def __init__(self, verbose=False):
config = ConfigProvider().getProcessingConfig()
self.maxNaNValues = config.get("maxNaNValues")
self.lowerFreq = config.get("lowerFreq")
self.upperFreq = config.get("upperFreq")
self.samplingRate = ConfigProvider().getEmotivConfig().get("samplingRate")
self.qualUtil = QualityUtil()
self.sigUtil = SignalUtil()
self.verbose = verbose
class SignalProcessor(object):
def __init__(self, verbose=False):
config = ConfigProvider().getProcessingConfig()
self.maxNaNValues = config.get("maxNaNValues")
self.lowerFreq = config.get("lowerFreq")
self.upperFreq = config.get("upperFreq")
self.samplingRate = ConfigProvider().getEmotivConfig().get("samplingRate")
self.qualUtil = QualityUtil()
self.sigUtil = SignalUtil()
self.verbose = verbose
def process(self, raw, quality):
raw = self._replaceBadQuality(raw, quality)
raw = self._replaceSequences(raw)
raw = self._replaceOutliners(raw)
raw = self._normalize(raw)
invalid = self.qualUtil.isInvalidData(raw)
return raw, invalid
def _replaceBadQuality(self, raw, quality):
if self.verbose:
print "badQuality: %d" % self.qualUtil.countBadQuality(raw, quality)
raw = self.qualUtil.replaceBadQuality(raw, quality, NaN)
self._printNaNCount(raw)
return raw
def _replaceSequences(self, raw):
if self.verbose:
print "sequences: %d" % self.qualUtil.countSequences(raw)
raw = self.qualUtil.replaceSequences(raw)
self._printNaNCount(raw)
return raw
def _replaceOutliners(self, raw):
if self.verbose:
print "outliners: %d" % self.qualUtil.countOutliners(raw)
raw = self.qualUtil.replaceOutliners(raw, NaN)
self._printNaNCount(raw)
return raw
def _normalize(self, raw):
if self.verbose:
print "normalize: min %.2f max %.2f" % (self.sigUtil.minimum(raw),self.sigUtil.maximum(raw))
raw = self.sigUtil.normalize(raw)
if self.verbose:
print "normalize: min %.2f max %.2f" % (self.sigUtil.minimum(raw),self.sigUtil.maximum(raw))
self._printNaNCount(raw)
return raw
def _printNaNCount(self, raw):
if self.verbose:
print "NaN count: %s" % self.qualUtil.countNans(raw)
class FFTProcessor(object):
def __init__(self, verbose=False):
self.samplingRate = ConfigProvider().getEmotivConfig().get("samplingRate")
self.qualUtil = QualityUtil()
self.fftUtil = FFTUtil()
self.verbose = verbose
def process(self, proc):
fft = self.fftUtil.fft(proc)
invalid = self.qualUtil.isInvalidData(fft)
return fft, invalid
class EEGProcessor(object):
def __init__(self, verbose=False):
self.samplingRate = ConfigProvider().getEmotivConfig().get("samplingRate")
self.qualUtil = QualityUtil()
self.eegUtil = EEGUtil()
self.verbose = verbose
def process(self, proc):
alpha = self.eegUtil.getAlphaWaves(proc, self.samplingRate)
invalid = self.qualUtil.isInvalidData(alpha)
return alpha, invalid
def __init__(self, verbose=False):
self.samplingRate = ConfigProvider().getEmotivConfig().get("samplingRate")
self.qualUtil = QualityUtil()
self.fftUtil = FFTUtil()
self.verbose = verbose
def setUp(self):
self.util = QualityUtil()
class TestQualityUtil(unittest.TestCase):
def setUp(self):
self.util = QualityUtil()
def test_replaceOutliners_withNaN(self):
value = np.NaN
testList = np.array([-10.0, -4, -3, -2, 0, 4, 5, 6, 10])
self.assertEqual(countOcc(testList, value), 0)
procList = self.util.replaceOutliners(testList, value, -3, 5)
self.assertEqual(np.count_nonzero(np.isnan(procList)), 4)
def test_replaceOutliners_withValue(self):
value = -99
testList = np.array([-10, -4, -3, -2, 0, 4, 5, 6, 10])
self.assertEqual(countOcc(testList, value), 0)
procList = self.util.replaceOutliners(testList, value, -3, 5)
self.assertEqual(countOcc(procList, value), 4)
def test_replaceOutliners_withoutValue(self):
testList = np.array([-10, -4, -3, -2, 0, 4, 5, 6, 10])
self.assertEqual(countOcc(testList, -3), 1)
self.assertEqual(countOcc(testList, 5), 1)
procList = self.util.replaceOutliners(testList, None, -3, 5)
self.assertEqual(countOcc(procList, -3), 3)
self.assertEqual(countOcc(procList, 5), 3)
def test_isInvalidData(self):
maxNaNValues = self.util.maxNaNValues
for length in range(maxNaNValues+1):
testList = self._getNaNList(length)
self.assertFalse(self.util.isInvalidData(testList))
for length in range(maxNaNValues+1, maxNaNValues + 4):
testList = self._getNaNList(length)
self.assertTrue(self.util.isInvalidData(testList))
def _getNaNList(self, length):
return np.array([np.NaN]*length)
def test_countOutliners(self):
testList = np.array([-10.0, -4, -3, -2, 0, 4, 5, 6, 10])
self.assertEqual(self.util.countOutliners(testList, -3, 5), 4)
def test_countOutliners_defaultThreshold(self):
lb = self.util.lowerBound
ub = self.util.upperBound
testList = np.array([lb-1, lb, lb+1, -2, 0, 4, ub-1, ub, ub+1])
self.assertEqual(self.util.countOutliners(testList), 2)
def test_countOutliners_noOccurence(self):
testList = np.array([-10.0, -4, -3, -2, 0, 4, 5, 6, 10])
self.assertEqual(self.util.countOutliners(testList, -11, 11), 0)
def test_replaceBadQuality(self):
value = 99
testList = np.array([-10, -4, -3, -2, 0, 2, 4, 5, 6, 10])
qualList = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
procList = self.util.replaceBadQuality(testList, qualList, value, 4)
self.assertEqual(len(qualList), len(procList))
self.assertEqual(countOcc(procList, value), 4)
def test_replaceBadQuality_withNaN(self):
value = np.NaN
testList = np.array([-10.0, -4, -3, -2, 0, 2, 4, 5, 6, 10])
qualList = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
procList = self.util.replaceBadQuality(testList, qualList, value, 4)
self.assertEqual(len(qualList), len(procList))
self.assertEqual(np.count_nonzero(np.isnan(procList)), 4)
def test_replaceBadQuality_differentLengthError(self):
value = np.NaN
testList = np.array([-10.0, -4, -3, -2, 0, 2, 4, 5, 6, 10])
qualList = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8])
with self.assertRaises(ValueError):
_ = self.util.replaceBadQuality(testList, qualList, value, 4)
def test_countBadQuality(self):
testList = np.array([-10.0, -4, -3, -2, 0, 2, 4, 5, 6, 10])
qualList = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
count = self.util.countBadQuality(testList, qualList, 4)
self.assertEqual(len(qualList), len(testList))
self.assertEqual(count, 4)
def test_countBadQuality_defaultThreshold(self):
testList = np.array([-10.0, -4, -3, -2, 0, 2, 4, 5, 6, 10])
minQuality = self.util.minQuality
qualList = np.array([0, minQuality-1, minQuality, minQuality+1, 15, 15, 15, 15, 15, 15])
count = self.util.countBadQuality(testList, qualList)
self.assertEqual(len(qualList), len(testList))
self.assertEqual(count, 1)
def test_zeros(self):
countZeros = self.util.countZeros(TEST_DATA_ZERO)
self.assertEqual(countZeros, 10)
self.assertNotEqual(countZeros, len(TEST_DATA_ZERO))
def test_nans(self):
countNans = self.util.countNans(TEST_DATA_NAN)
self.assertEqual(countNans, 4)
self.assertEqual(countNans, len(TEST_DATA_NAN))
def test_nans_mixed(self):
countNans = self.util.countNans(TEST_DATA_MIXED)
self.assertEqual(countNans, 2)
self.assertNotEqual(countNans, len(TEST_DATA_MIXED))
#TODO make this flexible to maxSeqLegth change
@unittest.skip("fix leading zero is replaced")
def test_replaceZeroSequences(self):
zeros = np.array([0.0, -5.0, 0.0, 0, 2.0, 0.0, 0.0, 0.0, 3.5, 0, 0, 0, 0, 0, 1.0, 1.0, 1.0, 1.0, 1.0, 0, 0, 0, 0, 0, 0])
l = self.util.replaceZeroSequences(zeros)
self.assertNotEquals(self.util.countZeros(zeros), self.util.countZeros(l))
self.assertEquals(self.util.countZeros(l), 6)
self.assertEquals(self.util.countNans(l), 16)
#TODO make this flexible to maxSeqLegth change
def test_replaceAnySequences(self):
zeros = np.array([0, 0.0, 0.0, 0, 0, 2.0, 0, 2.0, 1.0, 1.0, 1.0, 1.0, 1.0])
l = self.util.replaceSequences(zeros)
self.assertNotEquals(self.util.countZeros(zeros), self.util.countZeros(l))
self.assertEquals(self.util.countZeros(l), 1)
self.assertEquals(self.util.countNans(l), 10)
def test_countAnySequences(self):
a = np.array([0, 0.0, 0.0, 0, 2.0, 0, 2.0, 1.0, 1.0, 1.0, 1.0, 1.0])
l = self.util.countSequences(a)
self.assertEquals(l, 1)
