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 __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, 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, 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):
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 understand(image_file):
try:
tag = FormatHDF5.open_file(image_file, 'rb').read(8)
except IOError:
return False
# check that this is a HDF5 file (should not have got here if not
# anyway...)
if tag != "\211HDF\r\n\032\n":
return False
import h5py
h5_handle = h5py.File(image_file, 'r')
try:
desc = h5_handle['entry/instrument/detector/description']
except KeyError:
h5_handle.close()
return False
if 'Lambda' in desc.value[0]:
h5_handle.close()
return True
return False
def __init__(self, image_file):
assert(self.understand(image_file))
FormatHDF5.__init__(self, image_file)
self._raw_data = None
self.pixel_size = 50 / 1000 # 50 um
self.RECONST_SIZE = 2398 # compatible with DataConvert3 -reconst mode
self.RECONST_MODE = True
self.RECONST_64 = True
self.distance = 52.0 # mm
# TODO: These should be read from geometry file.
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]
def understand(image_file):
try:
tag = FormatHDF5.open_file(image_file, "rb").read(8)
except IOError:
return False
# check that this is a HDF5 file (should not have got here if not
# anyway...)
if tag != "\211HDF\r\n\032\n":
return False
with h5py.File(image_file, "r") as h5_handle:
try:
desc = h5_handle["entry/instrument/detector/description"]
except KeyError:
return False
if "Lambda" in desc[()][0]:
return True
return False
def __init__(self, image_file, **kwargs):
assert (self.understand(image_file))
FormatHDF5.__init__(self, image_file, **kwargs)
def understand(image_file):
try:
tag = FormatHDF5.open_file(image_file, 'rb').read(8)
except IOError, e:
return False
def __init__(self, image_file, **kwargs): assert(self.understand(image_file)) FormatHDF5.__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)
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
# Default value for Phase I MPCCD
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,
]
self.thickness = 0.050
self.mask = None
# Read metadata if possible
self.read_metadata()
# Override by environmental variables
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 = [
float(i) for i in os.environ["MPCCD_GEOMETRY"].split(",")
]
if len(tmp) != 24:
raise EnvironmentError(
"Environment variable MPCCD_GEOMETRY must contain 24 comma-separated parts"
)
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 as e:
raise EnvironmentError(
"Invalid MPCCD Geometry specified in environment variable MPCCD_GEOMETRY: {}"
.format(e))
if "MPCCD_DISTANCE" in os.environ:
self.distance = float(os.environ["MPCCD_DISTANCE"])
