DiadFit 1.0.8__tar.gz → 1.0.9__tar.gz

{DiadFit-1.0.8 → DiadFit-1.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.8
+Version: 1.0.9
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

{DiadFit-1.0.8 → DiadFit-1.0.9}/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__ = '1.0.8'
+__version__ = '1.0.9'

{DiadFit-1.0.8 → DiadFit-1.0.9}/src/DiadFit/densimeter_fitting.py

@@ -15,6 +15,7 @@ from scipy import stats
 
 encode="ISO-8859-1"
 
+## Files are fit using the folder UCB_cali_fitting_1117_1447
 
 def calculate_generic_std_err_values(*, pickle_str, new_x, CI=0.67):
 

{DiadFit-1.0.8 → DiadFit-1.0.9}/src/DiadFit/densimeters.py

@@ -994,7 +994,7 @@ CI_split=0.67, CI_neon=0.67,  Ne_pickle_str=None, pref_Ne=None, Ne_err=None, cor
     corrected_split: pd.Series
         Corrected splitting  (cm-1)  
         
-    Split_err: float, int
+    split_err: float, int
         Error on corrected splitting
 
     temp: str

{DiadFit-1.0.8 → DiadFit-1.0.9}/src/DiadFit/diads.py

@@ -33,54 +33,7 @@ allowed_models = ["VoigtModel", "PseudoVoigtModel", "Pearson4Model", "SkewedVoig
 #warnings.simplefilter('error')
 
 encode="ISO-8859-1"
-## Ratio of different peaks
 
-
-def calculate_SO2_CO2_ratio(SO2_area, diad1_area, diad2_area, SO2_cross_sec=5.3, diad1_cross_sec=0.89, diad2_cross_sec=1.4):
-    """ Calculates SO2:CO2 ratio using the parameters from Marie-Camille Caumons lab"""
-
-
-    A_CO2_star=( diad1_area + diad2_area)/(diad2_cross_sec+diad1_cross_sec)
-    A_SO2_star=(SO2_area)/(SO2_cross_sec)
-    Ratio=A_SO2_star/(A_SO2_star+A_CO2_star)
-
-    return Ratio
-
-def calculate_mole_fraction_2comp(peak_area_a, peak_area_b, cross_section_a, cross_section_b, instrument_eff_a, instrument_eff_b):
-    """ This function calculates the molar ration of 2 components a and b based on peak areas,
-    cross section and instrument efficiency
-
-    Parameters
-    ------------
-
-    peak_area_a: int, float, pd.Series, np.array
-        Peak area of component a
-
-    peak_area_b: int, float, pd.Series, np.array
-        Peak area of component b
-
-    cross_section_a, cross_section_a: int, float
-        Raman cross section for component a and b
-
-    instrument_eff_a, instrument_eff_b: int, float
-        Instrument effeciency of a and b.
-
-    Returns
-    ------------
-    pd.DataFrame
-        Molar ratio of a/b
-
-
-    """
-
-    Sum_phase_a=peak_area_a/(cross_section_a*instrument_eff_a)
-    Sum_phase_b=peak_area_b/(cross_section_b*instrument_eff_b)
-
-    df=pd.DataFrame(data={'% A': 100*Sum_phase_a/(Sum_phase_b+Sum_phase_a),
-    '% B': 100-100*Sum_phase_a/(Sum_phase_b+Sum_phase_a)}
-    )
-
-    return df
 def plot_diad(*,path=None, filename=None, filetype='Witec_ASCII', Spectra_x=None, Spectra_y=None):
     """This function makes a plot of the spectra for a specific file to allow visual inspectoin
 

DiadFit-1.0.9/src/DiadFit/molar_gas_proportions.py

@@ -0,0 +1,231 @@
+import math
+import pandas as pd
+import numpy as np
+
+
+
+
+
+
+# def calculate_sigma(wavelength, vi_dict, T_K):
+#     """
+#     This function calculates the σ cross section according to wavelength based on Burke (2001) EQ(1), you must provide:
+# ### 1) the peak shift of the species, 2) temp (doesn't really matter) and 3) Σ (wavelength-independent relative Raman scattering cross-sections).
+#     """
+#     c = 2.998 * 10**10  # cm/s light speed
+#     h = 6.626 * 10**-27  # erg.s Planck constant
+#     k = 1.381 * 10**-16  # erg/K Boltzmann's constant
+#
+#     v0 = 1 / (wavelength * 10**-7)
+#
+#     sigma_results = {}
+#     for name, vi_info in vi_dict.items():
+#         vi = vi_info["Peak_shift_cm-1"]
+#         BigSigma = vi_info["Σ"]
+#
+#         result = BigSigma / (((v0 - vi)**-4 / (v0 - 2331)**-4) * (1 - math.exp(-h * c * vi / (k * T_K))))
+#         sigma_results[name] = round(result, 2)
+#
+#     return sigma_results
+#
+#
+#
+#
+# def calculate_mole_percent(components):
+#     """ This function calculates the mole percents of the components entered, based on Burke (2001) EQ(2)
+#     """
+#     def partial_molec_contribution_single(A, sigma, squiggle):
+#         return A / (sigma * squiggle)
+#
+#     def partial_molec_contribution_double(A1, sigma1, A2, sigma2, squiggle):
+#         return (A1 + A2) / ((sigma1 + sigma2) * squiggle)
+#
+#     total_partials = 0
+#     partials = []
+#
+#     for component in components:
+#         if component['name'] == 'CO2':
+#             partial = partial_molec_contribution_double(component['peak_area_1'], component['cross_section_1'],
+#                                                        component['peak_area_2'], component['cross_section_2'],
+#                                                        component['efficiency'])
+#         else:
+#             partial = partial_molec_contribution_single(component['peak_area'], component['cross_section'],
+#                                                         component['efficiency'])
+#
+#         partials.append(partial)
+#         total_partials += partial
+#
+#     mole_percentages = [round((partial / total_partials) * 100, 1) for partial in partials]
+#
+#     mole_percent_dict = {component['name']: mole_percent for component, mole_percent in zip(components, mole_percentages)}
+#     mole_percent_dict['Mole_Percent_Sum'] = sum(mole_percentages)
+#
+#     return mole_percent_dict
+
+
+#
+#
+# def calculate_CO2_SO2_ratio(*, peak_area_SO2, peak_area_diad1, peak_area_diad2,wavelength=532.067, T_K=37+273.15,efficiency_SO2=1, efficiency_CO2=0.5, sigma_SO2=4.03, sigma_CO2_v1=0.8, sigma_CO2_v2=1.23):
+#
+#   # First we need to calculate the oarameters
+#
+#   component_dict = {
+#     "SO2": {"Peak_shift_cm-1": 1151, "Σ": sigma_SO2},
+#     "CO2_v1": {"Peak_shift_cm-1": 1285, "Σ": sigma_CO2_v1},
+#     "CO2_2v2": {"Peak_shift_cm-1": 1388, "Σ": sigma_CO2_v2}}
+# ### "Σ" is the wavelength independent relative cross-section
+#
+#   sigma_results = calculate_sigma(wavelength=wavelength, vi_dict=component_dict, T_K=T_K)
+#
+#     # Now lets allocate these calculations
+#   components = [
+#         {'name': 'SO2',
+#         'peak_area': peak_area_SO2,
+#         'cross_section':  sigma_results['SO2'],
+#         'efficiency': efficiency_SO2},
+#         {'name': 'CO2',
+#           'peak_area_1':peak_area_diad2, 'cross_section_1': sigma_results['CO2_2v2'],
+#         'peak_area_2': peak_area_diad1, 'cross_section_2': sigma_results['CO2_v1'], 'efficiency': efficiency_CO2}
+#     ]
+#   mol_perc=calculate_mole_percent(components)
+#
+#
+#   return pd.DataFrame(mol_perc)
+
+
+
+  ## Math for converting back and forth between Raman scattering cross sections
+
+def calculate_wavelength_dependent_cross_section(wavelength_nm, T_C, Raman_shift_cm, wavelength_independent_cross_section ):
+    """ This function calculates the wavelength dependent cross section (lower case sigma) from the wavelength independent Raman scattering efficiency (Upper case sigma)
+
+      Parameters
+       ----------------
+        wavelength_nm:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
+
+        wavelength_independent_cross_section:
+            Wavelength independent cross section
+
+        T_K:
+            absolute temperature in Kelvin
+
+        Raman_shift_cm:
+            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
+
+        Returns
+        -----------------
+        Wavelength dependent cross section
+
+          """
+    Wavelength_cm1=1/wavelength_nm*10000000
+    constant =1-np.exp(((-6.626*10**-27)*(2.998*10**10)*Raman_shift_cm)/((1.381*10**-16)*(273.15+T_C)))
+    Wavelength_dependent = wavelength_independent_cross_section/(((Wavelength_cm1-Raman_shift_cm)**(-4)/(Wavelength_cm1-2331)**(-4))*constant)
+    return Wavelength_dependent
+
+def calculate_wavelength_independent_cross_section(wavelength_nm, T_C, Raman_shift_cm, wavelength_dependent_cross_section ):
+    """ This function calculates the wavelength independent cross section (capital Sigma) from the wavelength dependent Raman scattering efficiency (lower case sigma)
+
+      Parameters
+       ----------------
+        wavelength_nm:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
+
+        wavelength_dependent_cross_section:
+            Wavelength dependent cross section
+
+        T_K:
+            absolute temperature in Kelvin
+
+        Raman_shift_cm:
+            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
+
+        Returns
+        -----------------
+        Wavelength independent cross section
+
+          """
+    Wavelength_cm1=1/wavelength_nm*10000000
+    constant =1-np.exp(((-6.626*10**-27)*(2.998*10**10)*Raman_shift_cm)/((1.381*10**-16)*(273.15+T_C)))
+    Wavelength_independent = wavelength_dependent_cross_section*((Wavelength_cm1-Raman_shift_cm)**(-4)/(Wavelength_cm1-2331)**(-4)*constant)
+    return Wavelength_independent
+
+def convert_cross_section_wavelength1_wavelength2(wavelength_nm_1,wavelength_nm_2,  Raman_shift_cm, wavelength_dependent_cross_section_wavelength1, T_C):
+   """ This function calculates the wavelength dependent cross section (lower case sigma) for laser wavelength 2 from the wavelength-dependent cross section for laser wavelength 1.
+
+
+      Parameters
+       ----------------
+        wavelength_nm_1:
+            laser wavelength used in nm to calculate the wavelength dependent cross section
+
+        wavelength_nm_2:
+            laser wavelength of the system of interest you are trying to calculate the wavelength dependent cross section for
+
+        wavelength_dependent_cross_section_wavelength1:
+            Wavelength dependent cross section
+
+        T_K:
+            absolute temperature in Kelvin
+
+        Raman_shift_cm:
+            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
+
+        Returns
+        -----------------
+        Wavelength dependent cross section for wavelength2
+
+          """
+
+   # First calculate the independent cross section
+   ind_cross_sec=calculate_wavelength_independent_cross_section(wavelength_nm=wavelength_nm_1, T_C=T_C, Raman_shift_cm=Raman_shift_cm,
+                                                         wavelength_dependent_cross_section =wavelength_dependent_cross_section_wavelength1)
+   print(ind_cross_sec)
+   dep_cross_sec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm_2, T_C=T_C, Raman_shift_cm=Raman_shift_cm, wavelength_independent_cross_section =ind_cross_sec)
+
+   return dep_cross_sec
+
+def calculate_SO2_CO2_mol_prop_wave_indep(SO2_wavelength_ind, CO2_diad1_wavelength_ind, CO2_diad2_wavelength_ind, wavelength_nm, T_C,
+                               A_SO2, A_CO2_Tot):
+    """ Takes wavelength independnet cross sections and CO2 and SO2 peak areas and converts them into SO2 mol proportions
+    Parameters
+    ------------------
+
+    SO2_wavelength_ind: Wavelength independent cross section for SO2
+
+    CO2_diad1_wavelength_ind: Wavelength independent cross section for diad 1 (at 1285)
+
+    CO2_diad2_wavelength_ind: Wavelength independent cross section for diad 2 (at 1388)
+
+    wavelength_nm: Laser wavelenth of system in nm
+
+    T_C: Temperature of analysis in C.
+
+    Returns
+    ---------------
+
+    SO2 mol proportion
+
+
+    """
+
+    SO2_cross_sec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm, T_C=T_C, Raman_shift_cm=1151, wavelength_independent_cross_section=SO2_wavelength_ind)
+    CO2_diad1_xsec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm, T_C=T_C, Raman_shift_cm=1285, wavelength_independent_cross_section=CO2_diad1_wavelength_ind)
+    CO2_diad2_xsec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm, T_C=T_C, Raman_shift_cm=1388, wavelength_independent_cross_section=CO2_diad2_wavelength_ind)
+
+
+    SO2_prop=(A_SO2/SO2_cross_sec)/(A_CO2_Tot /(CO2_diad1_xsec + CO2_diad2_xsec) +  (A_SO2/SO2_cross_sec) )
+
+    return SO2_prop
+
+
+def calculate_SO2_CO2_ratio(SO2_area, diad1_area, diad2_area, SO2_cross_sec=5.3, diad1_cross_sec=0.89, diad2_cross_sec=1.4):
+    """ Calculates SO2:CO2 ratio using the parameters from Marie-Camille Caumons lab"""
+
+
+    A_CO2_star=( diad1_area + diad2_area)/(diad2_cross_sec+diad1_cross_sec)
+    A_SO2_star=(SO2_area)/(SO2_cross_sec)
+    Ratio=A_SO2_star/(A_SO2_star+A_CO2_star)
+
+    return Ratio
+

{DiadFit-1.0.8 → DiadFit-1.0.9}/src/DiadFit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.8
+Version: 1.0.9
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

DiadFit-1.0.8/src/DiadFit/molar_gas_proportions.py

@@ -1,183 +0,0 @@
-import math
-import pandas as pd
-import numpy as np
-
-def calculate_sigma(wavelength, vi_dict, T_K):
-    """
-    This function calculates the σ cross section according to wavelength based on Burke (2001) EQ(1), you must provide:
-### 1) the peak shift of the species, 2) temp (doesn't really matter) and 3) Σ (wavelength-independent relative Raman scattering cross-sections).
-    """
-    c = 2.998 * 10**10  # cm/s light speed
-    h = 6.626 * 10**-27  # erg.s Planck constant
-    k = 1.381 * 10**-16  # erg/K Boltzmann's constant
-
-    v0 = 1 / (wavelength * 10**-7)
-
-    sigma_results = {}
-    for name, vi_info in vi_dict.items():
-        vi = vi_info["Peak_shift_cm-1"]
-        BigSigma = vi_info["Σ"]
-
-        result = BigSigma / (((v0 - vi)**-4 / (v0 - 2331)**-4) * (1 - math.exp(-h * c * vi / (k * T_K))))
-        sigma_results[name] = round(result, 2)
-
-    return sigma_results
-
-
-
-
-def calculate_mole_percent(components):
-    """ This function calculates the mole percents of the components entered, based on Burke (2001) EQ(2)
-    """
-    def partial_molec_contribution_single(A, sigma, squiggle):
-        return A / (sigma * squiggle)
-
-    def partial_molec_contribution_double(A1, sigma1, A2, sigma2, squiggle):
-        return (A1 + A2) / ((sigma1 + sigma2) * squiggle)
-
-    total_partials = 0
-    partials = []
-
-    for component in components:
-        if component['name'] == 'CO2':
-            partial = partial_molec_contribution_double(component['peak_area_1'], component['cross_section_1'],
-                                                       component['peak_area_2'], component['cross_section_2'],
-                                                       component['efficiency'])
-        else:
-            partial = partial_molec_contribution_single(component['peak_area'], component['cross_section'],
-                                                        component['efficiency'])
-
-        partials.append(partial)
-        total_partials += partial
-
-    mole_percentages = [round((partial / total_partials) * 100, 1) for partial in partials]
-
-    mole_percent_dict = {component['name']: mole_percent for component, mole_percent in zip(components, mole_percentages)}
-    mole_percent_dict['Mole_Percent_Sum'] = sum(mole_percentages)
-
-    return mole_percent_dict
-
-
-
-
-def calculate_CO2_SO2_ratio(*, peak_area_SO2, peak_area_diad1, peak_area_diad2,wavelength=532.067, T_K=37+273.15,efficiency_SO2=1, efficiency_CO2=0.5, sigma_SO2=4.03, sigma_CO2_v1=0.8, sigma_CO2_v2=1.23):
-
-  # First we need to calculate the oarameters
-
-  component_dict = {
-    "SO2": {"Peak_shift_cm-1": 1151, "Σ": sigma_SO2},
-    "CO2_v1": {"Peak_shift_cm-1": 1285, "Σ": sigma_CO2_v1},
-    "CO2_2v2": {"Peak_shift_cm-1": 1388, "Σ": sigma_CO2_v2}}
-### "Σ" is the wavelength independent relative cross-section
-
-  sigma_results = calculate_sigma(wavelength=wavelength, vi_dict=component_dict, T_K=T_K)
-
-    # Now lets allocate these calculations
-  components = [
-        {'name': 'SO2',
-        'peak_area': peak_area_SO2,
-        'cross_section':  sigma_results['SO2'],
-        'efficiency': efficiency_SO2},
-        {'name': 'CO2',
-          'peak_area_1':peak_area_diad2, 'cross_section_1': sigma_results['CO2_2v2'],
-        'peak_area_2': peak_area_diad1, 'cross_section_2': sigma_results['CO2_v1'], 'efficiency': efficiency_CO2}
-    ]
-  mol_perc=calculate_mole_percent(components)
-
-
-  return pd.DataFrame(mol_perc)
-
-
-
-  ## Math for converting back and forth between Raman scattering cross sections
-
-def calculate_wavelength_dependent_cross_section(wavelength_nm, T_C, Raman_shift_cm, wavelength_independent_cross_section ):
-    """ This function calculates the wavelength dependent cross section (lower case sigma) from the wavelength independent Raman scattering efficiency (Upper case sigma)
-
-      Parameters
-       ----------------
-        wavelength_nm:
-            laser wavelength used in nm to calculate the wavelength dependent cross section
-
-        wavelength_independent_cross_section:
-            Wavelength independent cross section
-
-        T_K:
-            absolute temperature in Kelvin
-
-        Raman_shift_cm:
-            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
-
-        Returns
-        -----------------
-        Wavelength dependent cross section
-
-          """
-    Wavelength_cm1=1/wavelength_nm*10000000
-    constant =1-np.exp(((-6.626*10**-27)*(2.998*10**10)*Raman_shift_cm)/((1.381*10**-16)*(273.15+T_C)))
-    Wavelength_dependent = wavelength_independent_cross_section/(((Wavelength_cm1-Raman_shift_cm)**(-4)/(Wavelength_cm1-2331)**(-4))*constant)
-    return Wavelength_dependent
-
-def calculate_wavelength_independent_cross_section(wavelength_nm, T_C, Raman_shift_cm, wavelength_dependent_cross_section ):
-    """ This function calculates the wavelength independent cross section (capital Sigma) from the wavelength dependent Raman scattering efficiency (lower case sigma)
-
-      Parameters
-       ----------------
-        wavelength_nm:
-            laser wavelength used in nm to calculate the wavelength dependent cross section
-
-        wavelength_dependent_cross_section:
-            Wavelength dependent cross section
-
-        T_K:
-            absolute temperature in Kelvin
-
-        Raman_shift_cm:
-            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
-
-        Returns
-        -----------------
-        Wavelength independent cross section
-
-          """
-    Wavelength_cm1=1/wavelength_nm*10000000
-    constant =1-np.exp(((-6.626*10**-27)*(2.998*10**10)*Raman_shift_cm)/((1.381*10**-16)*(273.15+T_C)))
-    Wavelength_independent = wavelength_dependent_cross_section*((Wavelength_cm1-Raman_shift_cm)**(-4)/(Wavelength_cm1-2331)**(-4)*constant)
-    return Wavelength_independent
-
-def convert_cross_section_wavelength1_wavelength2(wavelength_nm_1,wavelength_nm_2,  Raman_shift_cm, wavelength_dependent_cross_section_wavelength1, T_C):
-   """ This function calculates the wavelength dependent cross section (lower case sigma) for laser wavelength 2 from the wavelength-dependent cross section for laser wavelength 1.
-
-
-      Parameters
-       ----------------
-        wavelength_nm_1:
-            laser wavelength used in nm to calculate the wavelength dependent cross section
-
-        wavelength_nm_2:
-            laser wavelength of the system of interest you are trying to calculate the wavelength dependent cross section for
-
-        wavelength_dependent_cross_section_wavelength1:
-            Wavelength dependent cross section
-
-        T_K:
-            absolute temperature in Kelvin
-
-        Raman_shift_cm:
-            Raman shift in cm-1 of peak of interest (e.g. 1151 for SO$_2$)
-
-        Returns
-        -----------------
-        Wavelength dependent cross section for wavelength2
-
-          """
-
-   # First calculate the independent cross section
-   ind_cross_sec=calculate_wavelength_independent_cross_section(wavelength_nm=wavelength_nm_1, T_C=T_C, Raman_shift_cm=Raman_shift_cm,
-                                                         wavelength_dependent_cross_section =wavelength_dependent_cross_section_wavelength1)
-   print(ind_cross_sec)
-   dep_cross_sec=calculate_wavelength_dependent_cross_section(wavelength_nm=wavelength_nm_2, T_C=T_C, Raman_shift_cm=Raman_shift_cm, wavelength_independent_cross_section =ind_cross_sec)
-
-   return dep_cross_sec
-
-