WIP: Roundtrip Tests

.gitignore

@@ -0,0 +1,5 @@
+build/
+dist/
+pyEDF.egg-info/
+*.pyc
+*.*~

README.rst

@@ -0,0 +1,27 @@
+pyEDF
+=====
+
+Python package to read from and write EEG data to European Data Format
+files. It is implemented in pure Python with very limited dependencies
+on external packages.
+
+See also
+--------
+
+-  https://github.com/holgern/pyedflib
+-  https://github.com/MNE-tools/MNE-python
+
+Assuming a standard Python environment is installed on your machine
+(including pip), pyEDF can be installed from PyPI:
+
+::
+
+    python -m pip install --user --upgrade  pyEDF
+
+For the current pre-release version, you can install from GitHub:
+
+::
+
+    python -m pip install --user --upgrade  git+https://github.com/robertoostenveld/pyEDF.git
+
+Dependencies should be handled automatically by pip.

pyEDF/__init__.py

@@ -0,0 +1,2 @@
+__version__ = 0.1
+from .EDF import EDFWriter, EDFReader

pyEDF/tests/config_vars.py

@@ -0,0 +1,6 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2018 Phillip Alday <me@phillipalday.com>
+# License: BSD (3-clause)
+
+import os.path as op
+data_path = op.expanduser('~/edf_data')

pyEDF/tests/test_edfreader.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2018 Phillip Alday <me@phillipalday.com>
+# License: BSD (3-clause)
+"""Tests for reading EDF files"""
+
+from nose.tools import assert_dict_equal, assert_raises
+
+from config_vars import data_path
+from os.path import join

pyEDF/tests/test_edfwriter.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2018 Phillip Alday <me@phillipalday.com>
+# License: BSD (3-clause)
+"""Tests for writing EDF files"""
+
+from nose.tools import assert_dict_equal, assert_raises
+
+from config_vars import data_path
+from os.path import join

pyEDF/tests/test_roundtrip.py

@@ -0,0 +1,87 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2018 Phillip Alday <me@phillipalday.com>
+# License: BSD (3-clause)
+"""Round Trip Data IO tests.
+
+    Note that these tests are *slow*. The entirety of each file is effectively
+    read in 3 times and written to disk once.
+"""
+
+from nose.tools import assert_dict_equal, assert_true, assert_sequence_equal
+import numpy as np
+
+from config_vars import data_path
+from os.path import join
+
+import pyEDF
+
+try:
+    # Python 2
+    from os import tempnam, unlink
+except ImportError:
+    # Python 3
+    from os import unlink
+    from tempfile import NamedTemporaryFile
+
+    tempnam = lambda: NamedTemporaryFile(delete=False).name
+
+def _roundtrip(edf_file):
+    edfin = pyEDF.EDFReader(edf_file)
+
+    fout = tempnam()
+    edfout = pyEDF.EDFWriter(fout)
+
+    header = edfin.readHeader()
+    edfout.writeHeader(header)
+
+    meas_info = header[0]
+    for i in range(int(meas_info['n_records'])):
+        edfout.writeBlock(edfin.readBlock(i))
+
+    edfin.close()
+    edfout.close()
+
+    original = pyEDF.EDFReader(edf_file)
+    copy = pyEDF.EDFReader(fout)
+
+    copy_header = copy.readHeader()
+
+    assert_dict_equal(header[0], copy_header[0])
+    for key in header[1]:
+        assert_sequence_equal(list(header[1][key]), list(copy_header[1][key]))
+
+    for i in range(int(meas_info['n_records'])):
+        # although this is floating point, it's not really numerics.
+        # it's just comparing copies of the same data, so exact equality
+        # should be a doable goal.
+        for ch_orig, ch_copy in zip(original.readBlock(i), copy.readBlock(i)):
+            assert_sequence_equal(list(ch_orig), list(ch_copy))
+
+    unlink(fout)
+
+def test_roundtrip_0601_s():
+    '''Roundtrip of file 0601_s.edf'''
+    # this file seems to have bad physical_min values
+    _roundtrip(join(data_path, '0601_s.edf'))
+
+def test_roundtrip_composition1_0s_to_1892s_fs20_15channels_tap127():
+    '''Roundtrip of file composition1_0s_to_1892s_fs20_15channels_tap127.edf'''
+    _roundtrip(join(data_path, 'composition1_0s_to_1892s_fs20_15channels_tap127.edf'))
+
+
+def test_roundtrip_NY394_VisualLoc_R1():
+    '''Roundtrip of file NY394_VisualLoc_R1.edf'''
+    _roundtrip(join(data_path, 'NY394_VisualLoc_R1.edf'))
+
+
+def test_roundtrip_shhs1_200001():
+    '''Roundtrip of file shhs1-200001.edf'''
+    _roundtrip(join(data_path, 'shhs1-200001.edf'))
+
+def test_roundtrip_testAlphaIR20170321_0():
+    '''Roundtrip of file testAlphaIR20170321-0.edf'''
+    _roundtrip(join(data_path, 'testAlphaIR20170321-0.edf'))
+
+def test_roundtrip_test_generator():
+    '''Roundtrip of file test_generator.edf'''
+    _roundtrip(join(data_path, 'test_generator.edf'))

setup.py

@@ -0,0 +1,101 @@
+#! /usr/bin/env python
+#
+# Copyright (C) 2018 Phillip Alday <me@phillipalday.com>
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+
+import os
+from os import path as op
+
+from setuptools import setup
+
+PACKAGE_NAME = 'pyEDF'
+
+# get the version (don't import mne here, so dependencies are not needed)
+version = None
+with open(os.path.join(PACKAGE_NAME, '__init__.py'), 'r') as fid:
+    for line in (line.strip() for line in fid):
+        if line.startswith('__version__'):
+            version = line.split('=')[1].strip().strip('\'')
+            break
+if version is None:
+    raise RuntimeError('Could not determine version')
+
+descr = """Reader and Writer for the European Data Format (EDF)"""
+
+DISTNAME = PACKAGE_NAME
+DESCRIPTION = descr
+AUTHOR = 'Robert Oostenveld'
+AUTHOR_EMAIL = 'r.oostenveld@donders.ru.nl'
+MAINTAINER = 'Phillip Alday'
+MAINTAINER_EMAIL = 'me@phillipalday.com'
+URL = 'https://github.com/robertoostenveld/pyEDF'
+LICENSE = 'BSD (3-clause)'
+DOWNLOAD_URL = 'https://github.com/robertoostenveld/pyEDF'
+VERSION = version
+
+def package_tree(pkgroot):
+    """Get the submodule list."""
+    # Adapted from MNE-Python
+    path = os.path.dirname(__file__)
+    subdirs = [os.path.relpath(i[0], path).replace(os.path.sep, '.')
+               for i in os.walk(os.path.join(path, pkgroot))
+               if '__init__.py' in i[2]]
+    return sorted(subdirs)
+
+if __name__ == "__main__":
+    if os.path.exists('MANIFEST'):
+        os.remove('MANIFEST')
+
+    setup(name=DISTNAME,
+          author=AUTHOR,
+          author_email=AUTHOR_EMAIL,
+          maintainer=MAINTAINER,
+          maintainer_email=MAINTAINER_EMAIL,
+          include_package_data=True,
+          description=DESCRIPTION,
+          license=LICENSE,
+          url=URL,
+          version=VERSION,
+          download_url=DOWNLOAD_URL,
+          long_description=open('README.md').read(),
+          zip_safe=True,  # the package can run out of an .egg file
+          classifiers=['Intended Audience :: Science/Research',
+                       'Intended Audience :: Developers',
+                       'License :: OSI Approved',
+                       'Programming Language :: Python',
+                       'Topic :: Software Development',
+                       'Topic :: Scientific/Engineering',
+                       'Operating System :: Microsoft :: Windows',
+                       'Operating System :: POSIX',
+                       'Operating System :: Unix',
+                       'Operating System :: MacOS'],
+          platforms='any',
+          packages=package_tree(PACKAGE_NAME),
+    )