def display(self):
"""
Display the Chromatogram
"""
self.constrain_zoom("x")
display = Display(self.fig, self.ax)
self.ax.clear()
# Read the TIC from the tic.dat file in the experiment tarfile
intensity_array, tic = self.experiment.tic_data
# peak_list = load_peaks(os.path.join(ExprDir, "{}_peaks.dat".format(self.experiment.name)))
display.plot_tic(tic, label=self.experiment.name, minutes=True)
# display.plot_peaks(filtered_peak_list, "Peaks")
# display.do_plotting('TIC and PyMS Detected Peaks')
# display.do_plotting(f'{self.experiment.name} TIC')
display.do_plotting('')
x = [time / 60 for time in tic.time_list]
self.ax.set_xlim(left=0, right=max(x))
self.ax.set_ylim(bottom=0)
self.ax.set_xlabel("Retention Time")
self.ax.set_ylabel("Intensity")
self.fig.subplots_adjust(left=0.1, bottom=0.125, top=0.9, right=0.97)
# figure.tight_layout()
self.canvas.draw()
self.setup_ylim_refresher(intensity_array, x)
area = peak_sum_area(im, peak)
peak.area = area
# print some details
UID = peak.UID
# height as sum of the intensities of the apexing ions
height = sum(peak.get_mass_spectrum().mass_spec.tolist())
print(UID + f", {rt:.2f}, {height:.2f}, {peak.area:.2f}")
# 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_list = []
for m in range(n_mz):
ic_list.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')
for ic in ic_list:
display.plot_ic(ic)
display.plot_peaks(new_peak_list, 'Peaks')
display.do_plotting('TIC, and PyMassSpec Detected Peaks')
display.show_chart()