DiadFit 0.0.79__tar.gz → 0.0.81__tar.gz

{DiadFit-0.0.79 → DiadFit-0.0.81}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 0.0.79
+Version: 0.0.81
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

{DiadFit-0.0.79 → DiadFit-0.0.81}/src/DiadFit/CO2_H2O_EOS.py

@@ -10,6 +10,7 @@ from pathlib import Path
 from pickle import load
 import pickle
 import math
+from DiadFit.CO2_EOS import *
 
 
 DiadFit_dir=Path(__file__).parent
@@ -101,7 +102,107 @@ aH2[13] = -4.13039220 / 10**1  # alpha for CO2
 aH2[14] = -8.47988634  # beta for CO2
 aH2[15] = 2.800 / 10**2  # gamma for CO2
 
+## This is for when you only feed a numpy array
+# def ensure_series(a, b, c):
+#     # Determine the target length
+#     lengths = [len(a) if isinstance(a, pd.Series) else None,
+#                len(b) if isinstance(b, pd.Series) else None,
+#                len(c) if isinstance(c, pd.Series) else None]
+#     lengths = [l for l in lengths if l is not None]
+#     target_length = max(lengths) if lengths else 1
+#
+#     # Convert each input to a Series of the target length
+#     if not isinstance(a, pd.Series):
+#         a = pd.Series([a] * target_length)
+#     if not isinstance(b, pd.Series):
+#         b = pd.Series([b] * target_length)
+#     if not isinstance(c, pd.Series):
+#         c = pd.Series([c] * target_length)
+#
+#     return a, b, c
+#
+#
+# def ensure_series_4(a, b, c, d):
+#     # Determine the target length
+#     lengths = [len(a) if isinstance(a, pd.Series) else None,
+#                len(b) if isinstance(b, pd.Series) else None,
+#                len(c) if isinstance(c, pd.Series) else None,
+#                len(d) if isinstance(d, pd.Series) else None]
+#     lengths = [l for l in lengths if l is not None]
+#     target_length = max(lengths) if lengths else 1
+#
+#     # Convert each input to a Series of the target length
+#     if not isinstance(a, pd.Series):
+#         a = pd.Series([a] * target_length)
+#     if not isinstance(b, pd.Series):
+#         b = pd.Series([b] * target_length)
+#     if not isinstance(c, pd.Series):
+#         c = pd.Series([c] * target_length)
+#     if not isinstance(d, pd.Series):
+#         d = pd.Series([d] * target_length)
+#     return a, b, c, d
 
+import pandas as pd
+import numpy as np
+
+def ensure_series(a, b, c):
+    # Determine the target length
+    lengths = [len(a) if isinstance(a, (pd.Series, np.ndarray)) else None,
+               len(b) if isinstance(b, (pd.Series, np.ndarray)) else None,
+               len(c) if isinstance(c, (pd.Series, np.ndarray)) else None]
+    lengths = [l for l in lengths if l is not None]
+    target_length = max(lengths) if lengths else 1
+
+    # Convert each input to a Series of the target length
+    if not isinstance(a, (pd.Series, np.ndarray)):
+        a = pd.Series([a] * target_length)
+    else:
+        a = pd.Series(a)
+
+    if not isinstance(b, (pd.Series, np.ndarray)):
+        b = pd.Series([b] * target_length)
+    else:
+        b = pd.Series(b)
+
+    if not isinstance(c, (pd.Series, np.ndarray)):
+        c = pd.Series([c] * target_length)
+    else:
+        c = pd.Series(c)
+
+    return a, b, c
+
+
+def ensure_series_4(a, b, c, d):
+    # Determine the target length
+    lengths = [len(a) if isinstance(a, (pd.Series, np.ndarray)) else None,
+               len(b) if isinstance(b, (pd.Series, np.ndarray)) else None,
+               len(c) if isinstance(c, (pd.Series, np.ndarray)) else None,
+               len(d) if isinstance(d, (pd.Series, np.ndarray)) else None]
+    lengths = [l for l in lengths if l is not None]
+    target_length = max(lengths) if lengths else 1
+
+    # Convert each input to a Series of the target length
+    if not isinstance(a, (pd.Series, np.ndarray)):
+        a = pd.Series([a] * target_length)
+    else:
+        a = pd.Series(a)
+
+    if not isinstance(b, (pd.Series, np.ndarray)):
+        b = pd.Series([b] * target_length)
+    else:
+        b = pd.Series(b)
+
+    if not isinstance(c, (pd.Series, np.ndarray)):
+        c = pd.Series([c] * target_length)
+    else:
+        c = pd.Series(c)
+
+    if not isinstance(d, (pd.Series, np.ndarray)):
+        d = pd.Series([d] * target_length)
+    else:
+        d = pd.Series(d)
+
+    return a, b, c, d
 
 
 
@@ -178,7 +279,7 @@ def purevolume(i, V, P, B, C, D, E, F, Vc, TK, b, g):
     # Return the final estimated volume
     return V
 
-def purepressure(i, V, P, B, C, D, E, F, Vc, TK, b, g):
+def purepressure(i, V, P, TK):
     """ Using the pure EOS, this function solves for the best pressure using the pureEOS residual calculated above
 
     It returns the pressure.
@@ -186,6 +287,8 @@ def purepressure(i, V, P, B, C, D, E, F, Vc, TK, b, g):
     """
     for iter in range(1, 51):
         # Calculate the derivative of the pureEOS function at (V, P)
+        k1_temperature, k2_temperature, k3_temperature, a1, a2, g, b, Vc, B, C, D, E, F, Vguess=get_EOS_params(P, TK)
+
         diff = (pureEOS(i, V, P + 0.0001, B, C, D, E, F, Vc, TK, b, g) - pureEOS(i, V, P, B, C, D, E, F, Vc, TK, b, g)) / 0.0001
 
         # Update the pressure using the Newton-Raphson method
@@ -201,6 +304,9 @@ def purepressure(i, V, P, B, C, D, E, F, Vc, TK, b, g):
     # Return the final estimated pressure
     return P
 
+
+
+
 def mol_vol_to_density(mol_vol, XH2O):
     """ Converts molar mass to molar density for a given XH2O"""
     density=((1-XH2O)*44 + (XH2O)*18)/mol_vol
@@ -265,11 +371,14 @@ def mixvolume(V, P, BVc, CVc2, DVc4, EVc5, FVc2, bmix, gVc2, TK):
 
     return V
 
-def mixpressure(V, P, BVc, CVc2, DVc4, EVc5, FVc2, bmix, gVc2, TK):
+def mixpressure(P, V, TK, Y):
     """ This function iterates in pressure space to get the best match to the entered volume using the mixEOS function above.
 
     """
     for iter in range(1, 51):
+        k1_temperature, k2_temperature, k3_temperature, a1, a2, g, b, Vc, B, C, D, E, F, Vguess=get_EOS_params(P, TK)
+        Bij, Vcij, BVc_prm, BVc, Cijk, Vcijk, CVc2_prm, CVc2, Dijklm, Vcijklm, DVc4_prm, DVc4, Eijklmn, Vcijklmn, EVc5_prm,  EVc5, Fij, FVc2_prm, FVc2, bmix, b_prm, gijk, gVc2_prm, gVc2=mixing_rules(B, C,D, E, F, Vc, Y, b,    g, k1_temperature, k2_temperature, k3_temperature)
+
         diff = ((mixEOS(V, P + 0.0001, BVc, CVc2, DVc4, EVc5, FVc2, bmix, gVc2, TK)
         - mixEOS(V, P, BVc, CVc2, DVc4, EVc5, FVc2, bmix, gVc2, TK)) / 0.0001)
         Pnew = P - mixEOS(V, P, BVc, CVc2, DVc4, EVc5, FVc2, bmix, gVc2, TK) / diff
@@ -280,8 +389,10 @@ def mixpressure(V, P, BVc, CVc2, DVc4, EVc5, FVc2, bmix, gVc2, TK):
     return P
 
 
+
 def mix_lnphi(i, Zmix, BVc_prm, CVc2_prm, DVc4_prm, EVc5_prm, FVc2_prm, FVc2, bmix, b_prm, gVc2, gVc2_prm, Vmix):
     lnph=0
+
     lnph = -math.log(Zmix)
     lnph += (BVc_prm[i] / Vmix)
     lnph += (CVc2_prm[i] / (2.0 * Vmix ** 2))
@@ -735,13 +846,8 @@ def calculate_molar_volume_DZ2006(*, P_kbar, T_K, XH2O):
 
 
     """
-    # Make all a panda series
-    if not isinstance(P_kbar, pd.Series):
-        P_kbar = pd.Series(P_kbar)
-    if not isinstance(T_K, pd.Series):
-        T_K = pd.Series(T_K)
-    if not isinstance(XH2O, pd.Series):
-        XH2O = pd.Series(XH2O)
+
+    P_kbar, T_K, XH2O=ensure_series(P_kbar, T_K, XH2O)
 
     # Check all the same length
     lengths = [len(P_kbar), len(T_K), len(XH2O)]
@@ -760,6 +866,67 @@ def calculate_molar_volume_DZ2006(*, P_kbar, T_K, XH2O):
 
     return mol_vol
 
+def calculate_Pressure_ind_DZ2006(*, mol_vol, T_K, XH2O, Pguess=None):
+    """ This function calculates pressure for a known molar volume, T in K and XH2O (mol frac) for a single value
+    """
+    V=mol_vol
+    if Pguess is None:
+        if V>1000:
+            Pguess=1000
+        elif V<10:
+            Pguess=20000
+        else:
+            Pguess=200
+
+    TK=T_K
+
+    # lets do for low pressure initially
+
+
+    if XH2O==0:
+        P=purepressure(1,  V, Pguess, TK)
+
+    elif XH2O==1:
+        P=purepressure(0, V, Pguess, TK)
+
+    else:
+        XCO2=1-XH2O
+        Y = [0] * 2
+        Y[0]=XH2O
+        Y[1]=XCO2
+
+        P=mixpressure(Pguess, V, T_K, Y)
+
+    return P
+
+def calculate_Pressure_DZ2006(*, mol_vol=None, density=None, T_K, XH2O):
+    """ Used to calculate molar volume in a loop for multiple inputs
+
+
+    """
+    # Make all a panda series
+
+
+
+    if mol_vol is None and density is not None:
+        mol_vol=density_to_mol_vol(density=density, XH2O=XH2O)
+
+    mol_vol, T_K, XH2O=ensure_series(mol_vol, T_K, XH2O)
+
+    # Check all the same length
+    lengths = [len(mol_vol), len(T_K), len(XH2O)]
+    if len(set(lengths)) != 1:
+        raise ValueError("All input Pandas Series must have the same length.")
+
+    # Set up loop
+    P=np.empty(len(mol_vol), float)
+
+    for i in range(0, len(mol_vol)):
+        P[i]=calculate_Pressure_ind_DZ2006(mol_vol=mol_vol.iloc[i].astype(float), T_K=T_K.iloc[i].astype(float), XH2O=XH2O.iloc[i].astype(float))
+
+
+
+    return P
 
 
 def mix_fugacity(*, P_kbar, T_K, XH2O, Vmix):
@@ -768,14 +935,10 @@ def mix_fugacity(*, P_kbar, T_K, XH2O, Vmix):
 
     """
     # Make everything a pandas series
-    if not isinstance(P_kbar, pd.Series):
-        P_kbar = pd.Series(P_kbar)
-    if not isinstance(T_K, pd.Series):
-        T_K = pd.Series(T_K)
-    if not isinstance(XH2O, pd.Series):
-        XH2O = pd.Series(XH2O)
-    if not isinstance(Vmix, pd.Series):
-        Vmix = pd.Series(Vmix)
+
+    P_kbar, T_K, XH2O, Vmix=ensure_series_4(P_kbar, T_K, XH2O, Vmix)
+
+
 
     #Check all the same length
     lengths = [len(P_kbar), len(T_K), len(XH2O), len(Vmix)]
@@ -796,16 +959,44 @@ def mix_fugacity(*, P_kbar, T_K, XH2O, Vmix):
 
 
 def mol_vol_to_density(*, mol_vol, XH2O):
-    """ Converts molar mass to molar density for a given XH2O"""
+    """ Converts molar mass to density for a given XH2O"""
     density=((1-XH2O)*44 + (XH2O)*18)/mol_vol
     return density
 
+def density_to_mol_vol(*, density, XH2O):
+    """ Converts density in g/cm3 to molar volume for a given XH2O"""
+    mol_vol=((1-XH2O)*44 + (XH2O)*18)/density
+    return mol_vol
+
+
+
+def calc_prop_knownP_EOS_DZ2006(*, P_kbar=1, T_K=1200, XH2O=1):
+    """ This function calculates molar volume, density, compressability factor, fugacity, and activity for mixed H2O-CO2 fluids
+    using the EOS of Span and Wanger. It assumes you know P, T, and XH2O.
+
+    Parameters
+    -------------------
+    P_kbar: float, np.array, pd.Series
+        Pressure in kbar
+    T_K: float, np.array, pd.Series
+        Temperature in Kelvin
+    XH2O: float, np.array, pd.Series
+        Molar fraction of H2O in the fluid phase.
+
+    Returns
+    -------------------
+    pd.DataFrame
+
+    """
+
 
 
+    # First, check all pd Series
+
 
-def H2O_CO2_EOS_DZ2006_knownP(*, P_kbar=1, T_K=1200, XH2O=1):
-    """ Function to return a dataframe of outputs when you know P, T_K and XH2O"""
     mol_vol=calculate_molar_volume_DZ2006(P_kbar=P_kbar, T_K=T_K, XH2O=XH2O)
+
+
     f_H2O, f_CO2, a_H2O, a_CO2, Zmix=mix_fugacity(P_kbar=P_kbar, T_K=T_K, XH2O=XH2O,
                                                       Vmix=mol_vol)
     density=mol_vol_to_density(mol_vol=mol_vol, XH2O=XH2O)
@@ -831,6 +1022,62 @@ def H2O_CO2_EOS_DZ2006_knownP(*, P_kbar=1, T_K=1200, XH2O=1):
 
 
 
+def calculate_entrapment_P_XH2O(*, XH2O, CO2_dens_gcm3, T_K):
+    """" 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
+    pure CO2 equation of states for comparison
+
+    Parameters
+    ----------------------
+    XH2O: float, pd.Series.
+        The molar fraction of H2O in the fluid. Should be between 0 and 1. Can get an estimate from say VESical.
+
+    CO2_dens_gcm3: float, pd.Series
+        Measured CO2 density in g/cm3
+
+    T_K: float, pd.Series
+        Temperature in Kelvin.
+
+    Returns
+    -----------------------------
+    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
+        CO2_dens_gcm3: Input CO2 density
+        T_K: input temperature
+        XH2O: input molar fraction of H2O
+
+    """
+    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})
+
+    return df
 
 
 

{DiadFit-0.0.79 → DiadFit-0.0.81}/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-0.0.79 → DiadFit-0.0.81}/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__ = '0.0.79'
+__version__ = '0.0.81'

{DiadFit-0.0.79 → DiadFit-0.0.81}/src/DiadFit/diads.py

@@ -154,7 +154,7 @@ class diad_id_config:
 
 
 
-def identify_diad_peaks(*, config: diad_id_config=diad_id_config(), path=None, filename,
+def identify_diad_peaks(*, config: diad_id_config=diad_id_config(), path=None, filename=None, diad_array=None,
  filetype='Witec_ASCII',  plot_figure=True):
 
     """ This function fits a spline to the spectral data. It then uses Scipy find peaks to identify the diad,
@@ -205,10 +205,11 @@ def identify_diad_peaks(*, config: diad_id_config=diad_id_config(), path=None, f
 
 
     """
-    Diad_df=get_data(path=path, filename=filename, filetype=filetype)
-
-
-    Diad=np.array(Diad_df)
+    if diad_array is None:
+        Diad_df=get_data(path=path, filename=filename, filetype=filetype)
+        Diad=np.array(Diad_df)
+    else:
+        Diad=diad_array
 
 
 
@@ -1037,7 +1038,7 @@ def plot_diad_groups(*, x_cord,  Weak_np=None, Medium_np=None, Strong_np=None, y
     return fig
 
 
-def remove_diad_baseline(*, path=None, filename=None, Diad_files=None, filetype='Witec_ASCII',
+def remove_diad_baseline(*, path=None, filename=None, Diad_files=None, filetype='Witec_ASCII', diad_array=None,
             exclude_range1=None, exclude_range2=None,N_poly=1, x_range_baseline=10,
             lower_bck=[1200, 1250], upper_bck=[1320, 1330], sigma=4,
             plot_figure=True):
@@ -1100,11 +1101,12 @@ def remove_diad_baseline(*, path=None, filename=None, Diad_files=None, filetype=
 
     """
 
-    Diad_df=get_data(path=path, filename=filename, filetype=filetype)
-
-
+    if diad_array is None:
+        Diad_df=get_data(path=path, filename=filename, filetype=filetype)
+        Diad=np.array(Diad_df)
+    else:
+        Diad=diad_array
 
-    Diad=np.array(Diad_df)
 
 
     if exclude_range1 is not None and exclude_range2 is None:
@@ -2280,7 +2282,7 @@ def fit_gaussian_voigt_generic_diad(config1, *, diad1=False, diad2=False, path=N
 
 
 def fit_diad_2_w_bck(*, config1: diad2_fit_config=diad2_fit_config(), config2: diad_id_config=diad_id_config(),
-    path=None, filename=None, peak_pos_voigt=None,filetype=None,
+    path=None, filename=None, peak_pos_voigt=None,filetype=None, diad_array=None,
     plot_figure=True, close_figure=False, Diad_pos=None, HB_pos=None, C13_pos=None):
     """ This function fits the background (using the function remove_diad_baseline) and then
     fits the peaks using fit_gaussian_voigt_generic_diad()
@@ -2390,8 +2392,11 @@ def fit_diad_2_w_bck(*, config1: diad2_fit_config=diad2_fit_config(), config2: d
 
     # Check number of peaks makes sense
     fit_peaks=config1.fit_peaks
-    Diad_df=get_data(path=path, filename=filename, filetype=filetype)
-    Diad=np.array(Diad_df)
+    if diad_array is None:
+        Diad_df=get_data(path=path, filename=filename, filetype=filetype)
+        Diad=np.array(Diad_df)
+    else:
+        Diad=diad_array
 
 
     if fit_peaks==2:
@@ -2433,7 +2438,7 @@ def fit_diad_2_w_bck(*, config1: diad2_fit_config=diad2_fit_config(), config2: d
 
     y_corr_diad2, Py_base_diad2, x_diad2,  Diad_short_diad2, Py_base_diad2, Pf_baseline_diad2,  Baseline_ysub_diad2, Baseline_x_diad2, Baseline_diad2, span_diad2=remove_diad_baseline(
    path=path, filename=filename, filetype=filetype, exclude_range1=config2.exclude_range1, exclude_range2=config2.exclude_range2, N_poly=config1.N_poly_bck_diad2,
-    lower_bck=config1.lower_bck_diad2, upper_bck=config1.upper_bck_diad2, plot_figure=False)
+    lower_bck=config1.lower_bck_diad2, upper_bck=config1.upper_bck_diad2, plot_figure=False, diad_array=diad_array)
 
 
 
@@ -2544,8 +2549,8 @@ def fit_diad_2_w_bck(*, config1: diad2_fit_config=diad2_fit_config(), config2: d
     ybase_xlin=Pf_baseline_diad2(x_lin)
 
     # We extract the full spectra to plot at the end, and convert to a dataframe
-    Spectra_df=get_data(path=path, filename=filename, filetype=filetype)
-    Spectra=np.array(Spectra_df)
+    #Spectra_df=get_data(path=path, filename=filename, filetype=filetype)
+    Spectra=Diad
 
 
 
@@ -2749,9 +2754,9 @@ def fit_diad_2_w_bck(*, config1: diad2_fit_config=diad2_fit_config(), config2: d
 
     # Lets calculate peak skewness here.
     Skew50=assess_diad2_skewness(config1=diad2_fit_config(), int_cut_off=0.5, path=path, filename=filename, filetype=filetype,
-    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False)
+    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False, diad_array=diad_array)
     Skew80=assess_diad2_skewness(config1=diad2_fit_config(), int_cut_off=0.3, path=path, filename=filename, filetype=filetype,
-    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False)
+    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False, diad_array=diad_array)
     df_out['Diad2_Asym50']=Skew50['Skewness_diad2']
     df_out['Diad2_Asym70']=Skew80['Skewness_diad2']
     df_out['Diad2_Yuan2017_sym_factor']=(df_out['Diad2_fwhm'])*(df_out['Diad2_Asym50']-1)
@@ -2767,7 +2772,7 @@ def fit_diad_2_w_bck(*, config1: diad2_fit_config=diad2_fit_config(), config2: d
 
 
 def fit_diad_1_w_bck(*, config1: diad1_fit_config=diad1_fit_config(), config2: diad_id_config=diad_id_config(),
-    path=None, filename=None, filetype=None,  plot_figure=True, close_figure=True, Diad_pos=None, HB_pos=None):
+    path=None, filename=None, filetype=None,  plot_figure=True, close_figure=True, Diad_pos=None, HB_pos=None, diad_array=None):
     """ This function fits the background (using the function remove_diad_baseline) and then fits the peaks
     using fit_gaussian_voigt_generic_diad()
     It then checks if any parameters are right at the permitted edge (meaning fitting didnt converge),
@@ -2876,13 +2881,16 @@ def fit_diad_1_w_bck(*, config1: diad1_fit_config=diad1_fit_config(), config2: d
             config1.fit_gauss=False
             #print('Either no hb position, or prominence<-50, using 1 fit')
 
-    Diad_df=get_data(path=path, filename=filename, filetype=filetype)
-    Diad=np.array(Diad_df)
+    if diad_array is None:
+        Diad_df=get_data(path=path, filename=filename, filetype=filetype)
+        Diad=np.array(Diad_df)
+    else:
+        Diad=diad_array
     # First, we feed data into the remove baseline function, which returns corrected data
 
     y_corr_diad1, Py_base_diad1, x_diad1,  Diad_short_diad1, Py_base_diad1, Pf_baseline_diad1,  Baseline_ysub_diad1, Baseline_x_diad1, Baseline_diad1, span_diad1=remove_diad_baseline(
    path=path, filename=filename, filetype=filetype, exclude_range1=config2.exclude_range1, exclude_range2=config2.exclude_range2, N_poly=config1.N_poly_bck_diad1,
-    lower_bck=config1.lower_bck_diad1, upper_bck=config1.upper_bck_diad1, plot_figure=False)
+    lower_bck=config1.lower_bck_diad1, upper_bck=config1.upper_bck_diad1, plot_figure=False, diad_array=diad_array)
 
 
 
@@ -2997,8 +3005,9 @@ def fit_diad_1_w_bck(*, config1: diad1_fit_config=diad1_fit_config(), config2: d
     ybase_xlin=Pf_baseline_diad1(x_lin)
 
     # We extract the full spectra to plot at the end, and convert to a dataframe
-    Spectra_df=get_data(path=path, filename=filename, filetype=filetype)
-    Spectra=np.array(Spectra_df)
+
+
+    Spectra=Diad
 
 
 
@@ -3193,9 +3202,9 @@ def fit_diad_1_w_bck(*, config1: diad1_fit_config=diad1_fit_config(), config2: d
 
     # Lets calculate peak skewness here.
     Skew50=assess_diad1_skewness(config1=diad1_fit_config(), int_cut_off=0.5, path=path, filename=filename, filetype=filetype,
-    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False)
+    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False, diad_array=diad_array)
     Skew80=assess_diad1_skewness(config1=diad1_fit_config(), int_cut_off=0.3, path=path, filename=filename, filetype=filetype,
-    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False)
+    skewness='abs', height=1, prominence=5, width=0.5, plot_figure=False, diad_array=diad_array)
 
     df_out['Diad1_Asym50']=Skew50['Skewness_diad1']
     df_out['Diad1_Asym70']=Skew80['Skewness_diad1']
@@ -4181,7 +4190,7 @@ encode="ISO-8859-1"
 
 
 def assess_diad1_skewness(*,  config1: diad1_fit_config=diad1_fit_config(), int_cut_off=0.3, path=None, filename=None, filetype=None,
-skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, peak_fit_routine=False, peak_pos=None, peak_height=None, dpi=200):
+skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, peak_fit_routine=False, peak_pos=None, peak_height=None, dpi=200, diad_array=None):
     """ Assesses Skewness of Diad peaks. Useful for identifying mixed L + V phases
     (see DeVitre et al. in review)
 
@@ -4243,7 +4252,7 @@ skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, peak_fit_ro
 
     y_corr_diad1, Py_base_diad1, x_diad1,  Diad_short, Py_base_diad1, Pf_baseline,  Baseline_ysub_diad1, Baseline_x_diad1, Baseline, span=remove_diad_baseline(
     path=path, filename=filename, filetype=filetype, N_poly=config1.N_poly_bck_diad1,
-    lower_bck=config1.lower_bck_diad1, upper_bck=config1.upper_bck_diad1, plot_figure=False)
+    lower_bck=config1.lower_bck_diad1, upper_bck=config1.upper_bck_diad1, plot_figure=False, diad_array=diad_array)
 
 
 
@@ -4434,7 +4443,7 @@ skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, peak_fit_ro
 
 
 def assess_diad2_skewness(*,  config1: diad2_fit_config=diad1_fit_config(), int_cut_off=0.3, path=None, filename=None, filetype=None,
-skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, dpi=200, peak_fit_routine=False, peak_pos=None, peak_height=None):
+skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, dpi=200, peak_fit_routine=False, peak_pos=None, peak_height=None, diad_array=None):
 
     """ Assesses Skewness of Diad peaks. Useful for identifying mixed L + V phases
     (see DeVitre et al. in review)
@@ -4498,7 +4507,7 @@ skewness='abs', height=1, prominence=5, width=0.5, plot_figure=True, dpi=200, pe
 # First, do the background subtraction
     y_corr_diad2, Py_base_diad2, x_diad2,  Diad_short, Py_base_diad2, Pf_baseline,  Baseline_ysub_diad2, Baseline_x_diad2, Baseline, span=remove_diad_baseline(
     path=path, filename=filename, filetype=filetype, N_poly=config1.N_poly_bck_diad2,
-    lower_bck=config1.lower_bck_diad2, upper_bck=config1.upper_bck_diad2, plot_figure=False)
+    lower_bck=config1.lower_bck_diad2, upper_bck=config1.upper_bck_diad2, plot_figure=False, diad_array=diad_array)
 
 
 

{DiadFit-0.0.79 → DiadFit-0.0.81}/src/DiadFit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 0.0.79
+Version: 0.0.81
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser