perslev
commented
4 years ago Hi, thank you for raising this issue! I will look into it as soon as possible, but it might be a few days from now.
Closed aluquecerp closed 4 years ago
perslev
commented
4 years ago Hi, thank you for raising this issue! I will look into it as soon as possible, but it might be a few days from now.
waves-lee
commented
4 years ago Hi, thank you for raising this issue! I will look into it as soon as possible, but it might be a few days from now.
Hello, I am very interested in your project, I want to be an entry project for me to learn brain signals, but I have the same problem when I run it（windows+python3.7+tensorflow-gpu2.0.0）. Like this： `utime.errors.ChannelNotFoundError: Unexpected channel loading error. Should have loaded 1 channels (['EEG Fpz-Cz']), but the PSG array ha s shape (8220000, 2). There might be an error in the code. Please rais an issue on GitHub.
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "d:\workspace\pythonspace\u-time\utime\dataset\sleep_study.py", line 595, in load self._load() File "d:\workspace\pythonspace\u-time\utime\dataset\sleep_study.py", line 535, in _load self._psg, header, loaded_chanls = self._load_with_any_in(try_channels) File "d:\workspace\pythonspace\u-time\utime\dataset\sleep_study.py", line 517, in _load_with_any_in raise err from e utime.errors.ChannelNotFoundError: Could not load select_channels ['EEG Fpz-Cz'] or alternative_select_channels [[]]
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "d:\workspace\pythonspace\u-time\utime\dataset\sleep_study_dataset.py", line 158, in load
for i, ss in enumerate(res):
File "D:\Program Files\Anaconda3\lib\concurrent\futures_base.py", line 598, in result_iterator
yield fs.pop().result()
File "D:\Program Files\Anaconda3\lib\concurrent\futures_base.py", line 435, in result
return self.get_result()
File "D:\Program Files\Anaconda3\lib\concurrent\futures_base.py", line 384, in get_result
raise self._exception
File "D:\Program Files\Anaconda3\lib\concurrent\futures\thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "d:\workspace\pythonspace\u-time\utime\dataset\sleep_study_dataset.py", line 156, in
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\Program Files\Anaconda3\Scripts\ut-script.py", line 11, in
It is difficult for a beginner like me ,to solve this problem. , I hope to get your help, thank you!
aluquecerp
commented
4 years ago Hi, @waves-lee
I made a fork of the repository and modified a bit of the code. It works on the example (I work usually on Google Colab) and at some cases. I am also a begginer, and I don't trust so much my code to work on every case. I would wait until @perslev develops a coherent and trustful solution, but you could try my code meanwhile.
waves-lee
commented
4 years ago Hi， @aluquecerp
I just tried the changes you made，it worked! Thank you soooooo much, you helped a lot. Also thanks @perslev for sharing your code. Now I can start to learn about it, hope you two have a nice day~
perslev
commented
4 years ago Thanks @aluquecerp for sharing your working version. Would one of you mind sharing your environment details so that I can try and reproduce this bug on my side?
E.g. output of pip freeze or conda env export.
Thanks!
aluquecerp
commented
4 years ago Hi, @perslev . I used a Google Colab Notebook. After using these two lines:
!git clone https://github.com/perslev/U-Time
!pip3 install -e U-Time
The pip freeze output is:
absl-py==0.9.0
alabaster==0.7.12
albumentations==0.1.12
altair==4.1.0
asgiref==3.2.7
astor==0.8.1
astropy==4.0.1.post1
astunparse==1.6.3
atari-py==0.2.6
atomicwrites==1.4.0
attrs==19.3.0
audioread==2.1.8
autograd==1.3
Babel==2.8.0
backcall==0.1.0
beautifulsoup4==4.6.3
bleach==3.1.5
blis==0.4.1
bokeh==1.4.0
boto==2.49.0
boto3==1.13.1
botocore==1.16.1
Bottleneck==1.3.2
branca==0.4.0
bs4==0.0.1
CacheControl==0.12.6
cachetools==3.1.1
catalogue==1.0.0
certifi==2020.4.5.1
cffi==1.14.0
chainer==6.5.0
chardet==3.0.4
click==7.1.2
cloudpickle==1.3.0
cmake==3.12.0
cmdstanpy==0.4.0
colorlover==0.3.0
community==1.0.0b1
contextlib2==0.5.5
convertdate==2.2.0
coverage==3.7.1
coveralls==0.5
crcmod==1.7
cufflinks==0.17.3
cvxopt==1.2.5
cvxpy==1.0.31
cycler==0.10.0
cymem==2.0.3
Cython==0.29.17
daft==0.0.4
dask==2.12.0
dataclasses==0.7
datascience==0.10.6
decorator==4.4.2
defusedxml==0.6.0
descartes==1.1.0
dill==0.3.1.1
distributed==1.25.3
Django==3.0.5
dlib==19.18.0
docopt==0.6.2
docutils==0.15.2
dopamine-rl==1.0.5
earthengine-api==0.1.220
easydict==1.9
ecos==2.0.7.post1
editdistance==0.5.3
en-core-web-sm==2.2.5
entrypoints==0.3
ephem==3.7.7.1
et-xmlfile==1.0.1
fa2==0.3.5
fancyimpute==0.4.3
fastai==1.0.61
fastdtw==0.3.4
fastprogress==0.2.3
fastrlock==0.4
fbprophet==0.6
feather-format==0.4.1
featuretools==0.4.1
filelock==3.0.12
firebase-admin==4.1.0
fix-yahoo-finance==0.0.22
Flask==1.1.2
folium==0.8.3
fsspec==0.7.3
future==0.16.0
gast==0.3.3
GDAL==2.2.2
gdown==3.6.4
gensim==3.6.0
geographiclib==1.50
geopy==1.17.0
gin-config==0.3.0
glob2==0.7
google==2.0.3
google-api-core==1.16.0
google-api-python-client==1.7.12
google-auth==1.7.2
google-auth-httplib2==0.0.3
google-auth-oauthlib==0.4.1
google-cloud-bigquery==1.21.0
google-cloud-core==1.0.3
google-cloud-datastore==1.8.0
google-cloud-firestore==1.6.2
google-cloud-language==1.2.0
google-cloud-storage==1.18.1
google-cloud-translate==1.5.0
google-colab==1.0.0
google-pasta==0.2.0
google-resumable-media==0.4.1
googleapis-common-protos==1.51.0
googledrivedownloader==0.4
graphviz==0.10.1
grpcio==1.28.1
gspread==3.0.1
gspread-dataframe==3.0.6
gym==0.17.1
h5py==2.10.0
HeapDict==1.0.1
holidays==0.9.12
html5lib==1.0.1
httpimport==0.5.18
httplib2==0.17.3
httplib2shim==0.0.3
humanize==0.5.1
hyperopt==0.1.2
ideep4py==2.0.0.post3
idna==2.9
image==1.5.31
imageio==2.4.1
imagesize==1.2.0
imbalanced-learn==0.4.3
imblearn==0.0
imgaug==0.2.9
importlib-metadata==1.6.0
imutils==0.5.3
inflect==2.1.0
intel-openmp==2020.0.133
intervaltree==2.1.0
ipykernel==4.10.1
ipython==5.5.0
ipython-genutils==0.2.0
ipython-sql==0.3.9
ipywidgets==7.5.1
itsdangerous==1.1.0
jax==0.1.64
jaxlib==0.1.45
jdcal==1.4.1
jedi==0.17.0
jieba==0.42.1
Jinja2==2.11.2
jmespath==0.9.5
joblib==0.14.1
jpeg4py==0.1.4
jsonschema==2.6.0
jupyter==1.0.0
jupyter-client==5.3.4
jupyter-console==5.2.0
jupyter-core==4.6.3
kaggle==1.5.6
kapre==0.1.3.1
Keras==2.3.1
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.0
keras-vis==0.4.1
kiwisolver==1.2.0
knnimpute==0.1.0
librosa==0.6.3
lightgbm==2.2.3
llvmlite==0.31.0
lmdb==0.98
lucid==0.3.8
LunarCalendar==0.0.9
lxml==4.2.6
Markdown==3.2.1
MarkupSafe==1.1.1
matplotlib==3.2.1
matplotlib-venn==0.11.5
missingno==0.4.2
mistune==0.8.4
mizani==0.6.0
mkl==2019.0
mlxtend==0.14.0
mne==0.20.3
more-itertools==8.2.0
moviepy==0.2.3.5
mpmath==1.1.0
msgpack==1.0.0
MultiPlanarUNet==0.2.3
multiprocess==0.70.9
multitasking==0.0.9
murmurhash==1.0.2
music21==5.5.0
natsort==5.5.0
nbconvert==5.6.1
nbformat==5.0.6
networkx==2.4
nibabel==3.0.2
nltk==3.2.5
notebook==5.2.2
np-utils==0.5.12.1
numba==0.48.0
numexpr==2.7.1
numpy==1.18.3
nvidia-ml-py3==7.352.0
oauth2client==4.1.3
oauthlib==3.1.0
okgrade==0.4.3
opencv-contrib-python==4.1.2.30
opencv-python==4.1.2.30
openpyxl==2.5.9
opt-einsum==3.2.1
osqp==0.6.1
packaging==20.3
palettable==3.3.0
pandas==1.0.3
pandas-datareader==0.8.1
pandas-gbq==0.11.0
pandas-profiling==1.4.1
pandocfilters==1.4.2
parso==0.7.0
pathlib==1.0.1
patsy==0.5.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==7.0.0
pip-tools==4.5.1
plac==1.1.3
plotly==4.4.1
plotnine==0.6.0
pluggy==0.7.1
portpicker==1.3.1
prefetch-generator==1.0.1
preshed==3.0.2
prettytable==0.7.2
progressbar2==3.38.0
prometheus-client==0.7.1
promise==2.3
prompt-toolkit==1.0.18
protobuf==3.10.0
psutil==5.7.0
psycopg2==2.7.6.1
ptvsd==5.0.0a12
ptyprocess==0.6.0
py==1.8.1
pyarrow==0.14.1
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycocotools==2.0.0
pycparser==2.20
pydata-google-auth==1.1.0
pydot==1.3.0
pydot-ng==2.0.0
pydotplus==2.0.2
PyDrive==1.3.1
pyemd==0.5.1
pyglet==1.5.0
Pygments==2.1.3
pygobject==3.26.1
pymc3==3.7
PyMeeus==0.3.7
pymongo==3.10.1
pymystem3==0.2.0
PyOpenGL==3.1.5
pyparsing==2.4.7
pyrsistent==0.16.0
pysndfile==1.3.8
PySocks==1.7.1
pystan==2.19.1.1
pytest==3.6.4
python-apt==1.6.5+ubuntu0.2
python-chess==0.23.11
python-dateutil==2.8.1
python-louvain==0.14
python-slugify==4.0.0
python-utils==2.4.0
pytz==2018.9
PyWavelets==1.1.1
PyYAML==3.13
pyzmq==19.0.0
qtconsole==4.7.3
QtPy==1.9.0
regex==2019.12.20
requests==2.23.0
requests-oauthlib==1.3.0
resampy==0.2.2
retrying==1.3.3
rpy2==3.2.7
rsa==4.0
ruamel.base==1.0.0
ruamel.yaml==0.16.10
ruamel.yaml.clib==0.2.0
s3fs==0.4.2
s3transfer==0.3.3
scikit-image==0.16.2
scikit-learn==0.22.2.post1
scipy==1.4.1
screen-resolution-extra==0.0.0
scs==2.1.2
seaborn==0.10.1
Send2Trash==1.5.0
setuptools-git==1.2
Shapely==1.7.0
simplegeneric==0.8.1
six==1.12.0
sklearn==0.0
sklearn-pandas==1.8.0
smart-open==2.0.0
snowballstemmer==2.0.0
sortedcontainers==2.1.0
spacy==2.2.4
Sphinx==1.8.5
sphinxcontrib-websupport==1.2.2
SQLAlchemy==1.3.16
sqlparse==0.3.1
srsly==1.0.2
statsmodels==0.10.2
sympy==1.1.1
tables==3.4.4
tabulate==0.8.7
tbb==2020.0.133
tblib==1.6.0
tensorboard==2.2.1
tensorboard-plugin-wit==1.6.0.post3
tensorboardcolab==0.0.22
tensorflow==2.2.0rc4
tensorflow-addons==0.8.3
tensorflow-datasets==2.1.0
tensorflow-estimator==2.2.0
tensorflow-gcs-config==2.1.8
tensorflow-hub==0.8.0
tensorflow-metadata==0.21.2
tensorflow-privacy==0.2.2
tensorflow-probability==0.10.0rc0
termcolor==1.1.0
terminado==0.8.3
testpath==0.4.4
text-unidecode==1.3
textblob==0.15.3
textgenrnn==1.4.1
Theano==1.0.4
thinc==7.4.0
toolz==0.10.0
torch==1.5.0+cu101
torchsummary==1.5.1
torchtext==0.3.1
torchvision==0.6.0+cu101
tornado==4.5.3
tqdm==4.38.0
traitlets==4.3.3
tweepy==3.6.0
typeguard==2.7.1
typing==3.6.6
typing-extensions==3.6.6
tzlocal==1.5.1
umap-learn==0.4.2
uritemplate==3.0.1
urllib3==1.24.3
-e git+https://github.com/perslev/U-Time@f4038e8d385254e8223fb05edb158417c0f9212f#egg=utime
vega-datasets==0.8.0
wasabi==0.6.0
wcwidth==0.1.9
webencodings==0.5.1
Werkzeug==1.0.1
widgetsnbextension==3.5.1
wordcloud==1.5.0
wrapt==1.12.1
xarray==0.15.1
xgboost==0.90
xkit==0.0.0
xlrd==1.1.0
xlwt==1.3.0
yellowbrick==0.9.1
zict==2.0.0
zipp==3.1.0
nengwp
commented
4 years ago My code also has errors. I have found a solution. mne==0.16.0 is enough, the higher version of mne uses a different api specifically to_data_frame() located in U-Time\utime\io\extractors\psg_extractors.py extract_from_mne_raw function _df = edf_obj.to_dataframe() Help you
nengwp
commented
4 years ago 感谢@aluquecerp分享您的工作版本。你们中的一个人介意共享您的环境详细信息，以便我可以尝试并重现此错误吗？
例如
pip freeze或的输出conda env export。谢谢！
My code also has errors. I have found a solution. mne==0.16.0 is enough, the higher version of mne uses a different api specifically to_data_frame() located in U-Time\utime\io\extractors\psg_extractors.py extract_from_mne_raw function df = edf_obj.to_data_frame() Help you
acrarshin
commented
4 years ago My code also has errors. I have found a solution. mne==0.16.0 is enough, the higher version of mne uses a different api specifically to_data_frame() located in U-Time\utime\io\extractors\psg_extractors.py extract_from_mne_raw function _df = edf_obj.to_dataframe() Help you
This worked for me. Thank you.
I tried to run the code following the instructions on Google Colab using Python 3 and GPU.
When I tried to run:
ut train --num_GPUs=1 --channels 'EEG Fpz-Cz'
I got the following error:
utime.errors.ChannelNotFoundError: Unexpected channel loading error. Should have loaded 1 channels (['EEG Fpz-Cz']), but the PSG array has shape (8406000, 2). There might be an error in the code. Please rais an issue on GitHub.
The previous steps were good. This is the whole message:
2020-04-07 00:58:08.072685: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudart.so.10.1
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/content/U-Time/utime/dataset/sleep_study.py", line 595, in load self._load() File "/content/U-Time/utime/dataset/sleep_study.py", line 535, in _load self._psg, header, loaded_chanls = self._load_with_any_in(try_channels) File "/content/U-Time/utime/dataset/sleep_study.py", line 517, in _load_with_any_in raise err from e utime.errors.ChannelNotFoundError: Could not load select_channels ['EEG Fpz-Cz'] or alternative_select_channels [[]]
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/content/U-Time/utime/dataset/sleep_study_dataset.py", line 158, in load for i, ss in enumerate(res): File "/usr/lib/python3.6/concurrent/futures/_base.py", line 586, in result_iterator yield fs.pop().result() File "/usr/lib/python3.6/concurrent/futures/_base.py", line 432, in result return self.get_result() File "/usr/lib/python3.6/concurrent/futures/_base.py", line 384, in get_result raise self._exception File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run result = self.fn(*self.args, **self.kwargs) File "/content/U-Time/utime/dataset/sleep_study_dataset.py", line 156, in
res = pool.map(lambda x: x.load(), to_load)
File "/content/U-Time/utime/dataset/sleep_study.py", line 600, in load
study_id=self.identifier) from e
utime.errors.CouldNotLoadError: Unexpected load error for sleep study SC4011E0. Please refer to the above traceback.
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/usr/local/bin/ut", line 11, in
load_entry_point('utime', 'console_scripts', 'ut')()
File "/content/U-Time/utime/bin/ut.py", line 55, in entry_func
mod.entry_func(parsed.args)
File "/content/U-Time/utime/bin/train.py", line 209, in entry_func
raise e
File "/content/U-Time/utime/bin/train.py", line 206, in entry_func
run(args=args, gpu_mon=gpu_mon)
File "/content/U-Time/utime/bin/train.py", line 142, in run
d.load(1 if args.just_one else None)
File "/content/U-Time/utime/dataset/sleep_study_dataset.py", line 163, in load
"traceback.".format(e.study_id)) from e
utime.errors.CouldNotLoadError: Could not load sleep study SC4011E0. Please refer to the above traceback.