In [4]:

    

%matplotlib inline


    

In [5]:

    

from matplotlib import pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns


    

    




:0: FutureWarning: IPython widgets are experimental and may change in the future.

In [6]:

    

import csv

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]

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:
    vol[sorted_x.index(r[0]), sorted_y.index(r[1]), sorted_z.index(r[2])] = r[-1]


    

In [7]:

    

x = [r[3] for r in rows]
y = [r[4] for r in rows]
plt.scatter(x=x, y=y, c='c')
plt.hold(True)
plt.plot([0, 150000], [0, 512], color="r")
plt.plot([0, 150000], [0, 300], color="r")
plt.xlabel("Unmasked Count")
plt.ylabel("Synapse Count")
plt.title("Synapse count with regards to unmasked count", fontdict={
        'fontsize': '16',
        'fontweight': 'bold'
})
plt.hold(False)


    

    




/usr/local/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  if self._edgecolors == str('face'):






    

In [1]:

    

from PIL import Image
import urllib, cStringIO

file = cStringIO.StringIO(urllib.urlopen("http://openconnecto.me/ocp/ca/bock11/image/xy/7/0,1050/0,936/2917/").read())
img = Image.open(file)
img_array = np.array(img)


    

    




---------------------------------------------------------------------------
KeyboardInterrupt                         Traceback (most recent call last)
<ipython-input-1-2122421ccba0> in <module>()
      2 import urllib, cStringIO
      3 
----> 4 file = cStringIO.StringIO(urllib.urlopen("http://openconnecto.me/ocp/ca/bock11/image/xy/7/0,1050/0,936/2917/").read())
      5 img = Image.open(file)
      6 img_array = np.array(img)

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in urlopen(url, data, proxies, context)
     85         opener = _urlopener
     86     if data is None:
---> 87         return opener.open(url)
     88     else:
     89         return opener.open(url, data)

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in open(self, fullurl, data)
    211         try:
    212             if data is None:
--> 213                 return getattr(self, name)(url)
    214             else:
    215                 return getattr(self, name)(url, data)

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in open_http(self, url, data)
    348         if realhost: h.putheader('Host', realhost)
    349         for args in self.addheaders: h.putheader(*args)
--> 350         h.endheaders(data)
    351         errcode, errmsg, headers = h.getreply()
    352         fp = h.getfile()

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in endheaders(self, message_body)
   1047         else:
   1048             raise CannotSendHeader()
-> 1049         self._send_output(message_body)
   1050 
   1051     def request(self, method, url, body=None, headers={}):

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in _send_output(self, message_body)
    891             msg += message_body
    892             message_body = None
--> 893         self.send(msg)
    894         if message_body is not None:
    895             #message_body was not a string (i.e. it is a file) and

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in send(self, data)
    853         if self.sock is None:
    854             if self.auto_open:
--> 855                 self.connect()
    856             else:
    857                 raise NotConnected()

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in connect(self)
    830         """Connect to the host and port specified in __init__."""
    831         self.sock = self._create_connection((self.host,self.port),
--> 832                                            self.timeout, self.source_address)
    833 
    834         if self._tunnel_host:

/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.pyc in create_connection(address, timeout, source_address)
    555     host, port = address
    556     err = None
--> 557     for res in getaddrinfo(host, port, 0, SOCK_STREAM):
    558         af, socktype, proto, canonname, sa = res
    559         sock = None

KeyboardInterrupt: 

In [ ]:

    

plt.imshow(img_array)
plt.hold(True)
plt.axis('off')
#plt.scatter(x=[r[0]/4.2 for r in rows], y=[(r[1]/3)-350 for r in rows], 'r-', alpha=0.2)