def create_h5_dataset(self, dataset, path):
"""
Create h5 file for the given dataset
"""
pprint('\nCreating %s'%dataset + ' h5 data set using fast, lossless ' +
'compression (lzf)...' , end='')
# read train and test data from original dataset
nparray_2D_train, label_train, label_names = \
self._read_set_from(dataset, 'train', path)
nparray_2D_test, label_test = \
self._read_set_from(dataset, 'test', path)[0:2]
# store in h5 file using lzf compression
h5file = h5py.File(self._h5path, 'w-')
h5file.create_dataset('/train/data', data=nparray_2D_train,
compression='lzf')
h5file.create_dataset('/train/label', data=label_train,
compression='lzf')
if (nparray_2D_test is not None):
h5file.create_dataset('/test/data', data=nparray_2D_test,
compression="lzf")
h5file.create_dataset('/test/label', data=label_test,
compression="lzf")
h5file.create_dataset('label_names', data=label_names,
compression="lzf")
h5file.close()
pprint(' Done.')
def initialize_multilayer(self, nmultilayer, config, dataset):
"""
Initialize given MultiLayer according to config.
The Layers get initialized with the data depending on their
InputSource
"""
# Set if theano and/or theano.scan should be used for learning
# iterations
try:
self._theano = config['config']['Theano']
except:
self._theano = False
try:
self._theanoscan = config['config']['Theano']*config['config']['Scan']
except:
self._theanoscan = False
try:
mini_batch_size = config['config']['mini_batch_size']
except:
mini_batch_size = 1
if self._theano and not self._theanoscan and (mini_batch_size > 1):
pprint("WARNING: theano (without scan) doesn't support " +
"mini-batches yet. mini_batch_size set to 1.")
mini_batch_size = 1
self.MultiLayer[nmultilayer]._mini_batch_size = mini_batch_size
try:
scan_batch_size = config['config']['scan_batch_size']
except:
scan_batch_size = None
self.MultiLayer[nmultilayer]._scan_batch_size = scan_batch_size
# Set the Data for the InputLayer of the MultiLayer depending on
# InputSource (DataSet or another MultiLayer)
InputSource = config['model']['MultiLayer'+str(nmultilayer+1)]\
['InputLayer']['InputSource']
self.MultiLayer[nmultilayer].Layer[0].set_inputsource(InputSource)
if (InputSource == 'DataSet'):
# If the InputSource is "DataSet" get the Training Data +
# Label from the given DataSet
Y = dataset.get_train_data()
Label = dataset.get_train_label()
elif (InputSource[0][0:10] == 'MultiLayer'):
# If the InputSource is a "MultiLayer[#]" get as Training
# Data the Output of that MultiLayer.
if not self._theanoscan:
Y = np.empty(shape=(dataset.get_train_data().shape[0],
config['model'][InputSource[0]][InputSource[1]]['C']),
dtype='float32')
for i in xrange(dataset.get_train_data().shape[0]):
Y[i,:] = self.output(dataset.get_train_data()[i],
int(InputSource[0][10])-1)
else:
# TODO: Implement Scan-Splitting for big data sets
inputdata = []
weights = {}
activations = {}
ml = self.MultiLayer[int(InputSource[0][10])-1]
if ml._scan_batch_size is None:
nbatches = 1
scan_batch_size = dataset.get_train_data().shape[0]
else:
nbatches = int(np.ceil(
dataset.get_train_data().shape[0]
/float(ml._scan_batch_size)))
scan_batch_size = ml._scan_batch_size
for layer in ml.Layer:
if layer.__class__.__name__ == 'InputLayer':
data = dataset.get_train_data()
label = dataset.get_train_label()
layer.set_input(data, label, shuffle=False)
layer.normalize_inputs()
data = layer.get_input_data().astype('float32')
# TODO: use layer.output() !
N = data.shape[0]
D = data.shape[1]
data = data.reshape((1, N, D))
inputdata.append(data)
elif layer.__class__.__name__ == 'ProcessingLayer':
weights[layer._layermodel.W_t.name] = \
layer.get_weights().astype('float32')
activations[layer._layermodel.s_t.name] = np.zeros(
(N, weights[layer._layermodel.W_t.name].shape[0]),
dtype='float32')
# TODO: reconstruct this from layers as in Train
# (done for outputs_info and non_sequences):
Y = np.empty(shape=(dataset.get_train_data().shape[0],
config['model'][InputSource[0]][InputSource[1]]['C']),
dtype='float32')
for nbatch in xrange(nbatches):
sequences = [inputdata[0][:,nbatch*scan_batch_size:\
(nbatch+1)*scan_batch_size,:]]
outputs_info = [activations[item.name]\
[nbatch*scan_batch_size:(nbatch+1)*scan_batch_size,:]
for layer in ml.Layer
for item in layer.outputs_info(mode='test')]
non_sequences = [weights[item.name]
for layer in ml.Layer
for item in layer.non_sequences(mode='test')]
args = sequences + outputs_info + non_sequences
Y[nbatch*scan_batch_size:(nbatch+1)*scan_batch_size] = \
ml._activation_scan(*args)[0]
Label = dataset.get_train_label()
self.MultiLayer[nmultilayer].set_iterations(
config['model']['MultiLayer'+str(nmultilayer+1)]['Iterations'])
plcount = 0
# if the number of datapoints changes on different layers/
# multilayers the next line must be changed
ndatapoints = Y.shape[0]
self.MultiLayer[nmultilayer].set_iteration(0)
for nlayer in xrange(self.MultiLayer[nmultilayer].number_of_layers()):
#--- Initialize Input Layer ---
if (self.MultiLayer[nmultilayer].Layer[nlayer].__class__.__name__
== 'InputLayer'):
InputSource = config['model']['MultiLayer'+str(nmultilayer+1)]\
['InputLayer']['InputSource']
A = config['model']['MultiLayer'+str(nmultilayer+1)]\
['InputLayer']['A']
if (A == 'Default'):
if (InputSource[0][0:10] == 'MultiLayer'):
A = config['model'][InputSource[0]][InputSource[1]]\
['C'] + 1
# if you change this formular remember to also
# change it in Output->WriteSetting (!)
else:
A = None
try:
theanoscan = config['config']['Theano']*config['config']['Scan']
except:
theanoscan = False
self.MultiLayer[nmultilayer].initialize_inputlayer(
Y,Label,A,nlayer,theanoscan)
#--- Processing Layer ---
elif (self.MultiLayer[nmultilayer].Layer[nlayer].__class__.__name__
== 'ProcessingLayer'):
plcount += 1
InputSource = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['InputSource']
if (type(InputSource) == str):
InputSource = (InputSource,)
C = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['C']
if (C == 'Default'):
try:
C = len(config['dataset']['classes'])
except:
C = config['dataset']['nclasses']
epsilon = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['epsilon']
try:
if (epsilon == 'Default'):
# if you change this formular remember to also change
# it in Output->WriteSetting (!)
if (config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Model']
== 'MM-LabeledOnly'):
epsilon = min(C/2.* \
1./config['dataset']['training_label_size'],
1.)
else:
epsilon = C/2. * \
1./config['dataset']['training_data_size']
elif (epsilon[0] == 'factor'):
if (config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Model']
== 'MM-LabeledOnly'):
epsilon = min(epsilon[1] * \
C/float(config['dataset']['training_label_size']),
1.)
else:
epsilon = min(epsilon[1] * \
C/float(config['dataset']['training_data_size']),
1.)
except:
pass
Model = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Model']
L = self.MultiLayer[nmultilayer].Layer[0].get_input_label()
if (InputSource[0] == 'InputLayer'):
Y = self.MultiLayer[nmultilayer].Layer[0].get_input_data()
D = Y.shape[1:]
elif (InputSource[0][0:15] == 'ProcessingLayer'):
D = (config['model']['MultiLayer'+str(nmultilayer+1)]\
[InputSource[0]]['C'],)
Y = None
else:
D = None
Y = None
print "ERROR: %s"%'model',
print "| MultiLayer%d"%(nmultilayer+1),
print "| ProcessingLayer%d:"%nlayer,
print "Invalid InputSource"
""" # obsolete
# for recurrent model: number of neurons in following layer
try:
K = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount+1)]['C']]
if (K == 'Default'):
K = len(config['dataset']['classes'])
except:
K = None
"""
# optional arguments:
try:
A = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['A']
if (A == 'Default'):
# if you change this formular remember to also change
# it in Output->WriteSetting (!)
if (InputSource[0][0:15] == 'ProcessingLayer'):
A = D + 1
else:
A = None
except:
A = None
try:
threshold = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['threshold']
except:
threshold = None
h5path = None
h5file = None
try:
InitMethod = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Initialization']
if isinstance(InitMethod, tuple):
InitMethod = InitMethod[0]
if (InitMethod == 'h5'):
h5path = config['model']\
['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]\
['Initialization'][1]
# expected h5 file name format:
# "Run[i]M[j]L[k].h5"
# e.g. "Run3M1L2.h5" for weights of 1st MultiLayer,
# 2nd Layer, the 3rd Run (counting starts with 1).
# For each Run, their must be an individual h5 file
# present.
try:
h5file = config['model']\
['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]\
['Initialization'][2]
except:
h5file = "Run%dM%dL%d.h5"%(
self._run+1,nmultilayer+1,nlayer)
except:
InitMethod = None
try:
Theano = config['config']['Theano']
except:
Theano = False
try:
Scan = config['config']['Scan']
except:
Scan = False
Parameters = {
'C':C,
'A':A,
'epsilon':epsilon,
'threshold':threshold
}
self.MultiLayer[nmultilayer].initialize_processinglayer(
Model,Parameters,InputSource,nlayer,Theano,
Scan,D,Y,L,InitMethod,h5path,h5file
)
if (np.ceil(float(config['dataset']['training_data_size'])/\
MPI.COMM_WORLD.Get_size() > ndatapoints)):
self.MultiLayer[nmultilayer]._blankstep = True
if self._theanoscan:
self.MultiLayer[nmultilayer].compile_theano_functions()
def train(self, nmultilayer, output, config, dataset):
ml = self.MultiLayer[nmultilayer]
ml.next_run()
pprint('%d.%d.2.1 - Visualize Weights' % (
self._run+1, nmultilayer+1), end='')
output.visualize_all_weights(self,nmultilayer,config)
pprint(' (%0.2f MB)' % mem_usage())
# if (len(self.MultiLayer) == 1):
# TODO: for greedy model: output Likelihood of up to the
# current MultiLayer
pprint('%d.%d.2.2 - LogLikelihood' % (
self._run+1, nmultilayer+1), end='')
output.write_loglikelihood(self, nmultilayer)
pprint(' (%0.2f MB)' % mem_usage())
# variables for stopping criterion
# TODO: generalize for all MultiLayers
try:
STOPPING_CRITERION = config.get()\
['model']['MultiLayer1']['StoppingCriterion']
except:
STOPPING_CRITERION = False
if STOPPING_CRITERION:
try:
mvngwidth = int(config.get()\
['model']['MultiLayer1']['MovingWidth'])
except:
pprint('WARNING (model.Model::Train): No width for \
moving average was given. It will be set to %d'%20)
mvngwidth = 20
loglikelihood = np.asarray([], dtype=np.float32)
mvng_avg, mvng_std = 0., 0.
max_mvng_avg = float('-inf')
last_weights = []
else:
loglikelihood = np.asarray([None])
STOP = False
MPI.COMM_WORLD.Barrier()
pprint('%d.%d.2.3 - Training Iterations' % (self._run+1,nmultilayer+1))
for niteration in xrange(ml.get_iterations()):
pprint('Iteration: %*d' % (
int(math.log10(ml.get_iterations()))+1,
ml.get_iteration()+1), end='')
# pprint('2.2.3.1 - Convergence', end='')
output.conv_pre(ml)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
MPI.COMM_WORLD.Barrier()
# pprint('2.2.3.2 - Learning Iteration', end='')
ml.learning_iteration(self._theanoscan)
# pprint(' - Memory usage: %s (Mb)\n' % mem_usage())
MPI.COMM_WORLD.Barrier()
# experimental: variing learning rates
# if ((niteration % 1 == 0) and
# (ml.Layer[1]._epsilon >= 0.0008)):
# ml.Layer[1]._epsilon *= 0.98
# MPI.COMM_WORLD.Barrier()
# to save learned weights every iteration
# output.save_weights(self.MultiLayer[nmultilayer])
# to save posterior distribution of training data every iteration
# if nmultilayer == self.number_of_multilayers()-1:
# output.save_posterior(self, config, dataset)
# Stopping criterion
if (len(self.MultiLayer) == 1):
# TODO: for greedy model: output Likelihood of up to the
# current MultiLayer
if STOPPING_CRITERION:
t0 = time.time()
loglikelihood = np.append(
loglikelihood,
self.loglikelihood()
)
if (niteration >= mvngwidth):
# save only the last #mvngwidth values
loglikelihood = loglikelihood[1:]
pprint(' | Log-Likelihood: %f (%f s)'%(
loglikelihood[-1], time.time()-t0), end='')
if STOPPING_CRITERION:
# save only the last #mvngwidht/2-1 weights
# for centered moving average
last_weights.append([ml.Layer[nlayer].get_weights()
for nlayer in xrange(1,len(ml.Layer))])
if (niteration > mvngwidth/2):
last_weights = last_weights[1:]
# calculate moving average over last #mvngwidth values
if (niteration >= mvngwidth-1):
mvng_avg = np.mean(loglikelihood)
mvng_std = np.std(loglikelihood)
pprint(' | Moving Average (%d): %f +- %f'%
((niteration+1 - mvngwidth/2),mvng_avg,mvng_std),
end='')
if (mvng_avg > max_mvng_avg):
max_mvng_avg = mvng_avg
elif (mvng_avg < max_mvng_avg - mvng_std):
# if the moving average drops below the maximum
# moving average by more than the moving standard
# deviation, stop the learning iteration and revert
# back to the point of the centered moving average
for nlayer in xrange(1,len(ml.Layer)):
ml.Layer[nlayer].set_weights(last_weights[0][nlayer-1])
stopping_iteration = niteration+1 - mvngwidth/2
pprint('\nStopping criterion met at iteration %d.'%
stopping_iteration)
STOP = True
ml.set_iteration(stopping_iteration)
ml.set_iterations(stopping_iteration)
# abort on numerical error (nan in any of the weights)
if any([np.any(np.isnan(ml.Layer[nlayer].get_weights()))
for nlayer in xrange(1,len(ml.Layer))]):
pprint('\nNumerical error: try to decrease learning ' +
'rate and/or mini-batch size.')
STOP = True
try:
ml.set_iteration(
stopping_iteration)
ml.set_iterations(
stopping_iteration)
except:
pass
this_loglikelihood = output.write_loglikelihood(self, nmultilayer, loglikelihood[-1])
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
if (len(self.MultiLayer) == 1):
# pprint('2.2.3.7 - Test Error', end='')
output.write_online_results(self, config, dataset, this_loglikelihood)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
# pprint('2.2.3.4 - Visualize Weights', end='')
output.visualize_all_weights(self,nmultilayer,config)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
# pprint('2.2.3.5 - Convergence 2', end='')
output.conv_post(self.MultiLayer[nmultilayer])
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
# pprint('2.2.3.6 - Visualize Convergence', end='')
output.visualize_convergence(self,nmultilayer)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
if STOP:
break
pprint('') #linebreak
def learning_iteration(self, theanoscan):
t0 = time.time()
if not theanoscan:
logn = int(math.log10(self.Layer[0].imagecount()))
pprint(' -- Image %*d'%(logn+1,0), end='')
for i in xrange(self.Layer[0].imagecount()):
if (((i+1)%1000 == 0) or ((i+1) == self.Layer[0].imagecount())):
pprint('\b'*(logn+1) + '%*d'%(logn+1, i+1), end='')
self.learningstep()
if self._blank_step:
self.blank_step()
self._niteration += 1
pprint('\b \b'*(10+logn+1), end='')
"""
from mpi4py import MPI
import time
if (MPI.COMM_WORLD.Get_rank() == 0):
if (self._nrun == 1):
print '%d Processes' % MPI.COMM_WORLD.Get_size()
print 'C\tL1 total\tL1 comm\tL1 calls\tL2 ',
print 'total\tL2 comm\tL2 calls'
print '%d\t%f\t%f\t%f\t%f\t%f\t%f' % (
self.Layer[1].GetNumberOfNeurons(), self.Layer[1].elapsed,
self.Layer[1].comm_time, self.Layer[1].ncomm,
self.Layer[2].elapsed, self.Layer[2].comm_time,
self.Layer[2].ncomm
)
self.Layer[1].elapsed = time.time() - time.time()
self.Layer[2].elapsed = time.time() - time.time()
self.Layer[1].comm_time = time.time() - time.time()
self.Layer[2].comm_time = time.time() - time.time()
self.Layer[1].ncomm = 0
self.Layer[2].ncomm = 0
"""
else:
inputs = {}
weights = {}
parameters = {}
mbs = self._mini_batch_size
if self._scan_batch_size is None:
nbatches = 1
scan_batch_size = self.Layer[0].get_input_data().shape[0]
# don't set self._scan_batch_size, because for testing
# the data shape will be different
else:
nbatches = int(np.ceil(
self.Layer[0].get_input_data().shape[0]
/float(self._scan_batch_size)))
scan_batch_size = self._scan_batch_size
for nbatch in xrange(nbatches):
for layer in self.Layer:
if layer.__class__.__name__ == 'InputLayer':
layer.shuffle()
try:
data = layer.get_input_data().astype('float32')[
nbatch*scan_batch_size:
(nbatch+1)*scan_batch_size]
label = layer.get_input_label().astype('int32')[
nbatch*scan_batch_size:
(nbatch+1)*scan_batch_size]
except:
data = layer.get_input_data().astype('float32')[
nbatch*scan_batch_size:]
label = layer.get_input_label().astype('int32')[
nbatch*scan_batch_size:]
# if mbs > 1: (...)
data = np.append(
data,
np.zeros(
((mbs - data.shape[0]%mbs)%mbs, data.shape[1]),
dtype='float32'),
axis=0)
data = data.reshape(
(data.shape[0]/mbs, mbs, data.shape[1]))
label = np.append(
label,
(-1)*np.ones((mbs - label.shape[0]%mbs)%mbs,
dtype='int32'),
axis=0)
label = label.reshape((label.shape[0]/mbs, mbs))
inputs[layer.s_t.name] = data
inputs[layer.L_t.name] = label
elif layer.__class__.__name__ == 'ProcessingLayer':
weights[layer._layermodel.W_t.name] = \
layer.get_weights().astype('float32')
# TODO: generalize parameters in Layer
parameters.update(dict(zip(
[item.name
for item in layer._layermodel.parameters_t],
[layer.parameters[item.name.rpartition('_')[0]]
for item in layer._layermodel.parameters_t]
)))
# parameters[layer._layermodel.epsilon_t.name] = \
# np.asarray(layer.get_learningrate(), dtype='float32')
sequences = [inputs[item.name]
for layer in self.Layer
for item in layer.sequences(mode='train')]
outputs_info = [weights[item.name]
for layer in self.Layer
for item in layer.outputs_info(mode='train')]
non_sequences = [parameters[item.name]
for layer in self.Layer
for item in layer.non_sequences(mode='train')]
args = sequences + outputs_info + non_sequences
learnedweights = self._learningiteration_scan(*args)
for n in xrange(len(learnedweights)):
self.Layer[n+1].set_weights(learnedweights[n])
self._niteration += 1
pprint(' (%f s)' % (time.time() - t0), end='')
def learning_iteration(self, theanoscan):
t0 = time.time()
if not theanoscan:
logn = int(math.log10(self.Layer[0].imagecount()))
pprint(' -- Image %*d' % (logn + 1, 0), end='')
for i in xrange(self.Layer[0].imagecount()):
if (((i + 1) % 1000 == 0)
or ((i + 1) == self.Layer[0].imagecount())):
pprint('\b' * (logn + 1) + '%*d' % (logn + 1, i + 1),
end='')
self.learningstep()
if self._blank_step:
self.blank_step()
self._niteration += 1
pprint('\b \b' * (10 + logn + 1), end='')
"""
from mpi4py import MPI
import time
if (MPI.COMM_WORLD.Get_rank() == 0):
if (self._nrun == 1):
print '%d Processes' % MPI.COMM_WORLD.Get_size()
print 'C\tL1 total\tL1 comm\tL1 calls\tL2 ',
print 'total\tL2 comm\tL2 calls'
print '%d\t%f\t%f\t%f\t%f\t%f\t%f' % (
self.Layer[1].GetNumberOfNeurons(), self.Layer[1].elapsed,
self.Layer[1].comm_time, self.Layer[1].ncomm,
self.Layer[2].elapsed, self.Layer[2].comm_time,
self.Layer[2].ncomm
)
self.Layer[1].elapsed = time.time() - time.time()
self.Layer[2].elapsed = time.time() - time.time()
self.Layer[1].comm_time = time.time() - time.time()
self.Layer[2].comm_time = time.time() - time.time()
self.Layer[1].ncomm = 0
self.Layer[2].ncomm = 0
"""
else:
inputs = {}
weights = {}
parameters = {}
mbs = self._mini_batch_size
if self._scan_batch_size is None:
nbatches = 1
scan_batch_size = self.Layer[0].get_input_data().shape[0]
# don't set self._scan_batch_size, because for testing
# the data shape will be different
else:
nbatches = int(
np.ceil(self.Layer[0].get_input_data().shape[0] /
float(self._scan_batch_size)))
scan_batch_size = self._scan_batch_size
for nbatch in xrange(nbatches):
for layer in self.Layer:
if layer.__class__.__name__ == 'InputLayer':
layer.shuffle()
try:
data = layer.get_input_data().astype(
'float32')[nbatch *
scan_batch_size:(nbatch + 1) *
scan_batch_size]
label = layer.get_input_label().astype(
'int32')[nbatch *
scan_batch_size:(nbatch + 1) *
scan_batch_size]
except:
data = layer.get_input_data().astype(
'float32')[nbatch * scan_batch_size:]
label = layer.get_input_label().astype(
'int32')[nbatch * scan_batch_size:]
# if mbs > 1: (...)
data = np.append(data,
np.zeros(
((mbs - data.shape[0] % mbs) %
mbs, data.shape[1]),
dtype='float32'),
axis=0)
data = data.reshape(
(data.shape[0] / mbs, mbs, data.shape[1]))
label = np.append(label, (-1) * np.ones(
(mbs - label.shape[0] % mbs) % mbs, dtype='int32'),
axis=0)
label = label.reshape((label.shape[0] / mbs, mbs))
inputs[layer.s_t.name] = data
inputs[layer.L_t.name] = label
elif layer.__class__.__name__ == 'ProcessingLayer':
weights[layer._layermodel.W_t.name] = \
layer.get_weights().astype('float32')
# TODO: generalize parameters in Layer
parameters.update(
dict(
zip([
item.name
for item in layer._layermodel.parameters_t
], [
layer.parameters[item.name.rpartition('_')
[0]]
for item in layer._layermodel.parameters_t
])))
# parameters[layer._layermodel.epsilon_t.name] = \
# np.asarray(layer.get_learningrate(), dtype='float32')
sequences = [
inputs[item.name] for layer in self.Layer
for item in layer.sequences(mode='train')
]
outputs_info = [
weights[item.name] for layer in self.Layer
for item in layer.outputs_info(mode='train')
]
non_sequences = [
parameters[item.name] for layer in self.Layer
for item in layer.non_sequences(mode='train')
]
args = sequences + outputs_info + non_sequences
learnedweights = self._learningiteration_scan(*args)
for n in xrange(len(learnedweights)):
self.Layer[n + 1].set_weights(learnedweights[n])
self._niteration += 1
pprint(' (%f s)' % (time.time() - t0), end='')
# Copyright (C) 2015, Dennis Forster <*****@*****.**>
#
# LICENSE: THE SOFTWARE IS PROVIDED "AS IS" UNDER THE
# ACADEMIC FREE LICENSE (AFL) v3.0.
#
"""Module docstring.
"""
from utils.sysfunctions import mem_usage
from utils.parallel import pprint
pprint('Start (RAM Usage: %0.2f MB)' % mem_usage())
# system imports
pprint('0.0.0 - System Imports', end='')
import sys
from mpi4py import MPI
pprint(' (%0.2f MB)' % mem_usage())
# custom imports
pprint('0.0.1 - Custom Imports')
from classes.model.Model import Model
from classes.input.DataSet import DataSet
from classes.config.Config import Config
from classes.output.Output import Output
# MPI definitions
pprint('0.1 - MPI Definitions', end='')
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
# Copyright (C) 2015, Dennis Forster <*****@*****.**>
#
# LICENSE: THE SOFTWARE IS PROVIDED "AS IS" UNDER THE
# ACADEMIC FREE LICENSE (AFL) v3.0.
#
"""Module docstring.
"""
from utils.sysfunctions import mem_usage
from utils.parallel import pprint
pprint('Start (RAM Usage: %0.2f MB)' % mem_usage())
# system imports
pprint('0.0.0 - System Imports', end='')
import sys
from mpi4py import MPI
pprint(' (%0.2f MB)' % mem_usage())
# custom imports
pprint('0.0.1 - Custom Imports')
from classes.model.Model import Model
from classes.input.DataSet import DataSet
from classes.config.Config import Config
from classes.output.Output import Output
# MPI definitions
pprint('0.1 - MPI Definitions', end='')
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
def pick_new_subset(self, config, dset, run=None):
"""
1. From the labeled data points the given number of data points
to use for training or testing are selected - these can be
either chosen completely randomly, or evenly distributed
between classes (and only randomly inside of each class);
all remaining labeled data points are declared as unlabeled
2. Then (for training) the remaining data points are chosen from
the unlabeled data points
"""
h5file = h5py.File(self._h5path, 'r')
if (dset == 'train'):
label = np.asarray(h5file['/train/label'].value, dtype=int)
label_size = min(config['dataset']['training_label_size'],
len(self._indexlist['full_train_labeled']))
data_size = min(config['dataset']['training_data_size'],
len(self._indexlist['full_train_labeled']) +\
len(self._indexlist['full_train_unlabeled']))
if (label_size > data_size):
label_size = data_size
pprint("ERROR: more training labels than training data. " +
"These values are now set as follows:")
pprint("training_data_size: %d", data_size)
pprint("training_label_size: %d", label_size)
elif (dset == 'test'):
label = np.asarray(h5file['/test/label'].value, dtype=int)
data_size = min(config['dataset']['test_size'],
len(self._indexlist['full_test']))
label_size = data_size
h5file.close()
# TODO: change data_size value in saved setting accordingly
# TODO: change label_size value in saved setting accordingly
try:
EVENLABELS = config['dataset']['EVENLABELS']
except:
EVENLABELS = False
try:
indexlist = config['dataset']['indexlist']
except:
indexlist = None
try:
labellist = config['dataset']['labellist']
except:
labellist = None
if ((indexlist is not None) and (labellist is not None)):
pprint('WARNING (classes.input.DataSet): when dataset.indexlist ' +
'is given, dataset.labellist will be ignored.')
if (indexlist is None):
if (labellist is None):
# draw labeled data
labeled_index = self.draw_indexlist(label, self._classes,
label_size, EVENLABELS)
else:
try:
filename = labellist
h5file = h5py.File(filename, 'r')
except:
filename = labellist + 'Run' + str(run+1) + 'Data.h5'
h5file = h5py.File(filename,'r')
if (dset == 'train'):
try:
labeled_index = h5file['train/labeled'].value
pprint('WARNING: labels set according to labellist - '+
'label_size will be ignored.')
# TODO: draw labels according to label_size from labellist
except:
pprint('WARNING (classes.input.DataSet): ' +
'training indexlist not found in provided ' +
'labellist, it will be drawn randomly')
labeled_index = self.draw_indexlist(
label, self._classes, label_size, EVENLABELS)
elif (dset == 'test'):
try:
labeled_index = h5file['test'].value
except:
pprint('WARNING (classes.input.DataSet): ' +
'testlist not found in provided labellist, it ' +
'will be drawn randomly')
labeled_index = self.draw_indexlist(
label, self._classes, label_size, EVENLABELS)
unlabeled_index = np.asarray([], dtype=int)
if (label_size < data_size):
# set remaining data points as unlabeled
remaining = [idx
for idx in self._indexlist['full_train_labeled']
if idx not in labeled_index]
label[remaining] = int(-1)
# draw additional unlabeled data
unlabeled_index = self.draw_indexlist(
label, [-1], data_size-label_size, False)
else:
try:
h5file = h5py.File(indexlist, 'r')
except:
h5file = h5py.File(indexlist+'Run'+str(run+1)+'Data.h5', 'r')
if (dset == 'train'):
labeled_index = h5file['train/labeled'].value
unlabeled_index = h5file['train/unlabeled'].value
elif (dset == 'test'):
labeled_index = h5file['test'].value
h5file.close()
if (dset == 'train'):
self._indexlist['train_labeled'] = labeled_index
self._indexlist['train_unlabeled'] = unlabeled_index
elif (dset == 'test'):
self._indexlist['test'] = labeled_index
def initialize_multilayer(self, nmultilayer, config, dataset):
"""
Initialize given MultiLayer according to config.
The Layers get initialized with the data depending on their
InputSource
"""
# Set if theano and/or theano.scan should be used for learning
# iterations
try:
self._theano = config['config']['Theano']
except:
self._theano = False
try:
self._theanoscan = config['config']['Theano'] * config['config'][
'Scan']
except:
self._theanoscan = False
try:
mini_batch_size = config['config']['mini_batch_size']
except:
mini_batch_size = 1
if self._theano and not self._theanoscan and (mini_batch_size > 1):
pprint("WARNING: theano (without scan) doesn't support " +
"mini-batches yet. mini_batch_size set to 1.")
mini_batch_size = 1
self.MultiLayer[nmultilayer]._mini_batch_size = mini_batch_size
try:
scan_batch_size = config['config']['scan_batch_size']
except:
scan_batch_size = None
self.MultiLayer[nmultilayer]._scan_batch_size = scan_batch_size
# Set the Data for the InputLayer of the MultiLayer depending on
# InputSource (DataSet or another MultiLayer)
InputSource = config['model']['MultiLayer'+str(nmultilayer+1)]\
['InputLayer']['InputSource']
self.MultiLayer[nmultilayer].Layer[0].set_inputsource(InputSource)
if (InputSource == 'DataSet'):
# If the InputSource is "DataSet" get the Training Data +
# Label from the given DataSet
Y = dataset.get_train_data()
Label = dataset.get_train_label()
elif (InputSource[0][0:10] == 'MultiLayer'):
# If the InputSource is a "MultiLayer[#]" get as Training
# Data the Output of that MultiLayer.
if not self._theanoscan:
Y = np.empty(shape=(
dataset.get_train_data().shape[0],
config['model'][InputSource[0]][InputSource[1]]['C']),
dtype='float32')
for i in xrange(dataset.get_train_data().shape[0]):
Y[i, :] = self.output(dataset.get_train_data()[i],
int(InputSource[0][10]) - 1)
else:
# TODO: Implement Scan-Splitting for big data sets
inputdata = []
weights = {}
activations = {}
ml = self.MultiLayer[int(InputSource[0][10]) - 1]
if ml._scan_batch_size is None:
nbatches = 1
scan_batch_size = dataset.get_train_data().shape[0]
else:
nbatches = int(
np.ceil(dataset.get_train_data().shape[0] /
float(ml._scan_batch_size)))
scan_batch_size = ml._scan_batch_size
for layer in ml.Layer:
if layer.__class__.__name__ == 'InputLayer':
data = dataset.get_train_data()
label = dataset.get_train_label()
layer.set_input(data, label, shuffle=False)
layer.normalize_inputs()
data = layer.get_input_data().astype('float32')
# TODO: use layer.output() !
N = data.shape[0]
D = data.shape[1]
data = data.reshape((1, N, D))
inputdata.append(data)
elif layer.__class__.__name__ == 'ProcessingLayer':
weights[layer._layermodel.W_t.name] = \
layer.get_weights().astype('float32')
activations[layer._layermodel.s_t.name] = np.zeros(
(N, weights[layer._layermodel.W_t.name].shape[0]),
dtype='float32')
# TODO: reconstruct this from layers as in Train
# (done for outputs_info and non_sequences):
Y = np.empty(shape=(
dataset.get_train_data().shape[0],
config['model'][InputSource[0]][InputSource[1]]['C']),
dtype='float32')
for nbatch in xrange(nbatches):
sequences = [inputdata[0][:,nbatch*scan_batch_size:\
(nbatch+1)*scan_batch_size,:]]
outputs_info = [activations[item.name]\
[nbatch*scan_batch_size:(nbatch+1)*scan_batch_size,:]
for layer in ml.Layer
for item in layer.outputs_info(mode='test')]
non_sequences = [
weights[item.name] for layer in ml.Layer
for item in layer.non_sequences(mode='test')
]
args = sequences + outputs_info + non_sequences
Y[nbatch*scan_batch_size:(nbatch+1)*scan_batch_size] = \
ml._activation_scan(*args)[0]
Label = dataset.get_train_label()
self.MultiLayer[nmultilayer].set_iterations(
config['model']['MultiLayer' + str(nmultilayer + 1)]['Iterations'])
plcount = 0
# if the number of datapoints changes on different layers/
# multilayers the next line must be changed
ndatapoints = Y.shape[0]
self.MultiLayer[nmultilayer].set_iteration(0)
for nlayer in xrange(self.MultiLayer[nmultilayer].number_of_layers()):
#--- Initialize Input Layer ---
if (self.MultiLayer[nmultilayer].Layer[nlayer].__class__.__name__
== 'InputLayer'):
InputSource = config['model']['MultiLayer'+str(nmultilayer+1)]\
['InputLayer']['InputSource']
A = config['model']['MultiLayer'+str(nmultilayer+1)]\
['InputLayer']['A']
if (A == 'Default'):
if (InputSource[0][0:10] == 'MultiLayer'):
A = config['model'][InputSource[0]][InputSource[1]]\
['C'] + 1
# if you change this formular remember to also
# change it in Output->WriteSetting (!)
else:
A = None
try:
theanoscan = config['config']['Theano'] * config['config'][
'Scan']
except:
theanoscan = False
self.MultiLayer[nmultilayer].initialize_inputlayer(
Y, Label, A, nlayer, theanoscan)
#--- Processing Layer ---
elif (self.MultiLayer[nmultilayer].Layer[nlayer].__class__.__name__
== 'ProcessingLayer'):
plcount += 1
InputSource = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['InputSource']
if (type(InputSource) == str):
InputSource = (InputSource, )
C = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['C']
if (C == 'Default'):
try:
C = len(config['dataset']['classes'])
except:
C = config['dataset']['nclasses']
epsilon = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['epsilon']
try:
if (epsilon == 'Default'):
# if you change this formular remember to also change
# it in Output->WriteSetting (!)
if (config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Model']
== 'MM-LabeledOnly'):
epsilon = min(C/2.* \
1./config['dataset']['training_label_size'],
1.)
else:
epsilon = C/2. * \
1./config['dataset']['training_data_size']
elif (epsilon[0] == 'factor'):
if (config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Model']
== 'MM-LabeledOnly'):
epsilon = min(epsilon[1] * \
C/float(config['dataset']['training_label_size']),
1.)
else:
epsilon = min(epsilon[1] * \
C/float(config['dataset']['training_data_size']),
1.)
except:
pass
Model = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Model']
L = self.MultiLayer[nmultilayer].Layer[0].get_input_label()
if (InputSource[0] == 'InputLayer'):
Y = self.MultiLayer[nmultilayer].Layer[0].get_input_data()
D = Y.shape[1:]
elif (InputSource[0][0:15] == 'ProcessingLayer'):
D = (config['model']['MultiLayer'+str(nmultilayer+1)]\
[InputSource[0]]['C'],)
Y = None
else:
D = None
Y = None
print "ERROR: %s" % 'model',
print "| MultiLayer%d" % (nmultilayer + 1),
print "| ProcessingLayer%d:" % nlayer,
print "Invalid InputSource"
""" # obsolete
# for recurrent model: number of neurons in following layer
try:
K = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount+1)]['C']]
if (K == 'Default'):
K = len(config['dataset']['classes'])
except:
K = None
"""
# optional arguments:
try:
A = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['A']
if (A == 'Default'):
# if you change this formular remember to also change
# it in Output->WriteSetting (!)
if (InputSource[0][0:15] == 'ProcessingLayer'):
A = D + 1
else:
A = None
except:
A = None
try:
threshold = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['threshold']
except:
threshold = None
h5path = None
h5file = None
try:
InitMethod = config['model']['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]['Initialization']
if isinstance(InitMethod, tuple):
InitMethod = InitMethod[0]
if (InitMethod == 'h5'):
h5path = config['model']\
['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]\
['Initialization'][1]
# expected h5 file name format:
# "Run[i]M[j]L[k].h5"
# e.g. "Run3M1L2.h5" for weights of 1st MultiLayer,
# 2nd Layer, the 3rd Run (counting starts with 1).
# For each Run, their must be an individual h5 file
# present.
try:
h5file = config['model']\
['MultiLayer'+str(nmultilayer+1)]\
['ProcessingLayer'+str(plcount)]\
['Initialization'][2]
except:
h5file = "Run%dM%dL%d.h5" % (
self._run + 1, nmultilayer + 1, nlayer)
except:
InitMethod = None
try:
Theano = config['config']['Theano']
except:
Theano = False
try:
Scan = config['config']['Scan']
except:
Scan = False
Parameters = {
'C': C,
'A': A,
'epsilon': epsilon,
'threshold': threshold
}
self.MultiLayer[nmultilayer].initialize_processinglayer(
Model, Parameters, InputSource, nlayer, Theano, Scan, D, Y,
L, InitMethod, h5path, h5file)
if (np.ceil(float(config['dataset']['training_data_size'])/\
MPI.COMM_WORLD.Get_size() > ndatapoints)):
self.MultiLayer[nmultilayer]._blankstep = True
if self._theanoscan:
self.MultiLayer[nmultilayer].compile_theano_functions()
def train(self, nmultilayer, output, config, dataset):
ml = self.MultiLayer[nmultilayer]
ml.next_run()
pprint('%d.%d.2.1 - Visualize Weights' %
(self._run + 1, nmultilayer + 1),
end='')
output.visualize_all_weights(self, nmultilayer, config)
pprint(' (%0.2f MB)' % mem_usage())
# if (len(self.MultiLayer) == 1):
# TODO: for greedy model: output Likelihood of up to the
# current MultiLayer
pprint('%d.%d.2.2 - LogLikelihood' % (self._run + 1, nmultilayer + 1),
end='')
output.write_loglikelihood(self, nmultilayer)
pprint(' (%0.2f MB)' % mem_usage())
# variables for stopping criterion
# TODO: generalize for all MultiLayers
try:
STOPPING_CRITERION = config.get()\
['model']['MultiLayer1']['StoppingCriterion']
except:
STOPPING_CRITERION = False
if STOPPING_CRITERION:
try:
mvngwidth = int(config.get()\
['model']['MultiLayer1']['MovingWidth'])
except:
pprint('WARNING (model.Model::Train): No width for \
moving average was given. It will be set to %d' % 20)
mvngwidth = 20
loglikelihood = np.asarray([], dtype=np.float32)
mvng_avg, mvng_std = 0., 0.
max_mvng_avg = float('-inf')
last_weights = []
else:
loglikelihood = np.asarray([None])
STOP = False
MPI.COMM_WORLD.Barrier()
pprint('%d.%d.2.3 - Training Iterations' %
(self._run + 1, nmultilayer + 1))
for niteration in xrange(ml.get_iterations()):
pprint('Iteration: %*d' % (int(math.log10(ml.get_iterations())) +
1, ml.get_iteration() + 1),
end='')
# pprint('2.2.3.1 - Convergence', end='')
output.conv_pre(ml)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
MPI.COMM_WORLD.Barrier()
# pprint('2.2.3.2 - Learning Iteration', end='')
ml.learning_iteration(self._theanoscan)
# pprint(' - Memory usage: %s (Mb)\n' % mem_usage())
MPI.COMM_WORLD.Barrier()
# experimental: variing learning rates
# if ((niteration % 1 == 0) and
# (ml.Layer[1]._epsilon >= 0.0008)):
# ml.Layer[1]._epsilon *= 0.98
# MPI.COMM_WORLD.Barrier()
# to save learned weights every iteration
# output.save_weights(self.MultiLayer[nmultilayer])
# to save posterior distribution of training data every iteration
# if nmultilayer == self.number_of_multilayers()-1:
# output.save_posterior(self, config, dataset)
# Stopping criterion
if (len(self.MultiLayer) == 1):
# TODO: for greedy model: output Likelihood of up to the
# current MultiLayer
if STOPPING_CRITERION:
t0 = time.time()
loglikelihood = np.append(loglikelihood,
self.loglikelihood())
if (niteration >= mvngwidth):
# save only the last #mvngwidth values
loglikelihood = loglikelihood[1:]
pprint(' | Log-Likelihood: %f (%f s)' %
(loglikelihood[-1], time.time() - t0),
end='')
if STOPPING_CRITERION:
# save only the last #mvngwidht/2-1 weights
# for centered moving average
last_weights.append([
ml.Layer[nlayer].get_weights()
for nlayer in xrange(1, len(ml.Layer))
])
if (niteration > mvngwidth / 2):
last_weights = last_weights[1:]
# calculate moving average over last #mvngwidth values
if (niteration >= mvngwidth - 1):
mvng_avg = np.mean(loglikelihood)
mvng_std = np.std(loglikelihood)
pprint(' | Moving Average (%d): %f +- %f' %
((niteration + 1 - mvngwidth / 2), mvng_avg,
mvng_std),
end='')
if (mvng_avg > max_mvng_avg):
max_mvng_avg = mvng_avg
elif (mvng_avg < max_mvng_avg - mvng_std):
# if the moving average drops below the maximum
# moving average by more than the moving standard
# deviation, stop the learning iteration and revert
# back to the point of the centered moving average
for nlayer in xrange(1, len(ml.Layer)):
ml.Layer[nlayer].set_weights(
last_weights[0][nlayer - 1])
stopping_iteration = niteration + 1 - mvngwidth / 2
pprint(
'\nStopping criterion met at iteration %d.' %
stopping_iteration)
STOP = True
ml.set_iteration(stopping_iteration)
ml.set_iterations(stopping_iteration)
# abort on numerical error (nan in any of the weights)
if any([
np.any(np.isnan(ml.Layer[nlayer].get_weights()))
for nlayer in xrange(1, len(ml.Layer))
]):
pprint('\nNumerical error: try to decrease learning ' +
'rate and/or mini-batch size.')
STOP = True
try:
ml.set_iteration(stopping_iteration)
ml.set_iterations(stopping_iteration)
except:
pass
this_loglikelihood = output.write_loglikelihood(
self, nmultilayer, loglikelihood[-1])
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
if (len(self.MultiLayer) == 1):
# pprint('2.2.3.7 - Test Error', end='')
output.write_online_results(self, config, dataset,
this_loglikelihood)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
# pprint('2.2.3.4 - Visualize Weights', end='')
output.visualize_all_weights(self, nmultilayer, config)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
# pprint('2.2.3.5 - Convergence 2', end='')
output.conv_post(self.MultiLayer[nmultilayer])
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
# pprint('2.2.3.6 - Visualize Convergence', end='')
output.visualize_convergence(self, nmultilayer)
# pprint(' - Memory usage: %s (Mb)' % mem_usage())
if STOP:
break
pprint('') #linebreak