# -*- coding: utf-8 -*- 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 from nose.tools import ok_, eq_, raises 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')) eq_(comments, []) eq_(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")) @raises(ValueError) def test_open_MPT_fails_for_bad_file(): mpt1 = 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')) eq_(comments, []) eq_(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"]) @raises(ValueError) def test_open_MPT_csv_fails_for_bad_file(): mpt1 = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr')) def test_open_MPR1(): mpr1 = MPRfile(os.path.join(testdata_dir, 'bio_logic1.mpr')) ## Check the dates as a basic test that it has been read properly eq_(mpr1.startdate, date(2011, 10, 29)) eq_(mpr1.enddate, date(2011, 10, 31)) def test_open_MPR2(): mpr2 = MPRfile(os.path.join(testdata_dir, 'bio_logic2.mpr')) ## Check the dates as a basic test that it has been read properly eq_(mpr2.startdate, date(2012, 9, 27)) eq_(mpr2.enddate, date(2012, 9, 27)) def test_open_MPR3(): mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic3.mpr')) ## Check the dates as a basic test that it has been read properly eq_(mpr.startdate, date(2013, 3, 27)) eq_(mpr.enddate, date(2013, 3, 27)) def test_open_MPR4(): mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic4.mpr')) ## Check the dates as a basic test that it has been read properly eq_(mpr.startdate, date(2011, 11, 1)) eq_(mpr.enddate, date(2011, 11, 2)) def test_open_MPR5(): mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic5.mpr')) ## Check the dates as a basic test that it has been read properly eq_(mpr.startdate, date(2013, 1, 28)) eq_(mpr.enddate, date(2013, 1, 28)) def test_open_MPR6(): mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic6.mpr')) ## Check the dates as a basic test that it has been read properly eq_(mpr.startdate, date(2012, 9, 11)) ## no end date because no VMP LOG module @raises(ValueError) def test_open_MPR_fails_for_bad_file(): mpr1 = 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: eq_(timestamp_from_comments(comments), mpr.timestamp) except AttributeError: pass def test_MPR1_matches_MPT1(): mpr1 = MPRfile(os.path.join(testdata_dir, 'bio_logic1.mpr')) mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt')) assert_MPR_matches_MPT(mpr1, mpt1, comments) def test_MPR2_matches_MPT2(): mpr2 = MPRfile(os.path.join(testdata_dir, 'bio_logic2.mpr')) mpt2, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic2.mpt')) assert_MPR_matches_MPT(mpr2, mpt2, comments) ## No bio_logic3.mpt file def test_MPR4_matches_MPT4(): mpr4 = MPRfile(os.path.join(testdata_dir, 'bio_logic4.mpr')) mpt4, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic4.mpt')) assert_MPR_matches_MPT(mpr4, mpt4, 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) ## Tests for issue #1 -- new dtypes ## def test_CV_C01(): mpr = MPRfile(os.path.join(testdata_dir, 'CV_C01.mpr')) mpt, comments = MPTfile(os.path.join(testdata_dir, 'CV_C01.mpt')) assert_MPR_matches_MPT(mpr, mpt, comments) def test_CA_455nm(): mpr = MPRfile(os.path.join(testdata_dir, '121_CA_455nm_6V_30min_C01.mpr')) mpt, comments = MPTfile(os.path.join(testdata_dir, '121_CA_455nm_6V_30min_C01.mpt')) assert_MPR_matches_MPT(mpr, mpt, comments)