File "/usr/local/lib/python3.8/dist-packages/cloudvolume/frontends/precomputed.py", line 551, in __getitem__
img = self.download(requested_bbox, self.mip)
File "/usr/local/lib/python3.8/dist-packages/cloudvolume/frontends/precomputed.py", line 731, in download
tup = self.image.download(
File "/usr/local/lib/python3.8/dist-packages/cloudvolume/datasource/precomputed/image/__init__.py", line 190, in download
return rx.download_sharded(
File "/usr/local/lib/python3.8/dist-packages/cloudvolume/datasource/precomputed/image/rx.py", line 99, in download_sharded
img3d = decode_fn(
File "/usr/local/lib/python3.8/dist-packages/cloudvolume/datasource/precomputed/image/rx.py", line 664, in decode_single_voxel
return _decode_helper(
File "/usr/local/lib/python3.8/dist-packages/cloudvolume/datasource/precomputed/image/rx.py", line 684, in _decode_helper
raise EmptyVolumeException(input_bbox)
cloudvolume.exceptions.EmptyVolumeException: Bbox([15940, 40089, 18946],[16004, 40153, 19010], dtype=int32)
I was observing the region Bbox([15940, 40089, 18946],[16004, 40153, 19010] on Neuroglancer and it seems to be at the edge of the entire electron microscopy dataset now. It is indeed a dark patch with no segmentation results.
In large-scale electron microscopy datasets, such as FAFB, MiCrONS, H01, etc., the vast majority of neuron segmentation results are in the middle region of the dataset, and it seems to be not uncommon to have no segmentation results in the edge region.
I'm wondering if there is another way to avoid this error, and I'm wondering if cloudvlomue, or igenous, has a relevant api parameter that defaults empty regions to 0 when accessed, which might avoid the above EmptyVolumeException.
Hi, I recently generated mesh and skeleton for the segmentation results of a larger electron microscopy dataset, and I used the following commands:
Generate mesh:
Generate skeleton:
When running the command
igneous execute
, the same error seems to occur in both scripts:The staus of
$skelforge_queue
Then, I try to access the autoseg data by CloudVolume
The same error seems to have occurred
The
cv.meta.info
of the autoseg(mip=2) isI was observing the region Bbox([15940, 40089, 18946],[16004, 40153, 19010] on Neuroglancer and it seems to be at the edge of the entire electron microscopy dataset now. It is indeed a dark patch with no segmentation results.
In large-scale electron microscopy datasets, such as FAFB, MiCrONS, H01, etc., the vast majority of neuron segmentation results are in the middle region of the dataset, and it seems to be not uncommon to have no segmentation results in the edge region.
I'm wondering if there is another way to avoid this error, and I'm wondering if
cloudvlomue
, origenous
, has a relevant api parameter that defaults empty regions to 0 when accessed, which might avoid the above EmptyVolumeException.