def run(self):
"""Execute the script."""
# Parse the command line
self.params, options, filelist = self.parser.parse_args(
show_diff_phil=True, return_unhandled=True
)
if len(filelist) != 1:
raise Sorry(
"Please provide input in the form:\n {0}".format(self.parser.usage)
)
# Read the filelist and tidy it up
try:
with open(filelist[0], "r") as f:
self.filelist = f.readlines()
except IOError:
raise Sorry("Cannot read the specified file list")
self.filelist = [l.rstrip() for l in self.filelist]
self.filelist = [l for l in self.filelist if l != ""]
# Create output directory if it does not already exist
self._directory = os.path.abspath(self.params.output.directory)
ensure_directory(self._directory)
print("Analysis will be performed in {0}".format(self._directory))
# locate centroid_analysis script
dials_dir = libtbx.env.find_in_repositories("dials")
self._ca = os.path.join(
dials_dir, "algorithms", "refinement", "analysis", "centroid_analysis.py"
)
# Do analysis for the files in filelist
for i, f in enumerate(self.filelist):
# strip newline from the filenames
s = "{:%Y-%m-%d %H:%M:%S} ".format(datetime.datetime.now())
s += "Processing file {0}: ".format(i) + f
print(s)
status = self.process(f, i)
if status:
print("Incomplete:", status)
return
def run(self):
"""Execute the script."""
# Parse the command line
self.params, options, filelist = self.parser.parse_args(show_diff_phil=True, return_unhandled=True)
if len(filelist) != 1:
raise Sorry("Please provide input in the form:\n {0}".format(self.parser.usage))
# Read the filelist and tidy it up
try:
with open(filelist[0], "r") as f:
self.filelist = f.readlines()
except IOError:
raise Sorry("Cannot read the specified file list")
self.filelist = [l.rstrip() for l in self.filelist]
self.filelist = [l for l in self.filelist if l != ""]
# Create output directory if it does not already exist
self._directory = os.path.abspath(self.params.output.directory)
ensure_directory(self._directory)
print "Analysis will be performed in {0}".format(self._directory)
# locate centroid_analysis script
dials_dir = libtbx.env.find_in_repositories("dials")
self._ca = os.path.join(dials_dir, "algorithms", "refinement", "analysis", "centroid_analysis.py")
# Do analysis for the files in filelist
for i, f in enumerate(self.filelist):
# strip newline from the filenames
s = "{:%Y-%m-%d %H:%M:%S} ".format(datetime.datetime.now())
s += "Processing file {0}: ".format(i) + f
print s
status = self.process(f, i)
if status:
print "Incomplete:", status
return
def run(self):
"""Run the script."""
from dials.util.options import flatten_experiments
params, options = self.parser.parse_args()
if len(params.input.experiments) == 0:
self.parser.print_help()
raise Sorry("No experiments found in the input")
experiments = flatten_experiments(params.input.experiments)
# Determine output path
self._directory = os.path.join(params.output.directory, "scan-varying_crystal")
self._directory = os.path.abspath(self._directory)
ensure_directory(self._directory)
self._format = "." + params.output.format
self._debug = params.output.debug
# Decomposition axes
self._e1 = params.orientation_decomposition.e1
self._e2 = params.orientation_decomposition.e2
self._e3 = params.orientation_decomposition.e3
# cell plot
dat = []
for iexp, exp in enumerate(experiments):
crystal = exp.crystal
scan = exp.scan
if crystal.num_scan_points == 0:
print "Ignoring scan-static crystal"
continue
scan_pts = range(crystal.num_scan_points)
cells = [crystal.get_unit_cell_at_scan_point(t) for t in scan_pts]
cell_params = [e.parameters() for e in cells]
a, b, c, aa, bb, cc = zip(*cell_params)
phi = [scan.get_angle_from_array_index(t) for t in scan_pts]
vol = [e.volume() for e in cells]
cell_dat = {"phi": phi, "a": a, "b": b, "c": c, "alpha": aa, "beta": bb, "gamma": cc, "volume": vol}
if self._debug:
print "Crystal in Experiment {0}".format(iexp)
print "Phi\ta\tb\tc\talpha\tbeta\tgamma\tVolume"
msg = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}"
line_dat = zip(phi, a, b, c, aa, bb, cc, vol)
for line in line_dat:
print msg.format(*line)
dat.append(cell_dat)
self.plot_cell(dat)
# orientation plot
dat = []
for iexp, exp in enumerate(experiments):
crystal = exp.crystal
scan = exp.scan
if crystal.num_scan_points == 0:
print "Ignoring scan-static crystal"
continue
scan_pts = range(crystal.num_scan_points)
phi = [scan.get_angle_from_array_index(t) for t in scan_pts]
Umats = [crystal.get_U_at_scan_point(t) for t in scan_pts]
if params.orientation_decomposition.relative_to_static_orientation:
# factor out static U
Uinv = crystal.get_U().inverse()
Umats = [U * Uinv for U in Umats]
# NB e3 and e1 definitions for the crystal are swapped compared
# with those used inside the solve_r3_rotation_for_angles_given_axes
# method
angles = [solve_r3_rotation_for_angles_given_axes(U, self._e3, self._e2, self._e1, deg=True) for U in Umats]
phi3, phi2, phi1 = zip(*angles)
angle_dat = {"phi": phi, "phi3": phi3, "phi2": phi2, "phi1": phi1}
if self._debug:
print "Crystal in Experiment {0}".format(iexp)
print "Image\tphi3\tphi2\tphi1"
msg = "{0}\t{1}\t{2}\t{3}"
line_dat = zip(phi, phi3, phi2, phi1)
for line in line_dat:
print msg.format(*line)
dat.append(angle_dat)
self.plot_orientation(dat)
def run(self):
"""Run the script."""
from dials.util.options import flatten_experiments
from scitbx import matrix
params, options = self.parser.parse_args()
if len(params.input.experiments) == 0:
self.parser.print_help()
return
experiments = flatten_experiments(params.input.experiments)
# Determine output path
self._directory = os.path.join(params.output.directory,
"scan-varying_model")
self._directory = os.path.abspath(self._directory)
ensure_directory(self._directory)
self._format = "." + params.output.format
self._debug = params.output.debug
# Decomposition axes
self._e1 = params.orientation_decomposition.e1
self._e2 = params.orientation_decomposition.e2
self._e3 = params.orientation_decomposition.e3
# cell plot
dat = []
for iexp, exp in enumerate(experiments):
crystal = exp.crystal
scan = exp.scan
if crystal.num_scan_points == 0:
print("Ignoring scan-static crystal")
continue
scan_pts = list(range(crystal.num_scan_points))
cells = [crystal.get_unit_cell_at_scan_point(t) for t in scan_pts]
cell_params = [e.parameters() for e in cells]
a, b, c, aa, bb, cc = zip(*cell_params)
phi = [scan.get_angle_from_array_index(t) for t in scan_pts]
vol = [e.volume() for e in cells]
cell_dat = {
"phi": phi,
"a": a,
"b": b,
"c": c,
"alpha": aa,
"beta": bb,
"gamma": cc,
"volume": vol,
}
try:
cell_esds = [
crystal.get_cell_parameter_sd_at_scan_point(t)
for t in scan_pts
]
sig_a, sig_b, sig_c, sig_aa, sig_bb, sig_cc = zip(*cell_esds)
cell_dat["sig_a"] = sig_a
cell_dat["sig_b"] = sig_b
cell_dat["sig_c"] = sig_c
cell_dat["sig_aa"] = sig_aa
cell_dat["sig_bb"] = sig_bb
cell_dat["sig_cc"] = sig_cc
except RuntimeError:
pass
if self._debug:
print("Crystal in Experiment {}".format(iexp))
print("Phi\ta\tb\tc\talpha\tbeta\tgamma\tVolume")
msg = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}"
line_dat = zip(phi, a, b, c, aa, bb, cc, vol)
for line in line_dat:
print(msg.format(*line))
dat.append(cell_dat)
if dat:
self.plot_cell(dat)
# orientation plot
dat = []
for iexp, exp in enumerate(experiments):
crystal = exp.crystal
scan = exp.scan
if crystal.num_scan_points == 0:
print("Ignoring scan-static crystal")
continue
scan_pts = list(range(crystal.num_scan_points))
phi = [scan.get_angle_from_array_index(t) for t in scan_pts]
Umats = [
matrix.sqr(crystal.get_U_at_scan_point(t)) for t in scan_pts
]
if params.orientation_decomposition.relative_to_static_orientation:
# factor out static U
Uinv = matrix.sqr(crystal.get_U()).inverse()
Umats = [U * Uinv for U in Umats]
# NB e3 and e1 definitions for the crystal are swapped compared
# with those used inside the solve_r3_rotation_for_angles_given_axes
# method
angles = [
solve_r3_rotation_for_angles_given_axes(U,
self._e3,
self._e2,
self._e1,
deg=True)
for U in Umats
]
phi3, phi2, phi1 = zip(*angles)
angle_dat = {"phi": phi, "phi3": phi3, "phi2": phi2, "phi1": phi1}
if self._debug:
print("Crystal in Experiment {}".format(iexp))
print("Image\tphi3\tphi2\tphi1")
msg = "{0}\t{1}\t{2}\t{3}"
line_dat = zip(phi, phi3, phi2, phi1)
for line in line_dat:
print(msg.format(*line))
dat.append(angle_dat)
if dat:
self.plot_orientation(dat)
# beam centre plot
dat = []
for iexp, exp in enumerate(experiments):
beam = exp.beam
detector = exp.detector
scan = exp.scan
if beam.num_scan_points == 0:
print("Ignoring scan-static beam")
continue
scan_pts = range(beam.num_scan_points)
phi = [scan.get_angle_from_array_index(t) for t in scan_pts]
p = detector.get_panel_intersection(beam.get_s0())
if p < 0:
print("Beam does not intersect a panel")
continue
panel = detector[p]
s0_scan_points = [
beam.get_s0_at_scan_point(i)
for i in range(beam.num_scan_points)
]
bc_scan_points = [
panel.get_beam_centre_px(s0) for s0 in s0_scan_points
]
bc_x, bc_y = zip(*bc_scan_points)
dat.append({
"phi": phi,
"beam_centre_x": bc_x,
"beam_centre_y": bc_y
})
if dat:
self.plot_beam_centre(dat)