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In [12]:



    


import os
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
import numpy as np
import h5py
import time
import nrrd
from voxnet.conn2d import map_to_surface

drive_path = os.path.join(os.getenv('HOME'), 'work/allen/data/sdk_new_100')

# When downloading 3D connectivity data volumes, what resolution do you want (in microns)?  
# Options are: 10, 25, 50, 100
resolution_um = 10

# Drop list criterion, in percent difference
volume_fraction = 20

# The manifest file is a simple JSON file that keeps track of all of
# the data that has already been downloaded onto the hard drives.
# If you supply a relative path, it is assumed to be relative to your
# current working directory.
manifest_file = os.path.join(drive_path, "manifest.json")

# Start processing data
mcc = MouseConnectivityCache(manifest_file = manifest_file,
                             resolution = resolution_um)
ontology = mcc.get_ontology()
# Injection structure of interest
isocortex = ontology['Isocortex']

# open up a pandas dataframe of all of the experiments
experiments = mcc.get_experiments(dataframe = True, 
                                  injection_structure_ids = [isocortex['id'].values[0]], 
                                  cre = False)
print "%d total experiments" % len(experiments)

view_paths_fn = os.path.join(os.getenv('HOME'), 'work/allen/data/TopView/top_view_paths_10.h5')
view_paths_file = h5py.File(view_paths_fn, 'r')
view_lut = view_paths_file['view lookup'][:]
view_paths = view_paths_file['paths'][:]
view_paths_file.close()

## Compute size of each path to convert path averages to sums
norm_lut = np.zeros(view_lut.shape, dtype=int)
ind = np.where(view_lut != -1)
ind = zip(ind[0], ind[1])
for curr_ind in ind:
    curr_path_id = view_lut[curr_ind]
    curr_path = view_paths[curr_path_id, :]
    norm_lut[curr_ind] = np.sum(curr_path > 0)

t0 = time.time()
expt_drop_list = []
full_vols = []
flat_vols = []



    


















    






/home/kamdh/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py:27: VisibleDeprecationWarning: Function get_ontology is deprecated. Use get_structure_tree instead.










    






126 total experiments

















In [13]:



    


eid = experiments.iloc[5].id
row = experiments.iloc[5]
print eid
print row



    


















    






180916954
gender                                                                   M
id                                                               180916954
injection-coordinates                                   [4800, 1220, 5930]
injection-structures     [{u'abbreviation': u'ACAd', u'color': u'40A666...
product-id                                                               5
strain                                                            C57BL/6J
structure-abbrev                                                       MOs
structure-color                                                     1F9D5A
structure-id                                                           993
structure-name                                        Secondary motor area
transgenic-line                                                           
Name: 180916954, dtype: object

















In [14]:



    


data_dir = os.path.join(os.getenv('HOME'),
                            "work/allen/data/sdk_new_100/experiment_%d/" % eid)
    # get and remap injection data
    print "getting injection density"
    in_d, in_info = mcc.get_injection_density(eid)
    print "mapping to surface"
    in_d_s = map_to_surface(in_d, view_lut, view_paths, scale = resolution_um/10., fun=np.mean)
    flat_vol = np.nansum(in_d_s * norm_lut) * (10./1000.)**3
    flat_vols.append(flat_vol)
    full_vol = np.nansum(in_d) * (10./1000.)**3
    full_vols.append(full_vol)



    


















    






getting injection density
mapping to surface

















In [15]:



    


expt_union = mcc.get_experiment_structure_unionizes(eid, hemisphere_ids = [2], is_injection = True,
                                                        structure_ids = [ontology['grey']['id'].values[0]])



    











In [16]:



    


flat_vols



    


















    
Out[16]:








[0.89908089262803303]

















In [17]:



    


full_vols



    


















    
Out[17]:








[0.51017865625000014]

















In [18]:



    


full_vol2 = float(expt_union['projection_volume'])
print expt_union
print full_vol2



    


















    






      hemisphere_id         id  is_injection  max_voxel_density  max_voxel_x  \
2206              2  533667735          True                1.0         4800   

      max_voxel_y  max_voxel_z  normalized_projection_volume  \
2206         1220         5930                      0.991312   

      projection_density  projection_energy  projection_intensity  \
2206            0.999986            12435.6               12435.8   

      projection_volume  experiment_id  structure_id  sum_pixel_intensity  \
2206             0.5557      180916954             8         5.641290e+12   

       sum_pixels  sum_projection_pixel_intensity  sum_projection_pixels  \
2206  453639000.0                    5.641280e+12            453632000.0   

        volume  
2206  0.555708  
0.5557

















In [19]:



    


print np.nansum(in_d_s * norm_lut)



    


















    






899080.892628

















In [20]:



    


in_d_sum = map_to_surface(in_d, view_lut, view_paths, scale = resolution_um/10., fun=np.sum)
np.nansum(in_d_sum) * (10./1000.)**3



    


















    
Out[20]:








0.89908087500000011

















In [21]:



    


print np.abs(flat_vol - full_vol)/full_vol*100
print np.abs(flat_vol - full_vol2)/full_vol2*100



    


















    






76.2286370889
61.7924946244

















In [23]:



    


import matplotlib.pyplot as plt
%matplotlib inline
tmp = norm_lut.astype(float)
tmp[tmp == 0] = np.nan

fig = plt.figure(figsize = (20,20))
ax = fig.add_subplot(121)
h = ax.imshow(in_d_s)
fig.colorbar(h)

a2 = fig.add_subplot(122)
h2 = a2.imshow(np.sum(in_d, axis=1))
fig.colorbar(h2)



    


















    
Out[23]:








<matplotlib.colorbar.Colorbar at 0x7fd5ec53ff50>










    
























In [20]:



    


experiments



    


















    
Out[20]:











  
    

      
      gender
      id
      injection-coordinates
      injection-structures
      product-id
      strain
      structure-abbrev
      structure-color
      structure-id
      structure-name
      transgenic-line
    

    

      id
      
      
      
      
      
      
      
      
      
      
      
    

  
  
    

      180435652
      M
      180435652
      [7820, 4250, 9870]
      [{u'abbreviation': u'TEa', u'color': u'15B0B3'...
      5
      C57BL/6J
      ECT
      0D9F91
      895
      Ectorhinal area
      
    

    

      180436360
      M
      180436360
      [4800, 4720, 8980]
      [{u'abbreviation': u'AId', u'color': u'219866'...
      5
      C57BL/6J
      VISC
      11AD83
      677
      Visceral area
      
    

    

      180719293
      M
      180719293
      [3140, 3330, 7390]
      [{u'abbreviation': u'AId', u'color': u'219866'...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      180709942
      M
      180709942
      [3360, 3120, 7520]
      [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      180917660
      M
      180917660
      [5570, 4540, 9540]
      [{u'abbreviation': u'AIp', u'color': u'219866'...
      5
      C57BL/6J
      VISC
      11AD83
      677
      Visceral area
      
    

    

      180916954
      M
      180916954
      [4800, 1220, 5930]
      [{u'abbreviation': u'ACAd', u'color': u'40A666...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      100141780
      M
      100141780
      [4070, 2600, 7500]
      [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...
      5
      C57BL/6J
      MOp
      1F9D5A
      985
      Primary motor area
      
    

    

      180720175
      M
      180720175
      [5710, 670, 6420]
      [{u'abbreviation': u'SSp-ll', u'color': u'1880...
      5
      C57BL/6J
      MOp
      1F9D5A
      985
      Primary motor area
      
    

    

      180717881
      M
      180717881
      [4580, 3610, 8670]
      [{u'abbreviation': u'SSp-m', u'color': u'18806...
      5
      C57BL/6J
      SSp-m
      188064
      345
      Primary somatosensory area, mouth
      
    

    

      127084296
      M
      127084296
      [4880, 1800, 6920]
      [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...
      5
      C57BL/6J
      MOp
      1F9D5A
      985
      Primary motor area
      
    

    

      112306316
      M
      112306316
      [3000, 3600, 6690]
      [{u'abbreviation': u'FRP', u'color': u'268F45'...
      5
      C57BL/6J
      ORBl
      248A5E
      723
      Orbital area, lateral part
      
    

    

      180709230
      M
      180709230
      [2360, 3870, 7100]
      [{u'abbreviation': u'AId', u'color': u'219866'...
      5
      C57BL/6J
      ORBl
      248A5E
      723
      Orbital area, lateral part
      
    

    

      180074890
      M
      180074890
      [6760, 4320, 9510]
      [{u'abbreviation': u'AIp', u'color': u'219866'...
      5
      C57BL/6J
      VISC
      11AD83
      677
      Visceral area
      
    

    

      112952510
      M
      112952510
      [3430, 1930, 6140]
      [{u'abbreviation': u'ACAd', u'color': u'40A666...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      112596790
      M
      112596790
      [3840, 4160, 8250]
      [{u'abbreviation': u'AId', u'color': u'219866'...
      5
      C57BL/6J
      AId
      219866
      104
      Agranular insular area, dorsal part
      
    

    

      112951804
      M
      112951804
      [6890, 2260, 8670]
      [{u'abbreviation': u'SSp-bfd', u'color': u'188...
      5
      C57BL/6J
      SSp-bfd
      188064
      329
      Primary somatosensory area, barrel field
      
    

    

      141603190
      M
      141603190
      [4100, 1810, 6110]
      [{u'abbreviation': u'ACAd', u'color': u'40A666...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      180718587
      M
      180718587
      [5200, 1310, 7300]
      [{u'abbreviation': u'SSp-ll', u'color': u'1880...
      5
      C57BL/6J
      SSp-ul
      188064
      369
      Primary somatosensory area, upper limb
      
    

    

      113036264
      M
      113036264
      [5600, 3510, 9100]
      [{u'abbreviation': u'SSp-m', u'color': u'18806...
      5
      C57BL/6J
      SSs
      188064
      378
      Supplemental somatosensory area
      
    

    

      100141796
      M
      100141796
      [9370, 2450, 9080]
      [{u'abbreviation': u'VISl', u'color': u'08858C...
      5
      C57BL/6J
      VISli
      08858C
      312782574
      Laterointermediate area
      
    

    

      112514915
      M
      112514915
      [6600, 3010, 9160]
      [{u'abbreviation': u'SSp-bfd', u'color': u'188...
      5
      C57BL/6J
      SSs
      188064
      378
      Supplemental somatosensory area
      
    

    

      146593590
      M
      146593590
      [5180, 1790, 5800]
      [{u'abbreviation': u'ACAd', u'color': u'40A666...
      5
      C57BL/6J
      ACAd
      40A666
      39
      Anterior cingulate area, dorsal part
      
    

    

      180296424
      M
      180296424
      [9570, 1750, 8510]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      117298988
      M
      117298988
      [6140, 3530, 9340]
      [{u'abbreviation': u'SSs', u'color': u'188064'...
      5
      C57BL/6J
      SSs
      188064
      378
      Supplemental somatosensory area
      
    

    

      170721670
      M
      170721670
      [2410, 3150, 6820]
      [{u'abbreviation': u'AOB', u'color': u'9DF0D2'...
      5
      C57BL/6J
      ORBl
      248A5E
      723
      Orbital area, lateral part
      
    

    

      157710335
      M
      157710335
      [2440, 2750, 7050]
      [{u'abbreviation': u'FRP', u'color': u'268F45'...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      126907302
      M
      126907302
      [7210, 1280, 8030]
      [{u'abbreviation': u'SSp-bfd', u'color': u'188...
      5
      C57BL/6J
      SSp-bfd
      188064
      329
      Primary somatosensory area, barrel field
      
    

    

      126861679
      M
      126861679
      [7450, 910, 7080]
      [{u'abbreviation': u'VISam', u'color': u'08858...
      5
      C57BL/6J
      VISam
      08858C
      394
      Anteromedial visual area
      
    

    

      127089669
      M
      127089669
      [9270, 2930, 9310]
      [{u'abbreviation': u'SUB', u'color': u'4FC244'...
      5
      C57BL/6J
      VISpor
      08858C
      312782628
      Postrhinal area
      
    

    

      141602484
      M
      141602484
      [4030, 1830, 7090]
      [{u'abbreviation': u'MOp', u'color': u'1F9D5A'...
      5
      C57BL/6J
      MOs
      1F9D5A
      993
      Secondary motor area
      
    

    

      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    

    

      112595376
      M
      112595376
      [8350, 1390, 6600]
      [{u'abbreviation': u'RSPd', u'color': u'1AA698...
      5
      C57BL/6J
      RSPv
      1AA698
      886
      Retrosplenial area, ventral part
      
    

    

      100141473
      M
      100141473
      [7370, 2110, 9000]
      [{u'abbreviation': u'SSp-bfd', u'color': u'188...
      5
      C57BL/6J
      SSp-bfd
      188064
      329
      Primary somatosensory area, barrel field
      
    

    

      158435116
      M
      158435116
      [2810, 3870, 6420]
      [{u'abbreviation': u'ORBl', u'color': u'248A5E...
      5
      C57BL/6J
      ORBvl
      248A5E
      746
      Orbital area, ventrolateral part
      
    

    

      126862385
      M
      126862385
      [9640, 620, 7060]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      100149109
      M
      100149109
      [7540, 2950, 9550]
      [{u'abbreviation': u'AUDp', u'color': u'019399...
      5
      C57BL/6J
      AUDp
      019399
      1002
      Primary auditory area
      
    

    

      139519496
      M
      139519496
      [7660, 2720, 9530]
      [{u'abbreviation': u'SSs', u'color': u'188064'...
      5
      C57BL/6J
      AUDd
      019399
      1011
      Dorsal auditory area
      
    

    

      112229103
      M
      112229103
      [7500, 770, 6790]
      [{u'abbreviation': u'VISam', u'color': u'08858...
      5
      C57BL/6J
      RSPagl
      1AA698
      894
      Retrosplenial area, lateral agranular part
      
    

    

      157062358
      M
      157062358
      [9260, 2830, 9490]
      [{u'abbreviation': u'TEa', u'color': u'15B0B3'...
      5
      C57BL/6J
      VISpor
      08858C
      312782628
      Postrhinal area
      
    

    

      100141219
      M
      100141219
      [8940, 1420, 7840]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      304565427
      M
      304565427
      [9280, 2040, 8630]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      304586645
      M
      304586645
      [8650, 1350, 8030]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      272916915
      M
      272916915
      [8510, 760, 6570]
      [{u'abbreviation': u'RSPd', u'color': u'1AA698...
      5
      C57BL/6J
      RSPd
      1AA698
      879
      Retrosplenial area, dorsal part
      
    

    

      272782668
      M
      272782668
      [9590, 950, 7230]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      112373124
      M
      112373124
      [5420, 2600, 8480]
      [{u'abbreviation': u'SSp-m', u'color': u'18806...
      5
      C57BL/6J
      SSp-n
      188064
      353
      Primary somatosensory area, nose
      
    

    

      116903230
      M
      116903230
      [7950, 3110, 9730]
      [{u'abbreviation': u'AUDp', u'color': u'019399...
      5
      C57BL/6J
      AUDp
      019399
      1002
      Primary auditory area
      
    

    

      100147853
      M
      100147853
      [9290, 1520, 8230]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      112424813
      M
      112424813
      [8030, 510, 6310]
      [{u'abbreviation': u'RSPd', u'color': u'1AA698...
      5
      C57BL/6J
      RSPd
      1AA698
      879
      Retrosplenial area, dorsal part
      
    

    

      174361040
      M
      174361040
      [9850, 850, 7110]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      277714322
      M
      277714322
      [8230, 1130, 8130]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      180403712
      M
      180403712
      [7470, 4370, 9850]
      [{u'abbreviation': u'TEa', u'color': u'15B0B3'...
      5
      C57BL/6J
      ECT
      0D9F91
      895
      Ectorhinal area
      
    

    

      277616630
      M
      277616630
      [8510, 1040, 7910]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      277713580
      M
      277713580
      [8130, 1110, 8120]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      277712166
      M
      277712166
      [8350, 1190, 8110]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      180073473
      M
      180073473
      [8400, 2500, 9540]
      [{u'abbreviation': u'TEa', u'color': u'15B0B3'...
      5
      C57BL/6J
      AUDpo
      019399
      1027
      Posterior auditory area
      
    

    

      304564721
      M
      304564721
      [8530, 1350, 8370]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      304585910
      M
      304585910
      [9230, 1370, 8200]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      148964212
      M
      148964212
      [5760, 1440, 7630]
      [{u'abbreviation': u'SSp-ll', u'color': u'1880...
      5
      C57BL/6J
      SSp-ul
      188064
      369
      Primary somatosensory area, upper limb
      
    

    

      272916202
      M
      272916202
      [9750, 2070, 8980]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISpl
      08858C
      425
      Posterolateral visual area
      
    

    

      304762965
      M
      304762965
      [8840, 1410, 8330]
      [{u'abbreviation': u'VISp', u'color': u'08858C...
      5
      C57BL/6J
      VISp
      08858C
      385
      Primary visual area
      
    

    

      180404418
      M
      180404418
      [5190, 4350, 9320]
      [{u'abbreviation': u'SSs', u'color': u'188064'...
      5
      C57BL/6J
      GU
      009C75
      1057
      Gustatory areas
      
    

  



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Content source: kharris/allen-voxel-network

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