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

DiadFit/CO2_EOS.py

@@ -12,6 +12,9 @@ import pickle
 import math
 DiadFit_dir=Path(__file__).parent
 
+## Visualizing coexisting phases
+
+
 
 
 ## Calculating density for a given homogenization temp - Only available with Span and Wanger, but have equations
@@ -70,7 +73,7 @@ def calculate_CO2_density_homog_T(T_h_C, EOS='SW96', Sample_ID=None, homog_to=No
             elif isinstance(T_h_C, np.ndarray):
 
                 T_h_C[T_h_C > 30.9782] = 30.9782
-                print('got into this loop')
+
 
 
 
@@ -167,6 +170,9 @@ def calculate_CO2_density_homog_T(T_h_C, EOS='SW96', Sample_ID=None, homog_to=No
 
 
 
+
+
+
     return df
 
 

DiadFit/H2O_fitting.py

@@ -872,13 +872,14 @@ fit_sil='poly', dpi=200):
     ydat_sil=y_corr_sil
 
     xspace_sil=xdat_sil[1]-xdat_sil[0]
-    area_trap = trapezoid(y_corr_sil, dx=xspace_sil)
+    area_trap = trapz(y_corr_sil, dx=xspace_sil)
     area_simps = simpson(y_corr_sil, dx=xspace_sil)
+
     # Just the LW area
     xsil_LW=xdat_sil[(xdat_sil>LW[0]) & (xdat_sil<LW[1])]
     y_corr_sil_LW=y_corr_sil[(xdat_sil>LW[0]) & (xdat_sil<LW[1])]
     xspace_sil_LW=xsil_LW[1]-xsil_LW[0]
-    area_trap_LW=trapezoid(y_corr_sil_LW, dx=xspace_sil_LW)
+    area_trap_LW=trapz(y_corr_sil_LW, dx=xspace_sil_LW)
     area_simp_LW=simpson(y_corr_sil_LW, dx=xspace_sil_LW)
 
 
@@ -886,7 +887,7 @@ fit_sil='poly', dpi=200):
     xsil_HW=xdat_sil[(xdat_sil>HW[0]) & (xdat_sil<HW[1])]
     y_corr_sil_HW=y_corr_sil[(xdat_sil>HW[0]) & (xdat_sil<HW[1])]
     xspace_sil_HW=xsil_HW[1]-xsil_HW[0]
-    area_trap_HW=trapezoid(y_corr_sil_HW, dx=xspace_sil_HW)
+    area_trap_HW=trapz(y_corr_sil_HW, dx=xspace_sil_HW)
     area_simp_HW=simpson(y_corr_sil_HW, dx=xspace_sil_HW)
 
     # MW
@@ -894,7 +895,7 @@ fit_sil='poly', dpi=200):
         xsil_MW=xdat_sil[(xdat_sil>MW[0]) & (xdat_sil<MW[1])]
         y_corr_sil_MW=y_corr_sil[(xdat_sil>MW[0]) & (xdat_sil<MW[1])]
         xspace_sil_MW=xsil_MW[1]-xsil_MW[0]
-        area_trap_MW=trapezoid(y_corr_sil_MW, dx=xspace_sil_MW)
+        area_trap_MW=trapz(y_corr_sil_MW, dx=xspace_sil_MW)
         area_simp_MW=simpson(y_corr_sil_MW, dx=xspace_sil_MW)
 
 
@@ -966,8 +967,8 @@ fit_sil='poly', dpi=200):
                           'Silicate_Simpson_Area': area_simps,
                           'LW_Silicate_Trapezoid_Area':area_trap_LW,
                           'LW_Silicate_Simpson_Area':area_simp_LW,
-                          'HW_Silicate_Trapezoid_Area':area_trap_LW,
-                          'HW_Silicate_Simpson_Area':area_simp_LW,
+                          'HW_Silicate_Trapezoid_Area':area_trap_HW,
+                          'HW_Silicate_Simpson_Area':area_simp_HW,
                            }, index=[0])
 
     if MW is not None:
@@ -1039,7 +1040,8 @@ def fit_area_for_water_region(*, path, filename, Spectra=None, config1: water_bc
     Returns
     -------
     pd.DataFrame
-        DataFrame with columns for 'Water_Trapezoid_Area', 'Water_Simpson_Area', as well as parameters for the selected background positions
+        DataFrame with columns for different areas, and parameters for choosen background positions.
+
 
     """
     Water=Spectra
@@ -1155,7 +1157,7 @@ def fit_area_for_water_region(*, path, filename, Spectra=None, config1: water_bc
 
 
     xspace_water=xdat_water[1]-xdat_water[0]
-    area_trap = trapezoid(y_corr_water, dx=xspace_water)
+    area_trap = trapz(y_corr_water, dx=xspace_water)
     area_simps = simpson(y_corr_water, dx=xspace_water)
 
 
@@ -1242,10 +1244,12 @@ def stitch_dataframes_together(df_sil, df_water,  MI_file, Host_file=None, save_
     Returns
     -----------
     pd.DataFrame
-        DataFrame with columns for MI filename, HW:LW_Trapezoid, HW:LW_Simpson, Water_Trapezoid_Area,
-        Water_Simpson_Area, Silicate_Trapezoid_Area, and Silicate_Simpson_Area.
-        If Host_file is provided,
-        the DataFrame will also include a column for Host filename.
+        DataFrame with columns for MI filename,
+        Silicate_Trapezoid_Area, Silicate_Simpson_Area = Total Silicate Area using trapezoid or Simpson method
+        LW_Trapezoid_Area, LW_Simpson_Area,  MW_Trapezoid_Area, MW_Simpson_Area, HW_Trapezoid_Area, HW_Simpson_Area = Areas of LW, MW and HW Silicate areas (following Shiavi) using Trapezoid or Simpson integration methodWater_Trapezoid_area,
+        Water_Simpson_area = Total area under water peak using Simpson or Trapezoid Integration method.
+        Water_to_HW_ratio_Simpson, Water_to_HW_ratio_Trapezoid: Ratio of Total water area divided by the HW silicate area
+        Water_to_Total_Silicate_ratio_Simpson, Water_to_Total_Silicate_ratio_Trapezoid: Ratio of Total water area divided by the HW silicate area
 
 
     """
@@ -1253,16 +1257,20 @@ def stitch_dataframes_together(df_sil, df_water,  MI_file, Host_file=None, save_
     if Host_file is not None:
         Combo_Area.insert(0, 'Host filename', Host_file)
     Combo_Area.insert(1, 'MI filename', MI_file)
-    Combo_Area.insert(2, 'HW:LW_Trapezoid',
+    Combo_Area.insert(2, 'Water_to_HW_ratio_Trapezoid',
                       Combo_Area['Water_Trapezoid_Area']/Combo_Area['HW_Silicate_Trapezoid_Area'])
-    Combo_Area.insert(3, 'HW:LW_Simpson',
+    Combo_Area.insert(3, 'Water_to_HW_ratio_Simpson',
                       Combo_Area['Water_Simpson_Area']/Combo_Area['HW_Silicate_Simpson_Area'])
+    Combo_Area.insert(4, 'Water_to_Total_Silicate_ratio_Trapezoid',
+                      Combo_Area['Water_Trapezoid_Area']/Combo_Area['Silicate_Trapezoid_Area'])
+    Combo_Area.insert(5, 'Water_to_Total_Silicate_ratio_Simpson',
+                      Combo_Area['Water_Simpson_Area']/Combo_Area['Silicate_Simpson_Area'])
 
     if Host_file is not None:
-        cols_to_move=['Host filename', 'MI filename', 'HW:LW_Trapezoid', 'HW:LW_Simpson',
+        cols_to_move=['Host filename', 'MI filename', 'Water_to_HW_ratio_Trapezoid', 'Water_to_HW_ratio_Simpson', 'Water_to_Total_Silicate_ratio_Trapezoid', 'Water_to_Total_Silicate_ratio_Simpson',
      'Water_Trapezoid_Area', 'Water_Simpson_Area', 'Silicate_Trapezoid_Area', 'Silicate_Simpson_Area']
     else:
-        cols_to_move=['MI filename', 'HW:LW_Trapezoid', 'HW:LW_Simpson',
+        cols_to_move=['MI filename', 'Water_to_HW_ratio_Trapezoid', 'Water_to_HW_ratio_Simpson', 'Water_to_Total_Silicate_ratio_Trapezoid', 'Water_to_Total_Silicate_ratio_Simpson',
      'Water_Trapezoid_Area', 'Water_Simpson_Area', 'Silicate_Trapezoid_Area', 'Silicate_Simpson_Area']
 
 

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__ = '1.0.2'
+__version__ = '1.0.8'

DiadFit/densimeters.py

@@ -267,8 +267,8 @@ def propagate_error_split_neon_peakfit(*, df_fits, Ne_corr=None, Ne_err=None, pr
 
 
     # Get the peak fit errors
-    Diad1_err=df_fits['Diad1_cent_err'].fillna(0)
-    Diad2_err=df_fits['Diad2_cent_err'].fillna(0)
+    Diad1_err=df_fits['Diad1_cent_err'].fillna(0).infer_objects()
+    Diad2_err=df_fits['Diad2_cent_err'].fillna(0).infer_objects()
     split_err=(Diad1_err**2 + Diad2_err**2)**0.5
     Combo_err= (((df_fits['Splitting']* (Ne_err))**2) +  (pref_Ne *split_err  )**2 )**0.5