issue in fresh installation: TypeError

[smallsr]

Getting this error when summarizing data using sample.cwa or any other file

Traceback (most recent call last): File "/mnt/c/Users/ScottS/accelerometer/baa/bin/accProcess", line 8, in sys.exit(main()) File "/mnt/c/Users/ScottS/accelerometer/baa/lib/python3.8/site-packages/accelerometer/accProcess.py", line 326, in main epochData, labels = accelerometer.summarisation.getActivitySummary( File "/mnt/c/Users/ScottS/accelerometer/baa/lib/python3.8/site-packages/accelerometer/summarisation.py", line 117, in getActivitySummary data = resolveInterrupts(data, epochPeriod, summary) File "/mnt/c/Users/ScottS/accelerometer/baa/lib/python3.8/site-packages/accelerometer/summarisation.py", line 176, in resolveInterrupts data['missing'] = data.isna().any(1) TypeError: any() takes 1 positional argument but 2 were given

[smallsr]

Per @chanshing, this is due to a recent pandas recent major update. Downgrading to pandas==1.5 fixes this error.

[chanshing]

https://github.com/OxWearables/biobankAccelerometerAnalysis/issues/222

[Rui127]

still facing the same error using.bin file after downgrading pandas

[chanshing]

@Rui127 Please can you say which version of accelerometer package are you using?

pip freeze | grep accelerometer

[Rui127]

accelerometer==6.2.3

[chanshing]

@Rui127 Thanks. Can you try upgrading to latest version of accelerometer? The TypeError issue mentioned should have been fixed in the later versions.

pip install -U accelerometer

[Rui127]

@chanshing I upgraded to the latest version. Unfortunately I am still getting the same error below 2024-06-15 07:11:45 === Summarizing === /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/accelerometer/summarisation.py:79: FutureWarning: The argument 'date_parser' is deprecated and will be removed in a future version. Please use 'date_format' instead, or read your data in as 'object' dtype and then call 'to_datetime'. data = pd.read_csv(epochFile, index_col=['time'], parse_dates=['time'], date_parser=utils.date_parser) /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/accelerometer/summarisation.py:169: FutureWarning: 'S' is deprecated and will be removed in a future version. Please use 's' instead of 'S'. epochPeriod = pd.Timedelta(epochPeriod, unit='S') Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/bin/accProcess", line 8, in sys.exit(main()) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/accelerometer/accProcess.py", line 326, in main epochData, labels = accelerometer.summarisation.getActivitySummary( File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/accelerometer/summarisation.py", line 117, in getActivitySummary data = resolveInterrupts(data, epochPeriod, summary) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/accelerometer/summarisation.py", line 176, in resolveInterrupts data['missing'] = data.isna().any(1) TypeError: any() takes 1 positional argument but 2 were given

[chanshing]

@Rui127 Please can you also share pandas version? pip freeze | grep pandas

[Rui127]

@chanshing pandas==1.3.5 pandas-flavor==0.6.0

[chanshing]

pandas-flavor is not in our package's dependency list so I am curious how it got there. Can you try uninstalling it and see if it works after that? pip uninstall pandas-flavor

[chanshing]

@Rui127 Also have you installed accelerometer in a separate environment? https://github.com/OxWearables/biobankAccelerometerAnalysis?tab=readme-ov-file#install

[Rui127]

@chanshing Thanks for pointing it out. I activate environment however it did not solve the problem. accelerometer==7.1.1 pandas==1.3.5

[chanshing]

@chanshing Thanks for pointing it out. I activate environment however it did not solve the problem.

accelerometer==7.1.1

pandas==1.3.5

Is there a way for you to share the file with me to debug the problem?

[Rui127]

@chanshing Thank you for helping and please let me know if you can download it https://drive.google.com/file/d/1PFJRLqMiB2f7Qt6u45JhEujq7TbdeE2E/view?usp=drive_link

[chanshing]

@Rui127 It doesn't seem to work - restricted access

[chanshing]

test-summary.json

@Rui127 I was able to process your file just fine. Maybe it's something wrong with your installation. You could try reinstalling it:

conda deactivate  # exit current environment
conda env remove -n accelerometer  # delete 'accelerometer' environment

then retry these steps: https://github.com/OxWearables/biobankAccelerometerAnalysis?tab=readme-ov-file#install

Can you also try pip freeze and paste here the list of packages installed?

[Rui127]

@chanshing I realized that the environment was built under Anaconda that i previously installed. I removed Anaconda and it works now. Sorry that I did not check it and thanks for the help

[chanshing]

Ok great! We do recommend anaconda for new Python users for env management, but glad you solved your problem!

[Rui127]

@chanshing I am checking the test-timeSeries.csv.gz file and wondering if there's a way to extract the light sensor data in the bin file as well e.g., mean or max lux of 30s bins

[chanshing]

@chanshing I am checking the test-timeSeries.csv.gz file and wondering if there's a way to extract the light sensor data in the bin file as well e.g., mean or max lux of 30s bins

Unfortunately we don't think this will be supported in the near future, but will let you know if things change!

[aidendoherty]

@Rui127 - just a note to say that we will of course welcome a pull request if you would like to try including this feature.