class RAXISHelper(object):
def __init__(self, image_file, **kwargs):
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
super(RAXISHelper, self).__init__(image_file, **kwargs)
def _start(self):
with Format.open_file(self._image_file) as fh:
self._header_bytes = fh.read(1024)
if self._header_bytes[812:822].strip() in (b"SGI", b"IRIS"):
self._f = ">f"
self._i = ">i"
else:
self._f = "<f"
self._i = "<i"
def detectorbase_start(self):
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
def get_raw_data(self):
"""Get the pixel intensities (i.e. read the image and return as a flex array."""
self.detectorbase_start()
# super() resolves to the other (true) parent class
return super(RAXISHelper, self).get_raw_data()
def _detector_helper(self):
"""Returns image header values as a dictionary."""
locations = {
"det_h": (self._i, 832),
"det_v": (self._i, 836),
"det_f": (self._i, 840),
"nx": (self._i, 768),
"ny": (self._i, 772),
"dx": (self._f, 776),
"dy": (self._f, 780),
"distance": (self._f, 344),
"two_theta": (self._f, 556),
"beam_x": (self._f, 540),
"beam_y": (self._f, 544),
}
values = {
name:
struct.unpack(location[0],
self._header_bytes[location[1]:location[1] + 4])[0]
for name, location in locations.items()
}
assert values["det_h"] == 0
assert values["det_v"] == 0
assert values["det_f"] == 0
values["beam"] = (
values["beam_x"] * values["dx"],
values["beam_y"] * values["dy"],
)
return values
def _start(self):
self._header_bytes = Format.open_file(self._image_file).read(1024)
if self._header_bytes[812:822].strip() in ['SGI', 'IRIS']:
self._f = '>f'
self._i = '>i'
else:
self._f = '<f'
self._i = '<i'
from iotbx.detectors.raxis import RAXISImage
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
def detectorbase_start(self):
from iotbx.detectors.raxis import RAXISImage
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
class FormatRAXISIVSPring8(Format):
'''Format class for R-AXIS4 images. Currently the only example we have is
from SPring-8, which requires a reverse axis goniometer. It is not clear how
to distinguish this detector from others that produce 'R-AXIS4' images that we
may come across in future. This will be a problem if other detectors do not
also require reverse axis.
'''
@staticmethod
def understand(image_file):
try:
header = Format.open_file(image_file, 'rb').read(1024)
except IOError:
return False
# A few items expected to be the same from image to image that we can use
# as a fingerprint for this instrument
if header[0:7] != "R-AXIS4": return False
# We expect an invalid goniometer section, indicated by wrong magic number
if struct.unpack(">i", header[852:856]) == 1: return False
if header[812:822].strip() != "IRIS": return False
return True
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
Format.__init__(self, image_file, **kwargs)
def _start(self):
self._header_bytes = Format.open_file(self._image_file).read(1024)
if self._header_bytes[812:822].strip() in ['SGI', 'IRIS']:
self._f = '>f'
self._i = '>i'
else:
self._f = '<f'
self._i = '<i'
def detectorbase_start(self):
from iotbx.detectors.raxis import RAXISImage
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
def _goniometer(self):
return self._goniometer_factory.single_axis_reverse()
def _detector(self):
'''Return a model for the detector as defined in the image header,
with the additional knowledge about how things are arranged i.e. that
the principle rotation axis vector points from the sample downwards.'''
i = self._i
f = self._f
header = self._header_bytes
det_h = struct.unpack(i, header[832:836])[0]
det_v = struct.unpack(i, header[836:840])[0]
det_f = struct.unpack(i, header[840:844])[0]
assert (det_h == 0)
assert (det_v == 0)
assert (det_f == 0)
nx = struct.unpack(i, header[768:772])[0]
ny = struct.unpack(i, header[772:776])[0]
dx = struct.unpack(f, header[776:780])[0]
dy = struct.unpack(f, header[780:784])[0]
distance = struct.unpack(f, header[344:348])[0]
two_theta = struct.unpack(f, header[556:560])[0]
beam_x = struct.unpack(f, header[540:544])[0]
beam_y = struct.unpack(f, header[544:548])[0]
beam = (beam_x * dx, beam_y * dy)
return self._detector_factory.simple('IMAGE_PLATE', distance, beam,
'+x', '+y', (dx, dy), (nx, ny),
(0, 1000000), [])
def _beam(self):
'''Return a simple model for the beam.'''
wavelength = struct.unpack(self._f, self._header_bytes[292:296])[0]
return self._beam_factory.simple(wavelength)
def _scan(self):
'''Return the scan information for this image.'''
import calendar
i = self._i
f = self._f
header = self._header_bytes
format = self._scan_factory.format('RAXIS')
exposure_time = struct.unpack(f, header[536:540])[0]
y, m, d = map(int, header[256:268].strip().split('-'))
epoch = calendar.timegm(
datetime.datetime(y, m, d, 0, 0, 0).timetuple())
# For this instrument, the header goniometer section is invalid. 3 floats
# starting at byte 520 specify phi0, phis and phie.
# (http://www.rigaku.com/downloads/software/readimage.html)
osc_dat = struct.unpack(f, header[520:524])[0]
osc_start = osc_dat + struct.unpack(f, header[524:528])[0]
osc_end = osc_dat + struct.unpack(f, header[528:532])[0]
osc_range = osc_end - osc_start
return self._scan_factory.single(self._image_file, format,
exposure_time, osc_start, osc_range,
epoch)
def get_raw_data(self):
'''Get the pixel intensities (i.e. read the image and return as a
flex array.'''
self.detectorbase_start()
try:
image = self.detectorbase
image.read()
raw_data = image.get_raw_data()
return raw_data
except Exception:
return None
class FormatRAXIS(Format):
'''A class to support the RAXIS detector format from Rigaku.'''
@staticmethod
def understand(image_file):
'''See if this looks like an RAXIS format image - clue is first
5 letters of file should be RAXIS.'''
if Format.open_file(image_file).read(5) == 'RAXIS':
return True
return False
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
Format.__init__(self, image_file, **kwargs)
return
def _start(self):
self._header_bytes = Format.open_file(self._image_file).read(1024)
if self._header_bytes[812:822].strip() in ['SGI', 'IRIS']:
self._f = '>f'
self._i = '>i'
else:
self._f = '<f'
self._i = '<i'
def detectorbase_start(self):
from iotbx.detectors.raxis import RAXISImage
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
def _goniometer(self):
'''Return a model for the goniometer from the values stored in the
header. Assumes same reference frame as is used for the Saturn
instrument.'''
# OK for the moment I am not completely clear on how omega, chi and
# phi are defined so for the moment assert (i) that only one rotation
# axis has a non-zero offset (ii) that this is the scan axis and
# (iii) that this is aligned with (1, 0, 0) in the file... N.B.
# with these scanners it is (I believe) always the case that the
# (1, 0, 0) direction points downwards from the sample to the
# goniometer.
i = self._i
f = self._f
header = self._header_bytes
# check magic number to see if this section is valid
if struct.unpack(i, header[852:856]) == 1:
n_axes = struct.unpack(i, header[856:860])[0]
else:
n_axes = 0
scan_axis = struct.unpack(i, header[980:984])[0]
for j in range(n_axes):
axis_x = struct.unpack(f, header[860 + j * 12:864 + j * 12])[0]
axis_y = struct.unpack(f, header[864 + j * 12:868 + j * 12])[0]
axis_z = struct.unpack(f, header[868 + j * 12:872 + j * 12])[0]
axis_start = struct.unpack(f, header[920 + j * 4:924 + j * 4])[0]
axis_end = struct.unpack(f, header[940 + j * 4:944 + j * 4])[0]
axis_offset = struct.unpack(f, header[960 + j * 4:964 + j * 4])[0]
if j == scan_axis:
assert(math.fabs(axis_x - 1) < 0.001)
assert(math.fabs(axis_y) < 0.001)
assert(math.fabs(axis_z) < 0.001)
else:
assert(math.fabs(axis_start % 180.0) < 0.001)
assert(math.fabs(axis_end % 180.0) < 0.001)
return self._goniometer_factory.single_axis()
def _detector(self):
'''Return a model for the detector as defined in the image header,
with the additional knowledge about how things are arranged i.e. that
the principle rotation axis vector points from the sample downwards.'''
# As above will have to make a bunch of assumptions about how the
# detector is set up, namely that the rotation axis points downwards,
# the fast axis points along and the slow axis points up. These will
# (as well as I can understand) be asserted. Also assuming that the
# two-theta axis is along (1, 0, 0) which is all that makes sense.
i = self._i
f = self._f
header = self._header_bytes
det_h = struct.unpack(i, header[832:836])[0]
det_v = struct.unpack(i, header[836:840])[0]
det_f = struct.unpack(i, header[840:844])[0]
assert(det_h == 0)
assert(det_v == 0)
assert(det_f == 0)
nx = struct.unpack(i, header[768:772])[0]
ny = struct.unpack(i, header[772:776])[0]
dx = struct.unpack(f, header[776:780])[0]
dy = struct.unpack(f, header[780:784])[0]
distance = struct.unpack(f, header[344:348])[0]
two_theta = struct.unpack(f, header[556:560])[0]
beam_x = struct.unpack(f, header[540:544])[0]
beam_y = struct.unpack(f, header[544:548])[0]
beam = (beam_x * dx, beam_y * dy)
return self._detector_factory.two_theta(
'IMAGE_PLATE', distance, beam, '+y', '-x', '+x', two_theta,
(dx, dy), (nx, ny), (0, 1000000), [])
def _beam(self):
'''Return a simple model for the beam. This assumes a laboratory source
which has an unpolarized beam.'''
wavelength = struct.unpack(self._f, self._header_bytes[292:296])[0]
return self._beam_factory.complex((0.0, 0.0, 1.0), 0.5,
(0.0, 1.0, 0.0), wavelength)
def _scan(self):
'''Return the scan information for this image.'''
import calendar
i = self._i
f = self._f
header = self._header_bytes
# We expect an invalid goniometer section, indicated by wrong magic number
magic_no = struct.unpack(">i", header[852:856])
format = self._scan_factory.format('RAXIS')
exposure_time = struct.unpack(f, header[536:540])[0]
y, m, d = map(int, header[256:268].strip().split('-'))
epoch = calendar.timegm(datetime.datetime(y, m, d, 0, 0, 0).timetuple())
if magic_no == 1:
s = struct.unpack(i, header[980:984])[0]
osc_start = struct.unpack(f, header[920 + s * 4:924 + s * 4])[0]
osc_end = struct.unpack(f, header[940 + s * 4:944 + s * 4])[0]
else:
osc_dat = struct.unpack(f, header[520:524])[0]
osc_start = osc_dat + struct.unpack(f, header[524:528])[0]
osc_end = osc_dat + struct.unpack(f, header[528:532])[0]
osc_range = osc_end - osc_start
return self._scan_factory.single(
self._image_file, format, exposure_time,
osc_start, osc_range, epoch)
def get_raw_data(self):
'''Get the pixel intensities (i.e. read the image and return as a
flex array.'''
self.detectorbase_start()
try:
image = self.detectorbase
image.read()
raw_data = image.get_raw_data()
return raw_data
except Exception:
return None
def detectorbase_start(self):
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
def __init__(self, filename):
RAXISImage.__init__(self, filename)
def __init__(self,filename): RAXISImage.__init__(self,filename)
class FormatRAXIS(Format):
'''A class to support the RAXIS detector format from Rigaku.'''
@staticmethod
def understand(image_file):
'''See if this looks like an RAXIS format image - clue is first
5 letters of file should be RAXIS.'''
if Format.open_file(image_file).read(5) == 'RAXIS':
return True
return False
def __init__(self, image_file):
assert(self.understand(image_file))
Format.__init__(self, image_file)
return
def _start(self):
self._header_bytes = Format.open_file(self._image_file).read(1024)
if self._header_bytes[812:822].strip() in ['SGI', 'IRIS']:
self._f = '>f'
self._i = '>i'
else:
self._f = '<f'
self._i = '<i'
from iotbx.detectors.raxis import RAXISImage
self.detectorbase = RAXISImage(self._image_file)
self.detectorbase.readHeader()
def _goniometer(self):
'''Return a model for the goniometer from the values stored in the
header. Assumes same reference frame as is used for the Saturn
instrument.'''
# OK for the moment I am not completely clear on how omega, chi and
# phi are defined so for the moment assert (i) that only one rotation
# axis has a non-zero offset (ii) that this is the scan axis and
# (iii) that this is aligned with (1, 0, 0) in the file... N.B.
# with these scanners it is (I believe) always the case that the
# (1, 0, 0) direction points downwards from the sample to the
# goniometer.
i = self._i
f = self._f
header = self._header_bytes
# check magic number to see if this section is valid
if struct.unpack(i, header[852:856]) == 1:
n_axes = struct.unpack(i, header[856:860])[0]
else:
n_axes = 0
scan_axis = struct.unpack(i, header[980:984])[0]
for j in range(n_axes):
axis_x = struct.unpack(f, header[860 + j * 12:864 + j * 12])[0]
axis_y = struct.unpack(f, header[864 + j * 12:868 + j * 12])[0]
axis_z = struct.unpack(f, header[868 + j * 12:872 + j * 12])[0]
axis_start = struct.unpack(f, header[920 + j * 4:924 + j * 4])[0]
axis_end = struct.unpack(f, header[940 + j * 4:944 + j * 4])[0]
axis_offset = struct.unpack(f, header[960 + j * 4:964 + j * 4])[0]
if j == scan_axis:
assert(math.fabs(axis_x - 1) < 0.001)
assert(math.fabs(axis_y) < 0.001)
assert(math.fabs(axis_z) < 0.001)
else:
assert(math.fabs(axis_start % 180.0) < 0.001)
assert(math.fabs(axis_end % 180.0) < 0.001)
return self._goniometer_factory.single_axis()
def _detector(self):
'''Return a model for the detector as defined in the image header,
with the additional knowledge about how things are arranged i.e. that
the principle rotation axis vector points from the sample downwards.'''
# As above will have to make a bunch of assumptions about how the
# detector is set up, namely that the rotation axis points downwards,
# the fast axis points along and the slow axis points up. These will
# (as well as I can understand) be asserted. Also assuming that the
# two-theta axis is along (1, 0, 0) which is all that makes sense.
i = self._i
f = self._f
header = self._header_bytes
det_h = struct.unpack(i, header[832:836])[0]
det_v = struct.unpack(i, header[836:840])[0]
det_f = struct.unpack(i, header[840:844])[0]
assert(det_h == 0)
assert(det_v == 0)
assert(det_f == 0)
nx = struct.unpack(i, header[768:772])[0]
ny = struct.unpack(i, header[772:776])[0]
dx = struct.unpack(f, header[776:780])[0]
dy = struct.unpack(f, header[780:784])[0]
distance = struct.unpack(f, header[344:348])[0]
two_theta = struct.unpack(f, header[556:560])[0]
beam_x = struct.unpack(f, header[540:544])[0]
beam_y = struct.unpack(f, header[544:548])[0]
beam = (beam_x * dx, beam_y * dy)
return self._detector_factory.two_theta(
'IMAGE_PLATE', distance, beam, '+y', '-x', '+x', two_theta,
(dx, dy), (nx, ny), (0, 1000000), [])
def _beam(self):
'''Return a simple model for the beam. This assumes a laboratory source
which has an unpolarized beam.'''
wavelength = struct.unpack(self._f, self._header_bytes[292:296])[0]
return self._beam_factory.complex((0.0, 0.0, 1.0), 0.5,
(0.0, 1.0, 0.0), wavelength)
def _scan(self):
'''Return the scan information for this image.'''
import calendar
i = self._i
f = self._f
header = self._header_bytes
# We expect an invalid goniometer section, indicated by wrong magic number
magic_no = struct.unpack(">i", header[852:856])
format = self._scan_factory.format('RAXIS')
exposure_time = struct.unpack(f, header[536:540])[0]
y, m, d = map(int, header[256:268].strip().split('-'))
epoch = calendar.timegm(datetime.datetime(y, m, d, 0, 0, 0).timetuple())
if magic_no == 1:
s = struct.unpack(i, header[980:984])[0]
osc_start = struct.unpack(f, header[920 + s * 4:924 + s * 4])[0]
osc_end = struct.unpack(f, header[940 + s * 4:944 + s * 4])[0]
else:
osc_dat = struct.unpack(f, header[520:524])[0]
osc_start = osc_dat + struct.unpack(f, header[524:528])[0]
osc_end = osc_dat + struct.unpack(f, header[528:532])[0]
osc_range = osc_end - osc_start
return self._scan_factory.single(
self._image_file, format, exposure_time,
osc_start, osc_range, epoch)
def detectorbase_start(self): from iotbx.detectors.raxis import RAXISImage self.detectorbase = RAXISImage(self._image_file) self.detectorbase.readHeader()