def _encode_data(self, dataset: SequenceDataset, params: EncoderParams):
sequence_objs = [obj for obj in dataset.get_data(params.pool_size)]
sequences = [obj.get_sequence() for obj in sequence_objs]
example_ids = dataset.get_example_ids()
max_seq_len = max([len(seq) for seq in sequences])
labels = self._get_labels(sequence_objs,
params) if params.encode_labels else None
examples = self._encode_sequence_list(
sequences,
pad_n_sequences=len(sequence_objs),
pad_sequence_len=max_seq_len)
feature_names = self._get_feature_names(max_seq_len)
if self.flatten:
examples = examples.reshape(
(len(sequence_objs),
max_seq_len * len(self.onehot_dimensions)))
feature_names = [
item for sublist in feature_names for item in sublist
]
encoded_data = EncodedData(examples=examples,
labels=labels,
example_ids=example_ids,
feature_names=feature_names,
encoding=OneHotEncoder.__name__)
return encoded_data
def _encode_data(self, dataset: SequenceDataset, params: EncoderParams):
sequence_objs = [obj for obj in dataset.get_data(params.pool_size)]
sequences = [
obj.get_sequence(self.sequence_type) for obj in sequence_objs
]
if any(seq is None for seq in sequences):
raise ValueError(
f"{OneHotEncoder.__name__}: sequence dataset {dataset.name} (id: {dataset.identifier}) contains empty sequences for the specified "
f"sequence type {self.sequence_type.name.lower()}. Please check that the dataset is imported correctly."
)
example_ids = dataset.get_example_ids()
max_seq_len = max([len(seq) for seq in sequences])
labels = self._get_labels(sequence_objs,
params) if params.encode_labels else None
examples = self._encode_sequence_list(
sequences,
pad_n_sequences=len(sequence_objs),
pad_sequence_len=max_seq_len)
feature_names = self._get_feature_names(max_seq_len)
if self.flatten:
examples = examples.reshape(
(len(sequence_objs),
max_seq_len * len(self.onehot_dimensions)))
feature_names = [
item for sublist in feature_names for item in sublist
]
encoded_data = EncodedData(examples=examples,
labels=labels,
example_ids=example_ids,
feature_names=feature_names,
encoding=OneHotEncoder.__name__)
return encoded_data