def get_encoded_dataset(self, encoder_fn, selectors):
"""
This version is intended for use with a data dict / indices.
:return:
"""
from deepthought.datasets.selection import DatasetMetaDB
from deepthought.util.function_util import process_dataset
import theano
# build lookup structure
metadb = DatasetMetaDB(self.full_meta, selectors.keys())
# get selected trial IDs
selected_trial_ids = metadb.select(selectors)
X, Y = process_dataset(self.full_hdf5, encoder_fn,
indices=selected_trial_ids,
input_sources=['indices'],
target_source=self.hyper_params['classification_target_source'])
meta = [self.full_meta[i] for i in selected_trial_ids]
# flatten X (2d) and Y (1d)
X = np.asarray(X, dtype=theano.config.floatX)
X = X.reshape(X.shape[0], np.prod(X.shape[1:]))
Y = Y.argmax(axis=1)
return X, Y, meta
def get_dataset(hdf5name,
selectors=None,
sources=('features', 'targets', 'subjects')):
if selectors is None:
selectors = {}
# load metadata
import deepthought.util.fs_util as fs_util
base_meta = fs_util.load(hdf5name + '.meta.pklz')
# build lookup structure
from deepthought.datasets.selection import DatasetMetaDB
metadb = DatasetMetaDB(base_meta, selectors.keys())
# get selected trial IDs
selected_trial_ids = metadb.select(selectors)
log.debug('selectors: {}'.format(selectors))
log.debug('selected trials: {}'.format(selected_trial_ids))
log.debug('selected sources: {}'.format(sources))
# load data and generate metadata
from fuel.datasets.hdf5 import H5PYDataset
hdf5 = H5PYDataset(hdf5name,
which_sets=('all', ),
subset=selected_trial_ids,
load_in_memory=True,
sources=sources)
meta = [base_meta[i] for i in selected_trial_ids]
log.debug('number of examples: {}'.format(hdf5.num_examples))
return hdf5, meta
def __init__(self, db, selectors):
metadb = DatasetMetaDB(db.metadata, selectors.keys())
selected_trial_ids = metadb.select(selectors)
self.data = [db.data[i] for i in selected_trial_ids]
self.metadata = [db.metadata[i] for i in selected_trial_ids]
if hasattr(db, 'targets'):
if db.targets is None:
self.targets = None
else:
self.targets = [db.targets[i] for i in selected_trial_ids]
def __init__(self, db, selectors):
metadb = DatasetMetaDB(db.metadata, selectors.keys())
selected_trial_ids = metadb.select(selectors)
self.data = [db.data[i] for i in selected_trial_ids]
self.metadata = [db.metadata[i] for i in selected_trial_ids]
if hasattr(db, 'targets'):
if db.targets is None:
self.targets = None
else:
self.targets = [db.targets[i] for i in selected_trial_ids]
def __init__(self, root_path, selectors=dict()):
# read metadata file: dict filename -> metadata
meta_map = load(os.path.join(root_path, 'metadata_db.pklz'))
filenames = list(meta_map.keys())
metadata = [meta_map[fn] for fn in filenames]
# filter files by metadata selectors
metadb = DatasetMetaDB(metadata, selectors.keys())
selected_file_ids = metadb.select(selectors)
# log.info('selected files: {}'.format(selected_file_ids))
# load selected files
self.data = []
self.metadata = []
for id in selected_file_ids:
log.debug('loading data file #{} {}'.format(id, filenames[id]))
f_data, f_metadata = load(os.path.join(root_path, filenames[id]))
self.data.append(f_data)
self.metadata.append(metadata[id])
print len(self.data), len(self.metadata)
def __init__(self, root_path, selectors=dict()):
# read metadata file: dict filename -> metadata
meta_map = load(os.path.join(root_path, 'metadata_db.pklz'))
filenames = list(meta_map.keys())
metadata = [meta_map[fn] for fn in filenames]
# filter files by metadata selectors
metadb = DatasetMetaDB(metadata, selectors.keys())
selected_file_ids = metadb.select(selectors)
# log.info('selected files: {}'.format(selected_file_ids))
# load selected files
self.data = []
self.metadata = []
for id in selected_file_ids:
log.debug('loading data file #{} {}'.format(id, filenames[id]))
f_data, f_metadata = load(os.path.join(root_path, filenames[id]))
self.data.append(f_data)
self.metadata.append(metadata[id])
print len(self.data), len(self.metadata)
def __init__(self,
db, # data source
name = '', # optional name
selectors = dict(),
partitioner = None,
meta_sources = [], # optional sources other than 'features' and 'targets' from metadata
channel_filter = NoChannelFilter(), # optional channel filter, default: keep all
channel_names = None, # optional channel names (for metadata)
label_attribute = 'label', # metadata attribute to be used as label
label_map = None, # optional conversion of labels
use_targets = True, # use targets if provides, otherwise labels are used
remove_dc_offset = False, # optional subtraction of channel mean, usually done already earlier
resample = None, # optional down-sampling
normalize = True, # normalize to max=1
# optional sub-sequences selection
start_sample = 0,
stop_sample = None, # optional for selection of sub-sequences
zero_padding = True, # if True (default) trials that are too short will be padded with
# otherwise they will rejected.
# optional signal filter to by applied before splitting the signal
signal_filter = None,
trial_processors = [], # optional processing of the trials
target_processor = None, # optional processing of the targets, e.g. zero-padding
transformers = [], # optional transformations of the dataset
layout='tf', # (0,1)-axes layout tf=time x features or ft=features x time
debug=False,
):
'''
Constructor
'''
# save params
self.params = locals().copy()
del self.params['self']
# print self.params
self.name = name
self.debug = debug
metadb = DatasetMetaDB(db.metadata, selectors.keys())
if partitioner is not None:
pass # FIXME
selected_trial_ids = metadb.select(selectors)
log.info('selectors: {}'.format(selectors))
log.info('selected trials: {}'.format(selected_trial_ids))
if normalize:
log.info('Data will be normalized to max amplitude 1 per channel (normalize=True).')
trials = list()
labels = list()
targets = list()
meta = list()
if stop_sample == 'auto-min':
stop_sample = np.min([db.data[trial_i].shape[-1] for trial_i in selected_trial_ids])
log.info('Using minimum trial length. stop_sample={}'.format(stop_sample))
elif stop_sample == 'auto-max':
stop_sample = np.max([db.data[trial_i].shape[-1] for trial_i in selected_trial_ids])
log.info('Using maximum trial length. stop_sample={}'.format(stop_sample))
for trial_i in selected_trial_ids:
trial_meta = db.metadata[trial_i]
if use_targets:
if targets is None:
target = None
else:
target = db.targets[trial_i]
assert not np.isnan(np.sum(target))
if target_processor is not None:
target = target_processor.process(target, trial_meta)
assert not np.isnan(np.sum(target))
else:
# get and process label
label = db.metadata[trial_i][label_attribute]
if label_map is not None:
label = label_map[label]
processed_trial = []
trial = db.data[trial_i]
if np.isnan(np.sum(trial)):
print trial_i, trial
assert not np.isnan(np.sum(trial))
rejected = False # flag for trial rejection
trial = np.atleast_2d(trial)
# process 1 channel at a time
for channel in xrange(trial.shape[0]):
# filter channels
if not channel_filter.keep_channel(channel):
continue
samples = trial[channel, :]
# subtract channel mean
if remove_dc_offset:
samples -= samples.mean()
# down-sample if requested
if resample is not None and resample[0] != resample[1]:
samples = librosa.resample(samples, resample[0], resample[1], res_type='sinc_best')
# apply optional signal filter after down-sampling -> requires lower order
if signal_filter is not None:
samples = signal_filter.process(samples)
# get sub-sequence in resampled space
# log.info('using samples {}..{} of {}'.format(start_sample,stop_sample, samples.shape))
if stop_sample is not None and stop_sample > len(samples):
if zero_padding:
tmp = np.zeros(stop_sample)
tmp[:len(samples)] = samples
samples = tmp
else:
rejected = True
break # stop processing this trial
s = samples[start_sample:stop_sample]
# TODO optional channel processing
# normalize to max amplitude 1
if normalize:
s = librosa.util.normalize(s)
# add 2nd data dimension
s = s.reshape(s.shape[0], 1)
# print s.shape
s = np.asfarray(s, dtype=theano.config.floatX)
processed_trial.append(s)
### end of channel iteration ###
if rejected:
continue # next trial
processed_trial = np.asfarray([processed_trial], dtype=theano.config.floatX)
# processed_trial = processed_trial.reshape((1, processed_trial.shape))
processed_trial = np.rollaxis(processed_trial, 1, 4)
# optional (external) trial processing, e.g. windowing
# trials will be in b01c format with tf layout for 01-axes
for trial_processor in trial_processors:
processed_trial = trial_processor.process(processed_trial, trial_meta)
trials.append(processed_trial)
for k in range(len(processed_trial)):
meta.append(trial_meta)
if use_targets:
targets.append(target)
else:
labels.append(label)
### end of datafile iteration ###
# turn into numpy arrays
self.trials = np.vstack(trials)
assert not np.isnan(np.sum(self.trials))
# prepare targets / labels
if use_targets:
self.targets = np.vstack(targets)
assert not np.isnan(np.sum(self.targets))
else:
labels = np.hstack(labels)
if label_map is None:
one_hot_formatter = OneHotFormatter(max(labels) + 1)
else:
one_hot_formatter = OneHotFormatter(max(label_map.values()) + 1)
one_hot_y = one_hot_formatter.format(labels)
self.targets = one_hot_y
self.metadata = meta
if layout == 'ft': # swap axes to (batch, feature, time, channels)
self.trials = self.trials.swapaxes(1, 2)
# transform after finalizing the data structure
for transformer in transformers:
self.trials, self.targets = transformer.process(self.trials, self.targets)
self.trials = np.asarray(self.trials, dtype=theano.config.floatX)
log.debug('final dataset shape: {} (b,0,1,c)'.format(self.trials.shape))
# super(EEGEpochsDataset, self).__init__(topo_view=self.trials, y=self.targets, axes=['b', 0, 1, 'c'])
self.X = self.trials.reshape(self.trials.shape[0], np.prod(self.trials.shape[1:]))
self.y = self.targets
log.info('generated dataset "{}" with shape X={}={} y={} targets={} '.
format(self.name, self.X.shape, self.trials.shape, self.y.shape, self.targets.shape))
# determine data specs
features_space = Conv2DSpace(
shape=[self.trials.shape[1], self.trials.shape[2]],
num_channels=self.trials.shape[3]
)
features_source = 'features'
targets_space = VectorSpace(dim=self.targets.shape[-1])
targets_source = 'targets'
space_components = [features_space, targets_space]
source_components = [features_source, targets_source]
# additional support for meta information
self.meta_maps = dict()
for meta_source in meta_sources:
self.meta_maps[meta_source] = sorted(list(set([m[meta_source] for m in self.metadata])))
space_components.extend([VectorSpace(dim=1)])
source_components.extend([meta_source])
log.info('Generated meta-source "{}" with value map: {}'
.format(meta_source, self.meta_maps[meta_source]))
space = CompositeSpace(space_components)
source = tuple(source_components)
self.data_specs = (space, source)
log.debug('data specs: {}'.format(self.data_specs))
def run(self, classifiers=(), verbose=False, debug=False):
print 'running job #{}'.format(self.job_id)
import deepthought.util.fs_util as fs_util
fs_util.ensure_dir_exists(self.output_path)
print 'output path: ', self.output_path
# prepare result objects
results = {k: ClassificationResult(k) for (k, _) in classifiers}
# load full dataset with all sources only once!
from deepthought.datasets.hdf5 import get_dataset
self.full_hdf5, self.full_meta = get_dataset(self.hdf5name, selectors=self.base_selectors, sources=None)
self.initialize()
# main loop ###
# outer cross-validation
outer_folds = self.fold_generator.get_outer_cv_folds()
for ofi, ofold in enumerate(outer_folds):
print 'processing outer fold', ofold
# phase I : pre-train features ###
encoder_fn = self.pretrain_encoder(ofi, ofold) # FIXME: add params
# phase II : classify ###
train_selectors = self.fold_generator.get_fold_selectors(outer_fold=ofold['train'])
X_train, Y_train, meta_train = self.get_encoded_dataset(encoder_fn, train_selectors)
test_selectors = self.fold_generator.get_fold_selectors(outer_fold=ofold['valid'])
X_test, Y_test, _ = self.get_encoded_dataset(encoder_fn, test_selectors)
for (classifier_name, classifier_factory) in classifiers:
result = results[classifier_name]
model_prefix = os.path.join(self.output_path, '{}_fold_{}'.format(classifier_name, ofi))
# generate index folds
idx_folds = []
from deepthought.datasets.selection import DatasetMetaDB
for ifold in self.fold_generator.get_inner_cv_folds(ofold):
train_selectors = self.fold_generator.get_fold_selectors(outer_fold=ofold['train'],
inner_fold=ifold['train'])
metadb = DatasetMetaDB(meta_train, train_selectors.keys())
if 'valid' in ifold.keys():
valid_selectors = self.fold_generator.get_fold_selectors(outer_fold=ofold['train'],
inner_fold=ifold['valid'])
else:
valid_selectors = None
if debug:
print 'train_selectors:', train_selectors
print 'valid_selectors:', valid_selectors
# get selected trial IDs
train_idx = metadb.select(train_selectors)
if valid_selectors is not None:
valid_idx = metadb.select(valid_selectors)
else:
valid_idx = []
idx_folds.append((train_idx, valid_idx))
if debug:
print idx_folds # print the generated folds before running the classifier
# train classifier
classifier, predict_fn = classifier_factory.train(X_train, Y_train, idx_folds, self.hyper_params, model_prefix)
# test classifier
train_Y_pred = predict_fn(X_train)
test_Y_pred = predict_fn(X_test)
# append to result
result.append_train(Y_train, train_Y_pred)
result.append_test(Y_test, test_Y_pred)
# result.fold_scores.append(classifier.score(X_test, Y_test))
result.fold_scores.append(np.mean(Y_test == test_Y_pred))
if verbose:
print '{} results for fold {}'.format(classifier_name, ofold)
print classification_report(Y_test, test_Y_pred)
print confusion_matrix(Y_test, test_Y_pred)
print 'overall test accuracy so far:', 1 - result.test_error()
print 'all folds completed'
for (classifier_name, _) in classifiers:
result = results[classifier_name]
fs_util.save(os.path.join(self.output_path, '{}_result.pklz'.format(classifier_name)), result) # result
print
print 'SUMMARY for classifier', classifier_name
print
print 'fold scores: ', np.asarray(result.fold_scores)
print
print classification_report(result.test_Y_real, result.test_Y_pred)
print confusion_matrix(result.test_Y_real, result.test_Y_pred)
print
print 'train accuracy:', 1 - result.train_error()
print 'test accuracy :', 1 - result.test_error()
return [results[classifier[0]].test_error() for classifier in classifiers] # error for each classifier
def __init__(
self,
db, # data source
name='', # optional name
selectors=dict(),
partitioner=None,
meta_sources=[], # optional sources other than 'features' and 'targets' from metadata
channel_filter=NoChannelFilter(
), # optional channel filter, default: keep all
channel_names=None, # optional channel names (for metadata)
label_attribute='label', # metadata attribute to be used as label
label_map=None, # optional conversion of labels
use_targets=True, # use targets if provides, otherwise labels are used
remove_dc_offset=False, # optional subtraction of channel mean, usually done already earlier
resample=None, # optional down-sampling
normalize=True, # normalize to max=1
# optional sub-sequences selection
start_sample=0,
stop_sample=None, # optional for selection of sub-sequences
zero_padding=True, # if True (default) trials that are too short will be padded with
# otherwise they will rejected.
# optional signal filter to by applied before splitting the signal
signal_filter=None,
trial_processors=[], # optional processing of the trials
target_processor=None, # optional processing of the targets, e.g. zero-padding
transformers=[], # optional transformations of the dataset
layout='tf', # (0,1)-axes layout tf=time x features or ft=features x time
debug=False,
):
'''
Constructor
'''
# save params
self.params = locals().copy()
del self.params['self']
# print self.params
self.name = name
self.debug = debug
metadb = DatasetMetaDB(db.metadata, selectors.keys())
if partitioner is not None:
pass # FIXME
selected_trial_ids = metadb.select(selectors)
log.info('selectors: {}'.format(selectors))
log.info('selected trials: {}'.format(selected_trial_ids))
if normalize:
log.info(
'Data will be normalized to max amplitude 1 per channel (normalize=True).'
)
trials = list()
labels = list()
targets = list()
meta = list()
if stop_sample == 'auto-min':
stop_sample = np.min(
[db.data[trial_i].shape[-1] for trial_i in selected_trial_ids])
log.info('Using minimum trial length. stop_sample={}'.format(
stop_sample))
elif stop_sample == 'auto-max':
stop_sample = np.max(
[db.data[trial_i].shape[-1] for trial_i in selected_trial_ids])
log.info('Using maximum trial length. stop_sample={}'.format(
stop_sample))
for trial_i in selected_trial_ids:
trial_meta = db.metadata[trial_i]
if use_targets:
if targets is None:
target = None
else:
target = db.targets[trial_i]
assert not np.isnan(np.sum(target))
if target_processor is not None:
target = target_processor.process(target, trial_meta)
assert not np.isnan(np.sum(target))
else:
# get and process label
label = db.metadata[trial_i][label_attribute]
if label_map is not None:
label = label_map[label]
processed_trial = []
trial = db.data[trial_i]
if np.isnan(np.sum(trial)):
print trial_i, trial
assert not np.isnan(np.sum(trial))
rejected = False # flag for trial rejection
trial = np.atleast_2d(trial)
# process 1 channel at a time
for channel in xrange(trial.shape[0]):
# filter channels
if not channel_filter.keep_channel(channel):
continue
samples = trial[channel, :]
# subtract channel mean
if remove_dc_offset:
samples -= samples.mean()
# down-sample if requested
if resample is not None and resample[0] != resample[1]:
samples = librosa.resample(samples,
resample[0],
resample[1],
res_type='sinc_best')
# apply optional signal filter after down-sampling -> requires lower order
if signal_filter is not None:
samples = signal_filter.process(samples)
# get sub-sequence in resampled space
# log.info('using samples {}..{} of {}'.format(start_sample,stop_sample, samples.shape))
if stop_sample is not None and stop_sample > len(samples):
if zero_padding:
tmp = np.zeros(stop_sample)
tmp[:len(samples)] = samples
samples = tmp
else:
rejected = True
break # stop processing this trial
s = samples[start_sample:stop_sample]
# TODO optional channel processing
# normalize to max amplitude 1
if normalize:
s = librosa.util.normalize(s)
# add 2nd data dimension
s = s.reshape(s.shape[0], 1)
# print s.shape
s = np.asfarray(s, dtype=theano.config.floatX)
processed_trial.append(s)
### end of channel iteration ###
if rejected:
continue # next trial
processed_trial = np.asfarray([processed_trial],
dtype=theano.config.floatX)
# processed_trial = processed_trial.reshape((1, processed_trial.shape))
processed_trial = np.rollaxis(processed_trial, 1, 4)
# optional (external) trial processing, e.g. windowing
# trials will be in b01c format with tf layout for 01-axes
for trial_processor in trial_processors:
processed_trial = trial_processor.process(
processed_trial, trial_meta)
trials.append(processed_trial)
for k in range(len(processed_trial)):
meta.append(trial_meta)
if use_targets:
targets.append(target)
else:
labels.append(label)
### end of datafile iteration ###
# turn into numpy arrays
self.trials = np.vstack(trials)
assert not np.isnan(np.sum(self.trials))
# prepare targets / labels
if use_targets:
self.targets = np.vstack(targets)
assert not np.isnan(np.sum(self.targets))
else:
labels = np.hstack(labels)
if label_map is None:
one_hot_formatter = OneHotFormatter(max(labels) + 1)
else:
one_hot_formatter = OneHotFormatter(
max(label_map.values()) + 1)
one_hot_y = one_hot_formatter.format(labels)
self.targets = one_hot_y
self.metadata = meta
if layout == 'ft': # swap axes to (batch, feature, time, channels)
self.trials = self.trials.swapaxes(1, 2)
# transform after finalizing the data structure
for transformer in transformers:
self.trials, self.targets = transformer.process(
self.trials, self.targets)
self.trials = np.asarray(self.trials, dtype=theano.config.floatX)
log.debug('final dataset shape: {} (b,0,1,c)'.format(
self.trials.shape))
# super(EEGEpochsDataset, self).__init__(topo_view=self.trials, y=self.targets, axes=['b', 0, 1, 'c'])
self.X = self.trials.reshape(self.trials.shape[0],
np.prod(self.trials.shape[1:]))
self.y = self.targets
log.info('generated dataset "{}" with shape X={}={} y={} targets={} '.
format(self.name, self.X.shape, self.trials.shape,
self.y.shape, self.targets.shape))
# determine data specs
features_space = Conv2DSpace(
shape=[self.trials.shape[1], self.trials.shape[2]],
num_channels=self.trials.shape[3])
features_source = 'features'
targets_space = VectorSpace(dim=self.targets.shape[-1])
targets_source = 'targets'
space_components = [features_space, targets_space]
source_components = [features_source, targets_source]
# additional support for meta information
self.meta_maps = dict()
for meta_source in meta_sources:
self.meta_maps[meta_source] = sorted(
list(set([m[meta_source] for m in self.metadata])))
space_components.extend([VectorSpace(dim=1)])
source_components.extend([meta_source])
log.info('Generated meta-source "{}" with value map: {}'.format(
meta_source, self.meta_maps[meta_source]))
space = CompositeSpace(space_components)
source = tuple(source_components)
self.data_specs = (space, source)
log.debug('data specs: {}'.format(self.data_specs))
def __init__(self,
dataset,
dataset_metadata,
base_selectors=None,
ext_selectors=None,
targets_source='targets',
group_attribute=None,
allow_self_comparison=False,
additional_sources=None,
**kwargs):
if base_selectors is None:
base_selectors = {}
if additional_sources is None:
additional_sources = []
# get selected trial IDs
from deepthought.datasets.selection import DatasetMetaDB
metadb = DatasetMetaDB(dataset_metadata, base_selectors.keys())
base_trial_ids = metadb.select(base_selectors)
log.debug('base selectors: {}'.format(base_selectors))
log.debug('selected base trials: {}'.format(base_trial_ids))
if ext_selectors is not None:
split_index = len(base_trial_ids)
metadb = DatasetMetaDB(dataset_metadata, ext_selectors.keys())
ext_trial_ids = metadb.select(ext_selectors)
else:
split_index = 0
ext_trial_ids = []
log.debug('ext selectors: {}'.format(ext_selectors))
log.debug('selected ext trials: {}'.format(ext_trial_ids))
# indices = np.concatenate((base_trial_ids, ext_trial_ids))
indices = base_trial_ids + ext_trial_ids
metadata = [dataset_metadata[i] for i in indices]
# load targets from dataset
state = dataset.open()
targets = dataset.get_data(
state=state,
request=indices)[dataset.sources.index(targets_source)]
dataset.close(state)
# print targets
# split data into partitions according to
groups = dict()
if group_attribute is not None:
for i, meta in enumerate(metadata):
group = meta[group_attribute]
if group not in groups:
groups[group] = []
groups[group].append(i)
else:
# default: all in one group
groups['default'] = np.arange(len(metadata))
# print groups
from itertools import product
pairs = []
others = []
# add group-wise
for group_ids in groups.values():
for i in range(targets.shape[-1]):
# 1st trial candidates
if split_index > 0:
trial_ids = np.where(targets[:split_index, i] == 1)[0]
else:
trial_ids = np.where(targets[:, i] == 1)[0]
# 2nd trial candidates (same class)
trial_ids2 = np.where(targets[:, i] == 1)[0]
# others candidates (different class)
others_ids = np.where(targets[:, i] == 0)[0]
# only retain ids within the group
trial_ids = np.intersect1d(trial_ids, group_ids)
trial_ids2 = np.intersect1d(trial_ids2, group_ids)
others_ids = np.intersect1d(others_ids, group_ids)
# combine with permutation
new_pairs = [
tuple(pair) for pair in product(trial_ids, trial_ids2)
]
if not allow_self_comparison: # remove repetitions
to_remove = []
for pair in new_pairs:
if pair[0] == pair[1]:
to_remove.append(pair)
for pair in to_remove:
new_pairs.remove(pair)
# print 'removed', to_remove
new_pairs = sorted(new_pairs)
# print pairs
# combine all pairs with all other trials
for pair, other in product(new_pairs, others_ids):
# print pair, other
pairs.append(pair)
others.append([other])
# NOTE: triplets uses internal ids
# (refencing into indices which contains hdfs-specific ids)
self.triplets = np.concatenate([pairs, others], axis=1)
self.indices = np.asarray(indices, dtype=np.int16)
# indices = indices.reshape((len(indices), 1)) # make 2D for VectorSpace
log.debug('triplets.shape={} indices.shape={}'.format(
self.triplets.shape, self.indices.shape))
sources = ['targets', '0_indices', '1_indices', '2_indices']
self.data_per_source = dict()
for source in additional_sources:
# load source data from hdf5 dataset
# hdf5 = H5PYDataset(hdf5name, which_sets=('all',),
# load_in_memory=True, sources=(source,)
# )
# state = hdf5.open()
# self.data_per_source[source] = hdf5.get_data(request=indices)[0]
# hdf5.close(state)
# load source data from dataset
state = dataset.open()
self.data_per_source[source] = dataset.get_data(
state=state, request=indices)[dataset.sources.index(source)]
dataset.close(state)
for i in range(3):
sources.append('{}_{}'.format(i, source))
self.sources = tuple(sources)
self.provides_sources = self.sources
log.debug('sources: {}'.format(self.sources))
super(TripletsIndexDataset, self).__init__(**kwargs)
def __init__(self,
dataset,
dataset_metadata,
base_selectors=None,
ext_selectors=None,
targets_source='targets',
group_attribute=None,
allow_self_comparison=False,
additional_sources=None,
**kwargs):
if base_selectors is None:
base_selectors = {}
if additional_sources is None:
additional_sources = []
# get selected trial IDs
from deepthought.datasets.selection import DatasetMetaDB
metadb = DatasetMetaDB(dataset_metadata, base_selectors.keys())
base_trial_ids = metadb.select(base_selectors)
log.debug('base selectors: {}'.format(base_selectors))
log.debug('selected base trials: {}'.format(base_trial_ids))
if ext_selectors is not None:
split_index = len(base_trial_ids)
metadb = DatasetMetaDB(dataset_metadata, ext_selectors.keys())
ext_trial_ids = metadb.select(ext_selectors)
else:
split_index = 0
ext_trial_ids = []
log.debug('ext selectors: {}'.format(ext_selectors))
log.debug('selected ext trials: {}'.format(ext_trial_ids))
# indices = np.concatenate((base_trial_ids, ext_trial_ids))
indices = base_trial_ids + ext_trial_ids
metadata = [dataset_metadata[i] for i in indices]
# load targets from dataset
state = dataset.open()
targets = dataset.get_data(
state=state,
request=indices)[dataset.sources.index(targets_source)]
dataset.close(state)
# print targets
# split data into partitions according to
groups = dict()
if group_attribute is not None:
for i, meta in enumerate(metadata):
group = meta[group_attribute]
if group not in groups:
groups[group] = []
groups[group].append(i)
else:
# default: all in one group
groups['default'] = np.arange(len(metadata))
# print groups
from itertools import product
pairs = []
pair_targets = []
# add group-wise
for group_ids in groups.values():
for i in range(targets.shape[-1]):
# 1st trial candidates
if split_index > 0:
trial_ids = np.where(targets[:split_index, i] == 1)[0]
else:
trial_ids = np.where(targets[:, i] == 1)[0]
# similar candidates (same class)
trial_ids2 = np.where(targets[:, i] == 1)[0]
# dissimilar candidates (different class)
others_ids = np.where(targets[:, i] == 0)[0]
# only retain ids within the group
trial_ids = np.intersect1d(trial_ids, group_ids)
trial_ids2 = np.intersect1d(trial_ids2, group_ids)
others_ids = np.intersect1d(others_ids, group_ids)
for pair in product(trial_ids, trial_ids2):
if allow_self_comparison or pair[0] != pair[1]:
pairs.append(tuple(pair))
pair_targets.append(0)
for pair in product(trial_ids, others_ids):
pairs.append(tuple(pair))
pair_targets.append(1)
# NOTE: pairs uses internal ids
# (refencing into indices which contains hdfs-specific ids)
self.pairs = np.asarray(pairs)
self.pair_targets = np.asarray(pair_targets)
self.indices = np.asarray(indices, dtype=np.int16)
log.debug('pairs.shape={} indices.shape={}'.format(
self.pairs.shape, self.indices.shape))
sources = ['targets', '0_indices', '1_indices']
self.data_per_source = dict()
for source in additional_sources:
# load source data from dataset
state = dataset.open()
self.data_per_source[source] = dataset.get_data(
state=state, request=indices)[dataset.sources.index(source)]
dataset.close(state)
for i in range(2):
sources.append('{}_{}'.format(i, source))
self.sources = tuple(sources)
self.provides_sources = self.sources
log.debug('sources: {}'.format(self.sources))
super(PairsIndexDataset, self).__init__(**kwargs)
