# -*- coding: utf-8 -*- import os.path import re from datetime import datetime import numpy as np from numpy.testing import assert_array_almost_equal, assert_array_equal import pytest from galvani import MPTfile, MPRfile from galvani.BioLogic import MPTfileCSV, str3 # not exported testdata_dir = os.path.join(os.path.dirname(__file__), 'testdata') def test_open_MPT(): 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(): with pytest.raises(ValueError, match='Bad first line'): MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpr')) def test_open_MPT_csv(): 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", "/mA", "(Q-Qo)/mA.h", "x", ] def test_open_MPT_csv_fails_for_bad_file(): with pytest.raises((ValueError, UnicodeDecodeError)): MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr')) @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'), ]) def test_MPR_dates(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(): 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(str3(time_match.group(1)), '%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=17) # 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 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', ]) def test_MPR_matches_MPT(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) assert_MPR_matches_MPT(mpr, mpt, comments) def test_MPR5_matches_MPT5(): 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(): 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)