part = os.path.join(tmpdir, "INTEGRATE_part.HKL")
inhkl = integrate_hkl_as_flex.reader(ihk, [], False)
inhkl.write_peak_corrected(ihk_part)
os.rename(ihk, ihk_full)
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),
("DATA_RANGE", "1 20000"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("SPACE_GROUP_NUMBER", "%d"%params.sgnum)] + tmp)
xac = os.path.join(tmpdir, "XDS_ASCII.HKL")
xac_full = os.path.join(tmpdir, "XDS_ASCII_full.HKL")
xac_part = os.path.join(tmpdir, "XDS_ASCII_part.HKL")
# CORRECT for full
os.symlink(ihk_full, ihk)
run_xds(wdir=tmpdir, comm="xds", show_progress=False)
if os.path.isfile(xac):
os.rename(xac, xac_full)
os.rename(os.path.join(tmpdir, "CORRECT.LP"),
os.path.join(tmpdir, "CORRECT_full.LP"))
os.remove(ihk)
# CORRECT for part
os.symlink(ihk_part, ihk)
run_xds(wdir=tmpdir, comm="xds", show_progress=False)
if os.path.isfile(xac):
os.rename(xac, xac_part)
os.rename(os.path.join(tmpdir, "CORRECT.LP"),
os.path.join(tmpdir, "CORRECT_part.LP"))
os.remove(ihk)
if params.pickle_hkl:
for f in filter(lambda x: os.path.isfile(x), (xac_part, xac_full)):
print >>decilog, "Pickling %s" % os.path.basename(f)
x = xds_ascii.XDS_ASCII(f, log_out=decilog)
if params.light_pickle: x.xd, x.yd, x.zd, x.rlp, x.corr = None, None, None, None, None # To make reading faster
pickle.dump(x, open(f+".pkl", "w"), -1)
if params.pickle_hkl:
for f in filter(lambda x: os.path.isfile(x), (ihk_part, ihk_full)):
print >>decilog, "Pickling %s" % os.path.basename(f)
inhkl = integrate_hkl_as_flex.reader(f, read_columns=["IOBS","SIGMA","XCAL","YCAL","RLP","PEAK","MAXC"])
pickle.dump(inhkl, open(f+".pkl", "w"), -1)
except ProcFailed, e:
print >>decilog, "Processing failed: %s" % e.message
def rescale_with_specified_symm(topdir, dirs, symms, out, sgnum=None, reference_symm=None):
assert (sgnum, reference_symm).count(None) == 1
if sgnum is not None:
sgnum_laue = sgtbx.space_group_info(sgnum).group().build_derived_reflection_intensity_group(False).type().number()
matches = filter(lambda x:x.reflection_intensity_symmetry(False).space_group_info().type().number()==sgnum_laue, symms)
matched_cells = numpy.array(map(lambda x: x.unit_cell().parameters(), matches))
median_cell = map(lambda x: numpy.median(matched_cells[:,x]), xrange(6))
reference_symm = crystal.symmetry(median_cell, sgnum)
else:
sgnum = reference_symm.space_group_info().type().number()
sgnum_laue = reference_symm.space_group().build_derived_reflection_intensity_group(False).type().number()
print >>out
print >>out, "Re-scaling with specified symmetry:", reference_symm.space_group_info().symbol_and_number()
print >>out, " reference cell:", reference_symm.unit_cell()
print >>out
print >>out
cells = {} # cell and file
for sym, wd in zip(symms, dirs):
print >>out, os.path.relpath(wd, topdir),
# Find appropriate data
xac_file = util.return_first_found_file(("XDS_ASCII.HKL_noscale.org", "XDS_ASCII.HKL_noscale",
"XDS_ASCII_fullres.HKL.org", "XDS_ASCII_fullres.HKL",
"XDS_ASCII.HKL.org", "XDS_ASCII.HKL"),
wd=wd)
if xac_file is None:
print >>out, "Can't find XDS_ASCII file in %s" % wd
continue
xac = XDS_ASCII(xac_file, read_data=False)
print >>out, "%s %s (%s)" % (os.path.basename(xac_file), xac.symm.space_group_info(),
",".join(map(lambda x: "%.2f"%x, xac.symm.unit_cell().parameters())))
if xac.symm.reflection_intensity_symmetry(False).space_group_info().type().number() == sgnum_laue:
if xac.symm.unit_cell().is_similar_to(reference_symm.unit_cell(), 0.1, 10):
print >>out, " Already scaled with specified symmetry"
cells[wd] = (numpy.array(xac.symm.unit_cell().parameters()), xac_file)
continue
xdsinp = os.path.join(wd, "XDS.INP")
cosets = reindex.reindexing_operators(reference_symm, xac.symm, 0.2, 20)
if len(cosets.combined_cb_ops())==0:
print >>out, "Can't find operator:"
sym.show_summary(out, " ")
reference_symm.show_summary(out, " ")
continue
newcell = reference_symm.space_group().average_unit_cell(xac.symm.change_basis(cosets.combined_cb_ops()[0]).unit_cell())
newcell = " ".join(map(lambda x: "%.3f"%x, newcell.parameters()))
print >>out, "Scaling with transformed cell:", newcell
#for f in xds_files.generated_by_CORRECT:
# util.rotate_file(os.path.join(wd, f))
bk_prefix = make_backup(xds_files.generated_by_CORRECT, wdir=wd, quiet=True)
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),
("SPACE_GROUP_NUMBER", "%d"%sgnum),
("UNIT_CELL_CONSTANTS", newcell),
("INCLUDE_RESOLUTION_RANGE", "50 0"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", None), # use default
("REFINE(CORRECT)", None), # use default
])
run_xds(wd)
for f in ("XDS.INP", "CORRECT.LP", "XDS_ASCII.HKL", "GXPARM.XDS"):
if os.path.exists(os.path.join(wd, f)):
shutil.copyfile(os.path.join(wd, f), os.path.join(wd, f+"_rescale"))
revert_files(xds_files.generated_by_CORRECT, bk_prefix, wdir=wd, quiet=True)
new_xac = os.path.join(wd, "XDS_ASCII.HKL_rescale")
new_gxparm = os.path.join(wd, "GXPARM.XDS_rescale")
if os.path.isfile(new_xac) and os.path.isfile(new_gxparm):
cells[wd] = (XPARM(new_gxparm).unit_cell, new_xac)
print "OK:", cells[wd][0]
else:
print >>out, "Error: rescaling failed (Can't find XDS_ASCII.HKL)"
continue
return cells, reference_symm
def xds_sequence(img_in, topdir, data_root_dir, params):
relpath = os.path.relpath(os.path.dirname(img_in), data_root_dir)
workdir = os.path.abspath(os.path.join(topdir, relpath, os.path.splitext(os.path.basename(img_in))[0]))
print workdir
frame_num = None
if not os.path.exists(img_in):
if "<>" in img_in:
img_in, num = img_in.split("<>")
frame_num = int(num)
if not os.path.exists(img_in):
print "Error: Not found!!", img_in
return
workdir += "_%.6d" % frame_num
assert img_in.endswith(".h5")
else:
for ext in (".bz2", ".gz", ".xz"):
if os.path.exists(img_in + ext):
img_in += ext
break
if params.tmpdir is not None:
tmpdir = tempfile.mkdtemp(prefix="xds", dir=params.tmpdir)
else:
tmpdir = workdir
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
xparm = os.path.join(tmpdir, "XPARM.XDS")
xdsinp = os.path.join(tmpdir, "XDS.INP")
integrate_hkl = os.path.join(tmpdir, "INTEGRATE.HKL")
decilog = open(os.path.join(tmpdir, "decision.log"), "w")
try:
print >> decilog, "Paramters:"
libtbx.phil.parse(master_params_str).format(params).show(out=decilog, prefix=" ")
print >> decilog, "\nStarting at %s" % time.strftime("%Y-%m-%d %H:%M:%S")
# Prepare XDS.INP
if params.sfx.cheetah_mpccd:
xdsinp_str = sfx_xds_inp(img_in, xdsinp, params)
else:
if frame_num is not None: # Eiger
from yamtbx.dataproc import eiger
img_in_work = os.path.join(os.path.dirname(xdsinp), "data_10000.cbf")
eiger.extract_to_minicbf(img_in, frame_num, img_in_work)
else:
ext = os.path.splitext(img_in)[1]
img_in_work = os.path.join(os.path.dirname(xdsinp), "data_10000" + ext)
os.symlink(img_in, img_in_work)
xdsinp_str = xds_inp.generate_xds_inp(
img_files=[img_in_work],
inp_dir=tmpdir,
reverse_phi=True,
anomalous=params.anomalous,
spot_range=None,
minimum=False,
crystal_symmetry=None,
integrate_nimages=None,
osc_range=params.osc_range,
orgx=params.orgx,
orgy=params.orgy,
rotation_axis=params.rotation_axis,
distance=params.distance,
)
ofs = open(xdsinp, "w")
ofs.write(xdsinp_str)
ofs.close()
# Start processing
modify_xdsinp(
xdsinp,
inp_params=[
("JOB", "XYCORR INIT COLSPOT IDXREF"),
("MAXIMUM_NUMBER_OF_PROCESSORS", "1"),
("MINPK", "%.2f" % params.minpk),
("PROFILE_FITTING", bool_to_str(params.profile_fitting)),
("STRONG_PIXEL", "%.2f" % params.strong_pixel),
("MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT", "%d" % params.minimum_number_of_pixels_in_a_spot),
("SEPMIN", "%.2f" % params.sepmin),
("CLUSTER_RADIUS", "%.2f" % params.cluster_radius),
("INDEX_ERROR", "%.4f" % params.index_error),
("INDEX_MAGNITUDE", "%d" % params.index_magnitude),
("INDEX_QUALITY", "%.2f" % params.index_quality),
("REFINE(IDXREF)", " ".join(params.refine_idxref)),
("INCLUDE_RESOLUTION_RANGE", "%.2f %.2f" % (params.d_max, params.idxref_d_min)),
(
"VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS",
"%.1f %.1f" % tuple(params.value_range_for_trusted_detector_pixels),
),
],
)
if len(params.extra_inp_str) > 0:
ofs = open(xdsinp, "a")
ofs.write("\n%s\n" % "\n".join(params.extra_inp_str))
ofs.close()
run_xds(wdir=tmpdir, show_progress=False)
if params.tryhard:
try_indexing_hard(tmpdir, show_progress=True, decilog=decilog)
# If Cell hint exists, try to use it..
if params.sgnum > 0:
flag_try_cell_hint = False
if not os.path.isfile(xparm):
flag_try_cell_hint = True
else:
xsxds = XPARM(xparm).crystal_symmetry()
cosets = check_cell(params, xsxds)
if cosets.double_cosets is None:
flag_try_cell_hint = True
if flag_try_cell_hint:
print >> decilog, " Worth trying to use prior cell for indexing."
modify_xdsinp(
xdsinp,
inp_params=[
("JOB", "IDXREF"),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f" % x, params.cell))),
("SPACE_GROUP_NUMBER", "%d" % params.sgnum),
],
)
run_xds(wdir=tmpdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[("SPACE_GROUP_NUMBER", "0")])
if not os.path.isfile(xparm):
raise ProcFailed("Indexing failed")
if params.checkcell.check and params.sgnum > 0:
xsxds = XPARM(xparm).crystal_symmetry()
cosets = check_cell(params, xsxds)
if cosets.double_cosets is None:
raise ProcFailed("Incompatible cell. Indexing failed.")
if not cosets.combined_cb_ops()[0].is_identity_op():
print >> decilog, "Re-idxref to match reference symmetry."
xsxds_cb = xsxds.change_basis(cosets.combined_cb_ops()[0]) # Really OK??
modify_xdsinp(
xdsinp,
inp_params=[
("JOB", "IDXREF"),
("SPACE_GROUP_NUMBER", "%d" % params.sgnum),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f" % x, xsxds_cb.unit_cell().parameters()))),
],
)
run_xds(wdir=tmpdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[("INCLUDE_RESOLUTION_RANGE", "%.2f %.2f" % (params.d_max, params.d_min))])
# To Integration
modify_xdsinp(xdsinp, inp_params=[("JOB", "DEFPIX INTEGRATE")])
run_xds(wdir=tmpdir, show_progress=False)
if not os.path.isfile(integrate_hkl):
raise ProcFailed("Integration failed.")
# Determine unit cell in CORRECT
if params.refine_correct:
tmp = [
("REFINE(CORRECT)", "ALL"),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f" % x, params.cell))),
]
else:
# XXX What if CELL is refined in INTEGRATE?
xsxds = XPARM(xparm).crystal_symmetry()
cosets = check_cell(params, xsxds)
if cosets.double_cosets is None:
raise ProcFailed(" Incompatible cell. Failed before CORRECT.")
xsxds_cb = xsxds.change_basis(cosets.combined_cb_ops()[0]) # Really OK??
tmp = [
("REFINE(CORRECT)", ""),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x: "%.3f" % x, xsxds_cb.unit_cell().parameters()))),
]
# PEAK-corrected INTEGRATE.HKL
ihk = os.path.join(tmpdir, "INTEGRATE.HKL")
ihk_full = os.path.join(tmpdir, "INTEGRATE_full.HKL")
ihk_part = os.path.join(tmpdir, "INTEGRATE_part.HKL")
inhkl = integrate_hkl_as_flex.reader(ihk, [], False)
inhkl.write_peak_corrected(ihk_part)
os.rename(ihk, ihk_full)
modify_xdsinp(
xdsinp,
inp_params=[
("JOB", "CORRECT"),
("DATA_RANGE", "1 20000"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("SPACE_GROUP_NUMBER", "%d" % params.sgnum),
]
+ tmp,
)
xac = os.path.join(tmpdir, "XDS_ASCII.HKL")
xac_full = os.path.join(tmpdir, "XDS_ASCII_full.HKL")
xac_part = os.path.join(tmpdir, "XDS_ASCII_part.HKL")
# CORRECT for full
os.symlink(ihk_full, ihk)
run_xds(wdir=tmpdir, comm="xds", show_progress=False)
if os.path.isfile(xac):
os.rename(xac, xac_full)
os.rename(os.path.join(tmpdir, "CORRECT.LP"), os.path.join(tmpdir, "CORRECT_full.LP"))
os.remove(ihk)
# CORRECT for part
os.symlink(ihk_part, ihk)
run_xds(wdir=tmpdir, comm="xds", show_progress=False)
if os.path.isfile(xac):
os.rename(xac, xac_part)
os.rename(os.path.join(tmpdir, "CORRECT.LP"), os.path.join(tmpdir, "CORRECT_part.LP"))
os.remove(ihk)
if params.pickle_hkl:
for f in filter(lambda x: os.path.isfile(x), (xac_part, xac_full)):
print >> decilog, "Pickling %s" % os.path.basename(f)
x = xds_ascii.XDS_ASCII(f, log_out=decilog)
if params.light_pickle:
x.xd, x.yd, x.zd, x.rlp, x.corr = None, None, None, None, None # To make reading faster
pickle.dump(x, open(f + ".pkl", "w"), -1)
if params.pickle_hkl:
for f in filter(lambda x: os.path.isfile(x), (ihk_part, ihk_full)):
print >> decilog, "Pickling %s" % os.path.basename(f)
inhkl = integrate_hkl_as_flex.reader(
f, read_columns=["IOBS", "SIGMA", "XCAL", "YCAL", "RLP", "PEAK", "MAXC"]
)
pickle.dump(inhkl, open(f + ".pkl", "w"), -1)
except ProcFailed, e:
print >> decilog, "Processing failed: %s" % e.message
