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I am trying to save contents of physiobank Normal Sinus Rhythm RR Interval Database into a numpy array but I keep getting an error:

Traceback (most recent call last):
  File "AverageRRI.py", line 20, in <module>
    averageArray = np.fromfile(file,dtype=float)
FileNotFoundError: [Errno 2] No such file or directory: 'nsr001.ecg'

but the file does exist in the directory.

import os
import numpy as np

for root, dirs, files in os.walk('normal-sinus-rhythm-rr-interval-database-1.0.0'):
    for file in files:
        if file.endswith(".ecg"):
            print(file)
            averageArray = np.fromfile(file,dtype=float)
            print(averageArray)

When I add the pathname like:

averageArray = np.fromfile('normal-sinus-rhythm-rr-interval-database-1.0.0/nsr001.ecg',dtype=float)
            print(averageArray)

It works.

Thanks so much!

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You just need to add the root directory in front of the filename so that the full filepath is correct. For this you can use os.path.join:

import os
import numpy as np

for root, dirs, files in os.walk('normal-sinus-rhythm-rr-interval-database-1.0.0'):
    for file in files:
        if file.endswith(".ecg"):
            print(os.path.join(root, file))
            averageArray = np.fromfile(os.path.join(root, file), dtype=float)
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  • $\begingroup$ Thanks so much, this worked! $\endgroup$
    – YJay
    Feb 3 at 15:03
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FileNotFoundError: [Errno 2] No such file or directory: --->'nsr001.ecg'

The directory path you wrote doesnt have the file which you are passing, check the path.

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