Allen Brain Institute - 鼠标连接 API 和鼠标连接缓存示例

Question

我正在尝试遵循 Mouse Connectivity sdk 并让他们的两个示例正常工作。

pd returns None 或所有投影信号密度实验。为什么会这样？

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))

结果：

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

尽管如此，experiments 确实收到了一个值，因此 MouseConnectivityApi 和 nrrd（我按照以下安装）似乎正在正常工作.

看这里：

对了，现在是第二个例子

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'])

这是从艾伦那里逐字复制的，但这是我收到的错误消息：

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

为什么会发生这种情况？

和以前一样（我假设不需要另一张图片），experiments 变量确实收到了每个实验的值。

Answer 1

不幸的是，现在这是 pynrrd/master github 存储库的一个 Windows 特定问题。我知道一个特定的修订有效：

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

要从 windows 命令提示符安装此修订版，您可以：

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

末尾的反斜杠很重要。它告诉 pip 从本地路径安装而不是检查 PyPI。

记录的问题：https://github.com/mhe/pynrrd/issues/18

Allen Brain Institute - 鼠标连接 API 和鼠标连接缓存示例

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

python

allen-sdk