import os import platform import re import time from datetime import datetime import numpy as np from numpy import log, abs, sqrt, exp from scipy import interpolate import pandas as pd from matplotlib import pyplot as plt from functools import lru_cache from tklib.tkparams import tkParams from tklib.tksci.tkFit_mxy_flex import tkFit_mxy from tklib.tksci.tkFit_lib import conv_input, save_data, add_history from tklib.tksci.tkFit_object import save_fit_config, read_fit_config_from_file import tklib.tksci.tkoptimize_flex as opt import peakfit as omodel #get_cmdで使う変数をapp.config_cmdに設定 def initialize_minimize_func(app): globals()["app"] = app cfg = app.cfg if app.get("config_cmd", None) is None: app.config_cmd = tkParams() config = app.config_cmd os = platform.system() config.script = 'mobility_polyOS240312.py' ''' if os == 'Linux': config.atlas_cmd = cfg.atlas_cmd_linux #'/home/share/sedatools/bin/deckbuild' config.atlas_options = cfg.atlas_options_linux # '-run -ascii' elif os == 'Windows': config.atlas_cmd = cfg.atlas_cmd_win # 'c:/sedatools/exe/deckbuild' config.atlas_options = cfg.atlas_options_win # '-run' else: config.atlas_cmd = cfg.atlas_cmd_linux #'/home/share/sedatools/bin/deckbuild' config.atlas_options = cfg.atlas_options_linux # '-run -ascii' # config.atlas_options = '-V 5.30.0.R -run -ascii' ''' #外部コマンドを使う場合、コマンドラインを返す def get_cmd(app, xk_all, fit): config = app.config_cmd config.mode = 'fit' config.infile = fit.infile config.datafile = fit.datafile config.fplot = 0 head = f"python {config.script} {config.mode} {config.infile} {config.datafile}" s = '' for x in xk_all: s += f" {x}" return head + s #iniファイル、フィッティング変数設定ファイルの読み込み def initialize(app): app.cfg = tkParams() app.cfg.figsize = [8, 6] app.arg_config_file, app.fit_config_file = opt.get_default_config_paths(app, app.cfg) app.fit_config_file = None if app.arg_config_file: opt.read_default_config_file(app, app.arg_config_file) if app.fit_config_file: opt.read_default_fit_file(app, app.fit_config_file) return app.cfg #fittingパラメータ以外をiniファイルに保存 def save_parameter_files(config_path, fitparam_path, fit, cfg, values = None, print_level = 1): flag_keys = ["fhistory", "ffitfiles", "fdisconnect_backward_data"] files_keys = ["templatepath", "datafile", "infile", "calfile", "outfile", "datafile", "historyfile", "fitfile"] condiction_keys = ["method", "jac", "nmaxiter", "nmaxcall", "tol", "xatol", "y_scale"] data_keys = ["sample", "Tmin", "Tmax", "Nmin", "Nmax"] scan_keys = ["target_var", "x0", "x1", "nx"] if fit.varname is None: fit.varname = [] exclude_keys = condiction_keys + flag_keys + fit.varname + files_keys + data_keys + scan_keys \ + ["infile", "logfile", "outfile", "parameterfile", "stopfile", "fplot", "mode", "daemon", "nohup"] print(f"Save configuration parameters to [{config_path}]") cfg.save_parameters(config_path, section = "Preferences", exclude_keys = exclude_keys, IsPrint = print_level) cfg.save_parameters(config_path, section = "Files", keys = files_keys, IsPrint = print_level) cfg.save_parameters(config_path, section = "Data", keys = data_keys, IsPrint = print_level) cfg.save_parameters(config_path, section = "Flags", keys = flag_keys, IsPrint = print_level) cfg.save_parameters(config_path, section = "Condition", keys = condiction_keys, IsPrint = print_level) cfg.save_parameters(config_path, section = "Scan", keys = scan_keys, IsPrint = print_level) if print_level: print(f"Save fitting parameters to [{fitparam_path}] (save_parameters)") fit.save_parameters(fitparam_path, section = "Parameters", keys = fit.varname, vars = fit, values = values, print_level = 0) # fit.print_variables(heading = "fitting parameters (save_parameters):") #iniファイルから、フィッティングパラメータ以外の設定を読み込む。 def read_parameters(path, cfg): #Parametersセクション以外のみ読み込む sectios = ["Preferences", "Flags", "Files", "Scan", "Condition"] ignore_keys = ["logfile", "outfile", "parameterfile", "parameterbkfile", "file1", "file2", "file3", "file4", "file5", "fplot", "mode", "daemon", "nohup"] print(f"Read parameters from [{path}]") for section in sectios: cfg.read_parameters(cfg.parameterfile, section = section, ignore_keys = ignore_keys) #fitオブジェクトを構成する def init_fit(app, cfg, print_level = 1): #パラメータファイルの読み込み。Parametersセクション以外のみ print("In tkminimize_func.read_parameters():") read_parameters(cfg.parameterfile, cfg) app.force_given_args(cfg) print("mode : {}".format(cfg.mode)) print("fplot : {}".format(cfg.fplot)) print("fhistory : {}".format(cfg.fhistory)) print("ffitfiles : {}".format(cfg.ffitfiles)) print("stop path : {}".format(cfg.stopfile)) print("infile : {}".format(cfg.infile)) print("outfile : {}".format(cfg.outfile)) fit = tkFit_mxy(app = app, method = cfg.method, jac = cfg.jac, tol = cfg.tol, xatol = cfg.get("xatol", 1.0e-4), nmaxiter = cfg.nmaxiter, nmaxcall = cfg.nmaxcall, fplot = cfg.fplot, fdisconnect_backward_data = cfg.get("fdisconnect_backward_data", False), print_interval = cfg.print_interval, plot_interval = cfg.plot_interval) app.fit = fit fit.fitfile_path = app.replace_path(cfg.infile, template = ["{dirname}", getattr(cfg, "fitfile_template", "{filebody}_parameters.csv")]) print() print("config parameter file : {}".format(cfg.parameterfile)) # print("parameter backup file: {}".format(cfg.parameterbkfile)) print("fitting parameter file: {}".format(fit.fitfile_path)) print("history file : {}".format(cfg.historyfile)) print() print(f"Fitting configuration") print(f" method : {cfg.method}") print(f" jac : {cfg.jac}") print(f" tol : {cfg.tol}") print(f" nmaxiter: {cfg.nmaxiter}") print(f" nmaxcall: {cfg.nmaxcall}") print(f" y_scale : {cfg.y_scale}") fit.configure(print_level = 0, cfg = cfg) fit.copy_attributes(cfg, ["T", "infile", "outfile", "historyfile", "fitfile", "templatepath", "datafile", "atlasfile", "logfile", "Cfile", "defectaccfile", "defectdonfile", "atlaslogfile", "calfile"]) fit.copy_attributes(cfg, ["fmax_record", "y_scale"]) fit.copy_attributes(cfg, ["initialize_method", "surrogate_model", "surrogate_method", "nparents", "ga_nmaxiter", "nmaxdata", "xatol", "mutation_rate", "n_restarts_optimizer", "alpha"]) # appに定義したフィッティングパラメータ設定をfitにコピー fit.copy_attributes(app, ["varname", "unit", "pk_scale", "optid", "linid", "dx", "kmin", "kmax", "kpenalty"]) # フィッティングパラメーターの初期値をfit変数から設定 # x0 = fit.build_parameter_list(fit.varname, source_obj = cfg) if hasattr(app, "x0"): fit.pk = app.x0.copy() # fit.print_variables(heading = f"Fitting parameters red from [{fit.fitfile_path}]:") # exit() # Fittingパラメータファイルからフィッティング変数の初期値を設定 fit.read_parameters(fit.fitfile_path, section = "Parameters", keys = fit.varname) nvars = len(fit.pk) fit.print_variables(heading = f"Fitting parameters red from [{fit.fitfile_path}]:") # exit() #起動時引数で与えられたパラメータを再設定 app.force_given_args(cfg) fit.initial_simplex = None if 'fit' in cfg.mode and (cfg.method == 'nelder-mead' or cfg.method == 'simplex'): if fit.dx: fit.initial_simplex = fit.build_initial_simplex() for i, splx in enumerate(fit.initial_simplex): print(f" {i}: ", end = '') for v in splx: print(f" {v:12.4g}", end = '') print() # fitから呼び出される関数の定義 if cfg.jac == 'func': fit.jac = lambda xk: diff1(xk, fit) else: fit.jac = cfg.jac fit.configure(cal_ylist = lambda xk_all, x_list = fit.x_list, run = cfg.run, print_level = 1: \ cal_ylist(app, xk_all, x_list = x_list, fit = fit, run = run, print_level = print_level), minimize_func = lambda pk, run = cfg.run, print_level = print_level: \ fit._minimize_func(pk, x_list = fit.x_list, y_list = fit.y_list, w_list = fit.w_list, run = cfg.run, print_level = print_level), callback = lambda pk, run = cfg.run, savefig_path = 'last_fit.png', use_so = False, print_level = 1: \ fit._callback(pk, run = cfg.run, savefig_path = savefig_path, use_so = use_so, print_level = print_level), cal_penalty = lambda xk_all, run = cfg.run, print_level = 1: \ fit._cal_penalty(xk_all, print_level), cal_fmin = lambda xk_all, x_list, y_list, w_list, run = cfg.run, print_level = 1: \ fit._cal_fmin(xk_all, x_list, y_list, w_list, run, print_level = print_level), save_parameter_files = lambda config_path, fitparam_path, cfg, values = None, print_level = 1: \ save_parameter_files(config_path, fitparam_path, fit, cfg, values = values, print_level = print_level), ) # fitのグラフ関連変数の定義 fit.configure(fplot = fit.fplot, plt = plt, iter = 0, xiter = [], yfmin = [], ycal_list = None, yfin_list = None) return fit def read_input_data(app, infile, cfg = None): print(f"minimize_func.read_input_data(): Read input data from [{infile}]") xlabels, ylabels, xlist, ylist, wlist = omodel.read_input_data(app, infile, cfg) if xlabels is None: print(f"Error in minimize_func.read_input_data(): Can not read [{infile}]") return None, None, None, None, None return xlabels, ylabels, xlist, ylist, wlist #2次元リストの変数x_listから、2次元リストの関数値y_listを返す def cal_ylist(app, xk_all, x_list, fit = None, run = True, print_level = 1): ylist = omodel.cal_ylist(app, xk_all, x_list, fit = fit, run = run, print_level = print_level) return ylist