def make_scan(self):
peaks = []
tids, ions = self.make_tids()
list(map(peaks.extend, tids))
peaks.sort(key=lambda x: x.mz)
mz = np.array([0])
intensity = np.array([0])
fpeaks = []
for p in peaks:
fpeaks.append(FittedPeak(
mz=p.mz, intensity=p.intensity, signal_to_noise=p.intensity, peak_count=-1, index=-1,
full_width_at_half_max=fwhm, area=p.intensity))
mz, intensity = reprofile(fpeaks)
scan = common.Scan(
{
"id": "test-scan",
"index": 0,
"m/z array": mz,
"intensity array": intensity,
"ms level": 1,
"scan time": 0.0,
"profile spectrum": "",
"negative scan": "",
},
mzml.MzMLDataInterface())
return scan
def make_broken_vendor_scan(self):
base = self.make_scan()
class BrokenVendorPeakPickingMzMLDataInterface(mzml.MzMLDataInterface):
def _pick_peaks_vendor(self, scan, *args, **kwargs):
raise ValueError("This was a horrible idea.")
scan = common.Scan(base._data,
BrokenVendorPeakPickingMzMLDataInterface())
return scan
def make_scan(self):
mz, intensity = make_profile(points, fwhm)
scan = common.Scan(
{
"id": "test-scan",
"index": 0,
"m/z array": mz,
"ms level": 1,
"scan time": 0.0,
"intensity array": intensity,
"profile spectrum": "",
"positive scan": "",
}, mzml.MzMLDataInterface())
return scan
def make_scan(self):
mz, intensity = make_profile(points, fwhm)
scan = common.Scan(
{
"id": "test-scan",
"index": 0,
"m/z array": mz,
"ms level": 1,
"scan time": 0.0,
"intensity array": intensity,
"profile spectrum": "",
"positive scan": "",
}, mzml.MzMLDataInterface())
scan.pick_peaks()
for point in points:
self.assertIsNotNone(scan.peak_set.has_peak(point[0]))
return scan
def make_scan(self):
mz, intensity = make_profile(points, fwhm)
scan = common.Scan(
{
"id": "spam",
"index": 0,
"ms level": 1,
"m/z array": mz,
"intensity array": intensity,
"profile spectrum": "",
"positive scan": "",
"scanList": {
"scan": [{
"scan start time": 0
}]
}
}, mzml.MzMLDataInterface())
return scan
def get_scan(self):
scan_data = gzload(datafile("test_scan.pkl.gz"))
scan = common.Scan(scan_data, mzml.MzMLDataInterface())
return scan