def _goniometer(self):
'''Return a model for a simple single-axis goniometer. This should
probably be checked against the image header.'''
from dxtbx.format.FormatCBFMiniPilatusHelpers import get_pilatus_timestamp
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary['timestamp'])
# Goniometer changed from reverse phi to conventional rotation direction
# on this date:
# calendar.timegm(time.strptime('2016-04-01T00:00:00', '%Y-%m-%dT%H:%M:%S'))
if timestamp < 1459468800:
return self._goniometer_factory.single_axis_reverse()
alpha = 50.0
if 'Phi' in self._cif_header_dictionary:
phi_value = float(self._cif_header_dictionary['Phi'].split()[0])
else:
phi_value = 0.0
if 'Kappa' in self._cif_header_dictionary:
kappa_value = float(self._cif_header_dictionary['Kappa'].split()[0])
else:
kappa_value = 0.0
if 'Omega' in self._cif_header_dictionary:
omega_value = float(self._cif_header_dictionary['Omega'].split()[0])
else:
omega_value = 0.0
return self._goniometer_factory.make_kappa_goniometer(
alpha, omega_value, kappa_value, phi_value, '-y', 'omega')
def _goniometer(self):
'''Return a model for a simple single-axis goniometer. This should
probably be checked against the image header.'''
from dxtbx.format.FormatCBFMiniPilatusHelpers import get_pilatus_timestamp
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary['timestamp'])
# Goniometer changed from reverse phi to conventional rotation direction
# on this date:
# calendar.timegm(time.strptime('2016-04-01T00:00:00', '%Y-%m-%dT%H:%M:%S'))
if timestamp < 1459468800:
return self._goniometer_factory.single_axis_reverse()
alpha = 50.0
if 'Phi' in self._cif_header_dictionary:
phi_value = float(self._cif_header_dictionary['Phi'].split()[0])
else:
phi_value = 0.0
if 'Kappa' in self._cif_header_dictionary:
kappa_value = float(
self._cif_header_dictionary['Kappa'].split()[0])
else:
kappa_value = 0.0
if 'Omega' in self._cif_header_dictionary:
omega_value = float(
self._cif_header_dictionary['Omega'].split()[0])
else:
omega_value = 0.0
return self._goniometer_factory.make_kappa_goniometer(
alpha, omega_value, kappa_value, phi_value, '-y', 'omega')
def _goniometer(self):
"""Return a model for a simple single-axis goniometer. This should
probably be checked against the image header."""
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary["timestamp"])
# Goniometer changed from reverse phi to conventional rotation direction
# on this date:
# calendar.timegm(time.strptime('2016-04-01T00:00:00', '%Y-%m-%dT%H:%M:%S'))
if timestamp < 1459468800:
return self._goniometer_factory.single_axis_reverse()
alpha = 50.0
if "Phi" in self._cif_header_dictionary:
phi_value = float(self._cif_header_dictionary["Phi"].split()[0])
else:
phi_value = 0.0
if "Kappa" in self._cif_header_dictionary:
kappa_value = float(
self._cif_header_dictionary["Kappa"].split()[0])
else:
kappa_value = 0.0
if "Omega" in self._cif_header_dictionary:
omega_value = float(
self._cif_header_dictionary["Omega"].split()[0])
else:
omega_value = 0.0
return self._goniometer_factory.make_kappa_goniometer(
alpha, omega_value, kappa_value, phi_value, "-y", "omega")
def _mask_bad_modules(self, detector):
# Mask out known bad modules
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary["timestamp"])
# https://photon-science.desy.de/research/technical_groups/detectors/e190302/e199162/CharacterizationandCalibrationofPilatus.pdf
nx = 487 # module pixels x
ny = 195 # module pixels y
cx = 60 # chip pixels x
cy = 97 # chip pixels y
dx = 7 # module gap size
if timestamp > calendar.timegm((2020, 9, 8, 0, 0, 0)):
# 2020 run 4
# Detector serviced by Dectris, no bad modules
pass
elif timestamp > calendar.timegm((2020, 2, 21, 0, 0, 0)):
# 2020 run 1
# module @ row 1 column 4
# blank chip @ row 15 column 4 (chip row 0, column 1)
# module @ row 17 column 0
# module @ row 17 column 4
if self._multi_panel:
detector[5 * 1 + 4].add_mask(0, 0, nx, ny)
detector[5 * 17].add_mask(0, 0, nx, ny)
detector[5 * 17 + 4].add_mask(0, 0, nx, ny)
detector[5 * 15 + 4].add_mask(cx, 0, cx * 2, cy)
else:
detector[1].add_mask((nx + dx) * 4, 0, (nx + dx) * 4 + nx, ny)
detector[17].add_mask(0, 0, nx, ny)
detector[17].add_mask((nx + dx) * 4, 0, (nx + dx) * 4 + nx, ny)
detector[15].add_mask((nx + dx) * 4 + cx, 0,
(nx + dx) * 4 + cx * 2, cy)
elif timestamp > calendar.timegm((2019, 11, 26, 0, 0, 0)):
# 2019 run 5
# module @ row 17 column 0
# module @ row 17 column 4
if self._multi_panel:
detector[5 * 17].add_mask(0, 0, nx, ny)
detector[5 * 17 + 4].add_mask(0, 0, nx, ny)
else:
detector[17].add_mask(0, 0, nx, ny)
detector[17].add_mask((nx + dx) * 4, 0, (nx + dx) * 4 + nx, ny)
elif timestamp > calendar.timegm((2019, 9, 3, 0, 0, 0)):
# 2019 run 4
# module @ row 15 column 2
# module @ row 17 column 0
if self._multi_panel:
detector[5 * 15 + 2].add_mask(0, 0, nx, ny)
detector[5 * 17].add_mask(0, 0, nx, ny)
else:
detector[15].add_mask((nx + dx) * 2, 0, (nx + dx) * 2 + nx, ny)
detector[17].add_mask(0, 0, nx, ny)
return detector
def _goniometer(self):
'''Return a model for a simple single-axis goniometer. This should
probably be checked against the image header.'''
from dxtbx.format.FormatCBFMiniPilatusHelpers import get_pilatus_timestamp
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary['timestamp'])
# Goniometer changed from reverse phi to conventional rotation direction
# on this date:
# calendar.timegm(time.strptime('2016-04-01T00:00:00', '%Y-%m-%dT%H:%M:%S'))
if timestamp < 1459468800:
return self._goniometer_factory.single_axis_reverse()
return self._goniometer_factory.single_axis()
def _scan(self):
exposure_time = float(self._cif_header_dictionary["Exposure_period"].split()[0])
osc_start = float(self._cif_header_dictionary["Start_angle"].split()[0])
osc_range = float(self._cif_header_dictionary["Angle_increment"].split()[0])
if "timestamp" in self._cif_header_dictionary:
timestamp = get_pilatus_timestamp(self._cif_header_dictionary["timestamp"])
else:
timestamp = 0.0
return self._scan_factory.single_file(
self._image_file, exposure_time, osc_start, osc_range, timestamp
)
def _scan(self):
"""Return the scan information for this image."""
format = self._scan_factory.format("CBF")
exposure_time = float(self._cif_header_dictionary["Exposure_period"].split()[0])
osc_start = float(self._cif_header_dictionary["Start_angle"].split()[0])
osc_range = float(self._cif_header_dictionary["Angle_increment"].split()[0])
timestamp = get_pilatus_timestamp(self._cif_header_dictionary["timestamp"])
return self._scan_factory.single(
self._image_file, format, exposure_time, osc_start, osc_range, timestamp
)
def _scan(self):
format = self._scan_factory.format('CBF')
exposure_time = float(
self._cif_header_dictionary['Exposure_period'].split()[0])
osc_start = float(
self._cif_header_dictionary['Start_angle'].split()[0])
osc_range = float(
self._cif_header_dictionary['Angle_increment'].split()[0])
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary['timestamp'])
return self._scan_factory.single(
self._image_file, format, exposure_time,
osc_start, osc_range, timestamp)
def _scan(self):
format = self._scan_factory.format('CBF')
exposure_time = float(
self._cif_header_dictionary['Exposure_period'].split()[0])
osc_start = float(
self._cif_header_dictionary['Start_angle'].split()[0])
osc_range = float(
self._cif_header_dictionary['Angle_increment'].split()[0])
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary['timestamp'])
return self._scan_factory.single(
self._image_file, format, exposure_time,
osc_start, osc_range, timestamp)
def _scan(self):
'''Return the scan information for this image.'''
format = self._scan_factory.format('CBF')
exposure_time = float(
self._cif_header_dictionary['Exposure_period'].split()[0])
osc_start = float(
self._cif_header_dictionary['Start_angle'].split()[0])
osc_range = float(
self._cif_header_dictionary['Angle_increment'].split()[0])
if "timestamp" in self._cif_header_dictionary:
timestamp = get_pilatus_timestamp(
self._cif_header_dictionary['timestamp'])
else:
timestamp = 0.0
return self._scan_factory.single(
self._image_file, format, exposure_time,
osc_start, osc_range, timestamp)
