class EpochAveraging(Block):
family = 'PreProcessing'
name = 'EpochAveraging'
def __init__(self):
self.epochs = BlockInput(
name='Epochs',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.EPOCHS
)
self.epochs_output = BlockOutput(
name='Epochs',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.EPOCHS
)
def input_params(self,data):
self.epochs.set_value(data['Epochs'])
def execute(self):
avgepoch = self.epochs.value.average()
self.epochs_output.set_value(avgepoch)
return None
class Subtraction(Block):
family = 'AddSub'
name = 'Subtraction'
def __init__(self):
self.num1 = BlockInput(name='num1',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER)
self.num2 = BlockInput(name='num2',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER)
self.output = BlockOutput(name='output',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER)
def input_params(self, data):
self.num1.set_value(data['num1'])
self.num2.set_value(data['num2'])
def execute(self):
value = self.num1.value - self.num2.value
self.output.set_value(value)
return (value, 'STRING')
class OfflineDataProvider(Block):
family = 'DataProvider'
name = 'OfflineDataProvider'
def __init__(self):
self.eeg_data = BlockParameter(
name='EEG File',
attribute_type=ParameterType.FILE,
defaultvalue='',
description='Select only the ".eeg" file, but folder must contain ".vhdr" and ".vmrk" files'
)
self.eeg_data_output = BlockOutput(
name='EEGData',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.EEGDATA
)
def input_params(self,data):
path = data['EEG File'].split('/')
path = Block.FILE_BASE_PATH + '/' + '/'.join(path[1:])
vhdr_path = '.'.join(path.split('.')[:-1]) + '.vhdr'
raw = mne.io.read_raw_brainvision(vhdr_path)
self.eeg_data.set_value(raw)
def execute(self):
value = self.eeg_data.value
value.load_data()
self.eeg_data_output.set_value(value)
return (value.get_data().shape,'STRING')
class Constant(Block):
family = 'Constant'
name = 'Constant'
def __init__(self):
self.num = BlockParameter(
name='constant value',
attribute_type=ParameterType.NUMBER,
defaultvalue=10
# defaultvalue=''
)
self.output = BlockOutput(
name='output',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER
)
def input_params(self,data):
self.num.set_value(int(data['constant value']))
def execute(self):
value = self.num.value
self.output.set_value(value)
return (value,'STRING')
class WaveletTransform(Block):
family = 'FeatureExtraction'
name = 'WaveletTransform'
def __init__(self):
self.epochs = BlockInput(name='Epochs',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.EPOCHS)
self.feature_vector = BlockOutput(
name='FeatureVector',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.FEATUREVECTOR)
def input_params(self, data):
self.epochs.set_value(data['Epochs'])
def execute(self):
feature_list = []
epochs = self.epochs.value
event_ids = epochs.event_id
event_id_class_mp = self.event_id_to_class(event_ids)
for event_name, event_id in event_ids.items():
event_epochs = epochs[event_name].get_data()
for epoch in event_epochs:
# feature_vector = self.extractFeatures(epoch,event_id_class_mp[event_id])
feature_vector = self.extractFeatures(epoch, event_id)
feature_list.append(feature_vector)
self.feature_vector.set_value(feature_list)
stdout_string = '<br>Total datapoints: {} <br> No. of Features: {}'.format(
len(feature_list), feature_list[0].features.shape)
return (stdout_string, 'STRING')
def event_id_to_class(self, event_ids):
event_id_class_mp = {}
i = 0
for event_name, event_id in event_ids.items():
if (event_id not in event_id_class_mp.keys()):
event_id_class_mp[event_id] = i
i += 1
return event_id_class_mp
def extractFeatures(self, epoch, event_id):
features = np.array([])
for channel_data in epoch:
coff_approx, coff_detail = pywt.dwt(channel_data, 'db1')
features = np.hstack([features, coff_approx])
norm = np.linalg.norm(features)
feature_vector = FeatureVector(features / norm, event_id)
return feature_vector
class FeatureLabeling(Block):
family = 'FeatureExtraction'
name = 'FeatureLabeling'
def __init__(self):
self.feature_vector = BlockInput(name='FeatureVector',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.EPOCHS)
self.labels = BlockParameter(
name='Labels',
attribute_type=ParameterType.STRING_ARRAY,
defaultvalue='',
description=
'All comma separated event ids are considered as one class.<br>Event id will not be considered if not added'
)
self.feature_vector_out = BlockOutput(
name='FeatureVector',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.FEATUREVECTOR)
def input_params(self, data):
self.feature_vector.set_value(data['FeatureVector'])
self.labels.set_value(data['Labels'])
def execute(self):
'''
Here every comma separated event ids are assigned same class.
For exmaple if the block parameter is:
- [ '2,4', '3', '5,6' ]
- So classes are assigned like:
- event id 2 and 4 are assigned class 0
- event id 3 is assigned class 1
- event id 5 and 5 are assigned class 2
'''
event_class_mp = self.event_class_mapping()
features = []
for feature in self.feature_vector.value:
class_id = feature.class_id
if (class_id in event_class_mp.keys()):
feature.set_class(event_class_mp[class_id])
features.append(feature)
self.feature_vector_out.set_value(features)
return (event_class_mp, 'STRING')
def event_class_mapping(self):
mapping = {}
class_i = 0
for label in self.labels.value:
event_ids = [int(x) for x in label.split(',')]
for event_id in event_ids:
mapping[event_id] = class_i
class_i += 1
return mapping
class NeuralNetworkLayer(Block):
family = 'Classification'
name = 'NeuralNetworkLayer'
def __init__(self):
self.model = BlockInput(name='Model',
min_cardinality=0,
max_cardinality=1,
attribute_type=ParameterType.MODEL)
self.units = BlockParameter(name='Number of Units',
attribute_type=ParameterType.NUMBER,
defaultvalue='',
description='Must be an Integer')
self.activation = BlockParameter(
name='Activation Function',
attribute_type=ParameterType.STRING,
defaultvalue='relu',
description=
"Either, 'sigmoid', 'relu', 'softmax', 'elu', 'leaky-relu', 'selu' or 'gelu'"
)
self.dropout = BlockParameter(
name='Dropout',
attribute_type=ParameterType.STRING,
defaultvalue='0',
description="Fraction of the input units to drop")
self.model_out = BlockOutput(name='Model',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.MODEL)
def input_params(self, data):
act_func = [
'sigmoid', 'relu', 'softmax', 'elu', 'leaky-relu', 'selu', 'gelu'
]
if ('Model' not in data.keys()):
self.model.set_value(None)
else:
self.model.set_value(data['Model'])
self.units.set_value(int(data['Number of Units']))
self.activation.set_value(data['Activation Function'])
self.dropout.set_value(float(data['Dropout']))
def execute(self):
if (self.model.value == None):
model = Sequential()
else:
model = self.model.value
model.add(Dense(self.units.value, activation=self.activation.value))
model.add(Dropout(self.dropout.value))
self.model_out.set_value(model)
return None
class Filter(Block):
family = 'PreProcessing'
name = 'Filter'
def __init__(self):
self.eeg_data = BlockInput(name='EEGData',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.EEGDATA)
self.low_cutoff_freq = BlockParameter(
name='Low Cutoff Frequency',
attribute_type=ParameterType.NUMBER,
defaultvalue='None',
description='If None the data are only low-passed')
self.high_cutoff_freq = BlockParameter(
name='High Cutoff Frequency',
attribute_type=ParameterType.NUMBER,
defaultvalue='None',
description='If None the data are only high-passed')
self.eeg_data_output = BlockOutput(
name='EEGData',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.EEGDATA)
def input_params(self, data):
self.eeg_data.set_value(data['EEGData'])
if (data['Low Cutoff Frequency'] == 'None'):
self.low_cutoff_freq.set_value(None)
else:
self.low_cutoff_freq.set_value(float(data['Low Cutoff Frequency']))
if (data['High Cutoff Frequency'] == 'None'):
self.high_cutoff_freq.set_value(None)
else:
self.high_cutoff_freq.set_value(
float(data['High Cutoff Frequency']))
def execute(self):
raw = self.eeg_data.value
raw.filter(self.low_cutoff_freq.value,
self.high_cutoff_freq.value,
fir_design='firwin')
self.eeg_data_output.set_value(raw)
return None
class ChannelSelection(Block):
family = 'PreProcessing'
name = 'ChannelSelection'
def __init__(self):
self.eeg_data = BlockInput(
name='EEGData',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.EEGDATA
)
self.channels = BlockParameter(
name='Channels',
attribute_type=ParameterType.STRING_ARRAY,
defaultvalue='',
description='Select channel'
)
self.eeg_data_output = BlockOutput(
name='EEGData',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.EEGDATA
)
def input_params(self,data):
self.channels.set_value(data['Channels'])
self.eeg_data.set_value(data['EEGData'])
def execute(self):
value = self.eeg_data.value
value = value.pick_channels(self.channels.value)
self.eeg_data_output.set_value(value)
return (value.get_data().shape,'STRING')
class SaveModel(Block):
family = 'Classification'
name = 'SaveModel'
def __init__(self):
self.model = BlockInput(name='Model',
min_cardinality=0,
max_cardinality=1,
attribute_type=ParameterType.MODEL)
self.model_out = BlockOutput(name='Model',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.MODEL)
def input_params(self, data):
if ('Model' not in data.keys()):
self.model.set_value(None)
else:
self.model.set_value(data['Model'])
def execute(self):
self.model_out.set_value(self.model.value)
return (self.model_out.value, 'MODEL')
class Multiplication(Block):
family = 'MultiDiv'
name = 'Multiplication'
def __init__(self):
self.num1 = BlockInput(
name='num1',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER
)
self.num2 = BlockInput(
name='num2',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER
)
self.output = BlockOutput(
name='output',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.NUMBER
)
def input_params(self,data):
# time.sleep(10)
# list(2)
self.num1.set_value(data['num1'])
self.num2.set_value(data['num2'])
def execute(self):
value = self.num1.value * self.num2.value
self.output.set_value(value)
return (value,'STRING')
class EpochExtraction(Block):
family = 'PreProcessing'
name = 'EpochExtraction'
def __init__(self):
self.eeg_data = BlockInput(name='EEGData',
min_cardinality=1,
max_cardinality=1,
attribute_type=ParameterType.EEGDATA)
self.pre_stimulus_onset = BlockParameter(
name='PreStimulus onset',
attribute_type=ParameterType.NUMBER,
defaultvalue='-0.2',
description='')
self.post_stimulus_onset = BlockParameter(
name='PostStimulus onset',
attribute_type=ParameterType.NUMBER,
defaultvalue='0.5',
description='')
self.baseline_start_time = BlockParameter(
name='Baseline Correction Start Time',
attribute_type=ParameterType.STRING,
defaultvalue='None',
description='None means beginning of the data')
self.baseline_end_time = BlockParameter(
name='Baseline Correction End Time',
attribute_type=ParameterType.STRING,
defaultvalue='0',
description='None means end of the data')
self.event_id = BlockParameter(name='Event Id',
attribute_type=ParameterType.STRING,
defaultvalue='None',
description='None means all the events')
self.eeg_data_output = BlockOutput(name='Epochs',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.EPOCHS)
def input_params(self, data):
self.eeg_data.set_value(data['EEGData'])
self.pre_stimulus_onset.set_value(float(data['PreStimulus onset']))
self.post_stimulus_onset.set_value(float(data['PostStimulus onset']))
if (data['Baseline Correction Start Time'] == 'None'):
self.baseline_start_time.set_value(None)
else:
self.baseline_start_time.set_value(
float(data['Baseline Correction Start Time']))
if (data['Baseline Correction End Time'] == 'None'):
self.baseline_end_time.set_value(None)
else:
self.baseline_end_time.set_value(
float(data['Baseline Correction End Time']))
if (data['Event Id'] == 'None'):
self.event_id.set_value(None)
else:
self.event_id.set_value(int(data['Event Id']))
def execute(self):
raw = self.eeg_data.value
events, event_id = mne.events_from_annotations(raw)
# https://mne.tools/stable/generated/mne.Epochs.html
epochs = mne.Epochs(raw,
events,
event_id=self.event_id.value,
tmin=self.pre_stimulus_onset.value,
tmax=self.post_stimulus_onset.value,
baseline=(self.baseline_start_time.value,
self.baseline_end_time.value),
preload=True)
self.eeg_data_output.set_value(epochs)
return (epochs.get_data().shape, 'STRING')
class NeuralNetworkClassifier(Block):
family = 'Classification'
name = 'NeuralNetworkClassifier'
def __init__(self):
self.model = BlockInput(name='Model',
min_cardinality=0,
max_cardinality=1,
attribute_type=ParameterType.MODEL)
self.feature_vector = BlockInput(
name='FeatureVector',
min_cardinality=0,
max_cardinality=1,
attribute_type=ParameterType.FEATUREVECTOR)
self.optimizer = BlockParameter(
name='Optimizer',
attribute_type=ParameterType.STRING,
defaultvalue='adam',
description="Either, 'adam', 'adagrad', 'rmsprop'")
self.test_size = BlockParameter(
name='Test Size',
attribute_type=ParameterType.NUMBER,
defaultvalue='0.33',
description="Test Train Split. Ratio of test size")
self.epochs = BlockParameter(name='Number of Epochs',
attribute_type=ParameterType.NUMBER,
defaultvalue='100',
description="")
self.classes = BlockParameter(
name='Number of Classes',
attribute_type=ParameterType.NUMBER,
defaultvalue='',
description="Number of Classification classes")
self.model_out = BlockOutput(name='Model',
min_cardinality=1,
max_cardinality=100,
attribute_type=ParameterType.MODEL)
def input_params(self, data):
self.model.set_value(data['Model'])
self.feature_vector.set_value(data['FeatureVector'])
self.optimizer.set_value(data['Optimizer'])
self.test_size.set_value(float(data['Test Size']))
self.epochs.set_value(int(data['Number of Epochs']))
self.classes.set_value(int(data['Number of Classes']))
def execute(self):
model = self.model.value
model.compile(loss='categorical_crossentropy',
optimizer=self.optimizer.value,
metrics=['accuracy'])
X = []
Y = []
for datapoint in self.feature_vector.value:
X.append(datapoint.features)
Y.append(datapoint.class_id)
X_train, X_test, y_train, y_test = train_test_split(
np.array(X),
np.array(Y),
test_size=self.test_size.value,
random_state=42)
number_of_training_sample = X_train.shape
print(number_of_training_sample)
print(X_test.shape)
print(set(y_train))
print(set(y_test))
y_train = keras.utils.to_categorical(y_train, self.classes.value)
y_test = keras.utils.to_categorical(y_test, self.classes.value)
# X_train = X_test = np.array(X)
# y_test = y_train = keras.utils.to_categorical(np.array(Y),self.classes.value)
history = model.fit(X_train,
y_train,
epochs=self.epochs.value,
validation_data=(X_test, y_test))
self.model_out.set_value(model)
validation_acc = history.history['val_accuracy'][-1]
training_acc = history.history['accuracy'][-1]
stdout = "<br>Training Accuracy: {}<br>Validation Accuracy: {}<br>No. of Training Samples: {}".format(
training_acc, validation_acc, number_of_training_sample[0])
return (stdout, 'STRING')