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