def _analyze_matrix(matrix, min_dist_between_max_peaks, calibration):
intensities = np.asarray(_mean_columns(matrix), dtype=np.int16)
(max_peaks_positions,
min_peaks_positions) = calculate_peaks(intensities,
min_dist_between_max_peaks)
max_peaks_intensities = _intensities_in_positions(intensities,
max_peaks_positions)
min_peaks_intensities = _intensities_in_positions(intensities,
min_peaks_positions)
return ({
"intensities":
intensities,
"max_peaks_positions":
max_peaks_positions,
"max_peaks_intensities":
max_peaks_intensities,
"min_peaks_positions":
min_peaks_positions,
"min_peaks_intensities":
min_peaks_intensities,
"amplitudes":
calculate_amplitudes(max_peaks_intensities, min_peaks_intensities),
"times_to_peaks":
calculate_time_to_peaks(max_peaks_positions, min_peaks_positions,
calibration),
"times_to_half_peaks":
calculate_times_to_half_peaks(intensities, max_peaks_positions,
min_peaks_positions, calibration),
"tau_s":
calculate_taus(intensities, max_peaks_positions, min_peaks_positions,
calibration)
})
def test_raise_error_if_the_only_founded_peak_is_in_the_last_position_of_the_vector(
self):
vector = [0, 0, 0, 0, 0, 0, 2]
min_dist_between_max_peaks = 2
self.assertRaises(
ValueError,
lambda: calculate_peaks(vector, min_dist_between_max_peaks))
def test_raise_error_when_no_max_peak_found_due_to_possible_peaks_bellow_threshold(
self):
# The threshold is calculated as 1.0 / max(vector)
# We use the threshold to avoid false positives
vector = [0, 1, 0, 0, 0, 1, 0, 0]
min_dist_between_max_peaks = 2
self.assertRaises(
ValueError,
lambda: calculate_peaks(vector, min_dist_between_max_peaks))
def test_with_one_peaks_there_are_two_minimum_peaks(self):
vector = [-1, 2, 3, 10, 9, 11, 6, 1, 3]
min_dist_between_max_peaks = 2
(max_peaks, min_peaks) = calculate_peaks(vector,
min_dist_between_max_peaks)
self.assertEqual(len(max_peaks), 1)
self.assertEqual(max_peaks[0], 5)
self.assertEqual(len(min_peaks), 2)
self.assertEqual(min_peaks[0], 0)
self.assertEqual(min_peaks[1], 7)
def test_finds_max_and_minumum_peaks(self):
vector = [-1, 2, 3, 10, 9, 8, 7, 15, 3]
min_dist_between_max_peaks = 2
(max_peaks, min_peaks) = calculate_peaks(vector,
min_dist_between_max_peaks)
self.assertEqual(len(max_peaks), 2)
self.assertEqual(max_peaks[0], 3)
self.assertEqual(max_peaks[1], 7)
self.assertEqual(len(min_peaks), 3)
self.assertEqual(min_peaks[0], 0)
self.assertEqual(min_peaks[1], 6)
self.assertEqual(min_peaks[2], 8)
def test_raise_error_when_no_max_peak_found(self):
vector = [0, 0, 0, 0]
min_dist_between_max_peaks = 2
self.assertRaises(
ValueError,
lambda: calculate_peaks(vector, min_dist_between_max_peaks))