NetworkCNNLayer.py

# general library
import numpy
from math import ceil, sqrt

# theano library
import theano
from theano import tensor as T
from theano.tensor.nnet import conv2d
try:
  from theano.tensor.signal import pool
except ImportError:
  pool = None
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams

# others
from NetworkHiddenLayer import _NoOpLayer
from ActivationFunctions import strtoact
from cuda_implementation.FractionalMaxPoolingOp import fmp
from theano.sandbox.cuda import dnn

class CNN(_NoOpLayer):
  recurrent = True

  def __init__(self, n_features=1, filter=1, d_row=-1, border_mode="valid",
               conv_stride=(1,1), pool_size=(1,1), filter_dilation=(1,1), ignore_border=1,
               pool_stride=0, pool_padding=(0,0), mode="max",
               activation="tanh", dropout=0.0, factor=1.0, base = None, transpose=False,
               force_sample=False, **kwargs):
    """
      :param int n_features: integer
        the number of feature map(s), e.g. 32, 64, or so on.
        the input will be interpret as (width|time, batch, height * n_in_features) and
        the output will be (width|time, batch, height * n_features).

      :param int|(int,int) filter: integer or tuple of length 2
        the filter size/shape, i.e. the number of row(s) and/or columns(s) from the filter shape.
        when this filter type is integer, it means the number of rows the same as the number of columns.
        e.g. 3, 5, (1,3), or so on.

      :param int d_row: integer
        the number of row(s) from the input
        the default value is -1, which the dimension comes from the n_out of the input.
        otherwise, this has to be filled only for the first convolutional layer and
        the rest layer will use the number of rows from the previous layer.

      :param str border_mode: string
        "valid" --  only apply filter to complete patches of the image.
                    Generates output of shape: (image_shape - filter_shape + 1).
        "full"  --  zero-pads image to multiple of filter shape to generate output of shape: (image_shape + filter_shape - 1).
        "same"  --  keep the dimension of convolutional layer output the same as the input dimension.

      :param (int,int) conv_stride: tuple of length 2
        factor by which to subsample the convolutional layer output.
        this stride is writen in (rows,columns).

      :param (int,int) pool_size: tuple of length 2
        factor by which to downscale in pooling layer.
        this is written in (rows,columns).
        the default value is (2,2), it will halve the input in each dimension.

      :param (int,int) filter_dilation: tuple of length 2
        factor by which to subsample (stride) the convolutional layer input.

      :param int|bool ignore_border: integer or boolean
        1 or True  -- (5, 5) input with pool_size = (2, 2), will generate a (2, 2) pooling layer output.
        0 or False -- (5, 5) input with pool_size = (2, 2), will generate a (3, 3) pooling layer output.

      :param (int,int) pool_stride: tuple of length 2
        stride size, which is the number of shifts over rows/cols to get the next pool region.
        the default value is 0, it will set equal to pool_size, which means no overlap on pooling regions.

      :param (int,int) pool_padding: tuple of length 2
        pad zeros to extend beyond four borders of the images.
        this is writen in (pad_h,pad_w), where pad_h is the size of the top and bottom margins, and pad_w is the size of the left and right margins.

      :param str mode: string
        pooling layer mode that excludes the padding in the computation.
        "max" --  max pooling
        "sum" --  sum pooling
        "avg" --  average pooling
        "fmp" --  fractional max pooling

      :param str activation: string
        activation function, e.g. "tanh", "sigmoid", "relu", "elu", "maxout", and so on.

      :param float factor: float
        factor by which scale the initial weights
    """

    super(CNN, self).__init__(**kwargs)
    self.base = base
    src = self.sources
    self.transpose = transpose
    self.status = self.get_status(src)  # [is_conv_layer, n_sources]
    self.is_1d = self.layer_class == "conv_1d"
    is_resnet = self.layer_class == "resnet"

    dimension = src[0].attrs["n_out"]  # input dimension

    if self.status[0]:  # if the previous layer is convolution layer
      stack_size = src[0].attrs["n_features"]  # set stack size from the number of feature maps of previous layer
      d_row = src[0].attrs["d_row"]
      dimension /= stack_size

      # check whether the number of inputs is more than 1 and not resnet for inception
      if self.status[1] != 1 and (not is_resnet):
        # check the spatial dimension of all inputs
        assert all((s.attrs["n_out"] / s.attrs["n_features"]) == dimension
                   for s in src), \
          "The spatial dimension of all inputs have to be the same!"
        stack_size = sum([s.attrs["n_features"] for s in src])  # set the stack_size by concatenating feature maps
    else:  # not convolution layer
      stack_size = 1  # set stack_size of first convolution layer as channel of the image (gray scale image)

      if self.is_1d:  # for processing entire image at once
        if d_row == -1:
          d_row = dimension
        else:
          stack_size = dimension / d_row
      elif d_row == -1:
        d_row = int(sqrt(dimension))

      assert self.status[1] == 1, "Except CNN, the input is only one!"

    # calculate the width of input
    d_col = dimension/d_row

    # set filter size to tuple
    if type(filter) == int:
      filter = [filter, filter]

    if filter == [1, 1]:
      border_mode = "valid"

    # set attributes for resnet
    if is_resnet:
      n_features = src[1].attrs['n_features']
      border_mode = "same"
      pool_size = [1, 1]

    assert ignore_border == 0 or ignore_border == 1, "Ignore border only accept true (1) or false (0)"

    # use no-overlap pooling
    if pool_stride == 0:
      pool_stride = pool_size

    # calculate the dimension of CNN output
    _, new_d_row = self.get_dim(d_row, filter[0], pool_size[0],
                                border_mode, conv_stride[0],
                                pool_stride[0], ignore_border,
                                pool_padding[0])
    border_mode, new_d_col = self.get_dim(d_col, filter[1], pool_size[1],
                                          border_mode, conv_stride[1],
                                          pool_stride[1], ignore_border,
                                          pool_padding[1])

    assert (mode == "max" or mode == "sum" or
            mode == "avg" or mode == "fmp"), "invalid pooling mode!"

    if mode == "fmp":
      new_d_row = int(ceil(new_d_row))
      new_d_col = int(ceil(new_d_col))

    assert (new_d_row > 0), "invalid spatial rows dimensions!"
    n_out = new_d_row * n_features

    if not self.is_1d:
      assert (new_d_col > 0), "invalid spatial columns dimensions!"
      n_out *= new_d_col

    # filter shape is tuple/list of length 4 which is (nb feature maps, stack size, filter row, filter col)
    self.filter_shape = (n_features, stack_size, filter[0], filter[1])
    self.filter_dilation = filter_dilation
    self.input_shape = [d_row, d_col]
    self.modes = [border_mode, ignore_border, mode, activation]
    self.pool_params = [pool_size, pool_stride, pool_padding, conv_stride]
    self.other_params = [dropout, factor]
    self.force_sample = force_sample

    # set attributes
    self.set_attr("n_features", n_features)
    self.set_attr("d_row", new_d_row)  # number of output row
    self.set_attr("n_out", n_out)  # number of output dimension

  def get_status(self, sources):
    n_sources = len(sources)
    is_conv_layer = all(s.layer_class in ("conv", "frac_conv", "conv_1d", "resnet")
                        for s in sources)
    return [is_conv_layer, n_sources]

  def get_dim(self, input, filters, pools, border_mode, stride, pool_stride, ignore_border, pad):
    if border_mode == "valid":
      result = (input - filters + 1)
    elif border_mode == "full":
      result = (input + filters - 1)
    elif border_mode == "same":
      border_mode = "half"
      result = input
    else:
      assert False, "Invalid border_mode"

    if stride != 1:
      result = int(ceil(result/float(stride)))

    result = (result - (pools - pool_stride)) / float(pool_stride)
    result = int(result) if ignore_border else int(ceil(result))
    result += (2 * pad)

    return border_mode, result

  def calculate_index(self, inputs):
    if inputs.ndim == 3:  # TBD
      return T.set_subtensor(
        inputs[((numpy.int8(1) - self.index.flatten()) > 0).nonzero()],
        T.zeros_like(inputs[0])
      )
    else:  # assume BFHW
      B = inputs.shape[0]
      inputs = inputs.dimshuffle(3, 0, 1, 2)  # WBFH
      inputs = self.calculate_index(
        inputs.reshape(
          (inputs.shape[0] * inputs.shape[1],
           inputs.shape[2],
           inputs.shape[3])
        )
      )
      return inputs.reshape((inputs.shape[0] / B, B, inputs.shape[1],
                             inputs.shape[2])).dimshuffle(1, 2, 3, 0)

  def calculate_dropout(self, dropout, inputs):
    assert dropout < 1.0, "Dropout have to be less than 1.0"
    mass = T.constant(1.0 / (1.0 - dropout), dtype="float32")
    random = RandomStreams(self.rng.randint(1234) + 1)

    if self.train_flag:
      inputs = inputs * T.cast(
        random.binomial(n=1, p=1 - dropout, size=inputs.shape),
        theano.config.floatX
      )
    else:
      inputs = inputs * mass
    return inputs

  def convolution(self, inputs, filter_shape, stride, border_mode, factor, pool_size, filter_dilation):
    fan_in = numpy.prod(filter_shape[1:])  # stack_size * filter_row * filter_col
    fan_out = (filter_shape[0] * numpy.prod(filter_shape[2:]) / numpy.prod(pool_size))
    #         (n_features * (filter_row * filter_col)) / (pool_size[0] * pool_size[1])

    W_bound = numpy.sqrt(6. / (fan_in + fan_out)) * factor
    if self.base:
      #W = self.base[0].W
      W = self.add_param(self.base[0].W)
    else:
      W = self.add_param(
        self.shared(
          value=numpy.asarray(
            self.rng.uniform(low=-W_bound, high=W_bound, size=filter_shape),
            dtype='float32'
          ),
          borrow=True,
          name="W_conv_" + self.name
        )
      )
    self.W = W

    if self.transpose:
      op = T.nnet.abstract_conv.AbstractConv2d_gradInputs(
        imshp=inputs.shape,
        kshp=W.shape,
        subsample=stride, border_mode=border_mode,
        filter_flip=False)
      conv_out = op(W, inputs, inputs[2:])
    else:
      conv_out = conv2d(
        input=inputs,
        filters=W,
        filter_shape=filter_shape,
        filter_dilation=filter_dilation,
        subsample=stride,
        border_mode=border_mode
      )

    conv_out.name = "conv_out_" + self.name
    conv_out = self.calculate_index(conv_out)
    return conv_out

  def pooling(self, inputs, pool_size, ignore_border, stride, pad, mode):
    if pool_size == [1, 1]:
      return inputs

    if mode == "avg":
      mode = "average_exc_pad"

    if mode == "fmp":
      height = inputs.shape[2]
      width = inputs.shape[3]
      batch = inputs.shape[0]
      X = inputs.dimshuffle(2, 3, 0, 1)  # (row, col, batches, filters)
      sizes = T.zeros((batch, 2))
      sizes = T.set_subtensor(sizes[:, 0], height)
      sizes = T.set_subtensor(sizes[:, 1], width)
      pooled_out, _ = fmp(X, sizes, pool_size[0])
      return pooled_out.dimshuffle(2, 3, 0, 1)

    pool_out = pool.pool_2d(
      input=inputs,
      ds=pool_size, # TODO(theano 0.9): change to ws
      ignore_border=ignore_border,
      st=stride, # TODO(theano 0.9): change to stride
      padding=pad, # TODO(theano 0.9): change to pad
      mode=mode
    )
    pool_out.name = "pool_out_"+self.name
    return pool_out

  def bias_term(self, inputs, n_features, activation):
    if self.base:
      #b = self.base[0].b
      b = self.add_param(self.base[0].b)
    else:
      b = self.add_param(
        self.shared(
          value=numpy.zeros((n_features,), dtype='float32'),
          borrow=True,
          name="b_conv_" + self.name
        )
      )
    self.b = b
    act = strtoact('identity') if activation == 'maxout' else strtoact(activation)
    output = act(inputs + b.dimshuffle("x", 0, "x", "x"))  # (time*batch, filter, out-row, out-col)
    output.name = "output_bias_term_"+self.name
    output = self.calculate_index(output)
    return output

  def run_cnn(self, inputs, filter_shape, filter_dilation, params, modes, others):
    # dropout
    if others[0] > 0.0:
      inputs = self.calculate_dropout(others[0], inputs)

    conv_out = self.convolution(inputs, filter_shape, params[3], modes[0], others[1], params[0], filter_dilation)
    pool_out = self.pooling(conv_out, params[0], modes[1], params[1], params[2], modes[2])

    if self.is_1d:
      self.index = self.pooling(self.index.dimshuffle(1, 'x', 0),
                                [1, params[0][1]],
                                modes[1],
                                params[1],
                                params[2],
                                modes[2]).dimshuffle(2, 0, 1).flatten(2)

    output = self.bias_term(pool_out, filter_shape[0], modes[3])

    return output


class NewConv(CNN):
  layer_class = "conv"

  '''
    this class is for standard CNN and inception
  '''
  def __init__(self, **kwargs):
    super(NewConv, self).__init__(**kwargs)

    # our CRNN input is 3D tensor that consists of (time, batch, dim)
    # however, the convolution function only accept 4D tensor which is (batch size, stack size, nb row, nb col)
    # therefore, we should convert our input into 4D tensor
    inputs = self.sources[0].output  # (time, batch, input-dim = row * col * stack_size)
    time = inputs.shape[0]
    batch = inputs.shape[1]

    if self.status[0]:  # the previous layer is convolutional layer
      self.input = T.concatenate([s.Output for s in self.sources], axis=1)  # (batch, stack size, row, col)
    else:
      # In case of spliced data, the last dim in inputs contains stacked frames (e.g. ASR).
      # Since Theano reshape will read _and_ write elements row-wise, we need to transpose the target matrix.
      # This is done by swapping target dimensions (reshape(.., input_shape[1], input_shape[0]) and subsequent
      # dimshuffle that puts row and col dim where Theano expects them.
      inputs2 = inputs.reshape((time * batch, self.input_shape[1],
                                self.input_shape[0], self.filter_shape[1]))  # (time*batch, row, col, stack)
      self.input = inputs2.dimshuffle(0, 3, 2, 1)  # (batch, stack_size, row, col)
    self.input.name = "conv_layer_input_final"

    if self.modes[3] != "tanh":
      act = strtoact(self.modes[3])
      self.modes[3] = "identity"

    self.Output = self.run_cnn(
      inputs=self.input,
      filter_shape=self.filter_shape,
      filter_dilation=self.filter_dilation,
      params=self.pool_params,
      modes=self.modes,
      others=self.other_params
    ) # (batch, nb feature maps, out-row, out-col)


    # our CRNN only accept 3D tensor (time, batch, dim)
    # so, we have to convert back the output to 3D tensor
    # self.make_output(self.Output2)
    if self.attrs['batch_norm']:
      self.Output = self.batch_norm(
        h=self.Output.reshape(
          (self.Output.shape[0],
           self.Output.shape[1] * self.Output.shape[2] * self.Output.shape[3])
        ),
        dim=self.attrs['n_out'],
        force_sample=self.force_sample
      ).reshape(self.Output.shape)
      if self.modes[3] != "tanh":
        self.Output = act(self.Output)

    if self.modes[3] == 'maxout':
      self.Output = T.max(self.Output, axis=1).dimshuffle(0, 'x', 1, 2)
      self.attrs['n_out'] /= self.attrs['n_features']
      self.attrs['n_features'] = 1

    output2 = self.Output.dimshuffle(0, 2, 3, 1)  # (batch, out-row, out-col, nb feature maps)
    self.output = output2.reshape((time, batch, output2.shape[1] * output2.shape[2] * output2.shape[3]))  # (time, batch, out-dim)


class ConcatConv(CNN):
  layer_class = "conv_1d"

  '''
    this class is for the CNN that processes an entire line image as the input by concatenated several frames by time axis.
  '''

  def __init__(self, padding=False, **kwargs):
    super(ConcatConv, self).__init__(**kwargs)

    inputs = T.concatenate([s.output for s in self.sources], axis=2)  # (time, batch, input-dim = row * features)
    time = inputs.shape[0]
    batch = inputs.shape[1]

    if self.status[0]:  # the previous layer is convolutional layer
      self.input = T.concatenate([s.Output for s in self.sources], axis=3)  # (batch, stack_size, row, time)
    else:
      d_row = kwargs['d_row'] if 'd_row' in kwargs else -1
      if d_row == -1:
        inputs2 = inputs.reshape((time, batch, inputs.shape[2], self.filter_shape[1]))  # (time, batch, row, stack)
      else:
        inputs2 = inputs.reshape((time, batch, d_row, self.filter_shape[1]))  # (time, batch, row, stack)
      self.input = inputs2.dimshuffle(1, 3, 2, 0)  # (batch, stack_size, row, time)
    self.input.name = "conv_layer_input_final"

    if self.pool_params[0][1] > 1 and padding:
      xp = T.constant(self.pool_params[0][1], 'int32')
      self.input = T.concatenate([self.input, T.zeros((batch, self.filter_shape[1], self.input.shape[2],
                                                       xp - T.mod(self.input.shape[3], xp)), 'float32')], axis=3)
      self.index = T.concatenate([self.index, T.zeros((xp - T.mod(self.index.shape[0], xp), batch), 'int8')], axis=0)

    if self.modes[0] == "valid":
      if self.filter_shape[3] > 1:
        idx = int(self.filter_shape[3] / 2)
        self.index = self.index[idx:-idx]

    self.Output = self.run_cnn(
      inputs=self.input,
      filter_shape=self.filter_shape,
      filter_dilation=self.filter_dilation,
      params=self.pool_params,
      modes=self.modes,
      others=self.other_params
    ) # (batch, nb feature maps, out-row, time)

    self.Output = self.Output #/ T.cast(self.Output.shape[1],'float32')

    if self.attrs['batch_norm']:
      if self.base is None:
        self.Output = self.batch_norm(
          h=self.Output.dimshuffle(0, 2, 3, 1).reshape(
            (self.Output.shape[0] * self.Output.shape[2] * self.Output.shape[3],
             self.Output.shape[1])
          ),
          dim=self.attrs['n_features'],
          force_sample=self.force_sample
        ).reshape((self.Output.shape[0],
                   self.Output.shape[2],
                   self.Output.shape[3],
                   self.Output.shape[1])).dimshuffle(0, 3, 1, 2)
      else:
        self.Output = self.batch_norm(
          h=self.Output.dimshuffle(0, 2, 3, 1).reshape(
            (self.Output.shape[0] * self.Output.shape[2] * self.Output.shape[3],
             self.Output.shape[1])
          ),
          dim=self.attrs['n_features'],
          force_sample=self.force_sample,
          sample_mean=self.base[0].sample_mean,
          gamma=self.base[0].gamma,
          beta=self.base[0].beta
        ).reshape((self.Output.shape[0],
                   self.Output.shape[2],
                   self.Output.shape[3],
                   self.Output.shape[1])).dimshuffle(0, 3, 1, 2)

    # our CRNN only accept 3D tensor (time, batch, dim)
    # so, we have to convert back the output to 3D tensor
    output2 = self.Output.dimshuffle(3, 0, 1, 2)  # (time, batch, nb feature maps, out-row)
    self.output = output2.reshape((output2.shape[0], output2.shape[1],
                                   output2.shape[2] * output2.shape[3]))  # (time, batch, out-dim)


class ResNet(CNN):
  layer_class = "resnet"

  '''
    this class is for resnet connection.
  '''

  def __init__(self, **kwargs):
    super(ResNet, self).__init__(**kwargs)

    assert self.status[1] == 2, "Only accept 2 sources!"
    assert self.status[0], "Only accept cnn layers!"

    x = self.sources[0]
    f_x = self.sources[1]

    time = x.output.shape[0]
    batch = x.output.shape[1]

    self.input = T.add(x.Output, f_x.Output)
    self.Output = T.nnet.relu(self.input)

    if self.attrs['batch_norm']:
      self.Output = self.batch_norm(
        h=self.Output.reshape(
          (self.Output.shape[0],
           self.Output.shape[1] * self.Output.shape[2] * self.Output.shape[3])
        ),
        dim=self.attrs['n_out'],
        force_sample=self.force_sample
      ).reshape(self.Output.shape)

    output2 = self.Output.dimshuffle(0, 2, 3, 1)  # (time*batch, out-row, out-col, nb feature maps)
    self.output = output2.reshape((time, batch, output2.shape[1] * output2.shape[2] * output2.shape[3]))  # (time, batch, out-dim)