def gen_cosine_matrix(self):
query = self.ions_list()
try:
cosine_matrix = compute_distance_matrix(
[fms.parent_mass for fms in query],
[
filter_data(
np.array(
fms.fragmolspectrum_set.get(energy=1).spectrum),
fms.parent_mass,
0.0,
0.0,
0.0,
0,
) for fms in query
],
0.002,
5,
)
cosine_matrix = Array2DModel.objects.create(
value=cosine_matrix.tolist())
self.cosine_matrix = cosine_matrix
self.save()
except Exception as ex:
pass
# raise ex
return self
def get_cosine(self, params):
parent_mass = [p[0].parent_mass for p in params]
spectrum = [
p[0].fragmolspectrum_set.get(energy=p[1]).spectrum for p in params
]
# filter_data(data, mz_parent, min_intensity, parent_filter_tolerance, matched_peaks_window,min_matched_peaks_search)
spectrum = [
filter_data(
np.array(spectrum[i]),
parent_mass[i],
self.frag_compare_conf.filter_min_intensity,
self.frag_compare_conf.filter_parent_filter_tolerance,
self.frag_compare_conf.filter_matched_peaks_window,
self.frag_compare_conf.filter_min_matched_peaks_search,
) for i in range(2)
]
# cosine_score(spectrum1_mz, spectrum1_data, spectrum2_mz, spectrum2_data, mz_tolerance, min_matched_peaks)
return cosine_score(
parent_mass[0],
spectrum[0],
parent_mass[1],
spectrum[1],
self.frag_compare_conf.cosine_mz_tolerance,
self.frag_compare_conf.cosine_min_matched_peaks,
)