pull_voxel() Issue

[johnduva]

The command: img, bbox, vox = ngl_sess.pull_voxel(2, v_id, radius) generates the error: >>AttributeError: 'Thread' object has no attribute 'isAlive'

This has error has never occurred until this week. Bijan hasn't seen this either but suggested to try using cloudvolume directly, or to modify the existing pull_voxel() code. I'm not sure exactly how this should be done and I'm wondering why this would be needed all of a sudden when we've never needed it before.

[johnduva]

This is the full error:

Downloading: 100%|██████████| 1/1 [00:00<00:00,  7.74it/s]
Downloading: 44it [00:01, 27.36it/s]                         
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-42-94e94b5c1366> in <module>
      1 # get image and center point
      2 ngl_sess = NeuroglancerSession(mip = mip, url = dir, url_segments=dir_segments)
----> 3 img, bbox, vox = ngl_sess.pull_voxel(2, v_id, radius)
      4 print(f"\n\nDownloaded volume is of shape {img.shape}, with total intensity {sum(sum(sum(img)))}.")

~/Desktop/Git/brainlit/brainlit/utils/session.py in pull_voxel(self, seg_id, v_id, radius)
    210         shape = [radius] * 3
    211         bounds = Bbox(np.subtract(seed[:3], shape), np.add(np.add(seed[3:], shape), 1))
--> 212         img = self.pull_bounds_img(bounds)
    213         # img = self.cv.download(bounds, mip=self.mip)
    214         vox_in_img = voxel - np.array(bounds.to_list()[:3])

~/Desktop/Git/brainlit/brainlit/utils/session.py in pull_bounds_img(self, bounds)
    314         check_iterable_type(bounds, (int, np.integer))
    315         check_iterable_nonnegative(bounds)
--> 316         img = self.cv.download(Bbox(bounds[:3], bounds[3:]), mip=self.mip)
    317         return np.squeeze(np.array(img))
    318 

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/frontends/precomputed.py in download(self, bbox, mip, parallel, segids, preserve_zeros)
    555       parallel = self.parallel
    556 
--> 557     img = self.image.download(bbox, mip, parallel=parallel)
    558 
    559     if segids is None:

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/datasource/precomputed/image/__init__.py in download(self, bbox, mip, parallel, location, retain, use_shared_memory, use_file, order)
    123       )
    124     else:
--> 125       return rx.download(
    126         bbox, mip,
    127         meta=self.meta,

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/datasource/precomputed/image/rx.py in download(requested_bbox, mip, meta, cache, fill_missing, progress, parallel, location, retain, use_shared_memory, use_file, compress, order, green)
    133       shade(renderbuffer, requested_bbox, img3d, bbox)
    134 
--> 135     download_chunks_threaded(
    136       meta, cache, mip, cloudpaths,
    137       fn=process, fill_missing=fill_missing,

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/datasource/precomputed/image/rx.py in download_chunks_threaded(meta, cache, mip, cloudpaths, fn, fill_missing, progress, compress_cache, green)
    284   downloads = itertools.chain( local_downloads, remote_downloads )
    285 
--> 286   schedule_jobs(
    287     fns=downloads,
    288     concurrency=DEFAULT_THREADS,

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/scheduler.py in schedule_jobs(fns, concurrency, progress, total, green)
     70     return schedule_green_jobs(fns, concurrency, progress, total)
     71 
---> 72   return schedule_threaded_jobs(fns, concurrency, progress, total)
     73 
     74 

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/scheduler.py in schedule_threaded_jobs(fns, concurrency, progress, total)
     17   with ThreadedQueue(n_threads=concurrency, progress=progress) as tq:
     18     for fn in fns:
---> 19       tq.put(wrap(fn))
     20 
     21 def schedule_green_jobs(

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/threaded_queue.py in __exit__(self, exception_type, exception_value, traceback)
    256   def __exit__(self, exception_type, exception_value, traceback):
    257     self.wait(progress=self.with_progress)
--> 258     self.kill_threads()

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/threaded_queue.py in kill_threads(self)
     96     """Kill all threads."""
     97     self._terminate.set()
---> 98     while self.are_threads_alive():
     99       time.sleep(0.001)
    100     self._threads = ()

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/threaded_queue.py in are_threads_alive(self)
     91   def are_threads_alive(self):
     92     """Returns: boolean indicating if any threads are alive"""
---> 93     return any(map(lambda t: t.isAlive(), self._threads))
     94 
     95   def kill_threads(self):

~/opt/anaconda3/envs/testenv/lib/python3.9/site-packages/cloudvolume/threaded_queue.py in <lambda>(t)
     91   def are_threads_alive(self):
     92     """Returns: boolean indicating if any threads are alive"""
---> 93     return any(map(lambda t: t.isAlive(), self._threads))
     94 
     95   def kill_threads(self):

AttributeError: 'Thread' object has no attribute 'isAlive'

[johnduva]

@bvarjavand I solved this: turns out threading.Thread 's method isAlive() was renamed to is_alive() since Python 3.9.0. I've updated my own version of threaded_queue.py but I'm not sure how you want to handle it because obviously not everyone is using Python 3.9. I'll keep this Issue open for now as a reminder in case you want to update the code.

[ryanlu41]

Can we use sys.version or sys.version_info to do that? https://docs.python.org/3/library/sys.html#sys.version

[johnduva]

That's what I would recommend.

[tirkarthi]

This seems to have been fixed in https://github.com/seung-lab/cloud-volume/commit/9e7195e410d201c98a03e3335874c8650143ec9e

[johnduva]

@tirkarthi is it strange that they don't check what the user's version is though? wouldn't that fail for someone who has <3.9?

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