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from ragGen import *
import csv
import numpy as np


    

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# Read in the data
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]

# These will come in handy later
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])))


    

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real_volume = np.zeros((len(sorted_y), len(sorted_x), len(sorted_z)))
for r in rows:
    real_volume[sorted_y.index(r[1]), sorted_x.index(r[0]), sorted_z.index(r[2])] = r[-1]


    

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test_im = real_volume[1]

ragu = generate_rag(test_im, False)
ragu.number_of_edges()
# ragu.adjacency_list()


    

    




---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-53-7231590aa225> in <module>()
      1 test_im = real_volume[1]
      2 
----> 3 ragu = rag.generate_rag(test_im, False)
      4 ragu.number_of_edges()
      5 # ragu.adjacency_list()

/Users/davidwestjr/git/uhhh/code/ragGen.py in generate_rag(im, linear)
      3 import numpy as np
      4 
----> 5 # Generates the Region Adjacency Graph
      6 def generate_rag(im, linear):
      7     G=nx.Graph()

NameError: global name 'nx' is not defined

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