def get_raw_data(self, index):
from boost.python import streambuf
from scitbx.array_family import flex
# is this image a type we can read?
assert self._data_type in ["h", "f", "B", "l", "b", "H", "I", "d"]
with FormatGatanDM4.open_file(self._image_file, "rb") as f:
f.seek(self._data_offset)
skip_bytes = index * self._image_num_elements * self._data_size
f.seek(skip_bytes, whence=1)
if self._data_type == "f":
from dxtbx import read_float32
raw_data = read_float32(streambuf(f), self._image_num_elements)
elif self._data_type == "B":
from dxtbx import read_uint8
raw_data = read_uint8(streambuf(f), self._image_num_elements)
elif self._data_type == "h":
from dxtbx import read_int16
raw_data = read_int16(streambuf(f), self._image_num_elements)
elif self._data_type == "H":
from dxtbx import read_uint16
raw_data = read_uint16(streambuf(f), self._image_num_elements)
elif self._data_type == "l":
from dxtbx import read_int32
raw_data = read_int32(streambuf(f), self._image_num_elements)
elif self._data_type == "I":
from dxtbx import read_uint32
raw_data = read_uint32(streambuf(f), self._image_num_elements)
# no C++ reader for remaining types (should be unusual anyway)
else:
vals = struct.unpack(
self._byteord + self._data_type * self._image_num_elements,
f.read(self._data_size * self._image_num_elements),
)
if self._data_type == "d":
raw_data = flex.double(vals)
if self._data_type in ["b", "?"]:
raw_data = flex.int(vals)
raw_data.reshape(flex.grid(self._image_size[1], self._image_size[0]))
return raw_data
def get_raw_data(self, index):
from boost.python import streambuf
from scitbx.array_family import flex
# is this image a type we can read?
assert self._data_type in ['h', 'f', 'B', 'l', 'b', 'H', 'I', 'd']
with FormatGatanDM4.open_file(self._image_file, 'rb') as f:
f.seek(self._data_offset)
skip_bytes = index * self._image_num_elements * self._data_size
f.seek(skip_bytes, whence=1)
if self._data_type == 'f':
from dxtbx import read_float32
raw_data = read_float32(streambuf(f), self._image_num_elements)
elif self._data_type == 'B':
from dxtbx import read_uint8
raw_data = read_uint8(streambuf(f), self._image_num_elements)
elif self._data_type == 'h':
from dxtbx import read_int16
raw_data = read_int16(streambuf(f), self._image_num_elements)
elif self._data_type == 'H':
from dxtbx import read_uint16
raw_data = read_uint16(streambuf(f), self._image_num_elements)
elif self._data_type == 'l':
from dxtbx import read_int32
raw_data = read_int32(streambuf(f), self._image_num_elements)
elif self._data_type == 'I':
from dxtbx import read_uint32
raw_data = read_uint32(streambuf(f), self._image_num_elements)
# no C++ reader for remaining types (should be unusual anyway)
else:
vals = struct.unpack(
self._byteord + self._data_type * self._image_num_elements,
f.read(self._data_size * self._image_num_elements))
if self._data_type == 'd':
raw_data = flex.double(vals)
if self._data_type in ['b', '?']:
raw_data = flex.int(vals)
raw_data.reshape(flex.grid(self._image_size[1], self._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