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%matplotlib notebook

Week 4



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import numpy as np
import seaborn as sns
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import csv



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data = open('../data/data.csv', 'r').readlines()
fieldnames = ['x', 'y', 'z', 'unmasked', 'synapses']
reader = csv.reader(data)
reader.next()

rows = [[int(col) for col in row] for row in reader]

xs = []
ys = []
zs = []
ss = []

sorted_x = sorted(list(set([r[0] for r in rows])))
sorted_y = sorted(list(set([r[1] for r in rows])))
sorted_z = sorted(list(set([r[2] for r in rows])))

vol = np.zeros((len(sorted_x), len(sorted_y), len(sorted_z)))
for r in rows:
    xs.append(r[0])
    ys.append(r[1])
    zs.append(r[2])
    ss.append(r[4])
    vol[sorted_x.index(r[0]), sorted_y.index(r[1]), sorted_z.index(r[2])] = r[-1]

1. 3D Heatmap

NOTE: This demo will be slow on low-spec computers (like mine).



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fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(xs,ys,zs, marker='o', s=ss, c="goldenrod", alpha=0.4)
for ii in xrange(0,360,1):
    ax.view_init(elev=10., azim=ii)
fig.show()

2. Heatmap after thresholding

Here, we assume that there is some level of noise, which can be defined by redefining THRESH below. The same heatmap is generated, but only for values where the synapse count is higher than the threshold, thus attempting to remove noise.



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THRESH = np.mean(ss) * 3/2



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print len(xs), len(ss)
ss_poppable = []
for s in range(len(ss)):
    if ss[s] < THRESH:
        ss_poppable.append(s)

for s in reversed(ss_poppable):
    xs.pop(s)
    ys.pop(s)
    zs.pop(s)
    ss.pop(s)
    
fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(xs,ys,zs, marker='o', s=ss, c="goldenrod", alpha=0.005)
ax.view_init(elev=11., azim=25)
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
ax.title("Heatmap of Synapses")
# fig.show()









    



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-------------------------------------------------------------------
TypeError                         Traceback (most recent call last)
<ipython-input-40-0e5e4b524d94> in <module>()
     18 ax.set_ylabel('y')
     19 ax.set_zlabel('z')
---> 20 ax.title("Heatmap of Synapses")
     21 # fig.show()

TypeError: 'Text' object is not callable



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ss[0]









    Out[31]:





0.0014990352637338398



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