def test_get_centroid_spectrum(self):
mzs = [0, 1, 2, 3]
vals = [1, 2, 1, 0]
this_spectrum = mass_spectrum()
this_spectrum.add_centroids(mzs, vals)
[mzs_, vals_] = this_spectrum.get_spectrum(source='centroids')
self.assertItemsEqual(mzs, mzs_)
self.assertItemsEqual(vals, vals_)
def test_get_centroid_spectrum(self):
mzs = [0, 1, 2, 3]
vals = [1, 2, 1, 0]
this_spectrum = mass_spectrum()
this_spectrum.add_centroids(mzs, vals)
[mzs_, vals_] = this_spectrum.get_spectrum(source='centroids')
self.assertItemsEqual(mzs, mzs_)
self.assertItemsEqual(vals, vals_)
def test_get_profile_spectrum(self):
mzs = [0, 1, 2, 3]
vals = [1, 2, 1, 0]
this_spectrum = mass_spectrum()
this_spectrum.add_spectrum(mzs, vals)
[mzs_, vals_] = this_spectrum.get_spectrum(source='profile')
self.assertItemsEqual(mzs, mzs_)
self.assertItemsEqual(vals, vals_)
def test_get_profile_spectrum(self):
mzs = [0, 1, 2, 3]
vals = [1, 2, 1, 0]
this_spectrum = mass_spectrum()
this_spectrum.add_spectrum(mzs, vals)
[mzs_, vals_] = this_spectrum.get_spectrum(source='profile')
self.assertItemsEqual(mzs, mzs_)
self.assertItemsEqual(vals, vals_)
def get_spectrum_imzml(self, index):
mzs, intensities = self.imzml.getspectrum(index)
## temp hack -> assume centroided
this_spectrum = mass_spectrum()
if self.spectrum_type == 'centroids':
this_spectrum.add_centroids(mzs, intensities)
else:
this_spectrum.add_spectrum(mzs, intensities)
return this_spectrum
def add_spectrum(self,
profile_mzs=[],
profile_intensities=[],
centroids_mz=[],
centroid_intensity=[],
index=[]):
if profile_mzs == [] & centroids_mz == []:
raise ValueError(
'one of profile or centroids mzs should be non-empty')
new_spectrum = mass_spectrum()
new_spectrum.add_spectrum(profile_mzs, profile_intensities)
new_spectrum.add_centroids(centroids_mz, centroid_intensity)
if index == []:
self.index_list.append(max(self.index_list) + 1)
self.spectra.append(new_spectrum)
def test_add_centroids(self):
mzs_counts_list = [[[0, 1, 2], [2, 2, 2]],
[[0, 0, 0], [0, 0, 0]],
[[0, 1, 2], [2, ]]
]
test_vals_should_add = [True,
True,
False,
]
for mzs_counts, should_add in zip(mzs_counts_list, test_vals_should_add):
this_spectrum = mass_spectrum()
if should_add:
this_spectrum.add_centroids(mzs_counts[0], mzs_counts[1])
self.assertItemsEqual(this_spectrum._centroids, mzs_counts[0])
self.assertItemsEqual(this_spectrum._centroids_intensity, mzs_counts[1])
else:
with self.assertRaises(IOError):
this_spectrum.add_centroids(mzs_counts[0], mzs_counts[1])
def get_spectrum_hdf5(self, index):
import h5py
this_spectrum = mass_spectrum()
tmp_str = '/spectral_data/%d' % (index)
try:
this_spectrum.add_spectrum(self.hdf[tmp_str + '/mzs/'],
self.hdf[tmp_str + '/intensities/'])
got_spectrum = True
except KeyError:
got_spectrum = False
try:
this_spectrum.add_centroids(
self.hdf[tmp_str + '/centroid_mzs/'],
self.hdf[tmp_str + '/centroid_intensities/'])
got_centroids = True
except KeyError:
got_centroids = False
if not any([got_spectrum, got_centroids]):
raise ValueError(
'No spectral data found in index {}'.format(index))
return this_spectrum
def test_add_centroids(self):
mzs_counts_list = [[[0, 1, 2], [2, 2, 2]], [[0, 0, 0], [0, 0, 0]],
[[0, 1, 2], [
2,
]]]
test_vals_should_add = [
True,
True,
False,
]
for mzs_counts, should_add in zip(mzs_counts_list,
test_vals_should_add):
this_spectrum = mass_spectrum()
if should_add:
this_spectrum.add_centroids(mzs_counts[0], mzs_counts[1])
self.assertItemsEqual(this_spectrum._centroids, mzs_counts[0])
self.assertItemsEqual(this_spectrum._centroids_intensity,
mzs_counts[1])
else:
with self.assertRaises(IOError):
this_spectrum.add_centroids(mzs_counts[0], mzs_counts[1])
def make_spectrum(self, mzs, vals, centroid_mzs, centroid_vals):
this_spectrum = mass_spectrum()
this_spectrum.add_spectrum(mzs, vals)
this_spectrum.add_centroids(centroid_mzs, centroid_vals)
return this_spectrum
def make_spectrum(self, mzs, vals, centroid_mzs, centroid_vals):
this_spectrum = mass_spectrum()
this_spectrum.add_spectrum(mzs, vals)
this_spectrum.add_centroids(centroid_mzs, centroid_vals)
return this_spectrum