chromaquant 0.3.1__py3-none-any.whl → 0.4.0__py3-none-any.whl

chromaquant/Quant/QuantSub/gasTCD.py

@@ -0,0 +1,425 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+COPYRIGHT STATEMENT:
+
+ChromaQuant – A quantification software for complex gas chromatographic data
+
+Copyright (c) 2024, by Julia Hancock
+              Affiliation: Dr. Julie Elaine Rorrer
+	      URL: https://www.rorrerlab.com/
+
+License: BSD 3-Clause License
+
+---
+
+SUBPACKAGE FOR PERFORMING GAS TCD QUANTIFICATION STEPS
+
+Julia Hancock
+Started 12-29-2024
+
+"""
+""" PACKAGES """
+from chemformula import ChemFormula
+
+#Function for quantifying gas TCD data w/ volume estimation method, no pressure adjustment
+def gasTCD_VE(BreakdownDF,DBRF,gasBag_cond,peak_error):
+    
+    #Unpack gas bag conditions
+    temp = gasBag_cond[0]       #temperature of gas bag, C
+    pressure = gasBag_cond[1]   #sample pressure in gas bag, psi
+    co2 = gasBag_cond[2]        #CO2 volume, mL
+
+    #Initialize compound name column in BreakdownDF
+    BreakdownDF['Compound Name'] = 'None'
+    
+    #Function to find if CO2 peak exists
+    def getCO2(BreakdownDF,DBRF,TCD_cond,peak_error):
+        
+        #Unpack TCD conditions
+        co2 = TCD_cond[0]
+        pressure = TCD_cond[1]
+        temp = TCD_cond[2]
+        R = TCD_cond[3]
+        
+        #Find the CO2 peak row in DBRF
+        CO2_row = DBRF.loc[DBRF['Compound Name'] == "Carbon Dioxide"].iloc[0]
+        
+        #Get the retention time
+        CO2_RT = CO2_row['RT (min)']
+        
+        #Get the minimum and maximum of the RT range using the peak error
+        CO2_RTmin = CO2_RT - peak_error
+        CO2_RTmax = CO2_RT + peak_error
+        
+        #Define boolean describing whether or not CO2 match has been found
+        CO2_bool = False
+        #Define volume estimate
+        volume = 0
+        
+        #Iterate through every row in BreakdownDF
+        for i, row in BreakdownDF.iterrows():
+            
+            #If the TCD retention time is within range of the CO2 entry...
+            if CO2_RTmin <= row['RT'] <= CO2_RTmax:
+                
+                #Add the compound name to the breakdown dataframe
+                BreakdownDF.at[i,'Compound Name'] = 'Carbon Dioxide'
+                
+                #Add the other relevant information to the breakdown dataframe
+                BreakdownDF.at[i,'Formula'] = 'CO2'
+                BreakdownDF.at[i,'RF (Area/vol.%)'] = CO2_row['RF']
+                BreakdownDF.at[i,'MW (g/mol)'] = ChemFormula('CO2').formula_weight
+                
+                #Get volume percent using response factor
+                volpercent = row['Area']/CO2_row['RF']
+                BreakdownDF.at[i,'Vol.%'] = volpercent
+                
+                #Calculate total volume using volume percent
+                volume = co2 * 100 / volpercent   #total volume, m^3
+                
+                #Assign CO2 volume
+                BreakdownDF.at[i,'Volume (m^3)'] = co2
+                
+                #Get moles using ideal gas law (PV=nRT)
+                BreakdownDF.at[i,'Moles (mol)'] = co2*pressure/(temp*R)
+                
+                #Get mass (mg) using moles and molar mass
+                BreakdownDF.at[i,'Mass (mg)'] = BreakdownDF.at[i,'Moles (mol)'] * BreakdownDF.at[i,'MW (g/mol)'] * 1000
+                
+                #Set CO2_bool to True
+                CO2_bool = True
+                
+                break
+            
+            #Otherwise, pass
+            else:
+                pass
+        
+        return CO2_bool, volume, BreakdownDF
+    
+    #Add min and max peak assignment values to DBRF
+    for i, row in DBRF.iterrows():
+        DBRF.at[i,'RT Max'] = DBRF.at[i,'RT (min)'] + peak_error
+        DBRF.at[i,'RT Min'] = DBRF.at[i,'RT (min)'] - peak_error
+    
+    #Convert sinfo variables to new units
+    co2 = co2 / 10**6                     #volume injected CO2, m^3
+    temp = temp + 273.15                  #reactor temperature, K
+    pressure = pressure / 14.504*100000   #reactor pressure, Pa
+    
+    #Define ideal gas constant, m^3*Pa/K*mol
+    R = 8.314
+    
+    #Define variable to total volume (m^3)
+    V_TC = 0
+    
+    #Define list of conditions
+    TCD_cond = [co2,pressure,temp,R]
+    
+    #Check if there is a peak in the BreakdownDF that can be assigned to CO2
+    CO2_bool, V_TC, BreakdownDF = getCO2(BreakdownDF,DBRF,TCD_cond,peak_error)
+    
+    if CO2_bool:
+        #Iterate through every row in BreakdownDF
+        for i, row in BreakdownDF.iterrows():
+            
+            #Iterate through every row in DBRF
+            for i2, row2 in DBRF.iterrows():
+                
+                #If the TCD retention time is within the range for a given DBRF entry...
+                if row2['RT Min'] <= row['RT'] <= row2['RT Max']:
+                    
+                    #Add the compound name to the breakdown dataframe
+                    BreakdownDF.at[i,'Compound Name'] = row2['Compound Name']
+                    
+                    #Add the other relevant information to the breakdown dataframe
+                    BreakdownDF.at[i,'Formula'] = row2['Formula']
+                    BreakdownDF.at[i,'RF (Area/vol.%)'] = row2['RF']
+                    BreakdownDF.at[i,'MW (g/mol)'] = ChemFormula(row2['Formula']).formula_weight
+                    
+                    #Get volume percent using response factor
+                    volpercent = row['Area']/row2['RF']
+                    BreakdownDF.at[i,'Vol.%'] = volpercent
+                    
+                    #Get volume using volume percent
+                    vol = V_TC*volpercent/100
+                    BreakdownDF.at[i,'Volume (m^3)'] = vol
+                    
+                    #Get moles using ideal gas law (PV=nRT)
+                    BreakdownDF.at[i,'Moles (mol)'] = vol*pressure/(temp*R)
+                    
+                    #Get mass (mg) using moles and molar mass
+                    BreakdownDF.at[i,'Mass (mg)'] = BreakdownDF.at[i,'Moles (mol)'] * BreakdownDF.at[i,'MW (g/mol)'] * 1000
+                
+                #Otherwise, pass    
+                else:
+                    pass
+    #Otherwise, pass
+    else:
+        pass
+    
+    #Convert total volume to mL
+    V_TC *= 10**6
+
+    return BreakdownDF, V_TC
+
+#Function for quantifying gas TCD data w/ scale factor method
+def gasTCD_SF(BreakdownDF,DBRF,gasBag_cond,reactor_cond,peak_error):
+    
+    #Initialize compound name column in BreakdownDF
+    BreakdownDF['Compound Name'] = 'None'
+    
+    #Function to determine total volume using ideal gas law
+    def volumeIGL(V_C,reactor_cond):
+
+        #Unpack reactor conditions
+        P_f = reactor_cond[0]       #reactor quench pressure, psig
+        V_R = reactor_cond[1]       #reactor internal volume, mL
+        P_0 = reactor_cond[2]       #atmospheric pressure, psi
+
+        #Estimate total volume of gas bag, mL
+        V_T = V_R * (P_f + P_0) / P_0
+
+        #Estimate total volume of gas bag plus volume CO2, mL
+        V_TC = V_T + V_C
+
+        return V_T, V_TC
+
+    # Function to estimate scale factor from CO2
+    def getScaleFactor(BreakdownDF,DBRF,V_C,V_TC):
+
+        #Find the CO2 peak row in DBRF
+        CO2_row = DBRF.loc[DBRF['Compound Name'] == "Carbon Dioxide"].iloc[0]
+        
+        #Get the retention time
+        CO2_RT = CO2_row['RT (min)']
+        
+        #Get the minimum and maximum of the RT range using the peak error
+        CO2_RTmin = CO2_RT - peak_error
+        CO2_RTmax = CO2_RT + peak_error
+        
+        #Define boolean describing whether or not CO2 match has been found
+        CO2_bool = False
+
+        #Iterate through every row in BreakdownDF
+        for i, row in BreakdownDF.iterrows():
+            
+            #If the TCD retention time is within range of the CO2 entry...
+            if CO2_RTmin <= row['RT'] <= CO2_RTmax:
+                
+                #Get estimated volume fraction of CO2
+                psiCO2_e = row['Area'] / (100 * CO2_row['RF'])
+
+                #Get actual volume fraction of CO2
+                psiCO2_a = V_C / V_TC
+
+                #Define scale factor as ratio of actual volume fraction to estimated volume fraction
+                SF = psiCO2_a / psiCO2_e
+
+                #Set CO2_bool to True
+                CO2_bool = True
+                
+                break
+            
+            #Otherwise, pass
+            else:
+                pass
+
+        #Raise error if no CO2 peak found
+        if CO2_bool == False:
+            raise Exception("[gasTCD][ERROR] No CO2 peak found in TCD")
+
+        else:
+            pass
+
+        return SF
+
+    #Function to calculate amounts of each species using the scale factor
+    def quantTCD(BreakdownDF,DBRF,gasBag_cond,reactor_cond):
+
+        # Unpack gas bag conditions
+        GB_temp = gasBag_cond[0]       # Temperature of gas bag, C
+        GB_pressure = gasBag_cond[1]   # Sample pressure in gas bag, psig
+        V_C = gasBag_cond[2]           # CO2 volume, mL
+
+        # Get total and total+CO2 gas bag volumes
+        V_T, V_TC = volumeIGL(V_C,reactor_cond)
+
+        # Define ideal gas constant, m^3*Pa/K*mol
+        R = 8.314
+
+        #Define conversion factor, Pa * m^3 * psi^-1 * mL^-1
+        C = 0.00689476
+
+        #Get scale factor
+        SF = getScaleFactor(BreakdownDF,DBRF,V_C,V_TC)
+
+        #Add min and max peak assignment values to DBRF
+        for i, row in DBRF.iterrows():
+            DBRF.at[i,'RT Max'] = DBRF.at[i,'RT (min)'] + peak_error
+            DBRF.at[i,'RT Min'] = DBRF.at[i,'RT (min)'] - peak_error
+
+        #Iterate through every row in BreakdownDF
+        for i, row in BreakdownDF.iterrows():
+            
+            #Iterate through every row in DBRF
+            for i2, row2 in DBRF.iterrows():
+                
+                #If the TCD retention time is within the range for a given DBRF entry...
+                if row2['RT Min'] <= row['RT'] <= row2['RT Max']:
+                    
+                    #Add the compound name to the breakdown dataframe
+                    BreakdownDF.at[i,'Compound Name'] = row2['Compound Name']
+                    
+                    #Add the other relevant information to the breakdown dataframe
+                    BreakdownDF.at[i,'Formula'] = row2['Formula']
+                    BreakdownDF.at[i,'RF (Area/vol.%)'] = row2['RF']
+                    BreakdownDF.at[i,'MW (g/mol)'] = ChemFormula(row2['Formula']).formula_weight
+                    
+                    #Get estimated volume percent using response factor
+                    volpercent_e = row['Area']/row2['RF']
+                    BreakdownDF.at[i,'Est. Vol.%'] = volpercent_e
+
+                    #Get adjusted volume percent using scale factor
+                    volpercent_a = volpercent_e * SF
+                    BreakdownDF.at[i,'Adj. Vol.%'] = volpercent_a
+                    
+                    #Get moles using ideal gas law (PV=nRT)
+                    BreakdownDF.at[i,'Moles (mol)'] = C * (GB_pressure * volpercent_a / 100 * V_TC)/(R * (GB_temp + 273.15))
+                    
+                    #Get mass (mg) using moles and molar mass
+                    BreakdownDF.at[i,'Mass (mg)'] = BreakdownDF.at[i,'Moles (mol)'] * BreakdownDF.at[i,'MW (g/mol)'] * 1000
+                
+                #Otherwise, pass    
+                else:
+                    pass
+        
+        return BreakdownDF, V_TC, SF
+    
+    BreakdownDF, V_TC, SF = quantTCD(BreakdownDF,DBRF,gasBag_cond,reactor_cond)
+    
+    return BreakdownDF, V_TC, SF
+
+#Function for quantifying gas TCD data w/ internal standard method
+def gasTCD_IS(BreakdownDF,DBRF,gasBag_cond,reactor_cond,peak_error):
+    
+    #Initialize compound name column in BreakdownDF
+    BreakdownDF['Compound Name'] = 'None'
+
+    #Define molar mass of CO2, g/mol
+    Mc = 44.009
+
+    # Function to estimate mass of CO2 from provided conditions and get area of CO2
+    def massCO2(BreakdownDF,DBRF,R,C,V_C,P_0,GB_temp):
+
+        #Find the CO2 peak row in DBRF
+        CO2_row = DBRF.loc[DBRF['Compound Name'] == "Carbon Dioxide"].iloc[0]
+        
+        #Get the retention time
+        CO2_RT = CO2_row['RT (min)']
+        
+        #Get the minimum and maximum of the RT range using the peak error
+        CO2_RTmin = CO2_RT - peak_error
+        CO2_RTmax = CO2_RT + peak_error
+        
+        #Define boolean describing whether or not CO2 match has been found
+        CO2_bool = False
+
+        #Iterate through every row in BreakdownDF
+        for i, row in BreakdownDF.iterrows():
+            
+            #If the TCD retention time is within range of the CO2 entry...
+            if CO2_RTmin <= row['RT'] <= CO2_RTmax:
+                
+                #Get mass of CO2, mg
+                mc = C * Mc * (P_0 * V_C) / (R * (GB_temp + 273.15)) * 1000
+
+                #Get area of CO2
+                Ac = row['Area']
+
+                #Set CO2_bool to True
+                CO2_bool = True
+                
+                break
+            
+            #Otherwise, pass
+            else:
+                pass
+
+        #Raise error if no CO2 peak found
+        if CO2_bool == False:
+            raise Exception("[gasTCD][ERROR] No CO2 peak found in TCD")
+
+        else:
+            pass
+
+        return mc, Ac
+
+    #Function to calculate amounts of each species using the scale factor
+    def quantTCD(BreakdownDF,DBRF,gasBag_cond,reactor_cond):
+
+        # Unpack gas bag conditions
+        GB_temp = gasBag_cond[0]       # Temperature of gas bag, C
+        GB_pressure = gasBag_cond[1]   # Sample pressure in gas bag, psig
+        V_C = gasBag_cond[2]           # CO2 volume, mL
+
+        #Unpack reactor conditions
+        P_f = reactor_cond[0]       #reactor quench pressure, psig
+        V_R = reactor_cond[1]       #reactor internal volume, mL
+        P_0 = reactor_cond[2]       #atmospheric pressure, psi
+
+        # Define ideal gas constant, m^3*Pa/K*mol
+        R = 8.314
+
+        #Define conversion factor, Pa * m^3 * psi^-1 * mL^-1
+        C = 0.00689476
+
+        #Get mass of CO2
+        mc, Ac = massCO2(BreakdownDF,DBRF,R,C,V_C,P_0,GB_temp)
+
+        #Get total volume plus CO2
+        V_T = V_R * (P_f + P_0) / P_0
+        V_TC = V_T + V_C
+        print(V_TC)
+        #Add min and max peak assignment values to DBRF
+        for i, row in DBRF.iterrows():
+            DBRF.at[i,'RT Max'] = DBRF.at[i,'RT (min)'] + peak_error
+            DBRF.at[i,'RT Min'] = DBRF.at[i,'RT (min)'] - peak_error
+
+        #Iterate through every row in BreakdownDF
+        for i, row in BreakdownDF.iterrows():
+            
+            #Iterate through every row in DBRF
+            for i2, row2 in DBRF.iterrows():
+                
+                #If the TCD retention time is within the range for a given DBRF entry...
+                if row2['RT Min'] <= row['RT'] <= row2['RT Max']:
+                    
+                    #Add the compound name to the breakdown dataframe
+                    BreakdownDF.at[i,'Compound Name'] = row2['Compound Name']
+                    
+                    #Add the other relevant information to the breakdown dataframe
+                    BreakdownDF.at[i,'Formula'] = row2['Formula']
+                    BreakdownDF.at[i,'RF'] = row2['RF']
+                    BreakdownDF.at[i,'MW (g/mol)'] = ChemFormula(row2['Formula']).formula_weight
+                    
+                    #If the peak is CO2...
+                    if row['Compound Name'] == "Carbon Dioxide":
+                        #Set mass to mc
+                        BreakdownDF.at[i,'Mass(mg)'] = mc
+                    
+                    #Otherwise...
+                    else:
+                        #Get mass (mg) using mass of carbon dioxide and response factor
+                        BreakdownDF.at[i,'Mass (mg)'] = (mc * (BreakdownDF.at[i,'Area'] / Ac)) / BreakdownDF.at[i,'RF']
+                
+                #Otherwise, pass    
+                else:
+                    pass
+        
+        return BreakdownDF, V_TC
+    
+    BreakdownDF, V_TC = quantTCD(BreakdownDF,DBRF,gasBag_cond,reactor_cond)
+    
+    return BreakdownDF, V_TC