def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
super(RAXISHelper, self).__init__(image_file, **kwargs)
def __init__(self, image_file, index=0, reconst_mode=False, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
self._raw_data = None
self.index = index
self.image_filename = image_file
FormatHDF5.__init__(self, image_file, **kwargs)
self.PIXEL_SIZE = 78.2 / 1000 # um
self.RECONST_SIZE = 3840
# This hard-coded value can be overwritten
# by RAYONIX_DISTANCE
self.distance = 240.0 # mm
self.mask = None
# Read metadata if possible
self.read_metadata()
# Override by environmental variables
import os
if "RAYONIX_DISTANCE" in os.environ:
self.distance = float(os.environ["RAYONIX_DISTANCE"])
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file."""
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
Format.__init__(self, image_file, **kwargs)
def __init__(self, image_file, **kwargs):
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatMultiImageLazy.__init__(self, **kwargs)
FormatStill.__init__(self, image_file, **kwargs)
Format.__init__(self, image_file, **kwargs)
self.current_index = None
self.current_event = None
self._psana_runs = {
} # empty container, to prevent breaking other formats
if "locator_scope" in kwargs:
self.params = FormatXTC.params_from_phil(
master_phil=kwargs["locator_scope"],
user_phil=image_file,
strict=True)
else:
self.params = FormatXTC.params_from_phil(master_phil=locator_scope,
user_phil=image_file,
strict=True)
assert self.params.mode == "idx", "idx mode should be used for analysis"
self._ds = FormatXTC._get_datasource(image_file, self.params)
self.populate_events()
self.n_images = len(self.times)
self._cached_psana_detectors = {}
self._beam_index = None
self._beam_cache = None
self._initialized = True
self._fee = None
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)
width, height, depth, order, bytes = FormatTIFF.get_tiff_header(
image_file)
# comment block - where the detector serial number may (or may not) be stored
# comments = bytes[1024+1440:1024+1440+512]
self._header_size = 4096
if order == FormatTIFF.LITTLE_ENDIAN:
self._I = '<I'
self._i = '<i'
self._ii = '<ii'
else:
self._I = '>I'
self._i = '>i'
self._ii = '>ii'
FormatTIFF.__init__(self, image_file, **kwargs)
return
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatMultiImage.__init__(self, **kwargs)
Format.__init__(self, image_file, **kwargs)
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)
Format.__init__(self, image_file, **kwargs)
def __init__(self, image_file, index=0, reconst_mode=False, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
self._raw_data = None
self.index = index
self.image_filename = image_file
FormatHDF5.__init__(self, image_file, **kwargs)
# This hard-coded value can be overwritten
# by RAYONIX_DISTANCE
self.distance = 240.0 # mm
self.mask = None
# Read metadata if possible
# Read pixel size from the metadata and determine the binning of rayonix
self.read_metadata()
self.PIXEL_SIZE = self.pixelsize_in_um / 1000 # convert um to mm
self.bin_size = int(self.pixelsize_in_um / 39.1)
self.RECONST_SIZE = 7680 // self.bin_size
# Override by environmental variables
if os.getenv("RAYONIX_DISTANCE"):
self.distance = float(os.environ["RAYONIX_DISTANCE"])
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatHDF5.__init__(self, image_file, **kwargs)
self._h5_handle = h5py.File(self.get_image_file(), 'r')
self._geometry_define()
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)
super(FormatNexusEigerDLS16M, self).__init__(image_file, **kwargs)
self._dynamic_shadowing = self.has_dynamic_shadowing(**kwargs)
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)
FormatSMVRigaku.__init__(self, image_file, **kwargs)
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)
self._dynamic_shadowing = self.has_dynamic_shadowing(**kwargs)
FormatCBFFullPilatus.__init__(self, image_file, **kwargs)
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)
FormatPYunspecified.__init__(self, image_file, **kwargs)
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)
FormatCBFFull.__init__(self, image_file, **kwargs)
self._raw_data = None
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)
FormatCBFMiniPilatus.__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. Easy from Rigaku A200 images as
they contain everything pretty much we need...'''
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatSMVRigakuA200.__init__(self, image_file, **kwargs)
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatSEReBIC.__init__(self, image_file, **kwargs)
self.pedestal = os.environ.get("ADD_PEDESTAL", 0)
self.pedestal = float(self.pedestal)
logger.info("WARNING: Using FormatSEReBICpedestal. The value {0} will "
"be added to all pixels".format(self.pedestal))
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file, including a
proper model of the experiment. Easy from Rigaku Saturn images as
they contain everything pretty much we need..."""
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
self._image_file = image_file
FormatBruker.__init__(self, image_file, **kwargs)
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)
self._dynamic_shadowing = kwargs.get('dynamic_shadowing', False)
FormatCBFFullPilatus.__init__(self, image_file, **kwargs)
return
def __init__(self, image_file, index=0, reconst_mode=False, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
self._raw_data = None
self.index = index
self.image_filename = image_file
FormatHDF5.__init__(self, image_file, **kwargs)
self.PIXEL_SIZE = 50 / 1000 # 50 um
self.RECONST_SIZE = 2398 # compatible with DataConvert3 -reconst mode
# These hard-coded values can be overwritten
# by MPCCD_GEOMETRY and MPCCD_DISTANCE
#
# These values can be retrieved from SACLA API.
# Alternatively, you can get it from a CrystFEL geometry file by
# awk '/corner_x/{x=50*$3} /corner_y/{y=50*$3; printf x","y","rot","}
# /\/ss/{rot=-atan2($3, $4)/3.141592*180}' input.geom
self.distance = 50.0 # mm
self.panel_origins = [(-1755.000000, 51711.000000, 0.000000),
(-1711.000000, 24944.000000, 0.000000),
(817.000000, -1808.000000, 0.000000),
(812.000000, -28466.000000, 0.000000),
(-792.000000, 28544.000000, 0.000000),
(-781.000000, 1840.000000, 0.000000),
(1650.000000, -24900.000000, 0.000000),
(1655.000000, -51626.000000, 0.000000)] # um
self.panel_rotations = [
-89.906197, -89.915802, -89.980003, -89.929298, 89.963097,
89.880798, 90.000000, 90.029503
]
import os
if 'MPCCD_RECONST_MODE' in os.environ:
reconst_mode = bool(os.environ['MPCCD_RECONST_MODE'])
self.RECONST_MODE = reconst_mode
self.RECONST_64 = True # Set False if you want to keep panels completely horizontal
# But this makes errors bigger.
if 'MPCCD_GEOMETRY' in os.environ:
try:
tmp = map(float, os.environ['MPCCD_GEOMETRY'].split(","))
if len(tmp) != 24:
raise
for i in range(8):
self.panel_origins[i] = (-tmp[i * 3], tmp[i * 3 + 1], 0)
self.panel_rotations[i] = tmp[i * 3 + 2]
except Exception:
raise "Invalid MPCCD Geomtry"
if 'MPCCD_DISTANCE' in os.environ:
self.distance = float(os.environ['MPCCD_DISTANCE'])
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)
FormatSMV.__init__(self, image_file, **kwargs)
detector_prefixes = self._header_dictionary['DETECTOR_NAMES'].split()
self._prefix = detector_prefixes[0]
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)
FormatCBFMiniEiger.__init__(self, image_file, **kwargs)
self._raw_data = None
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)
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)
self._raw_data = None
self._multi_panel = kwargs.get('multi_panel', False)
FormatCBFMiniPilatus.__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)
self._dynamic_shadowing = self.has_dynamic_shadowing(**kwargs)
self._multi_panel = kwargs.get("multi_panel", False)
FormatCBFMiniPilatus.__init__(self, image_file, **kwargs)
self._raw_data = None
def __init__(self, image_file, **kwargs):
"""Initialise the image structure from the given file, including a
proper model of the experiment. Easy from Rigaku Saturn images as
they contain everything pretty much we need..."""
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatSMVRigaku.__init__(self, image_file, **kwargs)
self.detector_class = "NOIR1"
self.detector = "adsc"
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatStill.__init__(self, image_file, **kwargs)
self._handle = h5py.File(image_file, "r")
# load image components
self._raw_panels = self._handle["raw"]
self._is_low_gain = self._handle["gain"][()]
self._pedestal = self._handle["dark"][()]
self._mask = self._handle["mask"][()]
self._low_gain_val = 6.85 # TODO : make this optional
# load geometry components
self._geometry_define()
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatHDF5.__init__(self, image_file, **kwargs)
#def _start(self):
self._h5_handle = h5py.File(self.get_image_file(), 'r')
self._decide_multi_panel()
self.load_dark()
self.load_gain()
self.load_mask()
self.load_xyz()
self._geometry_define()
self._assembler_define()
def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatMultiImageLazy.__init__(self, **kwargs)
FormatStill.__init__(self, image_file, **kwargs)
Format.__init__(self, image_file, **kwargs)
self.current_index = None
self.current_event = None
if 'locator_scope' in kwargs:
self.params = FormatXTC.params_from_phil(kwargs['locator_scope'],image_file,strict=True)
else:
self.params = FormatXTC.params_from_phil(locator_scope,image_file,strict=True)
assert self.params.mode == 'idx', 'idx mode should be used for analysis'
self._initialized = True
