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194 lines
7.4 KiB
Python
194 lines
7.4 KiB
Python
# -*- coding: utf-8 -*-
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# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr <chris.kerr@mykolab.ch>
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import os.path
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import re
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from datetime import datetime
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import numpy as np
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from numpy.testing import assert_array_almost_equal, assert_array_equal
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import pytest
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from galvani import BioLogic, MPTfile, MPRfile
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from galvani.BioLogic import MPTfileCSV # not exported
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def test_open_MPT(testdata_dir):
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mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt'))
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assert comments == []
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assert mpt1.dtype.names == (
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"mode", "ox/red", "error", "control changes", "Ns changes",
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"counter inc.", "time/s", "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W",
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"I/mA", "(Q-Qo)/mA.h", "x",
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)
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def test_open_MPT_fails_for_bad_file(testdata_dir):
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with pytest.raises(ValueError, match='Bad first line'):
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MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
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def test_open_MPT_csv(testdata_dir):
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mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpt'))
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assert comments == []
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assert mpt1.fieldnames == [
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"mode", "ox/red", "error", "control changes", "Ns changes",
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"counter inc.", "time/s", "control/V/mA", "Ewe/V", "dq/mA.h", "P/W",
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"<I>/mA", "(Q-Qo)/mA.h", "x",
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]
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def test_open_MPT_csv_fails_for_bad_file(testdata_dir):
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with pytest.raises((ValueError, UnicodeDecodeError)):
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MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr'))
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def test_colID_map_uniqueness():
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"""Check some uniqueness properties of the VMPdata_colID_xyz maps."""
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field_colIDs = set(BioLogic.VMPdata_colID_dtype_map.keys())
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flag_colIDs = set(BioLogic.VMPdata_colID_flag_map.keys())
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field_names = [v[0] for v in BioLogic.VMPdata_colID_dtype_map.values()]
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flag_names = [v[0] for v in BioLogic.VMPdata_colID_flag_map.values()]
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assert not field_colIDs.intersection(flag_colIDs)
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# 'I/mA' and 'dQ/mA.h' are duplicated
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# assert len(set(field_names)) == len(field_names)
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assert len(set(flag_names)) == len(flag_names)
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assert not set(field_names).intersection(flag_names)
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@pytest.mark.parametrize('colIDs, expected', [
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([1, 2, 3], [('flags', 'u1')]),
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([4, 6], [('time/s', '<f8'), ('Ewe/V', '<f4')]),
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([1, 4, 21], [('flags', 'u1'), ('time/s', '<f8')]),
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([4, 6, 4], [('time/s', '<f8'), ('Ewe/V', '<f4'), ('time/s 2', '<f8')]),
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([4, 9999], NotImplementedError),
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])
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def test_colID_to_dtype(colIDs, expected):
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"""Test converting column ID to numpy dtype."""
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if isinstance(expected, type) and issubclass(expected, Exception):
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with pytest.raises(expected):
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BioLogic.VMPdata_dtype_from_colIDs(colIDs)
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return
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expected_dtype = np.dtype(expected)
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dtype, flags_dict = BioLogic.VMPdata_dtype_from_colIDs(colIDs)
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assert dtype == expected_dtype
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@pytest.mark.parametrize('filename, startdate, enddate', [
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('bio_logic1.mpr', '2011-10-29', '2011-10-31'),
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('bio_logic2.mpr', '2012-09-27', '2012-09-27'),
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('bio_logic3.mpr', '2013-03-27', '2013-03-27'),
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('bio_logic4.mpr', '2011-11-01', '2011-11-02'),
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('bio_logic5.mpr', '2013-01-28', '2013-01-28'),
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# bio_logic6.mpr has no end date because it does not have a VMP LOG module
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('bio_logic6.mpr', '2012-09-11', None),
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# C019P-0ppb-A_C01.mpr stores the date in a different format
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('C019P-0ppb-A_C01.mpr', '2019-03-14', '2019-03-14'),
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])
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def test_MPR_dates(testdata_dir, filename, startdate, enddate):
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"""Check that the start and end dates in .mpr files are read correctly."""
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mpr = MPRfile(os.path.join(testdata_dir, filename))
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assert mpr.startdate.strftime('%Y-%m-%d') == startdate
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if enddate:
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assert mpr.enddate.strftime('%Y-%m-%d') == enddate
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else:
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assert not hasattr(mpr, 'enddate')
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def test_open_MPR_fails_for_bad_file(testdata_dir):
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with pytest.raises(ValueError, match='Invalid magic for .mpr file'):
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MPRfile(os.path.join(testdata_dir, 'arbin1.res'))
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def timestamp_from_comments(comments):
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for line in comments:
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time_match = re.match(b'Acquisition started on : ([0-9/]+ [0-9:]+)', line)
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if time_match:
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timestamp = datetime.strptime(time_match.group(1).decode('ascii'),
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'%m/%d/%Y %H:%M:%S')
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return timestamp
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raise AttributeError("No timestamp in comments")
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def assert_MPR_matches_MPT(mpr, mpt, comments):
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def assert_field_matches(fieldname, decimal):
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if fieldname in mpr.dtype.fields:
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assert_array_almost_equal(mpr.data[fieldname],
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mpt[fieldname],
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decimal=decimal)
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def assert_field_exact(fieldname):
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if fieldname in mpr.dtype.fields:
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assert_array_equal(mpr.data[fieldname], mpt[fieldname])
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assert_array_equal(mpr.get_flag("mode"), mpt["mode"])
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assert_array_equal(mpr.get_flag("ox/red"), mpt["ox/red"])
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assert_array_equal(mpr.get_flag("error"), mpt["error"])
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assert_array_equal(mpr.get_flag("control changes"), mpt["control changes"])
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if "Ns changes" in mpt.dtype.fields:
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assert_array_equal(mpr.get_flag("Ns changes"), mpt["Ns changes"])
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# Nothing uses the 0x40 bit of the flags
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assert_array_equal(mpr.get_flag("counter inc."), mpt["counter inc."])
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assert_array_almost_equal(mpr.data["time/s"],
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mpt["time/s"],
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decimal=2) # 2 digits in CSV
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assert_field_matches("control/V/mA", decimal=6)
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assert_field_matches("control/V", decimal=6)
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assert_array_almost_equal(mpr.data["Ewe/V"],
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mpt["Ewe/V"],
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decimal=6) # 32 bit float precision
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assert_field_matches("dQ/mA.h", decimal=17) # 64 bit float precision
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assert_field_matches("P/W", decimal=10) # 32 bit float precision for 1.xxE-5
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assert_field_matches("I/mA", decimal=6) # 32 bit float precision
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assert_field_exact("cycle number")
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assert_field_matches("(Q-Qo)/C", decimal=6) # 32 bit float precision
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try:
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assert timestamp_from_comments(comments) == mpr.timestamp
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except AttributeError:
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pass
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@pytest.mark.parametrize('basename', [
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'bio_logic1',
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'bio_logic2',
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# No bio_logic3.mpt file
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'bio_logic4',
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# bio_logic5 and bio_logic6 are special cases
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'CV_C01',
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'121_CA_455nm_6V_30min_C01',
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])
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def test_MPR_matches_MPT(testdata_dir, basename):
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"""Check the MPR parser against the MPT parser.
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Load a binary .mpr file and a text .mpt file which should contain
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exactly the same data. Check that the loaded data actually match.
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"""
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binpath = os.path.join(testdata_dir, basename + '.mpr')
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txtpath = os.path.join(testdata_dir, basename + '.mpt')
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mpr = MPRfile(binpath)
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mpt, comments = MPTfile(txtpath)
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assert_MPR_matches_MPT(mpr, mpt, comments)
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def test_MPR5_matches_MPT5(testdata_dir):
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mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic5.mpr'))
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mpt, comments = MPTfile((re.sub(b'\tXXX\t', b'\t0\t', line) for line in
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open(os.path.join(testdata_dir, 'bio_logic5.mpt'),
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mode='rb')))
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assert_MPR_matches_MPT(mpr, mpt, comments)
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def test_MPR6_matches_MPT6(testdata_dir):
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mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic6.mpr'))
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mpt, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic6.mpt'))
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mpr.data = mpr.data[:958] # .mpt file is incomplete
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assert_MPR_matches_MPT(mpr, mpt, comments)
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