Add polar plots code and example

examples/polar_plot_generation.py

@@ -0,0 +1,19 @@
+import tmd
+from view import polar_plots
+
+filename = './'
+
+pop = tmd.io.load_population(filename)
+
+# Get the data for a single cell
+res = polar_plots.get_histogram_polar_coordinates(pop.neurons[0], neurite_type='basal', N=30)
+
+# Plot the data for a single cell
+polar_plots.plot_polar_coordinates(res)
+
+# Extract the polar plots of all neurons in the population and save images
+# in a selected directory
+for n in pop.neurons:
+    res = polar_plots.get_histogram_polar_coordinates(n, neurite_type='basal', N=30)
+    polar_plots.plot_polar_coordinates(res, output_path='./PolarPlots/', output_name=n.name.split('/')[-1])
+    plt.close()

view/polar_plots.py

@@ -0,0 +1,49 @@
+import numpy as np
+from matplotlib import pylab as plt
+
+def get_histogram_polar_coordinates(neuron, neurite_type='basal', N=25):
+    '''
+    '''
+    def seg_angle(seg):
+        mean_x = np.mean([seg[0][0], seg[1][0]])
+        mean_y = np.mean([seg[0][1], seg[1][1]])
+
+        return np.arctan2(mean_y, mean_x)
+
+    segs = []
+    for tr in getattr(neuron, neurite_type):
+     segs = segs + tr.get_segments()
+
+    angles = np.array([seg_angle(s) for s in segs])
+    lens = []
+
+    for tr in getattr(neuron, neurite_type):
+        lens = lens + tr.get_segment_lengths().tolist()
+
+    angles = np.array(angles)
+    lens = np.array(lens)
+
+    step = 2*np.pi/N
+    ranges = [[i*step -np.pi, (i+1)*step-np.pi] for i in xrange(N)]
+
+    results = []
+
+    for r in ranges:
+        results.append(r + [np.sum(lens[np.where((angles > r[0]) & (angles < r[1]))[0]])])
+
+    return results
+
+
+def plot_polar_coordinates(input_data, output_name=None, output_path=None, output_format='png'):
+    '''
+    '''
+    fig = plt.figure()
+    ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], polar=True)
+
+    theta = np.array(input_data)[:,0]
+    radii = np.array(input_data)[:,2] / np.max(input_data)
+    width = 2*np.pi/len(input_data)
+    bars = ax.bar(theta, radii, width=width, bottom=0.0, alpha=0.8)
+
+    if output_path is not None:
+        plt.savefig(output_path + '/Polar_' + output_name, format=output_format)