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enram / vp-processing

Vertical profiles of birds (vp) data processing for analyses and visualizations
http://enram.github.io/vp-processing
MIT License
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Cannot open h5 file with bioRad #4

Closed peterdesmet closed 7 years ago

peterdesmet commented 7 years ago

When I try:

vp <- bioRad::readvp("../data/raw/se/ang/2017/03/03/23/seang_vp_20170303233000.h5")

I get the error:

Error in H5Fopen(file, "H5F_ACC_RDONLY") : HDF5. File accessability. Unable to open file.

Seems very similar to this unanswered stack overflow question. 🙁 I'm wondering if it is this specific file or something else?

peterdesmet commented 7 years ago

@stijnvanhoey The file is definitely at the right location (other wise I get does not exist..), so maybe files downloaded from the data-repository are locked in some way?

peterdesmet commented 7 years ago

Ok, so this example file does work, so it is specifically the files downloaded from the data repository.

plieper commented 7 years ago

I tried to load in with bioRad a few vp's with different time stamps from the data repo, turns out this error only occurs for vp's from 2017/03 on. Vp's from before that date I can load without problem. I also tried to open 'recent' vp's with HDFView, which didn't work either, giving the error:

java.io.IOException: Failed to open file

I'll inquire with Adriaan and Günther, maybe something changed to the h5-structures after januari 2017?

adokter commented 7 years ago

No idea what has caused this. On my Ubuntu machine I can't load these files either, I tried h5ls, hdfview and bioRad. It seems the later files are corrupted, my guess is something broke at baltrad as the latest vol2bird versions produce files I can read without any problem

stijnvanhoey commented 7 years ago

It could be the transfer from baltrad to S3 as well, I'll have a look at it the beginning of next week.

peterdesmet commented 7 years ago

Just tested with a Baltrad file from 2017-05 and that one load fine, so must be something in Baltrad to S3 processing. Assigned @stijnvanhoey

peterdesmet commented 7 years ago

Is an issue with data repository, moved it over there (https://github.com/enram/data-repository/issues/37) closing here.