view rankfilter_GCMS/test/test_rankfilter.py @ 22:cd4f13119afa

Small fix in filters part and improvement in query_metexp time logging

'''
Created on Mar 13, 2012

@author: marcelk
'''
from GCMS.rankfilter_GCMS.rankfilter import get_data, calibrate, calibrate_poly, convert_rt, convert_rt_poly
from pkg_resources import resource_filename  # @UnresolvedImport # pylint: disable=E0611
import unittest


class Test(unittest.TestCase):

    def setUp(self):
        self.calibration = resource_filename(__name__, "data/calibration.txt")
        self.sample = resource_filename(__name__, "data/sample.txt")

    def test_get_data(self):
        samples = get_data(self.sample, ['CAS', 'Name', 'R.T.', 'Forward', 'Reverse', 'Formula'])
        self.assertEqual(['C29H50O', 'C29H50O', 'C29H50O', 'C29H50O', 'C29H50O', 'C28H48O', 'C28H48O', 'C28H48O',
                          'C28H48O', 'C27H44O2', 'C29H50O2', 'C29H50O2', 'C29H50O2', 'C29H50O2', 'C29H50O2',
                          'C28H48O2', 'C28H48O2', 'C28H48O2', 'C28H48O2', 'C30H50O3', 'C29H50O', 'C29H50O',
                          'C29H50O', 'C29H50O'], samples['Formula'])

    def test_calibrate(self):
        standards = get_data(self.calibration, ['Name', 'R.T.', 'RI'])
        coeff = calibrate(standards)
        self.assertAlmostEqual(103.19073523551653, coeff[0], 5)
        self.assertAlmostEqual(277.14374835349395, coeff[1], 5)

    def test_calibrate_poly(self):
        standards = get_data(self.calibration, ['Name', 'R.T.', 'RI'])
        poly_cal = calibrate_poly(standards)
        self.assertAlmostEqual(0.028897105229818407, poly_cal[0], 5)
        self.assertAlmostEqual(0.704572097468386, poly_cal[1], 5)
        self.assertAlmostEqual(51.636852478526357, poly_cal[2], 5)
        self.assertAlmostEqual(704.95499738104672, poly_cal[3], 5)

    def test_convert_rt(self):
        standards = get_data(self.calibration, ['Name', 'R.T.', 'RI'])
        coeff = calibrate(standards)
        convert = convert_rt({'R.T.': [5, 10, 15, 20]}, coeff)
        self.assertAlmostEqual(793.09742453, convert['RIexp'][0], 5)
        self.assertAlmostEqual(1309.05110071, convert['RIexp'][1], 5)
        self.assertAlmostEqual(1825.00477689, convert['RIexp'][2], 5)
        self.assertAlmostEqual(2340.95845306, convert['RIexp'][3], 5)

    def test_convert_rt_poly(self):
        standards = get_data(self.calibration, ['Name', 'R.T.', 'RI'])
        poly_cal = calibrate_poly(standards)
        convert = convert_rt_poly({'R.T.': [5, 10, 15, 20]}, poly_cal)
        self.assertAlmostEqual(984.36570036, convert['RIexp'][0], 5)
        self.assertAlmostEqual(1320.67783714, convert['RIexp'][1], 5)
        self.assertAlmostEqual(1735.56423664, convert['RIexp'][2], 5)
        self.assertAlmostEqual(2250.69772778, convert['RIexp'][3], 5)

if __name__ == "__main__":
    #import sys;sys.argv = ['', 'Test.testName']
    unittest.main()