Load npy file from S3 in python

Question

is there anyway to load/read an external file(ie, AWS S3) in numpy?. I have several npy files stored in S3. I have tried to access them through a S3 presigned url but it seems neither numpy.load method or np.genfromtxt are able to read them.

I wouldn't want to save files on local file system and then load them on numpy.

Any idea?

Answer 1

Using s3fs

import numpy as np
from s3fs.core import S3FileSystem
s3 = S3FileSystem()

key = 'your_file.npy'
bucket = 'your_bucket'

df = np.load(s3.open('{}/{}'.format(bucket, key)))

You might have to set the allow_pickle=True depending on your file to be read.

Answer 2

I've compared s3fs and io.BytesIO for loading a 28G npz file from s3. s3fs takes 30 min while io takes 12 min.

obj = s3_session.resource("s3").Object(bucket, key)
with io.BytesIO(obj.get()["Body"].read()) as f:
    f.seek(0)  # rewind the file
    X, y = np.load(f).values()

s3fs = S3FileSystem()
with s3fs.open(f"s3://{bucket}/{key}") as s3file:
     X, y = np.load(s3file).values()

Answer 3

I had success using boto and StringIO. Connect to S3 using boto and get your bucket. Then read the file with following code into numpy:

  import numpy as np
  from StringIO import StringIO
  key=bucket.get_key('YOUR_KEY')
  data_string=StringIO(key.get_contents_as_string())
  data = np.load(data_string)

I am not sure it's the most efficient way, but it doesn't require a public URL.

Cheers, Michael