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.
