def _start(self):
"""Open the image file, read the image header, copy it into a
dictionary for future reference."""
FormatCBF._start(self)
cif_header = FormatCBF.get_cbf_header(self._image_file)
self._cif_header_dictionary = {}
for record in cif_header.split("\n"):
if record[:1] != "#":
continue
if len(record[1:].split()) <= 2 and record.count(":") == 2:
self._cif_header_dictionary["timestamp"] = record[1:].strip()
continue
tokens = record.replace("=", "").replace(":", "").split()
self._cif_header_dictionary[tokens[1]] = " ".join(tokens[2:])
for record in self._mime_header.split("\n"):
if not record.strip():
continue
token, value = record.split(":")
self._cif_header_dictionary[token.strip()] = value.strip()
def _start(self):
'''Open the image file, read the image header, copy it into a
dictionary for future reference.'''
FormatCBF._start(self)
cif_header = FormatCBF.get_cbf_header(self._image_file)
self._cif_header_dictionary = { }
for record in cif_header.split('\n'):
if not '#' in record[:1]:
continue
if len(record[1:].split()) <= 2 and record.count(':') == 2:
self._cif_header_dictionary['timestamp'] = record[1:].strip()
continue
tokens = record.replace('=', '').replace(':', '').split()[1:]
self._cif_header_dictionary[tokens[0]] = ' '.join(tokens[1:])
for record in self._mime_header.split('\n'):
if not record.strip():
continue
token, value = record.split(':')
self._cif_header_dictionary[token.strip()] = value.strip()
return
def _start(self):
'''Open the image file, read the image header, copy it into a
dictionary for future reference.'''
FormatCBF._start(self)
cif_header = FormatCBF.get_cbf_header(self._image_file)
self._cif_header_dictionary = {}
for record in cif_header.split('\n'):
if not '#' in record[:1]:
continue
if len(record[1:].split()) <= 2 and record.count(':') == 2:
self._cif_header_dictionary['timestamp'] = record[1:].strip()
continue
tokens = record.replace('=', '').replace(':', '').split()[1:]
self._cif_header_dictionary[tokens[0]] = ' '.join(tokens[1:])
for record in self._mime_header.split('\n'):
if not record.strip():
continue
token, value = record.split(':')
self._cif_header_dictionary[token.strip()] = value.strip()
return
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 __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 _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 __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)
assert (self.understand(image_file))
FormatCBF.__init__(self, image_file, **kwargs)
return
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 __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given 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 _start(self):
"""Read the image header and copy it into a dictionary for future reference.
In this case the header is useless, so we populate the dictionary manually
with dummy values"""
FormatCBF._start(self)
self._cif_header_dictionary = {}
self._cif_header_dictionary["Detector_distance"] = "3.523 m"
self._cif_header_dictionary["Beam_xy"] = "(1024.0, 1024.0) pixels"
self._cif_header_dictionary["Wavelength"] = "0.02508 A"
self._cif_header_dictionary["Pixel_size"] = "30e-6 m x 30e-6 m"
self._cif_header_dictionary["X-Binary-Size-Fastest-Dimension"] = "2048"
self._cif_header_dictionary["X-Binary-Size-Second-Dimension"] = "2048"
self._cif_header_dictionary["Count_cutoff"] = "65535 counts"
self._cif_header_dictionary["Phi"] = "0.0000 deg."
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" in header and "_diffrn_source" in header:
return False
def one_of_these_in(record):
these = [
"PILATUS",
"SLS",
"SSRL",
"?",
"XDS special",
"GENERIC_MINI", # intended for simulated PAD data, non-Pilatus array size
]
for convention in these:
if convention in record:
return True
return False
for record in header.split("\n"):
if "_array_data.header_convention" in record and one_of_these_in(record):
return True
if "# Detector" in record and "PILATUS" in record: # CBFlib v0.8.0 allowed
return True
if "# Detector" in record and "ADSC" in record and "HF-4M" in header:
return True
return False
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' in header and '_diffrn_source' in header:
return False
for record in header.split('\n'):
if '_array_data.header_convention' in record and \
'PILATUS' in record:
return True
if '_array_data.header_convention' in record and \
'SLS' in record:
return True
if '_array_data.header_convention' in record and \
'?' in record:
return True
if '# Detector' in record and \
'PILATUS' in record: #CBFlib v0.8.0 allowed
return True
if '# Detector' in record and \
'ADSC' in record and 'HF-4M' in header:
return True
return False
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
# According to ImageCIF, "Data items in the DIFFRN_MEASUREMENT_AXIS
# category associate axes with goniometers."
# http://www.iucr.org/__data/iucr/cifdic_html/2/cif_img.dic/Cdiffrn_measurement_axis.html
if "diffrn_measurement_axis" in header:
return False
# This implementation only supports single panel.
try:
cbf_handle = pycbf.cbf_handle_struct()
cbf_handle.read_widefile(image_file.encode(), pycbf.MSG_DIGEST)
except Exception as e:
if "CBFlib Error" in str(e):
return False
# check if multiple arrays
try:
return cbf_handle.count_elements() == 1
except Exception as e:
if "CBFlib Error" in str(e):
return False
return True
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' in header and '_diffrn_source' in header:
return False
def one_of_these_in(record):
these = [
'PILATUS',
'SLS',
'SSRL',
'?',
'XDS special',
'GENERIC_MINI', # intended for simulated PAD data, non-Pilatus array size
]
for convention in these:
if convention in record: return True
return False
for record in header.split('\n'):
if '_array_data.header_convention' in record and one_of_these_in(
record):
return True
if '# Detector' in record and \
'PILATUS' in record: #CBFlib v0.8.0 allowed
return True
if '# Detector' in record and \
'ADSC' in record and 'HF-4M' in header:
return True
return False
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 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 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 extract_header(self, cbf_filepath, npy_dir, bg=False):
'''Assume all headers (mostly) the same for a directory of image files (i.e directory
contains data from single aquisition experiment)
:param str cbf_filepath: path to cbf image
:param str npy_dir: path to destination
:param bool bg: if True, add 'background' to file name
'''
header = open(
os.path.join(npy_dir, "{}header.txt".format("bg" if bg else "")),
"w")
header.write(FormatCBF.get_cbf_header(cbf_filepath))
header.close()
def get_image_key(self, cbf_filepath, npy_filepath):
'''Keep the original image path from the header of each image as a means of
tracing data back to original image data.
:param str cbf_filepath: cbf image path
:param str npy_filepath: new numpy image path
:returns: string containing npy path followed by ramdisk path
'''
cbf_filedir, cbf_filename = os.path.split(cbf_filepath)
key = 'Image_path'
head = FormatCBF.get_cbf_header(cbf_filepath)
value = read_header(head, [key], file_string=True)
ans = os.path.join(value['Image_path'][0], cbf_filename)
return '{} {}'.format(npy_filepath, ans)
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)
# The header is minimal, but we want to avoid 'understanding' CBFs from
# other detectors. Use whatever we can in the header that might uniquely
# identify the right images
if "data_clip:_flipx" not in header:
return False
if "_array_data.header_convention" in header:
return False
if "Detector" in header:
return False
return True
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':
return False
# According to ImageCIF, "Data items in the DIFFRN_MEASUREMENT_AXIS
# category associate axes with goniometers."
# http://www.iucr.org/__data/iucr/cifdic_html/2/cif_img.dic/Cdiffrn_measurement_axis.html
if 'diffrn_measurement_axis' in header:
return False
# This implementation only supports single panel.
try:
cbf_handle = pycbf.cbf_handle_struct()
cbf_handle.read_widefile(image_file, pycbf.MSG_DIGEST)
except Exception, e:
if 'CBFlib Error' in str(e):
return False
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 _start(self):
'''Open the image file as a cbf file handle, and keep this somewhere
safe.'''
FormatCBF._start(self)
def _start(self):
"""Open the image file as a cbf file handle, and keep this somewhere
safe."""
FormatCBF._start(self) # Note, skip up an inheritance level
def _start(self):
"""Open the image file as a cbf file handle, and keep this somewhere
safe."""
FormatCBF._start(self)
def _start(self):
"""Open the image file as a cbf file handle, and keep this somewhere
safe."""
from dxtbx.format.FormatCBF import FormatCBF
FormatCBF._start(self) # Note, skip up an inhieritance level
def _start(self): '''Open the image file as a cbf file handle, and keep this somewhere safe.''' from dxtbx.format.FormatCBF import FormatCBF FormatCBF._start(self) # Note, skip up an inhieritance level
