file read issue on Windows

[dyf]

The recent merge from nocnokneo seems to have reintroduced a Windows file reading bug. Here's the error:

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
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

I believe MAP_PRIVATE is a linux-specific attribute, but I'm not sure about this.

Related stackoverflow question: http://stackoverflow.com/questions/32261480/allen-brain-institute-mouse-connectivity-api-and-mouse-connectivity-cache-exam/32279226#32279226

[mhe]

Thanks for reporting this. I will investigate.

[mhe]

@dyf I made a first attempt at a fix in the mmap-windows branch. Unfortunately this was a 'blind' fix: I do not have access to a windows machine at the moment to be able to properly test it. If someone in the meantime is able to test this on a windows machine: let me know the results.

[dyf]

Thanks, getting closer. I'm able to read the downloaded file with open(...), but get the following error with your updated pynrrd:

C:\Users\davidf\Anaconda\lib\site-packages\allensdk\core\mouse_connectivity_cache.pyc in get_projection_density(self, experiment_id, file_name)
168 self.api.download_projection_density(file_name, experiment_id, self.resolution)
169
--> 170 return nrrd.read(file_name)
171
172

C:\Users\davidf\Anaconda\lib\site-packages\nrrd.pyc in read(filename)
386 with open(filename,'rb') as filehandle:
387 header = read_header(filehandle)
--> 388 data = read_data(header, filehandle, filename)
389 return (data, header)
390

C:\Users\davidf\Anaconda\lib\site-packages\nrrd.pyc in read_data(fields, filehandle, filename, seek_past_header)
233 datafilehandle.seek(0)
234 if os.name == "nt":
--> 235 m = mmap.mmap(datafilehandle.fileno(), 0)
236 else:
237 m = mmap.mmap(datafilehandle.fileno(), 0,

WindowsError: [Error 5] Access is denied

[mhe]

I'm still doing this 'blind', but I've made slight modification in the same branch. It could be that the code I initially created to fix this requested write access to the file. Perhaps this fixes the issue.

[dyf]

Looks like it's working now. Thanks for the quick turnaround!