def run(file_name):
from libtbx.test_utils import approx_equal
py_image_obj = pyCBFImage(file_name)
py_image_obj.read()
c_image_obj = CBFImage(file_name)
c_image_obj.read()
assert_equal(py_image_obj.linearintdata, c_image_obj.linearintdata)
assert py_image_obj.size1 == c_image_obj.size1
assert py_image_obj.size2 == c_image_obj.size2
assert approx_equal(py_image_obj.saturation, c_image_obj.saturation)
assert approx_equal(py_image_obj.pixel_size, c_image_obj.pixel_size)
assert approx_equal(py_image_obj.osc_start, c_image_obj.osc_start)
assert approx_equal(py_image_obj.deltaphi, c_image_obj.deltaphi)
assert approx_equal(py_image_obj.wavelength, c_image_obj.wavelength)
assert approx_equal(py_image_obj.distance, c_image_obj.distance)
assert approx_equal(py_image_obj.beamx, c_image_obj.beamx)
assert approx_equal(py_image_obj.beamy, c_image_obj.beamy)
def run(file_name): from libtbx.test_utils import approx_equal py_image_obj = pyCBFImage(file_name) py_image_obj.read() c_image_obj = CBFImage(file_name) c_image_obj.read() assert_equal(py_image_obj.linearintdata, c_image_obj.linearintdata) assert py_image_obj.size1 == c_image_obj.size1 assert py_image_obj.size2 == c_image_obj.size2 assert approx_equal(py_image_obj.saturation, c_image_obj.saturation) assert approx_equal(py_image_obj.pixel_size, c_image_obj.pixel_size) assert approx_equal(py_image_obj.osc_start, c_image_obj.osc_start) assert approx_equal(py_image_obj.deltaphi, c_image_obj.deltaphi) assert approx_equal(py_image_obj.wavelength, c_image_obj.wavelength) assert approx_equal(py_image_obj.distance, c_image_obj.distance) assert approx_equal(py_image_obj.beamx, c_image_obj.beamx) assert approx_equal(py_image_obj.beamy, c_image_obj.beamy)
def _start(self):
'''Open the image file as a cbf file handle, and keep this somewhere
safe.'''
FormatCBF._start(self)
from iotbx.detectors.cbf import CBFImage
self.detectorbase = CBFImage(self._image_file)
self.detectorbase.readHeader()
def detectorbase_start(self):
self.detectorbase = CBFImage(self._image_file)
self.detectorbase.readHeader()
class FormatCBFFull(FormatCBF):
"""An image reading class for full CBF format images i.e. those from
a variety of cameras which support this format."""
@staticmethod
def understand(image_file):
"""Check to see if this looks like an CBF format image, i.e. we can
make sense of it."""
header = FormatCBF.get_cbf_header(image_file)
if "_diffrn.id" not in header and "_diffrn_source" not in header:
return False
return True
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file."""
# It appears Pycbf can not handle unicode filenames (see dials/dials#256)
self._raw_data = None
super(FormatCBFFull, self).__init__(str(image_file), **kwargs)
def __del__(self):
self._cbf_handle.__swig_destroy__(self._cbf_handle)
def _get_cbf_handle(self):
try:
return self._cbf_handle
except AttributeError:
self._cbf_handle = pycbf.cbf_handle_struct()
buffer = None
# Reopen to tell if it's a gzip - this should be cached, so fast
with FormatCBF.open_file(self._image_file, "rb") as fin:
# If this was a gzip or bzip file, read as a buffer
if (gzip and isinstance(fin._cache_object._file, gzip.GzipFile)
) or (bz2 and isinstance(fin._cache_object._file,
bz2.BZ2File)):
buffer = fin.read()
if buffer:
cbf_read_buffer(self._cbf_handle, buffer, pycbf.MSG_DIGEST)
else:
self._cbf_handle.read_widefile(self._image_file.encode(),
pycbf.MSG_DIGEST)
return self._cbf_handle
def _goniometer(self):
"""Return a working goniometer instance."""
return self._goniometer_factory.imgCIF_H(self._get_cbf_handle())
def _detector(self):
"""Return a working detector instance."""
return self._detector_factory.imgCIF_H(self._get_cbf_handle(),
"unknown")
def _beam(self):
"""Return a working beam instance."""
return self._beam_factory.imgCIF_H(self._get_cbf_handle())
def _scan(self):
"""Return a working scan instance."""
return self._scan_factory.imgCIF_H(self._image_file,
self._get_cbf_handle())
def detectorbase_start(self):
self.detectorbase = CBFImage(self._image_file)
self.detectorbase.readHeader()
def get_raw_data(self):
"""Get the pixel intensities (i.e. read the image and return as a
flex array."""
if self._raw_data is not None:
return self._raw_data
self.detectorbase_start()
try:
image = self.detectorbase
image.read()
self._raw_data = image.get_raw_data()
return self._raw_data
except Exception:
return None
def detectorbase_start(self): from iotbx.detectors.cbf import CBFImage self.detectorbase = CBFImage(self._image_file) self.detectorbase.readHeader()
class FormatCBFFull(FormatCBF):
'''An image reading class for full CBF format images i.e. those from
a variety of cameras which support this format.'''
@staticmethod
def understand(image_file):
'''Check to see if this looks like an CBF format image, i.e. we can
make sense of it.'''
header = FormatCBF.get_cbf_header(image_file)
if not '_diffrn.id' in header and not '_diffrn_source' in header:
return False
return True
def __init__(self, image_file, **kwargs):
'''Initialise the image structure from the given file.'''
assert(self.understand(image_file))
FormatCBF.__init__(self, image_file, **kwargs)
return
def __del__(self):
self._cbf_handle.__swig_destroy__(self._cbf_handle)
def _start(self):
'''Open the image file as a cbf file handle, and keep this somewhere
safe.'''
FormatCBF._start(self)
def _get_cbf_handle(self):
try:
return self._cbf_handle
except AttributeError:
self._cbf_handle = pycbf.cbf_handle_struct()
self._cbf_handle.read_widefile(self._image_file, pycbf.MSG_DIGEST)
return self._cbf_handle
def _goniometer(self):
'''Return a working goniometer instance.'''
return self._goniometer_factory.imgCIF_H(self._get_cbf_handle())
def _detector(self):
'''Return a working detector instance.'''
return self._detector_factory.imgCIF_H(self._get_cbf_handle(), 'unknown')
def _beam(self):
'''Return a working beam instance.'''
return self._beam_factory.imgCIF_H(self._get_cbf_handle())
def _scan(self):
'''Return a working scan instance.'''
return self._scan_factory.imgCIF_H(self._image_file, self._get_cbf_handle())
def detectorbase_start(self):
from iotbx.detectors.cbf import CBFImage
self.detectorbase = CBFImage(self._image_file)
self.detectorbase.readHeader()
def get_raw_data(self):
'''Get the pixel intensities (i.e. read the image and return as a
flex array.'''
self.detectorbase_start()
try:
image = self.detectorbase
image.read()
raw_data = image.get_raw_data()
return raw_data
except Exception:
return None
def detectorbase_start(self):
from iotbx.detectors.cbf import CBFImage
self.detectorbase = CBFImage(self._image_file)
self.detectorbase.readHeader()
class FormatCBFFull(FormatCBF):
"""An image reading class for full CBF format images i.e. those from
a variety of cameras which support this format."""
@staticmethod
def understand(image_file):
"""Check to see if this looks like an CBF format image, i.e. we can
make sense of it."""
header = FormatCBF.get_cbf_header(image_file)
if "_diffrn.id" not in header and "_diffrn_source" not in header:
return False
return True
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file."""
# It appears Pycbf can not handle unicode filenames (see dials/dials#256)
image_file = str(image_file)
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatCBF.__init__(self, image_file, **kwargs)
self._raw_data = None
def __del__(self):
self._cbf_handle.__swig_destroy__(self._cbf_handle)
def _start(self):
"""Open the image file as a cbf file handle, and keep this somewhere
safe."""
FormatCBF._start(self)
def _get_cbf_handle(self):
try:
return self._cbf_handle
except AttributeError:
self._cbf_handle = pycbf.cbf_handle_struct()
self._cbf_handle.read_widefile(self._image_file.encode(), pycbf.MSG_DIGEST)
return self._cbf_handle
def _goniometer(self):
"""Return a working goniometer instance."""
return self._goniometer_factory.imgCIF_H(self._get_cbf_handle())
def _detector(self):
"""Return a working detector instance."""
return self._detector_factory.imgCIF_H(self._get_cbf_handle(), "unknown")
def _beam(self):
"""Return a working beam instance."""
return self._beam_factory.imgCIF_H(self._get_cbf_handle())
def _scan(self):
"""Return a working scan instance."""
return self._scan_factory.imgCIF_H(self._image_file, self._get_cbf_handle())
def detectorbase_start(self):
from iotbx.detectors.cbf import CBFImage
self.detectorbase = CBFImage(self._image_file)
self.detectorbase.readHeader()
def get_raw_data(self):
"""Get the pixel intensities (i.e. read the image and return as a
flex array."""
if self._raw_data is not None:
return self._raw_data
self.detectorbase_start()
try:
image = self.detectorbase
image.read()
self._raw_data = image.get_raw_data()
return self._raw_data
except Exception:
return None