def __init__(self, image_file, **kwargs):
'''Initialise the image structure from the given file, including a
proper model of the experiment.'''
assert(self.understand(image_file))
FormatSMVRigaku.__init__(self, image_file, **kwargs)
def __init__(self, image_file):
"""Initialise the image structure from the given file, including a
proper model of the experiment."""
assert self.understand(image_file)
FormatSMVRigaku.__init__(self, image_file)
def __init__(self, image_file):
'''Initialise the image structure from the given file, including a
proper model of the experiment. Easy from Rigaku Saturn images as
they contain everything pretty much we need...'''
assert(self.understand(image_file))
FormatSMVRigaku.__init__(self, image_file)
return
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file, including a
proper model of the experiment. Easy from Rigaku Saturn images as
they contain everything pretty much we need..."""
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatSMVRigaku.__init__(self, image_file, **kwargs)
self.detector_class = "NOIR1"
self.detector = "adsc"
def get_raw_data(self):
'''Get the pixel intensities (i.e. read the image and return as a
flex array of integers.)'''
from boost.python import streambuf
from dxtbx import read_uint16, read_uint16_bs, is_big_endian
from scitbx.array_family import flex
assert(len(self.get_detector()) == 1)
image_pedestal = int(self._header_dictionary['DARK_PEDESTAL'])
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVRigaku.open_file(self._image_file, 'rb')
f.read(self._header_size)
if self._header_dictionary['BYTE_ORDER'] == 'big_endian':
big_endian = True
else:
big_endian = False
if big_endian == is_big_endian():
raw_data = read_uint16(streambuf(f), int(size[0] * size[1]))
else:
raw_data = read_uint16_bs(streambuf(f), int(size[0] * size[1]))
# apply image pedestal, will result in *negative pixel values*
raw_data -= image_pedestal
image_size = panel.get_image_size()
raw_data.reshape(flex.grid(image_size[1], image_size[0]))
return raw_data
def get_raw_data(self):
'''Get the pixel intensities (i.e. read the image and return as a
flex array of integers.)'''
from boost.python import streambuf
from dxtbx import read_uint16, read_uint16_bs, is_big_endian
from scitbx.array_family import flex
assert(len(self.get_detector()) == 1)
image_pedestal = int(self._header_dictionary['DARK_PEDESTAL'])
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVRigaku.open_file(self._image_file, 'rb')
f.read(self._header_size)
if self._header_dictionary['BYTE_ORDER'] == 'big_endian':
big_endian = True
else:
big_endian = False
if big_endian == is_big_endian():
raw_data = read_uint16(streambuf(f), int(size[0] * size[1]))
else:
raw_data = read_uint16_bs(streambuf(f), int(size[0] * size[1]))
# apply image pedestal, will result in *negative pixel values*
raw_data -= image_pedestal
image_size = panel.get_image_size()
raw_data.reshape(flex.grid(image_size[1], image_size[0]))
return raw_data
def understand(image_file):
'''Check to see if this looks like a ALS 4.2.2 NOIR SMV format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
wanted_header_items = [
'DETECTOR_NUMBER', 'DETECTOR_NAMES',
'CRYSTAL_GONIO_NUM_VALUES', 'CRYSTAL_GONIO_NAMES',
'CRYSTAL_GONIO_UNITS', 'CRYSTAL_GONIO_VALUES',
'NOIR1_CREATED',
'ROTATION', 'ROTATION_AXIS_NAME', 'ROTATION_VECTOR',
'SOURCE_VECTORS', 'SOURCE_WAVELENGTH',
'SOURCE_POLARZ', 'DIM', 'SIZE1', 'SIZE2',
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefix = header['DETECTOR_NAMES'].split()[0].strip()
more_wanted_header_items = [
'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS',
'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS',
'SPATIAL_BEAM_POSITION'
]
for header_item in more_wanted_header_items:
if not '%s%s' % (detector_prefix, header_item) in header:
return False
return True
def understand(image_file):
"""Check to see if this looks like a Rigaku A200 SMV format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for."""
size, header = FormatSMVRigaku.get_smv_header(image_file)
wanted_header_items = [
"DETECTOR_NUMBER",
"DETECTOR_NAMES",
"CRYSTAL_GONIO_NUM_VALUES",
"CRYSTAL_GONIO_NAMES",
"CRYSTAL_GONIO_UNITS",
"CRYSTAL_GONIO_VALUES",
"ROTATION",
"ROTATION_AXIS_NAME",
"ROTATION_VECTOR",
"SOURCE_VECTORS",
"SOURCE_WAVELENGTH",
"SOURCE_POLARZ",
"DIM",
"SIZE1",
"SIZE2",
]
if any(item not in header for item in wanted_header_items):
return False
detector_prefix = header["DETECTOR_NAMES"].split()[0].strip()
more_wanted_header_items = [
"DETECTOR_DIMENSIONS",
"DETECTOR_SIZE",
"DETECTOR_VECTORS",
"GONIO_NAMES",
"GONIO_UNITS",
"GONIO_VALUES",
"GONIO_VECTORS",
"SPATIAL_BEAM_POSITION",
"SPATIAL_DISTORTION_VECTORS",
]
if any(
"%s%s" % (detector_prefix, item) not in header
for item in more_wanted_header_items
):
return False
descriptive_items = ["DETECTOR_IDENTIFICATION", "DETECTOR_DESCRIPTION"]
for header_item in descriptive_items:
test = "%s%s" % (detector_prefix, header_item)
if test in header and (
"raxis" in header[test].lower() or "a200" in header[test].lower()
):
return True
return False
def understand(image_file):
'''Check to see if this looks like a Rigaku Saturn SMV format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
if 'DTREK_DATE_TIME' in header:
return False
wanted_header_items = [
'DETECTOR_NUMBER',
'DETECTOR_NAMES',
'CRYSTAL_GONIO_NUM_VALUES',
'CRYSTAL_GONIO_NAMES',
'CRYSTAL_GONIO_UNITS',
'CRYSTAL_GONIO_VALUES',
'ROTATION',
'ROTATION_AXIS_NAME',
'ROTATION_VECTOR',
'SOURCE_VECTORS',
'SOURCE_WAVELENGTH',
'SOURCE_POLARZ',
'DIM',
'SIZE1',
'SIZE2',
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefix = header['DETECTOR_NAMES'].split()[0].strip()
more_wanted_header_items = [
'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS',
'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS',
'SPATIAL_BEAM_POSITION'
]
for header_item in more_wanted_header_items:
if not '%s%s' % (detector_prefix, header_item) in header:
return False
descriptive_items = ['DETECTOR_IDENTIFICATION', 'DETECTOR_DESCRIPTION']
for header_item in descriptive_items:
test = '%s%s' % (detector_prefix, header_item)
if test in header and 'saturn' in header[test].lower():
return True
return False
def understand(image_file):
"""Check to see if this looks like a Rigaku d*TREK SMVRigaku format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for."""
size, header = FormatSMVRigaku.get_smv_header(image_file)
if "DETECTOR_TYPE" not in header:
return False
if header["DETECTOR_TYPE"] not in ["Pilatus 200K", "Pilatus 300K"]:
return False
return True
def understand(image_file):
'''Check to see if this looks like a Rigaku d*TREK SMVRigaku format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
if not 'DETECTOR_TYPE' in header:
return False
if header['DETECTOR_TYPE'] != 'Pilatus 300K':
return False
return True
def understand(image_file):
'''Check to see if this looks like a Rigaku d*TREK SMVRigaku format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
if not 'DETECTOR_TYPE' in header:
return False
if header['DETECTOR_TYPE'] != 'Pilatus 300K':
return False
return True
def understand(image_file):
"""Check to see if this looks like a ALS 4.2.2 NOIR SMV format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for."""
size, header = FormatSMVRigaku.get_smv_header(image_file)
wanted_header_items = [
"DETECTOR_NUMBER",
"DETECTOR_NAMES",
"CRYSTAL_GONIO_NUM_VALUES",
"CRYSTAL_GONIO_NAMES",
"CRYSTAL_GONIO_UNITS",
"CRYSTAL_GONIO_VALUES",
"NOIR1_CREATED",
"ROTATION",
"ROTATION_AXIS_NAME",
"ROTATION_VECTOR",
"SOURCE_VECTORS",
"SOURCE_WAVELENGTH",
"SOURCE_POLARZ",
"DIM",
"SIZE1",
"SIZE2",
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefix = header["DETECTOR_NAMES"].split()[0].strip()
more_wanted_header_items = [
"DETECTOR_DIMENSIONS",
"DETECTOR_SIZE",
"DETECTOR_VECTORS",
"GONIO_NAMES",
"GONIO_UNITS",
"GONIO_VALUES",
"GONIO_VECTORS",
"SPATIAL_BEAM_POSITION",
]
for header_item in more_wanted_header_items:
if not "%s%s" % (detector_prefix, header_item) in header:
return False
return True
def understand(image_file):
'''Check to see if this looks like a Rigaku d*TREK SMVRigaku format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
if not 'DETECTOR_NAMES' in header:
return False
name = header['DETECTOR_NAMES']
if not '%sDETECTOR_DESCRIPTION' % name in header:
return False
return 'Eiger1M' in header['%sDETECTOR_DESCRIPTION' % name]
def understand(image_file):
'''Check to see if this looks like a Rigaku d*TREK SMVRigaku format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
if not 'DETECTOR_NAMES' in header:
return False
name = header['DETECTOR_NAMES']
if not '%sDETECTOR_DESCRIPTION' % name in header:
return False
return 'Eiger1M' in header['%sDETECTOR_DESCRIPTION' % name]
def understand(image_file):
"""Check to see if this looks like a Rigaku d*TREK SMVRigaku format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for."""
size, header = FormatSMVRigaku.get_smv_header(image_file)
if "DETECTOR_NAMES" not in header:
return False
name = header["DETECTOR_NAMES"]
if "%sDETECTOR_DESCRIPTION" % name not in header:
return False
return "Eiger" in header["%sDETECTOR_DESCRIPTION" % name]
def understand(image_file):
'''Check to see if this looks like a Rigaku Saturn SMV format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
if 'DTREK_DATE_TIME' in header:
return False
wanted_header_items = [
'DETECTOR_NUMBER', 'DETECTOR_NAMES',
'CRYSTAL_GONIO_NUM_VALUES', 'CRYSTAL_GONIO_NAMES',
'CRYSTAL_GONIO_UNITS', 'CRYSTAL_GONIO_VALUES',
'ROTATION', 'ROTATION_AXIS_NAME', 'ROTATION_VECTOR',
'SOURCE_VECTORS', 'SOURCE_WAVELENGTH',
'SOURCE_POLARZ', 'DIM', 'SIZE1', 'SIZE2',
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefix = header['DETECTOR_NAMES'].split()[0].strip()
more_wanted_header_items = [
'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS',
'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS',
'SPATIAL_BEAM_POSITION'
]
for header_item in more_wanted_header_items:
if not '%s%s' % (detector_prefix, header_item) in header:
return False
descriptive_items = [
'DETECTOR_IDENTIFICATION', 'DETECTOR_DESCRIPTION'
]
for header_item in descriptive_items:
test = '%s%s' % (detector_prefix, header_item)
if test in header and 'saturn' in header[test].lower():
return True
return False
def understand(image_file):
'''Check to see if this looks like a ALS 4.2.2 NOIR SMV format image,
i.e. we can make sense of it. Essentially that will be if it contains
all of the keys we are looking for.'''
size, header = FormatSMVRigaku.get_smv_header(image_file)
wanted_header_items = [
'DETECTOR_NUMBER',
'DETECTOR_NAMES',
'CRYSTAL_GONIO_NUM_VALUES',
'CRYSTAL_GONIO_NAMES',
'CRYSTAL_GONIO_UNITS',
'CRYSTAL_GONIO_VALUES',
'NOIR1_CREATED',
'ROTATION',
'ROTATION_AXIS_NAME',
'ROTATION_VECTOR',
'SOURCE_VECTORS',
'SOURCE_WAVELENGTH',
'SOURCE_POLARZ',
'DIM',
'SIZE1',
'SIZE2',
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefix = header['DETECTOR_NAMES'].split()[0].strip()
more_wanted_header_items = [
'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS',
'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS',
'SPATIAL_BEAM_POSITION'
]
for header_item in more_wanted_header_items:
if not '%s%s' % (detector_prefix, header_item) in header:
return False
return True
def _start(self):
FormatSMVRigaku._start(self)
def _start(self):
FormatSMVRigaku._start(self)
from iotbx.detectors.dtrek import DTREKImage
self.detectorbase = DTREKImage(self._image_file)
self.detectorbase.readHeader()
def _start(self):
FormatSMVRigaku._start(self)
def _start(self):
FormatSMVRigaku._start(self)
from iotbx.detectors.saturn import SaturnImage
self.detectorbase = SaturnImage(self._image_file)
self.detectorbase.readHeader()
