DiadFit 1.0.2__py3-none-any.whl → 1.0.5__py3-none-any.whl

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__ = '1.0.5'

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
 

DiadFit/diads.py

@@ -7,6 +7,7 @@ from lmfit.models import GaussianModel, VoigtModel, LinearModel, ConstantModel,
 from scipy.signal import find_peaks
 from scipy.signal.windows import gaussian
 
+
 import os
 import re
 from os import listdir
@@ -21,6 +22,7 @@ from scipy.integrate import trapezoid
 from scipy.integrate import simpson
 from scipy.interpolate import interp1d
 
+
 # Allowed models
 
 allowed_models = ["VoigtModel", "PseudoVoigtModel", "Pearson4Model", "SkewedVoigtModel"]
@@ -2549,7 +2551,7 @@ def fit_gaussian_voigt_generic_diad(config1, *, diad1=False, diad2=False, path=N
         # Final check - that Gaussian isnt anywhere near the height of the diad
 
 
-    df_out=df_out.fillna(0)
+    df_out=df_out.fillna(0).infer_objects()
 
     return result, df_out, y_best_fit, x_lin, components, xdat, ydat, ax1_xlim, ax2_xlim, residual_diad_coords, ydat_inrange,  xdat_inrange
 

DiadFit/ne_lines.py

@@ -1531,9 +1531,9 @@ 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 +1568,7 @@ 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 +1576,15 @@ 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 +1592,14 @@ 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')

DiadFit/relaxifi.py

@@ -493,13 +493,27 @@ def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MP
     results = pd.DataFrame([{'Time(s)': 0,
                              'Step':0,
                              'dt(s)':0,
-                            'Pexternal(MPa)': Pexternal_MPa,
-                            'Pinternal(MPa)': Pinternal_MPa,
-                            'dR/dt(m/s)': calculate_dR_dt(R_m=R_m, b_m=b_m, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, T_K=T_K),
-                            'Fi_radius(μm)': R_m*10**6,
-                            'b (distance to xtal rim -μm)':b_m*10**6,
+                            'Pexternal(MPa)': float(Pexternal_MPa),
+                            'Pinternal(MPa)': float(Pinternal_MPa),
+                            'dR/dt(m/s)': float(calculate_dR_dt(R_m=R_m, b_m=b_m, Pinternal_MPa=Pinternal_MPa, Pexternal_MPa=Pexternal_MPa, T_K=T_K)),
+                            'Fi_radius(μm)': float(R_m*10**6),
+                            'b (distance to xtal rim -μm)':float(b_m*10**6),
                             '\u0394R/R0 (fractional change in radius)':0,
-                            'CO2_dens_gcm3': CO2_dens_initial}], index=range(steps))
+                            'CO2_dens_gcm3': float(CO2_dens_initial)}], index=range(steps))
+                            
+    results = results.astype({
+        'Time(s)': 'float64',
+        'Step': 'int64',
+        'dt(s)': 'float64',
+        'Pexternal(MPa)': 'float64',
+        'Pinternal(MPa)': 'float64',
+        'dR/dt(m/s)': 'float64',
+        'Fi_radius(μm)': 'float64',
+        'b (distance to xtal rim -μm)': 'float64',
+        '\u0394R/R0 (fractional change in radius)': 'float64',
+        'CO2_dens_gcm3': 'float64'
+    })
+
 
     dt_s=totaltime_s/steps
     
@@ -515,9 +529,10 @@ def stretch_at_constant_Pext(*,R_m,b_m,T_K,EOS='SW96',Pinternal_MPa,Pexternal_MP
         if update_b==True:
             b_m=1000*R_m
         
-        results.loc[step] = [step * dt_s, step, dt_s, Pexternal_MPa, Pinternal_MPa, dR_dt, R_m * 10 ** 6, b_m * 10 ** 6,
-                            (R_m * 10 ** 6 - results.loc[0, 'Fi_radius(μm)']) / results.loc[0, 'Fi_radius(μm)'],
-                                CO2_dens_new]
+        results.loc[step] = [float(step * dt_s), int(step), float(dt_s), float(Pexternal_MPa), float(Pinternal_MPa), 
+                     float(dR_dt), float(R_m * 10 ** 6), float(b_m * 10 ** 6), 
+                     float((R_m * 10 ** 6 - results.loc[0, 'Fi_radius(μm)']) / results.loc[0, 'Fi_radius(μm)']),
+                     float(CO2_dens_new)]
 
     if report_results == 'startendonly':
         results.drop(index=list(range(1, results.shape[0] - 1)), inplace=True)  # Drop all rows except first and last

{DiadFit-1.0.2.dist-info → DiadFit-1.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.2
+Version: 1.0.5
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser
@@ -12,11 +12,11 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Requires-Dist: pandas
-Requires-Dist: numpy <2
+Requires-Dist: numpy<2
 Requires-Dist: matplotlib
 Requires-Dist: scikit-learn
-Requires-Dist: scipy >1.6
-Requires-Dist: lmfit >=1.1.0
+Requires-Dist: scipy>1.6
+Requires-Dist: lmfit>=1.1.0
 Requires-Dist: tqdm
 Requires-Dist: python-docx
 

{DiadFit-1.0.2.dist-info → DiadFit-1.0.5.dist-info}/RECORD

@@ -1,6 +1,6 @@
 DiadFit/CO2_EOS.py,sha256=H2_th8DP5m9oJ-IZCg9XncuOogQy_AE8ihiT-4zlIOo,74170
 DiadFit/CO2_in_bubble_error.py,sha256=Nq5YEf2oa2rWRreEPXl2lEA86NXOGvll0Gca2AOu_RE,21224
-DiadFit/H2O_fitting.py,sha256=ZOLWL8j7HQYKlx1-ISm1twvH34jhrGFwukU8ElRj0Dw,43920
+DiadFit/H2O_fitting.py,sha256=XLNNgqmiIyj-ysRQeQFnk08Dlr6tFHFySY3Z-wEadxs,44914
 DiadFit/Highrho_polyfit_data.pkl,sha256=7t6uXxI-HdfsvreAWORzMa9dXxUsnXqKBSo1O3EgiBw,1213
 DiadFit/Highrho_polyfit_dataUCB_1117_1400.pkl,sha256=oBOarETLyfq2DJhYGQrJofgHjvRMLamE6G2b7EE5m-Y,1213
 DiadFit/Highrho_polyfit_dataUCB_1117_1447.pkl,sha256=OG1qip_xU1hl3xp3HC8e9_2497-KYEV3Xz3mx0gdJ4Y,1213
@@ -29,21 +29,21 @@ DiadFit/Mediumrho_polyfit_data_CCMR.pkl,sha256=U6ODSdurqS0-lynm1MG1zktg8NuhYRbrY
 DiadFit/Mediumrho_polyfit_data_CMASS.pkl,sha256=SBy1pIdqCAF9UtB9FLNTuD0-tFyD7swwJppdE2U_FsY,1557
 DiadFit/Psensor.py,sha256=C2xSlgxhUJIKIBDvUp02QaYRs5QsIqjGGRMP25ZLRZ0,10435
 DiadFit/__init__.py,sha256=F-HjhCYKL_U8PfiH8tZ9DUCkxPvo6lAslJS4fyvxkbY,1148
-DiadFit/_version.py,sha256=X0PLLhZnpIdwlS5nJADl6Y4cVKJ40aHv2hvu4kkgAGQ,295
+DiadFit/_version.py,sha256=599vLXXrjZtWlaxUrZujLY2-Ub1qzeOKj5Sk5VZAYKo,295
 DiadFit/argon_lines.py,sha256=vtzsuDdEgrAmEF9xwpejpFqKV9hKPS1JUYhIl4AfXZ0,7675
 DiadFit/cosmicray_filter.py,sha256=a45x2_nmpi9Qcjc_L39UA9JOd1NMorIjtTRGnCdG3MU,23634
 DiadFit/densimeter_fitting.py,sha256=zEyCwq1zDV3z6-MIu-eZqgp3YQPUGqwZiKczN3-22LQ,8247
-DiadFit/densimeters.py,sha256=p3jY9709vKegCfWZIwoU4Rt5jFfwJJQobLb71AXUxAY,55250
+DiadFit/densimeters.py,sha256=pSD8s9_9949bjWTbXU6SwoNgvsVBKGfQVf-JYMMtjrs,55282
 DiadFit/density_depth_crustal_profiles.py,sha256=b072IJaoGDydKpqWWKoJHeXKIkcIXxKf82whpvLAPpw,17761
-DiadFit/diads.py,sha256=RWFesTt_W52u_-N9Cr2VtHuKrR038XKf3-dDLx5CNYY,180888
+DiadFit/diads.py,sha256=ELG6wgEaGCYFj0IeA2F9QasYNmMVmFOi0rOl0oXv1pU,180906
 DiadFit/error_propagation.py,sha256=ipYI-Nwjv4f0sBdUiGeYV4wLcLGUXzKRrquNnc72d3c,50620
 DiadFit/importing_data_files.py,sha256=0Cx_CKJZR8efssMzQit0aPRh_rsjQFGXgLtI285FW_k,41961
 DiadFit/lookup_table.csv,sha256=Hs1tmSQ9ArTUDv3ymEXbvnLlPBxYUP0P51dz7xAKk-Q,2946857
 DiadFit/lookup_table_noneg.csv,sha256=HelvewKbBy4cqT2GAqsMo-1ps1lBYqZ-8hCJZWPGfhI,3330249
 DiadFit/molar_gas_proportions.py,sha256=_oEZn_vndHGDaXAjZ6UU8ycujBx_qB2KGCGqZSzotQU,3389
-DiadFit/ne_lines.py,sha256=6z9oo4lgh0iYv1mkSscgzCt_Pe4gQTnquG99pR6cJS8,63811
-DiadFit/relaxifi.py,sha256=hHzRsJPQIVohYi3liy9IQJpaomgsa2zbLQmhqkpdfrI,31549
-DiadFit-1.0.2.dist-info/METADATA,sha256=EjFCY1urZhZ_wc2Wxb8f0NC8gNgV-JaFY1ShqDBpnoQ,1174
-DiadFit-1.0.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-DiadFit-1.0.2.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
-DiadFit-1.0.2.dist-info/RECORD,,
+DiadFit/ne_lines.py,sha256=in27yyvtlONf80KA2SREJ8xEemHvYTiWmd2-LOeJ7Tk,63955
+DiadFit/relaxifi.py,sha256=ZJ1LPWU1qKM8kU1ym4Ltp8skI_lMlhbCVhW6C1UhLb8,32109
+DiadFit-1.0.5.dist-info/METADATA,sha256=rz8zJHYmknOrLusf8A65vAdHe3-T3JeTriprj6FT4RI,1171
+DiadFit-1.0.5.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
+DiadFit-1.0.5.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
+DiadFit-1.0.5.dist-info/RECORD,,

{DiadFit-1.0.2.dist-info → DiadFit-1.0.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: bdist_wheel (0.44.0)
 Root-Is-Purelib: true
 Tag: py3-none-any