[Neuroimaging] Thread-safe ArrayProxy/fileslice?

[paul mccarthy]

Hi Nathaniel,

True - perhaps such a method could be added to the Opener class (with the
internal seek/read calls protected by a mutex), and used by read_segments,
instead of separate seek/read calls. This would be a very simple change -
I'm happy to prepare a PR if it sounds like a good idea.

Cheers,

Paul

On 8 February 2017 at 20:23, Nathaniel Smith <njs at pobox.com> wrote:

> The best solution would be to use a pread-style interface that lets you
> read from a given offset without seeking at all, and thus without needing
> any locks. Unfortunately, Python hasn't historically had the best support
> for this, but it's available if you're using Python 3 on unix:
> https://docs.python.org/3/library/os.html#os.pread
>
> -n
>
> On Feb 8, 2017 5:55 AM, "paul mccarthy" <pauldmccarthy at gmail.com> wrote:
>
>> Howdy all,
>>
>> Does anybody have experience accessing image data through the ArrayProxy
>> class (or functions in the fileslice module) in a multi-threaded
>> environment? I am visualising large 4D images which are kept on disk (via
>> my indexed_gzip module), and am having trouble when accessing the data
>> from multiple threads, as the seek/read pairs from different threads
>> will occasionally become intertwined with each other.
>>
>>
>> My hacky workaround is to patch the ArrayProxy.__getitem__ method, and
>> add a threading.Lock to each instance, as follows:
>>
>>
>> import threading
>>
>> import nibabel            as nib
>> import nibabel.arrayproxy as ap
>>
>> def ArrayProxy__getitem__(self, slc):
>>
>>     if not hasattr(self, '_thread_lock'):
>>         return self.__real_getitem__(slc)
>>
>>     self._thread_lock.acquire()
>>
>>     try:
>>         return ap.ArrayProxy.__real_getitem__(self, slc)
>>
>>     finally:
>>         self._thread_lock.release()
>>
>> # Patch ArrayProxy.__getitem__
>> ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
>> ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__
>>
>>
>> # Then add a lock to instances
>> # which need to be thread-safe
>> img = nib.load('MNI152_T1_2mm.nii.gz')
>> img.dataobj._thread_lock = threading.Lock()
>>
>>
>> This is the first thing I came up with, although I will probably end up
>> adding the lock to the fileobj, and patching the fileslice.fileslice
>> function instead. Unless there are any better ideas?
>>
>> Cheers,
>>
>> Paul
>>
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>>
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