Python numpy.frombuffer() 使用实例

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Example 1

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 2

def test_tile_symmetry(self):
        '''
        Make sure that tiles are symmetric
        '''
        upload_file = open('data/Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool', 'rb')
        tileset = tm.Tileset.objects.create(
            datafile=dcfu.SimpleUploadedFile(upload_file.name, upload_file.read()),
            filetype='cooler',
            datatype='matrix',
            owner=self.user1,
            uuid='aa')

        ret = self.client.get('/api/v1/tiles/?d=aa.0.0.0')


        contents = json.loads(ret.content.decode('utf-8'))

        import base64
        r = base64.decodestring(contents['aa.0.0.0']['dense'].encode('utf-8'))
        q = np.frombuffer(r, dtype=np.float16)

        q = q.reshape((256,256)) 

Example 3

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 4

def unpack_packet(stream,vertex_type,size):
    # The entire packet is read into memory at once for speed
    packet = stream.read(size)
    primitives = []
    i = 0

    while i < size:
        opcode = packet[i]
        if opcode == 0x00:
            i += 1
            continue
        primitive_type = gx.PrimitiveType(opcode)
        vertex_count = uint16.unpack_from(packet,i + 1)
        vertices = numpy.frombuffer(packet,vertex_type,vertex_count,i + 3)
        primitives.append(Primitive(primitive_type,vertices))
        i += 3 + vertex_count*vertex_type.itemsize

    return primitives 

Example 5

def load_bytes(self, data_blocks, dtype='<i1', start=None, end=None, expected_size=None):
        """
        Return list of bytes contained
        in the specified set of blocks.
        
        NB : load all data as files cannot exceed 4Gb 
             find later other solutions to spare memory.
        """
        chunks = list()
        raw = ''
        # keep only data blocks having
        # a size greater than zero
        blocks = [k for k in data_blocks if k.size > 0]
        for data_block in blocks :
            self.file.seek(data_block.start)
            raw = self.file.read(data_block.size)[0:expected_size]
            databytes = np.frombuffer(raw, dtype=dtype)
            chunks.append(databytes)
        # concatenate all chunks and return
        # the specified slice
        if len(chunks)>0 :
            databytes = np.concatenate(chunks)
            return databytes[start:end]
        else :
            return np.array([]) 

Example 6

def load_channel_data(self, ep, ch):
        """
        Return a numpy array containing the
        list of bytes corresponding to the
        specified episode and channel.
        """
        #memorise the sample size and symbol
        sample_size = self.sample_size(ep, ch)
        sample_symbol = self.sample_symbol(ep, ch)
        
        #create a bit mask to define which
        #sample to keep from the file
        bit_mask = self.create_bit_mask(ep, ch)
        
        #load all bytes contained in an episode
        data_blocks = self.get_data_blocks(ep)
        databytes = self.load_bytes(data_blocks)
        raw = self.filter_bytes(databytes, bit_mask)
        
        #reshape bytes from the sample size
        dt = np.dtype(numpy_map[sample_symbol])
        dt.newbyteorder('<')
        return np.frombuffer(raw.reshape([len(raw) / sample_size, sample_size]), dt) 

Example 7

def load_bytes(self, data_blocks, dtype='<i1', start=None, end=None, expected_size=None):
        """
        Return list of bytes contained
        in the specified set of blocks.
        
        NB : load all data as files cannot exceed 4Gb 
             find later other solutions to spare memory.
        """
        chunks = list()
        raw = ''
        # keep only data blocks having
        # a size greater than zero
        blocks = [k for k in data_blocks if k.size > 0]
        for data_block in blocks :
            self.file.seek(data_block.start)
            raw = self.file.read(data_block.size)[0:expected_size]
            databytes = np.frombuffer(raw, dtype=dtype)
            chunks.append(databytes)
        # concatenate all chunks and return
        # the specified slice
        if len(chunks)>0 :
            databytes = np.concatenate(chunks)
            return databytes[start:end]
        else :
            return np.array([]) 

Example 8

def load_channel_data(self, ep, ch):
        """
        Return a numpy array containing the
        list of bytes corresponding to the
        specified episode and channel.
        """
        #memorise the sample size and symbol
        sample_size = self.sample_size(ep, ch)
        sample_symbol = self.sample_symbol(ep, ch)
        
        #create a bit mask to define which
        #sample to keep from the file
        bit_mask = self.create_bit_mask(ep, ch)
        
        #load all bytes contained in an episode
        data_blocks = self.get_data_blocks(ep)
        databytes = self.load_bytes(data_blocks)
        raw = self.filter_bytes(databytes, bit_mask)
        
        #reshape bytes from the sample size
        dt = np.dtype(numpy_map[sample_symbol])
        dt.newbyteorder('<')
        return np.frombuffer(raw.reshape([len(raw) / sample_size, sample_size]), dt) 

Example 9

def load_encoded_spikes(self, episode, evt_channel, identifier):
        """
        Return times stored as a 4-bytes integer
        in the specified spike channel.
        NB: it is meant for Blackrock-type, having an additional byte for each event time as spike sorting label.
            These additiona bytes are appended trailing the times.
        """
        # to load the requested spikes for the specified episode and event channel:
        # get all the elphy blocks having as identifier 'RSPK' (or whatever)
        all_rspk_blocks = [k for k in self.blocks if k.identifier == identifier]
        rspk_block = all_rspk_blocks[episode-1]
        # RDATA(h?dI) REVT(NbVeV:I, NbEv:256I ... spike data are 4byte integers
        rspk_header = 4*( rspk_block.size - rspk_block.data_size-2 + len(rspk_block.n_events))
        pre_events = np.sum(rspk_block.n_events[0:evt_channel-1], dtype=int, axis=0)
        # the real start is after header, preceeding events (which are 4byte) and preceeding labels (1byte)
        start = rspk_header + (4*pre_events) + pre_events
        end = start + 4*rspk_block.n_events[evt_channel-1]
        raw = self.load_bytes( [rspk_block], dtype='<i1', start=start, end=end, expected_size=rspk_block.size )
        # re-encoding after reading byte by byte
        res = np.frombuffer(raw[0:(4*rspk_block.n_events[evt_channel-1])], dtype='<i4')
        res.sort() # sometimes timings are not sorted
        #print "load_encoded_data() - spikes:",res
        return res 

Example 10

def extract_images(filename):
    """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
    log = logger.get()
    log.info('Extracting {}'.format(filename))
    with gzip.open(filename) as bytestream:
        magic = _read32(bytestream)
        if magic != 2051:
            raise ValueError(
                'Invalid magic number %d in MNIST image file: %s' %
                (magic, filename))
        num_images = _read32(bytestream)
        rows = _read32(bytestream)
        cols = _read32(bytestream)
        buf = bytestream.read(rows * cols * num_images)
        data = numpy.frombuffer(buf, dtype=numpy.uint8)
        data = data.reshape(num_images, rows, cols, 1)
        return data 

Example 11

def extract_labels(filename, one_hot=False):
    """Extract the labels into a 1D uint8 numpy array [index]."""
    log = logger.get()
    log.info('Extracting {}'.format(filename))
    with gzip.open(filename) as bytestream:
        magic = _read32(bytestream)
        if magic != 2049:
            raise ValueError(
                'Invalid magic number %d in MNIST label file: %s' %
                (magic, filename))
        num_items = _read32(bytestream)
        buf = bytestream.read(num_items)
        labels = numpy.frombuffer(buf, dtype=numpy.uint8)
        if one_hot:
            return dense_to_one_hot(labels)
        return labels 

Example 12

def read_pgm(filename, byteorder='>'):
    """Return image data from a raw PGM file as numpy array.

    Format specification: http://netpbm.sourceforge.net/doc/pgm.html

    """
    with open(filename, 'rb') as f:
        buffer = f.read()
    try:
        header, width, height, maxval = re.search(
            b"(^P5\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n]\s)*)", buffer).groups()
    except AttributeError:
        raise ValueError("Not a raw PGM file: '%s'" % filename)
    return np.frombuffer(buffer,
                         dtype='u1' if int(maxval) < 256 else byteorder + 'u2',
                         count=int(width) * int(height),
                         offset=len(header)
                         ).reshape((int(height), int(width))) 

Example 13

def extract_images(filename, verbose=True):
    """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
    if verbose:
        print('Extracting', filename)
    with gzip.open(filename) as bytestream:
        magic = _read32(bytestream)
        if magic != 2051:
            raise ValueError(
              'Invalid magic number %d in MNIST image file: %s' %
              (magic, filename))
        num_images = _read32(bytestream)
        rows = _read32(bytestream)
        cols = _read32(bytestream)
        buf = bytestream.read(rows * cols * num_images)
        data = np.frombuffer(buf, dtype=np.uint8)
        data = data.reshape(num_images, rows, cols, 1)
        return data 

Example 14

def test_buffer_numpy(self):
        """test non-copying numpy array messages"""
        try:
            import numpy
        except ImportError:
            raise SkipTest("numpy required")
        rand = numpy.random.randint
        shapes = [ rand(2,16) for i in range(5) ]
        for i in range(1,len(shapes)+1):
            shape = shapes[:i]
            A = numpy.random.random(shape)
            m = zmq.Frame(A)
            if view.__name__ == 'buffer':
                self.assertEqual(A.data, m.buffer)
                B = numpy.frombuffer(m.buffer,dtype=A.dtype).reshape(A.shape)
            else:
                self.assertEqual(memoryview(A), m.buffer)
                B = numpy.array(m.buffer,dtype=A.dtype).reshape(A.shape)
            self.assertEqual((A==B).all(), True) 

Example 15

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 16

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 17

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with tf.gfile.Open(filename, 'rb') as f, gzip.GzipFile(fileobj=f) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 18

def pickle_transitions_matrix_data():
    transitions = pickle.load( open( "/ssd/ddimitrov/pickle/transitions", "rb" ) )
    vocab = pickle.load( open( "/ssd/ddimitrov/pickle/vocab", "rb" ) )

    i_indices = array.array(str("l"))
    j_indices = array.array(str("l"))
    values = array.array(str("d"))

    for s, targets in transitions.iteritems():
        for t, v in targets.iteritems():
            i_indices.append(vocab[s])
            j_indices.append(vocab[t])
            values.append(v)

    i_indices = np.frombuffer(i_indices, dtype=np.int_)
    j_indices = np.frombuffer(j_indices, dtype=np.int_)
    values = np.frombuffer(values, dtype=np.float64)
    transition_matrix=[i_indices,j_indices,values]
    pickle.dump(transition_matrix, open("/ssd/ddimitrov/pickle/transition_matrix", "wb"), protocol=pickle.HIGHEST_PROTOCOL)
    print "transition_matrix" 

Example 19

def _read_datafile(self, path, expected_dims):
        """Helper function to read a file in IDX format."""
        base_magic_num = 2048
        with gzip.GzipFile(path) as f:
            magic_num = struct.unpack('>I', f.read(4))[0]
            expected_magic_num = base_magic_num + expected_dims
            if magic_num != expected_magic_num:
                raise ValueError('Incorrect MNIST magic number (expected '
                                 '{}, got {})'
                                 .format(expected_magic_num, magic_num))
            dims = struct.unpack('>' + 'I' * expected_dims,
                                 f.read(4 * expected_dims))
            buf = f.read(reduce(operator.mul, dims))
            data = np.frombuffer(buf, dtype=np.uint8)
            data = data.reshape(*dims)
            return data 

Example 20

def _ungzip(save_path, extract_path, database_name, _):
    """
    Unzip a gzip file and extract it to extract_path
    :param save_path: The path of the gzip files
    :param extract_path: The location to extract the data to
    :param database_name: Name of database
    :param _: HACK - Used to have to same interface as _unzip
    """
    # Get data from save_path
    with open(save_path, 'rb') as f:
        with gzip.GzipFile(fileobj=f) as bytestream:
            magic = _read32(bytestream)
            if magic != 2051:
                raise ValueError('Invalid magic number {} in file: {}'.format(magic, f.name))
            num_images = _read32(bytestream)
            rows = _read32(bytestream)
            cols = _read32(bytestream)
            buf = bytestream.read(rows * cols * num_images)
            data = np.frombuffer(buf, dtype=np.uint8)
            data = data.reshape(num_images, rows, cols)

    # Save data to extract_path
    for image_i, image in enumerate(
            tqdm(data, unit='File', unit_scale=True, miniters=1, desc='Extracting {}'.format(database_name))):
        Image.fromarray(image, 'L').save(os.path.join(extract_path, 'image_{}.jpg'.format(image_i))) 

Example 21

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 22

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 23

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 24

def receive_data(self, channel, oc):
        # push data from a socket into an OutputConnector (oc)
        self.last_timestamp = datetime.datetime.now()
        # wire format is just: [size, buffer...]
        sock = self._chan_to_rsocket[channel]
        # TODO receive 4 or 8 bytes depending on sizeof(size_t)
        msg = sock.recv(8)
        # reinterpret as int (size_t)
        msg_size = struct.unpack('n', msg)[0]
        buf = sock.recv(msg_size, socket.MSG_WAITALL)
        if len(buf) != msg_size:
            logger.error("Channel %s socket msg shorter than expected" % channel.channel)
            logger.error("Expected %s bytes, received %s bytes" % (msg_size, len(buf)))
            # assume that we cannot recover, so stop listening.
            loop = asyncio.get_event_loop()
            loop.remove_reader(sock)
            return
        data = np.frombuffer(buf, dtype=channel.dtype)
        asyncio.ensure_future(oc.push(data)) 

Example 25

def receive_data(self, channel, oc):
        # push data from a socket into an OutputConnector (oc)
        self.last_timestamp = datetime.datetime.now()
        self.fetch_count += 1
        # wire format is just: [size, buffer...]
        sock = self._chan_to_rsocket[channel]
        # TODO receive 4 or 8 bytes depending on sizeof(size_t)
        msg = sock.recv(8)
        # reinterpret as int (size_t)
        msg_size = struct.unpack('n', msg)[0]
        buf = sock.recv(msg_size, socket.MSG_WAITALL)
        if len(buf) != msg_size:
            logger.error("Channel %s socket msg shorter than expected" % channel.channel)
            logger.error("Expected %s bytes, received %s bytes" % (msg_size, len(buf)))
            # assume that we cannot recover, so stop listening.
            loop = asyncio.get_event_loop()
            loop.remove_reader(sock)
            return
        data = np.frombuffer(buf, dtype=np.float32)
        asyncio.ensure_future(oc.push(data)) 

Example 26

def loop(self):
        while self.running:
            evts = dict(self.poller.poll(50))
            if self.socket in evts and evts[self.socket] == zmq.POLLIN:
                msg = self.socket.recv_multipart()
                msg_type = msg[0].decode()
                name     = msg[1].decode()
                if msg_type == "done":
                    self.finished.emit(True)
                elif msg_type == "data":
                    result = [name]
                    # How many pairs of metadata and data are there?
                    num_arrays = int((len(msg) - 2)/2)
                    for i in range(num_arrays):
                        md, data = msg[2+2*i:4+2*i]
                        md = json.loads(md.decode())
                        A = np.frombuffer(data, dtype=md['dtype'])
                        result.append(A)
                    self.message.emit(tuple(result))
        self.socket.close() 

Example 27

def _reads(self, addr, length):
        if length > 65535:
            length = 65535
            self.logger.warning("Maximum read-length is %d", length)
        header = b'r' + bytes(bytearray([0,
                                         length & 0xFF, (length >> 8) & 0xFF,
                                         addr & 0xFF, (addr >> 8) & 0xFF, (addr >> 16) & 0xFF, (addr >> 24) & 0xFF]))
        self.socket.send(header)
        data = self.socket.recv(length * 4 + 8)
        while (len(data) < length * 4 + 8):
            data += self.socket.recv(length * 4 - len(data) + 8)
        if data[:8] == header:  # check for in-sync transmission
            return np.frombuffer(data[8:], dtype=np.uint32)
        else:  # error handling
            self.logger.error("Wrong control sequence from server: %s", data[:8])
            self.emptybuffer()
            return None 

Example 28

def read(self):
        """Return audio file as array of integer.
        Returns:
            audio_data: np.ndarray, shape of (frame_num,)
        """
        # Read wav file
        with wave.open(self.file_path, "r") as wav:
            # Move to head of the audio file
            wav.rewind()

            self.frame_num = wav.getnframes()
            self.sampling_rate = wav.getframerate()  # 16,000 Hz
            self.channels = wav.getnchannels()
            self.sample_size = wav.getsampwidth()  # 2

            # Read to buffer as binary format
            buf = wav.readframes(self.frame_num)

        if self.channels == 1:
            audio_data = np.frombuffer(buf, dtype="int16")
        elif self.channels == 2:
            audio_data = np.frombuffer(buf, dtype="int32")

        return audio_data 

Example 29

def extract_images(filename):
    """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
    print('Extracting', filename)
    with gzip.open(filename) as bytestream:
        magic = _read32(bytestream)
        if magic != 2051:
            raise ValueError(
                'Invalid magic number %d in MNIST image file: %s' %
                (magic, filename))
        num_images = _read32(bytestream)
        rows = _read32(bytestream)
        cols = _read32(bytestream)
        buf = bytestream.read(rows * cols * num_images)
        data = numpy.frombuffer(buf, dtype=numpy.uint8)
        data = data.reshape(num_images, rows, cols, 1)
        return data 

Example 30

def extract_images(filename):
    """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
    print('Extracting', filename)
    with gzip.open(filename) as bytestream:
        magic = _read32(bytestream)
        if magic != 2051:
            raise ValueError(
                'Invalid magic number %d in MNIST image file: %s' %
                (magic, filename))
        num_images = _read32(bytestream)
        rows = _read32(bytestream)
        cols = _read32(bytestream)
        buf = bytestream.read(rows * cols * num_images)
        data = numpy.frombuffer(buf, dtype=numpy.uint8)
        data = data.reshape(num_images, rows, cols, 1)
        return data 

Example 31

def make_array(shape=(1,), dtype=np.float32, shared=False, fill_val=None):  
    np_type_to_ctype = {np.float32: ctypes.c_float,
                        np.float64: ctypes.c_double,
                        np.bool: ctypes.c_bool,
                        np.uint8: ctypes.c_ubyte,
                        np.uint64: ctypes.c_ulonglong}
    
    if not shared:
        np_arr = np.empty(shape, dtype=dtype)
    else:
        numel = np.prod(shape)
        arr_ctypes = sharedctypes.RawArray(np_type_to_ctype[dtype], numel)
        np_arr = np.frombuffer(arr_ctypes, dtype=dtype, count=numel)
        np_arr.shape = shape
    
    if not fill_val is None:
        np_arr[...] = fill_val
    
    return np_arr 

Example 32

def __call__(self, bytez):
        output = np.zeros((16, 16), dtype=np.int)
        a = np.frombuffer(bytez, dtype=np.uint8)
        if a.shape[0] < self.window:
            Hbin, c = self._entropy_bin_counts(a)
            output[Hbin, :] += c
        else:
            # strided trick from here: http://www.rigtorp.se/2011/01/01/rolling-statistics-numpy.html
            shape = a.shape[:-1] + (a.shape[-1] - self.window + 1, self.window)
            strides = a.strides + (a.strides[-1],)
            blocks = np.lib.stride_tricks.as_strided(
                a, shape=shape, strides=strides)[::self.step, :]

            # from the blocks, compute histogram
            for block in blocks:
                Hbin, c = self._entropy_bin_counts(block)
                output[Hbin, :] += c

        return output.flatten().astype(self.dtype) 

Example 33

def _unpack_ndarray(cls, buf, offset):
        dtype, offset = cls._unpack_string(buf, offset)
        shape_len = unpack_from("I", buf, offset)[0]
        offset += 4
        shape = []
        for i in range(0, shape_len):
            item = unpack_from("I", buf, offset)[0]
            offset += 4
            shape.append(item)

        reslen = unpack_from("I", buf, offset)[0]
        offset += 4
        res = np.frombuffer(buf[offset:offset+reslen], dtype=np.dtype(dtype))
        res = res.reshape(shape)
        offset += reslen
        return res, offset 

Example 34

def _extract_images(filename, num_images):
  """Extract the images into a numpy array.

  Args:
    filename: The path to an MNIST images file.
    num_images: The number of images in the file.

  Returns:
    A numpy array of shape [number_of_images, height, width, channels].
  """
  print('Extracting images from: ', filename)
  with gzip.open(filename) as bytestream:
    bytestream.read(16)
    buf = bytestream.read(
        _IMAGE_SIZE * _IMAGE_SIZE * num_images * _NUM_CHANNELS)
    data = np.frombuffer(buf, dtype=np.uint8)
    data = data.reshape(num_images, _IMAGE_SIZE, _IMAGE_SIZE, _NUM_CHANNELS)
  return data 

Example 35

def _extract_labels(filename, num_labels):
  """Extract the labels into a vector of int64 label IDs.

  Args:
    filename: The path to an MNIST labels file.
    num_labels: The number of labels in the file.

  Returns:
    A numpy array of shape [number_of_labels]
  """
  print('Extracting labels from: ', filename)
  with gzip.open(filename) as bytestream:
    bytestream.read(8)
    buf = bytestream.read(1 * num_labels)
    labels = np.frombuffer(buf, dtype=np.uint8).astype(np.int64)
  return labels 

Example 36

def read_pgm(filename, byteorder='>'):
    """Return image data from a raw PGM file as numpy array.

    Format specification: http://netpbm.sourceforge.net/doc/pgm.html

    """
    with open(filename, 'rb') as f:
        buffer = f.read()
    try:
        header, width, height, maxval = re.search(
            b"(^P5\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n]\s)*)", buffer).groups()
    except AttributeError:
        raise ValueError("Not a raw PGM file: '%s'" % filename)
    return np.frombuffer(buffer,
                         dtype='u1' if int(maxval) < 256 else byteorder+'u2',
                         count=int(width)*int(height),
                         offset=len(header)
                         ).reshape((int(height), int(width))) 

Example 37

def mpraw_as_np(shape, dtype):
    """Construct a numpy array of the specified shape and dtype for which the
    underlying storage is a multiprocessing RawArray in shared memory.

    Parameters
    ----------
    shape : tuple
      Shape of numpy array
    dtype : data-type
      Data type of array

    Returns
    -------
    arr : ndarray
      Numpy array
    """

    sz = int(np.product(shape))
    csz = sz * np.dtype(dtype).itemsize
    raw = mp.RawArray('c', csz)
    return np.frombuffer(raw, dtype=dtype, count=sz).reshape(shape) 

Example 38

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 39

def native_to_builtin(value, native_type, data_count):
    '''Convert from a native EPICS DBR type to a builtin Python type

    Notes:
     - A waveform of characters is just a bytestring.
     - A waveform of strings is an array whose elements are fixed-length (40-
       character) strings.
     - Enums are just integers that happen to have special significance.
     - Everything else is, straightforwardly, an array of numbers.
    '''

    if USE_NUMPY:
        # Return an ndarray
        dt = _numpy_map[native_type]
        if native_type == ChannelType.STRING and len(value) < MAX_STRING_SIZE:
            # caput behaves this way
            return numpy.frombuffer(
                bytes(value).ljust(MAX_STRING_SIZE, b'\x00'), dtype=dt)

        return numpy.frombuffer(value, dtype=dt)
    else:
        # TODO
        raise NotImplementedError("the non-numpy version has not been "
                                  "written yet") 

Example 40

def extract_images(filename):
  """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
  print('Extracting %s' % filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2051:
      raise ValueError(
          'Invalid magic number %d in MNIST image file: %s' %
          (magic, filename))
    num_images = _read32(bytestream)
    rows = _read32(bytestream)
    cols = _read32(bytestream)
    buf = bytestream.read(rows * cols * num_images)
    data = numpy.frombuffer(buf, dtype=numpy.uint8)
    data = data.reshape(num_images, rows, cols, 1)
    return data 

Example 41

def test_history_recording_simple_model(self):
        """Test that history in memory matches with that recorded for test one-dimensional model."""
        self.param, self.like = onedmodel()
        model = Model(self.like, self.param)
        step = Dream(model=model, model_name='test_history_recording')
        history_arr = mp.Array('d', [0]*4*step.total_var_dimension)
        n = mp.Value('i', 0)
        nchains = mp.Value('i', 3)
        pydream.Dream_shared_vars.history = history_arr
        pydream.Dream_shared_vars.count = n
        pydream.Dream_shared_vars.nchains = nchains
        test_history = np.array([[1], [3], [5], [7]])
        for chainpoint in test_history:
            for point in chainpoint:
                step.record_history(nseedchains=0, ndimensions=step.total_var_dimension, q_new=point, len_history=len(history_arr))
        history_arr_np = np.frombuffer(pydream.Dream_shared_vars.history.get_obj())
        history_arr_np_reshaped = history_arr_np.reshape(np.shape(test_history))
        self.assertIs(np.array_equal(history_arr_np_reshaped, test_history), True)
        remove('test_history_recording_DREAM_chain_history.npy')
        remove('test_history_recording_DREAM_chain_adapted_crossoverprob.npy')
        remove('test_history_recording_DREAM_chain_adapted_gammalevelprob.npy') 

Example 42

def test_history_recording_multidim_model(self):
        """Test that history in memory matches with that recorded for test multi-dimensional model."""
        self.param, self.like = multidmodel()
        model = Model(self.like, self.param)
        dream = Dream(model=model, model_name='test_history_recording')
        history_arr = mp.Array('d', [0]*4*dream.total_var_dimension*3)
        n = mp.Value('i', 0)
        nchains = mp.Value('i', 3)
        pydream.Dream_shared_vars.history = history_arr
        pydream.Dream_shared_vars.count = n
        pydream.Dream_shared_vars.nchains = nchains
        test_history = np.array([[[1, 2, 3, 4], [3, 4, 5, 6], [5, 6, 7, 8]], [[7, 8, 9, 10], [9, 12, 18, 20], [11, 14, 18, 8]], [[13, 14, 18, 4], [15, 17, 11, 8], [17, 28, 50, 4]], [[19, 21, 1, 18], [21, 19, 19, 11], [23, 4, 3, 2]]])
        for chainpoint in test_history:
            for point in chainpoint:
                dream.record_history(nseedchains=0, ndimensions=dream.total_var_dimension, q_new=point, len_history=len(history_arr))
        history_arr_np = np.frombuffer(pydream.Dream_shared_vars.history.get_obj())
        history_arr_np_reshaped = history_arr_np.reshape(np.shape(test_history))
        self.assertIs(np.array_equal(history_arr_np_reshaped, test_history), True)
        remove('test_history_recording_DREAM_chain_history.npy')
        remove('test_history_recording_DREAM_chain_adapted_crossoverprob.npy')
        remove('test_history_recording_DREAM_chain_adapted_gammalevelprob.npy') 

Example 43

def _read32(bytestream):
  dt = numpy.dtype(numpy.uint32).newbyteorder('>')
  return numpy.frombuffer(bytestream.read(4), dtype=dt)[0] 

Example 44

def extract_labels(filename, one_hot=False):
  """Extract the labels into a 1D uint8 numpy array [index]."""
  print('Extracting', filename)
  with gzip.open(filename) as bytestream:
    magic = _read32(bytestream)
    if magic != 2049:
      raise ValueError(
          'Invalid magic number %d in MNIST label file: %s' %
          (magic, filename))
    num_items = _read32(bytestream)
    buf = bytestream.read(num_items)
    labels = numpy.frombuffer(buf, dtype=numpy.uint8)
    if one_hot:
      return dense_to_one_hot(labels)
    return labels 

Example 45

def _read32(bytestream):
  dt = numpy.dtype(numpy.uint32).newbyteorder('>')
  return numpy.frombuffer(bytestream.read(4), dtype=dt) 

Example 46

def decode_raw(bytestring, shape=(64,64,64), dtype=np.uint32):
    return np.frombuffer(bytestring, dtype=dtype).reshape(shape[::-1]).T 

Example 47

def capture(self, initial_sleep=0.01, poll=0.01, buffer_=None,
                filename=None):
        """Capture a still image. Type :class:`numpy.ndarray`."""
        self.start_exposure()
        if initial_sleep:
            time.sleep(initial_sleep)
        while self.get_exposure_status() == ASI_EXP_WORKING:
            if poll:
                time.sleep(poll)
            pass

        status = self.get_exposure_status()
        if status != ASI_EXP_SUCCESS:
            raise ZWO_CaptureError('Could not capture image', status)
        
        data = self.get_data_after_exposure(buffer_)
        whbi = self.get_roi_format()
        shape = [whbi[1], whbi[0]]
        if whbi[3] == ASI_IMG_RAW8 or whbi[3] == ASI_IMG_Y8:
            img = np.frombuffer(data, dtype=np.uint8)
        elif whbi[3] == ASI_IMG_RAW16:
            img = np.frombuffer(data, dtype=np.uint16)
        elif whbi[3] == ASI_IMG_RGB24:
            img = np.frombuffer(data, dtype=np.uint8)
            shape.append(3)
        else:
            raise ValueError('Unsupported image type')
        img = img.reshape(shape)

        if filename is not None:
            from PIL import Image
            mode = None
            if len(img.shape) == 3:
                img = img[:, :, ::-1]  # Convert BGR to RGB
            if whbi[3] == ASI_IMG_RAW16:
                mode = 'I;16'
            image = Image.fromarray(img, mode=mode)
            image.save(filename)
            logger.debug('wrote %s', filename)
        return img 

Example 48

def capture_video_frame(self, buffer_=None, filename=None, timeout=None):
        """Capture a single frame from video. Type :class:`numpy.ndarray`.

        Video mode must have been started previously otherwise a :class:`ZWO_Error` will be raised. A new buffer
        will be used to store the image unless one has been supplied with the `buffer` keyword argument.
        If `filename` is not ``None`` the image is saved using :py:meth:`PIL.Image.Image.save()`.
        :func:`capture_video_frame()` will wait indefinitely unless a `timeout` has been given.
        The SDK suggests that the `timeout` value, in milliseconds, should be twice the exposure plus 500 ms."""
        data = self.get_video_data(buffer_=buffer_, timeout=timeout)
        whbi = self.get_roi_format()
        shape = [whbi[1], whbi[0]]
        if whbi[3] == ASI_IMG_RAW8 or whbi[3] == ASI_IMG_Y8:
            img = np.frombuffer(data, dtype=np.uint8)
        elif whbi[3] == ASI_IMG_RAW16:
            img = np.frombuffer(data, dtype=np.uint16)
        elif whbi[3] == ASI_IMG_RGB24:
            img = np.frombuffer(data, dtype=np.uint8)
            shape.append(3)
        else:
            raise ValueError('Unsupported image type')
        img = img.reshape(shape)

        if filename is not None:
            from PIL import Image
            mode = None
            if len(img.shape) == 3:
                img = img[:, :, ::-1]  # Convert BGR to RGB
            if whbi[3] == ASI_IMG_RAW16:
                mode = 'I;16'
            image = Image.fromarray(img, mode=mode)
            image.save(filename)
            logger.debug('wrote %s', filename)

        return img 

Example 49

def __init__(self, buf, offset = 0, idmap = None, idmap_size = 1024):
        if idmap is None:
            idmap = Cache(idmap_size)
        self.offset = offset
        if offset != 0:
            self.buf = buf = buffer(buf, offset)
        else:
            self.buf = buf
        self.total_size, self.index_offset, self.index_elements = self._Header.unpack_from(buf, 0)
        self.index = numpy.frombuffer(buf, 
            offset = self.index_offset, 
            dtype = numpy.uint64, 
            count = self.index_elements)
        self.idmap = idmap

        if self.index_elements > 0 and self.index[0] >= (self._Header.size + self._NewHeader.size):
            # New version, most likely
            self.version, min_reader_version, self.schema_offset, self.schema_size = self._NewHeader.unpack_from(
                buf, self._Header.size)
            if self._CURRENT_VERSION < min_reader_version:
                raise ValueError((
                    "Incompatible buffer, this buffer needs a reader with support for version %d at least, "
                    "this reader supports up to version %d") % (
                        min_reader_version,
                        self._CURRENT_VERSION
                    ))
            if self.schema_offset and self.schema_size:
                if self.schema_offset > len(buf) or (self.schema_size + self.schema_offset) > len(buf):
                    raise ValueError("Corrupted input - bad schema location")
                stored_schema = cPickle.loads(bytes(buffer(buf, self.schema_offset, self.schema_size)))
                if not isinstance(stored_schema, Schema):
                    raise ValueError("Corrupted input - unrecognizable schema")
                if self.schema is None or not self.schema.compatible(stored_schema):
                    self.schema = stored_schema
            elif self.schema is None:
                raise ValueError("Cannot map schema-less buffer without specifying schema")
        elif self.index_elements > 0:
            raise ValueError("Cannot reliably map version-0 buffers") 

Example 50

def imageToArray(img, copy=False, transpose=True):
    """
    Convert a QImage into numpy array. The image must have format RGB32, ARGB32, or ARGB32_Premultiplied.
    By default, the image is not copied; changes made to the array will appear in the QImage as well (beware: if 
    the QImage is collected before the array, there may be trouble).
    The array will have shape (width, height, (b,g,r,a)).
    """
    fmt = img.format()
    ptr = img.bits()
    if USE_PYSIDE:
        arr = np.frombuffer(ptr, dtype=np.ubyte)
    else:
        ptr.setsize(img.byteCount())
        arr = np.asarray(ptr)
        if img.byteCount() != arr.size * arr.itemsize:
            # Required for Python 2.6, PyQt 4.10
            # If this works on all platforms, then there is no need to use np.asarray..
            arr = np.frombuffer(ptr, np.ubyte, img.byteCount())
    
    arr = arr.reshape(img.height(), img.width(), 4)
    if fmt == img.Format_RGB32:
        arr[...,3] = 255
    
    if copy:
        arr = arr.copy()
        
    if transpose:
        return arr.transpose((1,0,2))
    else:
        return arr