From 77d85c179cccf3e31187e5679d862c8c069382ed Mon Sep 17 00:00:00 2001 From: Morten Hjorth-Jensen Date: Thu, 9 Nov 2023 17:52:38 +0100 Subject: [PATCH] minor update --- .../__pycache__/__init__.cpython-39.pyc | Bin 0 -> 155 bytes .../_build/html/reports/chapter1.err.log | 90 ++++++ .../_build/html/reports/chapter1.log | 71 +++++ .../_build/html/reports/chapter10.err.log | 112 +++++++ .../_build/html/reports/chapter10.log | 30 ++ .../_build/html/reports/chapter11.err.log | 214 +++++++++++++ .../_build/html/reports/chapter11.log | 39 +++ .../_build/html/reports/chapter12.err.log | 87 ++++++ .../_build/html/reports/chapter12.log | 39 +++ .../_build/html/reports/chapter13.err.log | 138 +++++++++ .../_build/html/reports/chapter13.log | 39 +++ .../_build/html/reports/chapter2.err.log | 44 +++ .../_build/html/reports/chapter2.log | 290 ++++++++++++++++++ .../_build/html/reports/chapter3.err.log | 96 ++++++ .../_build/html/reports/chapter3.log | 30 ++ .../_build/html/reports/chapter4.err.log | 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a/doc/LectureNotes/_build/html/_static/__pycache__/__init__.cpython-39.pyc b/doc/LectureNotes/_build/html/_static/__pycache__/__init__.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..9ba76c9ec7a71eaf6f100d0f1ac95959bc8bba4c GIT binary patch literal 155 zcmYe~<>g`kg3D^9Ng(<$h(HF6K#l_t7qb9~6oz01O-8?!3`HPe1o6uuCo@UEpt2+* zKhIdtQolH}BvrQ{F*!RiJ+)ZBxF91luOdDvKR-LZBqKF9Rlm3-u_QBDKR!M)FS8^* YUaz3?7Kcr4eoARhsvXGW&p^xo0PQ{{mH+?% literal 0 HcmV?d00001 diff --git a/doc/LectureNotes/_build/html/reports/chapter1.err.log b/doc/LectureNotes/_build/html/reports/chapter1.err.log new file mode 100644 index 000000000..ad4d24e3f --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter1.err.log @@ -0,0 +1,90 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +# Importing various packages +import numpy as np +import matplotlib.pyplot as plt +from sklearn.linear_model import LinearRegression + +x = np.random.rand(100,1) +y = 2*x+np.random.randn(100,1) +linreg = LinearRegression() +linreg.fit(x,y) +# This is our new x-array to which we test our model +xnew = np.array([[0],[1]]) +ypredict = linreg.predict(xnew) + +plt.plot(xnew, ypredict, "r-") +plt.plot(x, y ,'ro') +plt.axis([0,1.0,0, 5.0]) +plt.xlabel(r'$x$') +plt.ylabel(r'$y$') +plt.title(r'Simple Linear Regression') +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 # Importing various packages + 4 import numpy as np + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter1.log b/doc/LectureNotes/_build/html/reports/chapter1.log new file mode 100644 index 000000000..ac23b4426 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter1.log @@ -0,0 +1,71 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# Read the experimental data with Pandas +Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11), + names=('N', 'Z', 'A', 'Element', 'Ebinding'), + widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1), + header=39, + index_col=False) + +# Extrapolated values are indicated by '#' in place of the decimal place, so +# the Ebinding column won't be numeric. Coerce to float and drop these entries. +Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce') +Masses = Masses.dropna() +# Convert from keV to MeV. +Masses['Ebinding'] /= 1000 + +# Group the DataFrame by nucleon number, A. +Masses = Masses.groupby('A') +# Find the rows of the grouped DataFrame with the maximum binding energy. +Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()]) +------------------ + +--------------------------------------------------------------------------- +ValueError Traceback (most recent call last) +Input In [8], in () + 1 # Read the experimental data with Pandas +----> 2 Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11), + 3  names=('N', 'Z', 'A', 'Element', 'Ebinding'), + 4  widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1), + 5  header=39, + 6  index_col=False) + 8 # Extrapolated values are indicated by '#' in place of the decimal place, so + 9 # the Ebinding column won't be numeric. Coerce to float and drop these entries. + 10 Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce') + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/util/_decorators.py:311, in deprecate_nonkeyword_arguments..decorate..wrapper(*args, **kwargs) + 305 if len(args) > num_allow_args: + 306 warnings.warn( + 307 msg.format(arguments=arguments), + 308 FutureWarning, + 309 stacklevel=stacklevel, + 310 ) +--> 311 return func(*args, **kwargs) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/io/parsers/readers.py:871, in read_fwf(filepath_or_buffer, colspecs, widths, infer_nrows, **kwds) + 869 len_index = len(index_col) + 870 if len(names) + len_index != len(colspecs): +--> 871 raise ValueError("Length of colspecs must match length of names") + 873 kwds["colspecs"] = colspecs + 874 kwds["infer_nrows"] = infer_nrows + +ValueError: Length of colspecs must match length of names +ValueError: Length of colspecs must match length of names + diff --git a/doc/LectureNotes/_build/html/reports/chapter10.err.log b/doc/LectureNotes/_build/html/reports/chapter10.err.log new file mode 100644 index 000000000..04a96e97d --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter10.err.log @@ -0,0 +1,112 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +# import necessary packages +import numpy as np +import matplotlib.pyplot as plt +from sklearn import datasets + + +# ensure the same random numbers appear every time +np.random.seed(0) + +# display images in notebook +%matplotlib inline +plt.rcParams['figure.figsize'] = (12,12) + + +# download MNIST dataset +digits = datasets.load_digits() + +# define inputs and labels +inputs = digits.images +labels = digits.target + +print("inputs = (n_inputs, pixel_width, pixel_height) = " + str(inputs.shape)) +print("labels = (n_inputs) = " + str(labels.shape)) + + +# flatten the image +# the value -1 means dimension is inferred from the remaining dimensions: 8x8 = 64 +n_inputs = len(inputs) +inputs = inputs.reshape(n_inputs, -1) +print("X = (n_inputs, n_features) = " + str(inputs.shape)) + + +# choose some random images to display +indices = np.arange(n_inputs) +random_indices = np.random.choice(indices, size=5) + +for i, image in enumerate(digits.images[random_indices]): + plt.subplot(1, 5, i+1) + plt.axis('off') + plt.imshow(image, cmap=plt.cm.gray_r, interpolation='nearest') + plt.title("Label: %d" % digits.target[random_indices[i]]) +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 # import necessary packages + 4 import numpy as np + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter10.log b/doc/LectureNotes/_build/html/reports/chapter10.log new file mode 100644 index 000000000..bd7db9a84 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter10.log @@ -0,0 +1,30 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +conda create -n tf tensorflow +conda activate tf +------------------ + + Input In [12] + conda create -n tf tensorflow + ^ +SyntaxError: invalid syntax + +SyntaxError: invalid syntax (2259440937.py, line 1) + diff --git a/doc/LectureNotes/_build/html/reports/chapter11.err.log b/doc/LectureNotes/_build/html/reports/chapter11.err.log new file mode 100644 index 000000000..04c508ee2 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter11.err.log @@ -0,0 +1,214 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import autograd.numpy as np +from autograd import grad, elementwise_grad +import autograd.numpy.random as npr +from matplotlib import pyplot as plt + +def sigmoid(z): + return 1/(1 + np.exp(-z)) + +# Assuming one input, hidden, and output layer +def neural_network(params, x): + + # Find the weights (including and biases) for the hidden and output layer. + # Assume that params is a list of parameters for each layer. + # The biases are the first element for each array in params, + # and the weights are the remaning elements in each array in params. + + w_hidden = params[0] + w_output = params[1] + + # Assumes input x being an one-dimensional array + num_values = np.size(x) + x = x.reshape(-1, num_values) + + # Assume that the input layer does nothing to the input x + x_input = x + + ## Hidden layer: + + # Add a row of ones to include bias + x_input = np.concatenate((np.ones((1,num_values)), x_input ), axis = 0) + + z_hidden = np.matmul(w_hidden, x_input) + x_hidden = sigmoid(z_hidden) + + ## Output layer: + + # Include bias: + x_hidden = np.concatenate((np.ones((1,num_values)), x_hidden ), axis = 0) + + z_output = np.matmul(w_output, x_hidden) + x_output = z_output + + return x_output + +# The trial solution using the deep neural network: +def g_trial(x,params, g0 = 10): + return g0 + x*neural_network(params,x) + +# The right side of the ODE: +def g(x, g_trial, gamma = 2): + return -gamma*g_trial + +# The cost function: +def cost_function(P, x): + + # Evaluate the trial function with the current parameters P + g_t = g_trial(x,P) + + # Find the derivative w.r.t x of the neural network + d_net_out = elementwise_grad(neural_network,1)(P,x) + + # Find the derivative w.r.t x of the trial function + d_g_t = elementwise_grad(g_trial,0)(x,P) + + # The right side of the ODE + func = g(x, g_t) + + err_sqr = (d_g_t - func)**2 + cost_sum = np.sum(err_sqr) + + return cost_sum / np.size(err_sqr) + +# Solve the exponential decay ODE using neural network with one input, hidden, and output layer +def solve_ode_neural_network(x, num_neurons_hidden, num_iter, lmb): + ## Set up initial weights and biases + + # For the hidden layer + p0 = npr.randn(num_neurons_hidden, 2 ) + + # For the output layer + p1 = npr.randn(1, num_neurons_hidden + 1 ) # +1 since bias is included + + P = [p0, p1] + + print('Initial cost: %g'%cost_function(P, x)) + + ## Start finding the optimal weights using gradient descent + + # Find the Python function that represents the gradient of the cost function + # w.r.t the 0-th input argument -- that is the weights and biases in the hidden and output layer + cost_function_grad = grad(cost_function,0) + + # Let the update be done num_iter times + for i in range(num_iter): + # Evaluate the gradient at the current weights and biases in P. + # The cost_grad consist now of two arrays; + # one for the gradient w.r.t P_hidden and + # one for the gradient w.r.t P_output + cost_grad = cost_function_grad(P, x) + + P[0] = P[0] - lmb * cost_grad[0] + P[1] = P[1] - lmb * cost_grad[1] + + print('Final cost: %g'%cost_function(P, x)) + + return P + +def g_analytic(x, gamma = 2, g0 = 10): + return g0*np.exp(-gamma*x) + +# Solve the given problem +if __name__ == '__main__': + # Set seed such that the weight are initialized + # with same weights and biases for every run. + npr.seed(15) + + ## Decide the vales of arguments to the function to solve + N = 10 + x = np.linspace(0, 1, N) + + ## Set up the initial parameters + num_hidden_neurons = 10 + num_iter = 10000 + lmb = 0.001 + + # Use the network + P = solve_ode_neural_network(x, num_hidden_neurons, num_iter, lmb) + + # Print the deviation from the trial solution and true solution + res = g_trial(x,P) + res_analytical = g_analytic(x) + + print('Max absolute difference: %g'%np.max(np.abs(res - res_analytical))) + + # Plot the results + plt.figure(figsize=(10,10)) + + plt.title('Performance of neural network solving an ODE compared to the analytical solution') + plt.plot(x, res_analytical) + plt.plot(x, res[0,:]) + plt.legend(['analytical','nn']) + plt.xlabel('x') + plt.ylabel('g(x)') + plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import autograd.numpy as np + 4 from autograd import grad, elementwise_grad + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter11.log b/doc/LectureNotes/_build/html/reports/chapter11.log new file mode 100644 index 000000000..fe5b658db --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter11.log @@ -0,0 +1,39 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply + msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async + result = await obj + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg + raise Empty +_queue.Empty + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell + exec_reply = await self.task_poll_for_reply + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply + await self._async_handle_timeout(timeout, cell) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout + raise CellTimeoutError.error_from_timeout_and_cell( +nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds. +The message was: Cell execution timed out. +Here is a preview of the cell contents: +------------------- +['import autograd.numpy as np', 'from autograd import jacobian,hessian,grad', 'import autograd.numpy.random as npr', 'from matplotlib import cm', 'from matplotlib import pyplot as plt'] +... +[' plt.plot(x, res3)', ' plt.plot(x,res_analytical3)', " plt.legend(['dnn','analytical'])", '', ' plt.show()'] +------------------- + diff --git a/doc/LectureNotes/_build/html/reports/chapter12.err.log b/doc/LectureNotes/_build/html/reports/chapter12.err.log new file mode 100644 index 000000000..aad510ff1 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter12.err.log @@ -0,0 +1,87 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import math +from scipy import signal +import matplotlib.pyplot as plt + +# number of points +n = 500 +# start and final times +t0 = 0.0 +tn = 1.0 +# Period +t = np.linspace(t0, tn, n, endpoint=False) +SqrSignal = np.zeros(n) +SqrSignal = 1.0+signal.square(2*np.pi*5*t) +plt.plot(t, SqrSignal) +plt.ylim(-0.5, 2.5) +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import math + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter12.log b/doc/LectureNotes/_build/html/reports/chapter12.log new file mode 100644 index 000000000..49de8aa50 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter12.log @@ -0,0 +1,39 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply + msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async + result = await obj + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg + raise Empty +_queue.Empty + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell + exec_reply = await self.task_poll_for_reply + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply + await self._async_handle_timeout(timeout, cell) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout + raise CellTimeoutError.error_from_timeout_and_cell( +nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds. +The message was: Cell execution timed out. +Here is a preview of the cell contents: +------------------- +['CNN_keras = np.zeros((len(eta_vals), len(lmbd_vals)), dtype=object)', ' ', 'for i, eta in enumerate(eta_vals):', ' for j, lmbd in enumerate(lmbd_vals):', ' CNN = create_convolutional_neural_network_keras(input_shape, receptive_field,'] +... +[' ', ' print("Learning rate = ", eta)', ' print("Lambda = ", lmbd)', ' print("Test accuracy: %.3f" % scores[1])', ' print()'] +------------------- + diff --git a/doc/LectureNotes/_build/html/reports/chapter13.err.log b/doc/LectureNotes/_build/html/reports/chapter13.err.log new file mode 100644 index 000000000..c2d1fa4d3 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter13.err.log @@ -0,0 +1,138 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +# Start importing packages +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt +import tensorflow as tf +from tensorflow.keras import datasets, layers, models +from tensorflow.keras.layers import Input +from tensorflow.keras.models import Model, Sequential +from tensorflow.keras.layers import Dense, SimpleRNN, LSTM, GRU +from tensorflow.keras import optimizers +from tensorflow.keras import regularizers +from tensorflow.keras.utils import to_categorical + + + +# convert into dataset matrix +def convertToMatrix(data, step): + X, Y =[], [] + for i in range(len(data)-step): + d=i+step + X.append(data[i:d,]) + Y.append(data[d,]) + return np.array(X), np.array(Y) + +step = 4 +N = 1000 +Tp = 800 + +t=np.arange(0,N) +x=np.sin(0.02*t)+2*np.random.rand(N) +df = pd.DataFrame(x) +df.head() + +plt.plot(df) +plt.show() + +values=df.values +train,test = values[0:Tp,:], values[Tp:N,:] + +# add step elements into train and test +test = np.append(test,np.repeat(test[-1,],step)) +train = np.append(train,np.repeat(train[-1,],step)) + +trainX,trainY =convertToMatrix(train,step) +testX,testY =convertToMatrix(test,step) +trainX = np.reshape(trainX, (trainX.shape[0], 1, trainX.shape[1])) +testX = np.reshape(testX, (testX.shape[0], 1, testX.shape[1])) + +model = Sequential() +model.add(SimpleRNN(units=32, input_shape=(1,step), activation="relu")) +model.add(Dense(8, activation="relu")) +model.add(Dense(1)) +model.compile(loss='mean_squared_error', optimizer='rmsprop') +model.summary() + +model.fit(trainX,trainY, epochs=100, batch_size=16, verbose=2) +trainPredict = model.predict(trainX) +testPredict= model.predict(testX) +predicted=np.concatenate((trainPredict,testPredict),axis=0) + +trainScore = model.evaluate(trainX, trainY, verbose=0) +print(trainScore) + +index = df.index.values +plt.plot(index,df) +plt.plot(index,predicted) +plt.axvline(df.index[Tp], c="r") +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 # Start importing packages + 4 import pandas as pd + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter13.log b/doc/LectureNotes/_build/html/reports/chapter13.log new file mode 100644 index 000000000..cc6e3f3b0 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter13.log @@ -0,0 +1,39 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply + msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async + result = await obj + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg + raise Empty +_queue.Empty + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell + exec_reply = await self.task_poll_for_reply + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply + await self._async_handle_timeout(timeout, cell) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout + raise CellTimeoutError.error_from_timeout_and_cell( +nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds. +The message was: Cell execution timed out. +Here is a preview of the cell contents: +------------------- +['%matplotlib inline', '', '# Start importing packages', 'import pandas as pd', 'import numpy as np'] +... +['index = df.index.values', 'plt.plot(index,df)', 'plt.plot(index,predicted)', 'plt.axvline(df.index[Tp], c="r")', 'plt.show()'] +------------------- + diff --git a/doc/LectureNotes/_build/html/reports/chapter2.err.log b/doc/LectureNotes/_build/html/reports/chapter2.err.log new file mode 100644 index 000000000..b078680ac --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter2.err.log @@ -0,0 +1,44 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import numpy as np +import pandas as pd +n = 10 +x = np.random.normal(size=n) +x = x - np.mean(x) +y = 4+3*x+np.random.normal(size=n) +y = y - np.mean(y) +# Note that we transpose the matrix in order to stay with our ordering n x p +X = (np.vstack((x, y))).T +print(X) +Xpd = pd.DataFrame(X) +print(Xpd) +correlation_matrix = Xpd.corr() +print(correlation_matrix) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[7], line 2 + 1 import numpy as np +----> 2 import pandas as pd + 3 n = 10 + 4 x = np.random.normal(size=n) + +ModuleNotFoundError: No module named 'pandas' + diff --git a/doc/LectureNotes/_build/html/reports/chapter2.log b/doc/LectureNotes/_build/html/reports/chapter2.log new file mode 100644 index 000000000..dc7ae5f01 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter2.log @@ -0,0 +1,290 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +from cvxopt import matrix, spdiag, mul, div, sqrt, normal, setseed +from cvxopt import blas, lapack, solvers, sparse, spmatrix +import math + +try: + import mosek + import sys + __MOSEK = True +except: __MOSEK = False + +if __MOSEK: + + def l1regls_mosek(A, b): + """ + + Returns the solution of l1-norm regularized least-squares problem + + minimize || A*x - b ||_2^2 + e'*u + + subject to -u <= x <= u + + """ + + m, n = A.size + + env = mosek.Env() + task = env.Task(0,0) + task.set_Stream(mosek.streamtype.log, lambda x: sys.stdout.write(x)) + + task.appendvars( 2*n) # number of variables + task.appendcons( 2*n) # number of constraints + + # input quadratic objective + Q = matrix(0.0, (n,n)) + blas.syrk(A, Q, alpha = 2.0, trans='T') + + I = [] + for i in range(n): + I.extend(range(i,n)) + + J = [] + for i in range(n): + J.extend((n-i)*[i]) + + task.putqobj(I, J, list(Q[matrix(I) + matrix(J)*n])) + task.putclist(range(2*n), list(-2*A.T*b) + n*[1.0]) # setup linear objective + + # input constraint matrix row by row + for i in range(n): + task.putarow( i, [i, n+i], [1.0, -1.0]) + task.putarow( n+i, [i, n+i], [1.0, 1.0]) + + # setup bounds on constraints + task.putboundslice(mosek.accmode.con, + 0, n, n*[mosek.boundkey.up], n*[0.0], n*[0.0]) + task.putboundslice(mosek.accmode.con, + n, 2*n, n*[mosek.boundkey.lo], n*[0.0], n*[0.0]) + + # setup variable bounds + task.putboundslice(mosek.accmode.var, + 0, 2*n, 2*n*[mosek.boundkey.fr], 2*n*[0.0], 2*n*[0.0]) + + # optimize the task + task.putobjsense(mosek.objsense.minimize) + task.optimize() + task.solutionsummary(mosek.streamtype.log) + x = n*[0.0] + task.getsolutionslice(mosek.soltype.itr, mosek.solitem.xx, 0, n, x) + + return matrix(x) + + def l1regls_mosek2(A, b): + """ + + Returns the solution of l1-norm regularized least-squares problem + + minimize w'*w + e'*u + + subject to -u <= x <= u + + A*x - w = b + + """ + + m, n = A.size + + env = mosek.Env() + task = env.Task(0,0) + task.set_Stream(mosek.streamtype.log, lambda x: sys.stdout.write(x)) + + task.appendvars(2*n + m) # number of variables + task.appendcons(2*n + m) # number of constraints + + # input quadratic objective + task.putqobj(range(2*n,2*n+m), range(2*n,2*n+m), m*[2.0]) + + task.putclist(range(2*n+m), n*[0.0] + n*[1.0] + m*[0.0]) # setup linear objective + + # input constraint matrix row by row + for i in range(n): + task.putarow( i, [i, n+i], [1.0, -1.0]) + task.putarow( n+i, [i, n+i], [1.0, 1.0]) + + for i in range(m): + task.putarow( 2*n+i, range(n) + [2*n+i], list(A[i,:]) + [-1.0]) + + # setup bounds on constraints + task.putboundslice(mosek.accmode.con, + 0, n, n*[mosek.boundkey.up], n*[0.0], n*[0.0]) + task.putboundslice(mosek.accmode.con, + n, 2*n, n*[mosek.boundkey.lo], n*[0.0], n*[0.0]) + task.putboundslice(mosek.accmode.con, + 2*n, 2*n+m, m*[mosek.boundkey.fx], list(b), list(b)) + + # setup variable bounds + task.putboundslice(mosek.accmode.var, 0, 2*n+m, (2*n+m)*[mosek.boundkey.fr], + (2*n+m)*[0.0], (2*n+m)*[0.0]) + + # optimize the task + task.putobjsense(mosek.objsense.minimize) + task.optimize() + task.solutionsummary(mosek.streamtype.log) + x = n*[0.0] + task.getsolutionslice(mosek.soltype.itr, mosek.solitem.xx, 0, n, x) + + return matrix(x) + +def l1regls(A, b): + """ + + Returns the solution of l1-norm regularized least-squares problem + + minimize || A*x - b ||_2^2 + || x ||_1. + + """ + + m, n = A.size + q = matrix(1.0, (2*n,1)) + q[:n] = -2.0 * A.T * b + + def P(u, v, alpha = 1.0, beta = 0.0 ): + """ + v := alpha * 2.0 * [ A'*A, 0; 0, 0 ] * u + beta * v + """ + v *= beta + v[:n] += alpha * 2.0 * A.T * (A * u[:n]) + + + def G(u, v, alpha=1.0, beta=0.0, trans='N'): + """ + v := alpha*[I, -I; -I, -I] * u + beta * v (trans = 'N' or 'T') + """ + + v *= beta + v[:n] += alpha*(u[:n] - u[n:]) + v[n:] += alpha*(-u[:n] - u[n:]) + + h = matrix(0.0, (2*n,1)) + + + # Customized solver for the KKT system + # + # [ 2.0*A'*A 0 I -I ] [x[:n] ] [bx[:n] ] + # [ 0 0 -I -I ] [x[n:] ] = [bx[n:] ]. + # [ I -I -D1^-1 0 ] [zl[:n]] [bzl[:n]] + # [ -I -I 0 -D2^-1 ] [zl[n:]] [bzl[n:]] + # + # where D1 = W['di'][:n]**2, D2 = W['di'][:n]**2. + # + # We first eliminate zl and x[n:]: + # + # ( 2*A'*A + 4*D1*D2*(D1+D2)^-1 ) * x[:n] = + # bx[:n] - (D2-D1)*(D1+D2)^-1 * bx[n:] + + # D1 * ( I + (D2-D1)*(D1+D2)^-1 ) * bzl[:n] - + # D2 * ( I - (D2-D1)*(D1+D2)^-1 ) * bzl[n:] + # + # x[n:] = (D1+D2)^-1 * ( bx[n:] - D1*bzl[:n] - D2*bzl[n:] ) + # - (D2-D1)*(D1+D2)^-1 * x[:n] + # + # zl[:n] = D1 * ( x[:n] - x[n:] - bzl[:n] ) + # zl[n:] = D2 * (-x[:n] - x[n:] - bzl[n:] ). + # + # The first equation has the form + # + # (A'*A + D)*x[:n] = rhs + # + # and is equivalent to + # + # [ D A' ] [ x:n] ] = [ rhs ] + # [ A -I ] [ v ] [ 0 ]. + # + # It can be solved as + # + # ( A*D^-1*A' + I ) * v = A * D^-1 * rhs + # x[:n] = D^-1 * ( rhs - A'*v ). + + S = matrix(0.0, (m,m)) + Asc = matrix(0.0, (m,n)) + v = matrix(0.0, (m,1)) + + def Fkkt(W): + + # Factor + # + # S = A*D^-1*A' + I + # + # where D = 2*D1*D2*(D1+D2)^-1, D1 = d[:n]**-2, D2 = d[n:]**-2. + + d1, d2 = W['di'][:n]**2, W['di'][n:]**2 + + # ds is square root of diagonal of D + ds = math.sqrt(2.0) * div( mul( W['di'][:n], W['di'][n:]), + sqrt(d1+d2) ) + d3 = div(d2 - d1, d1 + d2) + + # Asc = A*diag(d)^-1/2 + Asc = A * spdiag(ds**-1) + + # S = I + A * D^-1 * A' + blas.syrk(Asc, S) + S[::m+1] += 1.0 + lapack.potrf(S) + + def g(x, y, z): + + x[:n] = 0.5 * ( x[:n] - mul(d3, x[n:]) + + mul(d1, z[:n] + mul(d3, z[:n])) - mul(d2, z[n:] - + mul(d3, z[n:])) ) + x[:n] = div( x[:n], ds) + + # Solve + # + # S * v = 0.5 * A * D^-1 * ( bx[:n] - + # (D2-D1)*(D1+D2)^-1 * bx[n:] + + # D1 * ( I + (D2-D1)*(D1+D2)^-1 ) * bzl[:n] - + # D2 * ( I - (D2-D1)*(D1+D2)^-1 ) * bzl[n:] ) + + blas.gemv(Asc, x, v) + lapack.potrs(S, v) + + # x[:n] = D^-1 * ( rhs - A'*v ). + blas.gemv(Asc, v, x, alpha=-1.0, beta=1.0, trans='T') + x[:n] = div(x[:n], ds) + + # x[n:] = (D1+D2)^-1 * ( bx[n:] - D1*bzl[:n] - D2*bzl[n:] ) + # - (D2-D1)*(D1+D2)^-1 * x[:n] + x[n:] = div( x[n:] - mul(d1, z[:n]) - mul(d2, z[n:]), d1+d2 )\ + - mul( d3, x[:n] ) + + # zl[:n] = D1^1/2 * ( x[:n] - x[n:] - bzl[:n] ) + # zl[n:] = D2^1/2 * ( -x[:n] - x[n:] - bzl[n:] ). + z[:n] = mul( W['di'][:n], x[:n] - x[n:] - z[:n] ) + z[n:] = mul( W['di'][n:], -x[:n] - x[n:] - z[n:] ) + + return g + + return solvers.coneqp(P, q, G, h, kktsolver = Fkkt)['x'][:n] +------------------ + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) + in  +----> 1 from cvxopt import matrix, spdiag, mul, div, sqrt, normal, setseed + 2 from cvxopt import blas, lapack, solvers, sparse, spmatrix + 3 import math + 4  + 5 try: + +ModuleNotFoundError: No module named 'cvxopt' +ModuleNotFoundError: No module named 'cvxopt' + diff --git a/doc/LectureNotes/_build/html/reports/chapter3.err.log b/doc/LectureNotes/_build/html/reports/chapter3.err.log new file mode 100644 index 000000000..80d3d640c --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter3.err.log @@ -0,0 +1,96 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +from time import time +from scipy.stats import norm +import matplotlib.pyplot as plt + +# Returns mean of bootstrap samples +# Bootstrap algorithm +def bootstrap(data, datapoints): + t = np.zeros(datapoints) + n = len(data) + # non-parametric bootstrap + for i in range(datapoints): + t[i] = np.mean(data[np.random.randint(0,n,n)]) + # analysis + print("Bootstrap Statistics :") + print("original bias std. error") + print("%8g %8g %14g %15g" % (np.mean(data), np.std(data),np.mean(t),np.std(t))) + return t + +# We set the mean value to 100 and the standard deviation to 15 +mu, sigma = 100, 15 +datapoints = 10000 +# We generate random numbers according to the normal distribution +x = mu + sigma*np.random.randn(datapoints) +# bootstrap returns the data sample +t = bootstrap(x, datapoints) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[2], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 from time import time + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter3.log b/doc/LectureNotes/_build/html/reports/chapter3.log new file mode 100644 index 000000000..0b02b2c82 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter3.log @@ -0,0 +1,30 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +scipy.misc.imread +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [31], in () +----> 1 scipy.misc.imread + +NameError: name 'scipy' is not defined +NameError: name 'scipy' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/chapter4.err.log b/doc/LectureNotes/_build/html/reports/chapter4.err.log new file mode 100644 index 000000000..ce2627dac --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter4.err.log @@ -0,0 +1,124 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +# Common imports +import os +import numpy as np +import pandas as pd +import matplotlib.pyplot as plt +from sklearn.linear_model import LinearRegression, Ridge, Lasso +from sklearn.model_selection import train_test_split +from sklearn.utils import resample +from sklearn.metrics import mean_squared_error +from IPython.display import display +from pylab import plt, mpl +plt.style.use('seaborn') +mpl.rcParams['font.family'] = 'serif' + +# Where to save the figures and data files +PROJECT_ROOT_DIR = "Results" +FIGURE_ID = "Results/FigureFiles" +DATA_ID = "DataFiles/" + +if not os.path.exists(PROJECT_ROOT_DIR): + os.mkdir(PROJECT_ROOT_DIR) + +if not os.path.exists(FIGURE_ID): + os.makedirs(FIGURE_ID) + +if not os.path.exists(DATA_ID): + os.makedirs(DATA_ID) + +def image_path(fig_id): + return os.path.join(FIGURE_ID, fig_id) + +def data_path(dat_id): + return os.path.join(DATA_ID, dat_id) + +def save_fig(fig_id): + plt.savefig(image_path(fig_id) + ".png", format='png') + +infile = open(data_path("chddata.csv"),'r') + +# Read the chd data as csv file and organize the data into arrays with age group, age, and chd +chd = pd.read_csv(infile, names=('ID', 'Age', 'Agegroup', 'CHD')) +chd.columns = ['ID', 'Age', 'Agegroup', 'CHD'] +output = chd['CHD'] +age = chd['Age'] +agegroup = chd['Agegroup'] +numberID = chd['ID'] +display(chd) + +plt.scatter(age, output, marker='o') +plt.axis([18,70.0,-0.1, 1.2]) +plt.xlabel(r'Age') +plt.ylabel(r'CHD') +plt.title(r'Age distribution and Coronary heart disease') +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 # Common imports + 4 import os + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter4.log b/doc/LectureNotes/_build/html/reports/chapter4.log new file mode 100644 index 000000000..1eb3ce965 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter4.log @@ -0,0 +1,77 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import matplotlib.pyplot as plt +import numpy as np +from sklearn.model_selection import train_test_split +from sklearn.datasets import load_breast_cancer +from sklearn.linear_model import LogisticRegression + +# Load the data +cancer = load_breast_cancer() + +X_train, X_test, y_train, y_test = train_test_split(cancer.data,cancer.target,random_state=0) +print(X_train.shape) +print(X_test.shape) +# Logistic Regression +logreg = LogisticRegression(solver='lbfgs') +logreg.fit(X_train, y_train) +print("Test set accuracy with Logistic Regression: {:.2f}".format(logreg.score(X_test,y_test))) +#now scale the data +from sklearn.preprocessing import StandardScaler +scaler = StandardScaler() +scaler.fit(X_train) +X_train_scaled = scaler.transform(X_train) +X_test_scaled = scaler.transform(X_test) +# Logistic Regression +logreg.fit(X_train_scaled, y_train) +print("Test set accuracy Logistic Regression with scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test))) + + +from sklearn.preprocessing import LabelEncoder +from sklearn.model_selection import cross_validate +#Cross validation +accuracy = cross_validate(logreg,X_test_scaled,y_test,cv=10)['test_score'] +print(accuracy) +print("Test set accuracy with Logistic Regression and scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test))) + + +import scikitplot as skplt +y_pred = logreg.predict(X_test_scaled) +skplt.metrics.plot_confusion_matrix(y_test, y_pred, normalize=True) +plt.show() +y_probas = logreg.predict_proba(X_test_scaled) +skplt.metrics.plot_roc(y_test, y_probas) +plt.show() +skplt.metrics.plot_cumulative_gain(y_test, y_probas) +plt.show() +------------------ + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Input In [8], in () + 32 print(accuracy) + 33 print("Test set accuracy with Logistic Regression and scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test))) +---> 36 import scikitplot as skplt + 37 y_pred = logreg.predict(X_test_scaled) + 38 skplt.metrics.plot_confusion_matrix(y_test, y_pred, normalize=True) + +ModuleNotFoundError: No module named 'scikitplot' +ModuleNotFoundError: No module named 'scikitplot' + diff --git a/doc/LectureNotes/_build/html/reports/chapter5.err.log b/doc/LectureNotes/_build/html/reports/chapter5.err.log new file mode 100644 index 000000000..dc78d827b --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter5.err.log @@ -0,0 +1,136 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +from sklearn import datasets +from sklearn.svm import SVC, LinearSVC +from sklearn.linear_model import SGDClassifier +from sklearn.preprocessing import StandardScaler +import matplotlib +import matplotlib.pyplot as plt +plt.rcParams['axes.labelsize'] = 14 +plt.rcParams['xtick.labelsize'] = 12 +plt.rcParams['ytick.labelsize'] = 12 + + +iris = datasets.load_iris() +X = iris["data"][:, (2, 3)] # petal length, petal width +y = iris["target"] + +setosa_or_versicolor = (y == 0) | (y == 1) +X = X[setosa_or_versicolor] +y = y[setosa_or_versicolor] + + + +C = 5 +alpha = 1 / (C * len(X)) + +lin_clf = LinearSVC(loss="hinge", C=C, random_state=42) +svm_clf = SVC(kernel="linear", C=C) +sgd_clf = SGDClassifier(loss="hinge", learning_rate="constant", eta0=0.001, alpha=alpha, + max_iter=100000, random_state=42) + +scaler = StandardScaler() +X_scaled = scaler.fit_transform(X) + +lin_clf.fit(X_scaled, y) +svm_clf.fit(X_scaled, y) +sgd_clf.fit(X_scaled, y) + +print("LinearSVC: ", lin_clf.intercept_, lin_clf.coef_) +print("SVC: ", svm_clf.intercept_, svm_clf.coef_) +print("SGDClassifier(alpha={:.5f}):".format(sgd_clf.alpha), sgd_clf.intercept_, sgd_clf.coef_) + +# Compute the slope and bias of each decision boundary +w1 = -lin_clf.coef_[0, 0]/lin_clf.coef_[0, 1] +b1 = -lin_clf.intercept_[0]/lin_clf.coef_[0, 1] +w2 = -svm_clf.coef_[0, 0]/svm_clf.coef_[0, 1] +b2 = -svm_clf.intercept_[0]/svm_clf.coef_[0, 1] +w3 = -sgd_clf.coef_[0, 0]/sgd_clf.coef_[0, 1] +b3 = -sgd_clf.intercept_[0]/sgd_clf.coef_[0, 1] + +# Transform the decision boundary lines back to the original scale +line1 = scaler.inverse_transform([[-10, -10 * w1 + b1], [10, 10 * w1 + b1]]) +line2 = scaler.inverse_transform([[-10, -10 * w2 + b2], [10, 10 * w2 + b2]]) +line3 = scaler.inverse_transform([[-10, -10 * w3 + b3], [10, 10 * w3 + b3]]) + +# Plot all three decision boundaries +plt.figure(figsize=(11, 4)) +plt.plot(line1[:, 0], line1[:, 1], "k:", label="LinearSVC") +plt.plot(line2[:, 0], line2[:, 1], "b--", linewidth=2, label="SVC") +plt.plot(line3[:, 0], line3[:, 1], "r-", label="SGDClassifier") +plt.plot(X[:, 0][y==1], X[:, 1][y==1], "bs") # label="Iris-Versicolor" +plt.plot(X[:, 0][y==0], X[:, 1][y==0], "yo") # label="Iris-Setosa" +plt.xlabel("Petal length", fontsize=14) +plt.ylabel("Petal width", fontsize=14) +plt.legend(loc="upper center", fontsize=14) +plt.axis([0, 5.5, 0, 2]) + +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 from sklearn import datasets + 4 from sklearn.svm import SVC, LinearSVC + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter5.log b/doc/LectureNotes/_build/html/reports/chapter5.log new file mode 100644 index 000000000..5b4b7d4e4 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter5.log @@ -0,0 +1,41 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# Import the necessary packages +import numpy +from cvxopt import matrix +from cvxopt import solvers +P = matrix(numpy.diag([1,0]), tc=’d’) +q = matrix(numpy.array([3,4]), tc=’d’) +G = matrix(numpy.array([[-1,0],[0,-1],[-1,-3],[2,5],[3,4]]), tc=’d’) +h = matrix(numpy.array([0,0,-15,100,80]), tc=’d’) +# Construct the QP, invoke solver +sol = solvers.qp(P,q,G,h) +# Extract optimal value and solution +sol[’x’] +sol[’primal objective’] +------------------ + + Input In [5] + P = matrix(numpy.diag([1,0]), tc=’d’) + ^ +SyntaxError: invalid character '’' (U+2019) + +SyntaxError: invalid character '’' (U+2019) (3974140161.py, line 5) + diff --git a/doc/LectureNotes/_build/html/reports/chapter6.err.log b/doc/LectureNotes/_build/html/reports/chapter6.err.log new file mode 100644 index 000000000..82a357884 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter6.err.log @@ -0,0 +1,158 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import matplotlib.pyplot as plt +from sklearn.preprocessing import PolynomialFeatures +from sklearn.linear_model import LinearRegression + +steps=250 + +distance=0 +x=0 +distance_list=[] +steps_list=[] +while x 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import matplotlib.pyplot as plt + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapter6.log b/doc/LectureNotes/_build/html/reports/chapter6.log new file mode 100644 index 000000000..966c9a43c --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter6.log @@ -0,0 +1,100 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# Common imports +import numpy as np +import pandas as pd +import matplotlib.pyplot as plt +from sklearn.tree import DecisionTreeClassifier +from sklearn.model_selection import train_test_split +from sklearn.tree import export_graphviz +from sklearn.preprocessing import StandardScaler, OneHotEncoder +from sklearn.compose import ColumnTransformer +from IPython.display import Image +from pydot import graph_from_dot_data +import os + +# Where to save the figures and data files +PROJECT_ROOT_DIR = "Results" +FIGURE_ID = "Results/FigureFiles" +DATA_ID = "DataFiles/" + +if not os.path.exists(PROJECT_ROOT_DIR): + os.mkdir(PROJECT_ROOT_DIR) + +if not os.path.exists(FIGURE_ID): + os.makedirs(FIGURE_ID) + +if not os.path.exists(DATA_ID): + os.makedirs(DATA_ID) + +def image_path(fig_id): + return os.path.join(FIGURE_ID, fig_id) + +def data_path(dat_id): + return os.path.join(DATA_ID, dat_id) + +def save_fig(fig_id): + plt.savefig(image_path(fig_id) + ".png", format='png') + +infile = open(data_path("rideclass.csv"),'r') + +# Read the experimental data with Pandas +from IPython.display import display +ridedata = pd.read_csv(infile,names = ('Outlook','Temperature','Humidity','Wind','Ride')) +ridedata = pd.DataFrame(ridedata) + +# Features and targets +X = ridedata.loc[:, ridedata.columns != 'Ride'].values +y = ridedata.loc[:, ridedata.columns == 'Ride'].values + +# Create the encoder. +encoder = OneHotEncoder(handle_unknown="ignore") +# Assume for simplicity all features are categorical. +encoder.fit(X) +# Apply the encoder. +X = encoder.transform(X) +print(X) +# Then do a Classification tree +tree_clf = DecisionTreeClassifier(max_depth=2) +tree_clf.fit(X, y) +print("Train set accuracy with Decision Tree: {:.2f}".format(tree_clf.score(X,y))) +#transfer to a decision tree graph +export_graphviz( + tree_clf, + out_file="DataFiles/ride.dot", + rounded=True, + filled=True +) +cmd = 'dot -Tpng DataFiles/cancer.dot -o DataFiles/cancer.png' +os.system(cmd) +------------------ + +--------------------------------------------------------------------------- +FileNotFoundError Traceback (most recent call last) +Input In [6], in () + 34 def save_fig(fig_id): + 35 plt.savefig(image_path(fig_id) + ".png", format='png') +---> 37 infile = open(data_path("rideclass.csv"),'r') + 39 # Read the experimental data with Pandas + 40 from IPython.display import display + +FileNotFoundError: [Errno 2] No such file or directory: 'DataFiles/rideclass.csv' +FileNotFoundError: [Errno 2] No such file or directory: 'DataFiles/rideclass.csv' + diff --git a/doc/LectureNotes/_build/html/reports/chapter7.err.log b/doc/LectureNotes/_build/html/reports/chapter7.err.log new file mode 100644 index 000000000..be4502783 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter7.err.log @@ -0,0 +1,43 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +heads_proba = 0.51 +coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32) +cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1) +plt.figure(figsize=(8,3.5)) +plt.plot(cumulative_heads_ratio) +plt.plot([0, 10000], [0.51, 0.51], "k--", linewidth=2, label="51%") +plt.plot([0, 10000], [0.5, 0.5], "k-", label="50%") +plt.xlabel("Number of coin tosses") +plt.ylabel("Heads ratio") +plt.legend(loc="lower right") +plt.axis([0, 10000, 0.42, 0.58]) +save_fig("votingsimple") +plt.show() +------------------ + + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Cell In[1], line 2 + 1 heads_proba = 0.51 +----> 2 coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32) + 3 cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1) + 4 plt.figure(figsize=(8,3.5)) + +NameError: name 'np' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/chapter7.log b/doc/LectureNotes/_build/html/reports/chapter7.log new file mode 100644 index 000000000..dfe36f408 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter7.log @@ -0,0 +1,45 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +heads_proba = 0.51 +coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32) +cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1) +plt.figure(figsize=(8,3.5)) +plt.plot(cumulative_heads_ratio) +plt.plot([0, 10000], [0.51, 0.51], "k--", linewidth=2, label="51%") +plt.plot([0, 10000], [0.5, 0.5], "k-", label="50%") +plt.xlabel("Number of coin tosses") +plt.ylabel("Heads ratio") +plt.legend(loc="lower right") +plt.axis([0, 10000, 0.42, 0.58]) +save_fig("votingsimple") +plt.show() +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [1], in () + 1 heads_proba = 0.51 +----> 2 coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32) + 3 cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1) + 4 plt.figure(figsize=(8,3.5)) + +NameError: name 'np' is not defined +NameError: name 'np' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/chapter8.err.log b/doc/LectureNotes/_build/html/reports/chapter8.err.log new file mode 100644 index 000000000..9ee6a3af1 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter8.err.log @@ -0,0 +1,43 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import numpy as np +import pandas as pd +n = 10 +x = np.random.normal(size=n) +x = x - np.mean(x) +y = 4+3*x+np.random.normal(size=n) +y = y - np.mean(y) +X = (np.vstack((x, y))).T +print(X) +Xpd = pd.DataFrame(X) +print(Xpd) +correlation_matrix = Xpd.corr() +print(correlation_matrix) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[3], line 2 + 1 import numpy as np +----> 2 import pandas as pd + 3 n = 10 + 4 x = np.random.normal(size=n) + +ModuleNotFoundError: No module named 'pandas' + diff --git a/doc/LectureNotes/_build/html/reports/chapter9.err.log b/doc/LectureNotes/_build/html/reports/chapter9.err.log new file mode 100644 index 000000000..32818ffd8 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapter9.err.log @@ -0,0 +1,144 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +"""The sigmoid function (or the logistic curve) is a +function that takes any real number, z, and outputs a number (0,1). +It is useful in neural networks for assigning weights on a relative scale. +The value z is the weighted sum of parameters involved in the learning algorithm.""" + +import numpy +import matplotlib.pyplot as plt +import math as mt + +z = numpy.arange(-5, 5, .1) +sigma_fn = numpy.vectorize(lambda z: 1/(1+numpy.exp(-z))) +sigma = sigma_fn(z) + +fig = plt.figure() +ax = fig.add_subplot(111) +ax.plot(z, sigma) +ax.set_ylim([-0.1, 1.1]) +ax.set_xlim([-5,5]) +ax.grid(True) +ax.set_xlabel('z') +ax.set_title('sigmoid function') + +plt.show() + +"""Step Function""" +z = numpy.arange(-5, 5, .02) +step_fn = numpy.vectorize(lambda z: 1.0 if z >= 0.0 else 0.0) +step = step_fn(z) + +fig = plt.figure() +ax = fig.add_subplot(111) +ax.plot(z, step) +ax.set_ylim([-0.5, 1.5]) +ax.set_xlim([-5,5]) +ax.grid(True) +ax.set_xlabel('z') +ax.set_title('step function') + +plt.show() + +"""Sine Function""" +z = numpy.arange(-2*mt.pi, 2*mt.pi, 0.1) +t = numpy.sin(z) + +fig = plt.figure() +ax = fig.add_subplot(111) +ax.plot(z, t) +ax.set_ylim([-1.0, 1.0]) +ax.set_xlim([-2*mt.pi,2*mt.pi]) +ax.grid(True) +ax.set_xlabel('z') +ax.set_title('sine function') + +plt.show() + +"""Plots a graph of the squashing function used by a rectified linear +unit""" +z = numpy.arange(-2, 2, .1) +zero = numpy.zeros(len(z)) +y = numpy.max([zero, z], axis=0) + +fig = plt.figure() +ax = fig.add_subplot(111) +ax.plot(z, y) +ax.set_ylim([-2.0, 2.0]) +ax.set_xlim([-2.0, 2.0]) +ax.grid(True) +ax.set_xlabel('z') +ax.set_title('Rectified linear unit') + +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 """The sigmoid function (or the logistic curve) is a  + 4 function that takes any real number, z, and outputs a number (0,1). + 5 It is useful in neural networks for assigning weights on a relative scale. + 6 The value z is the weighted sum of parameters involved in the learning algorithm.""" + 8 import numpy + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapteroptimization.err.log b/doc/LectureNotes/_build/html/reports/chapteroptimization.err.log new file mode 100644 index 000000000..22aebfc70 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapteroptimization.err.log @@ -0,0 +1,90 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import numpy.linalg as la + +import scipy.optimize as sopt + +import matplotlib.pyplot as pt +from mpl_toolkits.mplot3d import axes3d + +def f(x): + return 0.5*x[0]**2 + 2.5*x[1]**2 + +def df(x): + return np.array([x[0], 5*x[1]]) + +fig = pt.figure() +ax = fig.gca(projection="3d") + +xmesh, ymesh = np.mgrid[-2:2:50j,-2:2:50j] +fmesh = f(np.array([xmesh, ymesh])) +ax.plot_surface(xmesh, ymesh, fmesh) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import numpy.linalg as la + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/chapteroptimization.log b/doc/LectureNotes/_build/html/reports/chapteroptimization.log new file mode 100644 index 000000000..bed025caf --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/chapteroptimization.log @@ -0,0 +1,84 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import autograd.numpy as np +from autograd import grad +def f9(a): # Assume a is an array with 2 elements + b = np.array([1.0,2.0]) + return a.dot(b) + +f9_grad = grad(f9) + +x = np.array([1.0,0.0]) + +print("The derivative of f9 is:",f9_grad(x)) +------------------ + +--------------------------------------------------------------------------- +AttributeError Traceback (most recent call last) +Input In [23], in () + 7 f9_grad = grad(f9) + 9 x = np.array([1.0,0.0]) +---> 11 print("The derivative of f9 is:",f9_grad(x)) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:20, in unary_to_nary..nary_operator..nary_f(*args, **kwargs) + 18 else: + 19 x = tuple(args[i] for i in argnum) +---> 20 return unary_operator(unary_f, x, *nary_op_args, **nary_op_kwargs) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/differential_operators.py:25, in grad(fun, x) + 18 @unary_to_nary + 19 def grad(fun, x): + 20  """ + 21  Returns a function which computes the gradient of `fun` with respect to + 22  positional argument number `argnum`. The returned function takes the same + 23  arguments as `fun`, but returns the gradient instead. The function `fun` + 24  should be scalar-valued. The gradient has the same type as the argument.""" +---> 25 vjp, ans = _make_vjp(fun, x) + 26 if not vspace(ans).size == 1: + 27 raise TypeError("Grad only applies to real scalar-output functions. " + 28 "Try jacobian, elementwise_grad or holomorphic_grad.") + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/core.py:10, in make_vjp(fun, x) + 8 def make_vjp(fun, x): + 9 start_node = VJPNode.new_root() +---> 10 end_value, end_node = trace(start_node, fun, x) + 11 if end_node is None: + 12 def vjp(g): return vspace(x).zeros() + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/tracer.py:10, in trace(start_node, fun, x) + 8 with trace_stack.new_trace() as t: + 9 start_box = new_box(x, t, start_node) +---> 10 end_box = fun(start_box) + 11 if isbox(end_box) and end_box._trace == start_box._trace: + 12 return end_box._value, end_box._node + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:15, in unary_to_nary..nary_operator..nary_f..unary_f(x) + 13 else: + 14 subargs = subvals(args, zip(argnum, x)) +---> 15 return fun(*subargs, **kwargs) + +Input In [23], in f9(a) + 3 def f9(a): # Assume a is an array with 2 elements + 4 b = np.array([1.0,2.0]) +----> 5 return a.dot(b) + +AttributeError: 'ArrayBox' object has no attribute 'dot' +AttributeError: 'ArrayBox' object has no attribute 'dot' + diff --git a/doc/LectureNotes/_build/html/reports/clustering.err.log b/doc/LectureNotes/_build/html/reports/clustering.err.log new file mode 100644 index 000000000..9ef7ae598 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/clustering.err.log @@ -0,0 +1,79 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import time +import numpy as np +import tensorflow as tf +from matplotlib import image +import matplotlib.pyplot as plt +from sklearn.cluster import KMeans +from IPython.display import display + +np.random.seed(2021) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import time + 4 import numpy as np + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/clustering.log b/doc/LectureNotes/_build/html/reports/clustering.log new file mode 100644 index 000000000..208ee071b --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/clustering.log @@ -0,0 +1,239 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import time +import numpy as np +import tensorflow as tf +from matplotlib import image +import matplotlib.pyplot as plt +from sklearn.cluster import KMeans +from IPython.display import display + +np.random.seed(2021) +------------------ + +--------------------------------------------------------------------------- +AttributeError Traceback (most recent call last) +Input In [1], in () + 3 import time + 4 import numpy as np +----> 5 import tensorflow as tf + 6 from matplotlib import image + 7 import matplotlib.pyplot as plt + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/__init__.py:51, in  + 49 from ._api.v2 import autograph + 50 from ._api.v2 import bitwise +---> 51 from ._api.v2 import compat + 52 from ._api.v2 import config + 53 from ._api.v2 import data + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/__init__.py:37, in  + 3 """Compatibility functions. + 4 + 5 The `tf.compat` module contains two sets of compatibility functions. + (...) + 32 + 33 """ + 35 import sys as _sys +---> 37 from . import v1 + 38 from . import v2 + 39 from tensorflow.python.compat.compat import forward_compatibility_horizon + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/__init__.py:30, in  + 28 from . import autograph + 29 from . import bitwise +---> 30 from . import compat + 31 from . import config + 32 from . import data + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/compat/__init__.py:37, in  + 3 """Compatibility functions. + 4 + 5 The `tf.compat` module contains two sets of compatibility functions. + (...) + 32 + 33 """ + 35 import sys as _sys +---> 37 from . import v1 + 38 from . import v2 + 39 from tensorflow.python.compat.compat import forward_compatibility_horizon + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/compat/v1/__init__.py:47, in  + 45 from tensorflow._api.v2.compat.v1 import layers + 46 from tensorflow._api.v2.compat.v1 import linalg +---> 47 from tensorflow._api.v2.compat.v1 import lite + 48 from tensorflow._api.v2.compat.v1 import logging + 49 from tensorflow._api.v2.compat.v1 import lookup + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/__init__.py:9, in  + 6 import sys as _sys + 8 from . import constants +----> 9 from . import experimental + 10 from tensorflow.lite.python.lite import Interpreter + 11 from tensorflow.lite.python.lite import OpHint + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/experimental/__init__.py:8, in  + 3 """Public API for tf.lite.experimental namespace. + 4 """ + 6 import sys as _sys +----> 8 from . import authoring + 9 from tensorflow.lite.python.analyzer import ModelAnalyzer as Analyzer + 10 from tensorflow.lite.python.lite import OpResolverType + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/experimental/authoring/__init__.py:8, in  + 3 """Public API for tf.lite.experimental.authoring namespace. + 4 """ + 6 import sys as _sys +----> 8 from tensorflow.lite.python.authoring.authoring import compatible + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/authoring/authoring.py:43, in  + 39 import functools + 42 # pylint: disable=g-import-not-at-top +---> 43 from tensorflow.lite.python import convert + 44 from tensorflow.lite.python import lite + 45 from tensorflow.lite.python.metrics import converter_error_data_pb2 + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/convert.py:29, in  + 26 import six + 28 from tensorflow.lite.python import lite_constants +---> 29 from tensorflow.lite.python import util + 30 from tensorflow.lite.python import wrap_toco + 31 from tensorflow.lite.python.convert_phase import Component + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:51, in  + 47 # Jax functions used by TFLite + 48 # pylint: disable=g-import-not-at-top + 49 # pylint: disable=unused-import + 50 try: +---> 51 from jax import xla_computation as _xla_computation + 52 except ImportError: + 53 _xla_computation = None + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/__init__.py:116, in  + 40 from ._src.config import ( + 41 config as config, + 42 enable_checks as enable_checks, + (...) + 51 numpy_rank_promotion as numpy_rank_promotion, + 52 ) + 53 from ._src.api import ( + 54 ad, # TODO(phawkins): update users to avoid this. + 55 checkpoint as checkpoint, + (...) + 114 xla_computation as xla_computation, + 115 ) +--> 116 from .experimental.maps import soft_pmap as soft_pmap + 117 from .version import __version__ as __version__ + 119 # These submodules are separate because they are in an import cycle with + 120 # jax and rely on the names imported above. + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/experimental/maps.py:26, in  + 23 from functools import wraps, partial, partialmethod + 24 from enum import Enum +---> 26 from .. import numpy as jnp + 27 from .. import core + 28 from .. import linear_util as lu + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/__init__.py:19, in  + 1 # Copyright 2018 Google LLC + 2 # + 3 # Licensed under the Apache License, Version 2.0 (the "License"); + (...) + 17 + 18 # flake8: noqa: F401 +---> 19 from . import fft as fft + 20 from . import linalg as linalg + 22 from jax.interpreters.xla import DeviceArray as DeviceArray + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/fft.py:17, in  + 1 # Copyright 2020 Google LLC + 2 # + 3 # Licensed under the Apache License, Version 2.0 (the "License"); + (...) + 14 + 15 # flake8: noqa: F401 +---> 17 from jax._src.numpy.fft import ( + 18 ifft as ifft, + 19 ifft2 as ifft2, + 20 ifftn as ifftn, + 21 ifftshift as ifftshift, + 22 ihfft as ihfft, + 23 irfft as irfft, + 24 irfft2 as irfft2, + 25 irfftn as irfftn, + 26 fft as fft, + 27 fft2 as fft2, + 28 fftfreq as fftfreq, + 29 fftn as fftn, + 30 fftshift as fftshift, + 31 hfft as hfft, + 32 rfft as rfft, + 33 rfft2 as rfft2, + 34 rfftfreq as rfftfreq, + 35 rfftn as rfftn, + 36 ) + 38 # Module initialization is encapsulated in a function to avoid accidental + 39 # namespace pollution. + 40 _NOT_IMPLEMENTED = [] + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/numpy/fft.py:19, in  + 16 import operator + 17 import numpy as np +---> 19 from jax import lax + 20 from jax._src.lib import xla_client + 21 from jax._src.util import safe_zip + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/lax/__init__.py:332, in  + 299 from jax._src.lax.lax import (_reduce_sum, _reduce_max, _reduce_min, _reduce_or, + 300 _reduce_and, _reduce_window_sum, _reduce_window_max, + 301 _reduce_window_min, _reduce_window_prod, + (...) + 306 _upcast_fp16_for_computation, _broadcasting_shape_rule, + 307 _eye, _tri, _delta, _ones, _zeros, _dilate_shape) + 308 from jax._src.lax.control_flow import ( + 309 associative_scan as associative_scan, + 310 cond as cond, + (...) + 330 while_p as while_p, + 331 ) +--> 332 from jax._src.lax.fft import ( + 333 fft as fft, + 334 fft_p as fft_p, + 335 ) + 336 from jax._src.lax.parallel import ( + 337 all_gather as all_gather, + 338 all_to_all as all_to_all, + (...) + 355 xeinsum as xeinsum, + 356 ) + 357 from jax._src.lax.other import ( + 358 conv_general_dilated_patches as conv_general_dilated_patches + 359 ) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lax/fft.py:145, in  + 143 batching.primitive_batchers[fft_p] = fft_batching_rule + 144 if pocketfft: +--> 145 xla.backend_specific_translations['cpu'][fft_p] = pocketfft.pocketfft + +AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft' +AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft' + diff --git a/doc/LectureNotes/_build/html/reports/exercisesweek34.err.log b/doc/LectureNotes/_build/html/reports/exercisesweek34.err.log new file mode 100644 index 000000000..52c0836ef --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/exercisesweek34.err.log @@ -0,0 +1,30 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +x = np.random.rand(100,1) +y = 2.0+5*x*x+0.1*np.random.randn(100,1) +------------------ + + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 x = np.random.rand(100,1) + 2 y = 2.0+5*x*x+0.1*np.random.randn(100,1) + +NameError: name 'np' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/exercisesweek34.log b/doc/LectureNotes/_build/html/reports/exercisesweek34.log new file mode 100644 index 000000000..da58b1bdc --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/exercisesweek34.log @@ -0,0 +1,32 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +x = np.random.rand(100,1) +y = 2.0+5*x*x+0.1*np.random.randn(100,1) +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [1], in () +----> 1 x = np.random.rand(100,1) + 2 y = 2.0+5*x*x+0.1*np.random.randn(100,1) + +NameError: name 'np' is not defined +NameError: name 'np' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/linalg.err.log b/doc/LectureNotes/_build/html/reports/linalg.err.log new file mode 100644 index 000000000..0f6541948 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/linalg.err.log @@ -0,0 +1,81 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import matplotlib.pyplot as plt +from scipy import sparse +eye = np.eye(4) +print(eye) +sparse_mtx = sparse.csr_matrix(eye) +print(sparse_mtx) +x = np.linspace(-10,10,100) +y = np.sin(x) +plt.plot(x,y,marker='x') +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[15], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import matplotlib.pyplot as plt + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/linalg.log b/doc/LectureNotes/_build/html/reports/linalg.log new file mode 100644 index 000000000..b5403c763 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/linalg.log @@ -0,0 +1,31 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import numpy as np +x = np.log(np.array([4.0, 7.0, 8.0]) +print(x) +------------------ + + File "", line 3 + print(x) + ^ +SyntaxError: invalid syntax + +SyntaxError: invalid syntax (, line 3) + diff --git a/doc/LectureNotes/_build/html/reports/project1.err.log b/doc/LectureNotes/_build/html/reports/project1.err.log new file mode 100644 index 000000000..460e75b34 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/project1.err.log @@ -0,0 +1,109 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +from mpl_toolkits.mplot3d import Axes3D +import matplotlib.pyplot as plt +from matplotlib import cm +from matplotlib.ticker import LinearLocator, FormatStrFormatter +import numpy as np +from random import random, seed + +fig = plt.figure() +ax = fig.gca(projection='3d') + +# Make data. +x = np.arange(0, 1, 0.05) +y = np.arange(0, 1, 0.05) +x, y = np.meshgrid(x,y) + + +def FrankeFunction(x,y): + term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2)) + term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1)) + term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2)) + term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2) + return term1 + term2 + term3 + term4 + + +z = FrankeFunction(x, y) + +# Plot the surface. +surf = ax.plot_surface(x, y, z, cmap=cm.coolwarm, + linewidth=0, antialiased=False) + +# Customize the z axis. +ax.set_zlim(-0.10, 1.40) +ax.zaxis.set_major_locator(LinearLocator(10)) +ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f')) + +# Add a color bar which maps values to colors. +fig.colorbar(surf, shrink=0.5, aspect=5) + +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 from mpl_toolkits.mplot3d import Axes3D + 4 import matplotlib.pyplot as plt + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/project1.log b/doc/LectureNotes/_build/html/reports/project1.log new file mode 100644 index 000000000..94cb683ee --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/project1.log @@ -0,0 +1,30 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +scipy.misc.imread +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [2], in () +----> 1 scipy.misc.imread + +NameError: name 'scipy' is not defined +NameError: name 'scipy' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/statistics.err.log b/doc/LectureNotes/_build/html/reports/statistics.err.log new file mode 100644 index 000000000..db3036938 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/statistics.err.log @@ -0,0 +1,107 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +from math import acos, exp, sqrt +from matplotlib import pyplot as plt +from matplotlib import rc, rcParams +import matplotlib.units as units +import matplotlib.ticker as ticker +rc('text',usetex=True) +rc('font',**{'family':'serif','serif':['Gaussian distribution']}) +font = {'family' : 'serif', + 'color' : 'darkred', + 'weight' : 'normal', + 'size' : 16, + } +pi = acos(-1.0) +mu0 = 0.0 +sigma0 = 1.0 +mu1= 1.0 +sigma1 = 2.0 +mu2 = 2.0 +sigma2 = 4.0 + +x = np.linspace(-20.0, 20.0) +v0 = np.exp(-(x*x-2*x*mu0+mu0*mu0)/(2*sigma0*sigma0))/sqrt(2*pi*sigma0*sigma0) +v1 = np.exp(-(x*x-2*x*mu1+mu1*mu1)/(2*sigma1*sigma1))/sqrt(2*pi*sigma1*sigma1) +v2 = np.exp(-(x*x-2*x*mu2+mu2*mu2)/(2*sigma2*sigma2))/sqrt(2*pi*sigma2*sigma2) +plt.plot(x, v0, 'b-', x, v1, 'r-', x, v2, 'g-') +plt.title(r'{\bf Gaussian distributions}', fontsize=20) +plt.text(-19, 0.3, r'Parameters: $\mu = 0$, $\sigma = 1$', fontdict=font) +plt.text(-19, 0.18, r'Parameters: $\mu = 1$, $\sigma = 2$', fontdict=font) +plt.text(-19, 0.08, r'Parameters: $\mu = 2$, $\sigma = 4$', fontdict=font) +plt.xlabel(r'$x$',fontsize=20) +plt.ylabel(r'$p(x)$ [MeV]',fontsize=20) + +# Tweak spacing to prevent clipping of ylabel +plt.subplots_adjust(left=0.15) +plt.savefig('gaussian.pdf', format='pdf') +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 from math import acos, exp, sqrt + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/statistics.log b/doc/LectureNotes/_build/html/reports/statistics.log new file mode 100644 index 000000000..77f756b6e --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/statistics.log @@ -0,0 +1,58 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# Blocking + @timeFunction + def blocking(self, blockSizeMax = 500): + blockSizeMin = 1 + + self.blockSizes = [] + self.meanVec = [] + self.varVec = [] + + for i in range(blockSizeMin, blockSizeMax): + if(len(self.data) % i != 0): + pass#continue + blockSize = i + meanTempVec = [] + varTempVec = [] + startPoint = 0 + endPoint = blockSize + + while endPoint <= len(self.data): + meanTempVec.append(np.average(self.data[startPoint:endPoint])) + startPoint = endPoint + endPoint += blockSize + mean, var = np.average(meanTempVec), np.var(meanTempVec)/len(meanTempVec) + self.meanVec.append(mean) + self.varVec.append(var) + self.blockSizes.append(blockSize) + + self.blockingAvg = np.average(self.meanVec[-200:]) + self.blockingVar = (np.average(self.varVec[-200:])) + self.blockingStd = np.sqrt(self.blockingVar) +------------------ + + File "", line 2 + @timeFunction + ^ +IndentationError: unexpected indent + +IndentationError: unexpected indent (, line 2) + diff --git a/doc/LectureNotes/_build/html/reports/week34.err.log b/doc/LectureNotes/_build/html/reports/week34.err.log new file mode 100644 index 000000000..4212b15c2 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week34.err.log @@ -0,0 +1,81 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import matplotlib.pyplot as plt +from scipy import sparse +eye = np.eye(4) +print(eye) +sparse_mtx = sparse.csr_matrix(eye) +print(sparse_mtx) +x = np.linspace(-10,10,100) +y = np.sin(x) +plt.plot(x,y,marker='x') +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[16], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import matplotlib.pyplot as plt + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/week34.log b/doc/LectureNotes/_build/html/reports/week34.log new file mode 100644 index 000000000..813cc0c70 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week34.log @@ -0,0 +1,71 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# Read the experimental data with Pandas +Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11), + names=('N', 'Z', 'A', 'Element', 'Ebinding'), + widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1), + header=39, + index_col=False) + +# Extrapolated values are indicated by '#' in place of the decimal place, so +# the Ebinding column won't be numeric. Coerce to float and drop these entries. +Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce') +Masses = Masses.dropna() +# Convert from keV to MeV. +Masses['Ebinding'] /= 1000 + +# Group the DataFrame by nucleon number, A. +Masses = Masses.groupby('A') +# Find the rows of the grouped DataFrame with the maximum binding energy. +Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()]) +------------------ + +--------------------------------------------------------------------------- +ValueError Traceback (most recent call last) +Input In [30], in () + 1 # Read the experimental data with Pandas +----> 2 Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11), + 3  names=('N', 'Z', 'A', 'Element', 'Ebinding'), + 4  widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1), + 5  header=39, + 6  index_col=False) + 8 # Extrapolated values are indicated by '#' in place of the decimal place, so + 9 # the Ebinding column won't be numeric. Coerce to float and drop these entries. + 10 Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce') + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/util/_decorators.py:311, in deprecate_nonkeyword_arguments..decorate..wrapper(*args, **kwargs) + 305 if len(args) > num_allow_args: + 306 warnings.warn( + 307 msg.format(arguments=arguments), + 308 FutureWarning, + 309 stacklevel=stacklevel, + 310 ) +--> 311 return func(*args, **kwargs) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/io/parsers/readers.py:871, in read_fwf(filepath_or_buffer, colspecs, widths, infer_nrows, **kwds) + 869 len_index = len(index_col) + 870 if len(names) + len_index != len(colspecs): +--> 871 raise ValueError("Length of colspecs must match length of names") + 873 kwds["colspecs"] = colspecs + 874 kwds["infer_nrows"] = infer_nrows + +ValueError: Length of colspecs must match length of names +ValueError: Length of colspecs must match length of names + diff --git a/doc/LectureNotes/_build/html/reports/week35.err.log b/doc/LectureNotes/_build/html/reports/week35.err.log new file mode 100644 index 000000000..b09f8c4b6 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week35.err.log @@ -0,0 +1,110 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import os +import numpy as np +import pandas as pd +import matplotlib.pyplot as plt +from sklearn.model_selection import train_test_split + + +def R2(y_data, y_model): + return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2) +def MSE(y_data,y_model): + n = np.size(y_model) + return np.sum((y_data-y_model)**2)/n + +x = np.random.rand(100) +y = 2.0+5*x*x+0.1*np.random.randn(100) + + +# The design matrix now as function of a fourth-order polynomial +X = np.zeros((len(x),5)) +X[:,0] = 1.0 +X[:,1] = x +X[:,2] = x**2 +X[:,3] = x**3 +X[:,4] = x**4 +# We split the data in test and training data +X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2) +# matrix inversion to find beta +beta = np.linalg.inv(X_train.T @ X_train) @ X_train.T @ y_train +print(beta) +# and then make the prediction +ytilde = X_train @ beta +print("Training R2") +print(R2(y_train,ytilde)) +print("Training MSE") +print(MSE(y_train,ytilde)) +ypredict = X_test @ beta +print("Test R2") +print(R2(y_test,ypredict)) +print("Test MSE") +print(MSE(y_test,ypredict)) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[7], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import os + 4 import numpy as np + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/week35.log b/doc/LectureNotes/_build/html/reports/week35.log new file mode 100644 index 000000000..f18309f81 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week35.log @@ -0,0 +1,32 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +fit = np.linalg.lstsq(X, Energies, rcond =None)[0] +ytildenp = np.dot(fit,X.T) +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [2], in () +----> 1 fit = np.linalg.lstsq(X, Energies, rcond =None)[0] + 2 ytildenp = np.dot(fit,X.T) + +NameError: name 'Energies' is not defined +NameError: name 'Energies' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/week36.err.log b/doc/LectureNotes/_build/html/reports/week36.err.log new file mode 100644 index 000000000..fe6672d9b --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week36.err.log @@ -0,0 +1,38 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import numpy as np +X = np.array( [ [1,2,3],[2,4,5],[3,5,6]]) +Xinv = np.linlag.pinv(X) +------------------ + + +--------------------------------------------------------------------------- +AttributeError Traceback (most recent call last) +Cell In[1], line 3 + 1 import numpy as np + 2 X = np.array( [ [1,2,3],[2,4,5],[3,5,6]]) +----> 3 Xinv = np.linlag.pinv(X) + +File ~/miniforge3/lib/python3.9/site-packages/numpy/__init__.py:313, in __getattr__(attr) + 310 from .testing import Tester + 311 return Tester +--> 313 raise AttributeError("module {!r} has no attribute " + 314 "{!r}".format(__name__, attr)) + +AttributeError: module 'numpy' has no attribute 'linlag' + diff --git a/doc/LectureNotes/_build/html/reports/week36.log b/doc/LectureNotes/_build/html/reports/week36.log new file mode 100644 index 000000000..368486b5b --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week36.log @@ -0,0 +1,40 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import numpy as np +X = np.array( [ [1,2,3],[2,4,5],[3,5,6]]) +Xinv = np.linlag.pinv(X) +------------------ + +--------------------------------------------------------------------------- +AttributeError Traceback (most recent call last) +Input In [1], in () + 1 import numpy as np + 2 X = np.array( [ [1,2,3],[2,4,5],[3,5,6]]) +----> 3 Xinv = np.linlag.pinv(X) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/numpy/__init__.py:315, in __getattr__(attr) + 312 from .testing import Tester + 313 return Tester +--> 315 raise AttributeError("module {!r} has no attribute " + 316 "{!r}".format(__name__, attr)) + +AttributeError: module 'numpy' has no attribute 'linlag' +AttributeError: module 'numpy' has no attribute 'linlag' + diff --git a/doc/LectureNotes/_build/html/reports/week37.err.log b/doc/LectureNotes/_build/html/reports/week37.err.log new file mode 100644 index 000000000..8b161c9a8 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week37.err.log @@ -0,0 +1,96 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +from time import time +from scipy.stats import norm +import matplotlib.pyplot as plt + +# Returns mean of bootstrap samples +# Bootstrap algorithm +def bootstrap(data, datapoints): + t = np.zeros(datapoints) + n = len(data) + # non-parametric bootstrap + for i in range(datapoints): + t[i] = np.mean(data[np.random.randint(0,n,n)]) + # analysis + print("Bootstrap Statistics :") + print("original bias std. error") + print("%8g %8g %14g %15g" % (np.mean(data), np.std(data),np.mean(t),np.std(t))) + return t + +# We set the mean value to 100 and the standard deviation to 15 +mu, sigma = 100, 15 +datapoints = 10000 +# We generate random numbers according to the normal distribution +x = mu + sigma*np.random.randn(datapoints) +# bootstrap returns the data sample +t = bootstrap(x, datapoints) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 from time import time + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/week37.log b/doc/LectureNotes/_build/html/reports/week37.log new file mode 100644 index 000000000..f0de99fea --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week37.log @@ -0,0 +1,92 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +from sklearn import linear_model +np.random.seed(2018) +n = 10 +d = 2 +Lambda = 0.01 + +# Make data set. +x = np.linspace(-3, 3, n) +y = 2.0 + 0.5*x + 5.0*(x**2)+ np.random.randn(n) + +# Design matrix X does not include the intercept. +X = np.zeros((n, d)) +for p in range(d): + X[:, p] = x ** (p+1) + +#Split data in train and test +X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2) +# Scale data by subtracting mean value of the input using scikit-learn +scaler = StandardScaler(with_std=False) +scaler.fit(X_train) +X_train_mean = np.mean(X_train,axis=0) +X_train_scaled = scaler.transform(X_train) +X_test_scaled = scaler.transform(X_test) +# We scale also the output, here by our own code +y_scaler = np.mean(y_train) +y_train_scaled = y_train - y_scaler +y_test_scaled = y_test- y_scaler + +#Calculate beta +OLS = LinearRegression() +betaOLS=OLS.fit(X_train_scaled,y_train_scaled) +ypredictOLS = OLS.predict(X_test_scaled) +linear_model.Ridge(Lambda) +RegRidge.fit(X_train_scaled,y_train_scaled) +ypredictRidge = RegRidge.predict(X_test_scaled) +betaOLS = OLS.coef_ +betaRidge = RegRidge.coef_ +print(betaOLS) +print(betaRidge) +interceptOLS = np.mean(y_train) - X_train_mean @ betaOLS +interceptRidge = y_scaler - X_train_mean @ betaRidge +print(interceptOLS) +print(interceptRidge) +#predict value +ytilde_test_Ridge = X_test_scaled @ betaRidge+y_scaler +ytilde_test_OLS = X_test_scaled @ betaOLS+y_scaler + +#Calculate MSE +print(" ") +print("test MSE of OLS") +print(MSE(y_test,ytilde_test_OLS)) +print(" ") +print("test MSE of Ridge") +print(MSE(y_test,ytilde_test_Ridge)) +plt.scatter(x,y,label='Data') +plt.plot(x, X @ RegRidge.coef_ + RegRidge.intercept_ , label="Ridge_Fit") +plt.grid() +plt.legend() +plt.show() +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [11], in () + 32 ypredictOLS = OLS.predict(X_test_scaled) + 33 linear_model.Ridge(Lambda) +---> 34 RegRidge.fit(X_train_scaled,y_train_scaled) + 35 ypredictRidge = RegRidge.predict(X_test_scaled) + 36 betaOLS = OLS.coef_ + +NameError: name 'RegRidge' is not defined +NameError: name 'RegRidge' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/week38.err.log b/doc/LectureNotes/_build/html/reports/week38.err.log new file mode 100644 index 000000000..e6b8e0715 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week38.err.log @@ -0,0 +1,159 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import matplotlib.pyplot as plt +from sklearn.model_selection import KFold +from sklearn.linear_model import Ridge +from sklearn.model_selection import cross_val_score +from sklearn.preprocessing import PolynomialFeatures + +# A seed just to ensure that the random numbers are the same for every run. +# Useful for eventual debugging. +np.random.seed(3155) + +# Generate the data. +nsamples = 100 +x = np.random.randn(nsamples) +y = 3*x**2 + np.random.randn(nsamples) + +## Cross-validation on Ridge regression using KFold only + +# Decide degree on polynomial to fit +poly = PolynomialFeatures(degree = 6) + +# Decide which values of lambda to use +nlambdas = 500 +lambdas = np.logspace(-3, 5, nlambdas) + +# Initialize a KFold instance +k = 5 +kfold = KFold(n_splits = k) + +# Perform the cross-validation to estimate MSE +scores_KFold = np.zeros((nlambdas, k)) + +i = 0 +for lmb in lambdas: + ridge = Ridge(alpha = lmb) + j = 0 + for train_inds, test_inds in kfold.split(x): + xtrain = x[train_inds] + ytrain = y[train_inds] + + xtest = x[test_inds] + ytest = y[test_inds] + + Xtrain = poly.fit_transform(xtrain[:, np.newaxis]) + ridge.fit(Xtrain, ytrain[:, np.newaxis]) + + Xtest = poly.fit_transform(xtest[:, np.newaxis]) + ypred = ridge.predict(Xtest) + + scores_KFold[i,j] = np.sum((ypred - ytest[:, np.newaxis])**2)/np.size(ypred) + + j += 1 + i += 1 + + +estimated_mse_KFold = np.mean(scores_KFold, axis = 1) + +## Cross-validation using cross_val_score from sklearn along with KFold + +# kfold is an instance initialized above as: +# kfold = KFold(n_splits = k) + +estimated_mse_sklearn = np.zeros(nlambdas) +i = 0 +for lmb in lambdas: + ridge = Ridge(alpha = lmb) + + X = poly.fit_transform(x[:, np.newaxis]) + estimated_mse_folds = cross_val_score(ridge, X, y[:, np.newaxis], scoring='neg_mean_squared_error', cv=kfold) + + # cross_val_score return an array containing the estimated negative mse for every fold. + # we have to the the mean of every array in order to get an estimate of the mse of the model + estimated_mse_sklearn[i] = np.mean(-estimated_mse_folds) + + i += 1 + +## Plot and compare the slightly different ways to perform cross-validation + +plt.figure() + +plt.plot(np.log10(lambdas), estimated_mse_sklearn, label = 'cross_val_score') +plt.plot(np.log10(lambdas), estimated_mse_KFold, 'r--', label = 'KFold') + +plt.xlabel('log10(lambda)') +plt.ylabel('mse') + +plt.legend() + +plt.show() +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import matplotlib.pyplot as plt + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/week38.log b/doc/LectureNotes/_build/html/reports/week38.log new file mode 100644 index 000000000..ac1a85d80 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week38.log @@ -0,0 +1,32 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +x = 2*np.random.rand(m,1) +y = 4+3*x+np.random.randn(m,1) +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [13], in () +----> 1 x = 2*np.random.rand(m,1) + 2 y = 4+3*x+np.random.randn(m,1) + +NameError: name 'm' is not defined +NameError: name 'm' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/week39.err.log b/doc/LectureNotes/_build/html/reports/week39.err.log new file mode 100644 index 000000000..f95488573 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week39.err.log @@ -0,0 +1,90 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped + return loop.run_until_complete(inner) + File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +%matplotlib inline + +import numpy as np +import numpy.linalg as la + +import scipy.optimize as sopt + +import matplotlib.pyplot as pt +from mpl_toolkits.mplot3d import axes3d + +def f(x): + return x[0]**2 + 3.0*x[1]**2 + +def df(x): + return np.array([2*x[0], 6*x[1]]) + +fig = pt.figure() +ax = fig.gca(projection="3d") + +xmesh, ymesh = np.mgrid[-3:3:50j,-3:3:50j] +fmesh = f(np.array([xmesh, ymesh])) +ax.plot_surface(xmesh, ymesh, fmesh) +------------------ + + +--------------------------------------------------------------------------- +ModuleNotFoundError Traceback (most recent call last) +Cell In[1], line 1 +----> 1 get_ipython().run_line_magic('matplotlib', 'inline') + 3 import numpy as np + 4 import numpy.linalg as la + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth) + 2430 kwargs['local_ns'] = self.get_local_scope(stack_depth) + 2431 with self.builtin_trap: +-> 2432 result = fn(*args, **kwargs) + 2434 # The code below prevents the output from being displayed + 2435 # when using magics with decorator @output_can_be_silenced + 2436 # when the last Python token in the expression is a ';'. + 2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False): + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line) + 97 print("Available matplotlib backends: %s" % backends_list) + 98 else: +---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui) + 100 self._show_matplotlib_backend(args.gui, backend) + +File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui) + 3585 def enable_matplotlib(self, gui=None): + 3586  """Enable interactive matplotlib and inline figure support. + 3587 + 3588  This takes the following steps: + (...) + 3604  display figures inline. + 3605  """ +-> 3606 from matplotlib_inline.backend_inline import configure_inline_support + 3608 from IPython.core import pylabtools as pt + 3609 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select) + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1 +----> 1 from . import backend_inline, config # noqa + 2 __version__ = "0.1.6" # noqa + +File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6 + 1 """A matplotlib backend for publishing figures via display_data""" + 3 # Copyright (c) IPython Development Team. + 4 # Distributed under the terms of the BSD 3-Clause License. +----> 6 import matplotlib + 7 from matplotlib import colors + 8 from matplotlib.backends import backend_agg + +ModuleNotFoundError: No module named 'matplotlib' + diff --git a/doc/LectureNotes/_build/html/reports/week39.log b/doc/LectureNotes/_build/html/reports/week39.log new file mode 100644 index 000000000..0b636f0e1 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week39.log @@ -0,0 +1,32 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +x = 2*np.random.rand(m,1) +y = 4+3*x+np.random.randn(m,1) +------------------ + +--------------------------------------------------------------------------- +NameError Traceback (most recent call last) +Input In [6], in () +----> 1 x = 2*np.random.rand(m,1) + 2 y = 4+3*x+np.random.randn(m,1) + +NameError: name 'm' is not defined +NameError: name 'm' is not defined + diff --git a/doc/LectureNotes/_build/html/reports/week40.log b/doc/LectureNotes/_build/html/reports/week40.log new file mode 100644 index 000000000..774834f0f --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week40.log @@ -0,0 +1,84 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +import autograd.numpy as np +from autograd import grad +def f8(x): # Assume x is an array + x[2] = 3 + return x*2 + +f8_grad = grad(f8) + +x = 8.4 + +print("The derivative of f8 is:",f8_grad(x)) +------------------ + +--------------------------------------------------------------------------- +TypeError Traceback (most recent call last) +Input In [13], in () + 7 f8_grad = grad(f8) + 9 x = 8.4 +---> 11 print("The derivative of f8 is:",f8_grad(x)) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:20, in unary_to_nary..nary_operator..nary_f(*args, **kwargs) + 18 else: + 19 x = tuple(args[i] for i in argnum) +---> 20 return unary_operator(unary_f, x, *nary_op_args, **nary_op_kwargs) + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/differential_operators.py:25, in grad(fun, x) + 18 @unary_to_nary + 19 def grad(fun, x): + 20  """ + 21  Returns a function which computes the gradient of `fun` with respect to + 22  positional argument number `argnum`. The returned function takes the same + 23  arguments as `fun`, but returns the gradient instead. The function `fun` + 24  should be scalar-valued. The gradient has the same type as the argument.""" +---> 25 vjp, ans = _make_vjp(fun, x) + 26 if not vspace(ans).size == 1: + 27 raise TypeError("Grad only applies to real scalar-output functions. " + 28 "Try jacobian, elementwise_grad or holomorphic_grad.") + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/core.py:10, in make_vjp(fun, x) + 8 def make_vjp(fun, x): + 9 start_node = VJPNode.new_root() +---> 10 end_value, end_node = trace(start_node, fun, x) + 11 if end_node is None: + 12 def vjp(g): return vspace(x).zeros() + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/tracer.py:10, in trace(start_node, fun, x) + 8 with trace_stack.new_trace() as t: + 9 start_box = new_box(x, t, start_node) +---> 10 end_box = fun(start_box) + 11 if isbox(end_box) and end_box._trace == start_box._trace: + 12 return end_box._value, end_box._node + +File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:15, in unary_to_nary..nary_operator..nary_f..unary_f(x) + 13 else: + 14 subargs = subvals(args, zip(argnum, x)) +---> 15 return fun(*subargs, **kwargs) + +Input In [13], in f8(x) + 3 def f8(x): # Assume x is an array +----> 4 x[2] = 3 + 5 return x*2 + +TypeError: 'ArrayBox' object does not support item assignment +TypeError: 'ArrayBox' object does not support item assignment + diff --git a/doc/LectureNotes/_build/html/reports/week42.log b/doc/LectureNotes/_build/html/reports/week42.log new file mode 100644 index 000000000..156b429c4 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week42.log @@ -0,0 +1,29 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +pip3 install tensorflow +------------------ + + Input In [14] + pip3 install tensorflow + ^ +SyntaxError: invalid syntax + +SyntaxError: invalid syntax (2357089093.py, line 1) + diff --git a/doc/LectureNotes/_build/html/reports/week43.log b/doc/LectureNotes/_build/html/reports/week43.log new file mode 100644 index 000000000..c61efecd0 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week43.log @@ -0,0 +1,119 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# to categorical turns our integer vector into a onehot representation +from sklearn.metrics import accuracy_score + +# one-hot in numpy +def to_categorical_numpy(integer_vector): + n_inputs = len(integer_vector) + n_categories = np.max(integer_vector) + 1 + onehot_vector = np.zeros((n_inputs, n_categories)) + onehot_vector[range(n_inputs), integer_vector] = 1 + + return onehot_vector + +#Y_train_onehot, Y_test_onehot = to_categorical(Y_train), to_categorical(Y_test) +Y_train_onehot, Y_test_onehot = to_categorical_numpy(Y_train), to_categorical_numpy(Y_test) + +def feed_forward_train(X): + # weighted sum of inputs to the hidden layer + z_h = np.matmul(X, hidden_weights) + hidden_bias + # activation in the hidden layer + a_h = sigmoid(z_h) + + # weighted sum of inputs to the output layer + z_o = np.matmul(a_h, output_weights) + output_bias + # softmax output + # axis 0 holds each input and axis 1 the probabilities of each category + exp_term = np.exp(z_o) + probabilities = exp_term / np.sum(exp_term, axis=1, keepdims=True) + + # for backpropagation need activations in hidden and output layers + return a_h, probabilities + +def backpropagation(X, Y): + a_h, probabilities = feed_forward_train(X) + + # error in the output layer + error_output = probabilities - Y + # error in the hidden layer + error_hidden = np.matmul(error_output, output_weights.T) * a_h * (1 - a_h) + + # gradients for the output layer + output_weights_gradient = np.matmul(a_h.T, error_output) + output_bias_gradient = np.sum(error_output, axis=0) + + # gradient for the hidden layer + hidden_weights_gradient = np.matmul(X.T, error_hidden) + hidden_bias_gradient = np.sum(error_hidden, axis=0) + + return output_weights_gradient, output_bias_gradient, hidden_weights_gradient, hidden_bias_gradient + +print("Old accuracy on training data: " + str(accuracy_score(predict(X_train), Y_train))) + +eta = 0.01 +lmbd = 0.01 +for i in range(1000): + # calculate gradients + dWo, dBo, dWh, dBh = backpropagation(X_train, Y_train_onehot) + + # regularization term gradients + dWo += lmbd * output_weights + dWh += lmbd * hidden_weights + + # update weights and biases + output_weights -= eta * dWo + output_bias -= eta * dBo + hidden_weights -= eta * dWh + hidden_bias -= eta * dBh + +print("New accuracy on training data: " + str(accuracy_score(predict(X_train), Y_train))) +------------------ + +--------------------------------------------------------------------------- +RuntimeWarning Traceback (most recent call last) +Input In [26], in () + 53 lmbd = 0.01 + 54 for i in range(1000): + 55 # calculate gradients +---> 56 dWo, dBo, dWh, dBh = backpropagation(X_train, Y_train_onehot) + 58 # regularization term gradients + 59 dWo += lmbd * output_weights + +Input In [26], in backpropagation(X, Y) + 32 def backpropagation(X, Y): +---> 33 a_h, probabilities = feed_forward_train(X) + 35 # error in the output layer + 36 error_output = probabilities - Y + +Input In [26], in feed_forward_train(X) + 18 z_h = np.matmul(X, hidden_weights) + hidden_bias + 19 # activation in the hidden layer +---> 20 a_h = sigmoid(z_h) + 22 # weighted sum of inputs to the output layer + 23 z_o = np.matmul(a_h, output_weights) + output_bias + +Input In [25], in sigmoid(x) + 3 def sigmoid(x): +----> 4 return 1/(1 + np.exp(-x)) + +RuntimeWarning: overflow encountered in exp +RuntimeWarning: overflow encountered in exp + diff --git a/doc/LectureNotes/_build/html/reports/week44.log b/doc/LectureNotes/_build/html/reports/week44.log new file mode 100644 index 000000000..49de8aa50 --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week44.log @@ -0,0 +1,39 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply + msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async + result = await obj + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg + raise Empty +_queue.Empty + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell + exec_reply = await self.task_poll_for_reply + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply + await self._async_handle_timeout(timeout, cell) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout + raise CellTimeoutError.error_from_timeout_and_cell( +nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds. +The message was: Cell execution timed out. +Here is a preview of the cell contents: +------------------- +['CNN_keras = np.zeros((len(eta_vals), len(lmbd_vals)), dtype=object)', ' ', 'for i, eta in enumerate(eta_vals):', ' for j, lmbd in enumerate(lmbd_vals):', ' CNN = create_convolutional_neural_network_keras(input_shape, receptive_field,'] +... +[' ', ' print("Learning rate = ", eta)', ' print("Lambda = ", lmbd)', ' print("Test accuracy: %.3f" % scores[1])', ' print()'] +------------------- + diff --git a/doc/LectureNotes/_build/html/reports/week45.log b/doc/LectureNotes/_build/html/reports/week45.log new file mode 100644 index 000000000..51706797f --- /dev/null +++ b/doc/LectureNotes/_build/html/reports/week45.log @@ -0,0 +1,39 @@ +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply + msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async + result = await obj + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg + raise Empty +_queue.Empty + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete + return future.result() + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell + exec_reply = await self.task_poll_for_reply + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply + await self._async_handle_timeout(timeout, cell) + File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout + raise CellTimeoutError.error_from_timeout_and_cell( +nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds. +The message was: Cell execution timed out. +Here is a preview of the cell contents: +------------------- +['# Start importing packages', 'import pandas as pd', 'import numpy as np', 'import matplotlib.pyplot as plt', 'import tensorflow as tf'] +... +['trainScore = model.evaluate(trainX, trainY, verbose=0)', 'print(trainScore)', 'plt.plot(df)', 'plt.plot(predicted)', 'plt.show()'] +------------------- + diff --git a/doc/LectureNotes/week45.ipynb b/doc/LectureNotes/week45.ipynb index f3cbde629..d80fa50f3 100644 --- a/doc/LectureNotes/week45.ipynb +++ b/doc/LectureNotes/week45.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "7e9869f2", + "id": "967cdaca", "metadata": { "editable": true }, @@ -14,7 +14,7 @@ }, { "cell_type": "markdown", - "id": "fca263d7", + "id": "7f44e4d0", "metadata": { "editable": true }, @@ -27,7 +27,7 @@ }, { "cell_type": "markdown", - "id": "8c3d9fea", + "id": "3094316d", "metadata": { "editable": true }, @@ -58,6 +58,10 @@ "\n", " * These lecture notes\n", "\n", + " * [Video of lecture](https://youtu.be/z0x-vgyAZUk)\n", + "\n", + " * [Whiteboard notes](https://github.com/CompPhysics/MachineLearning/blob/master/doc/HandWrittenNotes/2023/NotesNov9.pdf)\n", + "\n", " * For a more in depth discussion on neural networks we recommend Goodfellow et al chapter 10. See also chapter 11 and 12 on practicalities and applications \n", "\n", " * Reading suggestions for implementation of RNNs: [Aurelien Geron's chapter 14](https://github.com/CompPhysics/MachineLearning/blob/master/doc/Textbooks/TensorflowML.pdf).\n", @@ -69,7 +73,7 @@ }, { "cell_type": "markdown", - "id": "d0107e8f", + "id": "46b1e9db", "metadata": { "editable": true }, @@ -79,7 +83,7 @@ }, { "cell_type": "markdown", - "id": "44ed2bb7", + "id": "19315bd5", "metadata": { "editable": true }, @@ -98,7 +102,7 @@ { "cell_type": "code", "execution_count": 1, - "id": "7d202a1c", + "id": "d03a6f44", "metadata": { "collapsed": false, "editable": true @@ -155,7 +159,7 @@ }, { "cell_type": "markdown", - "id": "0fcc974f", + "id": "e6cbd4ca", "metadata": { "editable": true }, @@ -167,7 +171,7 @@ }, { "cell_type": "markdown", - "id": "693475c8", + "id": "1ea723fc", "metadata": { "editable": true }, @@ -182,7 +186,7 @@ { "cell_type": "code", "execution_count": 2, - "id": "cdd8cf73", + "id": "0ebb62df", "metadata": { "collapsed": false, "editable": true @@ -235,7 +239,7 @@ }, { "cell_type": "markdown", - "id": "51ef3976", + "id": "0fb161e1", "metadata": { "editable": true }, @@ -250,7 +254,7 @@ }, { "cell_type": "markdown", - "id": "033bda9d", + "id": "8bdb137e", "metadata": { "editable": true }, @@ -270,7 +274,7 @@ { "cell_type": "code", "execution_count": 3, - "id": "0a320c52", + "id": "af61779f", "metadata": { "collapsed": false, "editable": true @@ -324,7 +328,7 @@ }, { "cell_type": "markdown", - "id": "bcd8ea70", + "id": "89f07674", "metadata": { "editable": true }, @@ -339,7 +343,7 @@ { "cell_type": "code", "execution_count": 4, - "id": "6fe70002", + "id": "37c8ca05", "metadata": { "collapsed": false, "editable": true @@ -366,7 +370,7 @@ }, { "cell_type": "markdown", - "id": "c4440f93", + "id": "509bf7a9", "metadata": { "editable": true }, @@ -380,7 +384,7 @@ { "cell_type": "code", "execution_count": 5, - "id": "96a74e80", + "id": "e9d06a0c", "metadata": { "collapsed": false, "editable": true @@ -425,7 +429,7 @@ }, { "cell_type": "markdown", - "id": "98525677", + "id": "ab1f9810", "metadata": { "editable": true }, @@ -450,7 +454,7 @@ { "cell_type": "code", "execution_count": 6, - "id": "d00d3339", + "id": "d8a5dabe", "metadata": { "collapsed": false, "editable": true @@ -462,7 +466,7 @@ }, { "cell_type": "markdown", - "id": "39d74647", + "id": "69fd6511", "metadata": { "editable": true }, @@ -473,7 +477,7 @@ { "cell_type": "code", "execution_count": 7, - "id": "382459a0", + "id": "b74de9e5", "metadata": { "collapsed": false, "editable": true @@ -485,7 +489,7 @@ }, { "cell_type": "markdown", - "id": "06da1caf", + "id": "24e267e4", "metadata": { "editable": true }, @@ -498,7 +502,7 @@ }, { "cell_type": "markdown", - "id": "2d846128", + "id": "77a9c527", "metadata": { "editable": true }, @@ -531,7 +535,7 @@ }, { "cell_type": "markdown", - "id": "23991e3b", + "id": "5f6ea3f0", "metadata": { "editable": true }, @@ -545,7 +549,7 @@ }, { "cell_type": "markdown", - "id": "4581b004", + "id": "b0d324b8", "metadata": { "editable": true }, @@ -557,7 +561,7 @@ }, { "cell_type": "markdown", - "id": "855fc1d5", + "id": "d5593af9", "metadata": { "editable": true }, @@ -569,7 +573,7 @@ }, { "cell_type": "markdown", - "id": "7b676376", + "id": "e857f89e", "metadata": { "editable": true }, @@ -581,7 +585,7 @@ }, { "cell_type": "markdown", - "id": "64e4f58f", + "id": "13dc6da3", "metadata": { "editable": true }, @@ -591,7 +595,7 @@ }, { "cell_type": "markdown", - "id": "6bef46ee", + "id": "0f77aa9a", "metadata": { "editable": true }, @@ -603,7 +607,7 @@ }, { "cell_type": "markdown", - "id": "ed7cfd1e", + "id": "3c560ddf", "metadata": { "editable": true }, @@ -613,7 +617,7 @@ }, { "cell_type": "markdown", - "id": "307589a6", + "id": "b46686df", "metadata": { "editable": true }, @@ -625,7 +629,7 @@ }, { "cell_type": "markdown", - "id": "24f17f38", + "id": "24aec375", "metadata": { "editable": true }, @@ -636,7 +640,7 @@ }, { "cell_type": "markdown", - "id": "e825c026", + "id": "8d288b9d", "metadata": { "editable": true }, @@ -655,7 +659,7 @@ }, { "cell_type": "markdown", - "id": "6dcb34a4", + "id": "e1663205", "metadata": { "editable": true }, @@ -667,7 +671,7 @@ }, { "cell_type": "markdown", - "id": "a975cae8", + "id": "b34d890c", "metadata": { "editable": true }, @@ -677,7 +681,7 @@ }, { "cell_type": "markdown", - "id": "d4971baf", + "id": "14e7f314", "metadata": { "editable": true }, @@ -689,7 +693,7 @@ }, { "cell_type": "markdown", - "id": "a4bd001d", + "id": "879bac6b", "metadata": { "editable": true }, @@ -701,7 +705,7 @@ }, { "cell_type": "markdown", - "id": "a8b1f114", + "id": "31d2b3b7", "metadata": { "editable": true }, @@ -713,7 +717,7 @@ }, { "cell_type": "markdown", - "id": "959cdbff", + "id": "34fd7537", "metadata": { "editable": true }, @@ -723,7 +727,7 @@ }, { "cell_type": "markdown", - "id": "59ee7f47", + "id": "4bebbe84", "metadata": { "editable": true }, @@ -735,7 +739,7 @@ }, { "cell_type": "markdown", - "id": "5cdba722", + "id": "690c8d76", "metadata": { "editable": true }, @@ -763,7 +767,7 @@ }, { "cell_type": "markdown", - "id": "35390ed4", + "id": "12d8a75e", "metadata": { "editable": true }, @@ -775,7 +779,7 @@ }, { "cell_type": "markdown", - "id": "b1651ea3", + "id": "1df29154", "metadata": { "editable": true }, @@ -800,7 +804,7 @@ }, { "cell_type": "markdown", - "id": "1bfac852", + "id": "9083178e", "metadata": { "editable": true }, @@ -818,7 +822,7 @@ }, { "cell_type": "markdown", - "id": "f655bb24", + "id": "e7719466", "metadata": { "editable": true }, @@ -829,7 +833,7 @@ { "cell_type": "code", "execution_count": 8, - "id": "31f4ee21", + "id": "bcddf060", "metadata": { "collapsed": false, "editable": true @@ -872,7 +876,7 @@ }, { "cell_type": "markdown", - "id": "098bfaec", + "id": "6ec55e94", "metadata": { "editable": true }, @@ -882,7 +886,7 @@ }, { "cell_type": "markdown", - "id": "55cc0e20", + "id": "690b1a08", "metadata": { "editable": true }, @@ -909,7 +913,7 @@ }, { "cell_type": "markdown", - "id": "8860da9c", + "id": "825bc136", "metadata": { "editable": true }, @@ -920,7 +924,7 @@ { "cell_type": "code", "execution_count": 9, - "id": "7252c0b8", + "id": "ce956b33", "metadata": { "collapsed": false, "editable": true @@ -993,7 +997,7 @@ }, { "cell_type": "markdown", - "id": "fcbca2f7", + "id": "002c4d99", "metadata": { "editable": true }, @@ -1013,7 +1017,7 @@ }, { "cell_type": "markdown", - "id": "1c5b70a2", + "id": "6572c07f", "metadata": { "editable": true }, @@ -1029,7 +1033,7 @@ }, { "cell_type": "markdown", - "id": "29c129fe", + "id": "fbd8e269", "metadata": { "editable": true }, @@ -1051,7 +1055,7 @@ }, { "cell_type": "markdown", - "id": "c2bc1aa3", + "id": "919bb09e", "metadata": { "editable": true }, @@ -1069,7 +1073,7 @@ }, { "cell_type": "markdown", - "id": "01ef7e17", + "id": "6e3360db", "metadata": { "editable": true }, @@ -1115,7 +1119,7 @@ }, { "cell_type": "markdown", - "id": "8dd26bf6", + "id": "0f284cbd", "metadata": { "editable": true }, @@ -1136,7 +1140,7 @@ }, { "cell_type": "markdown", - "id": "3b42d5ef", + "id": "b5e9785e", "metadata": { "editable": true }, @@ -1197,7 +1201,7 @@ }, { "cell_type": "markdown", - "id": "2f8de715", + "id": "50a43c30", "metadata": { "editable": true }, @@ -1222,7 +1226,7 @@ }, { "cell_type": "markdown", - "id": "9998cb2c", + "id": "f3e0d31b", "metadata": { "editable": true }, @@ -1241,7 +1245,7 @@ }, { "cell_type": "markdown", - "id": "45dfbeff", + "id": "b1571231", "metadata": { "editable": true }, @@ -1265,7 +1269,7 @@ }, { "cell_type": "markdown", - "id": "141b8f50", + "id": "e7886dd3", "metadata": { "editable": true }, @@ -1347,7 +1351,7 @@ }, { "cell_type": "markdown", - "id": "fbadc1e0", + "id": "f878b195", "metadata": { "editable": true }, @@ -1363,7 +1367,7 @@ { "cell_type": "code", "execution_count": 10, - "id": "9365f92f", + "id": "1889da48", "metadata": { "collapsed": false, "editable": true @@ -1402,7 +1406,7 @@ }, { "cell_type": "markdown", - "id": "55c2aa23", + "id": "5bf3bea4", "metadata": { "editable": true }, @@ -1446,7 +1450,7 @@ { "cell_type": "code", "execution_count": 11, - "id": "b57a3099", + "id": "6fc9b3dd", "metadata": { "collapsed": false, "editable": true @@ -1529,7 +1533,7 @@ }, { "cell_type": "markdown", - "id": "0b519f6c", + "id": "6b02bff4", "metadata": { "editable": true }, @@ -1540,7 +1544,7 @@ { "cell_type": "code", "execution_count": 12, - "id": "82db8594", + "id": "7030f585", "metadata": { "collapsed": false, "editable": true @@ -1642,7 +1646,7 @@ }, { "cell_type": "markdown", - "id": "4711b0d4", + "id": "53dc1510", "metadata": { "editable": true }, @@ -1664,7 +1668,7 @@ { "cell_type": "code", "execution_count": 13, - "id": "22123a0f", + "id": "62aa2c1c", "metadata": { "collapsed": false, "editable": true @@ -1761,7 +1765,7 @@ }, { "cell_type": "markdown", - "id": "50cd4d20", + "id": "56fb2d92", "metadata": { "editable": true }, @@ -1787,7 +1791,7 @@ { "cell_type": "code", "execution_count": 14, - "id": "5c3d5a53", + "id": "145ed525", "metadata": { "collapsed": false, "editable": true