def propagateOneStep(self, inputData, outputData, step, transientTime=0, verbose=0, steps="auto", learn=False):
if (verbose > 0):
bar = progressbar.ProgressBar(max_value=inputLength, redirect_stdout=True, poll_interval=0.0001)
bar.update(0)
x = self._x
#updates states
u, x = self.update(inputData=inputData, x=x)
self._x = x
self._X = B.vstack((B.array(self._outputBias), self._outputInputScaling*u, x))
# calculate output
#estimatedData = self.out_activation(B.dot(self._WOut, self._X).T)
#y_step = estimatedData
Y = B.dot(self._WOut, self._X)
if(learn):
#learning rate
rate = 0.1
#calculate target activation
y_target = self.out_inverse_activation(outputData).T
#solve for Wout by using expected_output and states
wout = B.dot(y_target.reshape(self.n_output,1), B.pinv(self._X)) #.reshape(self.n_output,1)
self._WOut = rate*wout + (1-rate)*self._WOut
if (verbose > 0):
bar.update(t)
if (verbose > 0):
bar.finish()
return self._X, Y
def _fitProcess(self, data):
try:
inData, outData, indices, state = data
transientTime = self.sharedNamespace.transientTime
partialLength = self.sharedNamespace.partialLength
totalLength = self.sharedNamespace.totalLength
timeseriesCount = self.sharedNamespace.timeseriesCount
workerID = self.parallelWorkerIDs.get()
self._x[workerID] = state
# propagate
X = B.empty((1 + self.n_input + self.n_reservoir, totalLength))
for i in range(timeseriesCount):
X[:, i * partialLength:(i + 1) * partialLength] = self.propagate(inData[i], transientTime=transientTime,
x=self._x[workerID], verbose=0)
# define the target values
Y_target = B.empty((1, totalLength))
for i in range(timeseriesCount):
Y_target[:, i * partialLength:(i + 1) * partialLength] = self.out_inverse_activation(outData[i]).T[:,
transientTime:]
# now fit
WOut = None
if self._solver == "pinv":
WOut = B.dot(Y_target, B.pinv(X))
elif self._solver == "lsqr":
X_T = X.T
WOut = B.dot(B.dot(Y_target, X_T), B.inv(
B.dot(X, X_T) + self._regressionParameters[0] * B.identity(1 + self.n_input + self.n_reservoir)))
# calculate the training prediction now
# trainingPrediction = self.out_activation(B.dot(WOut, X).T)
# store the state and the output matrix of the worker
SpatioTemporalESN._fitProcess.fitQueue.put(
([x - self._filterWidth for x in indices], self._x[workerID].copy(), WOut.copy()))
self.parallelWorkerIDs.put(workerID)
except Exception as ex:
print(ex)
import traceback
traceback.print_exc()
SpatioTemporalESN._fitProcess.fitQueue.put(([x - self._filterWidth for x in indices], None, None))
self.parallelWorkerIDs.put(workerID)
def fit(self,
inputData,
outputData,
transientTime="AutoReduce",
transientTimeCalculationEpsilon=1e-3,
transientTimeCalculationLength=20,
verbose=0):
#check the input data
if self.n_input != 0:
if len(inputData.shape) == 3 and len(outputData.shape) > 1:
#multiple time series are used with a shape (timeseries, time, dimension) -> (timeseries, time, dimension)
if inputData.shape[0] != outputData.shape[0]:
raise ValueError(
"Amount of input and output datasets is not equal - {0} != {1}"
.format(inputData.shape[0], outputData.shape[0]))
if inputData.shape[1] != outputData.shape[1]:
raise ValueError(
"Amount of input and output time steps is not equal - {0} != {1}"
.format(inputData.shape[1], outputData.shape[1]))
else:
if inputData.shape[0] != outputData.shape[0]:
raise ValueError(
"Amount of input and output time steps is not equal - {0} != {1}"
.format(inputData.shape[0], outputData.shape[0]))
else:
if inputData is not None:
raise ValueError(
"n_input has been set to zero. Therefore, the given inputData will not be used."
)
if inputData is not None:
inputData = B.array(inputData)
if outputData is not None:
outputData = B.array(outputData)
#reshape the input/output data to have the shape (timeseries, time, dimension)
if len(outputData.shape) <= 2:
outputData = outputData.reshape((1, -1, self.n_output))
if inputData is not None:
if len(inputData.shape) <= 2:
inputData = inputData.reshape((1, -1, self.n_input))
self.resetState()
# Automatic transient time calculations
if transientTime == "Auto":
transientTime = self.calculateTransientTime(
inputData[0], outputData[0], transientTimeCalculationEpsilon,
transientTimeCalculationLength)
if transientTime == "AutoReduce":
if (inputData is None
and outputData.shape[2] == 1) or inputData.shape[2] == 1:
transientTime = self.calculateTransientTime(
inputData[0], outputData[0],
transientTimeCalculationEpsilon,
transientTimeCalculationLength)
transientTime = self.reduceTransientTime(
inputData[0], outputData[0], transientTime)
else:
print(
"Transient time reduction is supported only for 1 dimensional input."
)
if inputData is not None:
partialLength = (inputData.shape[1] - transientTime)
totalLength = inputData.shape[0] * partialLength
timeseriesCount = inputData.shape[0]
elif outputData is not None:
partialLength = (outputData.shape[1] - transientTime)
totalLength = outputData.shape[0] * partialLength
timeseriesCount = outputData.shape[0]
else:
raise ValueError("Either input or output data must not to be None")
self._X = B.empty((1 + self.n_input + self.n_reservoir, totalLength))
if (verbose > 0):
bar = progressbar.ProgressBar(max_value=totalLength,
redirect_stdout=True,
poll_interval=0.0001)
bar.update(0)
for i in range(timeseriesCount):
if inputData is not None:
xx, yy = self.propagate(inputData[i], outputData[i],
transientTime, verbose - 1)
self._X[:, i * partialLength:(i + 1) * partialLength] = xx
else:
xx, yy = self.propagate(None, outputData[i], transientTime,
verbose - 1)
self._X[:, i * partialLength:(i + 1) * partialLength] = xx
if (verbose > 0):
bar.update(i)
if (verbose > 0):
bar.finish()
#define the target values
Y_target = B.empty((outputData.shape[2], totalLength))
for i in range(timeseriesCount):
Y_target[:, i * partialLength:(i + 1) *
partialLength] = self.out_inverse_activation(
outputData[i]).T[:, transientTime:]
if (self._solver == "pinv"):
self._WOut = B.dot(Y_target, B.pinv(self._X))
#calculate the training prediction now
train_prediction = self.out_activation((B.dot(self._WOut,
self._X)).T)
# elif (self._solver == "lsqr"):
# X_T = self._X.T
# self._WOut = B.dot(B.dot(Y_target, X_T),B.inv(B.dot(self._X,X_T) + self._regressionParameters[0]*B.identity(1+self.n_input+self.n_reservoir)))
# """
# #alternative representation of the equation
# Xt = X.T
# A = np.dot(X, Y_target.T)
# B = np.linalg.inv(np.dot(X, Xt) + regression_parameter*np.identity(1+self.n_input+self.n_reservoir))
# self._WOut = np.dot(B, A)
# self._WOut = self._WOut.T
# """
# #calculate the training prediction now
# train_prediction = self.out_activation(B.dot(self._WOut, self._X).T)
elif (self._solver in [
"sklearn_auto", "sklearn_lsqr", "sklearn_sag", "sklearn_svd"
]):
mode = self._solver[8:]
params = self._regressionParameters
params["solver"] = mode
self._ridgeSolver = Ridge(**params)
self._ridgeSolver.fit(self._X.T, Y_target.T)
#calculate the training prediction now
train_prediction = self.out_activation(
self._ridgeSolver.predict(self._X.T))
elif (self._solver in ["sklearn_svr", "sklearn_svc"]):
self._ridgeSolver = SVR(**self._regressionParameters)
self._ridgeSolver.fit(self._X.T, Y_target.T.ravel())
#calculate the training prediction now
train_prediction = self.out_activation(
self._ridgeSolver.predict(self._X.T))
#calculate the training error now
#flatten the outputData
outputData = outputData[:, transientTime:, :].reshape(totalLength, -1)
training_error = B.sqrt(B.mean((train_prediction - outputData)**2))
return training_error
def fit(
self,
inputData,
outputData,
transientTime="AutoReduce",
transientTimeCalculationEpsilon=1e-3,
transientTimeCalculationLength=20,
verbose=0,
):
# check the input data
if inputData.shape[0] != outputData.shape[0]:
raise ValueError(
"Amount of input and output datasets is not equal - {0} != {1}"
.format(inputData.shape[0], outputData.shape[0]))
nSequences = inputData.shape[0]
trainingLength = inputData.shape[1]
self._x = B.zeros((self.n_reservoir, 1))
# Automatic transient time calculations
if transientTime == "Auto":
transientTime = self.calculateTransientTime(
inputData,
outputData,
transientTimeCalculationEpsilon,
transientTimeCalculationLength,
)
if transientTime == "AutoReduce":
if (inputData is None
and outputData.shape[1] == 1) or inputData.shape[1] == 1:
transientTime = self.calculateTransientTime(
inputData,
outputData,
transientTimeCalculationEpsilon,
transientTimeCalculationLength,
)
transientTime = self.reduceTransientTime(
inputData, outputData, transientTime)
else:
print(
"Transient time reduction is supported only for 1 dimensional input."
)
self._X = B.zeros((
1 + self.n_input + self.n_reservoir,
nSequences * (trainingLength - transientTime),
))
Y_target = B.zeros(
(self.n_output, (trainingLength - transientTime) * nSequences))
if verbose > 0:
bar = progressbar.ProgressBar(max_value=len(inputData),
redirect_stdout=True,
poll_interval=0.0001)
bar.update(0)
for n in range(len(inputData)):
self._x = B.zeros((self.n_reservoir, 1))
self._X[:, n * (trainingLength - transientTime):(n + 1) *
(trainingLength - transientTime), ] = self.propagate(
inputData[n], transientTime=transientTime, verbose=0)
# set the target values
Y_target[:, n * (trainingLength - transientTime):(n + 1) *
(trainingLength - transientTime), ] = np.tile(
self.out_inverse_activation(outputData[n]),
trainingLength - transientTime,
).T
if verbose > 0:
bar.update(n)
if verbose > 0:
bar.finish()
if self._solver == "pinv":
self._WOut = B.dot(Y_target, B.pinv(self._X))
# calculate the training prediction now
train_prediction = self.out_activation((B.dot(self._WOut,
self._X)).T)
elif self._solver == "lsqr":
X_T = self._X.T
self._WOut = B.dot(
B.dot(Y_target, X_T),
B.inv(
B.dot(self._X, X_T) + self._regressionParameters[0] *
B.identity(1 + self.n_input + self.n_reservoir)),
)
"""
#alternative represantation of the equation
Xt = X.T
A = np.dot(X, Y_target.T)
B = np.linalg.inv(np.dot(X, Xt) + regression_parameter*np.identity(1+self.n_input+self.n_reservoir))
self._WOut = np.dot(B, A)
self._WOut = self._WOut.T
"""
# calculate the training prediction now
train_prediction = self.out_activation(
B.dot(self._WOut, self._X).T)
elif self._solver in [
"sklearn_auto",
"sklearn_lsqr",
"sklearn_sag",
"sklearn_svd",
]:
mode = self._solver[8:]
params = self._regressionParameters
params["solver"] = mode
self._ridgeSolver = Ridge(**params)
self._ridgeSolver.fit(self._X.T, Y_target.T)
# calculate the training prediction now
train_prediction = self.out_activation(
self._ridgeSolver.predict(self._X.T))
elif self._solver in ["sklearn_svr", "sklearn_svc"]:
self._ridgeSolver = SVR(**self._regressionParameters)
self._ridgeSolver.fit(self._X.T, Y_target.T.flatten())
# calculate the training prediction now
train_prediction = self.out_activation(
self._ridgeSolver.predict(self._X.T))
train_prediction = np.mean(train_prediction, 0)
# calculate the training error now
training_error = B.sqrt(B.mean((train_prediction - outputData.T)**2))
return training_error
def fit(self,
inputData,
outputData1,
outputData2,
transientTime="AutoReduce",
transientTimeCalculationEpsilon=1e-3,
transientTimeCalculationLength=20,
verbose=0):
#check the input data
if self.n_input != 0:
if len(inputData.shape) == 3 and len(outputData1.shape) > 1:
#multiple time series are used with a shape (timeseries, time, dimension) -> (timeseries, time, dimension)
if inputData.shape[0] != outputData1.shape[0]:
raise ValueError(
"Amount of input and output datasets is not equal - {0} != {1}"
.format(inputData.shape[0], outputData1.shape[0]))
if inputData.shape[1] != outputData1.shape[1]:
raise ValueError(
"Amount of input and output time steps is not equal - {0} != {1}"
.format(inputData.shape[1], outputData1.shape[1]))
else:
if inputData.shape[0] != outputData1.shape[0]:
raise ValueError(
"Amount of input and output time steps is not equal - {0} != {1}"
.format(inputData.shape[0], outputData1.shape[0]))
else:
if inputData is not None:
raise ValueError(
"n_input has been set to zero. Therefore, the given inputData will not be used."
)
inputData = B.array(inputData)
outputData1 = B.array(outputData1)
outputData2 = B.array(outputData2)
self._transientTime = transientTime
self._esn1.resetState()
self._esn2.resetState()
total_length = inputData.shape[0]
print("total_length ", total_length)
aggregated_y1 = B.empty((outputData1.shape))
aggregated_y2 = B.empty((outputData2.shape))
#put pixels and switch data together
inputDataWithFeedback = B.zeros(
(total_length, self.n_input + self._n_output2))
inputDataWithFeedback[:, :self.n_input] = inputData
inputDataWithFeedback[:, self.n_input:] = outputData2
X1, _ = self._esn1.propagate(inputData=inputDataWithFeedback,
outputData=outputData1,
transientTime=transientTime,
verbose=verbose - 1)
self._esn1._X = X1
Y_target = self.out_inverse_activation(outputData1).T
self._esn1._WOut = B.dot(Y_target, B.pinv(X1))
aggregated_y1 = self.out_activation((B.dot(self._esn1._WOut, X1)).T)
training_error1 = B.sqrt(
B.mean((aggregated_y1.reshape(
(total_length, self._n_output1)) - outputData1)**2))
training_error2 = 0
training_error1 = B.sqrt(B.mean((aggregated_y1 - outputData1)**2))
training_error2 = B.sqrt(B.mean((aggregated_y2 - outputData2)**2))
return training_error1, training_error2