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OxWearables / biobankAccelerometerAnalysis

Extracting meaningful health information from large accelerometer datasets
https://biobankaccanalysis.readthedocs.io/en/latest/index.html
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bug #252

Closed Bianlab2023 closed 5 months ago

Bianlab2023 commented 5 months ago

Error: java calibration failed, exit 254

Bianlab2023 commented 5 months ago

error reading/writing file data/sample-small.csv: java.lang.ArrayIndexOutOfBoundsException: 4 ['java', '-classpath', '/share/home/zlbian/.conda/envs/accelerometer/lib/python3.9/site-packages/accelerometer/java/:/share/home/zlbian/.conda/envs/accelerometer/lib/python3.9/site-packages/accelerometer/java/JTransforms-3.1-with-dependencies.jar', '-XX:ParallelGCThreads=1', 'AccelerometerParser', 'data/sample-small.csv', 'timeZone:Europe/London', 'timeShift:0', 'outputFile:/share2/home/zlbian/NHANES/data/sample-small-stationaryPoints.csv.gz', 'verbose:False', 'filter:True', 'getStationaryBouts:true', 'epochPeriod:10', 'stationaryStd:0.013', 'sampleRate:100', "csvTimeFormat:yyyy-MM-dd HH:mm:ss.SSSxxxx '['VV']'", 'csvStartRow:1', 'csvTimeXYZTempColsIndex:0,1,2,3,4'] Error: java calibration failed, exit 254

Bianlab2023 commented 5 months ago

it does not work with sample file .

chanshing commented 5 months ago

Hi @Bianlab2023 Could you share the sample file you are using?

Bianlab2023 commented 5 months ago

i used the sample file that you provided.

---- Replied Message ---- | From | Shing @.> | | Date | 04/18/2024 01:03 | | To | OxWearables/biobankAccelerometerAnalysis @.> | | Cc | Bianlab2023 @.>, Mention @.> | | Subject | Re: [OxWearables/biobankAccelerometerAnalysis] bug (Issue #252) |

Hi @Bianlab2023 Could you share the sample file you are using?

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Bianlab2023 commented 5 months ago

"http://gas.ndph.ox.ac.uk/aidend/accModels/sample-small.csv.gz"

chanshing commented 5 months ago

Ah sorry, for custom CSV files (not Axivity, Actigraph, GENEActiv) the flag --csvTimeXYZTempColsIndex needs to be specified, for example --csvTimeXYZTempColsIndex 0,1,2,3

https://biobankaccanalysis.readthedocs.io/en/latest/usage.html#processing-a-csv-file