def open_hdf5(self,
h5file,
frameno,
tmpdir="/dev/shm",
raise_window=True,
binning=1):
from yamtbx.dataproc import eiger
imgfile = os.path.join(
tmpdir, "adxvtmp-%s-%s.cbf" % (getpass.getuser(), os.getpid()))
eiger.extract_to_minicbf(h5file, frameno, imgfile, binning=binning)
self.open_image(imgfile, raise_window=raise_window)
def open_hdf5(self,
h5file,
frameno_or_path,
tmpdir=None,
raise_window=True,
binning=1):
from yamtbx.dataproc import eiger
if tmpdir is None:
tmpdir = "/dev/shm" if os.path.isdir(
"/dev/shm") else tempfile.gettempdir()
imgfile = os.path.join(
tmpdir, "adxvtmp-%s-%s.cbf" % (getpass.getuser(), os.getpid()))
eiger.extract_to_minicbf(h5file,
frameno_or_path,
imgfile,
binning=binning)
self.open_image(imgfile, raise_window=raise_window)
def open_hdf5(self, h5file, frameno, tmpdir="/dev/shm", raise_window=True, binning=1):
from yamtbx.dataproc import eiger
imgfile = os.path.join(tmpdir, "adxvtmp-%s-%s.cbf"%(getpass.getuser(), os.getpid()))
eiger.extract_to_minicbf(h5file, frameno, imgfile, binning=binning)
self.open_image(imgfile, raise_window=raise_window)
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 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