def get_spectrum(self, index):
this_spectrum = mass_spectrum()
tmp_str = '/spectral_data/%d/' % (index)
this_spectrum.add_centroids(
self.hdf[tmp_str + '/centroid_mzs/'],
self.hdf[tmp_str + '/centroid_intensities/'])
return this_spectrum
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_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_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 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 get_spectrum(self,index,datatype='profile'):
this_spectrum = mass_spectrum()
tmp_str='/spectral_data/%d/' %(index)
if datatype == 'profile':
this_spectrum.add_spectrum(self.hdf[tmp_str+'mzs/'],self.hdf[tmp_str+'/intensities/'])
elif datatype=='centroid':
this_spectrum.add_centroids(self.hdf[tmp_str+'centroid_mzs/'],self.hdf[tmp_str+'/centroid_intensities/'])
elif datatype == 'all':
if self.hdf[tmp_str+'mzs/']:
this_spectrum.add_spectrum(self.hdf[tmp_str+'mzs/'],self.hdf[tmp_str+'/intensities/'])
if self.hdf[tmp_str+'centroid_mzs/']:
this_spectrum.add_centroids(self.hdf[tmp_str+'centroid_mzs/'],self.hdf[tmp_str+'/centroid_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 get_spectrum(self,index):
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 get_spectrum(self, index, datatype='profile'):
this_spectrum = mass_spectrum()
tmp_str = '/spectral_data/%d/' % (index)
if datatype == 'profile':
this_spectrum.add_spectrum(self.hdf[tmp_str + 'mzs/'],
self.hdf[tmp_str + '/intensities/'])
elif datatype == 'centroid':
this_spectrum.add_centroids(
self.hdf[tmp_str + 'centroid_mzs/'],
self.hdf[tmp_str + '/centroid_intensities/'])
elif datatype == 'all':
if self.hdf[tmp_str + 'mzs/']:
this_spectrum.add_spectrum(self.hdf[tmp_str + 'mzs/'],
self.hdf[tmp_str + '/intensities/'])
if self.hdf[tmp_str + 'centroid_mzs/']:
this_spectrum.add_centroids(
self.hdf[tmp_str + 'centroid_mzs/'],
self.hdf[tmp_str + '/centroid_intensities/'])
return this_spectrum
def get_spectrum(self, index):
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_spectrum(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_spectrum(mzs_counts[0], mzs_counts[1])
self.assertItemsEqual(this_spectrum.mzs, mzs_counts[0])
self.assertItemsEqual(this_spectrum.intensities, mzs_counts[1])
else:
with self.assertRaises(IOError):
this_spectrum.add_spectrum(mzs_counts[0], mzs_counts[1])
def isodist(molecules, charges=0, output='', plot=False, sigma=0.35, resolution=250, cutoff=0.0001, do_centroid=True,
verbose=False):
exit = checkhelpcall(molecules)
save = checkoutput(output)
if exit == True:
sys.exit(0)
molecules = molecules.split(',')
for element in molecules:
element = formulaExpander(element)
if verbose:
print (
'The mass of %(substance)s is %(Mass)f and the calculated charge is %(Charge)d with m/z of %(Mz)f.' % {
'substance': \
element, 'Mass': molmass(element), 'Charge': molcharge(element),
'Mz': mz(molmass(element), molcharge(element), charges)})
if charges == 0:
charges = molcharge(element)
if charges == 0:
charges = 1
else:
if verbose:
print "Using user-supplied charge of %d for mass spectrum" % charges
isomasses = isotopemasses(element)
isoratios = isotoperatios(element)
if len(isomasses) != 1:
ratios, masses = isotopes(isoratios, isomasses, cutoff) # slow
final = genDict(masses, ratios, charges, cutoff) # very slow
else:
final = genDict(isomasses[0], isoratios[0], charges, cutoff)
# for i in sorted(final.keys()): #fast
# if final[i]>cutoff:
# print i,final[i]
ms_output = mass_spectrum()
if do_centroid:
from pyMS.centroid_detection import gradient
pts = resolution2pts(min(final.keys()), max(final.keys()), resolution)
xvector, yvector = genGaussian(final, sigma, pts) # slow
ms_output.add_spectrum(xvector, yvector)
mz_list, intensity_list, centroid_list = gradient(ms_output.get_spectrum()[0], ms_output.get_spectrum()[1],
max_output=-1, weighted_bins=5)
ms_output.add_centroids(mz_list, intensity_list)
else:
mz_idx = sorted(final.keys())
ms_output.add_centroids(mz_idx, [final[f] for f in mz_idx])
if plot == True:
import matplotlib.pyplot as plt # for plotting
plt.plot(xvector, yvector)
plt.plot(mz_list, intensity_list, 'rx')
plt.show()
if save == True:
g = open(savefile, 'w')
xs = xvector.tolist()
ys = yvector.tolist()
for i in range(0, len(xs)):
g.write(str(xs[i]) + "\t" + str(ys[i]) + "\n")
g.close
return ms_output
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 get_spectrum(self,index):
this_spectrum = mass_spectrum()
tmp_str='/spectral_data/%d/' %(index)
this_spectrum.add_centroids(self.hdf[tmp_str+'/centroid_mzs/'],self.hdf[tmp_str+'/centroid_intensities/'])
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
def get_spectrum_imzml(self,index):
mzs, intensities = self.imzml.getspectrum(index)
## temp hack -> assume centroided
this_spectrum = mass_spectrum()
this_spectrum.add_centroids(mzs,intensities)
return this_spectrum
