def _postprocess(self, stims, preds, tok, wds, ons, dur):
preds = preds[0].numpy()[:, 1:-1, :]
if self.return_softmax:
preds = scipy.special.softmax(preds, axis=-1)
out_idx = preds[0, self.mask_pos, :].argsort()[::-1]
if self.top_n:
sub_idx = out_idx[:self.top_n]
elif self.target:
sub_idx = self.tokenizer.convert_tokens_to_ids(self.target)
elif self.threshold:
sub_idx = np.where(preds[0, self.mask_pos, :] >= self.threshold)[0]
else:
sub_idx = out_idx
out_idx = [idx for idx in out_idx if idx in sub_idx]
feat = self.tokenizer.convert_ids_to_tokens(out_idx)
feat = [
f.capitalize() if len(f) == len(f.encode()) else f for f in feat
]
data = [listify(p) for p in preds[0, self.mask_pos, out_idx]]
if self.return_masked_word:
feat, data = self._return_masked_word(preds, feat, data)
if self.return_input:
data += [stims.name]
feat += ['sequence']
mask_ons = listify(stims.elements[self.mask_pos].onset)
mask_dur = listify(stims.elements[self.mask_pos].duration)
return data, feat, mask_ons, mask_dur
def __init__(self, functions=None, var_names=None,
subset_idx=None, **kwargs):
functions = listify(functions)
if var_names is not None:
var_names = listify(var_names)
if len(var_names) != len(functions):
raise ValueError('Length of var_names must match number of '
'functions')
for idx, f in enumerate(functions):
if isinstance(f, str):
try:
f_mod, f_func = f.rsplit('.', 1)
functions[idx] = getattr(import_module(f_mod),
f_func)
except:
try:
functions[idx] = eval(f)
except:
raise ValueError(f"{f} is not a valid function")
if var_names is None:
var_names = [f.__name__ for f in functions]
self.var_names = var_names
self.functions = functions
self.kwargs = kwargs
self.subset_idx = subset_idx
super().__init__()
def _preprocess(self, stim):
x = listify(stim.data)
if self.preprocessor_url_or_path:
preprocessor = hub.KerasLayer(self.preprocessor_url_or_path,
self.preprocessor_kwargs)
x = preprocessor(x)
return x
def get_converter(in_type, out_type, *args, **kwargs):
''' Scans the list of available Converters and returns an instantiation
of the first one whose input and output types match those passed in.
Args:
in_type (type): The type of input the converter must have.
out_type (type): The type of output the converter must have.
args, kwargs: Optional positional and keyword arguments to pass onto
matching Converter's initializer.
'''
convs = pliers.converters.__all__
# If config includes default converters for this combination, try them
# first
out_type = listify(out_type)[::-1]
default_convs = config.get_option('default_converters')
for ot in out_type:
conv_str = '%s->%s' % (in_type.__name__, ot.__name__)
if conv_str in default_convs:
convs = list(default_convs[conv_str]) + convs
for name in convs:
cls = getattr(pliers.converters, name)
if not inspect.isclass(cls) or not issubclass(cls, Converter):
continue
available = cls.available if issubclass(cls,
EnvironmentKeyMixin) else True
if cls._input_type == in_type and cls._output_type in out_type \
and available:
conv = cls(*args, **kwargs)
return conv
return None
def __init__(self, api_key=None, model='general-v1.3', min_value=None,
max_concepts=None, select_concepts=None, rate_limit=None,
batch_size=None):
verify_dependencies(['clarifai_client'])
if api_key is None:
try:
api_key = os.environ['CLARIFAI_API_KEY']
except KeyError:
raise ValueError("A valid Clarifai API API_KEY "
"must be passed the first time a Clarifai "
"extractor is initialized.")
self.api_key = api_key
try:
self.api = clarifai_client.ClarifaiApp(api_key=api_key)
self.model = self.api.models.get(model)
except clarifai_client.ApiError as e:
logging.warn(str(e))
self.api = None
self.model = None
self.model_name = model
self.min_value = min_value
self.max_concepts = max_concepts
self.select_concepts = select_concepts
if select_concepts:
select_concepts = listify(select_concepts)
self.select_concepts = [clarifai_client.Concept(concept_name=n)
for n in select_concepts]
super(ClarifaiAPIExtractor, self).__init__(rate_limit=rate_limit)
def __init__(self,
api_key=None,
model='general-v1.3',
min_value=None,
max_concepts=None,
select_concepts=None,
rate_limit=None):
verify_dependencies(['clarifai_client'])
if api_key is None:
try:
api_key = os.environ['CLARIFAI_API_KEY']
except KeyError:
raise ValueError("A valid Clarifai API API_KEY "
"must be passed the first time a Clarifai "
"extractor is initialized.")
self.api_key = api_key
try:
self.api = clarifai_client.ClarifaiApp(api_key=api_key)
self.model = self.api.models.get(model)
except clarifai_client.ApiError:
self.api = None
self.model = None
self.model_name = model
self.min_value = min_value
self.max_concepts = max_concepts
self.select_concepts = select_concepts
if select_concepts:
select_concepts = listify(select_concepts)
self.select_concepts = [
clarifai_client.Concept(concept_name=n)
for n in select_concepts
]
super(ClarifaiAPIExtractor, self).__init__(rate_limit=rate_limit)
def _transform(self, stim, *args, **kwargs):
# Check if we are requesting faster than the rate limit,
# if so, throttle by sleeping
time_diff = time.time() - self._last_request_time
if time_diff < self.rate_limit:
time.sleep(self.rate_limit - time_diff)
self._last_request_time = time.time()
# Check if we are trying to transform a large amount of data
self.transformed_stim_count += len(listify(stim))
if not config.get_option('allow_large_jobs'):
if not isiterable(stim) and stim.duration \
and stim.duration > config.get_option('long_job'):
raise ValueError("Attempted to run an API transformation "
"on a stimulus of duration %f, aborting. "
"To allow this transformation, set "
"config option 'allow_large_jobs' to "
"True." % stim.duration)
if self.transformed_stim_count > config.get_option('large_job'):
raise ValueError("Number of transformations using this %s "
"would exceed %d, aborting further "
"transformations. To allow, set config "
"option 'allow_large_jobs' to True." %
(self.__class__.__name__,
config.get_option('large_job')))
if config.get_option('api_key_validation') and not self.validate_keys():
raise ValueError("Error running %s, a provided environment key "
"was invalid or unauthorized. Please check that "
"you have authorized credentials for accessing "
"the target API." % self.__class__.__name__)
return super(APITransformer, self)._transform(stim, *args, **kwargs)
def _transform(self, stim, *args, **kwargs):
# Check if we are requesting faster than the rate limit,
# if so, throttle by sleeping
time_diff = time.time() - self._last_request_time
if time_diff < self.rate_limit:
time.sleep(self.rate_limit - time_diff)
self._last_request_time = time.time()
# Check if we are trying to transform a large amount of data
self.transformed_stim_count += len(listify(stim))
if not config.get_option('allow_large_jobs'):
if not isiterable(stim) and stim.duration \
and stim.duration > config.get_option('long_job'):
raise ValueError("Attempted to run an API transformation "
"on a stimulus of duration %f, aborting. "
"To allow this transformation, set "
"config option 'allow_large_jobs' to "
"True." % stim.duration)
if self.transformed_stim_count > config.get_option('large_job'):
raise ValueError("Number of transformations using this %s "
"would exceed %d, aborting further "
"transformations. To allow, set config "
"option 'allow_large_jobs' to True." %
(self.__class__.__name__,
config.get_option('large_job')))
if config.get_option('api_key_validation') and not self.validate_keys():
raise ValueError("Error running %s, a provided environment key "
"was invalid or unauthorized. Please check that "
"you have authorized credentials for accessing "
"the target API." % self.__class__.__name__)
return super(APITransformer, self)._transform(stim, *args, **kwargs)
def _transform(self, stim, *args, **kwargs):
new_stim = self._filter(stim, *args, **kwargs)
if not isinstance(new_stim, self._input_type) and \
not isinstance(listify(new_stim)[0], stim.__class__):
raise ValueError("Filter must return a Stim of the same type as "
"its input.")
return new_stim
def get_transformer(name, base=None, *args, **kwargs):
''' Scans list of currently available Transformer classes and returns an
instantiation of the first one whose name perfectly matches
(case-insensitive).
Args:
name (str): The name of the transformer to retrieve. Case-insensitive;
e.g., 'stftextractor' or 'CornerDetectionExtractor'.
base (str, list): Optional name of transformer modules to search.
Valid values are 'converters', 'extractors', and 'filters'.
args, kwargs: Optional positional or keyword arguments to pass onto
the Transformer.
'''
name = name.lower()
# Default to searching all kinds of Transformers
if base is None:
base = ['extractors', 'converters', 'filters']
base = listify(base)
for b in base:
importlib.import_module('pliers.%s' % b)
mod = getattr(pliers, b)
classes = getattr(mod, '__all__')
for cls_name in classes:
if cls_name.lower() == name.lower():
cls = getattr(mod, cls_name)
return cls(*args, **kwargs)
raise KeyError("No transformer named '%s' found." % name)
def _transform(self, stim, *args, **kwargs):
new_stim = self._filter(stim, *args, **kwargs)
if not isinstance(new_stim, self._input_type) and \
not isinstance(listify(new_stim)[0], stim.__class__):
raise ValueError("Filter must return a Stim of the same type as "
"its input.")
return new_stim
def get_converter(in_type, out_type, *args, **kwargs):
''' Scans the list of available Converters and returns an instantiation
of the first one whose input and output types match those passed in.
Args:
in_type (type): The type of input the converter must have.
out_type (type): The type of output the converter must have.
args, kwargs: Optional positional and keyword arguments to pass onto
matching Converter's initializer.
'''
convs = pliers.converters.__all__
# If config includes default converters for this combination, try them first
out_type = listify(out_type)[::-1]
for ot in out_type:
conv_str = '%s->%s' % (in_type.__name__, ot.__name__)
if conv_str in config.default_converters:
convs = list(config.default_converters[conv_str]) + convs
for name in convs:
cls = getattr(pliers.converters, name)
if not issubclass(cls, Converter):
continue
if cls._input_type == in_type and cls._output_type in out_type and cls.available:
try:
conv = cls(*args, **kwargs)
return conv
except ValueError:
# Important for API converters
pass
return None
def _extract(self, stim):
values = self._get_values(stim)
if self._feature == 'beat_track':
beats = np.array(values[1])
values = beats
values = values.T
n_frames = len(values)
feature_names = listify(self.get_feature_names())
onsets = librosa.frames_to_time(range(n_frames),
sr=stim.sampling_rate,
hop_length=self.hop_length)
onsets = onsets + stim.onset if stim.onset else onsets
durations = [self.hop_length / float(stim.sampling_rate)] * n_frames
return ExtractorResult(values,
stim,
self,
features=feature_names,
onsets=onsets,
durations=durations,
orders=list(range(n_frames)))
def _extract(self, stim):
values = self.func(stim.data)
feature_names = listify(self.get_feature_names())
return ExtractorResult(values,
stim,
self,
features=feature_names,
raw=values)
def _preprocess(self, stim):
if self.transform_inp:
return self.transform_inp(stim.data)
else:
if type(stim) == TextStim:
return listify(stim.data)
else:
return stim.data
def _stim_matches_input_types(self, stim):
# Checks if passed Stim meets all _input_type and _optional_input_type
# specifications.
mandatory = tuple(listify(self._input_type))
optional = tuple(listify(self._optional_input_type))
if isinstance(stim, CompoundStim):
return stim.has_types(mandatory) or (
not mandatory and stim.has_types(optional, False))
if len(mandatory) > 1:
msg = "Transformer of class %s requires multiple mandatory " + \
"inputs, so the passed input Stim must be a CompoundStim" + \
"--which it isn't." % self.__class__.__name__
raise ValueError(msg)
return isinstance(stim, mandatory) or (not mandatory
and isinstance(stim, optional))
def _transform(self, stim, *args, **kwargs):
stims = listify(stim)
if all(self._stim_matches_input_types(s) for s in stims):
result = super() \
._transform(stims, *args, **kwargs)
if isiterable(stim):
return result
else:
return result[0]
else:
return list(super()._iterate(stims, *args, **kwargs))
def has_types(self, types, all_=True):
''' Check whether the current component list matches all Stim types
in the types argument.
Args:
types (Stim, list): a Stim class or iterable of Stim classes.
all_ (bool): if True, all input types must match; if False, at least
one input type must match.
Return:
True if all passed types match at least one Stim in the component
list, otherwise False.
'''
func = all if all_ else any
return func([self.get_stim(t) for t in listify(types)])
def run_node(self, node, stim):
if isinstance(node, string_types):
node = self.nodes[node]
result = node.transformer.transform(stim)
if isinstance(node.transformer, Extractor):
return listify(result)
stim = result
# If result is a generator, the first child will destroy the
# iterable, so cache via list conversion
if len(node.children) > 1 and isgenerator(stim):
stim = list(stim)
return list(chain(*[self.run_node(c, stim) for c in node.children]))
def has_types(self, types, all_=True):
''' Check whether the current component list matches all Stim types
in the types argument.
Args:
types (Stim, list): a Stim class or iterable of Stim classes.
all_ (bool): if True, all input types must match; if False, at
least one input type must match.
Returns:
True if all passed types match at least one Stim in the component
list, otherwise False.
'''
func = all if all_ else any
return func([self.get_stim(t) for t in listify(types)])
def _postprocess(self, stims, preds, tok, wds, ons, dur):
data = preds[0].numpy().squeeze()
if self.return_softmax:
data = scipy.special.softmax(data)
data = [listify(d) for d in data.tolist()]
tok = [' '.join(wds)]
try:
dur = ons[-1] + dur[-1] - ons[0]
except:
dur = None
ons = ons[0]
feat = ['sent_pos', 'sent_neg']
if self.return_input:
data += tok
feat += ['sequence']
return data, feat, ons, dur
def _extract(self, stim):
values = self._get_values(stim)
values = values.T
feature_names = listify(self.get_feature_names())
n_frames = len(values)
onsets = librosa.frames_to_time(range(n_frames),
sr=stim.sampling_rate,
hop_length=self.hop_length)
onsets = onsets + stim.onset if stim.onset else onsets
durations = [self.hop_length / float(stim.sampling_rate)] * n_frames
return ExtractorResult(values,
stim,
self,
features=feature_names,
onsets=onsets,
durations=durations)
def __init__(self,
pretrained_model='bert-base-uncased',
tokenizer='bert-base-uncased',
framework='pt',
mask='MASK',
top_n=None,
threshold=None,
target=None,
return_softmax=False,
return_masked_word=False,
return_input=False,
model_kwargs=None,
tokenizer_kwargs=None):
if any([top_n and target, top_n and threshold, threshold and target]):
raise ValueError('top_n, threshold and target arguments '
'are mutually exclusive')
if type(mask) not in [int, str]:
raise ValueError('Mask must be a string or an integer.')
super(BertLMExtractor,
self).__init__(pretrained_model=pretrained_model,
tokenizer=tokenizer,
framework=framework,
return_input=return_input,
model_class='AutoModelWithLMHead',
model_kwargs=model_kwargs,
tokenizer_kwargs=tokenizer_kwargs)
self.target = listify(target)
if self.target:
missing = set(self.target) - set(self.tokenizer.vocab.keys())
if missing:
logging.warning(f'{missing} not in vocabulary. Dropping.')
present = set(self.target) & set(self.tokenizer.vocab.keys())
self.target = list(present)
if self.target == []:
raise ValueError(
'No valid target token. Import transformers'
' and run transformers.BertTokenizer.from_pretrained'
f'(\'{tokenizer}\').vocab.keys() to see available tokens')
self.mask = mask
self.top_n = top_n
self.threshold = threshold
self.return_softmax = return_softmax
self.return_masked_word = return_masked_word
def run_node(self, node, stim):
''' Executes the Transformer at a specific node.
Args:
node (str, Node): If a string, the name of the Node in the current
Graph. Otherwise the Node instance to execute.
stim (str, stim, list): Any valid input to the Transformer stored
at the target node.
'''
if isinstance(node, string_types):
node = self.nodes[node]
result = node.transformer.transform(stim)
if node.is_leaf():
return listify(result)
stim = result
# If result is a generator, the first child will destroy the
# iterable, so cache via list conversion
if len(node.children) > 1 and isgenerator(stim):
stim = list(stim)
return list(chain(*[self.run_node(c, stim) for c in node.children]))
def run_node(self, node, stim):
''' Executes the Transformer at a specific node.
Args:
node (str, Node): If a string, the name of the Node in the current
Graph. Otherwise the Node instance to execute.
stim (str, stim, list): Any valid input to the Transformer stored
at the target node.
'''
if isinstance(node, string_types):
node = self.nodes[node]
result = node.transformer.transform(stim)
if node.is_leaf():
return listify(result)
stim = result
# If result is a generator, the first child will destroy the
# iterable, so cache via list conversion
if len(node.children) > 1 and isgenerator(stim):
stim = list(stim)
return list(chain(*[self.run_node(c, stim) for c in node.children]))
def _extract(self, stim):
values = self._get_values(stim)
if self._feature=='beat_track':
beats=np.array(values[1])
values=beats
values = values.T
n_frames = len(values)
feature_names = listify(self.get_feature_names())
onsets = librosa.frames_to_time(range(n_frames),
sr=stim.sampling_rate,
hop_length=self.hop_length)
onsets = onsets + stim.onset if stim.onset else onsets
durations = [self.hop_length / float(stim.sampling_rate)] * n_frames
return ExtractorResult(values, stim, self, features=feature_names,
onsets=onsets, durations=durations,
orders=list(range(n_frames)))
def _extract(self, stim):
values = self.func(stim.data)
feature_names = listify(self.get_feature_names())
return ExtractorResult(values, stim, self, features=feature_names)
def env_keys(self):
return listify(self._env_keys)
def _to_df(self, result):
cols = listify(self._feature)
return pd.DataFrame([[r] for r in result._data], columns=cols)
def get_feature_names(self, out):
if self.features:
return listify(self.features)
else:
return ['feature_' + str(i) for i in range(out.shape[-1])]
def _to_df(self, result):
cols = listify(self._feature)
return pd.DataFrame([[r] for r in result._data], columns=cols)
def _extract(self, stim):
inp = self._preprocess(stim)
out = self.model(inp)
out = self._postprocess(out)
features = self.get_feature_names(out)
return ExtractorResult(listify(out), stim, self, features=features)
