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I have been trying to read the header (first 100 lines) of a netCDF file in Python, but have been facing some issues. I am familiar with the read_nc function available in the synoptReg package for R and with the ncread function that comes with MATLAB, as well as the read_csv function available in the pandas library. To my knowledge, however, there isn't anything similar for netCDF (.nc) files.

Noting this, and using answers from this question, I've tried the following (with no success):

with open(filepath,'r') as f:
    for i in range(100):
        line = next(f).strip()
        print(line)

However, I receive this error, even though I've ensured that tabs have not been mixed with spaces and that the for statement is within the with block (as given as explanations by the top answers to this question):

'utf-8' codec can't decode byte 0xbb in position 411: invalid start byte

I've also tried the following:

with open(filepath,'r') as f:
    for i in range(100):
        line = [next(f) for i in range(100)]
print(line)

and

from itertools import islice
with open('/Users/toshiro/Desktop/Projects/CCAR/Data/EDGAR/v6.0_CO2_excl_short-cycle_org_C_2010_TOTALS.0.1x0.1.nc','r') as f:
    for i in range(100):
        line = list(islice(f, 100))
print(line)

But receive the same error as above. Are there any workarounds for this?

ttoshiro
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    This nothing to do with how you're iterating over the file, but more with how you're opening the file. What codec is the file using? – Axe319 Aug 14 '22 at 04:47
  • I tried to check using the python-magic interface but I get the error `'utf-8' codec can't decode byte 0xbb in position 411: invalid start byte`. I'm guessing it's not utf-8? Is there a better way to check? – ttoshiro Aug 14 '22 at 06:31
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    yeah - just closing this loop - the encoding is netCDF. it's not text. so it's not utf-8 or ascii or latin-1 or any other type of text. you could open it as bytes and decode the whole thing as hex or something but you won't be able to make sense of it. so your best option really is to use the netCDF package or xarray with the netCDF driver. – Michael Delgado Aug 14 '22 at 06:57

1 Answers1

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You can't. netCDFs are binary files and can't be interpreted as text.

If the files are netCDF3 encoded, you can read them in with scipy.io.netcdf_file. But it's much more likely they are netCDF4, in which case you'll need the netCDF4 package.

On top of this, I'd highly recommend the xarray package for reading and working with netCDF data. It supports a labeled N-dimensional array interface - think pandas indexes on each dimension of a numpy array.

Whether you go with netCDF or xarray, netCDFs are self-describing and support arbitrary reads, so you don't need to load the whole file to view the metadata. So similar to viewing the head of a text file, you can simply do:

import xarray as xr
ds = xr.open_dataset("path/to/myfile.nc")
print(ds)  # this will give you a preview of your data

Additionally, xarray does have a xr.Dataset.head function which will display the first 5 (or N if you provide an int) elements along each dimension:

ds.head()  # display a 5x5x...x5 preview of your data

See the getting started guide and the User guide section on reading and writing netCDF files for more info.

Michael Delgado
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  • Thanks for the response. I tried `scipy.io.netcdf_file` but return to an earlier error: `I/O operation on closed file.` I saw this answer: https://stackoverflow.com/a/18952732/13430381, but my spacing/indenting is consistent... Any ideas why this is happening? – ttoshiro Aug 14 '22 at 06:01
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    I'd really recommend giving xarray a try. but I'd need to see the code you're using to debug it. and if it really is a netCDF, there's no spacing/indenting involved - it's binary and not human readible. Are you sure it's a netCDF file? if you can open it up in a text editor... it isn't one. – Michael Delgado Aug 14 '22 at 06:02
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    oh I see - you're talking about indentation using a with statement. are you using a context manager to open the file, and then trying to use the dataset object after the object is closed? you can't do that. just open the file without a with statement, or else do all your operations with the file inside the with block. – Michael Delgado Aug 14 '22 at 06:06
  • I see, but wouldn't I need to iterate it over the first 100 lines? Can I do that without a with statement/context manager? I'm trying xarray right now but get the error `'int' object has no attribute 'dims'`, so I must be using it incorrectly as well -- will have to read the documentation more. – ttoshiro Aug 14 '22 at 06:35
  • there aren't lines in the file. it's just a giant a block of 1s and 0s. I don't know what the dimensions of your file are, but it's not structured like a table - there isn't such a thing as "lines" even when loaded with xarray. and yeah - again I can't debug your errors if I don't know what you're doing - there are infinite ways to generate attribute errors in python :) but if you want to ask a new question go for it, and yeah I'd definitely recommend the docs and the [xarray tutorials page](https://tutorial.xarray.dev/intro.html). Have fun :) – Michael Delgado Aug 14 '22 at 06:53
  • and yeah - you don't need a context manager. if you want to explicitly release the file object you can call [`ds.close()`](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.close.html), but in most cases you don't need to - xarray will automatically close the file handler when your dataset falls out of scope. But while you're working with the data you can simply open the dataset and then work with it directly, as in my answer. – Michael Delgado Aug 14 '22 at 07:04