In [1]:

    

import urllib
import json
import vis3DConnect as vc


    

In [2]:

    

#http://connectivity.brain-map.org/?searchMode=spatial&sourceDomain=8,304325711&primaryStructureOnly=true&isi=false&targetCoordinates=9400,1250,6200&initImage=TWO_PHOTON&experimentCoordinates=9400,1250,6200&experiment=309113907

target_voxel = [9400,1250,6200]
experiment_id = 309113907


    

In [3]:

    

def get_path( target_voxel, experiment_id ) :
    
    url = "http://api.brain-map.org/api/v2/data/query.json?criteria=service::mouse_connectivity_target_spatial"
    url = url + "[seed_point$eq%s]" % ','.join([str(s) for s in target_voxel])
    url = url + "[section_data_set$eq%d]" % experiment_id
    
    response = urllib.urlopen(url)
    data = json.loads(response.read())
    data = [s['coord'] for s in data['msg'][0]['path']]
    return data


    

In [4]:

    

target_voxel = [9400,1250,6200]
experiment_id = 309113907
data = get_path( target_voxel, experiment_id )

# target voxel is starting point ending at the injection site


    

In [29]:

    

# unpack it for plotting
x, y, z = zip(*data)


    

In [30]:

    

# unpack it for plotting
x, y, z = zip(*data)

import numpy as np
# divide by 25 
nx = np.array(x).astype(float)/25
ny = np.array(y).astype(float)/25
nz = np.array(z).astype(float)/25


    

In [48]:

    

tst = np.vstack([nx,ny,nz]).transpose()
print tst
print len(tst)
print 'break'
print tst[0:len(tst):6,:]
print 'break'
print tst[::6]


    

    




[[ 376.     52.    248.  ]
 [ 375.52   55.52  248.  ]
 [ 374.2    58.64  248.  ]
 [ 371.52   60.88  248.44]
 [ 368.     62.64  249.32]
 [ 364.     63.52  250.64]
 [ 360.44   64.    252.  ]
 [ 357.32   64.    253.76]
 [ 354.64   64.44  256.  ]
 [ 352.     65.76  258.2 ]
 [ 349.32   68.44  260.  ]
 [ 347.08   71.52  261.32]
 [ 344.88   74.64  262.64]
 [ 342.64   77.32  263.52]
 [ 340.     80.44  264.  ]
 [ 337.76   83.52  264.  ]
 [ 336.     86.64  264.44]
 [ 334.64   89.32  265.32]
 [ 332.88   92.44  266.64]
 [ 331.08   96.    267.52]
 [ 328.88   99.52  268.  ]
 [ 326.64  102.64  268.44]
 [ 324.    104.88  269.76]
 [ 321.76  107.08  272.44]
 [ 320.    108.88  275.52]
 [ 318.2   110.64  278.64]
 [ 316.    111.52  280.88]
 [ 313.32  112.44  283.08]
 [ 311.08  113.76  284.88]
 [ 309.32  116.    287.08]
 [ 308.    118.2   289.32]
 [ 306.64  119.52  292.44]
 [ 305.32  120.44  296.  ]
 [ 304.    121.76  299.52]
 [ 302.64  124.    302.64]
 [ 300.88  126.2   305.32]
 [ 298.64  127.52  308.  ]
 [ 296.    128.44  310.2 ]
 [ 293.32  129.76  311.52]
 [ 290.64  132.    312.44]
 [ 288.    134.2   313.76]
 [ 285.32  135.52  316.  ]
 [ 283.08  136.44  318.2 ]
 [ 281.32  137.76  320.  ]
 [ 280.44  140.44  321.32]
 [ 280.    143.52  323.08]
 [ 280.    146.2   325.32]
 [ 280.    147.52  328.44]
 [ 280.    148.    332.  ]
 [ 280.    147.52  336.  ]
 [ 280.    146.2   340.  ]
 [ 280.    144.    343.52]
 [ 280.44  141.32  346.2 ]
 [ 281.32  138.64  348.  ]
 [ 282.64  135.52  349.76]
 [ 283.52  132.44  352.  ]
 [ 284.    129.32  354.2 ]
 [ 284.44  126.64  355.52]
 [ 285.32  123.52  356.  ]
 [ 286.64  120.    356.  ]
 [ 287.52  116.    356.  ]
 [ 288.44  112.44  356.  ]
 [ 289.76  109.32  356.  ]
 [ 292.    106.64  356.  ]
 [ 294.2   103.52  356.  ]
 [ 296.    100.44  356.  ]
 [ 297.32   97.32  356.  ]
 [ 299.08   94.64  356.  ]
 [ 300.88   91.52  356.  ]
 [ 303.08   88.44  356.  ]
 [ 304.88   85.32  356.  ]
 [ 307.08   83.08  356.  ]
 [ 308.88   81.32  356.  ]
 [ 311.08   80.44  356.  ]
 [ 313.32   79.52  356.  ]
 [ 316.44   78.2   356.  ]
 [ 319.52   75.52  355.52]
 [ 322.64   72.44  354.64]
 [ 324.88   69.32  352.88]
 [ 327.08   66.64  351.08]
 [ 330.64   63.52  348.  ]
 [ 336.     60.    344.  ]
 [ 347.6    51.6   311.2 ]]
83
break
[[ 376.     52.    248.  ]
 [ 360.44   64.    252.  ]
 [ 344.88   74.64  262.64]
 [ 332.88   92.44  266.64]
 [ 320.    108.88  275.52]
 [ 308.    118.2   289.32]
 [ 298.64  127.52  308.  ]
 [ 283.08  136.44  318.2 ]
 [ 280.    148.    332.  ]
 [ 282.64  135.52  349.76]
 [ 287.52  116.    356.  ]
 [ 297.32   97.32  356.  ]
 [ 308.88   81.32  356.  ]
 [ 324.88   69.32  352.88]]
break
[[ 376.     52.    248.  ]
 [ 360.44   64.    252.  ]
 [ 344.88   74.64  262.64]
 [ 332.88   92.44  266.64]
 [ 320.    108.88  275.52]
 [ 308.    118.2   289.32]
 [ 298.64  127.52  308.  ]
 [ 283.08  136.44  318.2 ]
 [ 280.    148.    332.  ]
 [ 282.64  135.52  349.76]
 [ 287.52  116.    356.  ]
 [ 297.32   97.32  356.  ]
 [ 308.88   81.32  356.  ]
 [ 324.88   69.32  352.88]]

In [31]:

    

%matplotlib inline

import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

fig = plt.figure()
ax = fig.gca(projection='3d')
ax.plot(nx, ny, nz, label='path')
ax.legend()
plt.show()


    

In [ ]: