Major refactoring to more closely conform to Python style best practi…

…ces.
BindsNET · Jun 11, 2018 · e48cbdd · e48cbdd
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diff --git a/bindsnet/analysis/plotting.py b/bindsnet/analysis/plotting.py
diff --git a/bindsnet/analysis/visualization.py b/bindsnet/analysis/visualization.py
@@ -14,10 +14,9 @@ def plot_weights_movie(ws, sample_every=1):
     
     Inputs:
     
-        | :code:`ws` (:code:`numpy.array`): Numpy array of shape :code:`[N_examples, source, target, time]`
-        | :code:`sample_every` (:code:`int`): Sub-sample using this parameter. For example if :code:`time` is
-                                                                  too large (500), set this parameter to 20 to sample weights 
-                                                                  every 20 iterations. 
+        | :code:`ws` (:code:`numpy.array`): Numpy array
+        of shape :code:`[n_examples, source, target, time]`
+        | :code:`sample_every` (:code:`int`): Sub-sample using this parameter. 
     """
     weights = []
 
@@ -49,10 +48,13 @@ def plot_spike_trains_for_example(spikes, n_ex=None, top_k=None, indices=None):
     
     Inputs:
         
-        | :code:`spikes` (:code:`torch.Tensor (n_examples, n_neurons, time)`): Spiking train data for a population of neurons for one example.
-        | :code:`n_ex` (:code:`int`): Allows user to pick which example to plot spikes for. Must be >= 0.
+        | :code:`spikes` (:code:`torch.Tensor (n_examples, n_neurons, time)`):
+        Spiking train data for a population of neurons for one example.
+        | :code:`n_ex` (:code:`int`): Allows user to pick
+        which example to plot spikes for. Must be >= 0.
         | :code:`top_k` (:code:`int`): Plot k neurons that spiked the most for n_ex example.
-        | :code:`indices` (:code:`list(int)`): Plot specific neurons' spiking activity instead of top_k. Meant to replace top_k. 
+        | :code:`indices` (:code:`list(int)`): Plot specific neurons'
+        spiking activity instead of top_k. Meant to replace top_k. 
     '''
 
     assert (n_ex is not None and n_ex >= 0 and n_ex < spikes.shape[0])
@@ -84,11 +86,16 @@ def plot_voltage(voltage, n_ex=0, n_neuron=0, time=None, threshold=None):
     
     Inputs:
         
-        | :code:`voltage` (:code:`torch.Tensor` or :code:`numpy.array`): Tensor or array of shape :code:`[n_examples, n_neurons, time]`.
-        | :code:`n_ex` (:code:`int`): Allows user to pick which example to plot voltage for.
-        | :code:`n_neuron` (:code:`int`): Neuron index for which to plot voltages for.
-        | :code:`time` (:code:`tuple(int)`): Plot spiking activity of neurons between the given range of time. 
-        | :code:`threshold` (:code:`float`): Neuron spiking threshold. Will be shown on the plot.
+        | :code:`voltage` (:code:`torch.Tensor` or :code:`numpy.array`):
+        Tensor or array of shape :code:`[n_examples, n_neurons, time]`.
+        | :code:`n_ex` (:code:`int`): Allows user
+        to pick which example to plot voltage for.
+        | :code:`n_neuron` (:code:`int`): Neuron
+        index for which to plot voltages for.
+        | :code:`time` (:code:`tuple(int)`): Plot spiking
+        activity of neurons between the given range of time. 
+        | :code:`threshold` (:code:`float`): Neuron
+        spiking threshold. Will be shown on the plot.
     '''
 
     assert (n_ex >= 0 and n_neuron >= 0)
@@ -105,7 +112,9 @@ def plot_voltage(voltage, n_ex=0, n_neuron=0, time=None, threshold=None):
 
     plt.figure()
     plt.plot(voltage[n_ex, n_neuron, timer])
-    plt.xlabel('Simulation Time'); plt.ylabel('Voltage'); plt.title('Membrane voltage of neuron %d for example %d'%(n_neuron, n_ex+1))
+    plt.xlabel('Simulation Time')
+    plt.ylabel('Voltage')
+    plt.title('Membrane voltage of neuron %d for example %d' % (n_neuron, n_ex + 1))
     locs, labels = plt.xticks()
     locs = range(int(locs[1]), int(locs[-1]), 10)
     plt.xticks(locs, time_ticks)

diff --git a/bindsnet/datasets/__init__.py b/bindsnet/datasets/__init__.py
diff --git a/bindsnet/datasets/preprocess.py b/bindsnet/datasets/preprocess.py
@@ -12,13 +12,12 @@ def gray_scale(im):
         
         | :code:`im` (:code:`numpy.array`): Grayscaled image
     '''
-    im = cv2.cvtColor(im, cv2.COLOR_RGB2GRAY)
-    return im
+    return cv2.cvtColor(im, cv2.COLOR_RGB2GRAY)
 
 
 def crop(im, x1, x2, y1, y2):
     return im[x1:x2, y1:y2, :]
-    
+
 
 def binary_image(im):
     '''
@@ -32,7 +31,7 @@ def binary_image(im):
         
         | :code:`im` (:code:`numpy.array`): Black and white image. 
     '''
-    ret, im = cv2.threshold(im, 0, 1, cv2.THRESH_BINARY)
+    _, im = cv2.threshold(im, 0, 1, cv2.THRESH_BINARY)
     return im
 
 
@@ -50,6 +49,4 @@ def subsample(im, x, y):
         
         | :code:`im` (:code:`numpy.array`): Rescaled image. 
     '''
-    im = cv2.resize(im, (x, y))
-    return im 
-
+    return cv2.resize(im, (x, y))                         
diff --git a/bindsnet/encoding/__init__.py b/bindsnet/encoding/__init__.py
@@ -4,7 +4,9 @@
 
 def bernoulli(datum, time=None, **kwargs):
     '''
-    Generates Bernoulli-distributed spike trains based on input intensity. Inputs must be non-negative. Spikes correspond to successful Bernoulli trials, with success probability equal to (normalized in [0, 1]) input value.
+    Generates Bernoulli-distributed spike trains based on input intensity.
+    Inputs must be non-negative. Spikes correspond to successful Bernoulli
+    trials, with success probability equal to (normalized in [0, 1]) input value.
 
     Inputs:
     
@@ -13,11 +15,13 @@ def bernoulli(datum, time=None, **kwargs):
         
         Keyword arguments:
             
-            | :code:`max_prob` (:code:`float`): Maximum probability of spike per Bernoulli trial.
+            | :code:`max_prob` (:code:`float`): Maximum
+            probability of spike per Bernoulli trial.
     
     Returns:
     
-        | (:code:`torch.Tensor`): Tensor of shape :code:`[time, n_1, ..., n_k]` of Bernoulli-distributed spikes.
+        | (:code:`torch.Tensor`): Tensor of shape :code:`[time, n_1, ..., n_k]`
+        of Bernoulli-distributed spikes.
     '''
     # Setting kwargs.
     max_prob = kwargs.get('max_prob', 1.0)
@@ -48,7 +52,8 @@ def bernoulli_loader(data, time=None, **kwargs):
 
     Inputs:
     
-        | :code:`data` (:code:`torch.Tensor` or iterable of :code:`torch.Tensor`s): Tensor of shape :code:`[n_samples, n_1, ..., n_k]`.
+        | :code:`data` (:code:`torch.Tensor` or iterable of :code:`torch.Tensor`s):
+        Tensor of shape :code:`[n_samples, n_1, ..., n_k]`.
         | :code:`time` (:code:`int`): Length of Bernoulli spike train per input variable.
         
         Keyword arguments:
@@ -57,7 +62,8 @@ def bernoulli_loader(data, time=None, **kwargs):
     
     Yields:
     
-        | (:code:`torch.Tensor`): Tensors of shape :code:`[time, n_1, ..., n_k]` of Bernoulli-distributed spikes.
+        | (:code:`torch.Tensor`): Tensors of shape :code:`[time, n_1, ..., n_k]`
+        of Bernoulli-distributed spikes.
     '''
 
     # Setting kwargs.
@@ -68,7 +74,8 @@ def bernoulli_loader(data, time=None, **kwargs):
 
 def poisson(datum, time, **kwargs):
     '''
-    Generates Poisson-distributed spike trains based on input intensity. Inputs must be non-negative.
+    Generates Poisson-distributed spike trains based
+    on input intensity. Inputs must be non-negative.
 
     Inputs:
     
@@ -77,7 +84,8 @@ def poisson(datum, time, **kwargs):
     
     Returns:
     
-        | (:code:`torch.Tensor`): Tensor of shape :code:`[time, n_1, ..., n_k]` of Poisson-distributed spikes.
+        | (:code:`torch.Tensor`): Tensor of shape :code:`[time, n_1, ..., n_k]`
+        of Poisson-distributed spikes.
     '''
     datum = np.copy(datum)
     shape, size = datum.shape, datum.size
@@ -107,29 +115,36 @@ def poisson_loader(data, time, **kwargs):
     
     Inputs:
     
-        | :code:`data` (:code:`torch.Tensor` or iterable of :code:`torch.Tensor`s): Tensor of shape :code:`[n_samples, n_1, ..., n_k]`
+        | :code:`data` (:code:`torch.Tensor` or iterable of :code:`torch.Tensor`s):
+        Tensor of shape :code:`[n_samples, n_1, ..., n_k]`
         | :code:`time` (:code:`int`): Length of Poisson spike train per input variable.
 
     Yields:
     
-        | (:code:`torch.Tensor`): Tensors of shape :code:`[time, n_1, ..., n_k]` of Poisson-distributed spikes.
+        | (:code:`torch.Tensor`): Tensors of shape :code:`[time, n_1, ..., n_k]`
+        of Poisson-distributed spikes.
     '''
     for i in range(len(data)):
         yield poisson(data[i], time)  # Encode datum as Poisson spike trains.
 
 
 def rank_order(datum, time, **kwargs):
     '''
-    Encodes data via a rank order coding-like representation. One spike per neuron, temporally ordered by decreasing intensity. Inputs must be non-negative.
+    Encodes data via a rank order coding-like representation. One
+    spike per neuron, temporally ordered by decreasing intensity.
+    Inputs must be non-negative.
     
     Inputs:
     
-        | :code:`data` (:code:`torch.Tensor`): Tensor of shape :code:`[n_samples, n_1, ..., n_k]`
-        | :code:`time` (:code:`int`): Length of Poisson spike train per input variable.
+        | :code:`data` (:code:`torch.Tensor`): Tensor
+        of shape :code:`[n_samples, n_1, ..., n_k]`
+        | :code:`time` (:code:`int`): Length of rank
+        order-encoded spike train per input variable.
 
     Returns:
     
-        | (:code:`torch.Tensor`): Tensor of shape :code:`[time, n_1, ..., n_k]` of Poisson-distributed spikes.
+        | (:code:`torch.Tensor`): Tensor of shape
+        :code:`[time, n_1, ..., n_k]` of rank order-encoded spikes.
     '''
     datum = np.copy(datum)
     shape, size = datum.shape, datum.size
@@ -155,16 +170,20 @@ def rank_order(datum, time, **kwargs):
 
 def rank_order_loader(data, time, **kwargs):
     '''
-    Lazily invokes :code:`bindsnet.encoding.rank_order` to iteratively encode a sequence of data.
+    Lazily invokes :code:`bindsnet.encoding.rank_order`
+    to iteratively encode a sequence of data.
     
     Inputs:
     
-        | :code:`data` (:code:`torch.Tensor` or iterable of :code:`torch.Tensor`s): Tensor of shape :code:`[n_samples, n_1, ..., n_k]`
-        | :code:`time` (:code:`int`): Length of Poisson spike train per input variable.
+        | :code:`data` (:code:`torch.Tensor` or iterable of :code:`torch.Tensor`s):
+        Tensor of shape :code:`[n_samples, n_1, ..., n_k]`
+        | :code:`time` (:code:`int`): Length of rank
+        order-encoded spike train per input variable.
 
     Yields:
     
-        | (:code:`torch.Tensor`): Tensors of shape :code:`[time, n_1, ..., n_k]` of rank order-encoded spikes.
+        | (:code:`torch.Tensor`): Tensors of shape :code:`[time, n_1, ..., n_k]`
+        of rank order-encoded spikes.
     '''
     for i in range(len(data)):
         yield rank_order(data[i], time)  # Encode datum as rank order-encoded spike trains.
diff --git a/bindsnet/environment/__init__.py b/bindsnet/environment/__init__.py
@@ -33,7 +33,8 @@ def __init__(self, dataset, train=True, time=350, **kwargs):
         self.intensity = kwargs.get('intensity', 1)
         self.max_prob = kwargs.get('max_prob', 1)
 
-        assert self.max_prob > 0 and self.max_prob <= 1, 'Maximum spiking probability must be in (0, 1].'
+        assert self.max_prob > 0 and self.max_prob <= 1, \
+            'Maximum spiking probability must be in (0, 1].'
 
         if train:
             self.data, self.labels = self.dataset.get_train()
@@ -50,14 +51,14 @@ def step(self, a=None):
         
         Inputs:
         
-            | :code:`a` (:code:`None`): There is no interaction of the network with the MNIST dataset.
+            | :code:`a` (:code:`None`): There is no interaction of the network the dataset.
 
         Returns:
 
-            | :code:`obs` (:code:`torch.Tensor`): Observation from the environment (spike train-encoded MNIST digit).
+            | :code:`obs` (:code:`torch.Tensor`): Observation from the environment.
             | :code:`reward` (:code:`float`): Fixed to :code:`0`.
             | :code:`done` (:code:`bool`): Fixed to :code:`False`.
-            | :code:`info` (:code:`dict`): Contains label of MNIST digit.
+            | :code:`info` (:code:`dict`): Contains label of data item.
         '''
         try:
             # Attempt to fetch the next observation.
@@ -140,7 +141,8 @@ def __init__(self, name, **kwargs):
         # Keyword arguments.
         self.max_prob = kwargs.get('max_prob', 1)
 
-        assert self.max_prob > 0 and self.max_prob <= 1, 'Maximum spiking probability must be in (0, 1].'
+        assert self.max_prob > 0 and self.max_prob <= 1, \
+            'Maximum spiking probability must be in (0, 1].'
 
     def step(self, a):
         '''

diff --git a/bindsnet/evaluation/__init__.py b/bindsnet/evaluation/__init__.py
@@ -7,16 +7,21 @@ def assign_labels(spikes, labels, n_labels, rates=None, alpha=1.0):
     
     Inputs:
     
-        | :code:`spikes` (:code:`torch.Tensor`): Binary tensor of shape :code:`(n_samples, time, n_neurons)` of a single layer's spiking activity.
-        | :code:`labels` (:code:`torch.Tensor`): Vector of shape :code:`(n_samples,)` with data labels corresponding to spiking activity.
+        | :code:`spikes` (:code:`torch.Tensor`): Binary tensor of shape
+        :code:`(n_samples, time, n_neurons)` of a single layer's spiking activity.
+        | :code:`labels` (:code:`torch.Tensor`): Vector of shape :code:`(n_samples,)`
+        with data labels corresponding to spiking activity.
         | :code:`n_labels` (:code:`int`): The number of target labels in the data.
-        | :code:`rates` (:code:`torch.Tensor`): If passed, these represent spike rates from a previous :code:`assign_labels()` call.
+        | :code:`rates` (:code:`torch.Tensor`): If passed, these represent spike
+        rates from a previous :code:`assign_labels()` call.
         | :code:`alpha` (:code:`float`): Rate of decay of label assignments.
     
     Returns:
     
-        | (:code:`torch.Tensor`): Vector of shape :code:`(n_neurons,)` of neuron label assignments.
-        | (:code:`torch.Tensor`): Vector of shape :code:`(n_neurons, n_labels)` of proportions of firing activity per neuron, per data label.
+        | (:code:`torch.Tensor`): Vector of shape
+        :code:`(n_neurons,)` of neuron label assignments.
+        | (:code:`torch.Tensor`): Vector of shape :code:`(n_neurons, n_labels)`
+        of proportions of firing activity per neuron, per data label.
     '''
     n_neurons = spikes.size(2)
 
@@ -53,13 +58,16 @@ def all_activity(spikes, assignments, n_labels):
     
     Inputs:
     
-        | :code:`spikes` (:code:`torch.Tensor`): Binary tensor of shape :code:`(n_samples, time, n_neurons)` of a layer's spiking activity.
-        | :code:`assignments` (:code:`torch.Tensor`): A vector of shape :code:`(n_neurons,)` of neuron label assignments.
+        | :code:`spikes` (:code:`torch.Tensor`): Binary tensor of shape
+        :code:`(n_samples, time, n_neurons)` of a layer's spiking activity.
+        | :code:`assignments` (:code:`torch.Tensor`): A vector of shape
+        :code:`(n_neurons,)` of neuron label assignments.
         | :code:`n_labels` (:code:`int`): The number of target labels in the data.
     
     Returns:
     
-        | (:code:`torch.Tensor`): Predictions tensor of shape :code:`(n_samples,)` resulting from the "all activity" classification scheme.
+        | (:code:`torch.Tensor`): Predictions tensor of shape :code:`(n_samples,)`
+        resulting from the "all activity" classification scheme.
     '''
     n_samples = spikes.size(0)
 
@@ -88,18 +96,23 @@ def all_activity(spikes, assignments, n_labels):
 
 def proportion_weighting(spikes, assignments, proportions, n_labels):
     '''
-    Classify data with the label with highest average spiking activity over all neurons, weighted by class-wise proportion..
+    Classify data with the label with highest average spiking
+    activity over all neurons, weighted by class-wise proportion.
     
     Inputs:
     
-        | :code:`spikes` (:code:`torch.Tensor`): Binary tensor of shape :code:`(n_samples, time, n_neurons)` of a single layer's spiking activity.
-        | :code:`assignments` (:code:`torch.Tensor`): A vector of shape :code:`(n_neurons,)` of neuron label assignments.
-        | :code:`proportions` (torch.Tensor): A matrix of shape :code:`(n_neurons, n_labels)` giving the per-class proportions of neuron spiking activity.
+        | :code:`spikes` (:code:`torch.Tensor`): Binary tensor of shape
+        :code:`(n_samples, time, n_neurons)` of a single layer's spiking activity.
+        | :code:`assignments` (:code:`torch.Tensor`): A vector of shape
+        :code:`(n_neurons,)` of neuron label assignments.
+        | :code:`proportions` (torch.Tensor): A matrix of shape :code:`(n_neurons, n_labels)`
+        giving the per-class proportions of neuron spiking activity.
         | :code:`n_labels` (:code:`int`): The number of target labels in the data.
     
     Returns:
     
-        | (:code:`torch.Tensor`): Predictions tensor of shape :code:`(n_samples,)` resulting from the "proportion weighting" classification scheme.
+        | (:code:`torch.Tensor`): Predictions tensor of shapez:code:`(n_samples,)`
+        resulting from the "proportion weighting" classification scheme.
     '''
     n_samples = spikes.size(0)