Curve fitting the white lines on zirconium oxide with hyperspy

fit_Zr_whitelines.py

def fit_Zr_L(sZr, ll=None):
    "Returns the model only"
    print("Will produce 10 progress bars")
    mZr = sZr.create_model(ll = ll, GOS="Hartree-Slater", auto_add_edges=False)
    mZr.fit_component(mZr["PowerLaw"], bounded=True, signal_range=[2150.,2210.], fit_independent=True, only_current=True)
    mZr.assign_current_values_to_all()
    mZr.fit_component(mZr["PowerLaw"], bounded=True, signal_range=[2150.,2210.], fit_independent=True, only_current=False)
    #mZr["PowerLaw"].set_parameters_not_free()


    Zr_L3 = hs.model.components1D.EELSCLEdge("Zr_L3", GOS="Hartree-Slater")
    Zr_L2 = hs.model.components1D.EELSCLEdge("Zr_L2", GOS="Hartree-Slater")

    Zr_L3_white = hs.model.components1D.Gaussian()
    Zr_L3_white.name = "Zr_L3 White Line"
    Zr_L3_white.centre.bmin = 2218.0
    Zr_L3_white.centre.bmax = 2240.0
    Zr_L3_white.A.bmin = 0
    Zr_L3_white.sigma.bmax=3
    mZr.append(Zr_L3_white)

    mZr.fit_component(Zr_L3_white,fitter="leastsq", signal_range=[Zr_L3_white.centre.bmin-3.0, Zr_L3_white.centre.bmax+3.0], bounded=True,)
    mZr.assign_current_values_to_all([Zr_L3_white])
    mZr.fit_component(Zr_L3_white,fitter="leastsq", signal_range=[Zr_L3_white.centre.bmin-3.0, Zr_L3_white.centre.bmax+3.0], bounded=True, only_current=False)

    mZr.append(Zr_L3)
    Zr_L3.onset_energy.twin = Zr_L3_white.centre
    mZr.fit_component(Zr_L3, bounded=True, signal_range=[2240., 2290.])
    mZr.assign_current_values_to_all([Zr_L3])
    mZr.fit_component(Zr_L3, bounded=True, signal_range=[2240., 2290.], only_current=False)

    Zr_L2_white = hs.model.components1D.Gaussian()
    Zr_L2_white.name = "Zr_L2 White Line"
    Zr_L2_white.centre.bmin = 2309.0
    Zr_L2_white.centre.bmax = 2317.0
    Zr_L2_white.A.bmin = 0
    Zr_L2_white.sigma.bmax=3

    mZr.append(Zr_L2_white)
    mZr.fit_component(Zr_L2_white, signal_range=[Zr_L2_white.centre.bmin-3.0, Zr_L2_white.centre.bmax+3.0], bounded=True,)

    mZr.assign_current_values_to_all([Zr_L2_white])
    mZr.fit_component(Zr_L2_white, signal_range=[Zr_L2_white.centre.bmin-3.0, Zr_L2_white.centre.bmax+3.0], bounded=True, only_current=False)

    mZr.append(Zr_L2)
    Zr_L2.onset_energy.twin = Zr_L2_white.centre
    mZr.fit_component(Zr_L2, bounded=True, signal_range=[2335., 2392.])
    mZr.assign_current_values_to_all([Zr_L2])
    mZr.fit_component(Zr_L2, bounded=True, signal_range=[2335., 2392.], only_current=False)
    mZr.fit_component(Zr_L2_white, signal_range=[Zr_L2_white.centre.bmin-3.0, Zr_L2_white.centre.bmax+3.0], bounded=True, only_current=False)

    mZr.fit_component(Zr_L3, bounded=True, signal_range=[2240., 2290.], only_current=False)
    mZr.fit_component(Zr_L3_white, signal_range=[Zr_L3_white.centre.bmin-3.0, Zr_L3_white.centre.bmax+3.0], bounded=True, only_current=False)
    mZr.fit_component(Zr_L2, bounded=True, signal_range=[2335., 2392.], only_current=False)
    mZr.fit_component(Zr_L2_white, signal_range=[Zr_L2_white.centre.bmin-3.0, Zr_L2_white.centre.bmax+3.0], bounded=True, only_current=False)
    print("Finished fitting Zirconium")
    return mZr

def fit_O_K(sO, ll=None):
    "Returns the model only"
    print("Will produce 5 progress bars")

    mO = sO.create_model(ll = ll, GOS="Hartree-Slater", auto_add_edges=False)
    mO.fit_component(mO["PowerLaw"], bounded=True, fit_independent=True, signal_range=[490.0,520.0], only_current=True)
    mO.assign_current_values_to_all()
    mO.fit_component(mO["PowerLaw"], bounded=True, fit_independent=True, signal_range=[490.0,520.0], only_current=False)
    O_K_white = hs.model.components1D.Gaussian()
    O_K_white.name = "O_K White Line"
    O_K_white.centre.bmin = 533.0
    O_K_white.centre.bmax = 537.0
    O_K_white.sigma.bmax = 3
    mO.append(O_K_white)
    mO.fit_component(O_K_white, bounded="True", signal_range=[532.0,538.0])
    mO.assign_current_values_to_all([O_K_white])
    mO.fit_component(O_K_white, bounded="True", signal_range=[532.0,538.0], only_current=False)


    O_K = hs.model.components1D.EELSCLEdge("O_K", GOS="Hartree-Slater")
    mO.append(O_K)
    O_K.onset_energy.twin = O_K_white.centre
    mO.fit_component(O_K, bounded="True", signal_range=[546.0,600.0])
    mO.assign_current_values_to_all([O_K])
    mO.fit_component(O_K, bounded="True", signal_range=[546.0,600.0], only_current=False)


    mO.fit_component(O_K_white, bounded="True", signal_range=[532.0,539.0], only_current=False)
    mO.fit_component(O_K, bounded="True", signal_range=[546.0,600.0], only_current=False)
    print("Finished fitting Oxygen")
    return mO