def get_colspot_result(frame_ranges, wdir):
assert all(map(lambda x: len(x) == 2 and x[0] <= x[1], frame_ranges))
# Check all needed files exist
if not check_needed_files(xds_files.needed_by_COLSPOT, wdir):
return
xdsinp = os.path.join(wdir, "XDS.INP")
backup_needed = xds_files.generated_by_COLSPOT + ("XDS.INP",)
# 1. Backup XDS.INP, etc. (Make copies; not renaming)
bk_prefix = make_backup(backup_needed, wdir=wdir)
try:
# 2. Modify XDS.INP
spot_ranges = map(lambda x: ("SPOT_RANGE", "%d %d" % tuple(x)), frame_ranges)
data_range = "%d %d" % (min(map(lambda x: min(x), frame_ranges)), max(map(lambda x: max(x), frame_ranges)))
modify_xdsinp(xdsinp, [("JOB", "COLSPOT"), ("DATA_RANGE", data_range)] + spot_ranges)
# 3. Run xds
p = subprocess.Popen("xds", cwd=wdir)
p.wait()
spotxds = SpotXds(os.path.join(wdir, "SPOT.XDS"))
finally:
# 6. Revert XDS.INP, etc.
revert_files(backup_needed, bk_prefix, wdir=wdir)
return spotxds
def run(params):
xdsinp = "XDS.INP"
kwds = dict(get_xdsinp_keyword(xdsinp))
orgx_org, orgy_org = map(float, (kwds["ORGX"], kwds["ORGY"]))
dx, dy = params.dx, params.dy
if params.unit == "mm":
assert "QX" in kwds
assert "QY" in kwds
dx /= float(kwds["QX"])
dy /= float(kwds["QY"])
backup_needed = files.generated_by_IDXREF + ("XDS.INP",)
bk_prefix = make_backup(backup_needed)
try:
results = []
for i in xrange(-params.nx, params.nx+1):
for j in xrange(-params.ny, params.ny+1):
work_name = "bs_x%+.2d_y%+.2d" % (i, j)
orgx = orgx_org + i * dx
orgy = orgy_org + j * dy
print "Trying", orgx, orgy
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF"),
("ORGX", orgx),
("ORGY", orgy),
])
call("xds")
make_backup(backup_needed, work_name+"_")
results.append([work_name, orgx, orgy])
for ret in results:
print ret,
analyze_result(ret[0]+"_IDXREF.LP")
finally:
revert_files(backup_needed, bk_prefix)
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 xds_sequence(root, params):
print
print os.path.relpath(root, params.topdir)
xparm = os.path.join(root, "XPARM.XDS")
gxparm = os.path.join(root, "GXPARM.XDS")
defpix_lp = os.path.join(root, "DEFPIX.LP")
correct_lp = os.path.join(root, "CORRECT.LP")
integrate_hkl = os.path.join(root, "INTEGRATE.HKL")
xac_hkl = os.path.join(root, "XDS_ASCII.HKL")
integrate_lp = os.path.join(root, "INTEGRATE.LP")
spot_xds = os.path.join(root, "SPOT.XDS")
xdsinp = os.path.join(root, "XDS.INP")
assert os.path.isfile(xdsinp)
xdsinp_dict = dict(get_xdsinp_keyword(xdsinp))
decilog = multi_out()
decilog.register("log",
open(os.path.join(root, "decision.log"), "a"),
atexit_send_to=None)
print >> decilog, "xds_sequence started at %s in %s\n" % (
time.strftime("%Y-%m-%d %H:%M:%S"), root)
if params.show_progress:
decilog.register("stdout", sys.stdout)
if params.mode == "initial" and params.resume and os.path.isfile(
correct_lp):
print " Already processed."
return
if params.mode == "recycle" and not os.path.isfile(gxparm):
print "GXPARM.XDS not found. Cannot do recycle."
return
if params.fast_delphi and (params.nproc is None or params.nproc > 1):
delphi = optimal_delphi_by_nproc(xdsinp=xdsinp, nproc=params.nproc)
print " Setting delphi to ", delphi
modify_xdsinp(xdsinp, inp_params=[
("DELPHI", str(delphi)),
])
if params.nproc is not None and params.nproc > 1:
modify_xdsinp(xdsinp,
inp_params=[
("MAXIMUM_NUMBER_OF_PROCESSORS", str(params.nproc)),
])
if params.mode == "initial":
# Peak search
modify_xdsinp(xdsinp, inp_params=[("JOB", "XYCORR INIT COLSPOT")])
run_xds(wdir=root, show_progress=params.show_progress)
if params.auto_frame_exclude_spot_based:
sx = idxreflp.SpotXds(spot_xds)
sx.set_xdsinp(xdsinp)
spots = filter(lambda x: 5 < x[-1] < 30,
sx.collected_spots()) # low-res (5 A)
frame_numbers = numpy.array(map(lambda x: int(x[2]) + 1, spots))
data_range = map(int, xdsinp_dict["DATA_RANGE"].split())
# XXX this assumes SPOT_RANGE equals to DATA_RANGE. Is this guaranteed?
h = numpy.histogram(frame_numbers,
bins=numpy.arange(data_range[0],
data_range[1] + 2,
step=1))
q14 = numpy.percentile(h[0], [25, 75])
iqr = q14[1] - q14[0]
cutoff = max(h[0][h[0] <= iqr * 1.5 + q14[1]]) / 5 # magic number
print "DEBUG:: IQR= %.2f, Q1/4= %s, cutoff= %.2f" % (iqr, q14,
cutoff)
cut_frames = h[1][h[0] < cutoff]
keep_frames = h[1][h[0] >= cutoff]
print "DEBUG:: keep_frames=", keep_frames
print "DEBUG:: cut_frames=", cut_frames
if len(cut_frames) > 0:
cut_ranges = [
[cut_frames[0], cut_frames[0]],
]
for fn in cut_frames:
if fn - cut_ranges[-1][1] <= 1: cut_ranges[-1][1] = fn
else: cut_ranges.append([fn, fn])
# Edit XDS.INP
cut_inp_str = "".join(
map(lambda x: "EXCLUDE_DATA_RANGE= %6d %6d\n" % tuple(x),
cut_ranges))
open(xdsinp, "a").write("\n" + cut_inp_str)
# Edit SPOT.XDS
shutil.copyfile(spot_xds, spot_xds + ".org")
sx.write(open(spot_xds, "w"), frame_selection=set(keep_frames))
# Indexing
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF")])
run_xds(wdir=root, show_progress=params.show_progress)
print # indexing stats like indexed percentage here.
if params.tryhard:
try_indexing_hard(root,
params.show_progress,
decilog,
known_sgnum=params.cell_prior.sgnum,
known_cell=params.cell_prior.cell,
tol_length=params.cell_prior.tol_length,
tol_angle=params.cell_prior.tol_angle)
if not os.path.isfile(xparm):
print >> decilog, " Indexing failed."
return
if params.cell_prior.check and params.cell_prior.sgnum > 0:
xsxds = XPARM(xparm).crystal_symmetry()
xsref = crystal.symmetry(params.cell_prior.cell,
params.cell_prior.sgnum)
cosets = reindex.reindexing_operators(xsref, xsxds,
params.cell_prior.tol_length,
params.cell_prior.tol_angle)
if cosets.double_cosets is None:
print >> decilog, " Incompatible cell. Indexing failed."
return
elif params.mode == "recycle":
print " Start recycle. original ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
for f in xds_files.generated_after_DEFPIX + ("XPARM.XDS",
"plot_integrate.log"):
util.rotate_file(os.path.join(root, f), copy=True)
shutil.copyfile(gxparm + ".1", xparm)
else:
raise "Unknown mode (%s)" % params.mode
# To Integration
modify_xdsinp(xdsinp,
inp_params=[("JOB", "DEFPIX INTEGRATE"),
("INCLUDE_RESOLUTION_RANGE", "50 0")])
run_xds(wdir=root, show_progress=params.show_progress)
if os.path.isfile(integrate_lp):
xds_plot_integrate.run(integrate_lp,
os.path.join(root, "plot_integrate.log"))
if not os.path.isfile(integrate_hkl):
print >> decilog, " Integration failed."
return
# Make _noscale.HKL if needed
if params.no_scaling:
bk_prefix = make_backup(("XDS.INP", ), wdir=root, quiet=True)
xparm_obj = XPARM(xparm)
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "CORRECT"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", "50"),
("REFINE(CORRECT)", ""),
("UNIT_CELL_CONSTANTS", " ".join(
map(lambda x: "%.3f" % x, xparm_obj.unit_cell))),
("SPACE_GROUP_NUMBER", "%d" % xparm_obj.spacegroup),
])
print >> decilog, " running CORRECT without empirical scaling"
run_xds(wdir=root, show_progress=params.show_progress)
for f in xds_files.generated_by_CORRECT + ("XDS.INP", ):
ff = os.path.join(root, f)
if not os.path.isfile(ff): continue
if ff.endswith(".cbf"):
os.remove(ff)
else:
os.rename(ff, ff + "_noscale")
revert_files(("XDS.INP", ), bk_prefix, wdir=root, quiet=True)
# Run pointless
symm_by_integrate = None
if params.use_pointless:
worker = Pointless()
result = worker.run_for_symm(xdsin=integrate_hkl,
logout=os.path.join(
root, "pointless_integrate.log"))
if "symm" in result:
symm = result["symm"]
print >> decilog, " pointless using INTEGRATE.HKL suggested", symm.space_group_info(
)
sgnum = symm.space_group_info().type().number()
cell = " ".join(
map(lambda x: "%.2f" % x,
symm.unit_cell().parameters()))
modify_xdsinp(xdsinp,
inp_params=[("SPACE_GROUP_NUMBER", "%d" % sgnum),
("UNIT_CELL_CONSTANTS", cell)])
symm_by_integrate = symm
else:
print >> decilog, " pointless failed."
# Do Scaling
modify_xdsinp(xdsinp, inp_params=[
("JOB", "CORRECT"),
])
run_xds(wdir=root, show_progress=params.show_progress)
if not os.path.isfile(gxparm):
print >> decilog, " Scaling failed."
return
print >> decilog, " OK. ISa= %.2f" % correctlp.get_ISa(correct_lp,
check_valid=True)
ret = calc_merging_stats(os.path.join(root, "XDS_ASCII.HKL"))
if params.cut_resolution:
if ret is not None and ret[0] is not None:
d_min = ret[0]
modify_xdsinp(xdsinp,
inp_params=[("JOB", "CORRECT"),
("INCLUDE_RESOLUTION_RANGE",
"50 %.2f" % d_min)])
print >> decilog, " Re-scale at %.2f A" % d_min
os.rename(os.path.join(root, "CORRECT.LP"),
os.path.join(root, "CORRECT_fullres.LP"))
os.rename(os.path.join(root, "XDS_ASCII.HKL"),
os.path.join(root, "XDS_ASCII_fullres.HKL"))
run_xds(wdir=root, show_progress=params.show_progress)
print >> decilog, " OK. ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
print >> decilog, " (Original files are saved as *_fullres.*)"
else:
print >> decilog, "error: Can't decide resolution."
last_ISa = correctlp.get_ISa(correct_lp, check_valid=True)
# Run pointless and (if result is different from INTEGRATE) re-scale.
if params.use_pointless:
worker = Pointless()
result = worker.run_for_symm(xdsin=xac_hkl,
logout=os.path.join(
root, "pointless_correct.log"))
if "symm" in result:
symm = result["symm"]
need_rescale = False
if symm_by_integrate is not None:
if not xtal.is_same_laue_symmetry(
symm_by_integrate.space_group(), symm.space_group()):
print >> decilog, "pointless suggested %s, which is different Laue symmetry from INTEGRATE.HKL (%s)" % (
symm.space_group_info(),
symm_by_integrate.space_group_info())
need_rescale = True
else:
print >> decilog, "pointless using XDS_ASCII.HKL suggested %s" % symm.space_group_info(
)
need_rescale = True
if need_rescale:
# make backup, and do correct and compare ISa
# if ISa got worse, revert the result.
backup_needed = ("XDS.INP", "XDS_ASCII_fullres.HKL",
"CORRECT_fullres.LP", "merging_stats.pkl",
"merging_stats.log")
backup_needed += xds_files.generated_by_CORRECT
bk_prefix = make_backup(backup_needed, wdir=root, quiet=True)
sgnum = symm.space_group_info().type().number()
cell = " ".join(
map(lambda x: "%.2f" % x,
symm.unit_cell().parameters()))
modify_xdsinp(xdsinp,
inp_params=[("JOB", "CORRECT"),
("SPACE_GROUP_NUMBER", "%d" % sgnum),
("UNIT_CELL_CONSTANTS", cell),
("INCLUDE_RESOLUTION_RANGE", "50 0")
])
run_xds(wdir=root, show_progress=params.show_progress)
ret = calc_merging_stats(os.path.join(root, "XDS_ASCII.HKL"))
if params.cut_resolution:
if ret is not None and ret[0] is not None:
d_min = ret[0]
modify_xdsinp(xdsinp,
inp_params=[("JOB", "CORRECT"),
("INCLUDE_RESOLUTION_RANGE",
"50 %.2f" % d_min)])
print >> decilog, " Re-scale at %.2f A" % d_min
os.rename(os.path.join(root, "CORRECT.LP"),
os.path.join(root, "CORRECT_fullres.LP"))
os.rename(os.path.join(root, "XDS_ASCII.HKL"),
os.path.join(root, "XDS_ASCII_fullres.HKL"))
run_xds(wdir=root, show_progress=params.show_progress)
print >> decilog, " OK. ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
print >> decilog, " (Original files are saved as *_fullres.*)"
else:
print >> decilog, "error: Can't decide resolution."
for f in ("CORRECT_fullres.LP",
"XDS_ASCII_fullres.HKL"):
if os.path.isfile(os.path.join(root, f)):
print >> decilog, "removing", f
os.remove(os.path.join(root, f))
ISa = correctlp.get_ISa(correct_lp, check_valid=True)
if ISa >= last_ISa or last_ISa != last_ISa: # if improved or last_ISa is nan
print >> decilog, "ISa improved= %.2f" % ISa
remove_backups(backup_needed, bk_prefix, wdir=root)
else:
print >> decilog, "ISa got worse= %.2f" % ISa
for f in backup_needed:
if os.path.isfile(os.path.join(root, f)):
os.remove(os.path.join(root, f))
revert_files(backup_needed,
bk_prefix,
wdir=root,
quiet=True)
run_xdsstat(wdir=root)
print
if params.make_report: html_report.make_individual_report(root, root)
print >> decilog, "xds_sequence finished at %s\n" % time.strftime(
"%Y-%m-%d %H:%M:%S")
decilog.close()
def try_indexing_hard(wdir,
show_progress,
decilog,
known_sgnum=None,
known_cell=None,
tol_length=None,
tol_angle=None):
idxref_lp = os.path.join(wdir, "IDXREF.LP")
xdsinp = os.path.join(wdir, "XDS.INP")
lp_org = idxreflp.IdxrefLp(idxref_lp)
if lp_org.is_cell_maybe_half():
backup_needed = ("XDS.INP", ) + xds_files.generated_by_IDXREF
print >> decilog, " !! Cell may be halved. Trying doubled cell."
bk_prefix = make_backup(backup_needed, wdir=wdir, quiet=True)
cell = lp_org.deduce_correct_cell_based_on_integerness()
cell = " ".join(map(lambda x: "%.2f" % x, cell.parameters()))
modify_xdsinp(xdsinp,
inp_params=[("JOB", "IDXREF"),
("SPACE_GROUP_NUMBER", "1"),
("UNIT_CELL_CONSTANTS", cell)])
run_xds(wdir=wdir, show_progress=show_progress)
if idxreflp.IdxrefLp(idxref_lp).is_cell_maybe_half():
revert_files(backup_needed, bk_prefix, wdir=wdir, quiet=True)
print >> decilog, " .. not solved. Next, try decreasing SEPMIN= and CLUSTER_RADIUS=."
bk_prefix = make_backup(backup_needed, wdir=wdir, quiet=True)
modify_xdsinp(xdsinp,
inp_params=[("JOB", "IDXREF"), ("SEPMIN", "4"),
("CLUSTER_RADIUS", "2")])
run_xds(wdir=wdir, show_progress=show_progress)
if idxreflp.IdxrefLp(idxref_lp).is_cell_maybe_half():
print >> decilog, " .. not solved. Give up."
revert_files(backup_needed, bk_prefix, wdir=wdir, quiet=True)
else:
print >> decilog, " Now OK."
remove_backups(backup_needed, bk_prefix, wdir=wdir)
modify_xdsinp(xdsinp, inp_params=[
("SPACE_GROUP_NUMBER", "0"),
])
# If Cell hint exists, try to use it..
if known_sgnum > 0:
flag_try_cell_hint = False
xparm = os.path.join(wdir, "XPARM.XDS")
if not os.path.isfile(xparm):
flag_try_cell_hint = True
else:
xsxds = XPARM(xparm).crystal_symmetry()
xsref = crystal.symmetry(known_cell, known_sgnum)
cosets = reindex.reindexing_operators(xsref, xsxds, tol_length,
tol_angle)
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,
known_cell))),
("SPACE_GROUP_NUMBER", "%d" % known_sgnum),
])
run_xds(wdir=wdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[
("SPACE_GROUP_NUMBER", "0"),
])
def run(params, out):
print >> out, "Frames:", params.frames
backup_needed = xds_files.generated_by_DEFPIX + (
"XDS.INP",
"BKGINIT.cbf",
)
bk_prefix = make_backup(backup_needed, wdir=params.xdsdir)
ret = {} # {frame: [matches, spots, predicted]}
try:
# run DEFPIX to limit resolution.
modify_xdsinp(os.path.join(params.xdsdir, "XDS.INP"),
[("JOB", "DEFPIX"),
("INCLUDE_RESOLUTION_RANGE", "50 %.2f" % params.d_min)])
p = subprocess.Popen("xds", cwd=params.xdsdir)
p.wait()
# copy BKGPIX.cbf -> BKGINIT.cbf (for COLSPOT)
shutil.copyfile(os.path.join(params.xdsdir, "BKGPIX.cbf"),
os.path.join(params.xdsdir, "BKGINIT.cbf"))
for frame in params.frames:
print >> out, "Frame %d" % frame
print >> out, "====================\n"
# search spots
if params.spotfinder == "xds":
spotxds = get_colspot_result(frame_ranges=[
[frame, frame],
],
wdir=params.xdsdir)
spots = map(lambda x: x[:2],
spotxds.collected_spots(with_resolution=False))
else:
raise "Sorry!"
# run INTEGRATE to collect predicted coords
integrate_results = xds_predict_mitai.run(
param_source=os.path.join(params.xdsdir, "XPARM.XDS"),
frame_num=frame,
wdir=params.xdsdir,
need_adx=False,
sigmar=params.sigmar,
sigmab=params.sigmab)
# read predicted coords
tmp = filter(lambda x: x.endswith(".HKL"), integrate_results)
if len(tmp) == 0:
print >> out, "Integration failed!"
ret[frame] = (0, len(spots), 0)
continue
integrate_hkl = tmp[0]
cols = integrate_hkl_as_flex.reader(integrate_hkl, [],
False).get_column_names()
i_xcal, i_ycal = cols.index("XCAL"), cols.index("YCAL")
predicted = []
for l in open(integrate_hkl):
if l.startswith("!"): continue
sp = l.split()
predicted.append(map(float, (sp[i_xcal], sp[i_ycal])))
# compare them
nmatch = calc_matches(
spots, predicted, params.distance_limit_in_px,
open(
os.path.join(params.xdsdir,
"matched_predicted_%.4d.adx" % frame), "w"))
#nmatch = calc_matches(predicted, spots, params.distance_limit_in_px,
# open(os.path.join(params.xdsdir, "matched_located_%.4d.adx"%frame), "w"))
ret[frame] = (nmatch, len(spots), len(predicted))
finally:
revert_files(backup_needed, bk_prefix, wdir=params.xdsdir)
print >> out
for frame in sorted(ret):
nmatch, nspots, npredicted = ret[frame]
print >> out, "Frame %4d Located/Predicted: %d/%d= %.2f%%" % (
frame, nmatch, npredicted, 100. * float(nmatch) /
npredicted if npredicted > 0 else float("nan"))
print >> out, "Frame %4d Predicted/Located: %d/%d= %.2f%%" % (
frame, nmatch, nspots,
100. * float(nmatch) / nspots if nspots > 0 else float("nan"))
print >> out
return ret
def xds_sequence(root, params):
print
print os.path.relpath(root, params.topdir)
init_lp = os.path.join(root, "INIT.LP")
xparm = os.path.join(root, "XPARM.XDS")
gxparm = os.path.join(root, "GXPARM.XDS")
defpix_lp = os.path.join(root, "DEFPIX.LP")
correct_lp = os.path.join(root, "CORRECT.LP")
integrate_hkl = os.path.join(root, "INTEGRATE.HKL")
xac_hkl = os.path.join(root, "XDS_ASCII.HKL")
integrate_lp = os.path.join(root, "INTEGRATE.LP")
spot_xds = os.path.join(root, "SPOT.XDS")
xdsinp = os.path.join(root, "XDS.INP")
assert os.path.isfile(xdsinp)
if params.cell_prior.force: assert params.cell_prior.check
xdsinp_dict = dict(get_xdsinp_keyword(xdsinp))
if params.cell_prior.sgnum > 0:
xs_prior = crystal.symmetry(params.cell_prior.cell,
params.cell_prior.sgnum)
else:
xs_prior = None
decilog = multi_out()
decilog.register("log",
open(os.path.join(root, "decision.log"), "a"),
atexit_send_to=None)
try:
print >> decilog, "xds_sequence started at %s in %s\n" % (
time.strftime("%Y-%m-%d %H:%M:%S"), root)
if not kamo_test_installation.tst_xds():
print >> decilog, "XDS is not installed or expired!!"
return
if params.show_progress:
decilog.register("stdout", sys.stdout)
if params.mode == "initial" and params.resume and os.path.isfile(
correct_lp):
print >> decilog, " Already processed."
return
if params.mode == "recycle" and not os.path.isfile(gxparm):
print >> decilog, "GXPARM.XDS not found. Cannot do recycle."
return
if params.fast_delphi and (params.nproc is None or params.nproc > 1):
delphi = optimal_delphi_by_nproc(xdsinp=xdsinp, nproc=params.nproc)
print >> decilog, " Setting delphi to ", delphi
modify_xdsinp(xdsinp, inp_params=[
("DELPHI", str(delphi)),
])
if params.nproc is not None and params.nproc > 1:
modify_xdsinp(xdsinp,
inp_params=[
("MAXIMUM_NUMBER_OF_PROCESSORS",
str(params.nproc)),
])
if params.mode == "initial":
modify_xdsinp(xdsinp, inp_params=[("JOB", "XYCORR INIT")])
run_xds(wdir=root, show_progress=params.show_progress)
initlp = InitLp(init_lp)
first_bad = initlp.check_bad_first_frames()
if first_bad:
print >> decilog, " first frames look bad (too weak) exposure:", first_bad
new_data_range = map(
int,
dict(get_xdsinp_keyword(xdsinp))["DATA_RANGE"].split())
new_data_range[0] = first_bad[-1] + 1
print >> decilog, " changing DATA_RANGE= to", new_data_range
modify_xdsinp(xdsinp,
inp_params=[("JOB", "INIT"),
("DATA_RANGE",
"%d %d" % tuple(new_data_range))])
for f in xds_files.generated_by_INIT:
util.rotate_file(os.path.join(root, f), copy=False)
run_xds(wdir=root, show_progress=params.show_progress)
# Peak search
modify_xdsinp(xdsinp, inp_params=[("JOB", "COLSPOT")])
run_xds(wdir=root, show_progress=params.show_progress)
if params.auto_frame_exclude_spot_based:
sx = idxreflp.SpotXds(spot_xds)
sx.set_xdsinp(xdsinp)
spots = filter(lambda x: 5 < x[-1] < 30,
sx.collected_spots()) # low-res (5 A)
frame_numbers = numpy.array(map(lambda x: int(x[2]) + 1,
spots))
data_range = map(
int,
dict(get_xdsinp_keyword(xdsinp))["DATA_RANGE"].split())
# XXX this assumes SPOT_RANGE equals to DATA_RANGE. Is this guaranteed?
h = numpy.histogram(frame_numbers,
bins=numpy.arange(data_range[0],
data_range[1] + 2,
step=1))
q14 = numpy.percentile(h[0], [25, 75])
iqr = q14[1] - q14[0]
cutoff = max(
h[0][h[0] <= iqr * 1.5 + q14[1]]) / 5 # magic number
print >> decilog, "DEBUG:: IQR= %.2f, Q1/4= %s, cutoff= %.2f" % (
iqr, q14, cutoff)
cut_frames = h[1][h[0] < cutoff]
keep_frames = h[1][h[0] >= cutoff]
print >> decilog, "DEBUG:: keep_frames=", keep_frames
print >> decilog, "DEBUG:: cut_frames=", cut_frames
if len(cut_frames) > 0:
cut_ranges = [
[cut_frames[0], cut_frames[0]],
]
for fn in cut_frames:
if fn - cut_ranges[-1][1] <= 1: cut_ranges[-1][1] = fn
else: cut_ranges.append([fn, fn])
# Edit XDS.INP
cut_inp_str = "".join(
map(
lambda x: "EXCLUDE_DATA_RANGE= %6d %6d\n" % tuple(
x), cut_ranges))
open(xdsinp, "a").write("\n" + cut_inp_str)
# Edit SPOT.XDS
shutil.copyfile(spot_xds, spot_xds + ".org")
sx.write(open(spot_xds, "w"),
frame_selection=set(keep_frames))
# Indexing
if params.cell_prior.method == "use_first":
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "IDXREF"),
("UNIT_CELL_CONSTANTS", " ".join(
map(lambda x: "%.3f" % x,
params.cell_prior.cell))),
("SPACE_GROUP_NUMBER",
"%d" % params.cell_prior.sgnum),
])
else:
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF")])
run_xds(wdir=root, show_progress=params.show_progress)
print >> decilog, "" # TODO indexing stats like indexed percentage here.
if params.tryhard:
try_indexing_hard(root,
params.show_progress,
decilog,
known_sgnum=params.cell_prior.sgnum,
known_cell=params.cell_prior.cell,
tol_length=params.cell_prior.tol_length,
tol_angle=params.cell_prior.tol_angle)
if not os.path.isfile(xparm):
print >> decilog, " Indexing failed."
return
if params.cell_prior.sgnum > 0:
# Check anyway
xsxds = XPARM(xparm).crystal_symmetry()
cosets = reindex.reindexing_operators(
xs_prior, xsxds, params.cell_prior.tol_length,
params.cell_prior.tol_angle)
if cosets.double_cosets is None:
if params.cell_prior.check:
print >> decilog, " Incompatible cell. Indexing failed."
return
else:
print >> decilog, " Warning: Incompatible cell."
elif params.cell_prior.method == "symm_constraint_only":
cell = xsxds.unit_cell().change_basis(
cosets.combined_cb_ops()[0])
print >> decilog, " Trying symmetry-constrained cell parameter:", cell
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "IDXREF"),
("UNIT_CELL_CONSTANTS", " ".join(
map(lambda x: "%.3f" % x,
cell.parameters()))),
("SPACE_GROUP_NUMBER",
"%d" % params.cell_prior.sgnum),
])
for f in xds_files.generated_by_IDXREF:
util.rotate_file(os.path.join(root, f),
copy=(f == "SPOT.XDS"))
run_xds(wdir=root, show_progress=params.show_progress)
if not os.path.isfile(xparm):
print >> decilog, " Indexing failed."
return
# Check again
xsxds = XPARM(xparm).crystal_symmetry()
if not xsxds.unit_cell().is_similar_to(
xs_prior.unit_cell(), params.cell_prior.tol_length,
params.cell_prior.tol_angle):
print >> decilog, " Resulted in different cell. Indexing failed."
return
elif params.mode == "recycle":
print >> decilog, " Start recycle. original ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
for f in xds_files.generated_after_DEFPIX + ("XPARM.XDS",
"plot_integrate.log"):
util.rotate_file(os.path.join(root, f), copy=True)
shutil.copyfile(gxparm + ".1", xparm)
else:
raise "Unknown mode (%s)" % params.mode
# To Integration
modify_xdsinp(xdsinp,
inp_params=[("JOB", "DEFPIX INTEGRATE"),
("INCLUDE_RESOLUTION_RANGE", "50 0")])
run_xds(wdir=root, show_progress=params.show_progress)
if os.path.isfile(integrate_lp):
xds_plot_integrate.run(integrate_lp,
os.path.join(root, "plot_integrate.log"))
if not os.path.isfile(integrate_hkl):
print >> decilog, " Integration failed."
return
# Make _noscale.HKL if needed
if params.no_scaling:
bk_prefix = make_backup(("XDS.INP", ), wdir=root, quiet=True)
xparm_obj = XPARM(xparm)
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "CORRECT"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", "50"),
("REFINE(CORRECT)", ""),
("UNIT_CELL_CONSTANTS", " ".join(
map(lambda x: "%.3f" % x,
xparm_obj.unit_cell))),
("SPACE_GROUP_NUMBER",
"%d" % xparm_obj.spacegroup),
])
print >> decilog, " running CORRECT without empirical scaling"
run_xds(wdir=root, show_progress=params.show_progress)
for f in xds_files.generated_by_CORRECT + ("XDS.INP", ):
ff = os.path.join(root, f)
if not os.path.isfile(ff): continue
if ff.endswith(".cbf"):
os.remove(ff)
else:
os.rename(ff, ff + "_noscale")
revert_files(("XDS.INP", ), bk_prefix, wdir=root, quiet=True)
# Run pointless
pointless_integrate = {}
if params.use_pointless:
worker = Pointless()
pointless_integrate = worker.run_for_symm(
xdsin=integrate_hkl,
logout=os.path.join(root, "pointless_integrate.log"))
if "symm" in pointless_integrate:
symm = pointless_integrate["symm"]
print >> decilog, " pointless using INTEGRATE.HKL suggested", symm.space_group_info(
)
if xs_prior:
if xtal.is_same_space_group_ignoring_enantiomorph(
symm.space_group(), xs_prior.space_group()):
print >> decilog, " which is consistent with given symmetry."
elif xtal.is_same_laue_symmetry(symm.space_group(),
xs_prior.space_group()):
print >> decilog, " which has consistent Laue symmetry with given symmetry."
else:
print >> decilog, " which is inconsistent with given symmetry."
sgnum = symm.space_group_info().type().number()
cell = " ".join(
map(lambda x: "%.2f" % x,
symm.unit_cell().parameters()))
modify_xdsinp(xdsinp,
inp_params=[("SPACE_GROUP_NUMBER", "%d" % sgnum),
("UNIT_CELL_CONSTANTS", cell)])
else:
print >> decilog, " pointless failed."
flag_do_not_change_symm = False
if xs_prior and params.cell_prior.force:
modify_xdsinp(xdsinp,
inp_params=[("UNIT_CELL_CONSTANTS", " ".join(
map(lambda x: "%.3f" % x,
params.cell_prior.cell))),
("SPACE_GROUP_NUMBER",
"%d" % params.cell_prior.sgnum)])
flag_do_not_change_symm = True
elif params.cell_prior.method == "correct_only":
xsxds = XPARM(xparm).crystal_symmetry()
cosets = reindex.reindexing_operators(xs_prior, xsxds,
params.cell_prior.tol_length,
params.cell_prior.tol_angle)
if cosets.double_cosets is not None:
cell = xsxds.unit_cell().change_basis(
cosets.combined_cb_ops()[0])
print >> decilog, " Using given symmetry in CORRECT with symmetry constraints:", cell
modify_xdsinp(xdsinp,
inp_params=[
("UNIT_CELL_CONSTANTS", " ".join(
map(lambda x: "%.3f" % x,
cell.parameters()))),
("SPACE_GROUP_NUMBER",
"%d" % params.cell_prior.sgnum),
])
flag_do_not_change_symm = True
else:
print >> decilog, " Tried to use given symmetry in CORRECT, but cell in integration is incompatible."
# Do Scaling
modify_xdsinp(xdsinp, inp_params=[
("JOB", "CORRECT"),
])
run_xds(wdir=root, show_progress=params.show_progress)
if not os.path.isfile(xac_hkl):
print >> decilog, " CORRECT failed."
return
if not os.path.isfile(gxparm):
print >> decilog, " Refinement in CORRECT failed."
print >> decilog, " OK. ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
ret = calc_merging_stats(xac_hkl)
if params.cut_resolution:
if ret is not None and ret[0] is not None:
d_min = ret[0]
modify_xdsinp(xdsinp,
inp_params=[("JOB", "CORRECT"),
("INCLUDE_RESOLUTION_RANGE",
"50 %.2f" % d_min)])
print >> decilog, " Re-scale at %.2f A" % d_min
os.rename(os.path.join(root, "CORRECT.LP"),
os.path.join(root, "CORRECT_fullres.LP"))
os.rename(xac_hkl, os.path.join(root, "XDS_ASCII_fullres.HKL"))
run_xds(wdir=root, show_progress=params.show_progress)
print >> decilog, " OK. ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
print >> decilog, " (Original files are saved as *_fullres.*)"
else:
print >> decilog, "error: Can't decide resolution."
last_ISa = correctlp.get_ISa(correct_lp, check_valid=True)
# Run pointless and (if result is different from INTEGRATE) re-scale.
if params.use_pointless:
worker = Pointless()
pointless_correct = worker.run_for_symm(
xdsin=xac_hkl,
logout=os.path.join(root, "pointless_correct.log"))
pointless_best_symm = None
if "symm" in pointless_correct:
symm = pointless_correct["symm"]
need_rescale = False
if pointless_integrate.get("symm"):
symm_by_integrate = pointless_integrate["symm"]
if not xtal.is_same_laue_symmetry(
symm_by_integrate.space_group(),
symm.space_group()):
print >> decilog, "pointless suggested %s, which is different Laue symmetry from INTEGRATE.HKL (%s)" % (
symm.space_group_info(),
symm_by_integrate.space_group_info())
prob_integrate = pointless_integrate.get(
"laue_prob", float("nan"))
prob_correct = pointless_correct.get(
"laue_prob", float("nan"))
print >> decilog, " Prob(%s |INTEGRATE), Prob(%s |CORRECT) = %.4f, %.4f." % (
symm_by_integrate.space_group_info(),
symm.space_group_info(), prob_integrate,
prob_correct)
if prob_correct > prob_integrate:
need_rescale = True
pointless_best_symm = symm
else:
pointless_best_symm = symm_by_integrate
else:
need_rescale = True
pointless_best_symm = symm
print >> decilog, "pointless using XDS_ASCII.HKL suggested %s" % symm.space_group_info(
)
if xs_prior:
if xtal.is_same_space_group_ignoring_enantiomorph(
symm.space_group(), xs_prior.space_group()):
print >> decilog, " which is consistent with given symmetry."
elif xtal.is_same_laue_symmetry(
symm.space_group(), xs_prior.space_group()):
print >> decilog, " which has consistent Laue symmetry with given symmetry."
else:
print >> decilog, " which is inconsistent with given symmetry."
if need_rescale and not flag_do_not_change_symm:
sgnum = symm.space_group_info().type().number()
cell = " ".join(
map(lambda x: "%.2f" % x,
symm.unit_cell().parameters()))
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "CORRECT"),
("SPACE_GROUP_NUMBER", "%d" % sgnum),
("UNIT_CELL_CONSTANTS", cell),
("INCLUDE_RESOLUTION_RANGE", "50 0")
])
run_xds(wdir=root, show_progress=params.show_progress)
ret = calc_merging_stats(xac_hkl)
if params.cut_resolution:
if ret is not None and ret[0] is not None:
d_min = ret[0]
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "CORRECT"),
("INCLUDE_RESOLUTION_RANGE",
"50 %.2f" % d_min)
])
print >> decilog, " Re-scale at %.2f A" % d_min
os.rename(os.path.join(root, "CORRECT.LP"),
os.path.join(root, "CORRECT_fullres.LP"))
os.rename(
xac_hkl,
os.path.join(root, "XDS_ASCII_fullres.HKL"))
run_xds(wdir=root,
show_progress=params.show_progress)
print >> decilog, " OK. ISa= %.2f" % correctlp.get_ISa(
correct_lp, check_valid=True)
print >> decilog, " (Original files are saved as *_fullres.*)"
else:
print >> decilog, "error: Can't decide resolution."
for f in ("CORRECT_fullres.LP",
"XDS_ASCII_fullres.HKL"):
if os.path.isfile(os.path.join(root, f)):
print >> decilog, "removing", f
os.remove(os.path.join(root, f))
ISa = correctlp.get_ISa(correct_lp, check_valid=True)
if ISa >= last_ISa or last_ISa != last_ISa: # if improved or last_ISa is nan
print >> decilog, "ISa improved= %.2f" % ISa
else:
print >> decilog, "ISa got worse= %.2f" % ISa
if pointless_best_symm:
xac_symm = XDS_ASCII(xac_hkl, read_data=False).symm
if not xtal.is_same_space_group_ignoring_enantiomorph(
xac_symm.space_group(),
pointless_best_symm.space_group()):
if xtal.is_same_laue_symmetry(
xac_symm.space_group(),
pointless_best_symm.space_group()):
tmp = "same Laue symmetry"
else:
tmp = "different Laue symmetry"
print >> decilog, "WARNING: symmetry in scaling is different from Pointless result (%s)." % tmp
run_xdsstat(wdir=root)
print
if params.make_report: html_report.make_individual_report(root, root)
except:
print >> decilog, traceback.format_exc()
finally:
print >> decilog, "\nxds_sequence finished at %s" % time.strftime(
"%Y-%m-%d %H:%M:%S")
decilog.close()
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 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(root, params):
print
print os.path.relpath(root, params.topdir)
xparm = os.path.join(root, "XPARM.XDS")
gxparm = os.path.join(root, "GXPARM.XDS")
defpix_lp = os.path.join(root, "DEFPIX.LP")
correct_lp = os.path.join(root, "CORRECT.LP")
integrate_hkl = os.path.join(root, "INTEGRATE.HKL")
xac_hkl = os.path.join(root, "XDS_ASCII.HKL")
integrate_lp = os.path.join(root, "INTEGRATE.LP")
xdsinp = os.path.join(root, "XDS.INP")
assert os.path.isfile(xdsinp)
decilog = multi_out()
decilog.register("log", open(os.path.join(root, "decision.log"), "a"), atexit_send_to=None)
print >>decilog, "xds_sequence started at %s in %s\n" % (time.strftime("%Y-%m-%d %H:%M:%S"), root)
if params.show_progress:
decilog.register("stdout", sys.stdout)
if params.mode=="initial" and params.resume and os.path.isfile(correct_lp):
print " Already processed."
return
if params.mode == "recycle" and not os.path.isfile(gxparm):
print "GXPARM.XDS not found. Cannot do recycle."
return
if params.fast_delphi and (params.nproc is None or params.nproc > 1):
delphi = optimal_delphi_by_nproc(xdsinp=xdsinp, nproc=params.nproc)
print " Setting delphi to ", delphi
modify_xdsinp(xdsinp, inp_params=[("DELPHI", str(delphi)),
])
if params.nproc is not None and params.nproc > 1:
modify_xdsinp(xdsinp, inp_params=[("MAXIMUM_NUMBER_OF_PROCESSORS", str(params.nproc)),
])
if params.mode == "initial":
# To Indexing
modify_xdsinp(xdsinp, inp_params=[("JOB", "XYCORR INIT COLSPOT IDXREF")])
run_xds(wdir=root, show_progress=params.show_progress)
print # indexing stats like indexed percentage here.
if params.tryhard:
try_indexing_hard(root, params.show_progress, decilog,
known_sgnum=params.cell_prior.sgnum,
known_cell=params.cell_prior.cell,
tol_length=params.cell_prior.tol_length,
tol_angle=params.cell_prior.tol_angle)
if not os.path.isfile(xparm):
print >>decilog, " Indexing failed."
return
if params.cell_prior.check and params.cell_prior.sgnum > 0:
xsxds = XPARM(xparm).crystal_symmetry()
xsref = crystal.symmetry(params.cell_prior.cell, params.cell_prior.sgnum)
cosets = reindex.reindexing_operators(xsref, xsxds,
params.cell_prior.tol_length, params.cell_prior.tol_angle)
if cosets.double_cosets is None:
print >>decilog, " Incompatible cell. Indexing failed."
return
elif params.mode == "recycle":
print " Start recycle. original ISa= %.2f" % correctlp.get_ISa(correct_lp, check_valid=True)
for f in xds_files.generated_after_DEFPIX + ("XPARM.XDS", "plot_integrate.log"):
util.rotate_file(os.path.join(root, f), copy=True)
shutil.copyfile(gxparm+".1", xparm)
else:
raise "Unknown mode (%s)" % params.mode
# To Integration
modify_xdsinp(xdsinp, inp_params=[("JOB", "DEFPIX INTEGRATE"),
("INCLUDE_RESOLUTION_RANGE", "50 0")])
run_xds(wdir=root, show_progress=params.show_progress)
if os.path.isfile(integrate_lp):
xds_plot_integrate.run(integrate_lp, os.path.join(root, "plot_integrate.log"))
if not os.path.isfile(integrate_hkl):
print >>decilog, " Integration failed."
return
# Make _noscale.HKL if needed
if params.no_scaling:
bk_prefix = make_backup(("XDS.INP",), wdir=root, quiet=True)
xparm_obj = XPARM(xparm)
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),
("CORRECTIONS", ""),
("NBATCH", "1"),
("MINIMUM_I/SIGMA", "50"),
("REFINE(CORRECT)", ""),
("UNIT_CELL_CONSTANTS", " ".join(map(lambda x:"%.3f"%x, xparm_obj.unit_cell))),
("SPACE_GROUP_NUMBER", "%d"%xparm_obj.spacegroup),])
print >>decilog, " running CORRECT without empirical scaling"
run_xds(wdir=root, show_progress=params.show_progress)
for f in xds_files.generated_by_CORRECT + ("XDS.INP",):
ff = os.path.join(root, f)
if not os.path.isfile(ff): continue
if ff.endswith(".cbf"):
os.remove(ff)
else:
os.rename(ff, ff+"_noscale")
revert_files(("XDS.INP",), bk_prefix, wdir=root, quiet=True)
# Run pointless
symm_by_integrate = None
if params.use_pointless:
worker = Pointless()
result = worker.run_for_symm(xdsin=integrate_hkl,
logout=os.path.join(root, "pointless_integrate.log"))
if "symm" in result:
symm = result["symm"]
print >>decilog, " pointless using INTEGRATE.HKL suggested", symm.space_group_info()
sgnum = symm.space_group_info().type().number()
cell = " ".join(map(lambda x:"%.2f"%x, symm.unit_cell().parameters()))
modify_xdsinp(xdsinp, inp_params=[("SPACE_GROUP_NUMBER", "%d"%sgnum),
("UNIT_CELL_CONSTANTS", cell)])
symm_by_integrate = symm
else:
print >>decilog, " pointless failed."
# Do Scaling
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),])
run_xds(wdir=root, show_progress=params.show_progress)
if not os.path.isfile(gxparm):
print >>decilog, " Scaling failed."
return
print >>decilog, " OK. ISa= %.2f" % correctlp.get_ISa(correct_lp, check_valid=True)
ret = calc_merging_stats(os.path.join(root, "XDS_ASCII.HKL"))
if params.cut_resolution:
if ret is not None and ret[0] is not None:
d_min = ret[0]
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),
("INCLUDE_RESOLUTION_RANGE", "50 %.2f"%d_min)])
print >>decilog, " Re-scale at %.2f A" % d_min
os.rename(os.path.join(root, "CORRECT.LP"), os.path.join(root, "CORRECT_fullres.LP"))
os.rename(os.path.join(root, "XDS_ASCII.HKL"), os.path.join(root, "XDS_ASCII_fullres.HKL"))
run_xds(wdir=root, show_progress=params.show_progress)
print >>decilog, " OK. ISa= %.2f" % correctlp.get_ISa(correct_lp, check_valid=True)
print >>decilog, " (Original files are saved as *_fullres.*)"
else:
print >>decilog, "error: Can't decide resolution."
last_ISa = correctlp.get_ISa(correct_lp, check_valid=True)
# Run pointless and (if result is different from INTEGRATE) re-scale.
if params.use_pointless:
worker = Pointless()
result = worker.run_for_symm(xdsin=xac_hkl,
logout=os.path.join(root, "pointless_correct.log"))
if "symm" in result:
symm = result["symm"]
need_rescale = False
if symm_by_integrate is not None:
if not xtal.is_same_laue_symmetry(symm_by_integrate.space_group(), symm.space_group()):
print >>decilog, "pointless suggested %s, which is different Laue symmetry from INTEGRATE.HKL (%s)" % (symm.space_group_info(), symm_by_integrate.space_group_info())
need_rescale = True
else:
print >>decilog, "pointless using XDS_ASCII.HKL suggested %s" % symm.space_group_info()
need_rescale = True
if need_rescale:
# make backup, and do correct and compare ISa
# if ISa got worse, revert the result.
backup_needed = ("XDS.INP", "XDS_ASCII_fullres.HKL","CORRECT_fullres.LP",
"merging_stats.pkl","merging_stats.log")
backup_needed += xds_files.generated_by_CORRECT
bk_prefix = make_backup(backup_needed, wdir=root, quiet=True)
sgnum = symm.space_group_info().type().number()
cell = " ".join(map(lambda x:"%.2f"%x, symm.unit_cell().parameters()))
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),
("SPACE_GROUP_NUMBER", "%d"%sgnum),
("UNIT_CELL_CONSTANTS", cell),
("INCLUDE_RESOLUTION_RANGE", "50 0")])
run_xds(wdir=root, show_progress=params.show_progress)
ret = calc_merging_stats(os.path.join(root, "XDS_ASCII.HKL"))
if params.cut_resolution:
if ret is not None and ret[0] is not None:
d_min = ret[0]
modify_xdsinp(xdsinp, inp_params=[("JOB", "CORRECT"),
("INCLUDE_RESOLUTION_RANGE", "50 %.2f"%d_min)])
print >>decilog, " Re-scale at %.2f A" % d_min
os.rename(os.path.join(root, "CORRECT.LP"), os.path.join(root, "CORRECT_fullres.LP"))
os.rename(os.path.join(root, "XDS_ASCII.HKL"), os.path.join(root, "XDS_ASCII_fullres.HKL"))
run_xds(wdir=root, show_progress=params.show_progress)
print >>decilog, " OK. ISa= %.2f" % correctlp.get_ISa(correct_lp, check_valid=True)
print >>decilog, " (Original files are saved as *_fullres.*)"
else:
print >>decilog, "error: Can't decide resolution."
for f in ("CORRECT_fullres.LP", "XDS_ASCII_fullres.HKL"):
if os.path.isfile(os.path.join(root, f)):
print >>decilog, "removing", f
os.remove(os.path.join(root, f))
ISa = correctlp.get_ISa(correct_lp, check_valid=True)
if ISa >= last_ISa or last_ISa!=last_ISa: # if improved or last_ISa is nan
print >>decilog, "ISa improved= %.2f" % ISa
remove_backups(backup_needed, bk_prefix, wdir=root)
else:
print >>decilog, "ISa got worse= %.2f" % ISa
for f in backup_needed:
if os.path.isfile(os.path.join(root, f)): os.remove(os.path.join(root, f))
revert_files(backup_needed, bk_prefix, wdir=root, quiet=True)
run_xdsstat(wdir=root)
print
if params.make_report: html_report.make_individual_report(root, root)
print >>decilog, "xds_sequence finished at %s\n" % time.strftime("%Y-%m-%d %H:%M:%S")
decilog.close()
def try_indexing_hard(wdir, show_progress, decilog,
known_sgnum=None, known_cell=None, tol_length=None, tol_angle=None):
idxref_lp = os.path.join(wdir, "IDXREF.LP")
xdsinp = os.path.join(wdir, "XDS.INP")
lp_org = idxreflp.IdxrefLp(idxref_lp)
if lp_org.is_cell_maybe_half():
backup_needed = ("XDS.INP",) + xds_files.generated_by_IDXREF
print >>decilog, " !! Cell may be halved. Trying doubled cell."
bk_prefix = make_backup(backup_needed, wdir=wdir, quiet=True)
cell = lp_org.deduce_correct_cell_based_on_integerness()
cell = " ".join(map(lambda x:"%.2f"%x, cell.parameters()))
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF"),
("SPACE_GROUP_NUMBER", "1"),
("UNIT_CELL_CONSTANTS", cell)
])
run_xds(wdir=wdir, show_progress=show_progress)
if idxreflp.IdxrefLp(idxref_lp).is_cell_maybe_half():
revert_files(backup_needed, bk_prefix, wdir=wdir, quiet=True)
print >>decilog, " .. not solved. Next, try decreasing SEPMIN= and CLUSTER_RADIUS=."
bk_prefix = make_backup(backup_needed, wdir=wdir, quiet=True)
modify_xdsinp(xdsinp, inp_params=[("JOB", "IDXREF"),
("SEPMIN", "4"),
("CLUSTER_RADIUS", "2")
])
run_xds(wdir=wdir, show_progress=show_progress)
if idxreflp.IdxrefLp(idxref_lp).is_cell_maybe_half():
print >>decilog, " .. not solved. Give up."
revert_files(backup_needed, bk_prefix, wdir=wdir, quiet=True)
else:
print >>decilog, " Now OK."
remove_backups(backup_needed, bk_prefix, wdir=wdir)
modify_xdsinp(xdsinp, inp_params=[("SPACE_GROUP_NUMBER", "0"),
])
# If Cell hint exists, try to use it..
if known_sgnum > 0:
flag_try_cell_hint = False
xparm = os.path.join(wdir, "XPARM.XDS")
if not os.path.isfile(xparm):
flag_try_cell_hint = True
else:
xsxds = XPARM(xparm).crystal_symmetry()
xsref = crystal.symmetry(known_cell, known_sgnum)
cosets = reindex.reindexing_operators(xsref, xsxds,
tol_length, tol_angle)
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, known_cell))),
("SPACE_GROUP_NUMBER", "%d"%known_sgnum),
])
run_xds(wdir=wdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[("SPACE_GROUP_NUMBER", "0"),
])
def run(params, out):
print >>out, "Frames:", params.frames
backup_needed = xds_files.generated_by_DEFPIX + ("XDS.INP","BKGINIT.cbf",)
bk_prefix = make_backup(backup_needed, wdir=params.xdsdir)
ret = {} # {frame: [matches, spots, predicted]}
try:
# run DEFPIX to limit resolution.
modify_xdsinp(os.path.join(params.xdsdir, "XDS.INP"),
[("JOB", "DEFPIX"), ("INCLUDE_RESOLUTION_RANGE", "50 %.2f"%params.d_min)])
p = subprocess.Popen("xds", cwd=params.xdsdir)
p.wait()
# copy BKGPIX.cbf -> BKGINIT.cbf (for COLSPOT)
shutil.copyfile(os.path.join(params.xdsdir, "BKGPIX.cbf"),
os.path.join(params.xdsdir, "BKGINIT.cbf"))
for frame in params.frames:
print >>out, "Frame %d" % frame
print >>out, "====================\n"
# search spots
if params.spotfinder == "xds":
spotxds = get_colspot_result(frame_ranges=[[frame, frame],], wdir=params.xdsdir)
spots = map(lambda x: x[:2], spotxds.collected_spots(with_resolution=False))
else:
raise "Sorry!"
# run INTEGRATE to collect predicted coords
integrate_results = xds_predict_mitai.run(param_source=os.path.join(params.xdsdir, "XPARM.XDS"),
frame_num=frame,
wdir=params.xdsdir, need_adx=False,
sigmar=params.sigmar, sigmab=params.sigmab)
# read predicted coords
tmp = filter(lambda x:x.endswith(".HKL"), integrate_results)
if len(tmp) == 0:
print >>out, "Integration failed!"
ret[frame] = (0, len(spots), 0)
continue
integrate_hkl = tmp[0]
cols = integrate_hkl_as_flex.reader(integrate_hkl, [], False).get_column_names()
i_xcal, i_ycal = cols.index("XCAL"), cols.index("YCAL")
predicted = []
for l in open(integrate_hkl):
if l.startswith("!"): continue
sp = l.split()
predicted.append(map(float, (sp[i_xcal], sp[i_ycal])))
# compare them
nmatch = calc_matches(spots, predicted, params.distance_limit_in_px,
open(os.path.join(params.xdsdir, "matched_predicted_%.4d.adx"%frame), "w"))
#nmatch = calc_matches(predicted, spots, params.distance_limit_in_px,
# open(os.path.join(params.xdsdir, "matched_located_%.4d.adx"%frame), "w"))
ret[frame] = (nmatch, len(spots), len(predicted))
finally:
revert_files(backup_needed, bk_prefix, wdir=params.xdsdir)
print >>out
for frame in sorted(ret):
nmatch, nspots, npredicted = ret[frame]
print >>out, "Frame %4d Located/Predicted: %d/%d= %.2f%%" % (frame, nmatch, npredicted,
100.*float(nmatch)/npredicted if npredicted>0 else float("nan"))
print >>out, "Frame %4d Predicted/Located: %d/%d= %.2f%%" % (frame, nmatch, nspots,
100.*float(nmatch)/nspots if nspots>0 else float("nan"))
print >>out
return ret
