chromaquant 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

chromaquant/Match/matchMain.py

@@ -1,233 +0,0 @@
-"""
-
-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 THAT MATCHES FID AND MS PEAKS
-
-Julia Hancock
-Started 12/10/2023
-
-"""
-""" PACKAGES """
-import sys
-import pandas as pd
-import os
-from molmass import Formula
-import math
-import numpy as np
-from chemformula import ChemFormula
-import json
-from datetime import datetime
-import logging
-import scipy
-import importlib.util
-
-""" DIRECTORIES (MANUAL) """
-"""
-testPath = "/Users/connards/Desktop/University/Rorrer Lab/Scripts/chromaquant/src/chromaquant/"
-#Define file directory
-D_files = "/Users/connards/Documents/ChromaQuant"
-
-#Define app directory
-D_app = "/Users/connards/Desktop/University/Rorrer Lab/Scripts/chromaquant/src/chromaquant"
-    
-#Define resources directory
-D_rsc = os.path.join(D_files,'resources')
-    
-#Define theme directory
-D_theme = os.path.join(D_rsc,'forest','forest-light.tcl')
-    
-#Define response factors directory
-D_rf = os.path.join(D_files,'response-factors')
-    
-#Define data directory
-D_data = os.path.join(D_files,'data')
-    
-#Define images directory
-D_img = os.path.join(D_files,'images')
-
-directories = {'files':D_files,'resources':D_rsc,'theme':D_theme,'rf':D_rf,'data':D_data,'images':D_img}
-"""
-
-""" VARIABLES FOR TESTING"""
-
-#sname = 'example2'
-#sphase = 'L'
-
-""" LOCAL PACKAGES """
-
-#Get package directory
-app_dir =  os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-
-#Get absolute directories for subpackages
-subpack_dir = {'Handle':os.path.join(app_dir,'Handle','__init__.py'),
-               'Manual':os.path.join(app_dir,'Manual','__init__.py'),
-               'MatchSub':os.path.join(app_dir,'Match','MatchSub','__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 modules
-    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'])
-mtsb = import_from_path("mtsb",subpack_dir['MatchSub'])
-
-""" FIT DEFINITION FUNCTION """
-
-#Function that defines fit lambda based on parameters in analysis-config
-def getFitLambda(fit_param):
-        """ This function requires a dictionary of polynomial parameters, with keys "a", "b", etc. """
-        
-        if fit_param['fit-type'] == "First Order":
-            
-            fit = lambda FID_RT: fit_param['a']*FID_RT + fit_param['b'] 
-
-        elif fit_param['fit-type'] == "Third Order":
-
-            fit = lambda FID_RT: fit_param['a']*FID_RT**3 + fit_param['b']*FID_RT**2 + fit_param['c']*FID_RT + fit_param['d']
-        
-        else:
-             
-             fit = None
-
-        return fit
-
-""" MATCH FUNCTION """
-def mainMatch(sname,sphase,model):
-
-    print("[matchMain] Beginning match...")
-
-    #Get current time
-    print("[matchMain] Getting current time...")
-    now = datetime.now()
-
-    """ DIRECTORIES """
-    print("[matchMain] Getting directories...")
-    #Get directories from handling script
-    directories = hd.handle(app_dir)
-
-    #Data file log directory
-    directories['log'] = os.path.join(directories['data'],sname,'log')
-
-    #Data file breakdowns directory
-    directories['break'] = os.path.join(directories['data'],sname,'breakdowns')
-
-    #Raw data file directory
-    directories['raw'] = os.path.join(directories['data'],sname,'raw data')
-
-    """ ANALYSIS CONFIGURATION """
-    print("[matchMain] Interpreting analysis configuration...")
-    #Read analysis configuration file
-    with open(os.path.join(directories['resources'],'analysis-config.json')) as f:
-        analysis_config = json.load(f)
-
-    #Extract analysis configuration info
-    #This dictionary contain lists of substrings to be checked against compound name strings to
-    #assign a compound type
-
-    #Six compound types exist: linear alkanes (L), branched alkanes (B), aromatics (A), cycloalkanes (C),
-    #alkenes/alkynes (E), and other (O)
-
-    #Each compound type abbreviation will have an entry in the dictionary corresponding to a list of
-    #substrings to be checked against a compound name string
-
-    contains = analysis_config["CT-assign-contains"]
-
-    #Tuple of contains keys in order of priority
-    keyloop = analysis_config["CT-assign-keyloop"]
-
-    #Tuple of elements to be excluded and automatically labelled as 'O'
-    element_exclude = analysis_config["CT-assign-element-exclude"]
-
-    #File suffixes to add to form data filenames
-    file_suffix = analysis_config["file-suffix"]
-
-    #Fit parameters for matching FID and MS accortding to polynomial fit
-    match_fit_parameters = analysis_config["match-fit-parameters"]
-
-    #Acceptable peak errors for matching
-    peak_errors = analysis_config["peak-errors"]
-
-    """ RUN FUNCTIONS """
-    print("[matchMain] Running match functions...")
-
-    #Run the file naming function – this function will create paths to all relevant files for matching FID and MS peaks according to sample name and phase
-    print("[matchMain] Getting data pths...")
-    paths = hd.fileNamer(sname,sphase,file_suffix,directories['raw'])
-
-    # Run the file checking function – this function will search for an existing FIDpMS file, creating one if it does not exist. 
-    # It will then read the file as a pandas DataFrame. The tf Boolean describes whether or not there exist manually-matched peaks.
-    print("[matchMain] Checking for FIDpMS file...")
-    fpmDF, tf = hd.checkFile(paths[2],paths[0])
-
-    # Import MS UPP data
-    print("[matchMain] Importing mass spectrometry data...")
-    mDF = pd.read_csv(paths[1])
-
-    # Get only relevant columns of MS UPP data
-    print("[matchMain] Cleaning mass spectrometry data...")
-    mDF = mDF.loc[:,['Component RT','Compound Name','Formula','Match Factor']]
-
-    # Third order function for testing
-    #fit = lambda FID_RT: 0.0252*FID_RT**3 - 0.5274*FID_RT**2 + 4.8067*FID_RT - 3.0243
-
-    # Get fit function using analysis-config
-    print("[matchMain] Extracting match fit parameters...")
-    fit = getFitLambda(match_fit_parameters)
-
-    #If model is polynomial...
-    if model == 'P':
-        # Run the matching function – this function takes a passed function describing an estimated relationship between MS RT's and FID RT's and matches peaks. 
-        # Function can be of any form as long as it returns a floating point value for the estimated MS RT
-        print("[matchMain] Matching peaks according to polynomial fit...")
-        fpmDF = mtsb.matchPeaks(fpmDF,mDF,fit,peak_errors['peak-error-third']) 
-
-    #If model is retention time...
-    if model == 'R':
-         # Run the matching function – this function takes a passed function describing an estimated relationship between MS RT's and FID RT's and matches peaks. 
-        # Function can be of any form as long as it returns a floating point value for the estimated MS RT
-        print("[matchMain] Matching peaks by retention time...")
-        fpmDF = mtsb.matchRT(fpmDF,mDF,peakError=peak_errors['peak-error-RT'])
-        fpmDF = mtsb.matchPeaks(fpmDF,mDF,fit,peak_errors['peak-error-third']) 
-
-    # Run the compound type abbreviation assignment function – this function takes a passed matched FID and MS list and assigns
-    # compound type abbreviations to each matched entry
-    print("[matchMain] Assigning compound types...")
-    fpmDF = mtsb.ctaAssign(fpmDF, contains, keyloop, element_exclude)
-
-    print("[matchMain] Handling duplicates...")
-    #Run the duplicate handling function
-    fpmDF = mtsb.duplicateHandle(fpmDF)
-
-    print("[AutoFpmMatch] Saving results...")
-    #Save the FIDpMS data
-    fpmDF.to_csv(paths[2],index=False)
-    
-    #Print computation time
-    compTime = datetime.now().timestamp()*1000 - now.timestamp()*1000
-    print("[matchMain] Time taken: {:.3f} ms".format(compTime))
-
-    #Close main function by returning
-    return None
-
-#For testing
-#mainMatch('example2','L','R')