python类recarray()的实例源码

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def get_signal_data(self, ep, ch):
        """
        Return a numpy array containing all samples of a
        signal, acquired on an Elphy analog channel, formatted
        as a list of (time, value) tuples.
        """
        #get data from the file
        y_data = self.load_encoded_data(ep, ch)
        x_data = np.arange(0, len(y_data))

        #create a recarray
        data = np.recarray(len(y_data), dtype=[('x', b_float), ('y', b_float)])

        #put in the recarray the scaled data
        x_factors = self.x_scale_factors(ep, ch)
        y_factors = self.y_scale_factors(ep, ch)
        data['x'] = x_factors.scale(x_data)
        data['y'] = y_factors.scale(y_data)

        return data

def get_tag_data(self, ep, tag_ch):
        """
        Return a numpy array containing all samples of a
        signal, acquired on an Elphy tag channel, formatted
        as a list of (time, value) tuples.
        """
        #get data from the file
        y_data = self.load_encoded_tags(ep, tag_ch)
        x_data = np.arange(0, len(y_data))

        #create a recarray
        data = np.recarray(len(y_data), dtype=[('x', b_float), ('y', b_int)])

        #put in the recarray the scaled data
        factors = self.x_tag_scale_factors(ep)
        data['x'] = factors.scale(x_data)
        data['y'] = y_data
        return data

def get_signal_data(self, ep, ch):
        """
        Return a numpy array containing all samples of a
        signal, acquired on an Elphy analog channel, formatted
        as a list of (time, value) tuples.
        """
        #get data from the file
        y_data = self.load_encoded_data(ep, ch)
        x_data = np.arange(0, len(y_data))

        #create a recarray
        data = np.recarray(len(y_data), dtype=[('x', b_float), ('y', b_float)])

        #put in the recarray the scaled data
        x_factors = self.x_scale_factors(ep, ch)
        y_factors = self.y_scale_factors(ep, ch)
        data['x'] = x_factors.scale(x_data)
        data['y'] = y_factors.scale(y_data)

        return data

def test_recfromtxt(self):
        #
        data = TextIO('A,B\n0,1\n2,3')
        kwargs = dict(delimiter=",", missing_values="N/A", names=True)
        test = np.recfromtxt(data, **kwargs)
        control = np.array([(0, 1), (2, 3)],
                           dtype=[('A', np.int), ('B', np.int)])
        self.assertTrue(isinstance(test, np.recarray))
        assert_equal(test, control)
        #
        data = TextIO('A,B\n0,1\n2,N/A')
        test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
        control = ma.array([(0, 1), (2, -1)],
                           mask=[(False, False), (False, True)],
                           dtype=[('A', np.int), ('B', np.int)])
        assert_equal(test, control)
        assert_equal(test.mask, control.mask)
        assert_equal(test.A, [0, 2])

def accumulate_user_vectors(users, max_prods, product_lookup, max_users, testmode):
  BUFFER_SIZE = float('inf') # XXX: see what mem usage looks like before over-engineering
  vec_accumulator = []
  nusers = 0
  for user in users:
    vecs = get_user_vectors(user, max_prods, product_lookup, testmode)
    vec_accumulator.append(vecs)
    nusers += 1
    if max_users and nusers >= max_users:
      break
    if nusers % 10000 == 0:
      print "{}... ".format(nusers)

  print "Accumulated vectors for {} users".format(len(vec_accumulator))
  concatted = np.concatenate(vec_accumulator)
  final_arr = concatted.view(np.recarray)
  return final_arr

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def test_recfromtxt(self):
        #
        data = TextIO('A,B\n0,1\n2,3')
        kwargs = dict(delimiter=",", missing_values="N/A", names=True)
        test = np.recfromtxt(data, **kwargs)
        control = np.array([(0, 1), (2, 3)],
                           dtype=[('A', np.int), ('B', np.int)])
        self.assertTrue(isinstance(test, np.recarray))
        assert_equal(test, control)
        #
        data = TextIO('A,B\n0,1\n2,N/A')
        test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
        control = ma.array([(0, 1), (2, -1)],
                           mask=[(False, False), (False, True)],
                           dtype=[('A', np.int), ('B', np.int)])
        assert_equal(test, control)
        assert_equal(test.mask, control.mask)
        assert_equal(test.A, [0, 2])

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def _join(files):
    from .io import load_locs, save_locs
    from os.path import splitext
    from numpy import append
    import numpy as np
    locs, info = load_locs(files[0])
    join_info = {'Generated by': 'Picasso Join',
                 'Files': [files[0]]}
    for path in files[1:]:
        locs_, info_ = load_locs(path)
        locs = append(locs, locs_)
        join_info['Files'].append(path)
    base, ext = splitext(files[0])
    info.append(join_info)
    locs.sort(kind='mergesort', order='frame')
    locs = locs.view(np.recarray)
    save_locs(base + '_join.hdf5', locs, info)

def groupprops(locs, callback=None):
    try:
        locs = locs[locs.dark != -1]
    except AttributeError:
        pass
    group_ids = _np.unique(locs.group)
    n = len(group_ids)
    n_cols = len(locs.dtype)
    names = ['group', 'n_events'] + list(_itertools.chain(*[(_ + '_mean', _ + '_std') for _ in locs.dtype.names]))
    formats = ['i4', 'i4'] + 2 * n_cols * ['f4']
    groups = _np.recarray(n, formats=formats, names=names)
    if callback is not None:
        callback(0)
    for i, group_id in enumerate(_tqdm(group_ids, desc='Calculating group statistics', unit='Groups')):
        group_locs = locs[locs.group == group_id]
        groups['group'][i] = group_id
        groups['n_events'][i] = len(group_locs)
        for name in locs.dtype.names:
            groups[name + '_mean'][i] = _np.mean(group_locs[name])
            groups[name + '_std'][i] = _np.std(group_locs[name])
        if callback is not None:
            callback(i+1)
    return groups

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def test_recfromtxt(self):
        #
        data = TextIO('A,B\n0,1\n2,3')
        kwargs = dict(delimiter=",", missing_values="N/A", names=True)
        test = np.recfromtxt(data, **kwargs)
        control = np.array([(0, 1), (2, 3)],
                           dtype=[('A', np.int), ('B', np.int)])
        self.assertTrue(isinstance(test, np.recarray))
        assert_equal(test, control)
        #
        data = TextIO('A,B\n0,1\n2,N/A')
        test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
        control = ma.array([(0, 1), (2, -1)],
                           mask=[(False, False), (False, True)],
                           dtype=[('A', np.int), ('B', np.int)])
        assert_equal(test, control)
        assert_equal(test.mask, control.mask)
        assert_equal(test.A, [0, 2])

def convert(self, other):
        """Convert a :class:`numpy.recarray` to a :class:`numpy.recarray` with additional fields, filling the additional fields with 0.

        :param other: The :class:`numpy.recarray` to be converted.
        :type other: :class:`numpy.recarray`"""

        a = self(np.zeros(self._nfields))
        if npv < (1,13,0):
            a[other.dtype.names] = other
        elif npv < (1,14,0):
            with warnings.catch_warnings():
                warnings.simplefilter('ignore', FutureWarning)
                a[:] = other
        else:
            for field_name in self._fields:
                a[field_name] = other[field_name]
        return a

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def test_recfromtxt(self):
        #
        data = TextIO('A,B\n0,1\n2,3')
        kwargs = dict(delimiter=",", missing_values="N/A", names=True)
        test = np.recfromtxt(data, **kwargs)
        control = np.array([(0, 1), (2, 3)],
                           dtype=[('A', np.int), ('B', np.int)])
        self.assertTrue(isinstance(test, np.recarray))
        assert_equal(test, control)
        #
        data = TextIO('A,B\n0,1\n2,N/A')
        test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
        control = ma.array([(0, 1), (2, -1)],
                           mask=[(False, False), (False, True)],
                           dtype=[('A', np.int), ('B', np.int)])
        assert_equal(test, control)
        assert_equal(test.mask, control.mask)
        assert_equal(test.A, [0, 2])

def writeCandidates(self,filename=None):
        if filename is None: filename = self.candfile

        threshold = self.config['search']['cand_threshold']
        select  = (self.assocs['CUT']==0)
        select &= (self.assocs['TS']>threshold)
        #select &= (self.assocs['ASSOC2']=='')

        self.candidates = self.assocs[select]
        # ADW: View as a recarray or selection doesn't work.
        # Why? I don't know, and I'm slightly terrified...
        hdu = pyfits.new_table(self.candidates.view(np.recarray))
        logger.info("Writing %s..."%filename)
        hdu.writeto(filename,clobber=True)

        # DEPRECATED: ADW 2017-09-15 
        ## Dump to txt file 
        #if which('fdump'):
        #    txtfile = filename.replace('.fits','.txt')
        #    columns = ['NAME','TS','GLON','GLAT','DISTANCE','MASS']
        #    cmd = 'fdump %(infile)s %(outfile)s columns="%(columns)s" rows="-" prhead="no" showcol="yes" clobber="yes" pagewidth="256" fldsep=" " showrow="no"'%(dict(infile=filename,outfile=txtfile,columns=','.join(columns)))
        #    print cmd
        #    subprocess.call(cmd,shell=True)

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def test_recfromtxt(self):
        #
        data = TextIO('A,B\n0,1\n2,3')
        kwargs = dict(delimiter=",", missing_values="N/A", names=True)
        test = np.recfromtxt(data, **kwargs)
        control = np.array([(0, 1), (2, 3)],
                           dtype=[('A', np.int), ('B', np.int)])
        self.assertTrue(isinstance(test, np.recarray))
        assert_equal(test, control)
        #
        data = TextIO('A,B\n0,1\n2,N/A')
        test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
        control = ma.array([(0, 1), (2, -1)],
                           mask=[(False, False), (False, True)],
                           dtype=[('A', np.int), ('B', np.int)])
        assert_equal(test, control)
        assert_equal(test.mask, control.mask)
        assert_equal(test.A, [0, 2])

def transform(self, posts):
        features = np.recarray(shape=(len(posts),),
                               dtype=[('subject', object), ('body', object)])
        for i, text in enumerate(posts):
            headers, _, bod = text.partition('\n\n')
            bod = strip_newsgroup_footer(bod)
            bod = strip_newsgroup_quoting(bod)
            features['body'][i] = bod

            prefix = 'Subject:'
            sub = ''
            for line in headers.split('\n'):
                if line.startswith(prefix):
                    sub = line[len(prefix):]
                    break
            features['subject'][i] = sub

        return features

def test_recarray_from_repr(self):
        a = np.array([(1,'ABC'), (2, "DEF")],
                     dtype=[('foo', int), ('bar', 'S4')])
        recordarr = np.rec.array(a)
        recarr = a.view(np.recarray)
        recordview = a.view(np.dtype((np.record, a.dtype)))

        recordarr_r = eval("numpy." + repr(recordarr), {'numpy': np})
        recarr_r = eval("numpy." + repr(recarr), {'numpy': np})
        recordview_r = eval("numpy." + repr(recordview), {'numpy': np})

        assert_equal(type(recordarr_r), np.recarray)
        assert_equal(recordarr_r.dtype.type, np.record)
        assert_equal(recordarr, recordarr_r)

        assert_equal(type(recarr_r), np.recarray)
        assert_equal(recarr_r.dtype.type, np.record)
        assert_equal(recarr, recarr_r)

        assert_equal(type(recordview_r), np.ndarray)
        assert_equal(recordview.dtype.type, np.record)
        assert_equal(recordview, recordview_r)

def test_recfromtxt(self):
        #
        data = TextIO('A,B\n0,1\n2,3')
        kwargs = dict(delimiter=",", missing_values="N/A", names=True)
        test = np.recfromtxt(data, **kwargs)
        control = np.array([(0, 1), (2, 3)],
                           dtype=[('A', np.int), ('B', np.int)])
        self.assertTrue(isinstance(test, np.recarray))
        assert_equal(test, control)
        #
        data = TextIO('A,B\n0,1\n2,N/A')
        test = np.recfromtxt(data, dtype=None, usemask=True, **kwargs)
        control = ma.array([(0, 1), (2, -1)],
                           mask=[(False, False), (False, True)],
                           dtype=[('A', np.int), ('B', np.int)])
        assert_equal(test, control)
        assert_equal(test.mask, control.mask)
        assert_equal(test.A, [0, 2])

def merge_table(self,name):
        """Merge an existing table in the database with the __self__ table.

        n = a.merge_table(<name>)

        Executes as 'INSERT INTO __self__ SELECT * FROM <name>'.
        However, this method is probably used less often than the simpler merge(recarray).

        :Arguments:
        name         name of the table in the database (must be compatible with __self__)

        :Returns:
        n            number of inserted rows
        """
        l_before = len(self)
        SQL = """INSERT OR ABORT INTO __self__ SELECT * FROM %s""" % name
        self.sql(SQL)
        l_after = len(self)
        return l_after - l_before

def extract_roi(self, top_left, size, is_normalize=False):
        """Extract Region of Interest
        Does not modify instance data
        Generates a set of td_events which fall into a rectangular region of interest with
        top left corner at 'top_left' and size 'size'
        top_left: [x: int, y: int]
        size: [width, height]
        is_normalize: bool. If True, x and y values will be normalized to the cropped region
        """
        min_x = top_left[0]
        min_y = top_left[1]
        max_x = size[0] + min_x
        max_y = size[1] + min_y
        extracted_data = self.data[(self.data.x >= min_x) & (self.data.x < max_x) & (self.data.y >= min_y) & (self.data.y < max_y)]

        if is_normalize:
            self.width = size[0]
            self.height = size[1]
            extracted_data = np.copy(extracted_data)
            extracted_data = extracted_data.view(np.recarray)
            extracted_data.x -= min_x
            extracted_data.y -= min_y

        return extracted_data

def parse_csv(csv_reader):
    previous_date = None
    data = []
    dtype = [('dt', 'int64'), ('sid', '|S14'), ('open', float),
             ('high', float), ('low', float), ('close', float),
             ('volume', int)]
    for line in csv_reader:
        row = process_line(line)
        current_date = line["dt"][:10].replace("-", "")
        if previous_date and previous_date != current_date:
            rows = np.array(data, dtype=dtype).view(np.recarray)
            yield current_date, rows
            data = []
        data.append(row)
        previous_date = current_date

def _compute_asset_lifetimes(self):
        """
        Compute and cache a recarry of asset lifetimes.
        """
        equities_cols = self.equities.c
        buf = np.array(
            tuple(
                sa.select((
                    equities_cols.sid,
                    equities_cols.start_date,
                    equities_cols.end_date,
                )).execute(),
            ), dtype='<f8',  # use doubles so we get NaNs
        )
        lifetimes = np.recarray(
            buf=buf,
            shape=(len(buf),),
            dtype=[
                ('sid', '<f8'),
                ('start', '<f8'),
                ('end', '<f8')
            ],
        )
        start = lifetimes.start
        end = lifetimes.end
        start[np.isnan(start)] = 0  # convert missing starts to 0
        end[np.isnan(end)] = np.iinfo(int).max  # convert missing end to INTMAX
        # Cast the results back down to int.
        return lifetimes.astype([
            ('sid', '<i8'),
            ('start', '<i8'),
            ('end', '<i8'),
        ])

def get_tag_data(self, episode, tag_channel):
        #memorise some useful properties
        block = self.episode_block(episode)
        sample_size = self.sample_size(episode, tag_channel)
        sample_symbol = self.sample_symbol(episode, tag_channel)

        #create a bit mask to define which
        #sample to keep from the file
        channel_mask = self.create_channel_mask(episode)
        bit_mask = self.create_bit_mask(channel_mask, 1)

        #get bytes from the file
        data_block = self.data_blocks[episode - 1]
        n_bytes = data_block.size
        self.file.seek(data_block.start)
        databytes = np.frombuffer(self.file.read(n_bytes), '<i1')

        #detect which bits keep to recompose the tag
        ep_mask = np.ones(n_bytes, dtype=int)
        np.putmask(ep_mask, ep_mask, bit_mask)
        to_keep = np.where(ep_mask > 0)[0]
        raw = databytes.take(to_keep)
        raw = raw.reshape([len(raw) / sample_size, sample_size])

        #create a recarray containing data
        dt = np.dtype(numpy_map[sample_symbol])
        dt.newbyteorder('<')
        tag_mask = 0b01 if (tag_channel == 1) else 0b10
        y_data = np.frombuffer(raw, dt) & tag_mask
        x_data = np.arange(0, len(y_data)) * block.dX + block.X0
        data = np.recarray(len(y_data), dtype=[('x', b_float), ('y', b_int)])
        data['x'] = x_data
        data['y'] = y_data

        return data

def get_tag_data(self, episode, tag_channel):
        #memorise some useful properties
        block = self.episode_block(episode)
        sample_size = self.sample_size(episode, tag_channel)
        sample_symbol = self.sample_symbol(episode, tag_channel)

        #create a bit mask to define which
        #sample to keep from the file
        channel_mask = self.create_channel_mask(episode)
        bit_mask = self.create_bit_mask(channel_mask, 1)

        #get bytes from the file
        data_block = self.data_blocks[episode - 1]
        n_bytes = data_block.size
        self.file.seek(data_block.start)
        databytes = np.frombuffer(self.file.read(n_bytes), '<i1')

        #detect which bits keep to recompose the tag
        ep_mask = np.ones(n_bytes, dtype=int)
        np.putmask(ep_mask, ep_mask, bit_mask)
        to_keep = np.where(ep_mask > 0)[0]
        raw = databytes.take(to_keep)
        raw = raw.reshape([len(raw) / sample_size, sample_size])

        #create a recarray containing data
        dt = np.dtype(numpy_map[sample_symbol])
        dt.newbyteorder('<')
        tag_mask = 0b01 if (tag_channel == 1) else 0b10
        y_data = np.frombuffer(raw, dt) & tag_mask
        x_data = np.arange(0, len(y_data)) * block.dX + block.X0
        data = np.recarray(len(y_data), dtype=[('x', b_float), ('y', b_int)])
        data['x'] = x_data
        data['y'] = y_data

        return data

def readVcf(inFile, logDebug):
    log.info("reading the VCF file")
    ## We read only one sample from the VCF file
    if logDebug:
        vcf = allel.read_vcf(inFile, samples = [0], fields = '*')
    else:
        sys.stderr = StringIO.StringIO()
        vcf = allel.read_vcf(inFile, samples = [0], fields = '*')
        #vcf = vcfnp.variants(inFile, cache=False).view(np.recarray)
        #vcfD = vcfnp.calldata_2d(inFile, cache=False).view(np.recarray)
        sys.stderr = sys.__stderr__
    (snpCHR, snpsREQ) = parseChrName(vcf['variants/CHROM'])
    try:
        snpGT = allel.GenotypeArray(vcf['calldata/GT']).to_gt()[snpsREQ, 0]
    except AttributeError:
        die("input VCF file doesnt have required GT field")
    snpsREQ = snpsREQ[np.where(snpGT != './.')[0]]
    snpGT = allel.GenotypeArray(vcf['calldata/GT']).to_gt()[snpsREQ, 0]
    if 'calldata/PL' in sorted(vcf.keys()):
        snpWEI = np.copy(vcf['calldata/PL'][snpsREQ, 0]).astype('float')
        snpWEI = snpWEI/(-10)
        snpWEI = np.exp(snpWEI)
    else:
        snpBinary = parseGT(snpGT)
        snpWEI = np.ones((len(snpsREQ), 3))  ## for homo and het
        snpWEI[np.where(snpBinary != 0),0] = 0
        snpWEI[np.where(snpBinary != 1),2] = 0
        snpWEI[np.where(snpBinary != 2),1] = 0
    snpCHR = snpCHR[snpsREQ]
    DPmean = np.mean(vcf['calldata/DP'][snpsREQ,0])
    snpPOS = np.array(vcf['variants/POS'][snpsREQ])
    return (DPmean, snpCHR, snpPOS, snpGT, snpWEI)

def test_endian_recarray(self,level=rlevel):
        # Ticket #2185
        dt = np.dtype([
               ('head', '>u4'),
               ('data', '>u4', 2),
            ])
        buf = np.recarray(1, dtype=dt)
        buf[0]['head'] = 1
        buf[0]['data'][:] = [1, 1]

        h = buf[0]['head']
        d = buf[0]['data'][0]
        buf[0]['head'] = h
        buf[0]['data'][0] = d
        assert_(buf[0]['head'] == 1)