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imageio and imageio-ffmpeg Using isAlive() in Python3.9
See original GitHub issueHello ImageIO Devs!
I’m currently using your reader with PIMS and Dask since it seems like ffmpeg backends are the way things are moving for video editing. It’s for this project.
While running my code on a Linux machine in an environment that has Python 3.9.2, I received the following error message:
Traceback (most recent call last):
File "/nadata/snlkt/data/facial_expression/specialk/MouseFacialExpressionAnalysis/dask_faces.py", line 635, in <module>
hog_images.to_zarr("/scratch/snlkt_facial_expression/hogs/data.zarr", overwrite=True)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/array/core.py", line 2784, in to_zarr
return to_zarr(self, *args, **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/array/core.py", line 3547, in to_zarr
return arr.store(z, lock=False, compute=compute, return_stored=return_stored)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/array/core.py", line 1710, in store
r = store([self], [target], **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/array/core.py", line 1184, in store
compute_as_if_collection(Array, store_dsk, map_keys, **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/base.py", line 319, in compute_as_if_collection
return schedule(dsk2, keys, **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/multiprocessing.py", line 220, in get
result = get_async(
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/local.py", line 508, in get_async
raise_exception(exc, tb)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/local.py", line 316, in reraise
raise exc
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/local.py", line 221, in execute_task
result = _execute_task(task, data)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in <genexpr>
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in <genexpr>
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in <genexpr>
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in <genexpr>
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 113, in _execute_task
return [_execute_task(a, cache) for a in arg]
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 113, in <listcomp>
return [_execute_task(a, cache) for a in arg]
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/optimization.py", line 990, in __call__
return core.get(self.dsk, self.outkey, dict(zip(self.inkeys, args)))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 149, in get
result = _execute_task(task, cache)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/utils.py", line 40, in apply
return func(*args, **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask/array/core.py", line 514, in _pass_extra_kwargs
return func(*args[len(keys) :], **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask_image/imread/__init__.py", line 99, in _map_read_frame
return _utils._read_frame(fn=fn, i=slice(i, j), **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/dask_image/imread/_utils.py", line 8, in _read_frame
return arrayfunc(imgs[i])
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/slicerator/__init__.py", line 226, in <genexpr>
return (self._get(i) for i in self.indices)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/slicerator/__init__.py", line 206, in _get
return self._ancestor[key]
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/slicerator/__init__.py", line 187, in __getitem__
return self._get(indices)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/pims/base_frames.py", line 100, in __getitem__
return self.get_frame(key)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/pims/base_frames.py", line 598, in get_frame
result = self._get_frame_wrapped(**coords)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/pims/imageio_reader.py", line 123, in get_frame_2D
frame = self.reader.get_data(i)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/imageio/core/format.py", line 340, in get_data
im, meta = self._get_data(index, **kwargs)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/imageio/plugins/ffmpeg.py", line 396, in _get_data
result, is_new = self._read_frame()
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/imageio/plugins/ffmpeg.py", line 585, in _read_frame
s, is_new = self._read_frame_data()
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/imageio/plugins/ffmpeg.py", line 569, in _read_frame_data
err2 = self._stderr_catcher.get_text(0.4)
File "/home/jdelahanty/miniconda3/envs/facial_expression2/lib/python3.9/site-packages/imageio/plugins/ffmpeg.py", line 901, in get_text
while self.isAlive() and time.time() < etime: # pragma: no cover
AttributeError: 'StreamCatcher' object has no attribute 'isAlive'
After googling around a little, I found a few other issues that talk about how isAlive was deprecated at some point. I’m not really sure why other than it seems like they wanted to move to snake_case instead of camelCase?
When I looked at the source code in my Conda environment as the Traceback describes, I indeed found the use of isAlive! Changing this to is_alive lets things work again!
Below is my full environment for reference.
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
blas 1.0 mkl
blosc 1.21.0 h8c45485_0
bokeh 2.4.2 py39hf3d152e_1 conda-forge
bottleneck 1.3.4 py39hce1f21e_0
brotli 1.0.9 h7f98852_5 conda-forge
brotli-bin 1.0.9 h7f98852_5 conda-forge
brotlipy 0.7.0 py39h3811e60_1001 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f8727e_0
ca-certificates 2021.10.8 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2021.10.8 py39hf3d152e_2 conda-forge
cffi 1.15.0 py39hd667e15_1
cfitsio 3.470 h2e3daa1_7 conda-forge
charls 2.2.0 h2531618_0
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
click 8.1.3 py39hf3d152e_0 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
cryptography 35.0.0 py39hbca0aa6_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.11.0 py39h27cfd23_0
dask 2022.4.2 pyhd8ed1ab_0 conda-forge
dask-core 2022.4.2 pyhd8ed1ab_0 conda-forge
dask-image 2021.12.0 pyhd8ed1ab_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
distributed 2022.4.2 pyhd8ed1ab_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
ffmpeg 4.3.2 hca11adc_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fsspec 2022.3.0 pyhd8ed1ab_0 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.6.13 h85f3911_1 conda-forge
h5py 3.2.1 nompi_py39h98ba4bc_100 conda-forge
hdf5 1.10.6 nompi_h7c3c948_1111 conda-forge
heapdict 1.0.1 py_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagecodecs 2021.8.26 py39h4cda21f_0
imageio 2.3.0 py_1 conda-forge
imageio-ffmpeg 0.4.7 pyhd8ed1ab_0 conda-forge
intel-openmp 2021.4.0 h06a4308_3561
jinja2 3.1.1 pyhd8ed1ab_0 conda-forge
jpeg 9e h7f8727e_0
jxrlib 1.1 h7f98852_2 conda-forge
kiwisolver 1.3.2 py39h295c915_0
krb5 1.19.2 hac12032_0
lame 3.100 h7f98852_1001 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.35.1 h7274673_9
lerc 3.0 h295c915_0
libaec 1.0.4 he6710b0_1
libbrotlicommon 1.0.9 h7f98852_5 conda-forge
libbrotlidec 1.0.9 h7f98852_5 conda-forge
libbrotlienc 1.0.9 h7f98852_5 conda-forge
libcurl 7.82.0 h0b77cf5_0
libdeflate 1.8 h7f98852_0 conda-forge
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h516909a_1 conda-forge
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 7.5.0 h14aa051_20 conda-forge
libgfortran4 7.5.0 h14aa051_20 conda-forge
libgomp 9.3.0 h5101ec6_17
libnghttp2 1.46.0 hce63b2e_0
libpng 1.6.37 h21135ba_2 conda-forge
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 9.3.0 hd4cf53a_17
libtiff 4.2.0 h85742a9_0
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4 3.1.3 py39h27cfd23_0
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markupsafe 2.0.1 py39h3811e60_0 conda-forge
matplotlib-base 3.3.4 py39h2fa2bec_0 conda-forge
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h3811e60_0 conda-forge
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39hde0f152_0 conda-forge
msgpack-python 1.0.2 py39hff7bd54_1
ncurses 6.3 h7f8727e_2
nettle 3.6 he412f7d_0 conda-forge
networkx 2.3 py_0 conda-forge
numcodecs 0.9.1 py39h295c915_0
numexpr 2.8.1 py39h6abb31d_0
numpy 1.21.5 py39he7a7128_1
numpy-base 1.21.5 py39hf524024_1
olefile 0.46 pyh9f0ad1d_1 conda-forge
openh264 2.1.1 h780b84a_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1n h7f8727e_0
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.2 py39h295c915_0
partd 1.2.0 pyhd8ed1ab_0 conda-forge
pillow 7.2.0 py39h6f3857e_2 conda-forge
pims 0.6.0 pyhd8ed1ab_0 conda-forge
pip 21.2.4 py39h06a4308_0
pooch 1.6.0 pyhd8ed1ab_0 conda-forge
psutil 5.8.0 py39h27cfd23_1
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py39hf3d152e_5 conda-forge
python 3.9.2 hdb3f193_0
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.3.0 py39h7f8727e_0
pyyaml 5.4.1 py39h3811e60_0 conda-forge
readline 8.1.2 h7f8727e_1
requests 2.27.1 pyhd8ed1ab_0 conda-forge
scikit-image 0.18.1 py39hde0f152_0 conda-forge
scipy 1.7.3 py39hc147768_0
setuptools 61.2.0 py39h06a4308_0
six 1.16.0 pyh6c4a22f_0 conda-forge
slicerator 1.1.0 pyhd8ed1ab_0 conda-forge
snappy 1.1.8 he1b5a44_3 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
sqlite 3.38.2 hc218d9a_0
tblib 1.7.0 pyhd8ed1ab_0 conda-forge
tifffile 2021.7.2 pyhd8ed1ab_0 conda-forge
tk 8.6.11 h1ccaba5_0
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39h3811e60_1 conda-forge
typing_extensions 4.2.0 pyha770c72_1 conda-forge
tzdata 2022a hda174b7_0
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
x264 1!161.3030 h7f98852_1 conda-forge
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h516909a_0 conda-forge
zarr 2.11.3 pyhd8ed1ab_0 conda-forge
zfp 0.5.5 h9c3ff4c_5 conda-forge
zict 2.2.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h7f8727e_2
zstd 1.4.9 ha95c52a_0 conda-forge
I’m not sure if this is actually more related to Dask or PIMS, but since the traceback came from the ffmpeg.py module I figured I’d post it here.
Issue Analytics
- State:
- Created a year ago
- Comments:15 (10 by maintainers)
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@jmdelahanty Okay, in that case, it was probably just an outdated library on your system and nothing major is preventing you from using a more recent version of ImageIO.
To sum up all the discussion above, the solution to this issue seems to be “update ImageIO, because the problem is fixed in more recent versions”.
@jmdelahanty Does that solve your problem? If so, I will go ahead and close this issue to stay organized, otherwise let me know what is missing.
@jmdelahanty: It was just meant as debugging tips, in case you’re looking for possible causes of issues. This is not the right thread for debugging conda setups. If you have issues with the conda package itself, I’d advise you open an issue at the repository for the package at https://github.com/conda-forge/imageio-feedstock/.