def failover_dxtbx(image_file):
'''Failover to use the dxtbx to read the image headers...'''
# replacement dxtbx for rigaku saturns sometimes
from dxtbx.format.Registry import Registry
from dxtbx.model.detector_helpers_types import detector_helpers_types
global last_format
if last_format:
iformat = last_format
else:
iformat = Registry.find(image_file)
from xia2.Handlers.Streams import Debug
Debug.write('Using dxtbx format instance: %s' % iformat.__name__)
if not iformat.understand(image_file):
raise RuntimeError('image file %s not understood by dxtbx' % \
image_file)
last_format = iformat
i = iformat(image_file)
b = i.get_beam()
g = i.get_goniometer()
d = i.get_detector()
s = i.get_scan()
header = {}
if not hasattr(d, 'get_image_size'):
# cope with new detector as array of panels dxtbx api
fast, slow = map(int, d[0].get_image_size())
_f, _s = d[0].get_pixel_size()
F = matrix.col(d[0].get_fast_axis())
S = matrix.col(d[0].get_slow_axis())
N = F.cross(S)
origin = matrix.col(d[0].get_origin())
else:
fast, slow = map(int, d.get_image_size())
_f, _s = d.get_pixel_size()
F = matrix.col(d.get_fast_axis())
S = matrix.col(d.get_slow_axis())
N = F.cross(S)
origin = matrix.col(d.get_origin())
beam = matrix.col(b.get_direction())
# FIXME detector has methods to compute the beam centre now...
centre = -(origin - origin.dot(N) * N)
x = centre.dot(F)
y = centre.dot(S)
header['fast_direction'] = F.elems
header['slow_direction'] = S.elems
header['rotation_axis'] = g.get_rotation_axis()
if hasattr(s, 'get_exposure_time'):
header['exposure_time'] = s.get_exposure_time()
else:
header['exposure_time'] = s.get_exposure_times()[0]
header['distance'] = math.fabs(origin.dot(N))
if math.fabs(beam.angle(N, deg=True) - 180) < 0.1:
header['two_theta'] = 180 - beam.angle(N, deg=True)
else:
header['two_theta'] = -beam.angle(N, deg=True)
header['raw_beam'] = x, y
header['phi_start'] = s.get_oscillation()[0]
header['phi_width'] = s.get_oscillation()[1]
header['phi_end'] = sum(s.get_oscillation())
header['pixel'] = _f, _s
# FIXME this is very bad as it relates to teh legacy backwards Mosflm
# beam centre standard still... FIXME-SCI-948
header['beam'] = y, x
header['epoch'] = s.get_image_epoch(s.get_image_range()[0])
header['date'] = time.ctime(header['epoch'])
header['wavelength'] = b.get_wavelength()
header['size'] = fast, slow
if hasattr(i, 'detector_class'):
header['detector_class'] = i.detector_class
header['detector'] = i.detector
else:
if hasattr(d, 'get_type'):
# cope with new detector as array of panels API
dtype = d.get_type()
else:
dtype = d[0].get_type()
detector_type = detector_helpers_types.get(dtype, fast, slow,
int(1000 * _f),
int(1000 * _s))
header['detector_class'] = detector_type.replace('-', ' ')
header['detector'] = detector_type.split('-')[0]
return header
def XDS(self):
sensor = self.get_detector().get_type()
fast, slow = map(int, self.get_detector().get_image_size())
f, s = self.get_detector().get_pixel_size()
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
R = matrix.col(
(1.0, 0.0, 0.0)).axis_and_angle_as_r3_rotation_matrix(180.0,
deg=True)
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = self.get_detector().get_trusted_range()
print("DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d" %
(detector, trusted[0] + 1, trusted[1]))
if detector == "PILATUS":
print("SENSOR_THICKNESS= 0.32")
print("DIRECTION_OF_DETECTOR_X-AXIS= %.3f %.3f %.3f" %
(R * self.get_detector().get_fast_axis()).elems)
print("DIRECTION_OF_DETECTOR_Y-AXIS= %.3f %.3f %.3f" %
(R * self.get_detector().get_slow_axis()).elems)
print("NX=%d NY=%d QX=%.4f QY=%.4f" % (fast, slow, f, s))
F = R * self.get_detector().get_fast_axis()
S = R * self.get_detector().get_slow_axis()
N = F.cross(S)
origin = R * self.get_detector().get_origin()
beam = (R * self.get_beam().get_direction() /
math.sqrt(matrix.col(self.get_beam().get_direction()).dot()))
centre = -(origin - origin.dot(N) * N)
x = centre.dot(F)
y = centre.dot(S)
print("DETECTOR_DISTANCE= %.3f" % origin.dot(N))
print("ORGX= %.1f ORGY= %.1f" % (x / f, y / s))
print("ROTATION_AXIS= %.3f %.3f %.3f" %
(R * self.get_goniometer().get_rotation_axis()).elems)
print("STARTING_ANGLE= %.3f" % self.get_scan().get_oscillation()[0])
print("OSCILLATION_RANGE= %.3f" % self.get_scan().get_oscillation()[1])
print("X-RAY_WAVELENGTH= %.5f" % self.get_beam().get_wavelength())
print("INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f" % (-beam).elems)
print("FRACTION_OF_POLARIZATION= %.3f" %
self.get_beam().get_polarization_fraction())
print("POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f" %
self.get_beam().get_polarization_normal())
print("NAME_TEMPLATE_OF_DATA_FRAMES= %s" %
self._template.replace("#", "?"))
print("TRUSTED_REGION= 0.0 1.41")
for f0, f1, s0, s1 in self.get_detector().get_mask():
print("UNTRUSTED_RECTANGLE= %d %d %d %d" %
(f0, f1 + 1, s0, s1 + 1))
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
print("DATA_RANGE= %d %d" % start_end)
print("JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT")
def imageset_to_xds(
imageset,
synchrotron=None,
refined_beam_vector=None,
refined_rotation_axis=None,
refined_distance=None,
):
"""A function to take an input header dictionary from Diffdump
and generate a list of records to start XDS - see Doc/INP.txt."""
# decide if we are at a synchrotron if we don't know already...
# that is, the wavelength is around either the Copper or Chromium
# K-alpha edge and this is an image plate.
beam = imageset.get_beam()
from dxtbx.serialize.xds import to_xds, xds_detector_name
converter = to_xds(imageset)
h5_names = ["h5", "nxs"]
if imageset.get_template().split(".")[-1] in h5_names:
if not check_xds_ok_with_h5():
raise RuntimeError("HDF5 input with no converter for XDS")
detector_class_is_square = {
"adsc q4": True,
"adsc q4 2x2 binned": True,
"adsc q210": True,
"adsc q210 2x2 binned": True,
"adsc q270": True,
"adsc q270 2x2 binned": True,
"adsc q315": True,
"adsc q315 2x2 binned": True,
"adsc HF4M": True,
"holton fake 01": True,
"unknown electron 57": True,
"mar 345": False,
"mar 180": False,
"mar 240": False,
"mar 300 ccd": True,
"mar 325 ccd": True,
"mar 225 ccd": True,
"mar ccd 225 hs": True,
"rayonix ccd 165": False,
"rayonix ccd 135": False,
"rayonix ccd 300": True,
"rayonix ccd 325": True,
"rayonix ccd 225": True,
"rayonix ccd 225 hs": True,
"rayonix ccd 300 hs": True,
"mar 165 ccd": False,
"mar 135 ccd": False,
"pilatus 12M": True,
"pilatus 6M": True,
"pilatus 2M": True,
"pilatus 1M": True,
"pilatus 200K": True,
"pilatus 300K": True,
"eiger 4M": True,
"eiger 9M": True,
"eiger 16M": True,
"rigaku saturn 92 2x2 binned": True,
"rigaku saturn 944 2x2 binned": True,
"rigaku saturn 724 2x2 binned": True,
"rigaku saturn 92": True,
"rigaku saturn 944": True,
"rigaku saturn 724": True,
"rigaku saturn a200": True,
"raxis IV": True,
"NOIR1": True,
}
sensor = converter.get_detector()[0].get_type()
fast, slow = converter.detector_size
f, s = converter.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
result = []
from dxtbx.model.detector_helpers_types import detector_helpers_types
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = converter.get_detector()[0].get_trusted_range()
# if CCD; undo dxtbx pedestal offset, hard code minimum 1; else use trusted
# range verbatim (i.e. for PAD) (later in pipeline sensor is SENSOR_UNKNOWN
# so additional test)
if sensor == "SENSOR_CCD" or detector == "CCDCHESS":
trusted = 1, trusted[1] - trusted[0]
# XDS upset if we trust < 0 see #193
if trusted[0] < 0:
trusted = 0, trusted[1]
result.append("DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d" %
(detector, trusted[0], trusted[1]))
result.append("DIRECTION_OF_DETECTOR_X-AXIS=%f %f %f" %
converter.detector_x_axis)
result.append("DIRECTION_OF_DETECTOR_Y-AXIS=%f %f %f" %
converter.detector_y_axis)
from xia2.Handlers.Phil import PhilIndex
params = PhilIndex.get_python_object()
if params.xds.trusted_region:
result.append("TRUSTED_REGION= %.2f %.2f" %
tuple(params.xds.trusted_region))
elif detector_class_is_square[detector_helpers_types.get(
sensor, fast, slow, df, ds).replace("-", " ")]:
result.append("TRUSTED_REGION=0.0 1.41")
else:
result.append("TRUSTED_REGION=0.0 0.99")
result.append("NX=%d NY=%d QX=%.4f QY=%.4f" % (fast, slow, f, s))
# RAXIS detectors have the distance written negative - why????
# this is ONLY for XDS - SATURN are the same - probably left handed
# goniometer rotation on rigaku X-ray sets.
if refined_distance:
result.append("DETECTOR_DISTANCE=%7.3f" % refined_distance)
else:
result.append("DETECTOR_DISTANCE=%7.3f" % converter.detector_distance)
result.append("OSCILLATION_RANGE=%4.2f" % converter.oscillation_range)
result.append("X-RAY_WAVELENGTH=%8.6f" % converter.wavelength)
# if user specified reversephi and this was not picked up in the
# format class reverse phi: n.b. double-negative warning!
if refined_rotation_axis:
result.append("ROTATION_AXIS= %f %f %f" % refined_rotation_axis)
else:
result.append("ROTATION_AXIS= %.3f %.3f %.3f" %
converter.rotation_axis)
if refined_beam_vector:
result.append("INCIDENT_BEAM_DIRECTION=%f %f %f" % refined_beam_vector)
else:
result.append("INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f" %
converter.beam_vector)
if hasattr(beam, "get_polarization_fraction"):
R = converter.imagecif_to_xds_transformation_matrix
result.append("FRACTION_OF_POLARIZATION= %.3f" %
beam.get_polarization_fraction())
result.append("POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f" %
(R * matrix.col(beam.get_polarization_normal())).elems)
# 24/NOV/14 XDS determines the air absorption automatically
# based on wavelength. May be useful to override this for in vacuo exps
# result.append('AIR=0.001')
if detector == "PILATUS":
try:
thickness = converter.get_detector()[0].get_thickness()
if not thickness:
thickness = 0.32
Debug.write(
"Could not determine sensor thickness. Assuming default PILATUS 0.32mm"
)
except e:
thickness = 0.32
Debug.write(
"Error occured during sensor thickness determination. Assuming default PILATUS 0.32mm"
)
result.append("SENSOR_THICKNESS=%f" % thickness)
# FIXME: Sensor absorption coefficient calculation probably requires a more general solution
# if converter.get_detector()[0].get_material() == 'CdTe':
# print "CdTe detector detected. Beam wavelength is %8.6f Angstrom" % converter.wavelength
if len(converter.panel_x_axis) > 1:
for panel_id in range(len(converter.panel_x_axis)):
result.append("")
result.append("!")
result.append("! SEGMENT %d" % (panel_id + 1))
result.append("!")
result.append("SEGMENT= %d %d %d %d" %
converter.panel_limits[panel_id])
result.append("DIRECTION_OF_SEGMENT_X-AXIS= %.3f %.3f %.3f" %
converter.panel_x_axis[panel_id])
result.append("DIRECTION_OF_SEGMENT_Y-AXIS= %.3f %.3f %.3f" %
converter.panel_y_axis[panel_id])
result.append("SEGMENT_DISTANCE= %.3f" %
converter.panel_distance[panel_id])
result.append("SEGMENT_ORGX= %.1f SEGMENT_ORGY= %.1f" %
converter.panel_origin[panel_id])
result.append("")
for f0, s0, f1, s1 in converter.get_detector()[0].get_mask():
result.append("UNTRUSTED_RECTANGLE= %d %d %d %d" %
(f0 - 1, f1 + 1, s0 - 1, s1 + 1))
if params.xds.untrusted_ellipse:
for untrusted_ellipse in params.xds.untrusted_ellipse:
result.append("UNTRUSTED_ELLIPSE= %d %d %d %d" %
tuple(untrusted_ellipse))
Debug.write(result[-1])
if params.xds.untrusted_rectangle:
for untrusted_rectangle in params.xds.untrusted_rectangle:
result.append("UNTRUSTED_RECTANGLE= %d %d %d %d" %
tuple(untrusted_rectangle))
Debug.write(result[-1])
return result
def XDS_INP(
self,
space_group_number=None,
real_space_a=None,
real_space_b=None,
real_space_c=None,
job_card="XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT",
as_str=None,
):
# as_str is deprecated and will be removed in the future
result = []
assert [real_space_a, real_space_b, real_space_c].count(None) in (0, 3)
sensor = self.get_detector()[0].get_type()
fast, slow = self.detector_size
f, s = self.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = self.get_detector()[0].get_trusted_range()
result.append("DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d" %
(detector, trusted[0] + 1, trusted[1]))
if detector == "PILATUS":
result.append("SENSOR_THICKNESS= %.3f" %
self.get_detector()[0].get_thickness())
if self.get_detector()[0].get_material():
from cctbx.eltbx import attenuation_coefficient
material = self.get_detector()[0].get_material()
table = attenuation_coefficient.get_table(material)
mu = table.mu_at_angstrom(self.wavelength) / 10.0
result.append(
"!SENSOR_MATERIAL / THICKNESS %s %.3f" %
(material, self.get_detector()[0].get_thickness()))
result.append("!SILICON= %f" % mu)
result.append("DIRECTION_OF_DETECTOR_X-AXIS= %.5f %.5f %.5f" %
self.detector_x_axis)
result.append("DIRECTION_OF_DETECTOR_Y-AXIS= %.5f %.5f %.5f" %
self.detector_y_axis)
result.append("NX=%d NY=%d QX=%.4f QY=%.4f" % (fast, slow, f, s))
result.append("DETECTOR_DISTANCE= %.6f" % self.detector_distance)
result.append("ORGX= %.2f ORGY= %.2f" % self.detector_origin)
result.append("ROTATION_AXIS= %.5f %.5f %.5f" % self.rotation_axis)
result.append("STARTING_ANGLE= %.3f" % self.starting_angle)
result.append("OSCILLATION_RANGE= %.3f" % self.oscillation_range)
result.append("X-RAY_WAVELENGTH= %.5f" % self.wavelength)
result.append("INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f" %
tuple([b / self.wavelength for b in self.beam_vector]))
# FIXME LATER
if hasattr(self.get_beam(), "get_polarization_fraction"):
result.append("FRACTION_OF_POLARIZATION= %.3f" %
self.get_beam().get_polarization_fraction())
result.append("POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f" %
self.get_beam().get_polarization_normal())
template = self.get_template()
if template.endswith("master.h5"):
template = template.replace("master", "??????")
result.append("NAME_TEMPLATE_OF_DATA_FRAMES= %s" %
template.replace("#", "?"))
result.append("TRUSTED_REGION= 0.0 1.41")
for f0, s0, f1, s1 in self.get_detector()[0].get_mask():
result.append("UNTRUSTED_RECTANGLE= %d %d %d %d" %
(f0, f1 + 1, s0, s1 + 1))
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
result.append("DATA_RANGE= %d %d" % start_end)
result.append("JOB=%s" % job_card)
if space_group_number is not None:
result.append("SPACE_GROUP_NUMBER= %i" % space_group_number)
if [real_space_a, real_space_b, real_space_c].count(None) == 0:
R = self.imagecif_to_xds_transformation_matrix
unit_cell_a_axis = R * matrix.col(real_space_a)
unit_cell_b_axis = R * matrix.col(real_space_b)
unit_cell_c_axis = R * matrix.col(real_space_c)
result.append("UNIT_CELL_A-AXIS= %.6f %.6f %.6f" %
unit_cell_a_axis.elems)
result.append("UNIT_CELL_B-AXIS= %.6f %.6f %.6f" %
unit_cell_b_axis.elems)
result.append("UNIT_CELL_C-AXIS= %.6f %.6f %.6f" %
unit_cell_c_axis.elems)
if len(self.panel_x_axis) > 1:
for panel_id, panel_x_axis in enumerate(self.panel_x_axis):
result.append("")
result.append("!")
result.append("! SEGMENT %d" % (panel_id + 1))
result.append("!")
result.append("SEGMENT= %d %d %d %d" %
self.panel_limits[panel_id])
result.append("DIRECTION_OF_SEGMENT_X-AXIS= %.5f %.5f %.5f" %
panel_x_axis)
result.append("DIRECTION_OF_SEGMENT_Y-AXIS= %.5f %.5f %.5f" %
self.panel_y_axis[panel_id])
result.append("SEGMENT_DISTANCE= %.3f" %
self.panel_distance[panel_id])
result.append("SEGMENT_ORGX= %.2f SEGMENT_ORGY= %.2f" %
self.panel_origin[panel_id])
return "\n".join(result)
def failover_dxtbx(image_file):
'''Failover to use the dxtbx to read the image headers...'''
# replacement dxtbx for rigaku saturns sometimes
from dxtbx.format.Registry import Registry
from dxtbx.model.detector_helpers_types import detector_helpers_types
global last_format
if last_format:
iformat = last_format
else:
iformat = Registry.find(image_file)
from xia2.Handlers.Streams import Debug
Debug.write('Using dxtbx format instance: %s' % iformat.__name__)
if not iformat.understand(image_file):
raise RuntimeError, 'image file %s not understood by dxtbx' % \
image_file
last_format = iformat
i = iformat(image_file)
b = i.get_beam()
g = i.get_goniometer()
d = i.get_detector()
s = i.get_scan()
header = { }
if not hasattr(d, 'get_image_size'):
# cope with new detector as array of panels dxtbx api
fast, slow = map(int, d[0].get_image_size())
_f, _s = d[0].get_pixel_size()
F = matrix.col(d[0].get_fast_axis())
S = matrix.col(d[0].get_slow_axis())
N = F.cross(S)
origin = matrix.col(d[0].get_origin())
else:
fast, slow = map(int, d.get_image_size())
_f, _s = d.get_pixel_size()
F = matrix.col(d.get_fast_axis())
S = matrix.col(d.get_slow_axis())
N = F.cross(S)
origin = matrix.col(d.get_origin())
beam = matrix.col(b.get_direction())
# FIXME detector has methods to compute the beam centre now...
centre = - (origin - origin.dot(N) * N)
x = centre.dot(F)
y = centre.dot(S)
header['fast_direction'] = F.elems
header['slow_direction'] = S.elems
header['rotation_axis'] = g.get_rotation_axis()
if hasattr(s, 'get_exposure_time'):
header['exposure_time'] = s.get_exposure_time()
else:
header['exposure_time'] = s.get_exposure_times()[0]
header['distance'] = math.fabs(origin.dot(N))
if math.fabs(beam.angle(N, deg = True) - 180) < 0.1:
header['two_theta'] = 180 - beam.angle(N, deg = True)
else:
header['two_theta'] = - beam.angle(N, deg = True)
header['raw_beam'] = x, y
header['phi_start'] = s.get_oscillation()[0]
header['phi_width'] = s.get_oscillation()[1]
header['phi_end'] = sum(s.get_oscillation())
header['pixel'] = _f, _s
# FIXME this is very bad as it relates to teh legacy backwards Mosflm
# beam centre standard still... FIXME-SCI-948
header['beam'] = y, x
header['epoch'] = s.get_image_epoch(s.get_image_range()[0])
header['date'] = time.ctime(header['epoch'])
header['wavelength'] = b.get_wavelength()
header['size'] = fast, slow
if hasattr(i, 'detector_class'):
header['detector_class'] = i.detector_class
header['detector'] = i.detector
else:
if hasattr(d, 'get_type'):
# cope with new detector as array of panels API
dtype = d.get_type()
else:
dtype = d[0].get_type()
detector_type = detector_helpers_types.get(
dtype, fast, slow, int(1000 * _f), int(1000 * _s))
header['detector_class'] = detector_type.replace('-', ' ')
header['detector'] = detector_type.split('-')[0]
return header
def XDS_INP(self,
out=None,
space_group_number=None,
real_space_a=None,
real_space_b=None,
real_space_c=None,
job_card="XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT",
as_str=False):
if out is None:
out = sys.stdout
# horrible hack to allow returning result as string; would be nice if the
# structure of this was to make the XDS.INP in memory then print it...
# see also show() method on things.
str_result = []
if as_str:
def print(str='', file=None):
str_result.append(str)
else:
from dxtbx import get_print
print = get_print()
assert [real_space_a, real_space_b, real_space_c].count(None) in (0, 3)
sensor = self.get_detector()[0].get_type()
fast, slow = self.detector_size
f, s = self.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = self.get_detector()[0].get_trusted_range()
print('DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d' % \
(detector, trusted[0] + 1, trusted[1]), file=out)
if detector == 'PILATUS':
print('SENSOR_THICKNESS= %.3f' % \
self.get_detector()[0].get_thickness(), file=out)
if self.get_detector()[0].get_material():
from cctbx.eltbx import attenuation_coefficient
material = self.get_detector()[0].get_material()
table = attenuation_coefficient.get_table(material)
mu = table.mu_at_angstrom(self.wavelength) / 10.0
print('!SENSOR_MATERIAL / THICKNESS %s %.3f' % \
(material, self.get_detector()[0].get_thickness()), file=out)
print('!SILICON= %f' % mu, file=out)
print('DIRECTION_OF_DETECTOR_X-AXIS= %.5f %.5f %.5f' % \
self.detector_x_axis, file=out)
print('DIRECTION_OF_DETECTOR_Y-AXIS= %.5f %.5f %.5f' % \
self.detector_y_axis, file=out)
print('NX=%d NY=%d QX=%.4f QY=%.4f' % (fast, slow, f, s), file=out)
print('DETECTOR_DISTANCE= %.6f' % self.detector_distance, file=out)
print('ORGX= %.2f ORGY= %.2f' % self.detector_origin, file=out)
print('ROTATION_AXIS= %.5f %.5f %.5f' % \
self.rotation_axis, file=out)
print('STARTING_ANGLE= %.3f' % \
self.starting_angle, file=out)
print('OSCILLATION_RANGE= %.3f' % \
self.oscillation_range, file=out)
print('X-RAY_WAVELENGTH= %.5f' % \
self.wavelength, file=out)
print('INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f' % \
tuple([b / self.wavelength for b in self.beam_vector]), file=out)
# FIXME LATER
if hasattr(self.get_beam(), "get_polarization_fraction"):
print('FRACTION_OF_POLARIZATION= %.3f' % \
self.get_beam().get_polarization_fraction(), file=out)
print('POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f' % \
self.get_beam().get_polarization_normal(), file=out)
template = self.get_template()
if template.endswith('master.h5'):
master_file = template
g = glob.glob(template.split('master.h5')[0] + 'data_*[0-9].h5')
assert g, 'No associated data files found for %s' % master_file
template = template_regex(g[0])[0]
template = master_file.split('master.h5')[0] + template.split(
'data_')[-1]
print('NAME_TEMPLATE_OF_DATA_FRAMES= %s' % \
template.replace('#', '?'), file=out)
print('TRUSTED_REGION= 0.0 1.41', file=out)
for f0, s0, f1, s1 in self.get_detector()[0].get_mask():
print('UNTRUSTED_RECTANGLE= %d %d %d %d' % \
(f0, f1 + 1, s0, s1 + 1), file=out)
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
print('DATA_RANGE= %d %d' % start_end, file=out)
print('JOB=%s' % job_card, file=out)
if space_group_number is not None:
print('SPACE_GROUP_NUMBER= %i' % space_group_number, file=out)
if [real_space_a, real_space_b, real_space_c].count(None) == 0:
R = self.imagecif_to_xds_transformation_matrix
unit_cell_a_axis = R * matrix.col(real_space_a)
unit_cell_b_axis = R * matrix.col(real_space_b)
unit_cell_c_axis = R * matrix.col(real_space_c)
print("UNIT_CELL_A-AXIS= %.6f %.6f %.6f" % unit_cell_a_axis.elems,
file=out)
print("UNIT_CELL_B-AXIS= %.6f %.6f %.6f" % unit_cell_b_axis.elems,
file=out)
print("UNIT_CELL_C-AXIS= %.6f %.6f %.6f" % unit_cell_c_axis.elems,
file=out)
if len(self.panel_x_axis) > 1:
for panel_id, panel_x_axis in enumerate(self.panel_x_axis):
print(file=out)
print("!", file=out)
print("! SEGMENT %d" % (panel_id + 1), file=out)
print("!", file=out)
print('SEGMENT= %d %d %d %d' % self.panel_limits[panel_id],
file=out)
print('DIRECTION_OF_SEGMENT_X-AXIS= %.5f %.5f %.5f' % \
panel_x_axis, file=out)
print('DIRECTION_OF_SEGMENT_Y-AXIS= %.5f %.5f %.5f' % \
self.panel_y_axis[panel_id], file=out)
print('SEGMENT_DISTANCE= %.3f' % self.panel_distance[panel_id],
file=out)
print('SEGMENT_ORGX= %.2f SEGMENT_ORGY= %.2f' %
self.panel_origin[panel_id],
file=out)
print(file=out)
if as_str:
return '\n'.join(str_result)
def XDS(self):
sensor = self.get_detector().get_type()
fast, slow = map(int, self.get_detector().get_image_size())
f, s = self.get_detector().get_pixel_size()
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
R = matrix.col((1.0, 0.0, 0.0)).axis_and_angle_as_r3_rotation_matrix(
180.0, deg = True)
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = self.get_detector().get_trusted_range()
print 'DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d' % \
(detector, trusted[0] + 1, trusted[1])
if detector == 'PILATUS':
print 'SENSOR_THICKNESS= 0.32'
print 'DIRECTION_OF_DETECTOR_X-AXIS= %.3f %.3f %.3f' % \
(R * self.get_detector().get_fast_axis()).elems
print 'DIRECTION_OF_DETECTOR_Y-AXIS= %.3f %.3f %.3f' % \
(R * self.get_detector().get_slow_axis()).elems
print 'NX=%d NY=%d QX=%.4f QY=%.4f' % (fast, slow, f, s)
F = R * self.get_detector().get_fast_axis()
S = R * self.get_detector().get_slow_axis()
N = F.cross(S)
origin = R * self.get_detector().get_origin()
beam = R * self.get_beam().get_direction() / \
math.sqrt(matrix.col(self.get_beam().get_direction()).dot())
centre = -(origin - origin.dot(N) * N)
x = centre.dot(F)
y = centre.dot(S)
print 'DETECTOR_DISTANCE= %.3f' % origin.dot(N)
print 'ORGX= %.1f ORGY= %.1f' % (x / f, y / s)
print 'ROTATION_AXIS= %.3f %.3f %.3f' % \
(R * self.get_goniometer().get_rotation_axis()).elems
print 'STARTING_ANGLE= %.3f' % \
self.get_scan().get_oscillation()[0]
print 'OSCILLATION_RANGE= %.3f' % \
self.get_scan().get_oscillation()[1]
print 'X-RAY_WAVELENGTH= %.5f' % \
self.get_beam().get_wavelength()
print 'INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f' % \
(- beam).elems
print 'FRACTION_OF_POLARIZATION= %.3f' % \
self.get_beam().get_polarization_fraction()
print 'POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f' % \
self.get_beam().get_polarization_normal()
print 'NAME_TEMPLATE_OF_DATA_FRAMES= %s' % self._template.replace(
'#', '?')
print 'TRUSTED_REGION= 0.0 1.41'
for f0, f1, s0, s1 in self.get_detector().get_mask():
print 'UNTRUSTED_RECTANGLE= %d %d %d %d' % \
(f0 - 1, f1 + 1, s0 - 1, s1 + 1)
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
print 'DATA_RANGE= %d %d' % start_end
print 'JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT'
def XDS_INP(self, out=None,
space_group_number=None,
real_space_a=None, real_space_b=None, real_space_c=None,
job_card="XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT"):
if out is None:
out = sys.stdout
assert [real_space_a, real_space_b, real_space_c].count(None) in (0,3)
sensor = self.get_detector()[0].get_type()
fast, slow = self.detector_size
f, s = self.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = self.get_detector()[0].get_trusted_range()
print >> out, 'DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d' % \
(detector, trusted[0] + 1, trusted[1])
if detector == 'PILATUS':
print >> out, 'SENSOR_THICKNESS= %.3f' % \
self.get_detector()[0].get_thickness()
if self.get_detector()[0].get_material():
from cctbx.eltbx import attenuation_coefficient
material = self.get_detector()[0].get_material()
table = attenuation_coefficient.get_table(material)
mu = table.mu_at_angstrom(self.wavelength) / 10.0
print >> out, '!SENSOR_MATERIAL / THICKNESS %s %.3f' % \
(material, self.get_detector()[0].get_thickness())
print >> out, '!SILICON= %f' % mu
print >> out, 'DIRECTION_OF_DETECTOR_X-AXIS= %.3f %.3f %.3f' % \
self.detector_x_axis
print >> out, 'DIRECTION_OF_DETECTOR_Y-AXIS= %.3f %.3f %.3f' % \
self.detector_y_axis
print >> out, 'NX=%d NY=%d QX=%.4f QY=%.4f' % (fast, slow, f, s)
print >> out, 'DETECTOR_DISTANCE= %.3f' % self.detector_distance
print >> out, 'ORGX= %.1f ORGY= %.1f' % self.detector_origin
print >> out, 'ROTATION_AXIS= %.3f %.3f %.3f' % \
self.rotation_axis
print >> out, 'STARTING_ANGLE= %.3f' % \
self.starting_angle
print >> out, 'OSCILLATION_RANGE= %.3f' % \
self.oscillation_range
print >> out, 'X-RAY_WAVELENGTH= %.5f' % \
self.wavelength
print >> out, 'INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f' % \
self.beam_vector
# FIXME LATER
if hasattr(self.get_beam(), "get_polarization_fraction"):
print >> out, 'FRACTION_OF_POLARIZATION= %.3f' % \
self.get_beam().get_polarization_fraction()
print >> out, 'POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f' % \
self.get_beam().get_polarization_normal()
print >> out, 'NAME_TEMPLATE_OF_DATA_FRAMES= %s' % \
self.get_template().replace('#', '?')
print >> out, 'TRUSTED_REGION= 0.0 1.41'
for f0, s0, f1, s1 in self.get_detector()[0].get_mask():
print >> out, 'UNTRUSTED_RECTANGLE= %d %d %d %d' % \
(f0 - 1, f1 + 1, s0 - 1, s1 + 1)
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
print >> out, 'DATA_RANGE= %d %d' % start_end
print >> out, 'JOB=%s' %job_card
if space_group_number is not None:
print >> out, 'SPACE_GROUP_NUMBER= %i' %space_group_number
if [real_space_a, real_space_b, real_space_c].count(None) == 0:
R = self.imagecif_to_xds_transformation_matrix
unit_cell_a_axis = R * matrix.col(real_space_a)
unit_cell_b_axis = R * matrix.col(real_space_b)
unit_cell_c_axis = R * matrix.col(real_space_c)
print >> out, "UNIT_CELL_A-AXIS= %.6f %.6f %.6f" %unit_cell_a_axis.elems
print >> out, "UNIT_CELL_B-AXIS= %.6f %.6f %.6f" %unit_cell_b_axis.elems
print >> out, "UNIT_CELL_C-AXIS= %.6f %.6f %.6f" %unit_cell_c_axis.elems
def XDS_INP(
self,
out=None,
space_group_number=None,
real_space_a=None,
real_space_b=None,
real_space_c=None,
job_card="XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT"):
if out is None:
out = sys.stdout
assert [real_space_a, real_space_b, real_space_c].count(None) in (0, 3)
sensor = self.get_detector()[0].get_type()
fast, slow = self.detector_size
f, s = self.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = self.get_detector()[0].get_trusted_range()
print >> out, 'DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d' % \
(detector, trusted[0] + 1, trusted[1])
if detector == 'PILATUS':
print >> out, 'SENSOR_THICKNESS= %.3f' % \
self.get_detector()[0].get_thickness()
if self.get_detector()[0].get_material():
from cctbx.eltbx import attenuation_coefficient
material = self.get_detector()[0].get_material()
table = attenuation_coefficient.get_table(material)
mu = table.mu_at_angstrom(self.wavelength) / 10.0
print >> out, '!SENSOR_MATERIAL / THICKNESS %s %.3f' % \
(material, self.get_detector()[0].get_thickness())
print >> out, '!SILICON= %f' % mu
print >> out, 'DIRECTION_OF_DETECTOR_X-AXIS= %.5f %.5f %.5f' % \
self.detector_x_axis
print >> out, 'DIRECTION_OF_DETECTOR_Y-AXIS= %.5f %.5f %.5f' % \
self.detector_y_axis
print >> out, 'NX=%d NY=%d QX=%.4f QY=%.4f' % (fast, slow, f, s)
print >> out, 'DETECTOR_DISTANCE= %.6f' % self.detector_distance
print >> out, 'ORGX= %.2f ORGY= %.2f' % self.detector_origin
print >> out, 'ROTATION_AXIS= %.5f %.5f %.5f' % \
self.rotation_axis
print >> out, 'STARTING_ANGLE= %.3f' % \
self.starting_angle
print >> out, 'OSCILLATION_RANGE= %.3f' % \
self.oscillation_range
print >> out, 'X-RAY_WAVELENGTH= %.5f' % \
self.wavelength
print >> out, 'INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f' % \
tuple([b / self.wavelength for b in self.beam_vector])
# FIXME LATER
if hasattr(self.get_beam(), "get_polarization_fraction"):
print >> out, 'FRACTION_OF_POLARIZATION= %.3f' % \
self.get_beam().get_polarization_fraction()
print >> out, 'POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f' % \
self.get_beam().get_polarization_normal()
print >> out, 'NAME_TEMPLATE_OF_DATA_FRAMES= %s' % \
self.get_template().replace('#', '?')
print >> out, 'TRUSTED_REGION= 0.0 1.41'
for f0, s0, f1, s1 in self.get_detector()[0].get_mask():
print >> out, 'UNTRUSTED_RECTANGLE= %d %d %d %d' % \
(f0 - 1, f1 + 1, s0 - 1, s1 + 1)
start_end = self.get_scan().get_image_range()
if start_end[0] == 0:
start_end = (1, start_end[1])
print >> out, 'DATA_RANGE= %d %d' % start_end
print >> out, 'JOB=%s' % job_card
if space_group_number is not None:
print >> out, 'SPACE_GROUP_NUMBER= %i' % space_group_number
if [real_space_a, real_space_b, real_space_c].count(None) == 0:
R = self.imagecif_to_xds_transformation_matrix
unit_cell_a_axis = R * matrix.col(real_space_a)
unit_cell_b_axis = R * matrix.col(real_space_b)
unit_cell_c_axis = R * matrix.col(real_space_c)
print >> out, "UNIT_CELL_A-AXIS= %.6f %.6f %.6f" % unit_cell_a_axis.elems
print >> out, "UNIT_CELL_B-AXIS= %.6f %.6f %.6f" % unit_cell_b_axis.elems
print >> out, "UNIT_CELL_C-AXIS= %.6f %.6f %.6f" % unit_cell_c_axis.elems
if len(self.panel_x_axis) > 1:
for panel_id, panel_x_axis in enumerate(self.panel_x_axis):
print >> out
print >> out, "!"
print >> out, "! SEGMENT %d" % (panel_id + 1)
print >> out, "!"
print >> out, 'SEGMENT= %d %d %d %d' % self.panel_limits[
panel_id]
print >> out, 'DIRECTION_OF_SEGMENT_X-AXIS= %.5f %.5f %.5f' % \
panel_x_axis
print >> out, 'DIRECTION_OF_SEGMENT_Y-AXIS= %.5f %.5f %.5f' % \
self.panel_y_axis[panel_id]
print >> out, 'SEGMENT_DISTANCE= %.3f' % self.panel_distance[
panel_id]
print >> out, 'SEGMENT_ORGX= %.2f SEGMENT_ORGY= %.2f' % self.panel_origin[
panel_id]
print >> out
def imageset_to_xds(imageset, synchrotron = None, refined_beam_vector = None,
refined_rotation_axis = None, refined_distance = None):
'''A function to take an input header dictionary from Diffdump
and generate a list of records to start XDS - see Doc/INP.txt.'''
# decide if we are at a synchrotron if we don't know already...
# that is, the wavelength is around either the Copper or Chromium
# K-alpha edge and this is an image plate.
beam = imageset.get_beam()
from dxtbx.serialize.xds import to_xds, xds_detector_name
converter = to_xds(imageset)
detector_class_is_square = {
'adsc q4':True,
'adsc q4 2x2 binned':True,
'adsc q210':True,
'adsc q210 2x2 binned':True,
'adsc q270':True,
'adsc q270 2x2 binned':True,
'adsc q315':True,
'adsc q315 2x2 binned':True,
'adsc HF4M':True,
'holton fake 01':True,
'mar 345':False,
'mar 180':False,
'mar 240':False,
'mar 300 ccd':True,
'mar 325 ccd':True,
'mar 225 ccd':True,
'mar ccd 225 hs':True,
'rayonix ccd 165':False,
'rayonix ccd 135':False,
'rayonix ccd 300':True,
'rayonix ccd 325':True,
'rayonix ccd 225':True,
'rayonix ccd 225 hs':True,
'rayonix ccd 300 hs':True,
'mar 165 ccd':False,
'mar 135 ccd':False,
'pilatus 12M':True,
'pilatus 6M':True,
'pilatus 2M':True,
'pilatus 1M':True,
'pilatus 200K':True,
'pilatus 300K':True,
'eiger 4M':True,
'eiger 9M':True,
'eiger 16M':True,
'rigaku saturn 92 2x2 binned':True,
'rigaku saturn 944 2x2 binned':True,
'rigaku saturn 724 2x2 binned':True,
'rigaku saturn 92':True,
'rigaku saturn 944':True,
'rigaku saturn 724':True,
'rigaku saturn a200':True,
'raxis IV':True,
'NOIR1':True}
sensor = converter.get_detector()[0].get_type()
fast, slow = converter.detector_size
f, s = converter.pixel_size
df = int(1000 * f)
ds = int(1000 * s)
# FIXME probably need to rotate by pi about the X axis
result = []
from dxtbx.model.detector_helpers_types import detector_helpers_types
detector = xds_detector_name(
detector_helpers_types.get(sensor, fast, slow, df, ds))
trusted = converter.get_detector()[0].get_trusted_range()
# FIXME what follows below should perhaps be 0 for the really weak
# pilatus data sets?
result.append('DETECTOR=%s MINIMUM_VALID_PIXEL_VALUE=%d OVERLOAD=%d' %
(detector, trusted[0] + 1, trusted[1]))
result.append('DIRECTION_OF_DETECTOR_X-AXIS=%f %f %f' %
converter.detector_x_axis)
result.append('DIRECTION_OF_DETECTOR_Y-AXIS=%f %f %f' %
converter.detector_y_axis)
from xia2.Handlers.Phil import PhilIndex
params = PhilIndex.get_python_object()
if params.xds.trusted_region:
result.append(
'TRUSTED_REGION= %.2f %.2f' % tuple(params.xds.trusted_region))
elif detector_class_is_square[
detector_helpers_types.get(sensor, fast, slow, df, ds).replace('-', ' ')]:
result.append('TRUSTED_REGION=0.0 1.41')
else:
result.append('TRUSTED_REGION=0.0 0.99')
result.append('NX=%d NY=%d QX=%.4f QY=%.4f' % (fast, slow, f, s))
# RAXIS detectors have the distance written negative - why????
# this is ONLY for XDS - SATURN are the same - probably left handed
# goniometer rotation on rigaku X-ray sets.
if refined_distance:
result.append('DETECTOR_DISTANCE=%7.3f' % refined_distance)
else:
result.append('DETECTOR_DISTANCE=%7.3f' % converter.detector_distance)
result.append('OSCILLATION_RANGE=%4.2f' % converter.oscillation_range)
result.append('X-RAY_WAVELENGTH=%8.6f' % converter.wavelength)
# if user specified reversephi and this was not picked up in the
# format class reverse phi: n.b. double-negative warning!
if refined_rotation_axis:
result.append('ROTATION_AXIS= %f %f %f' % \
refined_rotation_axis)
else:
result.append('ROTATION_AXIS= %.3f %.3f %.3f' % \
converter.rotation_axis)
if refined_beam_vector:
result.append('INCIDENT_BEAM_DIRECTION=%f %f %f' % \
refined_beam_vector)
else:
result.append(
'INCIDENT_BEAM_DIRECTION= %.3f %.3f %.3f' % converter.beam_vector)
if hasattr(beam, "get_polarization_fraction"):
R = converter.imagecif_to_xds_transformation_matrix
result.append('FRACTION_OF_POLARIZATION= %.3f' %
beam.get_polarization_fraction())
result.append('POLARIZATION_PLANE_NORMAL= %.3f %.3f %.3f' %
(R * matrix.col(beam.get_polarization_normal())).elems)
# 24/NOV/14 XDS determines the air absorption automatically
# based on wavelength. May be useful to override this for in vacuo exps
# result.append('AIR=0.001')
if detector == 'PILATUS':
try:
thickness = converter.get_detector()[0].get_thickness()
if not thickness:
thickness = 0.32
Debug.write('Could not determine sensor thickness. Assuming default PILATUS 0.32mm')
except e:
thickness = 0.32
Debug.write('Error occured during sensor thickness determination. Assuming default PILATUS 0.32mm')
result.append('SENSOR_THICKNESS=%f' % thickness)
# # FIXME: Sensor absorption coefficient calculation probably requires a more general solution
# if converter.get_detector()[0].get_material() == 'CdTe':
# print "CdTe detector detected. Beam wavelength is %8.6f Angstrom" % converter.wavelength
if len(converter.panel_x_axis) > 1:
for panel_id in range(len(converter.panel_x_axis)):
result.append('')
result.append('!')
result.append('! SEGMENT %d' %(panel_id+1))
result.append('!')
result.append('SEGMENT= %d %d %d %d' % converter.panel_limits[panel_id])
result.append('DIRECTION_OF_SEGMENT_X-AXIS= %.3f %.3f %.3f' % \
converter.panel_x_axis[panel_id])
result.append('DIRECTION_OF_SEGMENT_Y-AXIS= %.3f %.3f %.3f' % \
converter.panel_y_axis[panel_id])
result.append('SEGMENT_DISTANCE= %.3f' % converter.panel_distance[panel_id])
result.append(
'SEGMENT_ORGX= %.1f SEGMENT_ORGY= %.1f' % converter.panel_origin[panel_id])
result.append('')
for f0, s0, f1, s1 in converter.get_detector()[0].get_mask():
result.append('UNTRUSTED_RECTANGLE= %d %d %d %d' %
(f0 - 1, f1 + 1, s0 - 1, s1 + 1))
if params.xds.untrusted_ellipse:
for untrusted_ellipse in params.xds.untrusted_ellipse:
result.append(
'UNTRUSTED_ELLIPSE= %d %d %d %d' % tuple(untrusted_ellipse))
Debug.write(result[-1])
if params.xds.untrusted_rectangle:
for untrusted_rectangle in params.xds.untrusted_rectangle:
result.append(
'UNTRUSTED_RECTANGLE= %d %d %d %d' % tuple(untrusted_rectangle))
Debug.write(result[-1])
return result
