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)
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVADSC.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]))
image_size = panel.get_image_size()
raw_data.reshape(flex.grid(image_size[1], image_size[0]))
return raw_data
def read_smv_image(image_file):
from boost.python import streambuf
from dxtbx import read_uint16, read_uint16_bs, is_big_endian
from scitbx.array_family import flex
header_size, header_dictionary = get_smv_header(image_file)
f = open(image_file, 'rb')
f.read(header_size)
if header_dictionary['BYTE_ORDER'] == 'big_endian':
big_endian = True
else:
big_endian = False
image_size = (int(header_dictionary['SIZE1']),
int(header_dictionary['SIZE2']))
if big_endian == is_big_endian():
raw_data = read_uint16(streambuf(f),
int(image_size[0] * image_size[1]))
else:
raw_data = 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 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)
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVNOIR.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]))
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
f = self.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(512 * 512))
else:
raw_data = read_uint16_bs(streambuf(f), int(512 * 512))
image_size = (512, 512)
raw_data.reshape(flex.grid(image_size[1], image_size[0]))
# split into separate panels
self._raw_data = []
d = self.get_detector()
for panel in d:
xmin, ymin, xmax, ymax = self.coords[panel.get_name()]
self._raw_data.append(raw_data[ymin:ymax, xmin:xmax])
return tuple(self._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
f = self.open_file(self._image_file, 'rb')
f.read(self._header_size)
nx = int(self._header_dictionary['SIZE1']) # number of pixels
ny = int(self._header_dictionary['SIZE2']) # number of pixels
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(nx * ny))
else:
raw_data = read_uint16_bs(streambuf(f), int(nx * ny))
# note that x and y are reversed here
raw_data.reshape(flex.grid(ny, nx))
self._raw_data = raw_data
return self._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
f = self.open_file(self._image_file, 'rb')
header_size = int(self.header_dict['HDRBLKS']) * 512
f.read(header_size)
# 16 bits per pixel
assert int(self.header_dict['NPIXELB'].split()[0]) == 2
nrows = int(self.header_dict['NROWS'].split()[0])
ncols = int(self.header_dict['NCOLS'].split()[0])
if is_big_endian():
raw_data = read_uint16_bs(streambuf(f), nrows * ncols)
else:
raw_data = read_uint16(streambuf(f), nrows * ncols)
image_size = (nrows, ncols)
raw_data.reshape(flex.grid(image_size[0], image_size[1]))
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 = 40
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVADSCSN.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["IMAGE_PEDESTAL"])
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVADSCSN.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 read_smv_image(image_file):
from boost.python import streambuf
from dxtbx import read_uint16, read_uint16_bs, is_big_endian
from scitbx.array_family import flex
header_size, header_dictionary = get_smv_header(image_file)
with open(image_file, "rb") as f:
f.seek(header_size)
if header_dictionary["BYTE_ORDER"] == "big_endian":
big_endian = True
else:
big_endian = False
image_size = (int(header_dictionary["SIZE1"]),
int(header_dictionary["SIZE2"]))
if big_endian == is_big_endian():
raw_data = read_uint16(streambuf(f),
int(image_size[0] * image_size[1]))
else:
raw_data = 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 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 = 1
try:
image_pedestal = float(self._header_dictionary["ADC_OFFSET"])
except KeyError:
pass
panel = self.get_detector()[0]
size = panel.get_image_size()
f = FormatSMVJHSim.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*
# this is a horrible idea since raw_data is unsigned
# see all instances of image_pedestal in dxtbx
raw_data -= int(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.)"""
# It is better to catch FORMAT 86 here and fail with a sensible error msg
# as soon as something is attempted with the image data rather than in
# the understand method. Otherwise the user gets FormatBruker reading the
# image improperly but without failing
if self.header_dict["FORMAT"] != "100":
raise Sorry(
"Only FORMAT 100 images from the Photon II are currently "
"supported")
f = self.open_file(self._image_file, "rb")
header_size = int(self.header_dict["HDRBLKS"]) * 512
f.read(header_size)
if is_big_endian():
read_2b = read_uint16_bs
read_4b = read_uint32_bs
else:
read_2b = read_uint16
read_4b = read_uint32
# NPIXELB stores the number of bytes/pixel for the data and the underflow
# table. We expect 1 byte for underflows and either 2 or 1 byte per pixel
# for the data
npixelb = [int(e) for e in self.header_dict["NPIXELB"].split()]
assert npixelb[1] == 1
if npixelb[0] == 1:
read_data = read_uint8
elif npixelb[0] == 2:
read_data = read_2b
else:
raise IncorrectFormatError(
"{0} bytes per pixel is not supported".format(npixelb[0]))
nrows = int(self.header_dict["NROWS"].split()[0])
ncols = int(self.header_dict["NCOLS"].split()[0])
raw_data = read_data(streambuf(f), nrows * ncols)
image_size = (nrows, ncols)
raw_data.reshape(flex.grid(*image_size))
(num_underflows, num_2b_overflows, num_4b_overflows) = [
int(e) for e in self.header_dict["NOVERFL"].split()
]
# read underflows
if num_underflows > 0:
# stored values are padded to a multiple of 16 bytes
nbytes = num_underflows + 15 & ~(15)
underflow_vals = read_uint8(streambuf(f), nbytes)[:num_underflows]
else:
underflow_vals = None
# handle 2 byte overflows
if num_2b_overflows > 0:
# stored values are padded to a multiple of 16 bytes
nbytes = num_2b_overflows * 2 + 15 & ~(15)
overflow_vals = read_2b(streambuf(f),
nbytes // 2)[:num_2b_overflows]
overflow = flex.int(nrows * ncols, 0)
sel = (raw_data == 255).as_1d()
overflow.set_selected(sel, overflow_vals - 255)
overflow.reshape(flex.grid(*image_size))
raw_data += overflow
# handle 4 byte overflows
if num_4b_overflows > 0:
# stored values are padded to a multiple of 16 bytes
nbytes = num_4b_overflows * 4 + 15 & ~(15)
overflow_vals = read_4b(streambuf(f),
nbytes // 4)[:num_4b_overflows]
overflow = flex.int(nrows * ncols, 0)
sel = (raw_data == 65535).as_1d()
overflow.set_selected(sel, overflow_vals - 65535)
overflow.reshape(flex.grid(*image_size))
raw_data += overflow
# handle underflows
if underflow_vals is not None:
sel = (raw_data == 0).as_1d()
underflow = flex.int(nrows * ncols, 0)
underflow.set_selected(sel, underflow_vals)
underflow.reshape(flex.grid(*image_size))
raw_data += underflow
# handle baseline. num_underflows == -1 means no baseline subtraction. See
# https://github.com/cctbx/cctbx_project/files/1262952/BISFrameFileFormats.zip
if num_underflows != -1:
num_exposures = [int(e) for e in self.header_dict["NEXP"].split()]
baseline = num_exposures[2]
raw_data += baseline
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_uint8, read_uint16, read_uint16_bs, read_uint32, read_uint32_bs
from dxtbx import is_big_endian
from scitbx.array_family import flex
f = self.open_file(self._image_file, 'rb')
header_size = int(self.header_dict['HDRBLKS']) * 512
f.read(header_size)
if is_big_endian():
read_2b = read_uint16_bs
read_4b = read_uint32_bs
else:
read_2b = read_uint16
read_4b = read_uint32
# NPIXELB stores the number of bytes/pixel for the data and the underflow
# table. We expect 1 byte for underflows and either 2 or 1 byte per pixel
# for the data
npixelb = [int(e) for e in self.header_dict['NPIXELB'].split()]
assert npixelb[1] == 1
if npixelb[0] == 1:
read_data = read_uint8
elif npixelb[0] == 2:
read_data = read_2b
else:
from dxtbx import IncorrectFormatError
raise IncorrectFormatError(
"{0} bytes per pixel is not supported".format(npixelb[0]))
nrows = int(self.header_dict['NROWS'].split()[0])
ncols = int(self.header_dict['NCOLS'].split()[0])
raw_data = read_data(streambuf(f), nrows * ncols)
image_size = (nrows, ncols)
raw_data.reshape(flex.grid(*image_size))
(num_underflows, num_2b_overflows, num_4b_overflows) = [
int(e) for e in self.header_dict['NOVERFL'].split()
]
# read underflows
if num_underflows > 0:
# stored values are padded to a multiple of 16 bytes
nbytes = num_underflows + 15 & ~(15)
underflow_vals = read_uint8(streambuf(f), nbytes)[:num_underflows]
else:
underflow_vals = None
# handle 2 byte overflows
if num_2b_overflows > 0:
# stored values are padded to a multiple of 16 bytes
nbytes = num_2b_overflows * 2 + 15 & ~(15)
overflow_vals = read_2b(streambuf(f),
nbytes // 2)[:num_2b_overflows]
overflow = flex.int(nrows * ncols, 0)
sel = (raw_data == 255).as_1d()
overflow.set_selected(sel, overflow_vals - 255)
overflow.reshape(flex.grid(*image_size))
raw_data += overflow
# handle 4 byte overflows
if num_4b_overflows > 0:
# stored values are padded to a multiple of 16 bytes
nbytes = num_4b_overflows * 4 + 15 & ~(15)
overflow_vals = read_4b(streambuf(f),
nbytes // 4)[:num_4b_overflows]
overflow = flex.int(nrows * ncols, 0)
sel = (raw_data == 65535).as_1d()
overflow.set_selected(sel, overflow_vals - 65535)
overflow.reshape(flex.grid(*image_size))
raw_data += overflow
# handle underflows
if underflow_vals is not None:
sel = (raw_data == 0).as_1d()
underflow = flex.int(nrows * ncols, 0)
underflow.set_selected(sel, underflow_vals)
underflow.reshape(flex.grid(*image_size))
raw_data += underflow
# handle baseline. num_underflows == -1 means no baseline subtraction. See
# https://github.com/cctbx/cctbx_project/files/1262952/BISFrameFileFormats.zip
if num_underflows != -1:
num_exposures = [int(e) for e in self.header_dict['NEXP'].split()]
baseline = num_exposures[2]
raw_data += baseline
return raw_data
