DiadFit 1.0.5__py3-none-any.whl → 1.0.9__py3-none-any.whl

DiadFit/importing_data_files.py

@@ -1352,6 +1352,158 @@ def get_settings():
     # Return the settings
     return settings.get('meta_path'), settings.get('spectra_path'), settings.get('spectra_filetype'), \
            settings.get('prefix'), settings.get('prefix_str'), settings.get('spectra_file_ext'), settings.get('meta_file_ext'),settings.get('TruPower')
+           
+           ## Give nice column names
+           
+## Lets do the look up code.
+# 
+
+def add_column_name_descriptions(df):
+    
+    """ Adds a new to inputted dataframe, with a description of what the diadfit columns mean underneath
+    
+    Parameters
+    -------------------
+    df: pandas dataframe, including some columns from DiadFit (can have other columns too)
+    
+    Returns
+    ----------------------
+    df: A dataframe with a new row, with descriptions for columns matching our reference key. 
+    
+
+    
+    """
+    lookup_key = {
+    'filename': 'name of file',
+    'Density g/cm3': 'Density of CO2 in g/cm3',
+    'σ Density g/cm3': '1 sigma error on density (combined from peak fitting, Ne correction model, and densimeter equation)',
+    'σ Density g/cm3 (from Ne+peakfit)': '1 sigma error on density (from just peak fitting + Ne correction model)',
+    'σ Density g/cm3 (from densimeter)': '1 sigma error on density (from just the densimeter equation)',
+    'Corrected_Splitting': 'Splitting in cm-1 after correcting for instrument drift',
+    'Corrected_Splitting_σ': '1 sigma error on splitting (combined from peak fitting, Ne correction model)',
+    'Corrected_Splitting_σ_Ne': '1 sigma error on splitting just from Ne correction model',
+    'Corrected_Splitting_σ_peak_fit': '1 sigma error on splitting just from peak fitting',
+    'power (mW)': 'Laser power used in mW measured by WITEC TruPower',
+    'Spectral Center': 'Spectral Center used for analysis',
+    'in range': 'Y or N - Is the corrected splitting within the calibration range of the densimeter?',
+    'Notes': 'Which segment of the densimeter was used (e.g. which of several polynomials)',
+    'LowD_RT': 'Density calculated using the low density part of the Room Temp densimeter',
+    'HighD_RT': 'Density calculated using the high density part of the Room Temp densimeter',
+    'LowD_SC': 'Density calculated using the low density segment of the 37C densimeter',
+    'LowD_SC_σ': 'Error on density calculated using the low density segment of the 37C densimeter',
+    'MedD_RC': 'Density calculated using the medium density segment of the 37C densimeter',
+    'MedD_SC_σ': 'Error on density calculated using the medium density segment of the 37C densimeter',
+    'HighD_SC': 'Density calculated using the high density segment of the 37C densimeter',
+    'HighD_SC_σ': 'Error on density calculated using the high density segment of the 37C densimeter',
+    'Temperature': 'User entered Temp description: SupCrit or RoomT ',
+    'Splitting': 'Distance between fitted peak centers of Diad 1 and Diad 2 (cm-1)',
+    'Split_σ': 'Error on splitting',
+    'Diad1_Combofit_Cent': 'Fitted peak center (cm-1) of Diad1 (combined fit of diad, HB, gaussian background etc. )',
+    'Diad1_cent_err': 'Error on peak center of Diad1 (cm-1, calculated using lmfit)',
+    'Diad1_Combofit_Height': 'Height (intensity) of Diad1 combined fit',
+    'Diad1_Voigt_Cent': 'Fitted peak center (cm-1) of Diad1 for just the main peak',
+    'Diad1_Voigt_Area': 'Fitted area of Diad1 for just the main peak',
+    'Diad1_Voigt_Sigma': 'Fitted sigma of Diad1 for just the main peak',
+    'Diad1_Residual': 'Residual of fit to Diad1 (see DiadFit paper for explanation)',
+    'Diad1_Prop_Lor': 'Proportion of Lorentzian in Psuedovoigt peak for Diad1',
+    'Diad1_fwhm': 'Full Width Half Maximum of the fit to Diad1',
+    'Diad1_refit': 'Notes any warnings that flagged during iterative fitting',
+    'Diad2_Combofit_Cent': 'Fitted peak center (cm-1) of Diad2 (combined fit of diad, HB, gaussian background etc. )',
+    'Diad2_cent_err': 'Error on peak center of Diad2 (cm-1, calculated using lmfit)',
+    'Diad2_Combofit_Height': 'Height (intensity) of Diad2 combined fit',
+    'Diad2_Voigt_Cent': 'Fitted peak center (cm-1) of Diad2 for just the main peak',
+    'Diad2_Voigt_Area': 'Fitted area of Diad2 for just the main peak',
+    'Diad2_Voigt_Sigma': 'Fitted sigma of Diad2 for just the main peak',
+    'Diad2_Residual': 'Residual of fit to Diad2 (see DiadFit paper for explanation)',
+    'Diad2_Prop_Lor': 'Proportion of Lorentzian in Psuedovoigt peak for Diad2',
+    'Diad2_fwhm': 'Full Width Half Maximum of the fit to Diad2',
+    'Diad2_refit': 'Notes any warnings that flagged during iterative fitting',
+    'HB1_Cent': 'Fitted peak center of HB1 (cm-1)',
+    'HB1_Area': 'Fitted area of HB1',
+    'HB1_Sigma': 'Fitted sigma of HB1',
+    'HB2_Cent': 'Fitted peak center of HB2 (cm-1)',
+    'HB2_Area': 'Fitted area of HB2',
+    'HB2_Sigma': 'Fitted sigma of HB2',
+    'C13_Cent':  'Fitted peak center of the C13 peak (cm-1)',
+    'C13_Area': 'Fitted area of the C13 peak',
+    'C13_Sigma': 'Fitted sigma of the C13 peak',
+    'Diad2_Gauss_Cent': 'Fitted peak center (cm-1) of the Gaussian background on Diad2 (if used)',
+    'Diad2_Gauss_Area': 'Fitted area of the Gaussian background on Diad2',
+    'Diad2_Gauss_Sigma': 'Fitted sigma of the Gaussian backgroun on Diad2',
+    'Diad1_Gauss_Cent': 'Fitted peak center (cm-1) of the Gaussian background on Diad1 (if used)',
+    'Diad1_Gauss_Area': 'Fitted area of the Gaussian background on Diad1',
+    'Diad1_Gauss_Sigma': 'Fitted sigma of the Gaussian backgroun on Diad1',
+    'Diad1_Asym50': 'Asymmetry of Diad1 using a 50% intensity cut off (see DeVitre et al. 2023, Volcanica)',
+    'Diad1_Asym70': 'Asymmetry of Diad1 using a 70% intensity cut off (see DeVitre et al. 2023, Volcanica)',
+    'Diad1_Yuan2017_sym_factor': 'Symmetry factor of Diad1 following Yuan 2017',
+    'Diad1_Remigi2021_BSF': 'BSF factor of Diad1 following Remigi (2021)',
+    'Diad2_Asym50': 'Asymmetry of Diad2 using a 50% intensity cut off (see DeVitre et al. 2023, Volcanica)',
+    'Diad2_Asym70': 'Asymmetry of Diad2 using a 70% intensity cut off (see DeVitre et al. 2023, Volcanica)',
+    'Diad2_Yuan2017_sym_factor': 'Symmetry factor of Diad2 following Yuan 2017',
+    'Diad2_Remigi2021_BSF': 'BSF factor of Diad2 following Remigi (2021)',
+    'Diad1_PDF_Model': 'Name of the probability density function used to fit Diad1',
+    'Diad2_PDF_Model': 'Name of the probability density function used to fit Diad2',
+    'Standard': 'Is the analysis a standard (Yes/No)',
+    'date': 'Full date of analysis',
+    'Month': 'Month of analysis',
+    'Day': 'Day of the week of analysis',
+    'Int_time (s)': 'Integration time of each individual spectra in s',
+    'accumulations':'How many individual spectra are collected and averaged for a single reported spectra',
+    'Mag (X)': 'Objective used during analysis',
+    'duration': 'Duration of analysis as a string from WITEC',
+    '24hr_time': 'Time converted to a 24 hr clock',
+    'sec since midnight': 'time of acquisition as seconds after midnight on the day of analysis',
+    'Peak_Cent_SO2': 'Fitted peak center (cm-1) of the SO2 peak',
+    'Peak_Area_SO2': 'Fitted peak area (cm-1) of the SO2 peak',
+    'Peak_Height_SO2':  'Fitted peak height (cm-1) of the SO2 peak',
+    'Model_name_x': 'Model used to fit the SO2 peak',
+    'Peak_Cent_Carb': 'Fitted peak center (cm-1) of the Carb peak',
+    'Peak_Area_Carb': 'Fitted peak area (cm-1) of the Carb peak',
+    'Peak_Height_Carb':  'Fitted peak height (cm-1) of the Carb peak',
+    'Model_name_y': 'Model used to fit the SO2 peak',
+    'Carb_Diad_Ratio': 'Area of carbonate peak divided by sum of area of Diad1 and Diad2 ',
+    'SO2_Diad_Ratio': 'Area of the SO2 peak divided by sum of area of Diad1 and Diad2',
+    'SO2_mol_ratio': 'Molar proportion of SO2 in the gas species',
+    'time': 'seconds after midnight used for Ne correction ',
+    'preferred_values': 'Preferred value for Ne correction',
+    'lower_values': 'Preferred value - 1 sigma for Ne correction',
+    'upper_values': 'Preferred value + 1 sigma for Ne correction',
+   
+    'SingleCalc_D_km': 'Depth calculated using the preferred (average) value for the input parameters of the MC simulation',
+    'SingleCalc_P_kbar': 'Pressure calculated using the preferred (average) value for the input parameters of the MC simulation',    
+    'Mean_MC_P_kbar': 'Mean pressure calculated by averaging all the MC simulations for a single FI',
+    'Med_MC_P_kbar':'Median pressure calculated by averaging all the MC simulations for a single FI',
+    'std_dev_MC_P_kbar':'Std deviation of pressure calculated from all the MC simulations for a single FI',
+    'std_dev_MC_P_kbar_from_percentile':'Std deviation of pressure calculated from 84th-16th quantile/2 calculated from all the MC simulations for a single FI',
+    'Mean_MC_D_km': 'Mean depth calculated by averaging all the MC simulations for a single FI',
+    'Med_MC_D_km':'Median depth calculated by averaging all the MC simulations for a single FI',
+    'std_dev_MC_D_km':'Std deviation of depth calculated from all the MC simulations for a single FI',
+    'std_dev_MC_D_km_from_percentile':'Std deviation of depth calculated from 84th-16th quantile/2 calculated from all the MC simulations for a single FI',
+    'error_T_K': 'Input error in K for the Monte Carlo simulation',
+    'CO2_dens_gcm3_input': 'Input CO2 content in g/cm3 for the Monte Carlo simulation',
+    'error_CO2_dens_gcm3': 'Input CO2  error in g/cm3 for the Monte Carlo simulation',
+    'crust_dens_kgm3_input': 'Selected crustal density for the Monte Carlo simulation',
+    'error_crust_dens_kgm3':'Input crustal density error for the Monte Carlo simulation',
+    'model': 'Selected model to convert pressure to depth in the crust',
+    'EOS': 'Selected EOS to convert density to pressure'
+    
+    }
+    
+    # Create a list of descriptions based on the lookup key
+    description_row = [lookup_key.get(col, '') for col in df.columns]
+    
+    # Create a new DataFrame from the description row
+    description_df = pd.DataFrame([description_row], columns=df.columns)
+    
+    # Use pd.concat to combine the description row and original DataFrame
+    df_with_descriptions = pd.concat([description_df, df], ignore_index=True)
+    
+    # Display the DataFrame with descriptions
+    df_with_descriptions
+    
+    return df_with_descriptions
+
+           
 
 
 

DiadFit/molar_gas_proportions.py

@@ -1,87 +1,231 @@
 import math
 import pandas as pd
+import numpy as np
+
+
+
+
+
+
+# def calculate_sigma(wavelength, vi_dict, T_K):
+#     """
+#     This function calculates the σ cross section according to wavelength based on Burke (2001) EQ(1), you must provide:
+# ### 1) the peak shift of the species, 2) temp (doesn't really matter) and 3) Σ (wavelength-independent relative Raman scattering cross-sections).
+#     """
+#     c = 2.998 * 10**10  # cm/s light speed
+#     h = 6.626 * 10**-27  # erg.s Planck constant
+#     k = 1.381 * 10**-16  # erg/K Boltzmann's constant
+#
+#     v0 = 1 / (wavelength * 10**-7)
+#
+#     sigma_results = {}
+#     for name, vi_info in vi_dict.items():
+#         vi = vi_info["Peak_shift_cm-1"]
+#         BigSigma = vi_info["Σ"]
+#
+#         result = BigSigma / (((v0 - vi)**-4 / (v0 - 2331)**-4) * (1 - math.exp(-h * c * vi / (k * T_K))))
+#         sigma_results[name] = round(result, 2)
+#
+#     return sigma_results
+#
+#
+#
+#
+# def calculate_mole_percent(components):
+#     """ This function calculates the mole percents of the components entered, based on Burke (2001) EQ(2)
+#     """
+#     def partial_molec_contribution_single(A, sigma, squiggle):
+#         return A / (sigma * squiggle)
+#
+#     def partial_molec_contribution_double(A1, sigma1, A2, sigma2, squiggle):
+#         return (A1 + A2) / ((sigma1 + sigma2) * squiggle)
+#
+#     total_partials = 0
+#     partials = []
+#
+#     for component in components:
+#         if component['name'] == 'CO2':
+#             partial = partial_molec_contribution_double(component['peak_area_1'], component['cross_section_1'],
+#                                                        component['peak_area_2'], component['cross_section_2'],
+#                                                        component['efficiency'])
+#         else:
+#             partial = partial_molec_contribution_single(component['peak_area'], component['cross_section'],
+#                                                         component['efficiency'])
+#
+#         partials.append(partial)
+#         total_partials += partial
+#
+#     mole_percentages = [round((partial / total_partials) * 100, 1) for partial in partials]
+#
+#     mole_percent_dict = {component['name']: mole_percent for component, mole_percent in zip(components, mole_percentages)}
+#     mole_percent_dict['Mole_Percent_Sum'] = sum(mole_percentages)
+#
+#     return mole_percent_dict
+
+
+#
+#
+# def calculate_CO2_SO2_ratio(*, peak_area_SO2, peak_area_diad1, peak_area_diad2,wavelength=532.067, T_K=37+273.15,efficiency_SO2=1, efficiency_CO2=0.5, sigma_SO2=4.03, sigma_CO2_v1=0.8, sigma_CO2_v2=1.23):
+#
+#   # First we need to calculate the oarameters
+#
+#   component_dict = {
+#     "SO2": {"Peak_shift_cm-1": 1151, "Σ": sigma_SO2},
+#     "CO2_v1": {"Peak_shift_cm-1": 1285, "Σ": sigma_CO2_v1},
+#     "CO2_2v2": {"Peak_shift_cm-1": 1388, "Σ": sigma_CO2_v2}}
+# ### "Σ" is the wavelength independent relative cross-section
+#
+#   sigma_results = calculate_sigma(wavelength=wavelength, vi_dict=component_dict, T_K=T_K)
+#
+#     # Now lets allocate these calculations
+#   components = [
+#         {'name': 'SO2',
+#         'peak_area': peak_area_SO2,
+#         'cross_section':  sigma_results['SO2'],
+#         'efficiency': efficiency_SO2},
+#         {'name': 'CO2',
+#           'peak_area_1':peak_area_diad2, 'cross_section_1': sigma_results['CO2_2v2'],
+#         'peak_area_2': peak_area_diad1, 'cross_section_2': sigma_results['CO2_v1'], 'efficiency': efficiency_CO2}
+#     ]
+#   mol_perc=calculate_mole_percent(components)
+#
+#
+#   return pd.DataFrame(mol_perc)
+
+
+
+  ## Math for converting back and forth between Raman scattering cross sections
+
+def calculate_wavelength_dependent_cross_section(wavelength_nm, T_C, Raman_shift_cm, wavelength_independent_cross_section ):
+    """ This function calculates the wavelength dependent cross section (lower case sigma) from the wavelength independent Raman scattering efficiency (Upper case sigma)
+
+      Parameters
+       ----------------
+        wavelength_nm:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
+
+        wavelength_independent_cross_section:
+            Wavelength independent cross section
+
+        T_K:
+            absolute temperature in Kelvin
+
+        Raman_shift_cm:
+            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
+
+        Returns
+        -----------------
+        Wavelength dependent cross section
+
+          """
+    Wavelength_cm1=1/wavelength_nm*10000000
+    constant =1-np.exp(((-6.626*10**-27)*(2.998*10**10)*Raman_shift_cm)/((1.381*10**-16)*(273.15+T_C)))
+    Wavelength_dependent = wavelength_independent_cross_section/(((Wavelength_cm1-Raman_shift_cm)**(-4)/(Wavelength_cm1-2331)**(-4))*constant)
+    return Wavelength_dependent
+
+def calculate_wavelength_independent_cross_section(wavelength_nm, T_C, Raman_shift_cm, wavelength_dependent_cross_section ):
+    """ This function calculates the wavelength independent cross section (capital Sigma) from the wavelength dependent Raman scattering efficiency (lower case sigma)
+
+      Parameters
+       ----------------
+        wavelength_nm:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
+
+        wavelength_dependent_cross_section:
+            Wavelength dependent cross section
+
+        T_K:
+            absolute temperature in Kelvin
+
+        Raman_shift_cm:
+            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
+
+        Returns
+        -----------------
+        Wavelength independent cross section
+
+          """
+    Wavelength_cm1=1/wavelength_nm*10000000
+    constant =1-np.exp(((-6.626*10**-27)*(2.998*10**10)*Raman_shift_cm)/((1.381*10**-16)*(273.15+T_C)))
+    Wavelength_independent = wavelength_dependent_cross_section*((Wavelength_cm1-Raman_shift_cm)**(-4)/(Wavelength_cm1-2331)**(-4)*constant)
+    return Wavelength_independent
 
-def calculate_sigma(wavelength, vi_dict, T_K):
-    """
-    This function calculates the σ cross section according to wavelength based on Burke (2001) EQ(1), you must provide:
-### 1) the peak shift of the species, 2) temp (doesn't really matter) and 3) Σ (wavelength-independent relative Raman scattering cross-sections).
-    """
-    c = 2.998 * 10**10  # cm/s light speed
-    h = 6.626 * 10**-27  # erg.s Planck constant
-    k = 1.381 * 10**-16  # erg/K Boltzmann's constant
+def convert_cross_section_wavelength1_wavelength2(wavelength_nm_1,wavelength_nm_2,  Raman_shift_cm, wavelength_dependent_cross_section_wavelength1, T_C):
+   """ This function calculates the wavelength dependent cross section (lower case sigma) for laser wavelength 2 from the wavelength-dependent cross section for laser wavelength 1.
 
-    v0 = 1 / (wavelength * 10**-7)
 
-    sigma_results = {}
-    for name, vi_info in vi_dict.items():
-        vi = vi_info["Peak_shift_cm-1"]
-        BigSigma = vi_info["Σ"]
+      Parameters
+       ----------------
+        wavelength_nm_1:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
 
-        result = BigSigma / (((v0 - vi)**-4 / (v0 - 2331)**-4) * (1 - math.exp(-h * c * vi / (k * T_K))))
-        sigma_results[name] = round(result, 2)
+        wavelength_nm_2:
+            laser wavelength of the system of interest you are trying to calculate the wavelength dependent cross section for
 
-    return sigma_results
+        wavelength_dependent_cross_section_wavelength1:
+            Wavelength dependent cross section
 
+        T_K:
+            absolute temperature in Kelvin
 
+        Raman_shift_cm:
+            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
 
+        Returns
+        -----------------
+        Wavelength dependent cross section for wavelength2
 
-def calculate_mole_percent(components):
-    """ This function calculates the mole percents of the components entered, based on Burke (2001) EQ(2)
-    """
-    def partial_molec_contribution_single(A, sigma, squiggle):
-        return A / (sigma * squiggle)
+          """
+
+   # First calculate the independent cross section
+   ind_cross_sec=calculate_wavelength_independent_cross_section(wavelength_nm=wavelength_nm_1, T_C=T_C, Raman_shift_cm=Raman_shift_cm,
+                                                         wavelength_dependent_cross_section =wavelength_dependent_cross_section_wavelength1)
+   print(ind_cross_sec)
+   dep_cross_sec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm_2, T_C=T_C, Raman_shift_cm=Raman_shift_cm, wavelength_independent_cross_section =ind_cross_sec)
+
+   return dep_cross_sec
 
-    def partial_molec_contribution_double(A1, sigma1, A2, sigma2, squiggle):
-        return (A1 + A2) / ((sigma1 + sigma2) * squiggle)
+def calculate_SO2_CO2_mol_prop_wave_indep(SO2_wavelength_ind, CO2_diad1_wavelength_ind, CO2_diad2_wavelength_ind, wavelength_nm, T_C,
+                               A_SO2, A_CO2_Tot):
+    """ Takes wavelength independnet cross sections and CO2 and SO2 peak areas and converts them into SO2 mol proportions
+    Parameters
+    ------------------
 
-    total_partials = 0
-    partials = []
+    SO2_wavelength_ind: Wavelength independent cross section for SO2
 
-    for component in components:
-        if component['name'] == 'CO2':
-            partial = partial_molec_contribution_double(component['peak_area_1'], component['cross_section_1'],
-                                                       component['peak_area_2'], component['cross_section_2'],
-                                                       component['efficiency'])
-        else:
-            partial = partial_molec_contribution_single(component['peak_area'], component['cross_section'],
-                                                        component['efficiency'])
+    CO2_diad1_wavelength_ind: Wavelength independent cross section for diad 1 (at 1285)
 
-        partials.append(partial)
-        total_partials += partial
+    CO2_diad2_wavelength_ind: Wavelength independent cross section for diad 2 (at 1388)
 
-    mole_percentages = [round((partial / total_partials) * 100, 1) for partial in partials]
+    wavelength_nm: Laser wavelenth of system in nm
 
-    mole_percent_dict = {component['name']: mole_percent for component, mole_percent in zip(components, mole_percentages)}
-    mole_percent_dict['Mole_Percent_Sum'] = sum(mole_percentages)
+    T_C: Temperature of analysis in C.
 
-    return mole_percent_dict
+    Returns
+    ---------------
+
+    SO2 mol proportion
+
+
+    """
 
+    SO2_cross_sec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm, T_C=T_C, Raman_shift_cm=1151, wavelength_independent_cross_section=SO2_wavelength_ind)
+    CO2_diad1_xsec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm, T_C=T_C, Raman_shift_cm=1285, wavelength_independent_cross_section=CO2_diad1_wavelength_ind)
+    CO2_diad2_xsec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm, T_C=T_C, Raman_shift_cm=1388, wavelength_independent_cross_section=CO2_diad2_wavelength_ind)
 
 
+    SO2_prop=(A_SO2/SO2_cross_sec)/(A_CO2_Tot /(CO2_diad1_xsec + CO2_diad2_xsec) +  (A_SO2/SO2_cross_sec) )
 
-def calculate_CO2_SO2_ratio(*, peak_area_SO2, peak_area_diad1, peak_area_diad2,wavelength=532.067, T_K=37+273.15,efficiency_SO2=1, efficiency_CO2=0.5, sigma_SO2=4.03, sigma_CO2_v1=0.8, sigma_CO2_v2=1.23):
+    return SO2_prop
 
-  # First we need to calculate the oarameters
 
-  component_dict = {
-    "SO2": {"Peak_shift_cm-1": 1151, "Σ": sigma_SO2},
-    "CO2_v1": {"Peak_shift_cm-1": 1285, "Σ": sigma_CO2_v1},
-    "CO2_2v2": {"Peak_shift_cm-1": 1388, "Σ": sigma_CO2_v2}}
-### "Σ" is the wavelength independent relative cross-section
+def calculate_SO2_CO2_ratio(SO2_area, diad1_area, diad2_area, SO2_cross_sec=5.3, diad1_cross_sec=0.89, diad2_cross_sec=1.4):
+    """ Calculates SO2:CO2 ratio using the parameters from Marie-Camille Caumons lab"""
 
-  sigma_results = calculate_sigma(wavelength=wavelength, vi_dict=component_dict, T_K=T_K)
 
-    # Now lets allocate these calculations
-  components = [
-        {'name': 'SO2',
-        'peak_area': peak_area_SO2,
-        'cross_section':  sigma_results['SO2'],
-        'efficiency': efficiency_SO2},
-        {'name': 'CO2',
-          'peak_area_1':peak_area_diad2, 'cross_section_1': sigma_results['CO2_2v2'],
-        'peak_area_2': peak_area_diad1, 'cross_section_2': sigma_results['CO2_v1'], 'efficiency': efficiency_CO2}
-    ]
-  mol_perc=calculate_mole_percent(components)
+    A_CO2_star=( diad1_area + diad2_area)/(diad2_cross_sec+diad1_cross_sec)
+    A_SO2_star=(SO2_area)/(SO2_cross_sec)
+    Ratio=A_SO2_star/(A_SO2_star+A_CO2_star)
 
+    return Ratio
 
-  return pd.DataFrame(mol_perc)

DiadFit/ne_lines.py

@@ -348,6 +348,11 @@ def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
     
     Intensity=np.array([
     
+    
+    
+    
+    
+    
     1500,
     12,
     500,