DiadFit 0.0.80__tar.gz → 0.0.83__tar.gz

{DiadFit-0.0.80 → DiadFit-0.0.83}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 0.0.80
+Version: 0.0.83
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

{DiadFit-0.0.80 → DiadFit-0.0.83}/setup.py

@@ -31,11 +31,11 @@ setup(
     },
     install_requires=[
             'pandas',
-            'numpy',
+            'numpy<2',
             'matplotlib',
             'scikit-learn',
             'scipy',
-            'lmfit',
+            'lmfit>=1.1.0',
             'tqdm',
             'python-docx'
             ],

{DiadFit-0.0.80 → DiadFit-0.0.83}/src/DiadFit/CO2_EOS.py

@@ -19,7 +19,7 @@ DiadFit_dir=Path(__file__).parent
 
 def calculate_CO2_density_homog_T(T_h_C, EOS='SW96', Sample_ID=None, homog_to=None, set_to_critical=False):
     """ Calculates CO2 density for a specified homogenization temperature in Celcius
-    using the Span and Wanger (1996) equation of state.
+    using eq 3.14 and 3.15 from the Span and Wanger (1996) equation of state.
 
     Parameters
     --------------
@@ -52,18 +52,28 @@ def calculate_CO2_density_homog_T(T_h_C, EOS='SW96', Sample_ID=None, homog_to=No
         else:
             raise TypeError('unsupported input for homog_to, has to be L or V')
 
+
+    # IF its a float or integer, just tell people outright
     if isinstance(T_h_C, float) or isinstance(T_h_C, int):
         if T_h_C>=30.9782: # 29.878:
         #print('Sorry, algorithm cant converge for Ts above 29.878')
-            raise TypeError('Sorry, algorithm cant converge for Ts above 30.9782')
+            raise TypeError('Sorry, algorithm cant converge for T_h_C above 30.9782')
+
+    # If its a panda series, set critical is false, raise a type error
     if isinstance(T_h_C, pd.Series) or isinstance(T_h_C, np.ndarray):
-        if any(T_h_C)>=30.9782 and set_to_critical is False:
+
+        if any(T_h_C>=30.9782) and set_to_critical is False:
             raise TypeError('Sorry, algorithm cant converge for Ts above 30.9782. You can put set_to_critical=True and this T_ will be replacd with 30.9782')
-        elif any(T_h_C)>=30.9782 and set_to_critical is True:
+        elif any(T_h_C>=30.9782) and set_to_critical is True:
+            print('found some with too high temps, are setting to 30.9782C - the max homog T ')
             if isinstance(T_h_C, pd.Series):
                 T_h_C = np.where(T_h_C > 30.9782, 30.9782, T_h_C)
             elif isinstance(T_h_C, np.ndarray):
+
                 T_h_C[T_h_C > 30.9782] = 30.9782
+                print('got into this loop')
+
+
 
 
     if EOS!='SW96':
@@ -72,7 +82,10 @@ def calculate_CO2_density_homog_T(T_h_C, EOS='SW96', Sample_ID=None, homog_to=No
     T_K_hom=T_h_C+273.15
     TempTerm=1-T_K_hom/304.1282
     # This is equation 3.14 from Span and Wanger (1996)
+
+
     Liq_density=(np.exp(1.9245108*TempTerm**0.34-0.62385555*TempTerm**0.5-0.32731127*TempTerm**1.6666667+0.39245142*TempTerm**1.8333333)*0.4676)
+
     # This is equation 3.15 from Span and Wanger (1996)
     gas_density=(np.exp(-1.7074879*TempTerm**0.34-0.8227467*TempTerm**0.5-4.6008549*TempTerm**1-10.111178*TempTerm**2.333333-29.742252*TempTerm**4.6666667)*0.4676)
 
@@ -473,12 +486,6 @@ def calculate_P_for_rho_T_SW96(CO2_dens_gcm3, T_K):
     except ImportError:
         raise RuntimeError('You havent installed CoolProp, which is required to convert FI densities to pressures. If you have python through conda, run conda install -c conda-forge coolprop in your command line')
 
-    try:
-        import CoolProp.CoolProp as cp
-    except ImportError:
-        raise RuntimeError('You havent installed CoolProp, which is required to convert FI densities to pressures. If you have python through conda, run conda install -c conda-forge coolprop in your command line')
-
-
 
     P_kbar=cp.PropsSI('P', 'D', Density_kgm3, 'T', T_K, 'CO2')/10**8
     if isinstance(P_kbar, float):

{DiadFit-0.0.80 → DiadFit-0.0.83}/src/DiadFit/CO2_H2O_EOS.py

@@ -1022,7 +1022,7 @@ def calc_prop_knownP_EOS_DZ2006(*, P_kbar=1, T_K=1200, XH2O=1):
 
 
 
-def calculate_entrapment_P_XH2O(*, XH2O, CO2_dens_gcm3, T_K):
+def calculate_entrapment_P_XH2O(*, XH2O, CO2_dens_gcm3, T_K, T_K_ambient=37+273.15, fast_calcs=False, Hloss=True):
     """" This function calculates pressure for a measured CO$_2$ density, temperature and estimate of initial XH2O.
     It first corrects the density to obtain a bulk density for a CO2-H2O mix, assuming that H2O was lost from the inclusion.
     correcting for XH2O. It assumes that H2O has been lost from the inclusion (see Hansteen and Klugel, 2008 for method). It also calculates using other
@@ -1037,47 +1037,131 @@ def calculate_entrapment_P_XH2O(*, XH2O, CO2_dens_gcm3, T_K):
         Measured CO2 density in g/cm3
 
     T_K: float, pd.Series
-        Temperature in Kelvin.
+        Temperature in Kelvin fluid was trapped at
+
+    T_K_ambient: pd.Series
+        Temperature in Kelvin Raman measurement was made at.
+
+    fast_calcs: bool (default False)
+        If True, only performs one EOS calc for DZ06, not 4 (with water, without water, SP94 and SW96).
+        also specify H2Oloss=True or False
+
+
 
     Returns
     -----------------------------
+    if fast_calcs is False:
     pd.DataFrame:
         Columns showing:
         P_kbar_pureCO2_SW96: Pressure calculated for the measured CO$_2$ density using the pure CO2 EOS from Span and Wanger (1996)
         P_kbar_pureCO2_SP94: Pressure calculated for the measured CO$_2$ density using the pure CO2 EOS from Sterner and Pitzer (1994)
         P_kbar_pureCO2_DZ06: Pressure calculated from the measured CO$_2$ density using the pure CO2 EOs from Duan and Zhang (2006)
-        P_kbar_mixCO2_DZ06: Pressure calculated from the reconstructed mixed fluid density using the mixed EOS from Duan and Zhang (2006)
-        P Mix/P Pure DZ06: Correction factor - e.g. how much deeper the pressure is from the mixed EOS
-        rho_mix_calc: Bulk density calculated (C+H) at time of entrapment
+        P_kbar_mixCO2_DZ06_Hloss: Pressure calculated from the reconstructed mixed fluid density using the mixed EOS from Duan and Zhang (2006) assuming H loss
+        P_kbar_mixCO2_DZ06_noHloss: Pressure calculated from the reconstructed mixed fluid density using the mixed EOS from Duan and Zhang (2006) assuming H loss
+        P Mix_Hloss/P Pure DZ06: Correction factor - e.g. how much deeper the pressure is from the mixed EOS with H loss
+        P Mix_noHloss/P Pure DZ06: Correction factor - e.g. how much deeper the pressure is from the mixed EOS with H loss
+        rho_mix_calc_noHloss: Bulk density calculated (C+H)
+        rho_mix_calc_Hloss: Bulk density calculated (C+H) after h loss
         CO2_dens_gcm3: Input CO2 density
         T_K: input temperature
         XH2O: input molar fraction of H2O
 
+    if fast_calcs is True:
+        P_kbar_mixCO2_DZ06: Pressure calculated from the reconstructed mixed fluid density using the mixed EOS from Duan and Zhang (2006)
+
+
+
     """
     XH2O, rho_meas, T_K=ensure_series(a=XH2O, b=CO2_dens_gcm3, c=T_K)
     alpha=XH2O/(1-XH2O)
-    # This gets the bulk density of the CO2-H2O fluid
-    rho_orig=rho_meas*(1+alpha*(18/44))
-    # Lets calculate the pressure using SW96
-    P_SW=calculate_P_for_rho_T(T_K=T_K, CO2_dens_gcm3=rho_meas, EOS='SW96')
-    P_SP=calculate_P_for_rho_T(T_K=T_K, CO2_dens_gcm3=rho_meas, EOS='SP94')
-    # Same for DZ2006
-    P_DZ=calculate_Pressure_DZ2006(density=rho_meas, T_K=T_K, XH2O=XH2O*0)
-    # Now doing it with XH2O
-    P_DZ_mix=calculate_Pressure_DZ2006(density=rho_orig, T_K=T_K, XH2O=XH2O)
-
-    df=pd.DataFrame(data={
-        'P_kbar_pureCO2_SW96': P_SW['P_kbar'],
-        'P_kbar_pureCO2_SP94': P_SW['P_kbar'],
-        'P_kbar_pureCO2_DZ06': P_DZ/1000,
-        'P_kbar_mixCO2_DZ06': P_DZ_mix/1000,
-        'P Mix/P Pure DZ06': P_DZ_mix/P_DZ,
-        'rho_mix_calc': rho_orig,
-        'CO2_dens_gcm3': rho_meas,
-        'T_K': T_K,
-        'XH2O': XH2O})
+    # IF water is lost
+    rho_orig_H_loss=rho_meas*(1+alpha*(18/44))
+    # IF water isnt lost
 
-    return df
+    # Calculate mass ratio from molar ratio
+    mass_ratio=(XH2O*18)/((1-XH2O)*44)
+    # Calculate pressure in CO2 fluid
+    P=calculate_P_for_rho_T_SW96(CO2_dens_gcm3, T_K_ambient)
+    # Now calculate density of H2O fluid
+
+    # Calculate density of H2O
+    rho_H2O=calculate_rho_for_P_T_H2O(P['P_kbar'], T_K_ambient)
+
+
+
+    # Assume a system of unit 1. Calculate volume of CO2
+    VolCO2=(1-mass_ratio)/CO2_dens_gcm3
+    VolH2O=mass_ratio/rho_H2O
+    rho_orig_no_H_loss=1/(VolH2O+VolCO2)
+
+    if fast_calcs is True:
+        if Hloss is True:
+            P=calculate_Pressure_DZ2006(density=rho_orig_H_loss, T_K=T_K, XH2O=XH2O)
+        if Hloss is False:
+            P=calculate_Pressure_DZ2006(density=rho_orig_H_loss, T_K=T_K, XH2O=XH2O)
+        return P/1000
+
+    else:
+
+        # Lets calculate the pressure using SW96
+        P_SW=calculate_P_for_rho_T(T_K=T_K, CO2_dens_gcm3=rho_meas, EOS='SW96')
+        P_SP=calculate_P_for_rho_T(T_K=T_K, CO2_dens_gcm3=rho_meas, EOS='SP94')
+        # Same for DZ2006
+        P_DZ=calculate_Pressure_DZ2006(density=rho_meas, T_K=T_K, XH2O=XH2O*0)
+        # Now doing it with XH2O
+        P_DZ_mix_H_loss=calculate_Pressure_DZ2006(density=rho_orig_H_loss, T_K=T_K, XH2O=XH2O)
+        P_DZ_mix_noH_loss=calculate_Pressure_DZ2006(density=rho_orig_no_H_loss, T_K=T_K, XH2O=XH2O)
+
+        df=pd.DataFrame(data={
+            'P_kbar_pureCO2_SW96': P_SW['P_kbar'],
+            'P_kbar_pureCO2_SP94': P_SP['P_kbar'],
+            'P_kbar_pureCO2_DZ06': P_DZ/1000,
+            'P_kbar_mixCO2_DZ06_Hloss': P_DZ_mix_H_loss/1000,
+            'P_kbar_mixCO2_DZ06_no_Hloss': P_DZ_mix_noH_loss/1000,
+            'P Mix_Hloss/P Pure DZ06': P_DZ_mix_H_loss/P_DZ,
+            'P Mix_no_Hloss/P Pure DZ06': P_DZ_mix_noH_loss/P_DZ,
+            'rho_mix_calc_Hloss': rho_orig_H_loss,
+            'rho_mix_calc_noHloss': rho_orig_no_H_loss,
+            'CO2_dens_gcm3': rho_meas,
+            'T_K': T_K,
+            'XH2O': XH2O})
+
+        return df
+
+
+def calculate_rho_for_P_T_H2O(P_kbar, T_K):
+    """ This function calculates H2O density in g/cm3 for a known Pressure (in kbar), a known T (in K) using the Wanger and Pru (2002) EOS from CoolProp
+    doi:10.1063/1.1461829.
+
+    Parameters
+    ---------------------
+    P_kbar: int, float, pd.Series, np.array
+        Pressure in kbar
+
+    T_K: int, float, pd.Series, np.array
+        Temperature in Kelvin
+
+    Returns
+    --------------------
+    pd.Series
+        H2O density in g/cm3
+
+    """
+    if isinstance(P_kbar, pd.Series):
+        P_kbar=np.array(P_kbar)
+    if isinstance(T_K, pd.Series):
+        T_K=np.array(T_K)
+
+    P_Pa=P_kbar*10**8
+
+    try:
+        import CoolProp.CoolProp as cp
+    except ImportError:
+        raise RuntimeError('You havent installed CoolProp, which is required to convert FI densities to pressures. If you have python through conda, run conda install -c conda-forge coolprop in your command line')
+
+    H2O_dens_gcm3=cp.PropsSI('D', 'P', P_Pa, 'T', T_K, 'H2O')/1000
+
+    return pd.Series(H2O_dens_gcm3)
 
 
 

{DiadFit-0.0.80 → DiadFit-0.0.83}/src/DiadFit/H2O_fitting.py

@@ -305,8 +305,8 @@ def make_evaluate_mixed_spectra(*, path, filename, smoothed_host_y, smoothed_MI_
                                X_min=0, X_max=1, plot_figure=True, dpi=200):
 
     """
-    This function unmixes glass and host spectra, and fits the best fit proportion 
-    where the host peak and trough disapears. Specifically, it calculates the mixed spectra by 
+    This function unmixes glass and host spectra, and fits the best fit proportion
+    where the host peak and trough disapears. Specifically, it calculates the mixed spectra by
     taking the measured MI spectra and subtracting X*Ol spectra, where X is the mixing proportions
 
     Parameters
@@ -355,7 +355,7 @@ def make_evaluate_mixed_spectra(*, path, filename, smoothed_host_y, smoothed_MI_
     Dist: float
         Vertical distance between the host peak and trough (in intensity units)
     MI_Mix: np.array
-        Umixed spectra for each of the N_steps
+        Ubmixed spectra for each of the N_steps
     X: np.array
         X coordinates of unmixed spectra (along with MI_Mix and X allows plots of unmixing)
 
@@ -428,7 +428,7 @@ def make_evaluate_mixed_spectra(*, path, filename, smoothed_host_y, smoothed_MI_
         ax3.set_xlim([775, 900])
 
 
-        ax4.plot(MI_spectra[:, 0],MI_Mix_Best[:, 1], '-k', label='Umixed glass')
+        ax4.plot(MI_spectra[:, 0],MI_Mix_Best[:, 1], '-k', label='Unmixed glass')
         ax4.plot(MI_spectra[:, 0],MI_spectra[:, 1],  '-', color='salmon',label='Measured MI')
         ax4.plot(Host_spectra[:, 0],Host_spectra[:, 1], '-', color='g', label='Measured Host')
         ax4.legend()
@@ -456,7 +456,7 @@ override=False, flip=False, plot_figure=True, dpi=200):
     """
     This function checks if the unmixed specta is negative, based on two tie points.
     The first tie point is the mean y coordinate of the peak position of host +5 wavenumbers,
-    and the second tie point (tie_x_cord) is an optional input. If the specta is inverted, 
+    and the second tie point (tie_x_cord) is an optional input. If the specta is inverted,
     this function inverts it.
 
 

{DiadFit-0.0.80 → DiadFit-0.0.83}/src/DiadFit/_version.py

@@ -5,4 +5,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module
-__version__ = '0.0.80'
+__version__ = '0.0.83'

{DiadFit-0.0.80 → DiadFit-0.0.83}/src/DiadFit/cosmicray_filter.py

@@ -102,6 +102,7 @@ def filter_singleray(*,path=None,Diad_files=None,i=None,diad_peaks=None, exclude
 
     file=Diad_files.iloc[i]
     #open the spectrum in form of array
+
     Diad_array=pf.get_data(path=path, filename=file, filetype=filetype)
 
     # Get the intensity of the next and previous pixels
@@ -402,7 +403,7 @@ def filter_singleray(*,path=None,Diad_files=None,i=None,diad_peaks=None, exclude
 
     record=pd.DataFrame([])
     record.loc[file,'filename']=file
-    record.loc[file,'rays_present']=not all_rayswave.empty
+    record.loc[file,'rays_present']=float(not all_rayswave.empty)
 
     if second_pass==True:
         clean_spec_df=pxdf_filt_pass2[['Wavenumber','Intensity']]

{DiadFit-0.0.80 → DiadFit-0.0.83}/src/DiadFit/densimeters.py

@@ -619,8 +619,12 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
 
     df.loc[zero, 'Preferred D']=0
     df.loc[zero, 'Notes']=0
-
-
+    
+    # Get rid of pandas 2 issue with warning of setting item of incompatible dtype
+    df['Preferred D'] = df['Preferred D'].astype('float64', errors='ignore')
+    df['Preferred D_σ'] = df['Preferred D_σ'].astype('float64', errors='ignore')
+    df['Preferred D_σ_split'] = df['Preferred D_σ_split'].astype('float64', errors='ignore')
+    df['Preferred D_σ_dens'] = df['Preferred D_σ_dens'].astype('float64', errors='ignore')
 
 
 
@@ -692,23 +696,39 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
 
 
         
+    # if Ne_pickle_str is not None:
+    #     
+    #     df_merge1=pd.concat([df_combo_c, Ne_corr], axis=1).reset_index(drop=True)
+    # else:
+    #     df_merge1=df
+    # print('df')
+    # print(df['Preferred D'])
+    # print('df_merge1')
+    # print(df_merge1['Preferred D'])
     if Ne_pickle_str is not None:
         df_merge1=pd.concat([df_combo_c, Ne_corr], axis=1).reset_index(drop=True)
+        df_merge=pd.concat([df, df_merge1], axis=1).reset_index(drop=True)
+    elif Ne_pickle_str is None and df_combo is not None:
+        df_merge=pd.concat([df, df_combo_c], axis=1).reset_index(drop=True)
     else:
-        df_merge1=df
+        df_merge=df
+        
+    
 
-    df_merge=pd.concat([df, df_merge1], axis=1).reset_index(drop=True)
+    #df_merge=pd.concat([df, df_merge1], axis=1).reset_index(drop=True)
 
         
     
 
-    df_merge=pd.concat([df, df_merge1], axis=1).reset_index(drop=True)
+   
+    
 
     df_merge = df_merge.rename(columns={'Preferred D': 'Density g/cm3'})
     df_merge = df_merge.rename(columns={'Preferred D_σ': 'σ Density g/cm3'})
     df_merge = df_merge.rename(columns={'Preferred D_σ_split': 'σ Density g/cm3 (from Ne+peakfit)'})
     df_merge = df_merge.rename(columns={'Preferred D_σ_dens': 'σ Density g/cm3 (from densimeter)'})
     df_merge = df_merge.rename(columns={'filename_x': 'filename'})
+    
 
 
     #
@@ -727,6 +747,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
         df_merge = df_merge[cols_to_move + [
             col for col in df_merge.columns if col not in cols_to_move]]
 
+    
 
     return df_merge
 
@@ -968,7 +989,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
         Split=df_combo_c['Splitting']*pref_Ne
 
     else:
-       Split_err=(split_err*Split).astype(float)
+       Split_err=split_err
 
 
 
@@ -1129,6 +1150,14 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
 
     df.loc[zero, 'Preferred D']=0
     df.loc[zero, 'Notes']=0
+    
+    # Assign to the right type to avoid annoying pandas 2 warning
+    # Ensure the columns are of type float64
+    df['Preferred D'] = df['Preferred D'].astype('float64', errors='ignore')
+    df['Preferred D_σ'] = df['Preferred D_σ'].astype('float64', errors='ignore')
+    df['Preferred D_σ_split'] = df['Preferred D_σ_split'].astype('float64', errors='ignore')
+    df['Preferred D_σ_dens'] = df['Preferred D_σ_dens'].astype('float64', errors='ignore')
+    
 
 
 
@@ -1146,7 +1175,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
     df.loc[SupCrit&(min_MD_SC_Split&max_MD_SC_Split), 'Preferred D_σ_split'] = medD_error['MedD_Density_σ_split']
     df.loc[SupCrit&(min_MD_SC_Split&max_MD_SC_Split), 'Preferred D_σ_dens'] = medD_error['MedD_Density_σ_dens']
     df.loc[SupCrit&(min_MD_SC_Split&max_MD_SC_Split), 'Notes']='SupCrit, Med density'
-
+    
     # If SupCrit, low density
     df.loc[ SupCrit&(min_lowD_SC_Split&max_lowD_SC_Split), 'Preferred D'] = LowD_SC
     df.loc[ SupCrit&(min_lowD_SC_Split&max_lowD_SC_Split), 'Preferred D_σ'] = lowD_error['LowD_Density_σ']