DiadFit 0.0.88__py3-none-any.whl → 1.0.0__py3-none-any.whl

DiadFit/CO2_in_bubble_error.py

@@ -90,10 +90,16 @@ plot_figure=True, fig_i=0, neg_values=True):
     """
     # Constant for sphere calcs
 
+
      # Lets check what they entered for volume - if they didnt enter a volume % Bubble, lets calculate it
     if vol_perc_bub is None:
-        Vol_VB_sphere=const*VB_x*VB_y*VB_z
-        Vol_MI_sphere=const*MI_x*MI_y*MI_z
+        if VB_z is None:
+            VB_z=(VB_x+VB_y)/2
+        if MI_z is None:
+            MI_z=(MI_x+MI_y)/2
+
+        Vol_VB_sphere=const*VB_x*VB_y*VB_z*(0.5)**3
+        Vol_MI_sphere=const*MI_x*MI_y*MI_z*(0.5)**3
         vol_perc_bub=100* Vol_VB_sphere/Vol_MI_sphere
 
     # Now lets check how they entered error in volume
@@ -128,6 +134,7 @@ plot_figure=True, fig_i=0, neg_values=True):
 
 
 
+
     #This loops through each sample
     for i in range(0, len_loop):
         if i % 20 == 0:
@@ -152,6 +159,7 @@ plot_figure=True, fig_i=0, neg_values=True):
 
         # This is the function doing the work to actually make the simulations for each variable.
         if error_vol_perc_bub is not None:
+            print('didnt get inside else loop')
 
             df_synthetic=propagate_CO2_in_bubble_ind(
     N_dup=N_dup,
@@ -169,15 +177,27 @@ plot_figure=True, fig_i=0, neg_values=True):
     error_dist_melt_dens_kgm3=error_dist_melt_dens_kgm3,
     len_loop=1, neg_values=neg_values)
 
+
+
         else:
 
+
             # This is the more complex one where we have to account for x-y-z errors on all of them.
             MI_x_i = get_value(MI_x, i)
             MI_y_i = get_value(MI_y, i)
-            MI_z_i = get_value(MI_z, i)
+
+
+
             VB_x_i = get_value(VB_x, i)
             VB_y_i = get_value(VB_y, i)
+
+
+
+
             VB_z_i = get_value(VB_z, i)
+            MI_z_i = get_value(MI_z, i)
+
+
 
             error_MI_x_i = get_value(error_MI_x, i)
             error_MI_y_i = get_value(error_MI_y, i)
@@ -299,11 +319,33 @@ error_type_dimension=error_type_dimension, error_dist_dimension=error_dist_dimen
 
     return df_step, All_outputs, fig if 'fig' in locals() else None
 
-
+# Lets set the random seed
+np.random.seed(42)
 
 def add_noise_to_variable(original_value, error, error_type, error_dist, N_dup, neg_values, neg_threshold):
         """ This function adds noise to each variable for the monte-carloing
 
+        Parameters
+        -----------------
+        original_value: int, float
+            Preferred value (e.g. center of distribution)
+
+        error: int, float
+            Error value
+
+        error_type: str
+            'Abs' if absolute error, 'Perc' if percent
+
+        error_dist: str
+            'normal' if normally distributed, 'uniform' if uniformly distributed.
+
+        N_dup: int
+            number of duplicates
+
+        neg_values: bool
+            whether negative values are replaced with zeros
+
+
         """
 
         #  Depending on the error type, allocates an error
@@ -351,14 +393,47 @@ error_melt_dens_kgm3=0, error_type_melt_dens_kgm3='Abs', error_dist_melt_dens_kg
 
     Parameters
     ----------------
+    For volumes, either enter vol% bubble and associated errors...
+
+    vol_perc_bub: int, float, pd.series
+        Volume proportion of sulfide in melt inclusion
+
+
+    error_vol_perc_bub, CO2_bub_dens_gcm3, error_melt_dens_kgm3: int, float, pd.Series
+        Error for each variable, can be absolute or %
+
+    error_type_vol_perc_bub, error_type_bub_dens_gcm3, error_type_melt_dens_kgm3: 'Abs' or 'Perc'
+        whether given error is perc or absolute
+
+    error_dist_vol_perc_bub, error_dist_bub_dens_gcm3, error_dist_melt_dens_kgm3: 'normal' or 'uniform'
+        Distribution of simulated error
+
+
+    OR
+    Enter melt inclusion and vapour bubble dimensions (diameter, not radii), and their errors
+    MI_x, MI_y, MI_z, VB_x, VB_y, VB_z: int, float, series:
+        Diameter of melt inclusions.
+
+    error_MI_x, error_MI_y, error_MI_z, error_VB_x, error_VB_y, error_VB_z:
+        Error on diameter of melt inclusions
+
+    error_type_dimension='Abs' or 'Perc':
+        Specify whether errors on these dimensions are absolute or percentage
+
+    error_dist_dimension='normal' or 'uniform':
+        Specify error distribution
+
+
+
+
+
     SampleID: str, pd.series
         Sample_ID (e.g. sample names) which is returned on dataframe
 
     N_dup: int
         Number of duplicates when generating errors for Monte Carlo simulations
 
-    vol_perc_bub: int, float, pd.series
-        Volume proportion of sulfide in melt inclusion
+
 
     melt_dens_kgm3:int, float, pd.series
         Density of the silicate melt in kg/m3, e.g. from DensityX
@@ -367,14 +442,6 @@ error_melt_dens_kgm3=0, error_type_melt_dens_kgm3='Abs', error_dist_melt_dens_kg
         Density of the vapour bubble in g/cm3
 
 
-    error_vol_perc_bub, CO2_bub_dens_gcm3, error_melt_dens_kgm3: int, float, pd.Series
-        Error for each variable, can be absolute or %
-
-    error_type_vol_perc_bub, error_type_bub_dens_gcm3, error_type_melt_dens_kgm3: 'Abs' or 'Perc'
-        whether given error is perc or absolute
-
-    error_dist_vol_perc_bub, error_dist_bub_dens_gcm3, error_dist_melt_dens_kgm3: 'normal' or 'uniform'
-        Distribution of simulated error
 
     plot_figure: bool
         Default true - plots a figure of the row indicated by fig_i (default 1st row, fig_i=0)
@@ -412,32 +479,37 @@ error_melt_dens_kgm3=0, error_type_melt_dens_kgm3='Abs', error_dist_melt_dens_kg
 
     # Volume error distribution - if they give a volume percentage rather than dimensions
     if error_vol_perc_bub is not None:
+        print('using error on the bubble volume percent, not the entered dimensions, as error_vol_perc_bub was not None')
         # Easy peasy
         Vol_with_noise=add_noise_to_variable(vol_perc_bub, error_vol_perc_bub,
         error_type_vol_perc_bub, error_dist_vol_perc_bub,  N_dup, neg_values, neg_threshold=0.0000000001)
 
+
     else:
+
         x_MI_with_noise=add_noise_to_variable(MI_x, error_MI_x,
         error_type_dimension, error_dist_dimension, N_dup, neg_values, neg_threshold=0.0000000001)
 
         y_MI_with_noise=add_noise_to_variable(MI_y, error_MI_y,
         error_type_dimension, error_dist_dimension, N_dup, neg_values, neg_threshold=0.0000000001)
 
-        z_MI_with_noise=add_noise_to_variable(MI_z, error_MI_z,
-        error_type_dimension, error_dist_dimension, N_dup, neg_values, neg_threshold=0.0000000001)
-
         x_VB_with_noise=add_noise_to_variable(VB_x, error_VB_x,
         error_type_dimension, error_dist_dimension,  N_dup, neg_values, neg_threshold=0.0000000001)
 
         y_VB_with_noise=add_noise_to_variable(VB_y, error_VB_y,
         error_type_dimension, error_dist_dimension, N_dup, neg_values, neg_threshold=0.0000000001)
 
+
+        z_MI_with_noise=add_noise_to_variable(MI_z, error_MI_z,
+        error_type_dimension, error_dist_dimension, N_dup, neg_values, neg_threshold=0.0000000001)
+
+
         z_VB_with_noise=add_noise_to_variable(VB_z, error_VB_z,
         error_type_dimension, error_dist_dimension, N_dup, neg_values, neg_threshold=0.0000000001)
 
 
-        Vol_VB_sphere_with_noise=const*x_VB_with_noise*y_VB_with_noise*z_VB_with_noise
-        Vol_MI_sphere_with_noise=const*x_MI_with_noise*y_MI_with_noise*z_MI_with_noise
+        Vol_VB_sphere_with_noise=const*x_VB_with_noise*y_VB_with_noise*z_VB_with_noise*(0.5)**3
+        Vol_MI_sphere_with_noise=const*x_MI_with_noise*y_MI_with_noise*z_MI_with_noise*(0.5)**3
         Vol_with_noise=100* Vol_VB_sphere_with_noise/Vol_MI_sphere_with_noise
 
 

DiadFit/__init__.py

@@ -36,7 +36,7 @@ from DiadFit.error_propagation import *
 
 from DiadFit.density_depth_crustal_profiles import *
 from DiadFit.CO2_EOS import *
-from DiadFit.CO2_H2O_EOS import *
+
 
 from DiadFit.CO2_in_bubble_error import *
 

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__ = '0.0.88'
+__version__ = '1.0.0'

DiadFit/densimeters.py

@@ -512,6 +512,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
 
     # IF temp is 37
     if lab=='CMASS' and temp=='SupCrit':
+        print('yes')
         # This gets the densimeter at low density
         pickle_str_lowr='Lowrho_polyfit_data_CMASS.pkl'
         with open(DiadFit_dir/pickle_str_lowr, 'rb') as f:
@@ -529,7 +530,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
             
     
             
-    if lab=='CMASS' and temp=='RoomT':
+    elif lab=='CMASS' and temp=='RoomT':
         # This gets the densimeter at low density
         pickle_str_lowr='Lowrho_polyfit_data_CMASS_24C.pkl'
         with open(DiadFit_dir/pickle_str_lowr, 'rb') as f:
@@ -544,7 +545,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
             
             
             
-    elif lab=='CCMR':
+    elif lab=='CCMR' and temp=='SupCrit':
         pickle_str_lowr='Lowrho_polyfit_data_CCMR.pkl'
         with open(DiadFit_dir/pickle_str_lowr, 'rb') as f:
             lowrho_pickle_data = pickle.load(f)
@@ -556,11 +557,12 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
         # This gets the densimeter at high density.
         pickle_str_highr='Highrho_polyfit_data_CCMR.pkl'
         with open(DiadFit_dir/pickle_str_highr, 'rb') as f:
-            highrho_pickle_data = pickle.load(f)        
+            highrho_pickle_data = pickle.load(f)       
+            
         
     
     else:
-        raise TypeError('Lab name not recognised. enter CCMR or CMASS')
+        raise TypeError('Lab name not recognised. enter CCMR SupCrit, CMASS SupCrit, CMASS roomT (CCMR room T can be added on request to Penny)')
 
     # this allocates the model
     lowrho_model = lowrho_pickle_data['model']
@@ -626,7 +628,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
     # If splitting is 0
     zero=df['Corrected_Splitting']==0
 
-
+    # Cut off values -------------------------------------------
     # Range for SC low density
     min_lowD_SC_Split=df['Corrected_Splitting']>=102.7623598753032
     max_lowD_SC_Split=df['Corrected_Splitting']<=103.1741034592534
@@ -642,6 +644,8 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
     # Range for Room T high density
     min_HD_RoomT_Split=df['Corrected_Splitting']>=104.407308904012
     max_HD_RoomT_Split=df['Corrected_Splitting']<=105.1
+    
+
     # Impossible densities, room T
     Imposs_lower_end=(df['Corrected_Splitting']>103.350311768435) & (df['Corrected_Splitting']<103.88)
     # Impossible densities, room T

DiadFit/diads.py

@@ -5,6 +5,8 @@ from matplotlib import patches
 import lmfit
 from lmfit.models import GaussianModel, VoigtModel, LinearModel, ConstantModel, PseudoVoigtModel, Pearson4Model
 from scipy.signal import find_peaks
+from scipy.signal.windows import gaussian
+
 import os
 import re
 from os import listdir