from __future__ import print_function
import time
import numpy as np
np.random.seed(1234)
from functools import reduce
import math as m
import scipy.io
import theano
import theano.tensor as T
from scipy.interpolate import griddata
from sklearn.preprocessing import scale
from utils import augment_EEG, cart2sph, pol2cart
import lasagne
# from lasagne.layers.dnn import Conv2DDNNLayer as ConvLayer
from lasagne.layers import Conv2DLayer, MaxPool2DLayer, InputLayer
from lasagne.layers import DenseLayer, ElemwiseMergeLayer, FlattenLayer
from lasagne.layers import ConcatLayer, ReshapeLayer, get_output_shape
from lasagne.layers import Conv1DLayer, DimshuffleLayer, LSTMLayer, SliceLayer
import matplotlib.pyplot as plt
def azim_proj(pos):
"""
Computes the Azimuthal Equidistant Projection of input point in 3D Cartesian Coordinates.
Imagine a plane being placed against (tangent to) a globe. If
a light source inside the globe projects the graticule onto
the plane the result would be a planar, or azimuthal, map
projection.
:param pos: position in 3D Cartesian coordinates
:return: projected coordinates using Azimuthal Equidistant Projection
"""
[r, elev, az] = cart2sph(pos[0], pos[1], pos[2])
return pol2cart(az, m.pi / 2 - elev)
def gen_images(locs, features, n_gridpoints, normalize=True,
augment=False, pca=False, std_mult=0.1, n_components=2, edgeless=False):
"""
Generates EEG images given electrode locations in 2D space and multiple feature values for each electrode
:param locs: An array with shape [n_electrodes, 2] containing X, Y
coordinates for each electrode.
:param features: Feature matrix as [n_samples, n_features]
Features are as columns.
Features corresponding to each frequency band are concatenated.
(alpha1, alpha2, ..., beta1, beta2,...)
:param n_gridpoints: Number of pixels in the output images
:param normalize: Flag for whether to normalize each band over all samples
:param augment: Flag for generating augmented images
:param pca: Flag for PCA based data augmentation
:param std_mult Multiplier for std of added noise
:param n_components: Number of components in PCA to retain for augmentation
:param edgeless: If True generates edgeless images by adding artificial channels
at four corners of the image with value = 0 (default=False).
:return: Tensor of size [samples, colors, W, H] containing generated
images.
"""
feat_array_temp = []
nElectrodes = locs.shape[0] # Number of electrodes
# Test whether the feature vector length is divisible by number of electrodes
assert features.shape[1] % nElectrodes == 0 #feature.shape == 2670*192, nElectrodes == 64
n_colors = features.shape[1] / nElectrodes
for c in range(n_colors):
feat_array_temp.append(features[:, c * nElectrodes : nElectrodes * (c+1)])
if augment:
if pca:
for c in range(n_colors):
feat_array_temp[c] = augment_EEG(feat_array_temp[c], std_mult, pca=True, n_components=n_components)
else:
for c in range(n_colors):
feat_array_temp[c] = augment_EEG(feat_array_temp[c], std_mult, pca=False, n_components=n_components)
nSamples = features.shape[0]
# Interpolate the values
grid_x, grid_y = np.mgrid[
min(locs[:, 0]):max(locs[:, 0]):n_gridpoints*1j,
min(locs[:, 1]):max(locs[:, 1]):n_gridpoints*1j
]
temp_interp = []
for c in range(n_colors):
temp_interp.append(np.zeros([nSamples, n_gridpoints, n_gridpoints]))
# Generate edgeless images
if edgeless:
min_x, min_y = np.min(locs, axis=0)
max_x, max_y = np.max(locs, axis=0)
locs = np.append(locs, np.array([[min_x, min_y], [min_x, max_y],[max_x, min_y],[max_x, max_y]]),axis=0)
for c in range(n_colors):
feat_array_temp[c] = np.append(feat_array_temp[c], np.zeros((nSamples, 4)), axis=1)
# Interpolating
for i in xrange(nSamples):
for c in range(n_colors):
temp_interp[c][i, :, :] = griddata(locs, feat_array_temp[c][i, :], (grid_x, grid_y),
method='cubic', fill_value=np.nan)
print('Interpolating {0}/{1}\r'.format(i+1, nSamples), end='\r')
# Normalizing
for c in range(n_colors):
if normalize:
temp_interp[c][~np.isnan(temp_interp[c])] = \
scale(temp_interp[c][~np.isnan(temp_interp[c])])
temp_interp[c] = np.nan_to_num(temp_interp[c])
return np.swapaxes(np.asarray(temp_interp), 0, 1) # swap axes to have [samples, colors, W, H]
def build_cnn(input_var=None, w_init=None, n_layers=(4, 2, 1), n_filters_first=32, imsize=32, n_colors=3):
"""
Builds a VGG style CNN network followed by a fully-connected layer and a softmax layer.
Stacks are separated by a maxpool layer. Number of kernels in each layer is twice
the number in previous stack.
input_var: Theano variable for input to the network
outputs: pointer to the output of the last layer of network (softmax)
:param input_var: theano variable as input to the network
:param w_init: Initial weight values
:param n_layers: number of layers in each stack. An array of integers with each
value corresponding to the number of layers in each stack.
(e.g. [4, 2, 1] == 3 stacks with 4, 2, and 1 layers in each.
:param n_filters_first: number of filters in the first layer
:param imSize: Size of the image
:param n_colors: Number of color channels (depth)
:return: a pointer to the output of last layer
"""
weights = [] # Keeps the weights for all layers
count = 0
# If no initial weight is given, initialize with GlorotUniform
if w_init is None:
w_init = [lasagne.init.GlorotUniform()] * sum(n_layers)
# Input layer
network = InputLayer(shape=(None, n_colors, imsize, imsize),
input_var=input_var)
for i, s in enumerate(n_layers):
for l in range(s):
network = Conv2DLayer(network, num_filters=n_filters_first * (2 ** i), filter_size=(3, 3),
W=w_init[count], pad='same')
count += 1
weights.append(network.W)
network = MaxPool2DLayer(network, pool_size=(2, 2))
return network, weights
def build_convpool_max(input_vars, nb_classes, imsize=32, n_colors=3, n_timewin=3):
"""
Builds the complete network with maxpooling layer in time.
:param input_vars: list of EEG images (one image per time window)
:param nb_classes: number of classes
:param imsize: size of the input image (assumes a square input)
:param n_colors: number of color channels in the image
:param n_timewin: number of time windows in the snippet
:return: a pointer to the output of last layer
"""
convnets = []
w_init = None
# Build 7 parallel CNNs with shared weights
for i in range(n_timewin):
if i == 0:
convnet, w_init = build_cnn(input_vars[i], imsize=imsize, n_colors=n_colors)
else:
convnet, _ = build_cnn(input_vars[i], w_init=w_init, imsize=imsize, n_colors=n_colors)
convnets.append(convnet)
# convpooling using Max pooling over frames
convpool = ElemwiseMergeLayer(convnets, theano.tensor.maximum)
# A fully-connected layer of 512 units with 50% dropout on its inputs:
convpool = DenseLayer(lasagne.layers.dropout(convpool, p=.5),
num_units=512, nonlinearity=lasagne.nonlinearities.rectify)
# And, finally, the output layer with 50% dropout on its inputs:
convpool = lasagne.layers.DenseLayer(lasagne.layers.dropout(convpool, p=.5),
num_units=nb_classes, nonlinearity=lasagne.nonlinearities.softmax)
return convpool
def build_convpool_conv1d(input_vars, nb_classes, imsize=32, n_colors=3, n_timewin=3):
"""
Builds the complete network with 1D-conv layer to integrate time from sequences of EEG images.
:param input_vars: list of EEG images (one image per time window)
:param nb_classes: number of classes
:param imsize: size of the input image (assumes a square input)
:param n_colors: number of color channels in the image
:param n_timewin: number of time windows in the snippet
:return: a pointer to the output of last layer
"""
convnets = []
w_init = None
# Build 7 parallel CNNs with shared weights
for i in range(n_timewin):
if i == 0:
convnet, w_init = build_cnn(input_vars[i], imsize=imsize, n_colors=n_colors)
else:
convnet, _ = build_cnn(input_vars[i], w_init=w_init, imsize=imsize, n_colors=n_colors)
convnets.append(FlattenLayer(convnet))
# at this point convnets shape is [numTimeWin][n_samples, features]
# we want the shape to be [n_samples, features, numTimeWin]
convpool = ConcatLayer(convnets)
convpool = ReshapeLayer(convpool, ([0], n_timewin, get_output_shape(convnets[0])[1]))
convpool = DimshuffleLayer(convpool, (0, 2, 1))
# input to 1D convlayer should be in (batch_size, num_input_channels, input_length)
convpool = Conv1DLayer(convpool, 64, 3)
# A fully-connected layer of 512 units with 50% dropout on its inputs:
convpool = DenseLayer(lasagne.layers.dropout(convpool, p=.5),
num_units=512, nonlinearity=lasagne.nonlinearities.rectify)
# And, finally, the output layer with 50% dropout on its inputs:
convpool = DenseLayer(lasagne.layers.dropout(convpool, p=.5),
num_units=nb_classes, nonlinearity=lasagne.nonlinearities.softmax)
return convpool
def build_convpool_lstm(input_vars, nb_classes, grad_clip=110, imsize=32, n_colors=3, n_timewin=3):
"""
Builds the complete network with LSTM layer to integrate time from sequences of EEG images.
:param input_vars: list of EEG images (one image per time window)
:param nb_classes: number of classes
:param grad_clip: the gradient messages are clipped to the given value during
the backward pass.
:param imsize: size of the input image (assumes a square input)
:param n_colors: number of color channels in the image
:param n_timewin: number of time windows in the snippet
:return: a pointer to the output of last layer
"""
convnets = []
w_init = None
# Build 7 parallel CNNs with shared weights
for i in range(n_timewin):
if i == 0:
convnet, w_init = build_cnn(input_vars[i], imsize=imsize, n_colors=n_colors)
else:
convnet, _ = build_cnn(input_vars[i], w_init=w_init, imsize=imsize, n_colors=n_colors)
convnets.append(FlattenLayer(convnet))
# at this point convnets shape is [numTimeWin][n_samples, features]
# we want the shape to be [n_samples, features, numTimeWin]
convpool = ConcatLayer(convnets)
convpool = ReshapeLayer(convpool, ([0], n_timewin, get_output_shape(convnets[0])[1]))
# Input to LSTM should have the shape as (batch size, SEQ_LENGTH, num_features)
convpool = LSTMLayer(convpool, num_units=128, grad_clipping=grad_clip,
nonlinearity=lasagne.nonlinearities.tanh)
# We only need the final prediction, we isolate that quantity and feed it
# to the next layer.
convpool = SliceLayer(convpool, -1, 1) # Selecting the last prediction
# A fully-connected layer of 256 units with 50% dropout on its inputs:
convpool = DenseLayer(lasagne.layers.dropout(convpool, p=.5),
num_units=256, nonlinearity=lasagne.nonlinearities.rectify)
# And, finally, the output layer with 50% dropout on its inputs:
convpool = DenseLayer(lasagne.layers.dropout(convpool, p=.5),
num_units=nb_classes, nonlinearity=lasagne.nonlinearities.softmax)
return convpool
def build_convpool_mix(input_vars, nb_classes, grad_clip=110, imsize=32, n_colors=3, n_timewin=3):
"""
Builds the complete network with LSTM and 1D-conv layers combined
:param input_vars: list of EEG images (one image per time window)
:param nb_classes: number of classes
:param grad_clip: the gradient messages are clipped to the given value during
the backward pass.
:param imsize: size of the input image (assumes a square input)
:param n_colors: number of color channels in the image
:param n_timewin: number of time windows in the snippet
:return: a pointer to the output of last layer
"""
convnets = []
w_init = None
# Build 7 parallel CNNs with shared weights
for i in range(n_timewin):
if i == 0:
convnet, w_init = build_cnn(input_vars[i], imsize=imsize, n_colors=n_colors)
else:
convnet, _ = build_cnn(input_vars[i], w_init=w_init, imsize=imsize, n_colors=n_colors)
convnets.append(FlattenLayer(convnet))
# at this point convnets shape is [numTimeWin][n_samples, features]
# we want the shape to be [n_samples, features, numTimeWin]
convpool = ConcatLayer(convnets)
convpool = ReshapeLayer(convpool, ([0], n_timewin, get_output_shape(convnets[0])[1]))
reformConvpool = DimshuffleLayer(convpool, (0, 2, 1))
# input to 1D convlayer should be in (batch_size, num_input_channels, input_length)
conv_out = Conv1DLayer(reformConvpool, 64, 3)
conv_out = FlattenLayer(conv_out)
# Input to LSTM should have the shape as (batch size, SEQ_LENGTH, num_features)
lstm = LSTMLayer(convpool, num_units=128, grad_clipping=grad_clip,
nonlinearity=lasagne.nonlinearities.tanh)
lstm_out = SliceLayer(lstm, -1, 1)
# Merge 1D-Conv and LSTM outputs
dense_input = ConcatLayer([conv_out, lstm_out])
# A fully-connected layer of 256 units with 50% dropout on its inputs:
convpool = DenseLayer(lasagne.layers.dropout(dense_input, p=.5),
num_units=512, nonlinearity=lasagne.nonlinearities.rectify)
# And, finally, the 10-unit output layer with 50% dropout on its inputs:
convpool = DenseLayer(convpool,
num_units=nb_classes, nonlinearity=lasagne.nonlinearities.softmax)
return convpool
def iterate_minibatches(inputs, targets, batchsize, shuffle=False):
"""
Iterates over the samples returing batches of size batchsize.
:param inputs: input data array. It should be a 4D numpy array for images [n_samples, n_colors, W, H] and 5D numpy
array if working with sequence of images [n_timewindows, n_samples, n_colors, W, H].
:param targets: vector of target labels.
:param batchsize: Batch size
:param shuffle: Flag whether to shuffle the samples before iterating or not.
:return: images and labels for a batch
"""
if inputs.ndim == 4:
input_len = inputs.shape[0]
elif inputs.ndim == 5:
input_len = inputs.shape[1]
assert input_len == len(targets)
if shuffle:
indices = np.arange(input_len)
np.random.shuffle(indices)
for start_idx in range(0, input_len, batchsize):
if shuffle:
excerpt = indices[start_idx:start_idx + batchsize]
else:
excerpt = slice(start_idx, start_idx + batchsize)
if inputs.ndim == 4:
yield inputs[excerpt], targets[excerpt]
elif inputs.ndim == 5:
yield inputs[:, excerpt], targets[excerpt]
def train(images, labels, fold, model_type, batch_size=32, num_epochs=5):
"""
A sample training function which loops over the training set and evaluates the network
on the validation set after each epoch. Evaluates the network on the training set
whenever the
:param images: input images
:param labels: target labels
:param fold: tuple of (train, test) index numbers
:param model_type: model type ('cnn', '1dconv', 'maxpool', 'lstm', 'mix')
:param batch_size: batch size for training
:param num_epochs: number of epochs of dataset to go over for training
:return: none
"""
num_classes = len(np.unique(labels))
(X_train, y_train), (X_val, y_val), (X_test, y_test) = reformatInput(images, labels, fold)
X_train = X_train.astype("float32", casting='unsafe')
X_val = X_val.astype("float32", casting='unsafe')
X_test = X_test.astype("float32", casting='unsafe')
# Prepare Theano variables for inputs and targets
input_var = T.TensorType('floatX', ((False,) * 5))()
target_var = T.ivector('targets')
# Create neural network model (depending on first command line parameter)
print("Building model and compiling functions...")
# Building the appropriate model
if model_type == '1dconv':
network = build_convpool_conv1d(input_var, num_classes)
elif model_type == 'maxpool':
network = build_convpool_max(input_var, num_classes)
elif model_type == 'lstm':
network = build_convpool_lstm(input_var, num_classes, 100)
elif model_type == 'mix':
network = build_convpool_mix(input_var, num_classes, 100)
elif model_type == 'cnn':
input_var = T.tensor4('inputs')
network, _ = build_cnn(input_var)
network = DenseLayer(lasagne.layers.dropout(network, p=.5),
num_units=256,
nonlinearity=lasagne.nonlinearities.rectify)
network = DenseLayer(lasagne.layers.dropout(network, p=.5),
num_units=num_classes,
nonlinearity=lasagne.nonlinearities.softmax)
else:
raise ValueError("Model not supported ['1dconv', 'maxpool', 'lstm', 'mix', 'cnn']")
# Create a loss expression for training, i.e., a scalar objective we want
# to minimize (for our multi-class problem, it is the cross-entropy loss):
prediction = lasagne.layers.get_output(network)
loss = lasagne.objectives.categorical_crossentropy(prediction, target_var)
loss = loss.mean()
params = lasagne.layers.get_all_params(network, trainable=True)
updates = lasagne.updates.adam(loss, params, learning_rate=0.001)
# Create a loss expression for validation/testing. The crucial difference
# here is that we do a deterministic forward pass through the network,
# disabling dropout layers.
test_prediction = lasagne.layers.get_output(network, deterministic=True)
test_loss = lasagne.objectives.categorical_crossentropy(test_prediction,
target_var)
test_loss = test_loss.mean()
# As a bonus, also create an expression for the classification accuracy:
test_acc = T.mean(T.eq(T.argmax(test_prediction, axis=1), target_var),
dtype=theano.config.floatX)
# Compile a function performing a training step on a mini-batch (by giving
# the updates dictionary) and returning the corresponding training loss:
train_fn = theano.function([input_var, target_var], loss, updates=updates)
# Compile a second function computing the validation loss and accuracy:
val_fn = theano.function([input_var, target_var], [test_loss, test_acc])
# Finally, launch the training loop.
print("Starting training...")
best_validation_accu = 0
# We iterate over epochs:
for epoch in range(num_epochs):
# In each epoch, we do a full pass over the training data:
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(X_train, y_train, batch_size, shuffle=False):
inputs, targets = batch
train_err += train_fn(inputs, targets)
train_batches += 1
# And a full pass over the validation data:
val_err = 0
val_acc = 0
val_batches = 0
for batch in iterate_minibatches(X_val, y_val, batch_size, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
val_err += err
val_acc += acc
val_batches += 1
av_train_err = train_err / train_batches
av_val_err = val_err / val_batches
av_val_acc = val_acc / val_batches
# Then we print the results for this epoch:
print("Epoch {} of {} took {:.3f}s".format(
epoch + 1, num_epochs, time.time() - start_time))
print(" training loss:\t\t{:.6f}".format(av_train_err))
print(" validation loss:\t\t{:.6f}".format(av_val_err))
print(" validation accuracy:\t\t{:.2f} %".format(av_val_acc * 100))
if av_val_acc > best_validation_accu:
best_validation_accu = av_val_acc
# After training, we compute and print the test error:
test_err = 0
test_acc = 0
test_batches = 0
for batch in iterate_minibatches(X_test, y_test, batch_size, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
test_err += err
test_acc += acc
test_batches += 1
av_test_err = test_err / test_batches
av_test_acc = test_acc / test_batches
print("Final results:")
print(" test loss:\t\t\t{:.6f}".format(av_test_err))
print(" test accuracy:\t\t{:.2f} %".format(av_test_acc * 100))
# Dump the network weights to a file like this:
np.savez('weights_lasg_{0}'.format(model_type), *lasagne.layers.get_all_param_values(network))
print('-'*50)
print("Best validation accuracy:\t\t{:.2f} %".format(best_validation_accu * 100))
print("Best test accuracy:\t\t{:.2f} %".format(av_test_acc * 100))
if __name__ == '__main__':
from utils import reformatInput
# Load electrode locations
print('Loading data...')
locs = scipy.io.loadmat('../Sample data/Neuroscan_locs_orig.mat')
locs_3d = locs['A']
locs_2d = []
# Convert to 2D
for e in locs_3d:
locs_2d.append(azim_proj(e))
feats = scipy.io.loadmat('../Sample data/FeatureMat_timeWin.mat')['features']
subj_nums = np.squeeze(scipy.io.loadmat('../Sample data/trials_subNums.mat')['subjectNum'])
# Leave-Subject-Out cross validation
fold_pairs = []
for i in np.unique(subj_nums):
ts = subj_nums == i
tr = np.squeeze(np.nonzero(np.bitwise_not(ts)))
ts = np.squeeze(np.nonzero(ts))
np.random.shuffle(tr) # Shuffle indices
np.random.shuffle(ts)
fold_pairs.append((tr, ts))
# CNN Mode
print('Generating images...')
# Find the average response over time windows
av_feats = reduce(lambda x, y: x+y, [feats[:, i*192:(i+1)*192] for i in range(feats.shape[1] / 192)])
av_feats = av_feats / (feats.shape[1] / 192)
images = gen_images(np.array(locs_2d),
av_feats,
32, normalize=False)
print('\n')
print(images[0, :, :, :].shape)
pic = np.squeeze(images[0, :, :, :]).transpose(1, 2, 0)
plt.imshow(images[i, :, :, :].transpose(1, 2, 0))
plt.show()
print('\n')
# Class labels should start from 0
print('Training the CNN Model...')
train(images, np.squeeze(feats[:, -1]) - 1, fold_pairs[2], 'cnn')
# Conv-LSTM Mode
print('Generating images for all time windows...')
images_timewin = np.array([gen_images(np.array(locs_2d),
feats[:, i * 192:(i + 1) * 192], 32, normalize=False) for i in
range(feats.shape[1] / 192)
])
print('\n')
print('Training the LSTM-CONV Model...')
train(images_timewin, np.squeeze(feats[:, -1]) - 1, fold_pairs[2], 'mix')
print('Done!')
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