class FormatSMVRigakuA200SPring8BL26B1(FormatSMVRigakuA200): """A class for reading SMV format Rigaku A200 images written by a detector usually at SPring-8 BL26B1, which requires a reversed axis goniometer""" @staticmethod def understand(image_file): """Check to see if this looks like a Rigaku A200 SMV format image, i.e. we can make sense of it. Essentially that will be if it contains all of the keys we are looking for.""" size, header = FormatSMVRigakuA200SPring8BL26B1.get_smv_header( image_file) detector_prefix = header["DETECTOR_NAMES"].split()[0].strip() test = "%s%s" % (detector_prefix, "DETECTOR_IDENTIFICATION") if header.get(test) != "MSC_REIT_A200_SN09250183": return False test = "%s%s" % (detector_prefix, "DETECTOR_DESCRIPTION") if not header.get(test).startswith("A200"): return False test = "%s%s" % (detector_prefix, "GONIO_DESCRIPTION") if not header.get(test).startswith("SPring-8"): return False return True 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 _start(self): FormatSMVRigakuA200._start(self) def detectorbase_start(self): from iotbx.detectors.dtrek import DTREKImage self.detectorbase = DTREKImage(self._image_file) self.detectorbase.readHeader() def _goniometer(self): """Initialize the structure for the goniometer. Although ROTATION_VECTOR is written into the header, this might (?) always be 1. 1. 0. for this detector, and we want a reversed axis goniometer""" # axis = tuple(map(float, self._header_dictionary[ # 'ROTATION_VECTOR'].split())) return self._goniometer_factory.single_axis_reverse()
class FormatSMVRigakuA200SPring8BL26B1(FormatSMVRigakuA200): '''A class for reading SMV format Rigaku A200 images written by a detector usually at SPring-8 BL26B1, which requires a reversed axis goniometer''' @staticmethod def understand(image_file): '''Check to see if this looks like a Rigaku A200 SMV format image, i.e. we can make sense of it. Essentially that will be if it contains all of the keys we are looking for.''' size, header = FormatSMVRigakuA200SPring8BL26B1.get_smv_header(image_file) detector_prefix = header['DETECTOR_NAMES'].split()[0].strip() test = '%s%s' % (detector_prefix, 'DETECTOR_IDENTIFICATION') if header.get(test) != "MSC_REIT_A200_SN09250183": return False test = '%s%s' % (detector_prefix, 'DETECTOR_DESCRIPTION') if not header.get(test).startswith("A200"): return False test = '%s%s' % (detector_prefix, 'GONIO_DESCRIPTION') if not header.get(test).startswith("SPring-8"): return False return True def __init__(self, image_file): '''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...''' assert(self.understand(image_file)) FormatSMVRigakuA200.__init__(self, image_file) return def _start(self): FormatSMVRigakuA200._start(self) def detectorbase_start(self): from iotbx.detectors.dtrek import DTREKImage self.detectorbase = DTREKImage(self._image_file) self.detectorbase.readHeader() def _goniometer(self): '''Initialize the structure for the goniometer. Although ROTATION_VECTOR is written into the header, this might (?) always be 1. 1. 0. for this detector, and we want a reversed axis goniometer ''' #axis = tuple(map(float, self._header_dictionary[ # 'ROTATION_VECTOR'].split())) return self._goniometer_factory.single_axis_reverse()
class FormatSMVRigakuA200SPring8BL26B1(FormatSMVRigakuA200): """A class for reading SMV format Rigaku A200 images written by a detector usually at SPring-8 BL26B1, which requires a reversed axis goniometer""" @staticmethod def understand(image_file): """Check to see if this looks like a Rigaku A200 SMV format image, i.e. we can make sense of it. Essentially that will be if it contains all of the keys we are looking for.""" size, header = FormatSMVRigakuA200SPring8BL26B1.get_smv_header(image_file) detector_prefix = header["DETECTOR_NAMES"].split()[0].strip() test = "%s%s" % (detector_prefix, "DETECTOR_IDENTIFICATION") if header.get(test) != "MSC_REIT_A200_SN09250183": return False test = "%s%s" % (detector_prefix, "DETECTOR_DESCRIPTION") if not header.get(test).startswith("A200"): return False test = "%s%s" % (detector_prefix, "GONIO_DESCRIPTION") if not header.get(test).startswith("SPring-8"): return False return True def detectorbase_start(self): self.detectorbase = DTREKImage(self._image_file) self.detectorbase.readHeader() def _goniometer(self): """Initialize the structure for the goniometer. Although ROTATION_VECTOR is written into the header, this might (?) always be 1. 1. 0. for this detector, and we want a reversed axis goniometer""" # axis = tuple(map(float, self._header_dictionary[ # 'ROTATION_VECTOR'].split())) return self._goniometer_factory.single_axis_reverse()
class FormatSMVRigakuA200(FormatSMVRigaku): """A class for reading SMV format Rigaku A200 images, and correctly constructing a model for the experiment from this.""" @staticmethod def understand(image_file): """Check to see if this looks like a Rigaku A200 SMV format image, i.e. we can make sense of it. Essentially that will be if it contains all of the keys we are looking for.""" size, header = FormatSMVRigaku.get_smv_header(image_file) wanted_header_items = [ "DETECTOR_NUMBER", "DETECTOR_NAMES", "CRYSTAL_GONIO_NUM_VALUES", "CRYSTAL_GONIO_NAMES", "CRYSTAL_GONIO_UNITS", "CRYSTAL_GONIO_VALUES", "ROTATION", "ROTATION_AXIS_NAME", "ROTATION_VECTOR", "SOURCE_VECTORS", "SOURCE_WAVELENGTH", "SOURCE_POLARZ", "DIM", "SIZE1", "SIZE2", ] if any(item not in header for item in wanted_header_items): return False detector_prefix = header["DETECTOR_NAMES"].split()[0].strip() more_wanted_header_items = [ "DETECTOR_DIMENSIONS", "DETECTOR_SIZE", "DETECTOR_VECTORS", "GONIO_NAMES", "GONIO_UNITS", "GONIO_VALUES", "GONIO_VECTORS", "SPATIAL_BEAM_POSITION", "SPATIAL_DISTORTION_VECTORS", ] if any( "%s%s" % (detector_prefix, item) not in header for item in more_wanted_header_items ): return False descriptive_items = ["DETECTOR_IDENTIFICATION", "DETECTOR_DESCRIPTION"] for header_item in descriptive_items: test = "%s%s" % (detector_prefix, header_item) if test in header and ( "raxis" in header[test].lower() or "a200" in header[test].lower() ): return True return False 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) FormatSMVRigaku.__init__(self, image_file, **kwargs) def detectorbase_start(self): from iotbx.detectors.dtrek import DTREKImage self.detectorbase = DTREKImage(self._image_file) self.detectorbase.readHeader() def _goniometer(self): """Initialize the structure for the goniometer - this will need to correctly compose the axes given in the image header. In this case this is made rather straightforward as the image header has the calculated rotation axis stored in it. We could work from the rest of the header and construct a goniometer model.""" axis = tuple(map(float, self._header_dictionary["ROTATION_VECTOR"].split())) return self._goniometer_factory.known_axis(axis) def _detector(self): """Return a model for the detector, allowing for two-theta offsets and the detector position. This will be rather more complex...""" detector_name = self._header_dictionary["DETECTOR_NAMES"].split()[0].strip() detector_axes = self.get_detector_axes(detector_name) detector_x = matrix.col(tuple(detector_axes[:3])) detector_y = matrix.col(tuple(detector_axes[3:])) # Now map these to real axes distortion = self.get_distortion(detector_name) detector_fast = detector_x * distortion[0] + detector_y * distortion[1] detector_slow = detector_x * distortion[2] + detector_y * distortion[3] beam_pixels = self.get_beam_pixels(detector_name) pixel_size = self.get_pixel_size(detector_name) image_size = self.get_image_size(detector_name) detector_origin = -( beam_pixels[0] * pixel_size[0] * detector_fast + beam_pixels[1] * pixel_size[1] * detector_slow ) gonio_axes = self.get_gonio_axes(detector_name) gonio_values = self.get_gonio_values(detector_name) gonio_units = self._header_dictionary["%sGONIO_UNITS" % detector_name].split() gonio_num_axes = int( self._header_dictionary["%sGONIO_NUM_VALUES" % detector_name] ) rotations = [] translations = [] for j, unit in enumerate(gonio_units): axis = matrix.col(gonio_axes[3 * j : 3 * (j + 1)]) if unit == "deg": rotations.append( axis.axis_and_angle_as_r3_rotation_matrix(gonio_values[j], deg=True) ) translations.append(matrix.col((0.0, 0.0, 0.0))) elif unit == "mm": rotations.append( matrix.sqr((1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)) ) translations.append(gonio_values[j] * axis) else: raise RuntimeError("unknown axis unit %s" % unit) rotations.reverse() translations.reverse() for j in range(gonio_num_axes): detector_fast = rotations[j] * detector_fast detector_slow = rotations[j] * detector_slow detector_origin = rotations[j] * detector_origin detector_origin = translations[j] + detector_origin overload = int(float(self._header_dictionary["SATURATED_VALUE"])) underload = 0 return self._detector_factory.complex( "CCD", detector_origin.elems, detector_fast.elems, detector_slow.elems, pixel_size, image_size, (underload, overload), ) def _beam(self): """Return a simple model for the beam.""" beam_direction = self.get_beam_direction() p_fraction, p_plane = self.get_beam_polarization() wavelength = float(self._header_dictionary["SCAN_WAVELENGTH"]) return self._beam_factory.complex( beam_direction, p_fraction, p_plane, wavelength ) def _scan(self): """Return the scan information for this image.""" rotation = self.get_rotation() format = self._scan_factory.format("SMV") epoch = 0 exposure_time = rotation[3] osc_start = rotation[0] osc_range = rotation[2] return self._scan_factory.single( self._image_file, format, exposure_time, osc_start, osc_range, epoch )
class FormatSMVRigakuA200(FormatSMVRigaku): '''A class for reading SMV format Rigaku A200 images, and correctly constructing a model for the experiment from this.''' @staticmethod def understand(image_file): '''Check to see if this looks like a Rigaku A200 SMV format image, i.e. we can make sense of it. Essentially that will be if it contains all of the keys we are looking for.''' size, header = FormatSMVRigaku.get_smv_header(image_file) wanted_header_items = [ 'DETECTOR_NUMBER', 'DETECTOR_NAMES', 'CRYSTAL_GONIO_NUM_VALUES', 'CRYSTAL_GONIO_NAMES', 'CRYSTAL_GONIO_UNITS', 'CRYSTAL_GONIO_VALUES', 'ROTATION', 'ROTATION_AXIS_NAME', 'ROTATION_VECTOR', 'SOURCE_VECTORS', 'SOURCE_WAVELENGTH', 'SOURCE_POLARZ', 'DIM', 'SIZE1', 'SIZE2', ] for header_item in wanted_header_items: if not header_item in header: return False detector_prefix = header['DETECTOR_NAMES'].split()[0].strip() more_wanted_header_items = [ 'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS', 'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS', 'SPATIAL_BEAM_POSITION', 'SPATIAL_DISTORTION_VECTORS' ] for header_item in more_wanted_header_items: if not '%s%s' % (detector_prefix, header_item) in header: return False descriptive_items = ['DETECTOR_IDENTIFICATION', 'DETECTOR_DESCRIPTION'] for header_item in descriptive_items: test = '%s%s' % (detector_prefix, header_item) if test in header and ('raxis' in header[test].lower() or "a200" in header[test].lower()): return True return False 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) FormatSMVRigaku.__init__(self, image_file, **kwargs) return def _start(self): FormatSMVRigaku._start(self) def detectorbase_start(self): from iotbx.detectors.dtrek import DTREKImage self.detectorbase = DTREKImage(self._image_file) self.detectorbase.readHeader() def _goniometer(self): '''Initialize the structure for the goniometer - this will need to correctly compose the axes given in the image header. In this case this is made rather straightforward as the image header has the calculated rotation axis stored in it. We could work from the rest of the header and construct a goniometer model.''' axis = tuple( map(float, self._header_dictionary['ROTATION_VECTOR'].split())) return self._goniometer_factory.known_axis(axis) def _detector(self): '''Return a model for the detector, allowing for two-theta offsets and the detector position. This will be rather more complex...''' detector_name = self._header_dictionary['DETECTOR_NAMES'].split( )[0].strip() detector_axes = map( float, self._header_dictionary['%sDETECTOR_VECTORS' % detector_name].split()) detector_x = matrix.col(tuple(detector_axes[:3])) detector_y = matrix.col(tuple(detector_axes[3:])) # Now map these to real axes detector_remap = map( float, self._header_dictionary['%sSPATIAL_DISTORTION_VECTORS' % detector_name].split()) detector_fast = detector_x * detector_remap[0] + \ detector_y * detector_remap[1] detector_slow = detector_x * detector_remap[2] + \ detector_y * detector_remap[3] beam_pixels = map( float, self._header_dictionary['%sSPATIAL_DISTORTION_INFO' % detector_name].split()[:2]) pixel_size = map( float, self._header_dictionary['%sSPATIAL_DISTORTION_INFO' % detector_name].split()[2:]) image_size = map( int, self._header_dictionary['%sDETECTOR_DIMENSIONS' % detector_name].split()) detector_origin = - (beam_pixels[0] * pixel_size[0] * detector_fast + \ beam_pixels[1] * pixel_size[1] * detector_slow) gonio_axes = map( float, self._header_dictionary['%sGONIO_VECTORS' % detector_name].split()) gonio_values = map( float, self._header_dictionary['%sGONIO_VALUES' % detector_name].split()) gonio_units = self._header_dictionary['%sGONIO_UNITS' % detector_name].split() gonio_num_axes = int(self._header_dictionary['%sGONIO_NUM_VALUES' % detector_name]) rotations = [] translations = [] for j, unit in enumerate(gonio_units): axis = matrix.col(gonio_axes[3 * j:3 * (j + 1)]) if unit == 'deg': rotations.append( axis.axis_and_angle_as_r3_rotation_matrix(gonio_values[j], deg=True)) translations.append(matrix.col((0.0, 0.0, 0.0))) elif unit == 'mm': rotations.append( matrix.sqr((1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0))) translations.append(gonio_values[j] * axis) else: raise RuntimeError, 'unknown axis unit %s' % unit rotations.reverse() translations.reverse() for j in range(gonio_num_axes): detector_fast = rotations[j] * detector_fast detector_slow = rotations[j] * detector_slow detector_origin = rotations[j] * detector_origin detector_origin = translations[j] + detector_origin overload = int(float(self._header_dictionary['SATURATED_VALUE'])) underload = 0 return self._detector_factory.complex('CCD', detector_origin.elems, detector_fast.elems, detector_slow.elems, pixel_size, image_size, (underload, overload)) def _beam(self): '''Return a simple model for the beam.''' beam_direction = map( float, self._header_dictionary['SOURCE_VECTORS'].split()[:3]) polarization = map(float, self._header_dictionary['SOURCE_POLARZ'].split()) p_fraction = polarization[0] p_plane = polarization[1:] wavelength = float(self._header_dictionary['SCAN_WAVELENGTH']) return self._beam_factory.complex(beam_direction, p_fraction, p_plane, wavelength) def _scan(self): '''Return the scan information for this image.''' rotation = map(float, self._header_dictionary['ROTATION'].split()) format = self._scan_factory.format('SMV') epoch = 0 exposure_time = rotation[3] osc_start = rotation[0] osc_range = rotation[2] return self._scan_factory.single(self._image_file, format, exposure_time, osc_start, osc_range, epoch)
class FormatSMVRigakuA200(FormatSMVRigaku): '''A class for reading SMV format Rigaku A200 images, and correctly constructing a model for the experiment from this.''' @staticmethod def understand(image_file): '''Check to see if this looks like a Rigaku A200 SMV format image, i.e. we can make sense of it. Essentially that will be if it contains all of the keys we are looking for.''' size, header = FormatSMVRigaku.get_smv_header(image_file) wanted_header_items = [ 'DETECTOR_NUMBER', 'DETECTOR_NAMES', 'CRYSTAL_GONIO_NUM_VALUES', 'CRYSTAL_GONIO_NAMES', 'CRYSTAL_GONIO_UNITS', 'CRYSTAL_GONIO_VALUES', 'ROTATION', 'ROTATION_AXIS_NAME', 'ROTATION_VECTOR', 'SOURCE_VECTORS', 'SOURCE_WAVELENGTH', 'SOURCE_POLARZ', 'DIM', 'SIZE1', 'SIZE2', ] for header_item in wanted_header_items: if not header_item in header: return False detector_prefix = header['DETECTOR_NAMES'].split()[0].strip() more_wanted_header_items = [ 'DETECTOR_DIMENSIONS', 'DETECTOR_SIZE', 'DETECTOR_VECTORS', 'GONIO_NAMES', 'GONIO_UNITS', 'GONIO_VALUES', 'GONIO_VECTORS', 'SPATIAL_BEAM_POSITION', 'SPATIAL_DISTORTION_VECTORS' ] for header_item in more_wanted_header_items: if not '%s%s' % (detector_prefix, header_item) in header: return False descriptive_items = [ 'DETECTOR_IDENTIFICATION', 'DETECTOR_DESCRIPTION' ] for header_item in descriptive_items: test = '%s%s' % (detector_prefix, header_item) if test in header and ('raxis' in header[test].lower() or "a200" in header[test].lower()): return True return False def __init__(self, image_file): '''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...''' assert(self.understand(image_file)) FormatSMVRigaku.__init__(self, image_file) return def _start(self): FormatSMVRigaku._start(self) def detectorbase_start(self): from iotbx.detectors.dtrek import DTREKImage self.detectorbase = DTREKImage(self._image_file) self.detectorbase.readHeader() def _goniometer(self): '''Initialize the structure for the goniometer - this will need to correctly compose the axes given in the image header. In this case this is made rather straightforward as the image header has the calculated rotation axis stored in it. We could work from the rest of the header and construct a goniometer model.''' axis = tuple(map(float, self._header_dictionary[ 'ROTATION_VECTOR'].split())) return self._goniometer_factory.known_axis(axis) def _detector(self): '''Return a model for the detector, allowing for two-theta offsets and the detector position. This will be rather more complex...''' detector_name = self._header_dictionary[ 'DETECTOR_NAMES'].split()[0].strip() detector_axes = map(float, self._header_dictionary[ '%sDETECTOR_VECTORS' % detector_name].split()) detector_x = matrix.col(tuple(detector_axes[:3])) detector_y = matrix.col(tuple(detector_axes[3:])) # Now map these to real axes detector_remap = map(float, self._header_dictionary[ '%sSPATIAL_DISTORTION_VECTORS' % detector_name].split()) detector_fast = detector_x * detector_remap[0] + \ detector_y * detector_remap[1] detector_slow = detector_x * detector_remap[2] + \ detector_y * detector_remap[3] beam_pixels = map(float, self._header_dictionary[ '%sSPATIAL_DISTORTION_INFO' % detector_name].split()[:2]) pixel_size = map(float, self._header_dictionary[ '%sSPATIAL_DISTORTION_INFO' % detector_name].split()[2:]) image_size = map(int, self._header_dictionary[ '%sDETECTOR_DIMENSIONS' % detector_name].split()) detector_origin = - (beam_pixels[0] * pixel_size[0] * detector_fast + \ beam_pixels[1] * pixel_size[1] * detector_slow) gonio_axes = map(float, self._header_dictionary[ '%sGONIO_VECTORS' % detector_name].split()) gonio_values = map(float, self._header_dictionary[ '%sGONIO_VALUES' % detector_name].split()) gonio_units = self._header_dictionary[ '%sGONIO_UNITS' % detector_name].split() gonio_num_axes = int(self._header_dictionary[ '%sGONIO_NUM_VALUES' % detector_name]) rotations = [] translations = [] for j, unit in enumerate(gonio_units): axis = matrix.col(gonio_axes[3 * j:3 * (j + 1)]) if unit == 'deg': rotations.append(axis.axis_and_angle_as_r3_rotation_matrix( gonio_values[j], deg = True)) translations.append(matrix.col((0.0, 0.0, 0.0))) elif unit == 'mm': rotations.append(matrix.sqr((1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0))) translations.append(gonio_values[j] * axis) else: raise RuntimeError, 'unknown axis unit %s' % unit rotations.reverse() translations.reverse() for j in range(gonio_num_axes): detector_fast = rotations[j] * detector_fast detector_slow = rotations[j] * detector_slow detector_origin = rotations[j] * detector_origin detector_origin = translations[j] + detector_origin overload = int(float(self._header_dictionary['SATURATED_VALUE'])) underload = 0 return self._detector_factory.complex( 'CCD', detector_origin.elems, detector_fast.elems, detector_slow.elems, pixel_size, image_size, (underload, overload)) def _beam(self): '''Return a simple model for the beam.''' beam_direction = map(float, self._header_dictionary[ 'SOURCE_VECTORS'].split()[:3]) polarization = map(float, self._header_dictionary[ 'SOURCE_POLARZ'].split()) p_fraction = polarization[0] p_plane = polarization[1:] wavelength = float(self._header_dictionary['SCAN_WAVELENGTH']) return self._beam_factory.complex( beam_direction, p_fraction, p_plane, wavelength) def _scan(self): '''Return the scan information for this image.''' rotation = map(float, self._header_dictionary['ROTATION'].split()) format = self._scan_factory.format('SMV') epoch = 0 exposure_time = rotation[3] osc_start = rotation[0] osc_range = rotation[2] return self._scan_factory.single( self._image_file, format, exposure_time, osc_start, osc_range, epoch)