def detectorbase_start(self):
from xfel.cftbx.detector.cspad_detector import CSPadDetector
self.detectorbase = CSPadDetector(self._image_file)
self.detectorbase.readHeader()
self._metrology_params = self.detectorbase._metrology_params
self._tiles = self.detectorbase._tiles
# The lines above could eventually be replaced by the lines
# below.
"""
def detectorbase_start(self):
from xfel.cftbx.detector.cspad_detector import CSPadDetector
self.detectorbase = CSPadDetector(self._image_file)
self.detectorbase.readHeader()
self._metrology_params = self.detectorbase._metrology_params
self._tiles = self.detectorbase._tiles
# The lines above could eventually be replaced by the lines
# below.
"""
class FormatPYmultitile(FormatPY):
@staticmethod
def understand(image_file):
try:
import cPickle as pickle
stream = FormatPYmultitile.open_file(image_file, 'rb')
data = pickle.load(stream)
except IOError:
return False
wanted_header_items = ['TILES', 'METROLOGY']
for header_item in wanted_header_items:
if not header_item in data:
return False
unwanted_header_items = ['SIZE1', 'SIZE2']
for header_item in unwanted_header_items:
if header_item in data:
return False
return True
def __init__(self, image_file):
'''Initialise the image structure from the given file.'''
assert(self.understand(image_file))
FormatPY.__init__(self, image_file)
def _start(self):
# this Format class depends on stuff from detectorbase
self.detectorbase_start()
return
def detectorbase_start(self):
from xfel.cftbx.detector.cspad_detector import CSPadDetector
self.detectorbase = CSPadDetector(self._image_file)
self.detectorbase.readHeader()
self._metrology_params = self.detectorbase._metrology_params
self._tiles = self.detectorbase._tiles
# The lines above could eventually be replaced by the lines
# below.
"""
from cPickle import load
stream = FormatPYmultitile.open_file(self._image_file)
d = load(stream)
self._metrology_params = d['METROLOGY'].extract()
self._tiles = d['TILES']
stream.close()
"""
def _goniometer(self):
return self._goniometer_factory.single_axis()
def _detector(self):
'''The _detector() function returns a model for a CSPAD detector as
used at LCLS's CXI and XPP endstations. It converts the
metrology information in the pure Python object extracted from
the image pickle to DXTBX-style transformation vectors. Only
ASIC:s are considered, since DXTBX metrology is not concerned
with hierarchies.
Merged from xfel.cftbx.detector.cspad_detector.readHeader() and
xfel.cftbx.detector.metrology.metrology_as_dxtbx_vectors().
'''
from dxtbx.model import SimplePxMmStrategy
from dxtbx.model.detector import HierarchicalDetector
from scitbx.matrix import col
# XXX Introduces dependency on cctbx.xfel! Should probably be
# merged into the code here!
from xfel.cftbx.detector.metrology import \
_transform, get_projection_matrix
# Apply the detector distance to the translation of the root
# detector object.
d = self._metrology_params.detector
Tb_d = _transform(
col(d.orientation).normalize(),
col(d.translation) +
col((0, 0, -self._metrology_params.distance * 1e-3)))[1]
self._raw_data = []
detector = HierarchicalDetector()
for p in d.panel:
Tb_p = Tb_d * _transform(
col(p.orientation).normalize(),
col(p.translation))[1]
for s in p.sensor:
Tb_s = Tb_p * _transform(
col(s.orientation).normalize(),
col(s.translation))[1]
for a in s.asic:
Tb_a = Tb_s * _transform(
col(a.orientation).normalize(),
col(a.translation))[1]
Pb = get_projection_matrix(a.pixel_size, a.dimension)[1]
# The DXTBX-style metrology description consists of three
# vectors for each ASIC. The origin vector locates the
# (0, 0)-pixel in the laboratory frame in units of mm.
# The second and third vectors give the directions to the
# pixels immediately next to (0, 0) in the fast and slow
# directions, respectively, in arbitrary units.
origin = Tb_a * Pb * col((0, 0, 1))
fast = Tb_a * Pb * col((0, a.dimension[0], 1)) - origin
slow = Tb_a * Pb * col((a.dimension[1], 0, 1)) - origin
# Convert vector units from meter to millimeter. The
# default, SimplePxMmStrategy applies here. XXX Due to
# dark subtraction, a valid pixel intensity may be
# negative, and this is currently not reflected by
# trusted_range.
key = (d.serial, p.serial, s.serial, a.serial)
panel = detector.add_panel()
panel.set_type("PAD")
panel.set_name('%d:%d:%d:%d' % key)
panel.set_local_frame(
[t * 1e3 for t in fast.elems[0:3]],
[t * 1e3 for t in slow.elems[0:3]],
[t * 1e3 for t in origin.elems[0:3]])
panel.set_pixel_size([t * 1e3 for t in a.pixel_size])
panel.set_image_size(a.dimension)
panel.set_trusted_range((0, a.saturation))
self._raw_data.append(self._tiles[key])
return detector
def get_raw_data(self):
''' Return a tuple of flex arrays, one for each asic '''
return tuple(self._raw_data)
def _beam(self):
'''Return a simple model for the beam.'''
return self._beam_factory.simple(self._metrology_params.wavelength)
def _scan(self):
'''Return the scan information for this image.'''
from calendar import timegm
from time import strptime
# Convert textual ISO 8601 timestamp in UTC to
# millisecond-precision Unix epoch.
str_min = self._metrology_params.timestamp[:16] + 'UTC'
str_sec = self._metrology_params.timestamp[17:]
epoch = timegm(strptime(str_min, '%Y-%m-%dT%H:%M%Z')) + float(str_sec)
return self._scan_factory.make_scan(
image_range=(1, 1),
exposure_times=[1e-15 * self._metrology_params.pulse_length],
oscillation=(0, 0),
epochs={1: epoch})
class FormatPYmultitile(FormatPY):
@staticmethod
def understand(image_file):
try:
import six.moves.cPickle as pickle
stream = FormatPYmultitile.open_file(image_file, "rb")
data = pickle.load(stream)
except IOError:
return False
wanted_header_items = ["TILES", "METROLOGY"]
for header_item in wanted_header_items:
if not header_item in data:
return False
unwanted_header_items = ["SIZE1", "SIZE2"]
for header_item in unwanted_header_items:
if header_item in data:
return False
return True
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file."""
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatPY.__init__(self, image_file, **kwargs)
def _start(self):
# this Format class depends on stuff from detectorbase
self.detectorbase_start()
return
def detectorbase_start(self):
from xfel.cftbx.detector.cspad_detector import CSPadDetector
self.detectorbase = CSPadDetector(self._image_file)
self.detectorbase.readHeader()
self._metrology_params = self.detectorbase._metrology_params
self._tiles = self.detectorbase._tiles
# The lines above could eventually be replaced by the lines
# below.
"""
from cPickle import load
stream = FormatPYmultitile.open_file(self._image_file)
d = load(stream)
self._metrology_params = d['METROLOGY'].extract()
self._tiles = d['TILES']
stream.close()
"""
def _goniometer(self):
return self._goniometer_factory.single_axis()
def _detector(self):
"""The _detector() function returns a model for a CSPAD detector as
used at LCLS's CXI and XPP endstations. It converts the
metrology information in the pure Python object extracted from
the image pickle to DXTBX-style transformation vectors. Only
ASIC:s are considered, since DXTBX metrology is not concerned
with hierarchies.
Merged from xfel.cftbx.detector.cspad_detector.readHeader() and
xfel.cftbx.detector.metrology.metrology_as_dxtbx_vectors().
"""
from dxtbx.model import SimplePxMmStrategy
from dxtbx.model import Detector
from scitbx.matrix import col
# XXX Introduces dependency on cctbx.xfel! Should probably be
# merged into the code here!
from xfel.cftbx.detector.metrology import _transform, get_projection_matrix
# Apply the detector distance to the translation of the root
# detector object.
d = self._metrology_params.detector
Tb_d = _transform(
col(d.orientation).normalize(),
col(d.translation) + col((0, 0, -self._metrology_params.distance * 1e-3)),
)[1]
self._raw_data = []
detector = Detector()
for p in d.panel:
Tb_p = (
Tb_d * _transform(col(p.orientation).normalize(), col(p.translation))[1]
)
for s in p.sensor:
Tb_s = (
Tb_p
* _transform(col(s.orientation).normalize(), col(s.translation))[1]
)
for a in s.asic:
Tb_a = (
Tb_s
* _transform(
col(a.orientation).normalize(), col(a.translation)
)[1]
)
Pb = get_projection_matrix(a.pixel_size, a.dimension)[1]
# The DXTBX-style metrology description consists of three
# vectors for each ASIC. The origin vector locates the
# (0, 0)-pixel in the laboratory frame in units of mm.
# The second and third vectors give the directions to the
# pixels immediately next to (0, 0) in the fast and slow
# directions, respectively, in arbitrary units.
origin = Tb_a * Pb * col((0, 0, 1))
fast = Tb_a * Pb * col((0, a.dimension[0], 1)) - origin
slow = Tb_a * Pb * col((a.dimension[1], 0, 1)) - origin
# Convert vector units from meter to millimeter. The
# default, SimplePxMmStrategy applies here. XXX Due to
# dark subtraction, a valid pixel intensity may be
# negative, and this is currently not reflected by
# trusted_range.
key = (d.serial, p.serial, s.serial, a.serial)
panel = detector.add_panel()
panel.set_type("PAD")
panel.set_name("%d:%d:%d:%d" % key)
panel.set_local_frame(
[t * 1e3 for t in fast.elems[0:3]],
[t * 1e3 for t in slow.elems[0:3]],
[t * 1e3 for t in origin.elems[0:3]],
)
panel.set_pixel_size([t * 1e3 for t in a.pixel_size])
panel.set_image_size(a.dimension)
panel.set_trusted_range((0, a.saturation))
self._raw_data.append(self._tiles[key])
return detector
def get_raw_data(self):
""" Return a tuple of flex arrays, one for each asic """
return tuple(self._raw_data)
def _beam(self):
"""Return a simple model for the beam."""
return self._beam_factory.simple(self._metrology_params.wavelength)
def _scan(self):
"""Return the scan information for this image."""
from calendar import timegm
from time import strptime
# Convert textual ISO 8601 timestamp in UTC to
# millisecond-precision Unix epoch.
str_min = self._metrology_params.timestamp[:16] + "UTC"
str_sec = self._metrology_params.timestamp[17:]
epoch = timegm(strptime(str_min, "%Y-%m-%dT%H:%M%Z")) + float(str_sec)
return self._scan_factory.make_scan(
image_range=(1, 1),
exposure_times=[1e-15 * self._metrology_params.pulse_length],
oscillation=(0, 0),
epochs={1: epoch},
)
def detectorbase_start(self):
self.detectorbase = CSPadDetector(self._image_file)
self.detectorbase.readHeader()
self._metrology_params = self.detectorbase._metrology_params
self._tiles = self.detectorbase._tiles