DiadFit 1.0.2__py3-none-any.whl → 1.0.8__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

@@ -1,5 +1,6 @@
 import math
 import pandas as pd
+import numpy as np
 
 def calculate_sigma(wavelength, vi_dict, T_K):
     """
@@ -85,3 +86,98 @@ def calculate_CO2_SO2_ratio(*, peak_area_SO2, peak_area_diad1, peak_area_diad2,w
 
 
   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 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.
+
+
+      Parameters
+       ----------------
+        wavelength_nm_1:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
+
+        wavelength_nm_2:
+            laser wavelength of the system of interest you are trying to calculate the wavelength dependent cross section for
+
+        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
+
+          """
+
+   # 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
+
+

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,
@@ -1531,9 +1536,9 @@ plot_figure=True, loop=True,
                          
     df_combo=df
     pk1_peak_cent_values = df_combo['pk1_peak_cent'].values
-    pk1_peak_cent_errors = df_combo['error_pk1'].fillna(0).values
+    pk1_peak_cent_errors = df_combo['error_pk1'].fillna(0).infer_objects().values
     pk2_peak_cent_values = df_combo['pk2_peak_cent'].values
-    pk2_peak_cent_errors = df_combo['error_pk2'].fillna(0).values
+    pk2_peak_cent_errors = df_combo['error_pk2'].fillna(0).infer_objects().values
     
     constant=df_combo['deltaNe']
     
@@ -1568,7 +1573,7 @@ def plot_Ne_corrections(df=None, x_axis=None, x_label='index', marker='o', mec='
 
     # Pk1 center vs. X
 
-    ax5.errorbar(x, df['pk1_peak_cent'], xerr=0, yerr=df['error_pk1'].fillna(0),
+    ax5.errorbar(x, df['pk1_peak_cent'], xerr=0, yerr=df['error_pk1'].fillna(0).infer_objects(),
              fmt='o', ecolor='k', elinewidth=0.8, mfc='b', ms=5, mec='k', capsize=3)
     ax5.set_xlabel(x_label)
     ax5.set_ylabel('Peak 1 center')
@@ -1576,15 +1581,15 @@ def plot_Ne_corrections(df=None, x_axis=None, x_label='index', marker='o', mec='
     # Pk2 center vs. X
              
     ax6.plot(x, df['pk2_peak_cent'], marker,  mec='k', mfc='r')
-    ax6.errorbar(x, df['pk2_peak_cent'], xerr=0, yerr=df['error_pk2'].fillna(0),
+    ax6.errorbar(x, df['pk2_peak_cent'], xerr=0, yerr=df['error_pk2'].fillna(0).infer_objects(),
              fmt='o', ecolor='k', elinewidth=0.8, mfc='r', ms=5, mec='k', capsize=3)
     
     ax6.set_xlabel(x_label)
     ax6.set_ylabel('Peak 2 center')
     
     # 
-    ax3.errorbar(df['Ne_Corr'], df['pk2_peak_cent'], xerr=df['1σ_Ne_Corr'].fillna(0), 
-    yerr=df['error_pk2'].fillna(0),
+    ax3.errorbar(df['Ne_Corr'], df['pk2_peak_cent'], xerr=df['1σ_Ne_Corr'].fillna(0).infer_objects(), 
+    yerr=df['error_pk2'].fillna(0).infer_objects(),
              fmt='o', ecolor='k', elinewidth=0.8, mfc='b', ms=5, mec='k', capsize=3)
              
              
@@ -1592,14 +1597,14 @@ def plot_Ne_corrections(df=None, x_axis=None, x_label='index', marker='o', mec='
     ax3.set_ylabel('Peak 2 center')
 
 
-    ax4.errorbar(df['Ne_Corr'], df['pk1_peak_cent'], xerr=df['1σ_Ne_Corr'].fillna(0), 
-    yerr=df['error_pk1'].fillna(0),
+    ax4.errorbar(df['Ne_Corr'], df['pk1_peak_cent'], xerr=df['1σ_Ne_Corr'].fillna(0).infer_objects(), 
+    yerr=df['error_pk1'].fillna(0).infer_objects(),
              fmt='o', ecolor='k', elinewidth=0.8, mfc='b', ms=5, mec='k', capsize=3)
     ax4.set_xlabel('Ne Correction factor')
     ax4.set_ylabel('Peak 1 center')
     
     # Ne correction factor vs. time
-    ax1.errorbar(x, df['Ne_Corr'], xerr=0, yerr=df['1σ_Ne_Corr'].fillna(0),
+    ax1.errorbar(x, df['Ne_Corr'], xerr=0, yerr=df['1σ_Ne_Corr'].fillna(0).infer_objects(),
              fmt='o', ecolor='k', elinewidth=0.8, mfc='grey', ms=5, mec='k',capsize=3)
     
     ax1.set_ylabel('Ne Correction factor')