simplify the loading of input files in the io module #minor

efel/io.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 """IO handler for eFEL"""
 
 """
@@ -18,89 +19,22 @@
  along with this library; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 """
+from pathlib import Path
+import neo
+import numpy as np
 
-import os
 
-# pylint:disable=E0611, F0401
-import urllib.parse as up
-import urllib.request as ur
+def load_ascii_input(
+    file_path: Path | str, delimiter: str = " "
+) -> tuple[np.ndarray, np.ndarray]:
+    """Loads electrophysiology data from an ASCII file.
 
-# pylint:enable=E0611,F0401
-
-import mimetypes
-
-
-def windows_compatible(func):
-    """Decorator allowing to use urlparse with windows."""
-
-    def inner(fragment_url):
-        """Change windows path part to url."""
-        # if system is windows
-        if os.name == "nt":
-            fragment_url.replace("\\", "/")
-
-        parsed_url = func(fragment_url)
-
-        return parsed_url
-
-    return inner
-
-
-def load_fragment(fragment_url, mime_type=None):
-    """Load fragment
-
-    Load a fragment (e.g. time series data) from a given URL
+    Returns: A tuple containing two numpy arrays, one for time and one for voltage.
     """
-    parsed_url = windows_compatible(up.urlparse)(fragment_url)
-
-    scheme = parsed_url.scheme
-    server_loc = parsed_url.netloc
-    path = parsed_url.path
-    fragment_string = parsed_url.fragment
-
-    # reform path for windows files
-    if scheme == "file" and os.name == "nt":
-        path = ur.url2pathname(r"\\" + server_loc + path)
-
-    if mime_type is None:
-        mimetypes.init()
-        mime_type, _ = mimetypes.guess_type(path)
-        if mime_type is None:
-            raise TypeError(
-                'load_fragment: impossible to guess MIME type from url, '
-                'please specify the type manually as argument: %s' % path)
-
-    if scheme == 'file' and os.name == 'nt':
-        file_handle = open(path, 'r')
-    elif scheme == 'file':
-        file_handle = open(os.path.join(server_loc, path), 'r')
-
-    if 'text/' in mime_type:
-        import numpy
-
-        if fragment_string == '':
-            cols = None
-        else:
-            import re
-
-            match = re.match("col=([0-9]+)", fragment_string)
-            if match is None or len(match.groups()) != 1:
-                raise TypeError(
-                    "load_fragment: don't understand url fragment %s" %
-                    fragment_string)
-            else:
-                cols = int(match.groups()[0]) - 1
-
-        # Unfortunately we need this if statement
-        # Setting usecols to None throws an error in the loadtxt call
-        if cols is not None:
-            fragment_content = numpy.loadtxt(file_handle, usecols=[cols])
-        else:
-            fragment_content = numpy.loadtxt(file_handle)
-
-        return fragment_content
-    else:
-        raise TypeError('load_fragment: unknown mime type %s' % mime_type)
+    file_path = Path(file_path)
+    data = np.loadtxt(file_path, delimiter=delimiter)
+    time, voltage = data[:, 0], data[:, 1]
+    return time, voltage
 
 
 def extract_stim_times_from_neo_data(blocks, stim_start, stim_end):
@@ -242,37 +176,30 @@ def load_neo_file(file_name, stim_start=None, stim_end=None, **kwargs):
             returned object : [Segments_1, Segments_2, ..., Segments_n]
             Segments_1 = [Traces_1, Traces_2, ..., Traces_n]
     """
-
-    import neo
-
     reader = neo.io.get_io(file_name)
     blocks = reader.read(**kwargs)
 
     stim_start, stim_end = extract_stim_times_from_neo_data(
         blocks, stim_start, stim_end)
     if stim_start is None or stim_end is None:
         raise ValueError(
-            'No stim_start or stim_end has been found inside epochs or events.'
-            ' You can directly specify their value as argument "stim_start"'
-            ' and "stim_end"')
+            'No stim_start or stim_end found in epochs or events. '
+            'Please specify "stim_start" and "stim_end" arguments.')
 
-    # this part of the code transforms the data format.
+    # Convert data for eFEL
     efel_blocks = []
     for bl in blocks:
         efel_segments = []
         for seg in bl.segments:
             traces = []
-            count_traces = 0
-            analogsignals = seg.analogsignals
-
-            for sig in analogsignals:
-                traces.append({})
-                traces[count_traces]['T'] = sig.times.rescale('ms').magnitude
-                traces[count_traces]['V'] = sig.rescale('mV').magnitude
-                traces[count_traces]['stim_start'] = [stim_start]
-                traces[count_traces]['stim_end'] = [stim_end]
-                count_traces += 1
-
+            for sig in seg.analogsignals:
+                trace = {
+                    'T': sig.times.rescale('ms').magnitude,
+                    'V': sig.rescale('mV').magnitude,
+                    'stim_start': [stim_start],
+                    'stim_end': [stim_end]
+                }
+                traces.append(trace)
             efel_segments.append(traces)
         efel_blocks.append(efel_segments)
 

setup.py

@@ -80,8 +80,7 @@
     name="efel",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    install_requires=['numpy>=1.6'],
-    extras_require={'neo': ['neo[neomatlabio]>=0.5.1']},
+    install_requires=['numpy>=1.6', 'neo>=0.5.2'],
     packages=['efel', 'efel.pyfeatures', 'efel.units'],
     author="BlueBrain Project, EPFL",
     maintainer="Werner Van Geit",