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))
FormatSMV.__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))
FormatSMV.__init__(self, image_file)
def _start(self):
FormatSMV._start(self)
if not hasattr(self, "detectorbase") or self.detectorbase is None:
from iotbx.detectors import SMVImage
self.detectorbase = SMVImage(self._image_file)
self.detectorbase.readHeader()
def __init__(self, image_file, **kwargs):
'''Initialise the image structure from the given file, including a
proper model of the experiment.'''
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatSMV.__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))
FormatSMV.__init__(self, image_file)
detector_prefixes = self._header_dictionary['DETECTOR_NAMES'].split()
self._prefix = detector_prefixes[0]
return
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))
FormatSMV.__init__(self, image_file, **kwargs)
detector_prefixes = self._header_dictionary['DETECTOR_NAMES'].split()
self._prefix = detector_prefixes[0]
return
def __init__(self, image_file, **kwargs):
'''Initialise the image structure from the given file, including a
proper model of the experiment.'''
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatSMV.__init__(self, image_file, **kwargs)
detector_prefixes = self._header_dictionary['DETECTOR_NAMES'].split()
self._prefix = detector_prefixes[0]
def understand(image_file):
'''Check to see if this looks like an ADSC 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 and not some we are not (i.e. that belong
to a Rigaku Saturn.)'''
size, header = FormatSMV.get_smv_header(image_file)
# only recognise TimePix_SU
if header.get('BEAMLINE') != 'TimePix_SU': return False
# check the header contains the things we're going to use
wanted_header_items = ['BEAM_CENTER_X', 'BEAM_CENTER_Y',
'DISTANCE', 'WAVELENGTH', 'PIXEL_SIZE',
'OSC_START', 'OSC_RANGE', 'PHI', 'SIZE1', 'SIZE2',
'BYTE_ORDER', 'DETECTOR_SN']
for header_item in wanted_header_items:
if not header_item in header:
return False
# check the pixel size is 55 microns
if not float(header['PIXEL_SIZE']) == 0.055: return False
# check there are 512*512 pixels
if not (header['SIZE1']) == '512': return False
if not (header['SIZE2']) == '512': return False
return True
def understand(image_file):
'''Check to see if this looks like an ADSC 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 and not some we are not (i.e. that belong
to a Rigaku Saturn.)'''
size, header = FormatSMV.get_smv_header(image_file)
# do not understand JHSim images
if header.get('BEAMLINE') == 'fake': return False
# do not understand Timepix_SU images
if header.get('BEAMLINE', '').upper() == 'TIMEPIX_SU': return False
# this used to include TIME
wanted_header_items = [
'BEAM_CENTER_X', 'BEAM_CENTER_Y', 'DISTANCE', 'WAVELENGTH',
'PIXEL_SIZE', 'OSC_START', 'OSC_RANGE', 'SIZE1', 'SIZE2',
'BYTE_ORDER'
]
for header_item in wanted_header_items:
if not header_item in header:
return False
unwanted_header_items = ['DTREK_DATE_TIME']
for header_item in unwanted_header_items:
if header_item in header:
return False
return True
def understand(image_file):
'''Check to see if this looks like a Rigaku d*TREK 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 = FormatSMV.get_smv_header(image_file)
wanted_header_items = [
'DETECTOR_NUMBER', 'DETECTOR_NAMES',
'BYTE_ORDER', 'DIM', 'SIZE1', 'SIZE2', 'Data_type'
]
for header_item in wanted_header_items:
if not header_item in header:
return False
# code around CMOS1 on ALS 4.2.2
detector_prefixes = header['DETECTOR_NAMES'].split()
if len(detector_prefixes) == 1:
prefix = detector_prefixes[0]
det_desc = '%sDETECTOR_DESCRIPTION' % prefix
if 'CMOS-1' in header.get(det_desc, ''):
return False
detector_prefixes = header['DETECTOR_NAMES'].split()
try:
detector_number = int(header['DETECTOR_NUMBER'].strip())
except (KeyError,AttributeError,ValueError),e:
return False
def understand(image_file):
'''Check to see if this looks like a Rigaku d*TREK 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 = FormatSMV.get_smv_header(image_file)
wanted_header_items = [
'DETECTOR_NUMBER', 'DETECTOR_NAMES',
'BYTE_ORDER', 'DIM', 'SIZE1', 'SIZE2', 'Data_type'
]
for header_item in wanted_header_items:
if not header_item in header:
return False
# code around CMOS1 on ALS 4.2.2
detector_prefixes = header['DETECTOR_NAMES'].split()
if len(detector_prefixes) == 1:
prefix = detector_prefixes[0]
det_desc = '%sDETECTOR_DESCRIPTION' % prefix
if 'CMOS-1' in header.get(det_desc, ''):
return False
detector_prefixes = header['DETECTOR_NAMES'].split()
try:
detector_number = int(header['DETECTOR_NUMBER'].strip())
except (KeyError,AttributeError,ValueError),e:
return False
def understand(image_file):
size, header = FormatSMV.get_smv_header(image_file)
# only recognise TimePix_SU
if header.get("BEAMLINE", "").upper() != "TIMEPIX_SU":
return False
# check the header contains the things we're going to use
wanted_header_items = [
"BEAM_CENTER_X",
"BEAM_CENTER_Y",
"DISTANCE",
"WAVELENGTH",
"PIXEL_SIZE",
"OSC_START",
"OSC_RANGE",
"PHI",
"SIZE1",
"SIZE2",
"BYTE_ORDER",
"DETECTOR_SN",
]
if any(item not in header for item in wanted_header_items):
return False
return True
def understand(image_file):
'''Check to see if this looks like an JHSim SMV format image, i.e. we can
make sense of it. From JH: "The best way to identify images from any of my
simulators is to look for BEAMLINE=fake in the header."'''
size, header = FormatSMV.get_smv_header(image_file)
if header.get('BEAMLINE') == 'fake':
return True
else:
return False
def understand(image_file):
"""Check to see if this looks like a CMOS1 d*TREK 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 = FormatSMV.get_smv_header(image_file)
wanted_header_items = [
"DETECTOR_NUMBER",
"DETECTOR_NAMES",
"BYTE_ORDER",
"DIM",
"SIZE1",
"SIZE2",
"Data_type",
]
if any(item not in header for item in wanted_header_items):
return False
detector_prefixes = header["DETECTOR_NAMES"].split()
if len(detector_prefixes) != 1:
return False
detector_prefix = detector_prefixes[0]
more_wanted_header_items = [
"DETECTOR_DIMENSIONS",
"DETECTOR_SIZE",
"DETECTOR_VECTORS",
"GONIO_NAMES",
"GONIO_UNITS",
"GONIO_VALUES",
"GONIO_VECTORS",
]
if any(
"%s%s" % (detector_prefix, item) not in header
for item in more_wanted_header_items
):
return False
det_desc = "%sDETECTOR_DESCRIPTION" % detector_prefix
if "CMOS-1" in header.get(det_desc, ""):
return True
return False
def get_raw_data(self):
'''Get the pixel intensities (i.e. read the image and return as a
flex array of integers.)'''
# currently have no non-little-endian machines...
from boost.python import streambuf
from dxtbx import read_uint16
from scitbx.array_family import flex
assert (len(self.get_detector()) == 1)
size = self.get_detector()[0].get_image_size()
f = FormatSMV.open_file(self._image_file)
f.read(self._header_size)
raw_data = read_uint16(streambuf(f), int(size[0] * size[1]))
image_size = self.get_detector()[0].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.)'''
# currently have no non-little-endian machines...
from boost.python import streambuf
from dxtbx import read_uint16
from scitbx.array_family import flex
assert(len(self.get_detector()) == 1)
size = self.get_detector()[0].get_image_size()
f = FormatSMV.open_file(self._image_file)
f.read(self._header_size)
raw_data = read_uint16(streambuf(f), int(size[0] * size[1]))
image_size = self.get_detector()[0].get_image_size()
raw_data.reshape(flex.grid(image_size[1], image_size[0]))
return raw_data
def understand(image_file):
size, header = FormatSMV.get_smv_header(image_file)
# only recognise TimePix_SU
if header.get('BEAMLINE', '').upper() != 'TIMEPIX_SU': return False
# check the header contains the things we're going to use
wanted_header_items = [
'BEAM_CENTER_X', 'BEAM_CENTER_Y', 'DISTANCE', 'WAVELENGTH',
'PIXEL_SIZE', 'OSC_START', 'OSC_RANGE', 'PHI', 'SIZE1', 'SIZE2',
'BYTE_ORDER', 'DETECTOR_SN'
]
for header_item in wanted_header_items:
if not header_item in header:
return False
return True
def understand(image_file):
"""Check to see if this looks like an ADSC 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 and not some we are not (i.e. that belong
to a Rigaku Saturn.)"""
size, header = FormatSMV.get_smv_header(image_file)
# do not understand JHSim images
if header.get("BEAMLINE") == "fake":
return False
# do not understand Timepix_SU images
if header.get("BEAMLINE", "").upper() == "TIMEPIX_SU":
return False
# this used to include TIME
wanted_header_items = [
"BEAM_CENTER_X",
"BEAM_CENTER_Y",
"DISTANCE",
"WAVELENGTH",
"PIXEL_SIZE",
"OSC_START",
"OSC_RANGE",
"SIZE1",
"SIZE2",
"BYTE_ORDER",
]
for header_item in wanted_header_items:
if not header_item in header:
return False
unwanted_header_items = ["DTREK_DATE_TIME"]
for header_item in unwanted_header_items:
if header_item in header:
return False
return True
def understand(image_file):
"""Check to see if this looks like a Rigaku d*TREK 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 = FormatSMV.get_smv_header(image_file)
wanted_header_items = [
"DETECTOR_NUMBER",
"DETECTOR_NAMES",
"BYTE_ORDER",
"DIM",
"SIZE1",
"SIZE2",
"Data_type",
]
if any(header_item not in header
for header_item in wanted_header_items):
return False
# code around CMOS1 on ALS 4.2.2
detector_prefixes = header["DETECTOR_NAMES"].split()
if len(detector_prefixes) == 1:
prefix = detector_prefixes[0]
det_desc = "%sDETECTOR_DESCRIPTION" % prefix
if "CMOS-1" in header.get(det_desc, ""):
return False
detector_prefixes = header["DETECTOR_NAMES"].split()
try:
detector_number = int(header["DETECTOR_NUMBER"].strip())
except (KeyError, AttributeError, ValueError):
return False
if detector_number != len(detector_prefixes):
return False
return True
def read_smv_image(image_file):
header_size, header_dictionary = FormatSMV.get_smv_header(image_file)
with open(image_file, "rb") as f:
f.seek(header_size)
big_endian = header_dictionary["BYTE_ORDER"] == "big_endian"
image_size = (int(header_dictionary["SIZE1"]),
int(header_dictionary["SIZE2"]))
if big_endian == dxtbx.ext.is_big_endian():
raw_data = dxtbx.ext.read_uint16(
streambuf(f), int(image_size[0] * image_size[1]))
else:
raw_data = dxtbx.ext.read_uint16_bs(
streambuf(f), int(image_size[0] * image_size[1]))
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 CMOS1 d*TREK 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 = FormatSMV.get_smv_header(image_file)
wanted_header_items = [
'DETECTOR_NUMBER', 'DETECTOR_NAMES', 'BYTE_ORDER', 'DIM', 'SIZE1',
'SIZE2', 'Data_type'
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefixes = header['DETECTOR_NAMES'].split()
if len(detector_prefixes) != 1:
return False
detector_prefix = detector_prefixes[0]
more_wanted_header_items = [
'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS',
'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS'
]
for header_item in more_wanted_header_items:
if not '%s%s' % (detector_prefix, header_item) in header:
return False
det_desc = '%sDETECTOR_DESCRIPTION' % detector_prefix
if 'CMOS-1' in header.get(det_desc, ''):
return True
return False
def understand(image_file):
'''Check to see if this looks like a CMOS1 d*TREK 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 = FormatSMV.get_smv_header(image_file)
wanted_header_items = [
'DETECTOR_NUMBER', 'DETECTOR_NAMES',
'BYTE_ORDER', 'DIM', 'SIZE1', 'SIZE2', 'Data_type'
]
for header_item in wanted_header_items:
if not header_item in header:
return False
detector_prefixes = header['DETECTOR_NAMES'].split()
if len(detector_prefixes) != 1:
return False
detector_prefix = detector_prefixes[0]
more_wanted_header_items = [
'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS',
'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS'
]
for header_item in more_wanted_header_items:
if not '%s%s' % (detector_prefix, header_item) in header:
return False
det_desc = '%sDETECTOR_DESCRIPTION' % detector_prefix
if 'CMOS-1' in header.get(det_desc, ''):
return True
return False
def understand(image_file):
'''Check to see if this looks like an ADSC 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 and not some we are not (i.e. that belong
to a Rigaku Saturn.)'''
size, header = FormatSMV.get_smv_header(image_file)
wanted_header_items = ['BEAM_CENTER_X', 'BEAM_CENTER_Y',
'DISTANCE', 'WAVELENGTH', 'PIXEL_SIZE',
'OSC_START', 'OSC_RANGE', 'SIZE1', 'SIZE2',
'BYTE_ORDER', 'TIME']
for header_item in wanted_header_items:
if not header_item in header:
return 0
unwanted_header_items = ['DTREK_DATE_TIME']
for header_item in unwanted_header_items:
if header_item in header:
return False
return True
def _start(self):
FormatSMV._start(self)
self._header_size = int(self._header_dictionary['HEADER_BYTES'])
def _start(self): FormatSMV._start(self) self._header_size = int(self._header_dictionary['HEADER_BYTES'])
def _start(self):
FormatSMV._start(self)
def _start(self):
FormatSMV._start(self)
def understand(image_file):
size, header = FormatSMV.get_smv_header(image_file)
if header.get("BEAMLINE") != "fake": return False
if header.get("PREFIX") is None: return False
return header.get("PREFIX").find('batch')>=0