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))
FormatTIFFRayonix.__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.'''
assert (self.understand(image_file))
FormatTIFFRayonix.__init__(self, image_file, **kwargs)
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)
FormatTIFFRayonix.__init__(self, image_file, **kwargs)
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))
from iotbx.detectors.mar import MARImage
MARImage._read_header_asserts = lambda self: None
FormatTIFFRayonix.__init__(self, image_file, **kwargs)
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))
from iotbx.detectors.mar import MARImage
MARImage._read_header_asserts = lambda self: None
FormatTIFFRayonix.__init__(self, image_file, **kwargs)
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)
from iotbx.detectors.mar import MARImage
MARImage._read_header_asserts = lambda self: None
FormatTIFFRayonix.__init__(self, image_file, **kwargs)
def understand(image_file):
"""Check to see if this looks like an Rayonix TIFF format image,
i.e. we can make sense of it. Returns true if the beam center is specified
in pixels."""
width, height, depth, order, bytes = FormatTIFFRayonix.get_tiff_header(
image_file)
from scitbx.matrix import col
from dxtbx.format.FormatTIFFHelpers import LITTLE_ENDIAN, BIG_ENDIAN
format = {LITTLE_ENDIAN: "<", BIG_ENDIAN: ">"}[order]
offset = 1024
detector_size_pixels = col(
struct.unpack(format + "ii", bytes[offset + 80:offset + 88]))
detector_center_px = 0.5 * detector_size_pixels
# detector_pixel_sz_mm = 1.0e-6 * col( # convert from nano to milli
# struct.unpack(format + "ii", bytes[offset + 772 : offset + 780])
# )
header_beam_center = 0.001 * col( # Rayonix says this should be pixels
struct.unpack(format + "ii", bytes[offset + 644:offset + 652]))
disagreement = header_beam_center[0] / detector_center_px[0]
return (header_beam_center[0] > 0 and header_beam_center[1] > 0
and disagreement < 0.5
) # if header was in mm, disagreement should be
def understand(image_file):
'''Check to see if this looks like an Rayonix TIFF format image,
i.e. we can make sense of it. Returns true if the beam center is specified
in pixels.'''
width, height, depth, order, bytes = FormatTIFFRayonix.get_tiff_header(
image_file)
import struct
from scitbx.matrix import col
from dxtbx.format.FormatTIFFHelpers import LITTLE_ENDIAN, BIG_ENDIAN
format = {LITTLE_ENDIAN:'<', BIG_ENDIAN:'>'}[order]
offset = 1024
detector_size_pixels = col(struct.unpack(format+'ii',bytes[offset+80:offset+88]))
detector_center_px = 0.5 * detector_size_pixels
detector_pixel_sz_mm = 1.E-6 * col( # convert from nano to milli
struct.unpack(format+'ii',bytes[offset+772:offset+780]))
header_beam_center = 0.001 * col( # Rayonix says this should be pixels
struct.unpack(format+'ii',bytes[offset+644:offset+652]))
disagreement = header_beam_center[0]/detector_center_px[0]
return header_beam_center[0] > 0 and header_beam_center[1] > 0 \
and disagreement < 0.5 # if header was in mm, disagreement should be
def understand(image_file):
"""Check to see if this looks like an Rayonix TIFF format image,
i.e. we can make sense of it. This simply checks that records which
describe the size of the image match with the TIFF records which do
the same."""
width, height, depth, order, bytes = FormatTIFFRayonix.get_tiff_header(
image_file)
serial_number = -1
for record in bytes[2464:2464 + 512].strip().split("\n"):
if "detector serial number" in record.lower():
serial_number = int(record.split()[-1])
# only understand a square image
if width != height:
return
# BL26B2 MX225 with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 24 and width in [6144, 3072, 2046, 1536]:
return True
# BL32XU MX225-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 31 and width in [6144, 3072, 2046, 1536]:
return True
# BL44XU MX225-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 38 and width in [6144, 3072, 2046, 1536]:
return True
# BL44XU MX300-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 42 and width in [8192, 4096, 2728, 2048]:
return True
# BL41XU MX225-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 40 and width in [6144, 3072, 2046, 1536]:
return True
# BL32XU MX225-HS 1X1, 2X2, 3X3, 4X4, 5X5, 6X6, 8X8 or 10X10 binning
if serial_number == 106 and width in [
5760,
2880,
1920,
1440,
1152,
960,
720,
576,
]:
return True
return False
def understand(image_file):
'''Check to see if this looks like an Rayonix TIFF format image,
i.e. we can make sense of it. This simply checks that records which
describe the size of the image match with the TIFF records which do
the same.'''
width, height, depth, order, bytes = FormatTIFFRayonix.get_tiff_header(
image_file)
serial_number = -1
for record in bytes[2464:2464+512].strip().split('\n'):
if 'detector serial number' in record.lower():
serial_number = int(record.split()[-1])
# only understand a square image
if width != height: return
# BL26B2 MX225 with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 24 and width in [6144, 3072, 2046, 1536]:
return True
# BL32XU MX225-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 31 and width in [6144, 3072, 2046, 1536]:
return True
# BL44XU MX225-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 38 and width in [6144, 3072, 2046, 1536]:
return True
# BL44XU MX300-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 42 and width in [8192, 4096, 2728, 2048]:
return True
# BL41XU MX225-HE with 1X1, 2X2, 3X3 or 4X4 binning
if serial_number == 40 and width in [6144, 3072, 2046, 1536]:
return True
# BL32XU MX225-HS 1X1, 2X2, 3X3, 4X4, 5X5, 6X6, 8X8 or 10X10 binning
if serial_number == 106 and width in [5760, 2880, 1920, 1440, 1152, 960,
720, 576]:
return True
def _get_rayonix_scan_angles(self): return check(FormatTIFFRayonix._get_rayonix_scan_angles(self))
def _get_rayonix_detector_rotations(self): return check(FormatTIFFRayonix._get_rayonix_detector_rotations(self))
def _get_rayonix_distance(self): return check(FormatTIFFRayonix._get_rayonix_distance(self))
def _get_rayonix_pixel_size(self): return check(FormatTIFFRayonix._get_rayonix_pixel_size(self))
def _get_rayonix_distance(self): return check(FormatTIFFRayonix._get_rayonix_distance(self))
def _get_rayonix_detector_rotations(self): return check(FormatTIFFRayonix._get_rayonix_detector_rotations(self))
def _get_rayonix_scan_angles(self): return check(FormatTIFFRayonix._get_rayonix_scan_angles(self))
def _get_rayonix_timestamp(self): return check(FormatTIFFRayonix._get_rayonix_timestamp(self))
def _get_rayonix_pixel_size(self): return check(FormatTIFFRayonix._get_rayonix_pixel_size(self))
def _get_rayonix_times(self): return check(FormatTIFFRayonix._get_rayonix_times(self))
