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Project-MONAI
nightly tests: `deep_atlas/deep_atlas_tutorial.ipynb`
Describe the bug
Running ./deep_atlas/deep_atlas_tutorial.ipynb
Checking PEP8 compliance...
Running notebook...
Before:
"max_epochs = 60\n",
"max_epochs = 120\n",
After:
"max_epochs = 1\n",
"max_epochs = 1\n",
Before:
"val_interval = 5\n",
"val_interval = 5\n",
After:
"val_interval = 1\n",
"val_interval = 1\n",
Before:
"num_batches_for_histogram = 200 # sample this many batches\n",
After:
"num_batches_for_histogram = 1 # sample this many batches\n",
/opt/conda/lib/python3.8/site-packages/papermill/iorw.py:50: FutureWarning: pyarrow.HadoopFileSystem is deprecated as of 2.0.0, please use pyarrow.fs.HadoopFileSystem instead.
from pyarrow import HadoopFileSystem
Executing: 0%| | 0/97 [00:00<?, ?cell/s]
Executing: 1%| | 1/97 [00:01<02:05, 1.31s/cell]
Executing: 4%|▍ | 4/97 [00:09<03:57, 2.55s/cell]
Executing: 5%|▌ | 5/97 [00:11<03:42, 2.42s/cell]
Executing: 9%|▉ | 9/97 [1:50:32<24:52:15, 1017.45s/cell]
Executing: 26%|██▌ | 25/97 [1:50:33<4:30:49, 225.69s/cell]
Executing: 28%|██▊ | 27/97 [1:50:34<3:51:14, 198.21s/cell]
Executing: 28%|██▊ | 27/97 [1:50:35<4:46:43, 245.76s/cell]
Traceback (most recent call last):
File "/opt/conda/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
execute_notebook(
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [13]":
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/transforms/transform.py in apply_transform(transform, data, map_items, unpack_items)
81 return [_apply_transform(transform, item, unpack_items) for item in data]
---> 82 return _apply_transform(transform, data, unpack_items)
83 except Exception as e:
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/transforms/transform.py in _apply_transform(transform, parameters, unpack_parameters)
52
---> 53 return transform(parameters)
54
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/transforms/io/dictionary.py in __call__(self, data, reader)
120 for key, meta_key, meta_key_postfix in self.key_iterator(d, self.meta_keys, self.meta_key_postfix):
--> 121 data = self._loader(d[key], reader)
122 if self._loader.image_only:
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/transforms/io/array.py in __call__(self, filename, reader)
215
--> 216 img_array, meta_data = reader.get_data(img)
217 img_array = img_array.astype(self.dtype, copy=False)
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/image_reader.py in get_data(self, img)
242 for i in ensure_tuple(img):
--> 243 data = self._get_array_data(i)
244 img_array.append(data)
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/image_reader.py in _get_array_data(self, img)
327 """
--> 328 np_img = itk.array_view_from_image(img, keep_axes=False)
329 if img.GetNumberOfComponentsPerPixel() == 1: # handling spatial images
/opt/conda/lib/python3.8/site-packages/itk/support/extras.py in GetArrayViewFromImage(image_or_filter, keep_axes, update, ttype)
323 """Get an array view with the content of the image buffer"""
--> 324 return _GetArrayFromImage(
325 image_or_filter, "GetArrayViewFromImage", keep_axes, update, ttype
/opt/conda/lib/python3.8/site-packages/itk/support/extras.py in _GetArrayFromImage(image_or_filter, function_name, keep_axes, update, ttype)
293 ImageType = img.__class__
--> 294 keys = [k for k in itk.PyBuffer.keys() if k[0] == ImageType]
295 if len(keys) == 0:
/opt/conda/lib/python3.8/site-packages/itk/support/lazy.py in __getattribute__(self, attr)
131 namespace = {}
--> 132 base.itk_load_swig_module(module, namespace)
133 self.loaded_lazy_modules.add(module)
/opt/conda/lib/python3.8/site-packages/itk/support/base.py in itk_load_swig_module(name, namespace)
109 loader = LibraryLoader()
--> 110 l_module = loader.load(swig_module_name)
111
/opt/conda/lib/python3.8/site-packages/itk/support/base.py in load(self, name)
258 l_spec = importlib.util.find_spec(name)
--> 259 l_spec.loader.exec_module(l_module) # pytype: disable=attribute-error
260 return l_module
/opt/conda/lib/python3.8/importlib/_bootstrap_external.py in exec_module(self, module)
/opt/conda/lib/python3.8/importlib/_bootstrap.py in _call_with_frames_removed(f, *args, **kwds)
/opt/conda/lib/python3.8/site-packages/itk/support/../ITKBridgeNumPyPython.py in <module>
70 import itk.ITKCommonPython
---> 71 from itk.itkPyBufferPython import *
72 from itk.itkPyVectorContainerPython import *
/opt/conda/lib/python3.8/site-packages/itk/itkPyBufferPython.py in <module>
117 try:
--> 118 from distributed.protocol import dask_serialize, dask_deserialize
119 from typing import Dict, List, Tuple
/opt/conda/lib/python3.8/site-packages/distributed/__init__.py in <module>
7 from ._version import get_versions
----> 8 from .actor import Actor, ActorFuture
9 from .client import (
/opt/conda/lib/python3.8/site-packages/distributed/actor.py in <module>
4
----> 5 from .client import Future
6 from .protocol import to_serialize
/opt/conda/lib/python3.8/site-packages/distributed/client.py in <module>
52 from . import versions as version_module
---> 53 from .batched import BatchedSend
54 from .cfexecutor import ClientExecutor
/opt/conda/lib/python3.8/site-packages/distributed/batched.py in <module>
9
---> 10 from .core import CommClosedError
11
/opt/conda/lib/python3.8/site-packages/distributed/core.py in <module>
23 from . import profile, protocol
---> 24 from .comm import (
25 CommClosedError,
/opt/conda/lib/python3.8/site-packages/distributed/comm/__init__.py in <module>
24
---> 25 _register_transports()
/opt/conda/lib/python3.8/site-packages/distributed/comm/__init__.py in _register_transports()
16 def _register_transports():
---> 17 from . import inproc, tcp, ws
18
/opt/conda/lib/python3.8/site-packages/distributed/comm/tcp.py in <module>
379
--> 380 class BaseTCPConnector(Connector, RequireEncryptionMixin):
381 _executor = ThreadPoolExecutor(2, thread_name_prefix="TCP-Executor")
/opt/conda/lib/python3.8/site-packages/distributed/comm/tcp.py in BaseTCPConnector()
381 _executor = ThreadPoolExecutor(2, thread_name_prefix="TCP-Executor")
--> 382 _resolver = netutil.ExecutorResolver(close_executor=False, executor=_executor)
383 client = TCPClient(resolver=_resolver)
/opt/conda/lib/python3.8/site-packages/tornado/util.py in __new__(cls, *args, **kwargs)
287 # here too.
--> 288 instance.initialize(*args, **init_kwargs)
289 return instance
/opt/conda/lib/python3.8/site-packages/tornado/netutil.py in initialize(self, executor, close_executor)
426 ) -> None:
--> 427 self.io_loop = IOLoop.current()
428 if executor is not None:
/opt/conda/lib/python3.8/site-packages/tornado/ioloop.py in current(instance)
262 try:
--> 263 loop = asyncio.get_event_loop()
264 except (RuntimeError, AssertionError):
/opt/conda/lib/python3.8/asyncio/events.py in get_event_loop(self)
638 if self._local._loop is None:
--> 639 raise RuntimeError('There is no current event loop in thread %r.'
640 % threading.current_thread().name)
RuntimeError: There is no current event loop in thread 'Thread-9'.
The above exception was the direct cause of the following exception:
RuntimeError Traceback (most recent call last)
/tmp/ipykernel_11802/3916465789.py in <module>
----> 1 dataset_seg_available_train = monai.data.CacheDataset(
2 data=data_seg_available_train,
3 transform=transform_seg_available,
4 cache_num=16
5 )
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/dataset.py in __init__(self, data, transform, cache_num, cache_rate, num_workers, progress, copy_cache)
699 if self.num_workers is not None:
700 self.num_workers = max(int(self.num_workers), 1)
--> 701 self._cache: List = self._fill_cache()
702
703 def set_data(self, data: Sequence):
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/dataset.py in _fill_cache(self)
720 with ThreadPool(self.num_workers) as p:
721 if self.progress and has_tqdm:
--> 722 return list(
723 tqdm(
724 p.imap(self._load_cache_item, range(self.cache_num)),
/opt/conda/lib/python3.8/site-packages/tqdm/std.py in __iter__(self)
1178
1179 try:
-> 1180 for obj in iterable:
1181 yield obj
1182 # Update and possibly print the progressbar.
/opt/conda/lib/python3.8/multiprocessing/pool.py in next(self, timeout)
866 if success:
867 return value
--> 868 raise value
869
870 __next__ = next # XXX
/opt/conda/lib/python3.8/multiprocessing/pool.py in worker(inqueue, outqueue, initializer, initargs, maxtasks, wrap_exception)
123 job, i, func, args, kwds = task
124 try:
--> 125 result = (True, func(*args, **kwds))
126 except Exception as e:
127 if wrap_exception and func is not _helper_reraises_exception:
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/data/dataset.py in _load_cache_item(self, idx)
740 break
741 _xform = deepcopy(_transform) if isinstance(_transform, ThreadUnsafe) else _transform
--> 742 item = apply_transform(_xform, item)
743 return item
744
/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/transforms/transform.py in apply_transform(transform, data, map_items, unpack_items)
104 else:
105 _log_stats(data=data)
--> 106 raise RuntimeError(f"applying transform {transform}") from e
107
108
RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7f610d679ee0>
Seems like related to some ITK logic in the python / native connection? @thewtex , do you have any idea what's going on?
Thanks in advance.
Sorry I just noticed this issue; was this ultimately resolved? To close this, are we waiting on the change https://github.com/InsightSoftwareConsortium/ITK/pull/3011 to be included in the version of ITK used by MONAI?
