Feature: Support for file-like objects for EDF/BDF/GDF files (mne-tools#13156)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>
Co-authored-by: Eric Larson <[email protected]>

Author: 4 people

doc/changes/dev/13156.newfeature.rst

@@ -0,0 +1 @@
+Added support for file like objects in :func:`read_raw_bdf <mne.io.read_raw_bdf>`, :func:`read_raw_edf <mne.io.read_raw_edf>` and :func:`read_raw_gdf <mne.io.read_raw_gdf>`, by :newcontrib:`Santi Martínez`.

doc/changes/names.inc

@@ -283,6 +283,7 @@
 .. _Samuel Louviot: https://github.com/Sam54000
 .. _Samuel Powell: https://github.com/samuelpowell
 .. _Santeri Ruuskanen: https://github.com/ruuskas
+.. _Santi Martínez: https://github.com/szz-dvl
 .. _Sara Sommariva: https://github.com/sarasommariva
 .. _Sawradip Saha: https://sawradip.github.io/
 .. _Scott Huberty:  https://orcid.org/0000-0003-2637-031X

mne/_edf/open.py

@@ -0,0 +1,23 @@
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+# Maybe we can move this one to utils or something like that.
+from pathlib import Path
+
+from mne._fiff.open import _NoCloseRead
+
+from ..utils import _file_like, _validate_type, logger
+
+
+def _gdf_edf_get_fid(fname, **kwargs):
+    """Open a EDF/BDF/GDF file with no additional parsing."""
+    if _file_like(fname):
+        logger.debug("Using file-like I/O")
+        fid = _NoCloseRead(fname)
+        fid.seek(0)
+    else:
+        _validate_type(fname, [Path, str], "fname", extra="or file-like")
+        logger.debug("Using normal I/O")
+        fid = open(fname, "rb", **kwargs)  # Open in binary mode
+    return fid

mne/fixes.py

@@ -16,12 +16,14 @@
 # because this module is imported many places (but not always used)!
 
 import inspect
+import io
 import operator as operator_module
 import os
 import warnings
 from math import log
 
 import numpy as np
+import numpy.typing
 from packaging.version import parse
 
 ###############################################################################
@@ -733,3 +735,33 @@ def sph_harm_y(n, m, theta, phi, *, diff_n=0):
         return special.sph_harm_y(n, m, theta, phi, diff_n=diff_n)
     else:
         return special.sph_harm(m, n, phi, theta)
+
+
+###############################################################################
+# workaround: Numpy won't allow to read from file-like objects with numpy.fromfile,
+# we try to use numpy.fromfile, if a blob is used we use numpy.frombuffer to read
+# from the file-like object.
+def read_from_file_or_buffer(
+    file: str | bytes | os.PathLike | io.IOBase,
+    dtype: numpy.typing.DTypeLike = float,
+    count: int = -1,
+):
+    """numpy.fromfile() wrapper, handling io.BytesIO file-like streams.
+
+    Numpy requires open files to be actual files on disk, i.e., must support
+    file.fileno(), so it fails with file-like streams such as io.BytesIO().
+
+    If numpy.fromfile() fails due to no file.fileno() support, this wrapper
+    reads the required bytes from file and redirects the call to
+    numpy.frombuffer().
+
+    See https://github.com/numpy/numpy/issues/2230#issuecomment-949795210
+    """
+    try:
+        return np.fromfile(file, dtype=dtype, count=count)
+    except io.UnsupportedOperation as e:
+        if not (e.args and e.args[0] == "fileno" and isinstance(file, io.IOBase)):
+            raise  # Nothing I can do about it
+        dtype = np.dtype(dtype)
+        buffer = file.read(dtype.itemsize * count)
+        return np.frombuffer(buffer, dtype=dtype, count=count)