Python pycbf.cbf_handle_struct函数代码示例

def get_image_volume(cbf_paths):
  """Load the image volume from the list of cbf_paths. The list of paths is
  assumed to be is order from 1->n.

  :param cbf_paths: The list of cbf files
  :param width The width (xsize) of the volume
  :param height The height (ysize) of the volume
  :returns: The 3D volume array

  """
  # Read the first image and get the size
  cbf_handle = pycbf.cbf_handle_struct()
  cbf_handle.read_file(cbf_paths[0], pycbf.MSG_DIGEST)
  image = get_image(cbf_handle)
  height, width = image.shape

  # Initialise the image volume
  num_slices = len(cbf_paths)
  volume = numpy.zeros(shape=(num_slices, height, width), dtype=numpy.int32)
  volume[0,:,:] = image

  # For each CBF file, read the image and put into the image volume
  for i, filename in enumerate(cbf_paths[1:]):
    cbf_handle = pycbf.cbf_handle_struct()
    cbf_handle.read_file(filename, pycbf.MSG_DIGEST)
    volume[i+1,:,:] = get_image(cbf_handle)

  # Return the image volume
  return volume

def save_numpy_data_as_cbf(data, size1, size2, title, cbfout, pilatus_header=None):
    h = pycbf.cbf_handle_struct()
    h.new_datablock(title)

    h.require_category('array_data')

    if pilatus_header is not None:
        h.require_column('header_convention')
        h.set_value('"PILATUS_1.2"')
        h.require_column('header_contents')
        h.set_value(pilatus_header)


    h.require_category('array_data')
    h.require_column('data')
    
    elsigned = 1
    if data.dtype in (numpy.uint8, numpy.uint16, numpy.uint32, numpy.uint64):
        elsigned = 0

    h.set_integerarray_wdims_fs(pycbf.CBF_BYTE_OFFSET, 1, data.tostring(), data.dtype.itemsize,
                                elsigned, len(data), "little_endian",
                                size1, size2, 1, 0)
    h.write_file(cbfout, pycbf.CBF,
                 pycbf.MIME_HEADERS|pycbf.MSG_DIGEST|pycbf.PAD_4K, pycbf.ENC_NONE)

def read_image(filename):
    if os.path.splitext(filename)[1] == '.cbf':
        try:
            import pycbf
        except ImportError:
            raise NeXusError('Reading CBF files requires the pycbf module')
        cbf = pycbf.cbf_handle_struct()
        cbf.read_file(filename, pycbf.MSG_DIGEST)
        cbf.select_datablock(0)
        cbf.select_category(0)
        cbf.select_column(2)
        imsize = cbf.get_image_size(0)
        return np.fromstring(cbf.get_integerarray_as_string(), 
                             np.int32).reshape(imsize)
    else:
        try:
            from nexpy.readers.tifffile import tifffile as TIFF
        except ImportError:
            raise NeXusError('Reading TIFF files requires the TIFF reader installed with NeXpy')
        if filename.endswith('.bz2'):
            import bz2
            tiff_file = TIFF.TiffFile(bz2.BZ2File(filename))
        else:
            tiff_file = TIFF.TiffFile(filename)
        return tiff_file.asarray()

def open_file_return_array(filename):
  import pycbf
  import numpy

  # open file
  cbf_handle = pycbf.cbf_handle_struct()
  cbf_handle.read_file(filename, pycbf.MSG_DIGEST)
  cbf_handle.rewind_datablock()

  # find right datablock
  cbf_handle.select_datablock(0)
  cbf_handle.select_category(0)
  cbf_handle.select_column(2)
  cbf_handle.select_row(0)

  type = cbf_handle.get_typeofvalue()
  assert (type.find('bnry') > -1)

  # read and reshape
  image = numpy.fromstring(cbf_handle.get_integerarray_as_string(),
                           numpy.int32)
  parameters = cbf_handle.get_integerarrayparameters_wdims()
  image.shape = (parameters[10], parameters[9])

  return image

def read_metadata(filename):
    if filename.endswith('bz2'):
        fname = os.path.splitext(filename)[0]
    else:
        fname = filename
    if os.path.splitext(fname)[1] == '.cbf':
        try:
            import pycbf
        except ImportError:
            raise NeXusError('Reading CBF files requires the pycbf module')
        cbf = pycbf.cbf_handle_struct()
        cbf.read_file(fname, pycbf.MSG_DIGEST)
        cbf.select_datablock(0)
        cbf.select_category(0)
        cbf.select_column(1)
        meta_text = cbf.get_value().splitlines()
        date_string = meta_text[2][2:]
        time_stamp = epoch(date_string)
        exposure = float(meta_text[5].split()[2])
        summed_exposures = 1
        return time_stamp, exposure, summed_exposures
    elif os.path.exists(fname+'.metadata'):
        parser = ConfigParser()
        parser.read(fname+'.metadata')
        return (parser.getfloat('metadata', 'timeStamp'),
                parser.getfloat('metadata', 'exposureTime'),
                parser.getint('metadata', 'summedExposures'))
    else:
        return time.time(), 1.0, 1

  def imgCIF(cif_file):
    '''Initialize a scan model from an imgCIF file.'''

    cbf_handle = pycbf.cbf_handle_struct()
    cbf_handle.read_file(cif_file, pycbf.MSG_DIGEST)

    return scan_factory.imgCIF_H(cif_file, cbf_handle)

 def _get_cbf_handle(self):
   try:
     return self._cbf_handle
   except AttributeError:
     self._cbf_handle = pycbf.cbf_handle_struct()
     self._cbf_handle.read_widefile(self._image_file, pycbf.MSG_DIGEST)
     return self._cbf_handle

def load_cbf_as_numpy(filein, quiet=True):
    assert os.path.isfile(filein)
    if not quiet:
        print "reading", filein, "as cbf"
    h = pycbf.cbf_handle_struct()
    h.read_file(filein, pycbf.MSG_DIGEST)
    ndimfast, ndimslow = h.get_image_size_fs(0)
    arr = numpy.fromstring(h.get_image_fs_as_string(0, 4, 1, ndimfast, ndimslow), dtype=numpy.int32)
    return arr, ndimfast, ndimslow

  def understand(image_file):
    '''Check to see if this looks like an CBF format image, i.e. we can
    make sense of it.'''

    cbf_handle = pycbf.cbf_handle_struct()
    cbf_handle.read_widefile(image_file, pycbf.MSG_DIGEST)

    #check if multiple arrays
    return cbf_handle.count_elements() > 1

  def imgCIF(cif_file):
    '''Initialize a goniometer model from an imgCIF file.'''

    # FIXME in here work out how to get the proper setting matrix if != 1

    cbf_handle = pycbf.cbf_handle_struct()
    cbf_handle.read_file(cif_file, pycbf.MSG_DIGEST)

    return goniometer_factory.imgCIF_H(cbf_handle)

  def understand(image_file):
    '''Check to see if this looks like an CBF format image, i.e. we can
    make sense of it.'''

    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 load_xds_special(cbfin):
    h = pycbf.cbf_handle_struct()
    h.read_file(cbfin, pycbf.MSG_DIGEST)
    h.require_category("array_data")
    h.find_column("header_contents")
    header = h.get_value()

    M = cbf_binary_adaptor(cbfin)
    data = M.uncompress_implementation("buffer_based").uncompress_data()
    #print "slow, fast=", M.dim_slow(), M.dim_fast() # can be obtained after getting data
    return header, data, M.dim_slow(), M.dim_fast()

  def imgCIF(cif_file, sensor):
    '''Initialize a detector model from an imgCIF file.'''

    cbf_handle = pycbf.cbf_handle_struct()
    cbf_handle.read_file(cif_file, pycbf.MSG_DIGEST)

    cbf_detector = cbf_handle.construct_detector(0)

    pixel = (cbf_detector.get_inferred_pixel_size(1),
             cbf_detector.get_inferred_pixel_size(2))

    # FIXME can probably simplify the code which follows below by
    # making proper use of cctbx vector calls - should not be as
    # complex as it appears to be...

    origin = tuple(cbf_detector.get_pixel_coordinates(0, 0))
    fast = cbf_detector.get_pixel_coordinates(0, 1)
    slow = cbf_detector.get_pixel_coordinates(1, 0)

    dfast = [fast[j] - origin[j] for j in range(3)]
    dslow = [slow[j] - origin[j] for j in range(3)]

    lfast = math.sqrt(sum([dfast[j] * dfast[j] for j in range(3)]))
    lslow = math.sqrt(sum([dslow[j] * dslow[j] for j in range(3)]))

    fast = tuple([dfast[j] / lfast for j in range(3)])
    slow = tuple([dslow[j] / lslow for j in range(3)])

    size = tuple(reversed(cbf_handle.get_image_size(0)))

    try:
      underload = find_undefined_value(cbf_handle)
      overload = cbf_handle.get_overload(0) * dxtbx_overload_scale
      trusted_range = (underload, overload)
    except: # intentional
      trusted_range = (0.0, 0.0)

    cbf_detector.__swig_destroy__(cbf_detector)
    del(cbf_detector)

    # Get the sensor type
    dtype = detector_factory.sensor(sensor)

    # If the sensor type is PAD then create the detector with a
    # parallax corrected pixel to millimeter function
    #if dtype == detector_helper_sensors.SENSOR_PAD:
      #px_mm = ParallaxCorrectedPxMmStrategy(0.252500934883)
    #else:
    px_mm = SimplePxMmStrategy()

    return detector_factory.make_detector(
              dtype, fast, slow, origin, pixel, size,
              trusted_range, px_mm)

 def read_image(self, filename):
     if self.get_image_type() == 'CBF':
         import pycbf
         cbf = pycbf.cbf_handle_struct()
         cbf.read_file(str(filename), pycbf.MSG_DIGEST)
         cbf.select_datablock(0)
         cbf.select_category(0)
         cbf.select_column(2)
         imsize = cbf.get_image_size(0)
         return np.fromstring(cbf.get_integerarray_as_string(),np.int32).reshape(imsize)
     else:
         return TIFF.imread(filename)

  def imgCIF(cif_file):
    '''Initialize a goniometer model from an imgCIF file.'''

    cbf_handle = pycbf.cbf_handle_struct()
    cbf_handle.read_file(cif_file, pycbf.MSG_DIGEST)

    cbf_gonio = cbf_handle.construct_goniometer()

    axis, fixed = cbf_gonio_to_effective_axis_fixed(cbf_gonio)

    cbf_gonio.__swig_destroy__(cbf_gonio)
    del(cbf_gonio)

    return goniometer_factory.make_goniometer(axis, fixed)