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0d684af4705b990974626d9d0446d8ad21e56595
galvani/tests/test_BioLogic.py
Jonathan Schillings 0d684af470 Add loop_from_file and timestamp_from_file functions 
to extract loop_index and timestamp from the temporary _LOOP.txt and .mpl files during MPRfile initialization
Added unit tests but cannot upload test files due to LFS quota exceeded

Edited by Chris Kerr to fix flake8 warnings and resolve my comments from
the original PR https://github.com/echemdata/galvani/pull/102
2025-07-30 15:24:22 +03:00

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# -*- coding: utf-8 -*-
# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr <chris.kerr@mykolab.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
import os.path
import re
from datetime import date, datetime
import numpy as np
from numpy.testing import assert_array_almost_equal, assert_array_equal, assert_allclose
import pytest
from galvani import BioLogic, MPTfile, MPRfile
from galvani.BioLogic import MPTfileCSV # not exported
def test_open_MPT(testdata_dir):
mpt1, comments = MPTfile(os.path.join(testdata_dir, "bio_logic1.mpt"))
assert comments == []
assert mpt1.dtype.names == (
"mode",
"ox/red",
"error",
"control changes",
"Ns changes",
"counter inc.",
"time/s",
"control/V/mA",
"Ewe/V",
"dQ/mA.h",
"P/W",
"I/mA",
"(Q-Qo)/mA.h",
"x",
)
def test_open_MPT_fails_for_bad_file(testdata_dir):
with pytest.raises(ValueError, match="Bad first line"):
MPTfile(os.path.join(testdata_dir, "bio_logic1.mpr"))
def test_open_MPT_csv(testdata_dir):
mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, "bio_logic1.mpt"))
assert comments == []
assert mpt1.fieldnames == [
"mode",
"ox/red",
"error",
"control changes",
"Ns changes",
"counter inc.",
"time/s",
"control/V/mA",
"Ewe/V",
"dq/mA.h",
"P/W",
"<I>/mA",
"(Q-Qo)/mA.h",
"x",
]
def test_open_MPT_csv_fails_for_bad_file(testdata_dir):
with pytest.raises((ValueError, UnicodeDecodeError)):
MPTfileCSV(os.path.join(testdata_dir, "bio_logic1.mpr"))
def test_colID_map_uniqueness():
"""Check some uniqueness properties of the VMPdata_colID_xyz maps."""
field_colIDs = set(BioLogic.VMPdata_colID_dtype_map.keys())
flag_colIDs = set(BioLogic.VMPdata_colID_flag_map.keys())
field_names = [v[0] for v in BioLogic.VMPdata_colID_dtype_map.values()]
flag_names = [v[0] for v in BioLogic.VMPdata_colID_flag_map.values()]
assert not field_colIDs.intersection(flag_colIDs)
# 'I/mA' and 'dQ/mA.h' are duplicated
# assert len(set(field_names)) == len(field_names)
assert len(set(flag_names)) == len(flag_names)
assert not set(field_names).intersection(flag_names)
@pytest.mark.parametrize(
"colIDs, expected",
[
([1, 2, 3], [("flags", "u1")]),
([4, 6], [("time/s", "<f8"), ("Ewe/V", "<f4")]),
([1, 4, 21], [("flags", "u1"), ("time/s", "<f8")]),
([4, 6, 4], [("time/s", "<f8"), ("Ewe/V", "<f4"), ("time/s 2", "<f8")]),
([4, 9999], NotImplementedError),
],
)
def test_colID_to_dtype(colIDs, expected):
"""Test converting column ID to numpy dtype."""
if isinstance(expected, type) and issubclass(expected, Exception):
with pytest.raises(expected):
BioLogic.VMPdata_dtype_from_colIDs(colIDs)
return
expected_dtype = np.dtype(expected)
dtype, flags_dict = BioLogic.VMPdata_dtype_from_colIDs(colIDs)
assert np.dtype(dtype) == expected_dtype
@pytest.mark.parametrize(
"data, expected",
[
("02/23/17", date(2017, 2, 23)),
("10-03-05", date(2005, 10, 3)),
("11.12.20", date(2020, 11, 12)),
(b"01/02/03", date(2003, 1, 2)),
("13.08.07", ValueError),
("03-04/05", ValueError),
],
)
def test_parse_BioLogic_date(data, expected):
"""Test the parse_BioLogic_date function."""
if isinstance(expected, type) and issubclass(expected, Exception):
with pytest.raises(expected):
BioLogic.parse_BioLogic_date(data)
return
result = BioLogic.parse_BioLogic_date(data)
assert result == expected
@pytest.mark.parametrize(
"filename, startdate, enddate",
[
("bio_logic1.mpr", "2011-10-29", "2011-10-31"),
("bio_logic2.mpr", "2012-09-27", "2012-09-27"),
("bio_logic3.mpr", "2013-03-27", "2013-03-27"),
("bio_logic4.mpr", "2011-11-01", "2011-11-02"),
("bio_logic5.mpr", "2013-01-28", "2013-01-28"),
# bio_logic6.mpr has no end date because it does not have a VMP LOG module
("bio_logic6.mpr", "2012-09-11", None),
# C019P-0ppb-A_C01.mpr stores the date in a different format
("C019P-0ppb-A_C01.mpr", "2019-03-14", "2019-03-14"),
("Rapp_Error.mpr", "2010-12-02", "2010-12-02"),
("Ewe_Error.mpr", "2021-11-18", "2021-11-19"),
("col_27_issue_74.mpr", "2022-07-28", "2022-07-28"),
],
)
def test_MPR_dates(testdata_dir, filename, startdate, enddate):
"""Check that the start and end dates in .mpr files are read correctly."""
mpr = MPRfile(os.path.join(testdata_dir, filename))
assert mpr.startdate.strftime("%Y-%m-%d") == startdate
if enddate:
assert mpr.enddate.strftime("%Y-%m-%d") == enddate
else:
assert not hasattr(mpr, "enddate")
def test_open_MPR_fails_for_bad_file(testdata_dir):
with pytest.raises(ValueError, match="Invalid magic for .mpr file"):
MPRfile(os.path.join(testdata_dir, "arbin1.res"))
def timestamp_from_comments(comments):
for line in comments:
time_match = re.match(b"Acquisition started on : ([0-9/]+ [0-9:]+)", line)
if time_match:
timestamp = datetime.strptime(
time_match.group(1).decode("ascii"), "%m/%d/%Y %H:%M:%S"
)
return timestamp
raise AttributeError("No timestamp in comments")
def assert_MPR_matches_MPT(mpr, mpt, comments):
def assert_field_matches(fieldname, decimal):
if fieldname in mpr.dtype.fields:
assert_array_almost_equal(
mpr.data[fieldname], mpt[fieldname], decimal=decimal
)
def assert_field_exact(fieldname):
if fieldname in mpr.dtype.fields:
assert_array_equal(mpr.data[fieldname], mpt[fieldname])
assert_array_equal(mpr.get_flag("mode"), mpt["mode"])
assert_array_equal(mpr.get_flag("ox/red"), mpt["ox/red"])
assert_array_equal(mpr.get_flag("error"), mpt["error"])
assert_array_equal(mpr.get_flag("control changes"), mpt["control changes"])
if "Ns changes" in mpt.dtype.fields:
assert_array_equal(mpr.get_flag("Ns changes"), mpt["Ns changes"])
# Nothing uses the 0x40 bit of the flags
assert_array_equal(mpr.get_flag("counter inc."), mpt["counter inc."])
assert_array_almost_equal(
mpr.data["time/s"], mpt["time/s"], decimal=2
) # 2 digits in CSV
assert_field_matches("control/V/mA", decimal=6)
assert_field_matches("control/V", decimal=6)
assert_array_almost_equal(
mpr.data["Ewe/V"], mpt["Ewe/V"], decimal=6
) # 32 bit float precision
assert_field_matches("dQ/mA.h", decimal=16) # 64 bit float precision
assert_field_matches("P/W", decimal=10) # 32 bit float precision for 1.xxE-5
assert_field_matches("I/mA", decimal=6) # 32 bit float precision
assert_field_exact("cycle number")
assert_field_matches("(Q-Qo)/C", decimal=6) # 32 bit float precision
try:
assert timestamp_from_comments(comments) == mpr.timestamp.replace(microsecond=0)
except AttributeError:
pass
def assert_MPR_matches_MPT_v2(mpr, mpt, comments):
"""
Asserts that the fields in the MPR.data ar the same as in the MPT.
Modified from assert_MPR_matches_MPT. Automatically converts dtype from MPT data
to dtype from MPR data before comparing the columns.
Special case for EIS_indicators: these fields are valid only at f<100kHz so their
values are replaced by -1 or 0 at high frequency in the MPT file, this is not the
case in the MPR data.
Parameters
----------
mpr : MPRfile
Data extracted with the MPRfile class.
mpt : np.array
Data extracted with MPTfile method.
Returns
-------
None.
"""
def assert_field_matches(fieldname):
EIS_quality_indicators = [
"THD Ewe/%",
"NSD Ewe/%",
"NSR Ewe/%",
"|Ewe h2|/V",
"|Ewe h3|/V",
"|Ewe h4|/V",
"|Ewe h5|/V",
"|Ewe h6|/V",
"|Ewe h7|/V",
"THD I/%",
"NSD I/%",
"NSR I/%",
"|I h2|/A",
"|I h3|/A",
"|I h4|/A",
"|I h5|/A",
"|I h6|/A",
"|I h7|/A",
]
if fieldname in EIS_quality_indicators: # EIS quality indicators only valid for f < 100kHz
index_inf_100k = np.where(mpr.data["freq/Hz"] < 100000)[0]
assert_allclose(
mpr.data[index_inf_100k][fieldname],
mpt[index_inf_100k][fieldname].astype(mpr.data[fieldname].dtype),
)
elif fieldname == "<Ewe>/V":
assert_allclose(
mpr.data[fieldname],
mpt["Ewe/V"].astype(mpr.data[fieldname].dtype),
)
elif fieldname == "<I>/mA":
assert_allclose(
mpr.data[fieldname],
mpt["I/mA"].astype(mpr.data[fieldname].dtype),
)
elif fieldname == "dq/mA.h":
assert_allclose(
mpr.data[fieldname],
mpt["dQ/mA.h"].astype(mpr.data[fieldname].dtype),
)
else:
assert_allclose(
mpr.data[fieldname],
mpt[fieldname].astype(mpr.data[fieldname].dtype),
)
def assert_field_exact(fieldname):
if fieldname in mpr.dtype.fields:
assert_array_equal(mpr.data[fieldname], mpt[fieldname])
for key in mpr.flags_dict.keys():
assert_array_equal(mpr.get_flag(key), mpt[key])
for d in mpr.dtype.descr[1:]:
assert_field_matches(d[0])
try:
assert timestamp_from_comments(comments) == mpr.timestamp.replace(microsecond=0)
except AttributeError:
pass
@pytest.mark.parametrize(
"basename",
[
"bio_logic1",
"bio_logic2",
# No bio_logic3.mpt file
"bio_logic4",
# bio_logic5 and bio_logic6 are special cases
"CV_C01",
"121_CA_455nm_6V_30min_C01",
"020-formation_CB5",
],
)
def test_MPR_matches_MPT(testdata_dir, basename):
"""Check the MPR parser against the MPT parser.
Load a binary .mpr file and a text .mpt file which should contain
exactly the same data. Check that the loaded data actually match.
"""
binpath = os.path.join(testdata_dir, basename + ".mpr")
txtpath = os.path.join(testdata_dir, basename + ".mpt")
mpr = MPRfile(binpath)
mpt, comments = MPTfile(txtpath, encoding="latin1")
assert_MPR_matches_MPT(mpr, mpt, comments)
def test_MPR5_matches_MPT5(testdata_dir):
mpr = MPRfile(os.path.join(testdata_dir, "bio_logic5.mpr"))
mpt, comments = MPTfile(
(
re.sub(b"\tXXX\t", b"\t0\t", line)
for line in open(os.path.join(testdata_dir, "bio_logic5.mpt"), mode="rb")
)
)
assert_MPR_matches_MPT(mpr, mpt, comments)
def test_MPR6_matches_MPT6(testdata_dir):
mpr = MPRfile(os.path.join(testdata_dir, "bio_logic6.mpr"))
mpt, comments = MPTfile(os.path.join(testdata_dir, "bio_logic6.mpt"))
mpr.data = mpr.data[:958] # .mpt file is incomplete
assert_MPR_matches_MPT(mpr, mpt, comments)
@pytest.mark.parametrize(
"basename_v1150",
["v1150_CA", "v1150_CP", "v1150_GCPL", "v1150_GEIS", "v1150_MB", "v1150_OCV", "v1150_PEIS"],
)
def test_MPR_matches_MPT_v1150(testdata_dir, basename_v1150):
"""Check the MPR parser against the MPT parser.
Load a binary .mpr file and a text .mpt file which should contain
exactly the same data. Check that the loaded data actually match.
"""
binpath = os.path.join(testdata_dir, "v1150", basename_v1150 + ".mpr")
txtpath = os.path.join(testdata_dir, "v1150", basename_v1150 + ".mpt")
mpr = MPRfile(binpath)
mpt, comments = MPTfile(txtpath, encoding="latin1")
assert_MPR_matches_MPT_v2(mpr, mpt, comments)
def test_loop_from_file(testdata_dir):
"""Check if the loop_index is correctly extracted from the _LOOP.txt file
"""
mpr = MPRfile(os.path.join(testdata_dir, "running", "running_OCV.mpr"))
if mpr.loop_index is None:
raise AssertionError("No loop_index found")
elif not len(mpr.loop_index) == 4:
raise AssertionError("loop_index is not the right size")
elif not (mpr.loop_index == [0, 4, 8, 11]).all():
raise AssertionError("loop_index values are wrong")
def test_timestamp_from_file(testdata_dir):
"""Check if the loop_index is correctly extracted from the _LOOP.txt file
"""
mpr = MPRfile(os.path.join(testdata_dir, "running", "running_OCV.mpr"))
if not hasattr(mpr, "timestamp"):
raise AssertionError("No timestamp found")
elif not mpr.timestamp.timestamp() == 1707299985.908:
raise AssertionError("timestamp value is wrong")
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