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When converting an image, the program created a crashdump and exited.
/usr/local/bin/python /usr/local/bin/wsic convert -i /xxx.jp2 -o /xxx.tiff -rt 4096 4096 -w 30 -mpp 0.5 0.5 --no-ome --overwrite -to 180 -c jpeg -cl 90 -d 2 -d 4 -d 8
Reading: 1%| | 10/828 [00:23<31:10, 2.29s/it] Writing: 0%| | 106/204840 [00:23<12:07:59, 4.69it/s] /usr/local/lib/python3.9/site-packages/wsic/readers.py:385: UserWarning: Failed to get next tile after 100 attempts. Dumping debug information.9, 4.69it/s] warnings.warn( Reading: 1%| | 10/828 [03:23<4:37:56, 20.39s/it] Writing: 0%| | 160/204840 [03:23<72:26:45, 1.27s/it] Traceback (most recent call last): File "/usr/local/bin/wsic", line 8, in <module> Reader Shape (145456, 92000, 3) Read Tile Size (4096, 4096) Yield Tile Size (256, 256) sys.exit(main()) File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1130, in __call__ Read Mosaic Shape (36, 23) Yield Mosaic Shape (569, 360) Read Index (0, 10) Yield Index (0, 160) Remaining Reads (:10) [(1, 17), (1, 18), (1, 19), (1, 20), (1, 21), (1, 22), (2, 0), (2, 1), (2, 2), (2, 3)] Enqueued {(1, 0), (1, 6), (0, 14), (1, 3), (1, 9), (0, 11), (0, 17), (1, 12), (0, 20), (1, 15), (1, 2), (0, 10), (0, 16), (1, 5), (1, 11), (0, 13), (0, 19), (1, 8), (1, 14), (0, 22), (1, 1), (1, 4), (0, 12), (1, 7), (1, 13), (0, 15), (0, 21), (1, 10), (1, 16), (0, 18)} Reordering Dict (keys) dict_keys([(0, 22), (0, 21), (0, 18), (0, 15), (1, 1), (0, 14), (0, 11), (1, 4), (0, 13), (1, 5), (1, 3), (0, 12), (0, 17), (0, 19), (1, 0), (1, 6), (1, 8), (1, 10), (1, 7), (1, 13), (1, 14), (1, 15), (1, 12), (1, 16), (1, 9), (1, 11)]) Queue Size 0 Intermediate Read slices (slice(0, 256, None), slice(40960, 41216, None)) return self.main(*args, **kwargs) File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/usr/local/lib/python3.9/site-packages/wsic/cli.py", line 223, in convert writer.copy_from_reader( File "/usr/local/lib/python3.9/site-packages/wsic/writers.py", line 593, in copy_from_reader tif.write( File "/usr/local/lib/python3.9/site-packages/tifffile/tifffile.py", line 3116, in write for tileindex, chunk in enumerate( File "/usr/local/lib/python3.9/site-packages/tifffile/tifffile.py", line 20438, in encode_tiles tile = next(tileiter) File "/usr/local/lib/python3.9/site-packages/tifffile/tifffile.py", line 21536, in newiter yield from iterator File "/usr/local/lib/python3.9/site-packages/tqdm/std.py", line 1195, in __iter__ for obj in iterable: File "/usr/local/lib/python3.9/site-packages/wsic/readers.py", line 406, in __next__ raise IOError(f"Tile read timed out at index {self.yield_index}") OSError: Tile read timed out at index (0, 160) Exception ignored in: <function MultiProcessTileIterator.__del__ at 0x7f3a53e61160> Traceback (most recent call last): File "/usr/local/lib/python3.9/site-packages/wsic/readers.py", line 509, in __del__ self.close() File "/usr/local/lib/python3.9/site-packages/wsic/readers.py", line 501, in close executor.map(lambda p: p.join(1), self.processes) File "/usr/local/lib/python3.9/concurrent/futures/_base.py", line 598, in map fs = [self.submit(fn, *args) for args in zip(*iterables)] File "/usr/local/lib/python3.9/concurrent/futures/_base.py", line 598, in <listcomp> fs = [self.submit(fn, *args) for args in zip(*iterables)] File "/usr/local/lib/python3.9/concurrent/futures/thread.py", line 169, in submit raise RuntimeError('cannot schedule new futures after ' RuntimeError: cannot schedule new futures after interpreter shutdown
There is no other I/O intensive job while running the task.
The text was updated successfully, but these errors were encountered:
FYI it's more reproducible when using a high worker count.
Sorry, something went wrong.
Hi @himekifee I think I may have tracked down the cause of this issue and it should be fixed by #53 and #48.
This should be fixed in version 0.7.0 hopefully. Publishing to PyPI now.
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Description
When converting an image, the program created a crashdump and exited.
What I Did
/usr/local/bin/python /usr/local/bin/wsic convert -i /xxx.jp2 -o /xxx.tiff -rt 4096 4096 -w 30 -mpp 0.5 0.5 --no-ome --overwrite -to 180 -c jpeg -cl 90 -d 2 -d 4 -d 8
There is no other I/O intensive job while running the task.
The text was updated successfully, but these errors were encountered: