L=L, # the working distance in [m]
)
if True: # Change this to True to make subfigure c
# The code for the x-axis of subfigure c (the "F-vs-f" plot) is not yet implemented
# in ixdat, so this requires the old EC_MS package # TODO
from EC_MS import Molecule, recalibrate
mdict = {} # EC_MS works with a dictionary of Molecule objects.
for cal in calibration.ms_cal_results:
m = Molecule(cal.mol, primary=cal.mass, F_cal=cal.F)
mdict[cal.name] = m
# The analysis of the calibration is done with EC_MS's "recalibrate" function:
_, ax_c = recalibrate(
internal=[mdict["CO2_M44"], mdict["O2_M32"], mdict["H2_M2"]],
external=[mdict["He_M4"], mdict["CO_M28"], mdict["H2_M2_carrier"]],
labels=True,
)
# save it:
ax_c.get_figure().savefig("paper_I_fig_S1c.png")
# ----------------- Saving the calibration ----------------------
# We're also finished annotating figure a, so save that:
fig_a.savefig(
"paper_I_fig_S1a.png") # you can use eg .svg instead for vector graphics.
# save the calibration:
calibration.export() # this creates Scott2021a_ElectrocmimActa_calibration.ix
CO = point_calibration(data_MS,
mol="CO",
cal_type="external",
chip=chip,
tspan=tspan_CO,
tspan_bg=tspan_He)
mdict["CO"] = CO
H2_2 = point_calibration(
data_MS,
mol="H2",
cal_type="external",
chip=chip,
tspan=tspan_H2,
tspan_bg=tspan_air,
)
# f**k that, for some reason that looks even worse.
save_calibration_results(mdict, "20A31_calibration_results.pkl")
mdict, ax_F_vs_f = recalibrate(
internal=[mdict["CO2_M44"], mdict["O2_M32"], mdict["H2"]],
external=[He, CO, H2_2],
)
fig_0 = ax_0[0].get_figure()
fig_0.set_figwidth(fig_0.get_figwidth() * 2.5)
fig_0.savefig("calibration_experiment.svg")
ax_cal_curve_H2.get_figure().savefig("H2 calibration curve.svg")
ax_F_vs_f.get_figure().savefig("F vs f.svg")
chip = chip_calibration(data, mol=O2, gas='O2', composition=1, chip='microreactor', tspan=[8200, 8350])
chip.save('MR12')
print('\nAir flux through the chip in mol/s: ' + str(chip.capillary_flow(gas='air') / 6.02e23))
Ar = point_calibration(data, mol='Ar', mass='M40', cal_type='external', tspan=[10000, 10200], carrier='Ar', chip=chip)
CO = point_calibration(data, mol='CO', mass='M28', cal_type='external', tspan=[15400, 15600], carrier='CO', chip=chip)
H2 = point_calibration(data, mol='H2', mass='M2', cal_type='external', tspan=[20000, 20200], carrier='H2', chip=chip)
def T(M):
#return M**(-1/2)
return M**(-1/2.5)
quantify = {'CH4':'M15', 'CO2':'M44', #'CO':'M28', # CO has an external calibration
#'CH3OH':'M31' # we don't have a data file for methanol
}
mdict, ax = recalibrate(quantify=quantify, trusted=[O2], external=[O2, Ar, H2, CO],
transmission_function=T, labels=True)
save_calibration_results(mdict, '19F04_calibration.pkl')