DiadFit 1.0.1__py3-none-any.whl → 1.0.2__py3-none-any.whl

DiadFit/CO2_EOS.py

@@ -1028,7 +1028,7 @@ def ensure_series(a, b, c):
     else:
         c = pd.Series(c)
 
-    return a, b, c
+    return a.reset_index(drop=True), b.reset_index(drop=True), c.reset_index(drop=True)
 
 
 def ensure_series_4(a, b, c, d):
@@ -1061,7 +1061,7 @@ def ensure_series_4(a, b, c, d):
     else:
         d = pd.Series(d)
 
-    return a, b, c, d
+    return a.reset_index(drop=True), b.reset_index(drop=True), c.reset_index(drop=True), d.reset_index(drop=True)
 
 
 
@@ -2064,9 +2064,13 @@ def calculate_entrapment_P_XH2O(*, XH2O, CO2_dens_gcm3, T_K, T_K_ambient=37+273.
 
 
     """
+
     XH2O, rho_meas, T_K=ensure_series(a=XH2O, b=CO2_dens_gcm3, c=T_K)
     alpha=XH2O/(1-XH2O)
 
+    # All inputs 194 up to here
+
+
     # IF water is lost
     rho_orig_H_loss=rho_meas*(1+alpha*(18/44))
     # IF water isnt lost
@@ -2083,11 +2087,23 @@ def calculate_entrapment_P_XH2O(*, XH2O, CO2_dens_gcm3, T_K, T_K_ambient=37+273.
 
     # calculate density of H2O using EOS
     H2O_dens=calculate_rho_for_P_T_H2O(P_kbar=P_H2O,T_K=T_K_ambient)
+    H2O_dens=H2O_dens.reset_index(drop=True)
 
     # Calculate the bulk density by re-arranging the two volume equations
     nan_mask = H2O_dens==0
-    rho_orig_no_H_loss=(CO2_dens_gcm3*H2O_dens)/((1-XH2O_mass)*H2O_dens+XH2O_mass*CO2_dens_gcm3)
-    rho_orig_no_H_loss = np.where(nan_mask, CO2_dens_gcm3, rho_orig_no_H_loss)
+
+    # Debugging
+
+
+
+
+    rho_orig_no_H_loss=(rho_meas*H2O_dens)/((1-XH2O_mass)*H2O_dens+XH2O_mass*rho_meas)
+
+
+
+
+    rho_orig_no_H_loss = np.where(nan_mask, rho_meas, rho_orig_no_H_loss)
+
 
 
 

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__ = '1.0.1'
+__version__ = '1.0.2'

DiadFit/diads.py

@@ -17,7 +17,7 @@ from dataclasses import dataclass
 import matplotlib.patches as patches
 import warnings as w
 from tqdm import tqdm
-from numpy import trapz
+from scipy.integrate import trapezoid
 from scipy.integrate import simpson
 from scipy.interpolate import interp1d
 
@@ -832,6 +832,96 @@ def filter_splitting_prominence(*, fit_params, data_y_all,
 
     return fit_params_filt.reset_index(drop=True), data_y_filt, fit_params_disc.reset_index(drop=True), data_y_disc
 
+def filter_by_string(*, fit_params, data_y_all,
+                                x_cord,
+                                 str_filt=None):
+    """ Filters Spectra based on approximate splitting, draws a plot showing spectra to discard and those to keep
+
+    Parameters
+    --------------
+    fit_params: pd.dataframe
+        dataframe of fit parameters from loop_approx_diad_fits
+
+    data_y_all: np.array
+        y coordinates of each spectra from loop_approx_diad_fits, used for plotting visualizatoins
+
+    x_cord: np.array
+        x coordinates of 1 spectra. Assumes all x coordinates the same length
+
+
+
+    str_filt: str
+        Filters just based on string in filename. Keeps files with string in, discards those without.
+
+    Returns
+    --------------
+    fit_params_filt: pd.DataFrame
+        dataframe of fit parameters for spectra to keep
+    data_y_filt: np.array
+        y coordinates of spectra to keep
+    fit_params_disc: pd.DataFrame
+        dataframe of fit parameters for spectra to discard
+    data_y_disc: np.array
+        y coordinates of spectra to discard
+
+
+    """
+
+    filt=fit_params['filename'].str.contains(str_filt)
+
+
+    fit_params_filt=fit_params.loc[filt].reset_index(drop=True)
+    fit_params_disc=fit_params.loc[~(filt)].reset_index(drop=True)
+
+    print('Keeping N='+str(len(fit_params_filt)))
+    print('Discarding N='+str(len(fit_params_disc)))
+
+
+
+    # Then apply to get data
+    data_y_filt=data_y_all[:, (filt)]
+    data_y_disc=data_y_all[:, ~(filt)]
+
+    intc=800
+    prom_filt=0
+    prom_disc=0
+    fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12,5))
+    ax1.set_title('Samples')
+    ax2.set_title('Standards')
+    if sum(~filt)>0:
+        for i in range(0, np.shape(data_y_disc)[1]):
+            av_prom_disc=np.abs(np.nanmedian(fit_params_disc['Diad1_abs_prom'])/intc)
+            Diff=np.nanmax(data_y_disc[:, i])-np.nanmin(data_y_disc[:, i])
+            av_prom_Keep=fit_params_disc['Diad1_abs_prom'].iloc[i]
+            prom_disc=prom_disc+av_prom_disc
+            ax1.plot(x_cord+i*5, (data_y_disc[:, i]-np.nanmin(data_y_disc[:, i]))/Diff+i/3, '-r', lw=0.5)
+            yplot=np.quantile((data_y_disc[:, i]-np.nanmin(data_y_disc[:, i]))/Diff+i/3, 0.65)
+            file=fit_params_disc['filename'].iloc[i]
+            file = file.replace("_CRR_DiadFit", "")
+            ax1.annotate(str(file), xy=(1450+i*5, yplot),
+                    xycoords="data", fontsize=8, bbox=dict(facecolor='white', edgecolor='none', pad=2))
+
+        ax1.set_xlim([1250, 1500+i*5])
+        ax1.set_xticks([])
+        ax1.set_yticks([])
+    if sum(filt)>0:
+        for i in range(0, np.shape(data_y_filt)[1]):
+            Diff=np.nanmax(data_y_filt[:, i])-np.nanmin(data_y_filt[:, i])
+            av_prom_Keep=fit_params_filt['Diad1_abs_prom'].iloc[i]
+            prom_filt=prom_filt+av_prom_Keep
+            file=fit_params_filt['filename'].iloc[i]
+            ax2.plot(x_cord+i*5, (data_y_filt[:, i]-np.nanmin(data_y_filt[:, i]))/Diff+i/3, '-b', lw=0.5)
+            yplot=np.quantile((data_y_filt[:, i]-np.nanmin(data_y_filt[:, i]))/Diff+i/3, 0.65)
+            ax2.annotate(str(file), xy=(1450+i*5, yplot),
+                    xycoords="data", fontsize=8, bbox=dict(facecolor='white', edgecolor='none', pad=2))
+
+
+        ax2.set_xlim([1250, 1450+i*5])
+        ax2.set_xticks([])
+        ax2.set_yticks([])
+
+    return fit_params_filt.reset_index(drop=True), data_y_filt, fit_params_disc.reset_index(drop=True), data_y_disc
+
 
 def identify_diad_group(*, fit_params, data_y,  x_cord, filter_bool,y_fig_scale=0.1, grp_filter='Weak', str_filt=None):
 

DiadFit/error_propagation.py

@@ -331,6 +331,8 @@ error_CO2_dens=0, error_type_CO2_dens='Abs', error_dist_CO2_dens='normal',
 
 # Check for panda Series
 
+
+
 def convert_inputs_to_series(T_K, error_T_K, CO2_dens_gcm3, error_CO2_dens_gcm3, XH2O, error_XH2O):
     # Create a list of all inputs
     inputs = [T_K, error_T_K, CO2_dens_gcm3, error_CO2_dens_gcm3, XH2O, error_XH2O]
@@ -341,11 +343,17 @@ def convert_inputs_to_series(T_K, error_T_K, CO2_dens_gcm3, error_CO2_dens_gcm3,
     # Unpack the converted inputs back to their respective variables
     T_K, error_T_K, CO2_dens_gcm3, error_CO2_dens_gcm3, XH2O, error_XH2O = converted_inputs
     
-    # Continue with the function using the possibly converted inputs...
-    # For demonstration, just return the converted inputs
-    return T_K, error_T_K, CO2_dens_gcm3, error_CO2_dens_gcm3, XH2O, error_XH2O
-    
+    # Reset index only if the input is a pandas Series
+    T_K = T_K.reset_index(drop=True) if isinstance(T_K, pd.Series) else T_K
+    error_T_K = error_T_K.reset_index(drop=True) if isinstance(error_T_K, pd.Series) else error_T_K
+    CO2_dens_gcm3 = CO2_dens_gcm3.reset_index(drop=True) if isinstance(CO2_dens_gcm3, pd.Series) else CO2_dens_gcm3
+    error_CO2_dens_gcm3 = error_CO2_dens_gcm3.reset_index(drop=True) if isinstance(error_CO2_dens_gcm3, pd.Series) else error_CO2_dens_gcm3
+    XH2O = XH2O.reset_index(drop=True) if isinstance(XH2O, pd.Series) else XH2O
+    error_XH2O = error_XH2O.reset_index(drop=True) if isinstance(error_XH2O, pd.Series) else error_XH2O
     
+    # Return the possibly converted inputs
+    return T_K, error_T_K, CO2_dens_gcm3, error_CO2_dens_gcm3, XH2O, error_XH2O
+
 
 
 def propagate_FI_uncertainty(sample_ID, CO2_dens_gcm3, T_K, multiprocess='default',  cores='default', 

{DiadFit-1.0.1.dist-info → DiadFit-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.1
+Version: 1.0.2
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

{DiadFit-1.0.1.dist-info → DiadFit-1.0.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-DiadFit/CO2_EOS.py,sha256=ti9HEZynM-BoiPGYG1C7vUpO-RNZY-NqmjUl2FFnO3E,73918
+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/Highrho_polyfit_data.pkl,sha256=7t6uXxI-HdfsvreAWORzMa9dXxUsnXqKBSo1O3EgiBw,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=e_2FV9coO7Ff17u_XZSeherC0HKwQWI8n-EaEUoHEuU,295
+DiadFit/_version.py,sha256=X0PLLhZnpIdwlS5nJADl6Y4cVKJ40aHv2hvu4kkgAGQ,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/density_depth_crustal_profiles.py,sha256=b072IJaoGDydKpqWWKoJHeXKIkcIXxKf82whpvLAPpw,17761
-DiadFit/diads.py,sha256=PmCIxMXU6O5zFQWzQmhwkqEVoRDyw89ogKTYjIAvvMg,177423
-DiadFit/error_propagation.py,sha256=STJUqjdhwo0geXi0iZ9XN0RD3t7qYqbNGHzelfLOANQ,50038
+DiadFit/diads.py,sha256=RWFesTt_W52u_-N9Cr2VtHuKrR038XKf3-dDLx5CNYY,180888
+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-1.0.1.dist-info/METADATA,sha256=JVJSzMb7lAJj2u6IRmjuZRfn5i6um5XOl-jj3ISQU58,1174
-DiadFit-1.0.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-DiadFit-1.0.1.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
-DiadFit-1.0.1.dist-info/RECORD,,
+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,,