pims Doesn't Recognize ImageIO in Conda Environment/Jupyter Notebook
jmdelahanty opened this issue · 1 comments
jmdelahanty commented
Hello pims developers!
I'm super excited to use the package to help us get through some videos without cutting up video data into clips unnecessarily.
I'm trying to use it in a Jupyter Notebook or on the command line but am running into an import error I can't seem to solve.
Here's what it looks like from the command line:
Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pims
/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/skimage/io/manage_plugins.py:23: UserWarning: Your installed pillow version is < 7.1.0. Several security issues (CVE-2020-11538, CVE-2020-10379, CVE-2020-10994, CVE-2020-10177) have been fixed in pillow 7.1.0 or higher. We recommend to upgrade this library.
from .collection import imread_collection_wrapper
>>> import imageio
>>> pims.ImageIOReader("/nadata/snlkt/specialk_cs/2p/raw/CSE021/20211216/20211216_CSE021_plane1_-733.45.avi")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/pims/api.py", line 28, in raiser
raise ImportError(
ImportError: This reader requires ImageIO.
Here's some info about my conda environment:
# packages in environment at /home/jdelahanty/miniconda3/envs/facial_expression:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
anyio 3.5.0 py38h578d9bd_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py38h7f8727e_0
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py38h497a2fe_1001 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cairo 1.16.0 ha12eb4b_1010 conda-forge
certifi 2021.10.8 py38h578d9bd_2 conda-forge
cffi 1.15.0 py38hd667e15_1
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
cryptography 35.0.0 py38ha5dfef3_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.11.0 py38h7b6447c_0
dask-core 2022.2.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
enum34 1.1.10 py38h32f6830_2 conda-forge
executing 0.8.3 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
ffmpeg 4.3.2 h37c90e5_3 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freeglut 3.2.2 h9c3ff4c_1 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fsspec 2022.2.0 pyhd8ed1ab_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.6.13 h85f3911_1 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gst-plugins-base 1.18.5 hf529b03_3 conda-forge
gstreamer 1.18.5 h9f60fe5_3 conda-forge
harfbuzz 3.4.0 hb4a5f5f_0 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagecodecs-lite 2019.12.3 py38h5c078b8_3 conda-forge
imageio 2.6.1 py38_0 conda-forge
importlib-metadata 4.11.2 py38h578d9bd_0 conda-forge
importlib_resources 5.4.0 pyhd8ed1ab_0 conda-forge
ipykernel 5.5.5 py38hd0cf306_0 conda-forge
ipython 8.1.1 py38h578d9bd_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jasper 2.0.33 ha77e612_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.1 py38h578d9bd_0 conda-forge
jinja2 3.0.3 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9d h7f8727e_0
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.1.2 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.2 py38h578d9bd_0 conda-forge
jupyter_server 1.13.5 pyhd8ed1ab_1 conda-forge
jupyterlab 3.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_server 2.10.3 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.3.2 py38h295c915_0
krb5 1.19.3 h3790be6_0 conda-forge
lame 3.100 h7f98852_1001 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 11_linux64_openblas conda-forge
libcblas 3.9.0 11_linux64_openblas conda-forge
libclang 13.0.1 default_hc23dcda_0 conda-forge
libcurl 7.82.0 h7bff187_0 conda-forge
libdeflate 1.8 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_15 conda-forge
libgfortran-ng 11.2.0 h69a702a_13 conda-forge
libgfortran5 11.2.0 h5c6108e_13 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libglu 9.0.0 he1b5a44_1001 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 11_linux64_openblas conda-forge
liblapacke 3.9.0 11_linux64_openblas conda-forge
libllvm13 13.0.1 hf817b99_2 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.17 pthreads_h8fe5266_1 conda-forge
libopencv 4.5.5 py38hd60e7aa_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 14.2 hd57d9b9_0 conda-forge
libprotobuf 3.19.4 h780b84a_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_15 conda-forge
libtiff 4.3.0 h6f004c6_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
llvm-openmp 13.0.1 he0ac6c6_1 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markupsafe 2.0.1 py38h497a2fe_0 conda-forge
matplotlib-base 3.3.4 py38h0efea84_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py38h497a2fe_1004 conda-forge
mysql-common 8.0.28 haf5c9bc_3 conda-forge
mysql-libs 8.0.28 h28c427c_3 conda-forge
nbclassic 0.3.5 pyhd8ed1ab_0 conda-forge
nbclient 0.5.11 pyhd8ed1ab_0 conda-forge
nbconvert 6.4.2 py38h578d9bd_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h7f8727e_2
nest-asyncio 1.5.4 pyhd8ed1ab_0 conda-forge
nettle 3.6 he412f7d_0 conda-forge
networkx 2.7 pyhd8ed1ab_0 conda-forge
notebook 6.4.8 pyha770c72_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.77 h2350873_0 conda-forge
numpy 1.20.3 py38h9894fe3_1 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
opencv 4.5.5 py38h578d9bd_0 conda-forge
openh264 2.1.1 h780b84a_0 conda-forge
openssl 1.1.1n h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.2.3 py38h51da96c_0 conda-forge
pandoc 2.17.1.1 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.2.0 pyhd8ed1ab_0 conda-forge
pathlib 1.0.1 py38h578d9bd_5 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 6.2.1 py38h6b7be26_0 conda-forge
pims 0.5 pyh9f0ad1d_1 conda-forge
pip 21.2.4 py38h06a4308_0
pixman 0.40.0 h36c2ea0_0 conda-forge
pooch 1.6.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.13.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.27 pyha770c72_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-opencv 4.5.5 py38he5a9106_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.0 py38heee7806_0
pysocks 1.7.1 py38h578d9bd_4 conda-forge
python 3.8.13 h582c2e5_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pywavelets 1.1.1 py38h7b6447c_2
pyyaml 5.4.1 py38h497a2fe_0 conda-forge
pyzmq 19.0.2 py38ha71036d_2 conda-forge
qt 5.12.9 ha98a1a1_5 conda-forge
readline 8.1.2 h7f8727e_1
requests 2.27.1 pyhd8ed1ab_0 conda-forge
scikit-image 0.18.1 py38h51da96c_0 conda-forge
scikit-learn 0.23.2 py38h5d63f67_3 conda-forge
scipy 1.5.3 py38hb2138dd_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 58.0.4 py38h06a4308_0
six 1.16.0 pyh6c4a22f_0 conda-forge
slicerator 1.1.0 pyhd8ed1ab_0 conda-forge
sniffio 1.2.0 py38h578d9bd_2 conda-forge
sqlite 3.37.2 hc218d9a_0
stack_data 0.2.0 pyhd8ed1ab_0 conda-forge
terminado 0.13.2 py38h578d9bd_0 conda-forge
testpath 0.6.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2019.7.26.2 py38_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py38h497a2fe_1 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
urllib3 1.26.8 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.3.1 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
x264 1!161.3030 h7f98852_1 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h516909a_0 conda-forge
zeromq 4.3.4 h9c3ff4c_0 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
Any advice anyone?
jmdelahanty commented
I fixed it! Even though ImageIO was installed, there was a dependency that ImageIO required as well. Here's what I found when messing with ImageIO on it's own:
(facial_expression) jdelahanty@cheetos:/snlkt/data/facial_expression$ python3.8
Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import imageio as iio
>>> im = iio.get_reader
>>> im
<function get_reader at 0x7fdec3824790>
>>> test = iio.get_reader("/nadata/snlkt/specialk_cs/2p/raw/CSE014/20211211/20211211_CSE014_plane1_-320.375.avi")
Traceback (most recent call last):
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/imageio/plugins/ffmpeg.py", line 59, in _get_ffmpeg_api
import imageio_ffmpeg
ModuleNotFoundError: No module named 'imageio_ffmpeg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/imageio/core/functions.py", line 186, in get_reader
return format.get_reader(request)
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/imageio/core/format.py", line 170, in get_reader
return self.Reader(self, request)
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/imageio/core/format.py", line 221, in __init__
self._open(**self.request.kwargs.copy())
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/imageio/plugins/ffmpeg.py", line 257, in _open
self._ffmpeg_api = _get_ffmpeg_api()
File "/home/jdelahanty/miniconda3/envs/facial_expression/lib/python3.8/site-packages/imageio/plugins/ffmpeg.py", line 61, in _get_ffmpeg_api
raise ImportError(
ImportError: To use the imageio ffmpeg plugin you need to 'pip install imageio-ffmpeg'
After doing:
(facial_expression) jdelahanty@cheetos:/snlkt/data/facial_expression$ pip install imageio-ffmpeg
Collecting imageio-ffmpeg
Downloading imageio_ffmpeg-0.4.5-py3-none-manylinux2010_x86_64.whl (26.9 MB)
|████████████████████████████████| 26.9 MB 162 kB/s
Installing collected packages: imageio-ffmpeg
Successfully installed imageio-ffmpeg-0.4.5
I could then get the reader! Doing it looked like this:
(facial_expression) jdelahanty@cheetos:/snlkt/data/facial_expression$ python3.8
Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import imageio
>>> import pims
>>> pims.ImageIOReader
<class 'pims.imageio_reader.ImageIOReader'>
>>> pims.ImageIOReader("/nadata/snlkt/specialk_cs/2p/raw/CSE014/20211211/20211211_CSE014_plane1_-320.375.avi")
<FramesSequenceND>
Axes: 3
Axis 'x' size: 1280
Axis 'y' size: 1024
Axis 't' size: 45270
Pixel Datatype: uint8
Maybe the issue should remain open or some documentation for this being the potential reason for the exception could be added? I've never done that before, but would be happy to help if I could!