def modify_xds_ascii_files(self, suffix="_reidx", cells_dat_out=None):
#ofs_lst = open("for_merge_new.lst", "w")
if cells_dat_out: cells_dat_out.write("file a b c al be ga\n")
new_files = []
print >> self.log_out, "Writing reindexed files.."
for i, (f, op) in enumerate(zip(self.xac_files, self.best_operators)):
xac = XDS_ASCII(f, read_data=False)
if op.is_identity_op():
new_files.append(f)
if cells_dat_out:
cell = xac.symm.unit_cell().parameters()
cells_dat_out.write(
f + " " + " ".join(map(lambda x: "%7.3f" % x, cell)) +
"\n")
continue
newf = f.replace(
".HKL", suffix + ".HKL"
) if ".HKL" in f else os.path.splitext(f)[0] + suffix + ".HKL"
print >> self.log_out, "%4d %s" % (i, newf)
cell_tr = xac.write_reindexed(
op,
newf,
space_group=self.arrays[0].crystal_symmetry().space_group())
#ofs_lst.write(newf+"\n")
new_files.append(newf)
if cells_dat_out:
cells_dat_out.write(newf + " " + " ".join(
map(lambda x: "%7.3f" % x, cell_tr.parameters())) + "\n")
return new_files
def modify_xds_ascii_files(self, suffix="_reidx", cells_dat_out=None):
#ofs_lst = open("for_merge_new.lst", "w")
if cells_dat_out: cells_dat_out.write("file a b c al be ga\n")
new_files = []
print >>self.log_out, "Writing reindexed files.."
for i, (f, op) in enumerate(zip(self.xac_files, self.best_operators)):
xac = XDS_ASCII(f, read_data=False)
if op.is_identity_op():
new_files.append(f)
if cells_dat_out:
cell = xac.symm.unit_cell().parameters()
cells_dat_out.write(f+" "+" ".join(map(lambda x:"%7.3f"%x, cell))+"\n")
continue
newf = f.replace(".HKL", suffix+".HKL") if ".HKL" in f else os.path.splitext(f)[0]+suffix+".HKL"
print >>self.log_out, "%4d %s" % (i, newf)
cell_tr = xac.write_reindexed(op, newf, space_group=self.arrays[0].crystal_symmetry().space_group())
#ofs_lst.write(newf+"\n")
new_files.append(newf)
if cells_dat_out:
cells_dat_out.write(newf+" "+" ".join(map(lambda x:"%7.3f"%x, cell_tr.parameters()))+"\n")
return new_files
def reindex_with_specified_symm(topdir, reference_symm, dirs, out):
print >>out
print >>out, "Re-index to specified symmetry:"
reference_symm.show_summary(out, " ")
print >>out
print >>out
cells = {} # cell and file
sgnum_laue = reference_symm.space_group().build_derived_reflection_intensity_group(False).type().number()
for wd in dirs:
print >>out, "%s:" % 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
if xac_file.endswith(".org"): xac_file_org, xac_file = xac_file, xac_file[:-4]
else: xac_file_org = xac_file+".org"
if not os.path.isfile(xac_file_org):
os.rename(xac_file, xac_file_org)
xac = XDS_ASCII(xac_file_org, 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"
os.rename(xac_file_org, xac_file) # rename back
cells[wd] = (numpy.array(xac.symm.unit_cell().parameters()), xac_file)
continue
cosets = reindex.reindexing_operators(reference_symm, xac.symm, 0.2, 20)
if len(cosets.combined_cb_ops())==0:
print >>out, "Can't find operator:"
xac.symm.show_summary(out, " ")
reference_symm.show_summary(out, " ")
continue
newcell = xac.write_reindexed(op=cosets.combined_cb_ops()[0],
space_group=reference_symm.space_group(),
hklout=xac_file)
cells[wd] = (numpy.array(newcell.parameters()), xac_file)
newcell = " ".join(map(lambda x: "%.3f"%x, newcell.parameters()))
print >>out, " Reindexed to transformed cell: %s with %s" % (newcell, cosets.combined_cb_ops()[0].as_hkl())
return cells
def modify_xds_ascii_files(self, suffix="_reidx"):
#ofs_lst = open("for_merge_new.lst", "w")
new_files = []
print >>self.log_out, "Writing reindexed files.."
for i, (f, op) in enumerate(zip(self.xac_files, self.best_operators)):
if op.is_identity_op():
#ofs_lst.write(f+"\n")
new_files.append(f)
continue
newf = f.replace(".HKL", suffix+".HKL") if ".HKL" in f else os.path.splitext(f)[0]+suffix+".HKL"
print >>self.log_out, "%4d %s" % (i, newf)
xac = XDS_ASCII(f, read_data=False)
xac.write_reindexed(op, newf)
#ofs_lst.write(newf+"\n")
new_files.append(newf)
return new_files
def reindex_with_specified_symm_worker(wd,
wdr,
topdir,
log_out,
reference_symm,
sgnum_laue,
prep_dials_files=False):
"""
wd: directory where XDS file exists
wdr: wd to return; a directory where transformed file should be saved.
If wd!=wdr, files in wd/ are unchanged during procedure. Multiprocessing is unsafe when wd==wdr.
"""
out = StringIO()
print >> out, "%s:" % 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", "DIALS.HKL.org", "DIALS.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 (wdr, None)
if xac_file.endswith(".org"): xac_file_out = xac_file[:-4]
else: xac_file_out = xac_file
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): # XXX Check unit cell consistency!!
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 and "DIALS.HKL" not in xac_file:
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))))
cosets = reindex.reindexing_operators(reference_symm, xac.symm, 0.2,
20) # XXX ISN'T THIS TOO LARGE?
if len(cosets.combined_cb_ops()) == 0:
print >> out, "Can't find operator:"
xac.symm.show_summary(out, " ")
reference_symm.show_summary(out, " ")
log_out.write(out.getvalue())
log_out.flush()
return (wdr, None)
if wd == wdr:
dest = tempfile.mkdtemp(prefix="multiprep", dir=wd)
else:
dest = wdr
hklout = os.path.join(dest, os.path.basename(xac_file_out))
newcell = xac.write_reindexed(op=cosets.combined_cb_ops()[0],
space_group=reference_symm.space_group(),
hklout=hklout)
if "DIALS.HKL" in os.path.basename(xac_file):
outstr = 'output.experiments="%sreindexed_experiments.json" ' % os.path.join(
dest, "")
outstr += 'output.reflections="%sreindexed_reflections.pickle" ' % os.path.join(
dest, "")
for f in ("experiments.json", "indexed.pickle"):
if not os.path.isfile(os.path.join(os.path.dirname(xac_file), f)):
continue
util.call(
'dials.reindex %s change_of_basis_op=%s space_group="%s" %s' %
(f, cosets.combined_cb_ops()[0].as_abc(),
reference_symm.space_group_info(), outstr),
wdir=os.path.dirname(xac_file))
elif prep_dials_files:
prepare_dials_files(wd,
out,
space_group=reference_symm.space_group(),
reindex_op=cosets.combined_cb_ops()[0],
moveto=dest)
newcell_str = " ".join(map(lambda x: "%.3f" % x, newcell.parameters()))
print >> out, " Reindexed to transformed cell: %s with %s" % (
newcell_str, cosets.combined_cb_ops()[0].as_hkl())
log_out.write(out.getvalue())
log_out.flush()
if wd == wdr:
for f in glob.glob(os.path.join(dest, "*")):
f_in_wd = os.path.join(wd, os.path.basename(f))
if os.path.exists(f_in_wd) and not os.path.exists(f_in_wd +
".org"):
os.rename(f_in_wd, f_in_wd + ".org")
os.rename(f, f_in_wd)
shutil.rmtree(dest)
ret = (numpy.array(newcell.parameters()),
os.path.join(wd, os.path.basename(xac_file_out)))
else:
ret = (numpy.array(newcell.parameters()), hklout)
return (wdr, ret)
def reindex_with_specified_symm(topdir, reference_symm, dirs, out):
print >> out
print >> out, "Re-index to specified symmetry:"
reference_symm.show_summary(out, " ")
print >> out
print >> out
cells = {} # cell and file
sgnum_laue = reference_symm.space_group(
).build_derived_reflection_intensity_group(False).type().number()
for wd in dirs:
print >> out, "%s:" % 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
if xac_file.endswith(".org"):
xac_file_org, xac_file = xac_file, xac_file[:-4]
else:
xac_file_org = xac_file + ".org"
if not os.path.isfile(xac_file_org):
os.rename(xac_file, xac_file_org)
xac = XDS_ASCII(xac_file_org, 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"
os.rename(xac_file_org, xac_file) # rename back
cells[wd] = (numpy.array(xac.symm.unit_cell().parameters()),
xac_file)
continue
cosets = reindex.reindexing_operators(reference_symm, xac.symm, 0.2,
20)
if len(cosets.combined_cb_ops()) == 0:
print >> out, "Can't find operator:"
xac.symm.show_summary(out, " ")
reference_symm.show_summary(out, " ")
continue
newcell = xac.write_reindexed(op=cosets.combined_cb_ops()[0],
space_group=reference_symm.space_group(),
hklout=xac_file)
cells[wd] = (numpy.array(newcell.parameters()), xac_file)
newcell = " ".join(map(lambda x: "%.3f" % x, newcell.parameters()))
print >> out, " Reindexed to transformed cell: %s with %s" % (
newcell, cosets.combined_cb_ops()[0].as_hkl())
return cells
