chromaquant 0.3.1__py3-none-any.whl

chromaquant/Quant/__init__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+ChromaQuant.Quant package initialization
+
+Julia Hancock
+Created 10-19-2024
+
+"""
+
+from .AutoQuantification import main_AutoQuantification

chromaquant/__init__.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+ChromaQuant package initialization
+
+Julia Hancock
+Created 10-20-2024
+
+"""

chromaquant/__main__.py

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+#!/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
+
+---
+
+SCRIPT FOR SIMPLIFYING ANALYSIS WORKFLOW
+
+Julia Hancock
+Started 01-04-2024
+
+"""
+
+""" PACKAGES """
+print("[__main__] Loading packages...")
+import tkinter as tk
+from tkinter import ttk
+from ttkthemes import ThemedTk
+import tkinter.font as tkFont
+import os
+import subprocess
+import sys
+from PIL import Image, ImageTk
+from datetime import datetime
+import importlib.util
+
+""" LOCAL PACKAGES """
+print("[__main__] Importing local packages...")
+#Get current file absolute directory
+file_dir = os.path.dirname(os.path.abspath(__file__))
+#Get absolute directories for subpackages
+subpack_dir = {'Handle':os.path.join(file_dir,'Handle','__init__.py'),
+               'Manual':os.path.join(file_dir,'Manual','__init__.py'),
+               'Match':os.path.join(file_dir,'Match','__init__.py'),
+               'Quant':os.path.join(file_dir,'Quant','__init__.py')}
+
+#Define function to import from path
+def import_from_path(module_name,path):
+    #Define spec
+    spec = importlib.util.spec_from_file_location(module_name,path)
+    #Define module
+    module = importlib.util.module_from_spec(spec)
+    #Expand sys.modules dict
+    sys.modules[module_name] = module
+    #Load module
+    spec.loader.exec_module(module)
+    return module
+
+#Import all local packages
+hd = import_from_path("hd",subpack_dir['Handle'])
+mn = import_from_path("mn",subpack_dir['Manual'])
+qt = import_from_path("qt",subpack_dir['Quant'])
+mt = import_from_path("mt",subpack_dir['Match'])
+
+""" PARAMETERS """
+print("[__main__] Defining parameters...")
+version = "0.3.1"
+__version__ = "0.3.1"
+
+""" UI FUNCTION """
+
+def runUI():
+
+    """ DIRECTORIES """
+    print("[__main__] Defining directories...")
+    print("[__main__] Using Handle package...")
+    #Get directories from handling script
+    directories = hd.handle(os.path.dirname(os.path.abspath(__file__)))
+    #Unpack directories
+    #Primary files directory
+    files = directories['files']
+    #Resources directory
+    RE_Dir = directories['resources']
+    #Theme directory
+    theme_Dir = directories['theme']
+    #Response factor directory
+    RF_Dir = directories['rf']
+    #Data directory
+    DF_Dir = directories['data']
+    #Images directory
+    img_Dir = directories['images']
+    #AutoFpmMatch directory + file
+    afm_Dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),'AutoFpmMatch.py')
+    #AutoQuantification directory + file
+    aq_Dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),'AutoQuantification.py')
+    
+    """ DATA SEARCH """
+    print("[__main__] Searching for valid data files...")
+    #Get a list of all available sample data directories (excluding "old") in the data files directory
+    sampleList = [f.name for f in os.scandir(DF_Dir) if f.is_dir() if f.name != "old"]
+      
+    """ FUNCTIONS """
+    print("[__main__] Defining functions...")
+    #Function for setting up the UI
+    def uiSetup(theme_Dir):
+        
+        #Initialize UI window
+        root = ThemedTk(theme='adapta')
+    
+        # Import the tcl file with the tk.call method
+        root.tk.call('source', theme_Dir)
+    
+        # Set the theme with the theme_use method
+        style = ttk.Style(root)
+        style.theme_use('forest-light')
+        #Set up style button font
+        style.configure('QuantButton.TButton',font=('TKDefaultFont',16))
+        #Set up style accent button font
+        style.configure('Accent.TButton',font=('TKDefaultFont',16))
+        #Set up labelframe font
+        style.configure('QuantLabelframe.TLabelframe.Label',font=('TKDefaultFont',16))
+    
+        root.geometry("1090x560")
+        root.title("ChromaQuant – Quantification Made Easy")
+        root.resizable(0,0)
+    
+        #style.theme_use('forest')
+        #Configure the grid
+        root.columnconfigure(0,weight=2)
+        root.columnconfigure(1,weight=2)
+        root.columnconfigure(2,weight=2)
+        root.columnconfigure(3,weight=2)
+    
+        #Create a main frame
+        mainframe = ttk.Frame(root)
+        mainframe.grid(column=0,row=0)
+        
+        return root, mainframe
+    #Function for sample selection combobox
+    def on_select(event):
+        
+       sname = sampleBox.get()
+       print("User selected "+sampleBox.get())
+       return sname
+    
+    #Function for fidpms phase selection combobox
+    def fidpms_select():
+        
+        sphase = fpmVar.get()
+        print("User selected " + sphase)
+        
+        if sphase == "Liquid":
+            #Set variable to first order
+            fpmMVar.set('First order (linear)')
+            #Disable third order
+            third.config(state=tk.DISABLED)
+        else:
+            third.config(state=tk.NORMAL)
+        
+        return sphase
+    
+    #Function for model selection combobox
+    def fidpms_select_model():
+        
+        model = fpmMVar.get()
+        print("User selected " + model)
+        
+        return model
+        
+    #Function for fidpms speculative labeling combobox
+    def fidpms_select2():
+        
+        specLabTF = fpm2Var.get()
+        print("User selected " + specLabTF)
+    
+        return specLabTF
+    
+    #Function for quant phase selection combobox
+    def quant_select(event):
+        
+        global quantphases
+        quantphases = logBox.get
+    
+    #Function for running method functions
+    def runProcess(sname,pythonFun,varList):
+        """
+        Function that runs an external main function
+        Parameters
+        ----------
+        sname : String
+            Name of sample to be analyzed.
+        pythonFun : Function
+            Function to be run.
+        varList : List
+            List of reformatted variables to be passed to the function.
+    
+        Returns
+        -------
+        None.
+    
+        """
+        #Start time for execution time
+        exec_start = datetime.now()
+        #Insert sname at the beginning of the variables list
+        varList.insert(0,sname)
+        #Run the method function
+        pythonFun(*varList)
+        #End time for execution time
+        exec_end = datetime.now()
+        #Execution time
+        exec_time = (exec_end-exec_start).total_seconds()*10**3
+        print("Time to execute: {:.03f}ms".format(exec_time))
+        print("Program complete")
+        
+        return None
+    
+    #Function for running FIDpMS script
+    def runFIDpMS(sname,specLabTF,sphase,model):
+        """
+        Parameters
+        ----------
+        sname : STRING
+            Name of sample to be analyzed.
+        specLabTF : STRING
+            True/false string describing whether speculative labeling is to be performed.
+        sphase : TYPE
+            String describing whether liquid or gas is to be performed.
+        model : TYPE
+            String describing which model is to be performed.
+    
+        Returns
+        -------
+        NONE
+    
+        """
+        
+        #Function for reformatting provided variables
+        def reformatVar(var_initial,ifTF_list):
+            """
+            Parameters
+            ----------
+            var_initial : STRING, BOOLEAN
+                The initial variable to be reformatted.
+            ifTF_list : LIST
+                A list containing two lists, the first containing the variable options and the second containing reformatted values.
+    
+            Returns
+            -------
+            var_final : STRING
+                The final, reformatted variable.
+    
+            """
+            
+            #Set default value of reformatted value
+            var_final = "N/A"
+            
+            #Get the length of the variable option list
+            listLength = len(ifTF_list[0])
+            
+            #For every entry in the variable option list...
+            for i in range(listLength):
+                
+                #If the variable is equal to the ith variable option...
+                if var_initial == ifTF_list[0][i]:
+                    #Assign the variable to the first reformatted value
+                    var_final = ifTF_list[1][i]
+                #Otherwise, pass
+                else:
+                    pass
+    
+            return var_final
+        
+        #A dictionary containing the ifTF_lists for every passed variable
+        ifTF_Dict = {'specLabTF':[[1,0],['True','False']],'sphase':[['Gas','Liquid'],['G','L']],'model':[['First order (linear)','Third order','Retention time'],['F','T','R']]}
+        
+        #A dictionary of all passed variables excluding sname
+        passed_dict = {'sphase':sphase,'specLabTF':specLabTF,'model':model}
+        
+        print("User selected sample name {0} with phase {2} and entered {1} for running speculative labeling. Modeling is {3}".format(sname,specLabTF,sphase,model))
+        
+        #A dictionary for all reformatted variables
+        reformatVar_dict = {}
+        
+        #A dictionary of booleans describing whether or not values in reformatVar_dict are "N/A"
+        reformatBool_dict = {}
+        
+        #Reformat all variables
+        for i in passed_dict.keys():
+            
+            #Print reformatted variable name
+            print("Reformatting " + i + "...")
+            #Reformat variable, append to dictionary
+            reformatVar_dict[i] = reformatVar(passed_dict[i],ifTF_Dict[i])
+            #Print resulting reformatted value
+            print("Variable has been reformatted to {0}".format(reformatVar_dict[i]))
+            
+            #Check if reformatted variable is equal to "N/A". If it is, assign False
+            if reformatVar_dict[i] == "N/A":
+                reformatBool_dict[i] = False
+            #Otherwise, assign True
+            else:
+                reformatBool_dict[i] = True
+        
+        #If any of the required fields are empty, pass
+        if False in list(reformatBool_dict.values()) or sname == "":
+            print("Cannot run FIDpMS script, one or more variables are not defined")
+            pass
+        
+        #Otherwise, run the FIDpMS script
+        else:
+            print("Running FIDpMS script...")
+            
+            try:
+                #Get list of reformatVar_dict values
+                reformatVar_list = list(reformatVar_dict.values())
+                print(reformatVar_list)
+                #Append list with directories list
+                reformatVar_list.append(directories)
+                print(reformatVar_list)
+                #Run subprocess
+                runProcess(sname,mt.main_AutoFpmMatch,reformatVar_list)
+                
+            except subprocess.CalledProcessError as e:
+                print(f'Command {e.cmd} failed with error {e.returncode}')
+        
+        return None
+    
+    #Function for running quant script
+    def runQuant(sname,quantphases):
+    
+        print("User selected sample name {0} with phase(s) {1}".format(sname,quantphases))
+        #If any of the required fields are empty, pass
+        if sname == "" or quantphases == "":
+            print("User did not enter a value for at least one required argument, canceling script run")
+            pass
+        #Otherwise, run the FIDpMS script
+        else:
+            print("Running Quantification script...")
+            
+            try:
+                #Run subprocess
+                runProcess(sname,qt.main_AutoQuantification,[quantphases,directories])
+                
+            except subprocess.CalledProcessError as e:
+                print(f'Command {e.cmd} failed with error {e.returncode}')
+        
+        return None
+    
+    """ CODE """
+    print("[__main__] Initializing UI mainframe...")
+    #Run the UI setup
+    root, mainframe = uiSetup(theme_Dir)
+    
+    #Create font objects
+    title_font = tkFont.Font(size=18)   #Title font
+        
+    #IMAGE AND TITLE
+    #Add a frame for the logo and title/sample info
+    topFrame = ttk.Frame(mainframe)
+    topFrame.grid(column=0,row=0,sticky='w',padx=(350,0))
+    
+    #Add a frame for the ChromaQuant logo
+    logoFrame = ttk.Frame(topFrame)
+    logoFrame.grid(column=0,row=0)
+    
+    #Add a frame for the title text and sample selection
+    tsFrame = ttk.Frame(topFrame)
+    tsFrame.grid(column=1,row=0)
+    
+    #Add title text
+    tk.Label(tsFrame,text="ChromaQuant v"+version,font=title_font).grid(column=0,row=0,pady=10,padx=10)
+    
+    #Add an image for the ChromaQuant logo
+    #Load the image
+    #image = tk.PhotoImage(file=img_Dir+'ChromaQuantIcon.png')
+    image_i = Image.open(os.path.join(img_Dir,'ChromaQuantIcon.png'))
+    #Resize the image
+    resize_image = image_i.resize((100,100))
+    #Redefine the image
+    image = ImageTk.PhotoImage(resize_image)
+    #Add the image to a label
+    image_label = tk.Label(logoFrame, image=image)
+    image_label.grid(column=0,row=0,pady=10,padx=10)
+    
+    #SAMPLE SELECTION
+    #Add a frame for selecting the sample
+    sampleFrame = ttk.Frame(tsFrame)
+    sampleFrame.grid(column=0,row=1,pady=10,padx=10)
+    
+    #Add text to the top of the sample frame
+    tk.Label(sampleFrame,text='Select a sample to analyze:').grid(column=0,row=0)
+    sampleVar = tk.StringVar()
+    sampleBox = ttk.Combobox(sampleFrame,textvariable=sampleVar)
+    sampleBox['values'] = sampleList
+    sampleBox.state(["readonly"])
+    sampleBox.grid(column=0,row=1)
+    
+    #Bind the sampleBox to a function
+    sampleBox.bind("<<ComboboxSelected>>",on_select)
+    
+    #WIDGET FRAME
+    #Add a frame for the fidpms and quantification widgets
+    widgetFrame = ttk.Frame(mainframe)
+    widgetFrame.grid(column=0,row=1)
+    
+    #FIDPMS WIDGET
+    #Add a frame
+    fidpms_content = ttk.LabelFrame(widgetFrame,text='Peak Matching',style='QuantLabelframe.TLabelframe')
+    fidpms_content.grid(column=0,row=0,pady=10,padx=10)
+    
+    #Add text to the top of the frame
+    tk.Label(fidpms_content,text='Please enter all information').grid(column=0,row=0,columnspan=4,padx=20)
+    
+    #Set up a radiobutton for selecting liquid or gas
+    tk.Label(fidpms_content,text='Please select the sample type:').grid(column=0,row=1,padx=10,pady=20,sticky='e')
+    fpmVar = tk.StringVar()
+    Liquid = ttk.Radiobutton(fidpms_content,text='Liquid',variable=fpmVar,value="Liquid",command=fidpms_select)
+    Gas = ttk.Radiobutton(fidpms_content,text='Gas',variable=fpmVar,value="Gas",command=fidpms_select)
+    Liquid.grid(column=1,row=1,padx=1,sticky='w')
+    Gas.grid(column=2,row=1,padx=1,sticky='w')
+    
+    #Initially start with liquid selected
+    fpmVar.set('Liquid')
+    
+    #Set up a radiobutton for selecting the model type
+    tk.Label(fidpms_content,text='Please select the desired matching fit model:').grid(column=0,row=2,padx=10,pady=20,sticky='e')
+    fpmMVar = tk.StringVar()
+    third = ttk.Radiobutton(fidpms_content,text='Third order',variable=fpmMVar,value='Third order',command=fidpms_select_model)
+    first = ttk.Radiobutton(fidpms_content,text='First order (linear)',variable=fpmMVar,value='First order (linear)',command=fidpms_select_model)
+    rt = ttk.Radiobutton(fidpms_content,text='Retention time',variable=fpmMVar,value='Retention time',command=fidpms_select_model)
+    third.grid(column=1,row=2,padx=1,sticky='w')
+    first.grid(column=2,row=2,padx=1,sticky='w')
+    rt.grid(column=3,row=2,padx=1,sticky='w')
+    
+    #Initially start with first order selected and third order disabled
+    fpmMVar.set('First order (linear')
+    third.config(state=tk.DISABLED)
+    
+    #Set up a checkbox for selecting whether or not to perform speculative labeling
+    tk.Label(fidpms_content,text='Perform speculative labeling?').grid(column=0,row=3,padx=10,pady=20,sticky='e')
+    fpm2Var = tk.IntVar()
+    fpm2Box = tk.Checkbutton(fidpms_content,text='',variable=fpm2Var,onvalue=1,offvalue=0,command=fidpms_select2)
+    fpm2Box.grid(column=1,row=3,padx=1,sticky='w')
+    
+    #Add a start button
+    fidpms_sbutton = ttk.Button(fidpms_content,text="\n\n\nRun Script\n\n\n",width=20,style='Accent.TButton',command=lambda: runFIDpMS(sampleVar.get(),fpm2Var.get(),fpmVar.get(),fpmMVar.get()))
+    fidpms_sbutton.grid(column=0,row=4,pady=20,padx=20,columnspan=2)
+    
+    #DISABLING SPECULATIVE LABELING
+    fpm2Box.config(state=tk.DISABLED)
+    
+    #Bind the button to a function to run the appropriate script
+    #fidpms_sbutton.bind("<Button-1>",runFIDpMS)
+    
+    #QUANT WIDGET
+    #Add a frame
+    quant_content = ttk.LabelFrame(widgetFrame,text='Quantification',style='QuantLabelframe.TLabelframe')
+    quant_content.grid(column=1,row=0,pady=10,padx=10,sticky="n")
+    
+    #Add text to the top of the frame
+    tk.Label(quant_content,text='Please enter all information').grid(column=0,row=0,columnspan=2,padx=20)
+    #Set up a combobox for selecting liquid or gas
+    tk.Label(quant_content,text='Does the sample have liquid and/or gas components?').grid(column=0,row=1,padx=10,pady=20)
+    logVar = tk.StringVar()
+    logBox = ttk.Combobox(quant_content,textvariable=logVar)
+    logBox['values'] = ['Liquid','Gas','Liquid and Gas']
+    logBox.state(["readonly"])
+    logBox.grid(column=1,row=1,padx=10)
+    
+    #Bind the combobox to a function
+    logBox.bind("<<ComboboxSelected>>",quant_select)
+    
+    #Add a start button 
+    quant_sbutton = ttk.Button(quant_content,text="\n\n\nRun Script\n\n\n",width=20,style='Accent.TButton',command=lambda: runQuant(sampleVar.get(),logVar.get()))
+    quant_sbutton.grid(column=0,row=2,pady=20,padx=20,columnspan=2)
+    
+    #Bind the start button to a function
+    #quant_sbutton.bind("<Button-1>",runQuant)
+    
+    #var = ""
+    #togglebutton = ttk.Checkbutton(root, text='Switch', style='Switch',variable=var)
+    #togglebutton.grid(row=3,column=0)
+    
+    #Main loop
+    root.mainloop()
+    
+    #End of runUI function
+    return None
+
+""" RUN MAIN FUNCTION """
+print("[__main__] Starting UI...")
+if __name__ == "__main__":
+	runUI()
+

chromaquant/properties.json

@@ -0,0 +1,4 @@
+{
+    "app-directory": "/Users/[user]/Desktop/University/Rorrer Lab/Scripts/chromaquant/src/chromaquant",
+    "file-directory": "/Users/[user]/Documents/ChromaQuant"
+}