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NetworkTwoDLayer.py
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NetworkTwoDLayer.py
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from NetworkHiddenLayer import Layer
from Log import log
from cuda_implementation.OneDToTwoDOp import OneDToTwoDOp
from cuda_implementation.CropToBatchImageSizeOp import CropToBatchImageSizeInstance, CropToBatchImageSizeZeroInstance
from cuda_implementation.MultiDirectionalTwoDLSTMOp import MultiDirectionalTwoDLSTMOpInstance
from cuda_implementation.BiDirectionalTwoDLSTMOp import BidirectionalTwoDLSTMOpInstance
from cuda_implementation.CuDNNConvHWBCOp import CuDNNConvHWBCOpValidInstance
from cuda_implementation.PoolHWBCOp import PoolHWBCOp
from cuda_implementation.FractionalMaxPoolingOp import fmp
import theano
import theano.tensor as T
from theano.tensor.nnet import conv
try:
from theano.tensor.signal import pool
except ImportError: # old Theano or so...
pool = None
import numpy
from math import sqrt
from ActivationFunctions import strtoact
import theano.printing
from theano.ifelse import ifelse
class TwoDBaseLayer(Layer):
def __init__(self, n_out, **kwargs):
kwargs['n_out'] = n_out
super(TwoDBaseLayer, self).__init__(**kwargs)
#like in _NoOpLayer
self.params = {} # Reset all params.
self.set_attr('from', ",".join([s.name for s in self.sources]))
def create_xavier_weights(self, shape, name):
p = shape[0] + numpy.prod(shape[1:]) * 4
W = numpy.asarray(self.rng.uniform(low=-sqrt(6) / sqrt(p), high = sqrt(6) / sqrt(p), size=shape),
dtype=theano.config.floatX)
return theano.shared(value=W, borrow=True, name=name + "_" + self.name)
class OneDToTwoDLayer(TwoDBaseLayer):
layer_class = "1Dto2D"
recurrent = False
def __init__(self, **kwargs):
super(OneDToTwoDLayer, self).__init__(1, **kwargs)
assert len(self.sources) == 2
n_in = self.sources[0].attrs['n_out']
n_out = n_in
sizes = T.cast(self.sources[1].output, "float32")
assert sizes.ndim == 2
sizes = sizes.reshape((2, sizes.size // 2)).dimshuffle(1, 0)
self.output_sizes = sizes
X = self.sources[0].output
assert X.ndim == 3
assert X.dtype == "float32"
Y = OneDToTwoDOp()(X, sizes)
if self.attrs['batch_norm']:
Y = self.batch_norm(Y, n_out, index=sizes, force_sample=True)
self.output = Y
self.set_attr('n_out', n_out)
class OneDToTwoDFixedSizeLayer(TwoDBaseLayer):
layer_class = "1Dto2D_fixed_size"
recurrent = True
def __init__(self, pad_x=0, pad_y=0, d_row=-1, **kwargs):
super(OneDToTwoDFixedSizeLayer, self).__init__(1, **kwargs)
assert len(self.sources) == 1
X = self.sources[0].output
assert X.ndim == 3
assert X.dtype == "float32"
if d_row > 0:
X = X.reshape((X.shape[0],X.shape[1],d_row,X.shape[2] / d_row))
Y = T.unbroadcast(X.dimshuffle(2, 0, 1, 3), 3)
n_out = self.sources[0].attrs['n_out'] / d_row
else:
Y = X.dimshuffle(2, 0, 1, 'x')
n_out = 1
if pad_x + pad_y > 0:
tmp = T.zeros((Y.shape[1] + 2 * pad_x, Y.shape[2]), 'int8')
self.index = T.set_subtensor(tmp[pad_x: pad_x + Y.shape[1]], self.sources[0].index)
tmp = T.zeros((Y.shape[0] + 2 * pad_y, Y.shape[1] + 2 * pad_x, Y.shape[2], Y.shape[3]), 'float32')
Y = T.set_subtensor(tmp[pad_y:pad_y + Y.shape[0],pad_x:pad_x + Y.shape[1]], Y)
Y = T.unbroadcast(Y, 3)
height = Y.shape[0] # if n_out <= 0 else n_out
width = T.maximum(T.sum(self.index, axis=0), T.ones_like(self.index[0]))
batch = Y.shape[2]
sizes = T.zeros((batch, 2), dtype="float32")
sizes = T.set_subtensor(sizes[:, 0], height)
sizes = T.set_subtensor(sizes[:, 1], width)
self.output = Y
self.output_sizes = sizes
self.set_attr('n_out', n_out)
class TwoDToOneDLayer(TwoDBaseLayer):
layer_class = "2Dto1D"
recurrent = False
def __init__(self, collapse='mean', maxout=False, transpose=False, **kwargs):
super(TwoDToOneDLayer, self).__init__(1, **kwargs)
self.set_attr('collapse', collapse)
self.set_attr('transpose', transpose)
Y = self.sources[0].output
if transpose:
Y = Y.dimshuffle(1, 0, 2, 3)
#index handling
def index_fn(index, size):
return T.set_subtensor(index[:size], numpy.cast['int8'](1))
index_init = T.zeros((Y.shape[2],Y.shape[1]), dtype='int8')
self.index, _ = theano.scan(index_fn, [index_init, T.cast(self.sources[0].output_sizes[:,1],"int32")])
self.index = self.index.dimshuffle(1, 0)
n_out = self.sources[0].attrs['n_out']
if maxout:
Y = Y.max(axis=3).dimshuffle(0,1,2,'x')
if collapse == 'sum' or collapse == True:
Y = Y.sum(axis=0)
elif collapse == 'mean':
Y = Y.mean(axis=0)
elif collapse == 'conv':
from TheanoUtil import circular_convolution
Y, _ = theano.scan(lambda x_i,x_p:circular_convolution(x_i,x_p),Y,Y[0])
Y = Y[-1]
elif collapse == 'flatten':
self.index = T.ones((Y.shape[0] * Y.shape[1], Y.shape[2]), dtype='int8')
Y = Y.reshape((Y.shape[0]*Y.shape[1],Y.shape[2],Y.shape[3]))
elif str(collapse).startswith('pad_'):
pad = numpy.int32(collapse.split('_')[-1])
Y = ifelse(T.lt(Y.shape[0],pad),T.concatenate([Y,T.zeros((pad-Y.shape[0],Y.shape[1],Y.shape[2],Y.shape[3]),'float32')],axis=0),
ifelse(T.gt(Y.shape[0],pad),Y[:pad],Y))
Y = Y.dimshuffle(1,2,3,0).reshape((Y.shape[1],Y.shape[2],Y.shape[3]*Y.shape[0]))
n_out *= pad
elif collapse != False:
assert False, "invalid collapse mode"
if self.attrs['batch_norm']:
Y = self.batch_norm(Y, n_out, force_sample=False)
self.output = Y
self.act = [Y, Y]
self.set_attr('n_out', n_out)
forget_gate_initial_bias = 1.0
lambda_gate_initial_bias = 0.0
class DeepLSTM(TwoDBaseLayer):
layer_class = "deep_lstm"
recurrent = True
def __init__(self, n_out, depth, **kwargs):
super(DeepLSTM, self).__init__(n_out, **kwargs)
X = T.concatenate([s.output for s in self.sources],axis=2).dimshuffle('x',0,1,2).repeat(depth,axis=0)
n_in = sum([s.attrs['n_out'] for s in self.sources])
assert X.dtype == "float32"
width = T.maximum(T.sum(self.index, axis=0), T.ones_like(self.index[0]))
batch = X.shape[2]
sizes = T.zeros((batch, 2), dtype="float32")
sizes = T.set_subtensor(sizes[:, 0], numpy.float32(depth))
sizes = T.set_subtensor(sizes[:, 1], T.cast(width,'float32'))
X = T.unbroadcast(X, 0)
self.output_sizes = sizes
# dropout
assert len(self.masks) == 1
mask = self.masks[0]
if mask is not None:
X = self.mass * mask * X
b1 = self.create_and_add_bias(n_out, "1")
b2 = self.create_and_add_bias(n_out, "2")
W1, V_h1, V_v1 = self.create_and_add_2d_lstm_weights(n_in, n_out, "1")
W2, V_h2, V_v2 = self.create_and_add_2d_lstm_weights(n_in, n_out, "2")
if str(theano.config.device).startswith('cpu'):
Y = T.dot(X,W1)[:n_out*2]
else:
Y1, Y2 = BidirectionalTwoDLSTMOpInstance(X, W1, W2, V_h1, V_h2, V_v1, V_v2, b1, b2, sizes)[:2]
Y = T.concatenate([Y1,Y2],axis=3)
Y.name = 'Y'
self.set_attr('n_out', n_out*2)
self.output = Y[-1]
def create_and_add_2d_lstm_weights(self, n, m, name_suffix):
W, U, V = self.create_xavier_weights((n, 5 * m), "W" + name_suffix), \
self.create_xavier_weights((m, 5 * m), "U" + name_suffix), \
self.create_xavier_weights((m, 5 * m), "V" + name_suffix)
W = self.add_param(W)
U = self.add_param(U)
V = self.add_param(V)
return W, U, V
def create_and_add_bias(self, n_cells, name_suffix):
b_val = numpy.zeros((5 * n_cells,), dtype=theano.config.floatX)
b_val[1 * n_cells:2 * n_cells] = forget_gate_initial_bias
b_val[2 * n_cells:3 * n_cells] = lambda_gate_initial_bias
b = theano.shared(b_val, borrow=True, name="b" + name_suffix + "_" + self.name)
b = self.add_param(b)
return b
class TwoDLSTMLayer(TwoDBaseLayer):
layer_class = "mdlstm"
recurrent = True
def __init__(self, n_out, collapse_output=False, directions=4, projection='average', base=None, **kwargs):
if base is None:
base = []
super(TwoDLSTMLayer, self).__init__(n_out, **kwargs)
assert len(self.sources) == 1
source = self.sources[0]
n_in = source.attrs['n_out']
X = source.output
assert X.ndim == 4
sizes = source.output_sizes
if source.layer_class == "1Dto2D":
#sizes has the wrong layout if coming directly from a 1Dto2D layer
sizes = sizes.reshape((2, sizes.size // 2)).dimshuffle(1, 0)
self.output_sizes = sizes
assert directions in [1,2,4], "only 1, 2 or 4 directions are supported"
assert projection in ['average', 'concat'], "invalid projection"
if base:
#self.b1 = self.add_param(base[0].b1)
#self.b2 = self.add_param(base[0].b2)
#if directions >= 1:
# self.b3 = self.add_param(base[0].b3)
# self.b4 = self.add_param(base[0].b4)
#self.W1, self.V_h1, self.V_v1 = self.add_param(base[0].W1), self.add_param(base[0].V_h1), self.add_param(base[0].V_v1)
#self.W2, self.V_h2, self.V_v2 = self.add_param(base[0].W2), self.add_param(base[0].V_h2), self.add_param(base[0].V_v2)
#if directions >= 1:
# self.W3, self.V_h3, self.V_v3 = self.add_param(base[0].W3), self.add_param(base[0].V_h3), self.add_param(base[0].V_v3)
# self.W4, self.V_h4, self.V_v4 = self.add_param(base[0].W4), self.add_param(base[0].V_h4), self.add_param(base[0].V_v4)
#self.mass = base[0].mass
#self.masks = base[0].masks
self.b1 = base[0].b1
self.b2 = base[0].b2
if directions >= 1:
self.b3 = base[0].b3
self.b4 = base[0].b4
self.W1, self.V_h1, self.V_v1 = base[0].W1, base[0].V_h1, base[0].V_v1
self.W2, self.V_h2, self.V_v2 = base[0].W2, base[0].V_h2, base[0].V_v2
if directions >= 1:
self.W3, self.V_h3, self.V_v3 = base[0].W3, base[0].V_h3, base[0].V_v3
self.W4, self.V_h4, self.V_v4 = base[0].W4, base[0].V_h4, base[0].V_v4
self.mass = base[0].mass
self.masks = base[0].masks
else:
self.b1 = self.create_and_add_bias(n_out, "1")
self.b2 = self.create_and_add_bias(n_out, "2")
if directions >= 1:
self.b3 = self.create_and_add_bias(n_out, "3")
self.b4 = self.create_and_add_bias(n_out, "4")
self.W1, self.V_h1, self.V_v1 = self.create_and_add_2d_lstm_weights(n_in, n_out, "1")
self.W2, self.V_h2, self.V_v2 = self.create_and_add_2d_lstm_weights(n_in, n_out, "2")
if directions >= 1:
self.W3, self.V_h3, self.V_v3 = self.create_and_add_2d_lstm_weights(n_in, n_out, "3")
self.W4, self.V_h4, self.V_v4 = self.create_and_add_2d_lstm_weights(n_in, n_out, "4")
# dropout
assert len(self.masks) == 1
mask = self.masks[0]
if mask is not None:
X = self.mass * mask * X
if str(theano.config.device).startswith('cpu'):
Y = T.zeros_like(X)
if projection == 'concat':
Y = Y.repeat(directions,axis=-1)
n_out *= directions
else:
if directions <= 2:
Y = BidirectionalTwoDLSTMOpInstance(X, self.W1, self.W2, self.V_h1, self.V_h2, self.V_v1, self.V_v2, self.b1, self.b2, sizes)
else:
Y = MultiDirectionalTwoDLSTMOpInstance(X, self.W1, self.W2, self.W3, self.W4, self.V_h1, self.V_h2, self.V_h3, self.V_h4,
self.V_v1, self.V_v2, self.V_v3, self.V_v4, self.b1, self.b2, self.b3, self.b4, sizes)
if directions > 1:
Y = T.stack(Y[:directions],axis=-1)
if projection == 'average':
Y = Y.mean(axis=-1)
elif projection == 'concat':
Y = Y.reshape((Y.shape[0],Y.shape[1],Y.shape[2],Y.shape[3]*Y.shape[4]))
n_out *= directions
else:
Y = Y[0]
Y.name = 'Y'
self.set_attr('n_out', n_out)
self.set_attr('collapse_output', collapse_output)
self.set_attr('directions', directions)
self.set_attr('projection', projection)
#index handling
def index_fn(index, size):
return T.set_subtensor(index[:size], numpy.cast['int8'](1))
index_init = T.zeros((Y.shape[2],Y.shape[1]), dtype='int8')
self.index, _ = theano.scan(index_fn, [index_init, T.cast(sizes[:,1],"int32")])
self.index = self.index.dimshuffle(1, 0)
if collapse_output == 'sum' or collapse_output == True:
Y = Y.sum(axis=0)
elif collapse_output == 'mean':
Y = Y.mean(axis=0)
elif collapse_output == 'conv':
from TheanoUtil import circular_convolution
Y, _ = theano.scan(lambda x_i,x_p:circular_convolution(x_i,x_p),Y,Y[0])
Y = Y[-1]
elif collapse_output == 'flatten':
self.index = T.ones((Y.shape[0] * Y.shape[1], Y.shape[2]), dtype='int8')
Y = Y.reshape((Y.shape[0]*Y.shape[1],Y.shape[2],Y.shape[3]))
elif str(collapse_output).startswith('pad_'):
pad = numpy.int32(collapse_output.split('_')[-1])
Y = ifelse(T.lt(Y.shape[0],pad),T.concatenate([Y,T.zeros((pad-Y.shape[0],Y.shape[1],Y.shape[2],Y.shape[3]),'float32')],axis=0),
ifelse(T.gt(Y.shape[0],pad),Y[:pad],Y))
Y = Y.dimshuffle(1,2,3,0).reshape((Y.shape[1],Y.shape[2],Y.shape[3]*Y.shape[0]))
self.attrs['n_out'] *= pad
elif collapse_output != False:
assert False, "invalid collapse mode"
if self.attrs['batch_norm']:
Y = self.batch_norm(Y,self.attrs['n_out'],index=sizes if not collapse_output else self.index, force_sample=False)
self.output = Y
def create_and_add_2d_lstm_weights(self, n, m, name_suffix):
W, U, V = self.create_xavier_weights((n, 5 * m), "W" + name_suffix), \
self.create_xavier_weights((m, 5 * m), "U" + name_suffix), \
self.create_xavier_weights((m, 5 * m), "V" + name_suffix)
W = self.add_param(W)
U = self.add_param(U)
V = self.add_param(V)
return W, U, V
def create_and_add_bias(self, n_cells, name_suffix):
b_val = numpy.zeros((5 * n_cells,), dtype=theano.config.floatX)
b_val[1 * n_cells:2 * n_cells] = forget_gate_initial_bias
b_val[2 * n_cells:3 * n_cells] = lambda_gate_initial_bias
b = theano.shared(b_val, borrow=True, name="b" + name_suffix + "_" + self.name)
b = self.add_param(b)
return b
def conv_crop_pool_op(X, sizes, output_sizes, W, b, n_in, n_maps, filter_height, filter_width, filter_dilation, poolsize):
from Device import is_using_gpu
if is_using_gpu():
conv_op = CuDNNConvHWBCOpValidInstance
pool_op = PoolHWBCOp(poolsize)
conv_out = conv_op(X, W, b) if filter_height * filter_width > 0 else X
crop_out = CropToBatchImageSizeInstance(conv_out, sizes)
Y = pool_op(crop_out)
Y = CropToBatchImageSizeZeroInstance(Y, output_sizes)
else:
Y = X
return Y
class ConvBaseLayer(TwoDBaseLayer):
layer_class = "conv_base"
recurrent = False
def __init__(self, n_features, filter, base = None, activation="tanh", **kwargs):
if base is None:
base = []
kwargs['n_out'] = n_features
super(ConvBaseLayer, self).__init__(**kwargs)
assert len(self.sources) == 1
self.source = self.sources[0]
self.n_in = self.source.attrs['n_out']
self.X = self.source.output
assert self.X.ndim == 4
self.n_features = n_features
self.set_attr('n_features', n_features)
self.set_attr('filter', filter)
self.set_attr('activation', activation)
self.set_attr('n_out', n_features if numpy.prod(filter) > 0 else self.n_in)
#TODO: maybe this ordering is not consistent with Dewis implementation
self.filter_height = filter[0]
self.filter_width = filter[1]
self.activation = strtoact(activation)
if base:
#self.W = self.add_param(base[0].W)
#self.b = self.add_param(base[0].b)
self.W = base[0].W
self.b = base[0].b
else:
self.W = self.create_conv_weights(n_features, self.n_in, self.filter_height, self.filter_width)
self.b = self.create_and_add_bias(n_features)
def create_conv_weights(self, n_features, n_in, filter_height, filter_width, name_suffix = ""):
filter_shape = (n_features, n_in, filter_height, filter_width)
W = self.create_xavier_weights(filter_shape, "W" + name_suffix)
W = self.add_param(W)
return W
def create_and_add_bias(self, n_out, name_suffix=""):
b_val = numpy.zeros((n_out,), dtype=theano.config.floatX)
b = theano.shared(b_val, borrow=True, name="b" + name_suffix + "_" + self.name)
b = self.add_param(b)
return b
def conv_output_size_from_input_size(self, sizes):
heights = sizes[:, 0]
widths = sizes[:, 1]
heights = heights - self.filter_height + 1
widths = widths - self.filter_width + 1
return T.concatenate((heights[:, None], widths[:, None]), axis=1)
printed_pad_warning = False
def maybe_print_pad_warning(_, x):
global printed_pad_warning
if x != 0 and not printed_pad_warning:
print >> log.v2, "Warning, input for conv layer too small, applying padding on the fly, this can cause increased memory usage, longer runtimes and worse results. Consider padding your input data manually. This warning is only printed once, even if the problem occurs multiple times."
printed_pad_warning = True
class ConvPoolLayer2(ConvBaseLayer):
layer_class = "conv2"
recurrent = True
def __init__(self, pool_size, filter_dilation = None, padding=False, **kwargs):
super(ConvPoolLayer2, self).__init__(**kwargs)
self.pool_size = pool_size
self.set_attr('padding', padding)
sizes_raw = self.source.output_sizes
if not filter_dilation:
filter_dilation = [1,1]
#handle size problems
self.output_sizes = self.output_size_from_input_size(sizes_raw)
if not padding:
padding = T.min(self.output_sizes) <= 0
padding = theano.printing.Print(global_fn=maybe_print_pad_warning)(padding)
else:
padding = int(padding)
fixed_sizes = T.maximum(sizes_raw, numpy.array([self.pool_size[0] + self.filter_height - 1, self.pool_size[1] + self.filter_width - 1], dtype="float32"))
sizes = ifelse(padding, fixed_sizes, sizes_raw)
X_size = T.cast(T.max(sizes, axis=0), "int32")
def pad_fn(x_t, s):
x = T.alloc(numpy.cast["float32"](0), X_size[0], X_size[1], self.X.shape[3])
x = T.set_subtensor(x[:s[0], :s[1]], x_t[:s[0], :s[1]])
return x
fixed_X, _ = theano.scan(pad_fn, [self.X.dimshuffle(2,0,1,3), T.cast(sizes_raw, "int32")])
fixed_X = fixed_X.dimshuffle(1,2,0,3)
self.X = ifelse(padding, T.unbroadcast(fixed_X,3), self.X)
#end handle size problems
self.output_sizes = self.output_size_from_input_size(sizes)
Z = conv_crop_pool_op(self.X, sizes, self.output_sizes, self.W, self.b, self.n_in, self.n_features, self.filter_height,
self.filter_width, filter_dilation, pool_size)
Y = self.activation(Z)
if self.attrs['batch_norm']:
Y = self.batch_norm(Y,self.attrs['n_out'], index=sizes, force_sample=False)
self.output = Y
#index handling
def index_fn(index, size):
return T.set_subtensor(index[:size], numpy.cast['int8'](1))
index_init = T.zeros((Y.shape[2],Y.shape[1]), dtype='int8')
self.index, _ = theano.scan(index_fn, [index_init, T.cast(self.output_sizes[:,1],"int32")])
self.index = self.index.dimshuffle(1, 0)
def output_size_from_input_size(self, sizes):
heights = sizes[:, 0]
widths = sizes[:, 1]
heights = heights - self.filter_height + 1
widths = widths - self.filter_width + 1
p1, p2 = self.pool_size
heights //= p1
widths //= p2
return T.concatenate((heights[:, None], widths[:, None]), axis=1)
class ConvFMPLayer(ConvBaseLayer):
layer_class = "conv_fmp"
recurrent = False
def __init__(self, factor=numpy.sqrt(2), decay=1.0, min_factor=None, padding=False, **kwargs):
super(ConvFMPLayer, self).__init__(**kwargs)
if min_factor is None:
min_factor = factor
factor = T.maximum(factor * (decay ** self.network.epoch), numpy.float32(min_factor))
sizes_raw = self.source.output_sizes
# handle size problems
if not padding:
padding = T.min(self.source.output_sizes / factor) <= 0
padding = theano.printing.Print(global_fn=maybe_print_pad_warning)(padding)
fixed_sizes = T.maximum(sizes_raw, T.cast(T.as_tensor(
[factor + self.filter_height - 1, factor + self.filter_width - 1]), 'float32'))
sizes = ifelse(padding, fixed_sizes, sizes_raw)
X_size = T.cast(T.max(sizes, axis=0), "int32")
def pad_fn(x_t, s):
x = T.alloc(numpy.cast["float32"](0), X_size[0], X_size[1], self.X.shape[3])
x = T.set_subtensor(x[:s[0], :s[1]], x_t[:s[0], :s[1]])
return x
fixed_X, _ = theano.scan(pad_fn, [self.X.dimshuffle(2, 0, 1, 3), T.cast(sizes_raw, "int32")])
fixed_X = fixed_X.dimshuffle(1, 2, 0, 3)
self.X = ifelse(padding, T.unbroadcast(fixed_X, 3), self.X)
conv_out = CuDNNConvHWBCOpValidInstance(self.X, self.W, self.b)
conv_out_sizes = self.conv_output_size_from_input_size(sizes)
self.output, self.output_sizes = fmp(conv_out, conv_out_sizes, T.cast(factor,'float32'))