Error in io._read_bin - Githubissues

leewujung commented 5 years ago

I ran into the following error when trying to read source data files in example_data:

In[16]: dolfyn.read('RDI_withBT.000')
Reading file RDI_withBT.000 ...
Traceback (most recent call last):
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3291, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-16-1b2a3777040f>", line 1, in <module>
    dolfyn.read('RDI_withBT.000')
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/api.py", line 35, in read
    dat = func(fname, userdata=userdata, nens=nens)
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/rdi.py", line 38, in read_rdi
    with adcp_loader(fname) as ldr:
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/rdi.py", line 831, in __init__
    self.read_hdr()
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/rdi.py", line 699, in read_hdr
    nextbyte = fd.read_ui8(1)
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/_read_bin.py", line 171, in read_ui8
    return self.read(n, 'B')
  File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/_read_bin.py", line 163, in read
    raise eofException
dolfyn.io._read_bin.eofException

I tested it using python 3.7 and 3.5. The same error occurred for reading ad2cp files and a few others I tried to read. This must be something stupid but I couldn't figure it out. Any help will be much appreciated!

lkilcher commented 5 years ago

What system are you on (win, mac, linux)? Can you share a data file that is generating the error message?

On Tue, Aug 6, 2019 at 11:27 AM Wu-Jung Lee notifications@github.com wrote:

I ran into the following error when trying to read source data files in example_data:

In[16]: dolfyn.read('RDI_withBT.000') Reading file RDI_withBT.000 ... Traceback (most recent call last): File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3291, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "", line 1, in dolfyn.read('RDI_withBT.000') File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/api.py", line 35, in read dat = func(fname, userdata=userdata, nens=nens) File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/rdi.py", line 38, in read_rdi with adcp_loader(fname) as ldr: File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/rdi.py", line 831, in init self.read_hdr() File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/rdi.py", line 699, in read_hdr nextbyte = fd.read_ui8(1) File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/_read_bin.py", line 171, in read_ui8 return self.read(n, 'B') File "/Users/wu-jung/miniconda3/envs/echopype/lib/python3.7/site-packages/dolfyn/io/_read_bin.py", line 163, in read raise eofException dolfyn.io._read_bin.eofException

I tested it using python 3.7 and 3.5. The same error occurred for reading ad2cp files and a few others I tried to read. This must be something stupid but I couldn't figure it out. Any help will be much appreciated!

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leewujung commented 5 years ago

I am on a Mac. The data file I tried to read is one of the example files: dolfyn/dolfyn/example_data/RDI_withBT.000

Thanks!

lkilcher commented 5 years ago

Did you git-clone the repo, or install via pip? Assuming the former, this is probably because you don't have git-lfs installed. Go here https://dolfyn.readthedocs.io/en/stable/install.html#data-files-and-test-files, and especially here https://help.github.com/en/articles/installing-git-large-file-storage for more info.

If you installed via pip this may be a bug in the pip distribution.

leewujung commented 5 years ago

You are right that I messed up the git lfs part. I installed git-lfs using brew and executed git lfs install once earlier. For some reason when I do git lfs install again just now, it updated the hook and was able to pull the files correctly, before each file only had a few bytes instead of MB.

The problem is now resolved. Thanks for responding so promptly!

lkilcher / dolfyn

Error in io._read_bin #62