# trim by threshold
new_peak_list = num_ions_threshold(pl, n, t)
print "Number of filtered peaks: ", len(new_peak_list)
# TIC from raw data
tic = data.get_tic()
# save TIC to a file
# Get Ion Chromatograms for all m/z channels
n_mz = len(im.get_mass_list())
ic = []
for m in range(n_mz):
ic.append(im.get_ic_at_index(m))
# Create a new display object, this time plot the ICs
# and the TIC, as well as the peak list
display = Display()
display.plot_tic(tic, 'TIC')
display.plot_ics(ic)
display.plot_peaks(new_peak_list, 'Peaks')
display.do_plotting('TIC, and PyMS Detected Peaks')
# determine and set area
area = peak_sum_area(im, peak)
peak.set_area(area)
# print some details
UID = peak.get_UID()
# height as sum of the intensities of the apexing ions
height = sum(peak.get_mass_spectrum().mass_spec)
print UID + ", %.2f, %.2f, %.2f" % (rt, height, peak.get_area())
# TIC from raw data
tic = data.get_tic()
# baseline correction for TIC
tic_bc = tophat(tic, struct="1.5m")
# Get Ion Chromatograms for all m/z channels
n_mz = len(im.get_mass_list())
ic = []
for m in range(n_mz):
ic.append(im.get_ic_at_index(m))
# Create a new display object, this time plot the ICs
# and the TIC, as well as the peak list
display = Display()
display.plot_tic(tic_bc, 'TIC BC')
display.plot_ics(ic)
display.plot_peaks(new_peak_list, 'Peaks')
display.do_plotting('TIC, and PyMS Detected Peaks')
# trim by relative intensity
pl = rel_threshold(peak_list, r)
# trim by threshold
new_peak_list = num_ions_threshold(pl, n, t)
print "Number of filtered peaks: ", len(new_peak_list)
# TIC from raw data
tic = data.get_tic()
# save TIC to a file
# Get Ion Chromatograms for all m/z channels
n_mz = len(im.get_mass_list())
ic = []
# All plotting from here on
for m in range(n_mz):
ic.append(im.get_ic_at_index(m))
# Create a new display object, this time plot the ICs
# and the TIC, as well as the peak list
display = Display()
display.plot_tic(tic, 'TIC')
display.plot_ics(ic)
display.plot_peaks(new_peak_list, 'PyMS peaks')
display.do_plotting()
# determine and set area
area = peak_sum_area(im, peak)
peak.set_area(area)
# print some details
UID = peak.get_UID()
# height as sum of the intensities of the apexing ions
height = sum(peak.get_mass_spectrum().mass_spec)
print UID + ", %.2f, %.2f, %.2f" % (rt, height, peak.get_area())
# TIC from raw data
tic = data.get_tic()
# baseline correction for TIC
tic_bc = tophat(tic, struct="1.5m")
# Get Ion Chromatograms for all m/z channels
n_mz = len(im.get_mass_list())
ic = []
for m in range(n_mz):
ic.append(im.get_ic_at_index(m))
# Create a new display object, this time plot the ICs
# and the TIC, as well as the peak list
display = Display()
display.plot_tic(tic_bc, 'TIC BC')
display.plot_ics(ic)
display.plot_peaks(new_peak_list, 'Peaks')
display.do_plotting('TIC, and PyMS Detected Peaks')
