Allen Brain Institute - Mouse Connectivity API and Mouse Connectivity Cache examples

Question

I'm trying to follow the Mouse Connectivity sdk and get their two examples working.

pd returns None or all projection signal density experiments. Why might this be?

from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi

mca = MouseConnectivityApi()

# get metadata for all non-Cre experiments
experiments = mca.experiment_source_search(injection_structures='root', transgenic_lines=0)

# download the projection density volume for one of the experiments
#pd = mca.download_projection_density('example.nrrd', experiments[0]['id'], resolution=25)

for exp in range(len(experiments)):
    pd = mca.download_projection_density('example.nrrd', experiments[exp]['id'], resolution=25)
    print(type(pd))

Results:

C:\Anaconda\python.exe C:/Users/user/PycharmProjects/MyFirstAllenBrain/Test.py
<type 'NoneType'>
<type 'NoneType'>
<type 'NoneType'>
<type 'NoneType'>
<type 'NoneType'>
<type 'NoneType'>
... etc

The thing though is, is that experiments does recieve a value so it appears to be the case that the MouseConnectivityApi and nrrd (which I installed as per the following post) are working appropriately.

See here:

Right, and now the second example

from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache

# tell the cache class what resolution (in microns) of data you want to download
mcc = MouseConnectivityCache(resolution=25)

# use the ontology class to get the id of the isocortex structure
ontology = mcc.get_ontology()
isocortex = ontology['Isocortex']

# a list of dictionaries containing metadata for non-Cre experiments
experiments = mcc.get_experiments(injection_structure_ids=isocortex['id'])

# download the projection density volume for one of the experiments
pd = mcc.get_projection_density(experiments[0]['id'])

This is copied word for word from Allen and yet this is the error message I get:

C:\Anaconda\python.exe C:/Users/user/PycharmProjects/MyFirstAllenBrain/Test.py
Traceback (most recent call last):
  File "C:/Users/user/PycharmProjects/MyFirstAllenBrain/Test.py", line 14, in <module>
    pd = mcc.get_projection_density(experiments[0]['id'])
  File "C:\Users\user\AppData\Roaming\Python\Python27\site-packages\allensdk\core\mouse_connectivity_cache.py", line 170, in get_projection_density
    return nrrd.read(file_name)
  File "C:\Anaconda\lib\site-packages\nrrd.py", line 384, in read
    data = read_data(header, filehandle, filename)
  File "C:\Anaconda\lib\site-packages\nrrd.py", line 235, in read_data
    mmap.MAP_PRIVATE, mmap.PROT_READ)
AttributeError: 'module' object has no attribute 'MAP_PRIVATE'

Process finished with exit code 1

Why might this occur?

And again as before (no need for another picture I assume), the experiments variable does recieve what appears to be values for each experiment.

Answer 1

Unfortunately this is a Windows-specific issue with the pynrrd/master github repository right now. I know that one specific revision works:

https://github.com/mhe/pynrrd/commit/3c0f3d577b0b435fb4825c14820322a574311af0

To install this revision from a windows command prompt, you can:

> git clone https://github.com/mhe/pynrrd.git
> cd pynrrd
> git checkout 3c0f3d5
> cd ..
> pip install --upgrade pynrrd\

The backslash on the end is important. It tells pip to install from a local path instead of checking PyPI.

Issue logged: https://github.com/mhe/pynrrd/issues/18